diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000..e9f0bd7694 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,6 @@ +*.svg filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.jpg filter=lfs diff=lfs merge=lfs -text +*.jpeg filter=lfs diff=lfs merge=lfs -text +*.gif filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text diff --git a/.github/ISSUE_TEMPLATE/03_science_discussion.md b/.github/ISSUE_TEMPLATE/02_science_discussion.md similarity index 100% rename from .github/ISSUE_TEMPLATE/03_science_discussion.md rename to .github/ISSUE_TEMPLATE/02_science_discussion.md diff --git a/.github/ISSUE_TEMPLATE/02_support_needed.md b/.github/ISSUE_TEMPLATE/02_support_needed.md deleted file mode 100644 index d3c69aaf6a..0000000000 --- a/.github/ISSUE_TEMPLATE/02_support_needed.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -name: Support needed for model use -about: Ask for help with using CTSM - ---- - -### NOTE: Be sure to read the relevant documentation and user forums - -We have limited staff and ability to provide support. Here are some resources that might provide help: -- User's Guide: https://escomp.github.io/ctsm-docs/doc/build/html/users_guide/index.html -- CLM Forum: https://bb.cgd.ucar.edu/forums/land-modeling-clm -- README files amongst the source code -- GitHub CTSM issues: https://github.com/escomp/ctsm/issues/ -- Also make sure this issue is unique to CTSM and not really an issue with CESM or CIME - -### Details of support request - -[Fill in details here.] - -### Important details of your setup / configuration so we can better assist you - -**CTSM version you are using:** [output of `git describe`] - -**Have you made any modifications to code, xml files, etc.?** [Yes / No] - -[If Yes: Please point us to your modifications. However: In general we can NOT support problems with modified code. Try to show the problem without modifications.] - -**If you are having problems with a specific case: Is your case on a machine accessible to most CTSM developers (e.g., an NCAR machine)?** [Yes / No] - -If Yes: - -- Location of case directory: [Fill this in] - -- Location of run directory: [Fill this in] - -[If No: Please make sure you have included all important input and output needed to understand your issue, either by pasting it into the issue text, or by attaching relevant files. However: We are less likely to be able to reproduce your problem if the issue is NOT on an NCAR machine.] diff --git a/.github/ISSUE_TEMPLATE/04_other.md b/.github/ISSUE_TEMPLATE/03_other.md similarity index 100% rename from .github/ISSUE_TEMPLATE/04_other.md rename to .github/ISSUE_TEMPLATE/03_other.md diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 0000000000..b01aba8e3c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,5 @@ +blank_issues_enabled: true +contact_links: + - name: CESM forums + url: https://xenforo.cgd.ucar.edu/cesm/ + about: For support with model use, troubleshooting, etc., please use the CTSM forum diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 36a87f49f1..306ee7b1f3 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -14,7 +14,7 @@ Testing performed, if any: (List what testing you did to show your changes worked as expected) (This can be manual testing or running of the different test suites) (Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide) -(aux_clm on cheyenne for gnu/pgi and hobart for gnu/pgi/nag is the standard for tags on master) +(aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master) **NOTE: Be sure to check your Coding style against the standard:** https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines diff --git a/.gitignore b/.gitignore index 789237bc12..7948b49eed 100644 --- a/.gitignore +++ b/.gitignore @@ -41,6 +41,8 @@ tags build/ CMakeFiles/ +# symbolic links generated by run_sys_tests +/tests_* # unit testing directories /src/unit_tests.* @@ -57,7 +59,6 @@ CMakeFiles/ # cime_config buildnmlc -buildcppc # configure / build files /bld/**/CESM_cppdefs diff --git a/.lfsconfig b/.lfsconfig new file mode 100644 index 0000000000..3d2778fad3 --- /dev/null +++ b/.lfsconfig @@ -0,0 +1,2 @@ +[lfs] + fetchexclude = * diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 7ed198ec02..cd478587d1 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,49 +1,107 @@ -# Contributor Covenant Code of Conduct +# Contributor Code of Conduct +_The Contributor Code of Conduct is for participants in our software projects and community._ ## Our Pledge - -In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, politcal affiliation, veteran status, pregnancy, genetic information, personal appearance, choice of text editor or operating system, race, religion, or sexual identity and orientation, or any other characteristic protected under applicable US federal or state law. +We, as contributors, creators, stewards, and maintainers (participants), of **Community Terrestrial Systems Model (CTSM)** pledge to make participation in +our software, system or hardware project and community a safe, productive, welcoming and inclusive experience for everyone. +All participants are required to abide by this Code of Conduct. +This includes respectful treatment of everyone regardless of age, body size, disability, ethnicity, gender identity or expression, +level of experience, nationality, political affiliation, veteran status, pregnancy, genetic information, physical appearance, race, +religion, or sexual orientation, as well as any other characteristic protected under applicable US federal or state law. ## Our Standards - -Examples of behavior that contributes to creating a positive environment include: - -* Using welcoming and inclusive language -* Being respectful of differing viewpoints and experiences -* Gracefully accepting constructive criticism -* Focusing on what is best for the community -* Showing empathy towards other community members - -Examples of unacceptable behavior by participants include: - -* The use of sexualized language or imagery and unwelcome sexual attention or advances -* Trolling, insulting/derogatory comments, and personal or political attacks -* Public or private harassment +Examples of behaviors that contribute to a positive environment include: + +* All participants are treated with respect and consideration, valuing a diversity of views and opinions +* Be considerate, respectful, and collaborative +* Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism +* Acknowledging the contributions of others +* Avoid personal attacks directed toward other participants +* Be mindful of your surroundings and of your fellow participants +* Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress +* Respect the rules and policies of the project and venue + +Examples of unacceptable behavior include, but are not limited to: + +* Harassment, intimidation, or discrimination in any form +* Physical, verbal, or written abuse by anyone to anyone, including repeated use of pronouns other than those requested +* Unwelcome sexual attention or advances +* Personal attacks directed at other guests, members, participants, etc. * Publishing others' private information, such as a physical or electronic address, without explicit permission +* Alarming, intimidating, threatening, or hostile comments or conduct +* Inappropriate use of nudity and/or sexual images +* Threatening or stalking anyone, including a participant * Other conduct which could reasonably be considered inappropriate in a professional setting -* Refusing to use the pronouns that someone requests -* Intimidating, threatening, or hostile conduct; physical or verbal abuse; vandalism; arson; and sabotage -* Alarming or threatening comments that might refer to, suggest, or promote a violent, intimidating, or threatening action - -## Our Responsibilities - -Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. - -Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. ## Scope - -This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at ctsm-core@ucar.edu. Alternatively, this behavior can be reported to individuals on the CTSM team, who will then have the responsibility to talk about the behavior to the core team. Another alternative for NCAR employees (when all individuals involved are NCAR employees) is to use the reporting methods of NCAR for this behavior (these options include anonymous reporting methods). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Retaliation against a person who initiates a complaint or an inquiry about such behaviors is equally prohibited. - -Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. +This Code of Conduct applies to all spaces managed by the Project whether they be physical, online or face-to-face. +This includes project code, code repository, associated web pages, documentation, mailing lists, project websites and wiki pages, +issue tracker, meetings, telecons, events, project social media accounts, and any other forums created by the project team which the +community uses for communication. +In addition, violations of this Code of Conduct outside these spaces may affect a person's ability to participate within them. +Representation of a project may be further defined and clarified by project maintainers. + +## Community Responsibilities +Everyone in the community is empowered to respond to people who are showing unacceptable behavior. +They can talk to them privately or publicly. +Anyone requested to stop unacceptable behavior is expected to comply immediately. +If the behavior continues concerns may be brought to the project administrators or to any other party listed in the +[Reporting](#reporting) section below. + +## Project Administrator Responsibilities +Project administrators are responsible for clarifying the standards of acceptable behavior and are encouraged to model appropriate +behavior and provide support when people in the community point out inappropriate behavior. +Project administrator(s) are normally the ones that would be tasked to carry out the actions in the [Consequences](#consequences) +section below. + +Project administrators are also expected to keep this Code of Conduct updated with the main one housed at UCAR, as listed below in +the [Attribution](#attribution) section. + +## Reporting +Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as +outlined in the [Consequences](#consequences) section below. +However, making a report to a project administrator is not considered an 'official report' to UCAR. + +Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint +Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's +EthicsPoint Hotline](https://www2.fin.ucar.edu/ethics/anonymous-reporting). + +Complaints received by UCAR will be handled pursuant to the procedures outlined in UCAR's Harassment Reporting and Complaint +Procedure. +Complaints to UCAR will be held as confidential as practicable under the circumstances, and retaliation against a person who +initiates a complaint or an inquiry about inappropriate behavior will not be tolerated. + +Any Contributor can use these reporting methods even if they are not directly affiliated with UCAR. +The Frequently Asked Questions (FAQ) page for reporting is [here](https://www2.fin.ucar.edu/procedures/hr/reporting-faqs). + +## Consequences +Upon receipt of a complaint, the project administrator(s) may take any action deemed necessary and appropriate under the +circumstances. +Such action can include things such as: removing, editing, or rejecting comments, commits, code, wiki edits, email, issues, and +other contributions that are not aligned to this Code of Conduct, or banning temporarily or permanently any contributor for other +behaviors that are deemed inappropriate, threatening, offensive, or harmful. +Project administrators also have the right to report violations to UCAR HR and/or UCAR's Office of Diversity, Equity and Inclusion +(ODEI), as well as a participant's home institution and/or law enforcement. +In the event an incident is reported to UCAR, UCAR will follow its Harassment Reporting and Complaint Procedure. + +## Process for Changes +All UCAR managed projects are required to adopt this Contributor Code of Conduct. +Adoption is assumed even if not expressly stated in the repository. +Projects should fill in sections where prompted with project-specific information, including, project name and adoption date. + +Projects that adopt this Code of Conduct need to stay up to date with UCAR's Contributor Code of Conduct, linked with a DOI in the +[Attribution](#attribution) section below. +Projects can make limited substantive changes to the Code of Conduct, however, the changes must be limited in scope and may not +contradict the UCAR Contributor Code of Conduct. ## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version] - -[homepage]: http://contributor-covenant.org -[version]: http://contributor-covenant.org/version/1/4/ +This Code of Conduct was originally adapted from the [Contributor Covenant](http://contributor-covenant.org/version/1/4), version +1.4. +We then aligned it with the UCAR Participant Code of Conduct, which also borrows from the American Geophysical Union (AGU) Code of +Conduct. +The UCAR Participant Code of Conduct applies to both UCAR employees as well as participants in activities run by UCAR. +The original version of this for all software projects that have strong management from UCAR or UCAR staff is available on the UCAR +website at https://doi.org/10.5065/6w2c-a132. +The date that it was adopted by this project was **Feb/13/2018**. +When responding to complaints, UCAR HR and ODEI will do so based on the latest published version. +Therefore, any project-specific changes should follow the [Process for Changes](#process-for-changes) section above. diff --git a/Copyright b/Copyright deleted file mode 100644 index 21b9688874..0000000000 --- a/Copyright +++ /dev/null @@ -1,75 +0,0 @@ -CESM1.5: Copyright Notice and Disclaimer - -The Community Earth System Model (CESM was developed in cooperation with -the National Science Foundation, the Department of Energy, -the National Aeronautics and Space Administration, and -the University Corporation for Atmospheric Research National Center for Atmospheric Research. - -Except for the segregable components listed below, CESM is public domain software. -There may be other third party tools and libraries that are embedded, and -they may have their own copyright notices and terms. - -The following components are copyrighted and may only be used, modified, -or redistributed under the terms indicated below. - -Code Institution Copyright Terms of Use/Disclaimer ----- ----------- --------- ----------------------- -ESMF University of Copyright University of Illinois/NCSA Open Source License - Illinois/NCSA 2002-2009, - University of - Illinois/NCSA - Open Source - License - -POP,SCRIP,CICE Los Alamos National Copyright 2008 Los Alamos National Security, LLC - Laboratory Los Alamos - National - Security, LLC - -CISM NCAR/LANL/ORNL/SNL/ Copyright GNU Lesser General Public License v. 3 - LBNL/NYU/U. Bristol/ 2004-2018, CISM is free software: you can redistribute it - U. Edinburgh/ GNU Lesser and/or modify it under the terms of the GNU - U. Montana/U. Swansea General Public Lesser General Public License as published by the - License v. 3 Free Software Foundation, either version 3 of the - License, or (at your option) any later version. - -AER RRTMG Atmospheric Copyright AER RRTMG Copyright - and 2002-2010, - Environmental Atmospheric - Research, Inc. and - Environmental - Research, Inc. - -MCT Argonne Copyright 2000, MCT Copyright - National 2010, - Laboratory University of - Chicago. - -ICSSP N/A Copyright 2003, ISCCP Simulator Software - 2010, Steve - Klein and Mark - Webb - -XML/Lite Wadsack-Allen Copyright 2001, The documentation for the Perl XML-Lite - Digital Group 2010 module is no longer available on-line. - Wadsack-Allen - Digital Group - -Inf_NaN Lahey Copyright(c) Copies of this source code, or standalone compiled -_Detection Computer 2003, Lahey files derived from this source may not be sold -module Systems, Inc. Computer without permission from Lahey Computers Systems. - Systems, Inc. All or part of this module may be freely incorporated - into executable programs which are offered for sale. - Otherwise, distribution of all or part of this file is - permitted, provided this copyright notice and header - are included. - - -THIS SOFTWARE IS PROVIDED BY UCAR AND ANY CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, -INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL UCAR OR ANY CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER -IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF -THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/Externals.cfg b/Externals.cfg index 090732ee79..0a0f4d24e9 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -8,7 +8,7 @@ required = True local_path = components/cism protocol = git repo_url = https://github.com/ESCOMP/CISM-wrapper -tag = cism-release-cesm2.1.2_01 +tag = cism2_1_68 externals = Externals_CISM.cfg required = True @@ -16,21 +16,22 @@ required = True local_path = components/rtm protocol = git repo_url = https://github.com/ESCOMP/RTM -tag = release-cesm2.0.04 +tag = rtm1_0_71 required = True [mosart] local_path = components/mosart protocol = git repo_url = https://github.com/ESCOMP/MOSART -tag = release-cesm2.0.04 +tag = mosart1_0_36 required = True [cime] local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime5.6.28 +tag = cime5.8.19 +externals = ../Externals_cime.cfg required = True [externals_description] diff --git a/Externals_cime.cfg b/Externals_cime.cfg new file mode 100644 index 0000000000..4751386a44 --- /dev/null +++ b/Externals_cime.cfg @@ -0,0 +1,9 @@ +[cmeps] +hash = 253f612acae07b2b1dc73c84f1bb30b8e1b86ddd +protocol = git +repo_url = https://github.com/ESCOMP/CMEPS.git +local_path = src/drivers/nuopc/ +required = True + +[externals_description] +schema_version = 1.0.0 diff --git a/README b/README index 92e7a77e81..e8db3de87f 100644 --- a/README +++ b/README @@ -32,6 +32,7 @@ test -------------- CLM Testing scripts for CLM offline tools. tools ------------- CLM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CLM settings manage_externals -- Script to manage the external source directories +python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere) Directory structure only for a CTSM checkout: @@ -61,15 +62,22 @@ README.rst --------------- File that displays under the project in github README_EXTERNALS.rst ----- Information on how to work with subversion externals for clm CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project Copyright ---------------- CESM Copyright file -doc/UpdateChangeLog.pl ------- Script to add documentation on a tag to the +doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the ChangeLog/ChangeSum files -doc/ChangeLog ---------------- Documents different CLM versions -doc/ChangeSum ---------------- Summary documentation of different CLM versions +doc/ChangeLog ------------ Documents different CLM versions +doc/ChangeSum ------------ Summary documentation of different CLM versions + +doc/design --------------- Software Engineering and code design document files + +Checklists for standard Software Engineering tasks + +./doc/README.CHECKLIST.master_tags +./bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md Documentation of Namelist Items: (view the following in a web browser) -bld/namelist_files/namelist_definition.xml --- Definition of all namelist items -bld/namelist_files/namelist_defaults_clm4_5.xml - Default values for CLM4.5/CLM5.0 +bld/namelist_files/namelist_definition_ctsm.xml --- Definition of all namelist items +bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values ============================================================================================= Important files in main directories (under $CTSMROOT): @@ -77,7 +85,13 @@ Important files in main directories (under $CTSMROOT): Externals.cfg --------------- File for management of the main high level externals Externals_CLM.cfg ----------- File for management of the CLM specific externals (i.e. FATES) + +run_sys_tests --------------- Python script to send the standard CTSM testing off (submits + the create_test test suite for several different compilers on the + machines we do standard CTSM testing on). + parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test + (can be used along with run_sys_tests) doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts. doc/IMPORTANT_NOTES --------- Some important notes about this version of clm, configuration modes and namelist items @@ -87,7 +101,7 @@ doc/ChangeSum --------------- Summary one-line list of changes for each model version. doc/README ------------------ Documentation similar to this file doc/UsersGuide -------------- CLM Users Guide -doc/CodeReference ----------- CLM Code Reference Guide +doc/IMPORTANT_NOTES --------- Some important notes on caveats for some configurations/namelist items bld/README ------------------ Description of how to use the configure and build-namelist scripts. @@ -144,8 +158,6 @@ src/utils --------- Utility codes src/unit_test_shr - Unit test shared modules for unit testing src/unit_test_stubs Unit test stubs that replicate CTSM code simpler -src_clm40 --------- CLM4.0 source code directory - ============================================================================================= QUICKSTART: using the CPL7 scripts ============================================================================================= diff --git a/README.rst b/README.rst index 6569f5f809..193d806898 100644 --- a/README.rst +++ b/README.rst @@ -2,6 +2,9 @@ CTSM ==== +.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3739617.svg + :target: https://doi.org/10.5281/zenodo.3739617 + The Community Terrestrial Systems Model. This includes the Community Land Model (CLM5.0 and CLM4.5) of the Community Earth System Model. @@ -23,6 +26,11 @@ and https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup +For support with model use, troubleshooting, etc., please use the CTSM forum (or other +appropriate forum) here: + +https://xenforo.cgd.ucar.edu/cesm/ + To get updates on CTSM tags and important notes on CTSM developments join our low traffic email list: diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 5f5d86e5e3..32f2bdd255 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -62,6 +62,9 @@ REQUIRED OPTIONS -cimeroot "directory" Path to cime directory -config "filepath" Read the given CLM configuration cache file. Default: "config_cache.xml". + -configuration "cfg" The overall configuration being used [ clm | nwp ] + clm = Climate configuration + nwp = Numerical Weather Prediction configuration -d "directory" Directory where output namelist file will be written Default: current working directory. -envxml_dir "directory" Directory name of env_*.xml case files to read in. @@ -78,6 +81,7 @@ REQUIRED OPTIONS (i.e. PtVg, 1850, 2000, 2010, 1850-2000, 1850-2100) "-sim_year list" to list valid simulation years (default 2000) + -structure "structure" The overall structure being used [ standard | fast ] OPTIONS -bgc "value" Build CLM with BGC package [ sp | cn | bgc | fates ] (default is sp). @@ -85,11 +89,9 @@ OPTIONS sp = Satellite Phenology (SP) This toggles off the namelist variable: use_cn cn = Carbon Nitrogen model (CN) - (or CLM45CN if phys=clm4_5/clm5_0) This toggles on the namelist variable: use_cn bgc = Carbon Nitrogen with methane, nitrification, vertical soil C, CENTURY decomposition - (or CLM45BGC if phys=clm4_5/clm5_0) This toggles on the namelist variables: use_cn, use_lch4, use_nitrif_denitrif, use_vertsoilc, use_century_decomp fates = FATES/Ecosystem Demography with below ground BGC @@ -106,9 +108,6 @@ OPTIONS , also by default turn on Accelerated Decomposition mode which is controlled by the namelist variable spinup_state. - BGC Spinup for CLM4.5/5.0 Only (for CLM4.0 BGC spinup is controlled from configure) - - Turn on given spinup mode for BGC setting of CN on : Turn on Accelerated Decomposition (spinup_state = 1 or 2) off : run in normal mode (spinup_state = 0) @@ -162,13 +161,14 @@ OPTIONS -dynamic_vegetation Toggle for dynamic vegetation model. (default is off) (can ONLY be turned on when BGC type is 'cn' or 'bgc') This turns on the namelist variable: use_cndv + (Deprecated, this will be removed) -fire_emis Produce a fire_emis_nl namelist that will go into the "drv_flds_in" file for the driver to pass fire emissions to the atm. (Note: buildnml copies the file for use by the driver) -glc_nec Glacier number of elevation classes [0 | 3 | 5 | 10 | 36] (default is 0) (standard option with land-ice model is 10) -help [or -h] Print usage to STDOUT. - -light_res Resolution of lightning dataset to use for CN fire (hcru or T62) + -light_res Resolution of lightning dataset to use for CN fire (360x720 or 94x192) -ignore_ic_date Ignore the date on the initial condition files when determining what input initial condition file to use. -ignore_ic_year Ignore just the year part of the date on the initial condition files @@ -189,9 +189,6 @@ OPTIONS form \$CASEDIR/user_nl_clm/user_nl_clm_????) -inputdata "filepath" Writes out a list containing pathnames for required input datasets in file specified. - -irrig "value" If .true. week surface datasets with irrigation turned on. (only allowed for CLM4.0 physics) - Default: .false. - (for CLM4.5/CLM5.0 physics set the namelist flag irrigate=.true.) -l_ncpl "LND_NCPL" Number of CLM coupling time-steps in a day. -lnd_tuning_mode "value" Use the parameters tuned for the given configuration (CLM version and atmospheric forcing) -mask "landmask" Type of land-mask (default, navy, gx3v5, gx1v5 etc.) @@ -249,6 +246,7 @@ sub process_commandline { my %opts = ( cimeroot => undef, config => "config_cache.xml", + configuration => undef, csmdata => undef, clm_usr_name => undef, co2_type => undef, @@ -263,6 +261,7 @@ sub process_commandline { dir => "$cwd", ssp_rcp => "default", sim_year => "default", + structure => undef, clm_accelerated_spinup=> "default", chk_res => undef, note => undef, @@ -270,7 +269,6 @@ sub process_commandline { output_reals_filename => undef, fire_emis => 0, megan => "default", - irrig => "default", res => "default", silent => 0, ignore_warnings => 0, @@ -290,6 +288,7 @@ sub process_commandline { "co2_ppmv=f" => \$opts{'co2_ppmv'}, "co2_type=s" => \$opts{'co2_type'}, "config=s" => \$opts{'config'}, + "configuration=s" => \$opts{'configuration'}, "csmdata=s" => \$opts{'csmdata'}, "clm_usr_name=s" => \$opts{'clm_usr_name'}, "envxml_dir=s" => \$opts{'envxml_dir'}, @@ -301,7 +300,6 @@ sub process_commandline { "megan!" => \$opts{'megan'}, "glc_nec=i" => \$opts{'glc_nec'}, "light_res=s" => \$opts{'light_res'}, - "irrig=s" => \$opts{'irrig'}, "d:s" => \$opts{'dir'}, "h|help" => \$opts{'help'}, "ignore_ic_date" => \$opts{'ignore_ic_date'}, @@ -317,6 +315,7 @@ sub process_commandline { "ssp_rcp=s" => \$opts{'ssp_rcp'}, "s|silent" => \$opts{'silent'}, "sim_year=s" => \$opts{'sim_year'}, + "structure=s" => \$opts{'structure'}, "output_reals=s" => \$opts{'output_reals_filename'}, "clm_accelerated_spinup=s" => \$opts{'clm_accelerated_spinup'}, "clm_start_type=s" => \$opts{'clm_start_type'}, @@ -428,7 +427,7 @@ sub read_configure_definition { if ( -f $opts->{'config'} ) { $configfile = $opts->{'config'}; } else { - $configfile = "$cfgdir/config_files/config_definition.xml"; + $configfile = "$cfgdir/config_files/config_definition_ctsm.xml"; } # Check that configuration cache file exists. @@ -445,14 +444,13 @@ sub read_configure_definition { #----------------------------------------------------------------------------------------------- sub read_namelist_definition { - my ($cfgdir, $opts, $nl_flags, $physv) = @_; + my ($cfgdir, $opts, $nl_flags) = @_; # The namelist definition file contains entries for all namelist # variables that can be output by build-namelist. - my $phys = $physv->as_filename( ); my @nl_definition_files = ( "$cfgdir/namelist_files/namelist_definition_drv.xml", "$cfgdir/namelist_files/namelist_definition_drv_flds.xml", - "$cfgdir/namelist_files/namelist_definition_$phys.xml" ); + "$cfgdir/namelist_files/namelist_definition_ctsm.xml" ); foreach my $nl_defin_file ( @nl_definition_files ) { (-f "$nl_defin_file") or $log->fatal_error("Cannot find namelist definition file \"$nl_defin_file\""); @@ -504,12 +502,11 @@ sub read_envxml_case_files { #----------------------------------------------------------------------------------------------- sub read_namelist_defaults { - my ($cfgdir, $opts, $nl_flags, $cfg, $physv) = @_; + my ($cfgdir, $opts, $nl_flags, $cfg) = @_; - my $phys = $physv->as_filename( ); # The namelist defaults file contains default values for all required namelist variables. my @nl_defaults_files = ( "$cfgdir/namelist_files/namelist_defaults_overall.xml", - "$cfgdir/namelist_files/namelist_defaults_$phys.xml", + "$cfgdir/namelist_files/namelist_defaults_ctsm.xml", "$cfgdir/namelist_files/namelist_defaults_drv.xml", "$cfgdir/namelist_files/namelist_defaults_fire_emis.xml", "$cfgdir/namelist_files/namelist_defaults_drydep.xml" ); @@ -608,12 +605,12 @@ sub process_namelist_user_input { process_namelist_commandline_infile($opts, $definition, $nl, $envxml_ref); # Apply the commandline options and make sure the user didn't change it above - process_namelist_commandline_options($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv); + process_namelist_commandline_options($opts, $nl_flags, $definition, $defaults, $nl, $physv); # The last two process command line arguments for usr_name and use_case # They require that process_namelist_commandline_options was called before this process_namelist_commandline_clm_usr_name($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $envxml_ref); - process_namelist_commandline_use_case($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $envxml_ref, $physv); + process_namelist_commandline_use_case($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $envxml_ref); # Set the start_type by the command line setting for clm_start_type process_namelist_commandline_clm_start_type($opts, $nl_flags, $definition, $defaults, $nl); @@ -628,29 +625,26 @@ sub process_namelist_commandline_options { # First get the command-line specified overall values or their defaults # Obtain default values for the following build-namelist input arguments # : res, mask, ssp_rcp, sim_year, sim_year_range, and clm_accelerated_spinup. - # - # NOTE: cfg only needs to be passed to functions that work with - # clm4_0 compile time functionality! - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; setup_cmdl_chk_res($opts, $defaults); setup_cmdl_resolution($opts, $nl_flags, $definition, $defaults); setup_cmdl_mask($opts, $nl_flags, $definition, $defaults, $nl); - setup_cmdl_bgc($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv); - setup_cmdl_fire_light_res($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv); - setup_cmdl_spinup($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv); - setup_cmdl_crop($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv); - setup_cmdl_maxpft($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv); + setup_cmdl_configuration_and_structure($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_bgc($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_fire_light_res($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_spinup($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_crop($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_maxpft($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_glc_nec($opts, $nl_flags, $definition, $defaults, $nl); - setup_cmdl_irrigation($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_cmdl_ssp_rcp($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_simulation_year($opts, $nl_flags, $definition, $defaults, $nl); - setup_cmdl_dynamic_vegetation($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_cmdl_fates_mode($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_cmdl_vichydro($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_cmdl_dynamic_vegetation($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_fates_mode($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_vichydro($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_run_type($opts, $nl_flags, $definition, $defaults, $nl); - setup_cmdl_output_reals($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_cmdl_output_reals($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_lnd_tuning($opts, $nl_flags, $definition, $defaults, $nl, $physv); } @@ -725,15 +719,15 @@ sub setup_cmdl_fates_mode { # # call this at least after crop check is called # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var = "bgc_mode"; - if ( $physv->as_long() == $physv->as_long("clm4_0") || $nl_flags->{'crop'} eq "on" ) { + if ( $nl_flags->{'crop'} eq "on" ) { if ( $nl_flags->{$var} eq "fates" ) { - # ED is not a clm4_0 option and should not be used with crop and not with clm4_0 - $log->fatal_error("** Cannot turn fates mode on with crop or with clm4_0 physics." ); + # FATES should not be used with crop + $log->fatal_error("** Cannot turn fates mode on with crop." ); } } elsif ($nl_flags->{"bgc_mode"} eq "fates" && ! &value_is_true($nl_flags->{"use_fates"}) ) { $log->fatal_error("DEV_ERROR: internal logic error: bgc_mode = fates and use_fates = false."); @@ -786,11 +780,36 @@ sub setup_cmdl_fates_mode { } } +#------------------------------------------------------------------------------- +sub setup_cmdl_configuration_and_structure { + # Error-check and set the 'configuration' and 'structure' namelist flags + + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + my $val; + + my $var = "configuration"; + $val = $opts->{$var}; + if (defined($val) && ($val eq "clm" || $val eq "nwp")) { + $nl_flags->{$var} = $val; + } else { + $log->fatal_error("$var has a value (".$val.") that is NOT valid. Valid values are: clm, nwp."); + } + + $var = "structure"; + $val = $opts->{$var}; + if (defined($val) && ($val eq "standard" || $val eq "fast")) { + $nl_flags->{$var} = $val; + } else { + $log->fatal_error("$var has a value (".$val.") that is NOT valid. Valid values are: standard, fast."); + } +} + #------------------------------------------------------------------------------- sub setup_cmdl_bgc { # BGC - alias for group of biogeochemistry related use_XXX namelists - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var = "bgc"; @@ -798,95 +817,87 @@ sub setup_cmdl_bgc { $val = $opts->{$var}; $nl_flags->{'bgc_mode'} = $val; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - if ( $nl_flags->{'bgc_mode'} ne "default" ) { - $log->fatal_error("-bgc option used with clm4_0 physics. -bgc can ONLY be used with clm4_5/clm5_0 physics"); - } - $nl_flags->{'bgc_mode'} = $cfg->get($var); + my $var = "bgc_mode"; + if ( $nl_flags->{$var} eq "default" ) { + $nl_flags->{$var} = $defaults->get_value($var); + } + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, quote_string( $nl_flags->{$var} ) ); + if ( ! $definition->is_valid_value( $var, quote_string( $nl_flags->{$var}) ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); + } + $log->verbose_message("Using $nl_flags->{$var} for bgc."); + + # now set the actual name list variables based on the bgc alias + if ($nl_flags->{$var} eq "cn" ) { + $nl_flags->{'use_cn'} = ".true."; + $nl_flags->{'use_fates'} = ".false."; + } elsif ($nl_flags->{$var} eq "bgc" ) { + $nl_flags->{'use_cn'} = ".true."; + $nl_flags->{'use_fates'} = ".false."; + } elsif ($nl_flags->{$var} eq "fates" ) { + $nl_flags->{'use_cn'} = ".false."; + $nl_flags->{'use_fates'} = ".true."; } else { - my $var = "bgc_mode"; - if ( $nl_flags->{$var} eq "default" ) { - $nl_flags->{$var} = $defaults->get_value($var); - } - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, quote_string( $nl_flags->{$var} ) ); - if ( ! $definition->is_valid_value( $var, quote_string( $nl_flags->{$var}) ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); - } - $log->verbose_message("Using $nl_flags->{$var} for bgc."); - - # now set the actual name list variables based on the bgc alias - if ($nl_flags->{$var} eq "cn" ) { - $nl_flags->{'use_cn'} = ".true."; - $nl_flags->{'use_fates'} = ".false."; - } elsif ($nl_flags->{$var} eq "bgc" ) { - $nl_flags->{'use_cn'} = ".true."; - $nl_flags->{'use_fates'} = ".false."; - } elsif ($nl_flags->{$var} eq "fates" ) { - $nl_flags->{'use_cn'} = ".false."; - $nl_flags->{'use_fates'} = ".true."; - } else { - $nl_flags->{'use_cn'} = ".false."; - $nl_flags->{'use_fates'} = ".false."; - } - if ( defined($nl->get_value("use_cn")) && ($nl_flags->{'use_cn'} ne $nl->get_value("use_cn")) ) { - $log->fatal_error("The namelist variable use_cn is inconsistent with the -bgc option"); - } - if ( defined($nl->get_value("use_fates")) && ($nl_flags->{'use_fates'} ne $nl->get_value("use_fates")) ) { - $log->fatal_error("The namelist variable use_fates is inconsistent with the -bgc option"); - } + $nl_flags->{'use_cn'} = ".false."; + $nl_flags->{'use_fates'} = ".false."; + } + if ( defined($nl->get_value("use_cn")) && ($nl_flags->{'use_cn'} ne $nl->get_value("use_cn")) ) { + $log->fatal_error("The namelist variable use_cn is inconsistent with the -bgc option"); + } + if ( defined($nl->get_value("use_fates")) && ($nl_flags->{'use_fates'} ne $nl->get_value("use_fates")) ) { + $log->fatal_error("The namelist variable use_fates is inconsistent with the -bgc option"); + } - { - # If the variable has already been set use it, if not set to the value defined by the bgc_mode - my @list = ( "use_lch4", "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp" ); - my $ndiff = 0; - my %settings = ( 'bgc_mode'=>$nl_flags->{'bgc_mode'} ); - foreach my $var ( @list ) { - my $default_setting = $defaults->get_value($var, \%settings ); - if ( ! defined($nl->get_value($var)) ) { - $nl_flags->{$var} = $default_setting; - } else { - if ( $nl->get_value($var) ne $default_setting ) { - $ndiff += 1; - } - $nl_flags->{$var} = $nl->get_value($var); - } - $val = $nl_flags->{$var}; - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } - } - # If all the variables are different report it as an error - if ( $ndiff == ($#list + 1) ) { - $log->fatal_error("You are contradicting the -bgc setting with the namelist variables: @list" ); - } - } + { + # If the variable has already been set use it, if not set to the value defined by the bgc_mode + my @list = ( "use_lch4", "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp" ); + my $ndiff = 0; + my %settings = ( 'bgc_mode'=>$nl_flags->{'bgc_mode'} ); + foreach my $var ( @list ) { + my $default_setting = $defaults->get_value($var, \%settings ); + if ( ! defined($nl->get_value($var)) ) { + $nl_flags->{$var} = $default_setting; + } else { + if ( $nl->get_value($var) ne $default_setting ) { + $ndiff += 1; + } + $nl_flags->{$var} = $nl->get_value($var); + } + $val = $nl_flags->{$var}; + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $val); + if ( ! $definition->is_valid_value( $var, $val ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); + } + } + # If all the variables are different report it as an error + if ( $ndiff == ($#list + 1) ) { + $log->fatal_error("You are contradicting the -bgc setting with the namelist variables: @list" ); + } + } - # Now set use_cn and use_fates - foreach $var ( "use_cn", "use_fates" ) { - $val = $nl_flags->{$var}; - $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } - } + # Now set use_cn and use_fates + foreach $var ( "use_cn", "use_fates" ) { + $val = $nl_flags->{$var}; + $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $val); + if ( ! $definition->is_valid_value( $var, $val ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); + } } - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - my $var = "use_fun"; - if ( ! defined($nl->get_value($var)) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, - 'use_nitrif_denitrif'=>$nl_flags->{'use_nitrif_denitrif'} ); - } - if ( (! &value_is_true($nl_flags->{'use_nitrif_denitrif'}) ) && &value_is_true($nl->get_value('use_fun')) ) { - $log->fatal_error("When FUN is on, use_nitrif_denitrif MUST also be on!"); - } + + my $var = "use_fun"; + if ( ! defined($nl->get_value($var)) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, + 'use_nitrif_denitrif'=>$nl_flags->{'use_nitrif_denitrif'} ); + } + if ( (! &value_is_true($nl_flags->{'use_nitrif_denitrif'}) ) && &value_is_true($nl->get_value('use_fun')) ) { + $log->fatal_error("When FUN is on, use_nitrif_denitrif MUST also be on!"); } } # end bgc @@ -895,170 +906,129 @@ sub setup_cmdl_bgc { sub setup_cmdl_fire_light_res { # light_res - alias for lightning resolution - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = "light_res"; my $val = $opts->{$var}; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - if ( $val !~ /default|none/ ) { - $log->fatal_error("-$var option used with clm4_0 physics. -$var can ONLY be used with clm4_5/clm5_0 physics"); - } + if ( $val eq "default" ) { + $nl_flags->{$var} = remove_leading_and_trailing_quotes($defaults->get_value($var)); } else { - if ( $val eq "default" ) { - $nl_flags->{$var} = remove_leading_and_trailing_quotes($defaults->get_value($var)); - } else { - my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); - if ( defined($fire_method) && $val ne "none" ) { - if ( $fire_method eq "nofire" ) { + my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); + if ( defined($fire_method) && $val ne "none" ) { + if ( $fire_method eq "nofire" ) { $log->fatal_error("-$var option used with fire_method='nofire'. -$var can ONLY be used without the nofire option"); - } - } - my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') ); - if ( defined($stream_fldfilename_lightng) && $val ne "none" ) { - $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); - } - if ( ! &value_is_true($nl->get_value('use_cn')) ) { - $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); - } - if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { - $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); - } - $nl_flags->{$var} = $val; - } - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); - if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); - } - $log->verbose_message("Using $nl_flags->{$var} for $var."); - # - # Set flag if cn-fires are on or not - # - $var = "cnfireson"; - if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl->get_value('use_cn')) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method'); - } - my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); - if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) ) { - $log->fatal_error("fire_method is being set even though bgc is NOT cn or bgc."); - } - if ( defined($fire_method) && $fire_method eq "nofire" ) { - $nl_flags->{$var} = ".false."; - } elsif ( &value_is_true($nl->get_value('use_cn')) ) { - $nl_flags->{$var} = ".true."; - } else { - $nl_flags->{$var} = ".false."; - } + } + } + my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') ); + if ( defined($stream_fldfilename_lightng) && $val ne "none" ) { + $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); + } + if ( ! &value_is_true($nl->get_value('use_cn')) ) { + $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); + } + if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { + $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); + } + $nl_flags->{$var} = $val; + } + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); + if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); + } + $log->verbose_message("Using $nl_flags->{$var} for $var."); + # + # Set flag if cn-fires are on or not + # + $var = "cnfireson"; + if ( &value_is_true($nl->get_value('use_cn')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method'); + } + my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); + if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) ) { + $log->fatal_error("fire_method is being set even though bgc is NOT cn or bgc."); + } + if ( defined($fire_method) && $fire_method eq "nofire" ) { + $nl_flags->{$var} = ".false."; + } elsif ( &value_is_true($nl->get_value('use_cn')) ) { + $nl_flags->{$var} = ".true."; + } else { + $nl_flags->{$var} = ".false."; } } #------------------------------------------------------------------------------- sub setup_cmdl_crop { - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; $nl_flags->{'use_crop'} = ".false."; my $val; my $var = "crop"; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - $nl_flags->{'crop'} = $cfg->get($var); - if ( $nl_flags->{'crop'} eq "on" ) { - $nl_flags->{'use_crop'} = ".true."; - } - } else { - $val = $opts->{$var}; - $nl_flags->{'crop'} = $val; - if ( $nl_flags->{'crop'} eq 1 ) { - $nl_flags->{'use_crop'} = ".true."; - } - if ( defined($nl->get_value("use_crop")) && ($nl_flags->{'use_crop'} ne $nl->get_value("use_crop")) ) { - $log->fatal_error("Namelist item use_crop contradicts the command-line option -crop, use the command line option"); - } - if ( ($nl_flags->{'crop'} eq 1 ) && ($nl_flags->{'bgc_mode'} eq "sp") ) { - $log->fatal_error("** Cannot turn crop mode on mode bgc=sp\n" . - "**\n" . - "** Set the bgc mode to 'cn' or 'bgc' by the following means from highest to lowest precedence:\n" . - "** * by the command-line options -bgc cn\n" . - "** * by a default configuration file, specified by -defaults"); - } + $val = $opts->{$var}; + $nl_flags->{'crop'} = $val; + if ( $nl_flags->{'crop'} eq 1 ) { + $nl_flags->{'use_crop'} = ".true."; + } + if ( defined($nl->get_value("use_crop")) && ($nl_flags->{'use_crop'} ne $nl->get_value("use_crop")) ) { + $log->fatal_error("Namelist item use_crop contradicts the command-line option -crop, use the command line option"); + } + if ( ($nl_flags->{'crop'} eq 1 ) && ($nl_flags->{'bgc_mode'} eq "sp") ) { + $log->fatal_error("** Cannot turn crop mode on mode bgc=sp\n" . + "**\n" . + "** Set the bgc mode to 'cn' or 'bgc' by the following means from highest to lowest precedence:\n" . + "** * by the command-line options -bgc cn\n" . + "** * by a default configuration file, specified by -defaults"); + } - $var = "use_crop"; - $val = ".false."; - if ($nl_flags->{'crop'} eq 1) { - $val = ".true."; - } - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } + $var = "use_crop"; + $val = ".false."; + if ($nl_flags->{'crop'} eq 1) { + $val = ".true."; + } + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $val); + if ( ! $definition->is_valid_value( $var, $val ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); } } #------------------------------------------------------------------------------- sub setup_cmdl_maxpft { - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var = "maxpft"; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - $nl_flags->{'maxpft'} = $cfg->get($var); - # NOTE: maxpatchpft sizes already checked for clm4_0 by configure. + my %maxpatchpft; + $maxpatchpft{'.true.'} = 79; + $maxpatchpft{'.false.'} = 17; + if ( $opts->{$var} ne "default") { + $val = $opts->{$var}; } else { - my %maxpatchpft; - $maxpatchpft{'.true.'} = 79; - $maxpatchpft{'.false.'} = 17; - if ( $opts->{$var} ne "default") { - $val = $opts->{$var}; - } else { - $val = $maxpatchpft{$nl_flags->{'use_crop'}}; - } - $nl_flags->{'maxpft'} = $val; - - if ( ($nl_flags->{'bgc_mode'} ne "sp") && ($nl_flags->{'maxpft'} != $maxpatchpft{$nl_flags->{'use_crop'}}) ) { - $log->fatal_error("** For CN or BGC mode you MUST set max patch PFT's to $maxpatchpft{$nl_flags->{'use_crop'}}\n" . - "**\n" . - "** When the crop model is on then it must be set to $maxpatchpft{'crop'} otherwise to $maxpatchpft{'nocrop'}\n" . - "** Set the bgc mode, crop and maxpft by the following means from highest to lowest precedence:\n" . - "** * by the command-line options -bgc, -crop and -maxpft\n" . - "** * by a default configuration file, specified by -defaults\n" . - "**"); - } - if ( $nl_flags->{'maxpft'} > $maxpatchpft{$nl_flags->{'use_crop'}} ) { - $log->fatal_error("** Max patch PFT's can NOT exceed $maxpatchpft{$nl_flags->{'use_crop'}}\n" . - "**\n" . - "** Set maxpft by the following means from highest to lowest precedence:\n" . - "** * by the command-line options -maxpft\n" . - "** * by a default configuration file, specified by -defaults\n" . - "**"); - } - if ( $nl_flags->{'maxpft'} != $maxpatchpft{$nl_flags->{'use_crop'}} ) { - $log->warning("running with maxpft NOT equal to $maxpatchpft{$nl_flags->{'use_crop'}} is " . - "NOT validated / scientifically supported." ); - } - $log->verbose_message("Using $nl_flags->{'maxpft'} for maxpft."); + $val = $maxpatchpft{$nl_flags->{'use_crop'}}; + } + $nl_flags->{'maxpft'} = $val; - $var = "maxpatch_pft"; - my $group = $definition->get_group_name($var); - if ( ! defined($nl->get_variable_value($group, $var)) ) { - $val = $nl_flags->{'maxpft'}; - $nl->set_variable_value($group, $var, $val); - } - $val = $nl->get_variable_value($group, $var); - my @valid_values = ($maxpatchpft{'.true.'}, $maxpatchpft{'.false.'} ); - my $found = 0; - foreach my $valid_val ( @valid_values ) { - if ( $val == $valid_val ) { - $found = 1; - last; - } - } - if ( ! $found ) { - $log->warning("$var has a value ($val) that is normally NOT valid. Normal valid values are: @valid_values"); - } + $var = "maxpatch_pft"; + my $group = $definition->get_group_name($var); + if ( ! defined($nl->get_variable_value($group, $var)) ) { + $val = $nl_flags->{'maxpft'}; + $nl->set_variable_value($group, $var, $val); + } + $val = $nl->get_variable_value($group, $var); + my @valid_values = ($maxpatchpft{'.true.'}, $maxpatchpft{'.false.'} ); + my $found = 0; + foreach my $valid_val ( @valid_values ) { + if ( $val == $valid_val ) { + $found = 1; + last; + } + } + if ( ! $found ) { + $log->warning("$var has a value ($val) that is normally NOT valid. Normal valid values are: @valid_values"); } } @@ -1089,43 +1059,6 @@ sub setup_cmdl_glc_nec { #------------------------------------------------------------------------------- -sub setup_cmdl_irrigation { - # Must be after setup_cmdl_crop - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - - my $var = "irrig"; - - if ( $opts->{$var} eq "default" ) { - my %settings; - $settings{'use_crop'} = $nl_flags->{'use_crop'}; - $nl_flags->{$var} = $defaults->get_value($var, \%settings); - } else { - $nl_flags->{$var} = $opts->{$var}; - } - my $val = $nl_flags->{$var}; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } - $log->verbose_message("Irrigation $val"); - if ( &value_is_true($nl_flags->{'irrig'}) && &value_is_true($nl_flags->{'use_crop'}) ) { - $log->fatal_error("You've turned on both irrigation and crop.\n" . - "Irrigation is only applied to generic crop currently,\n" . - "which negates it's practical usage.\n." . - "We also have a known problem when both are on " . - "(see bug 1326 in the components/clm/doc/KnownBugs file)\n" . - "both irrigation and crop can NOT be on."); - } - } elsif ( $opts->{$var} ne "default" ) { - $log->fatal_error("The -irrig option can ONLY be used with clm4_0 physics"); - } -} - -#------------------------------------------------------------------------------- - sub setup_cmdl_ssp_rcp { # shared socioeconmic pathway and representative concentration pathway combination my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; @@ -1151,9 +1084,8 @@ sub setup_cmdl_ssp_rcp { #------------------------------------------------------------------------------- sub setup_cmdl_spinup { - # CLM 4.0 --> BGC spinup mode controlled from "spinup" in configure - # CLM 4.5/5.0 --> BGC spinup mode controlled from "clm_accelerated_spinup" in build-namelist - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_; + # BGC spinup mode controlled from "clm_accelerated_spinup" in build-namelist + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var; @@ -1172,57 +1104,50 @@ sub setup_cmdl_spinup { $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values"); } $log->verbose_message("CLM accelerated spinup mode is $val"); - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - $nl_flags->{'spinup'} = $cfg->get('spinup'); - } elsif ( $physv->as_long() >= $physv->as_long("clm4_5")) { - if ( &value_is_true($nl_flags->{'use_cn'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, - $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{$var}, - use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'} ); - if ( $nl->get_value("spinup_state") ne 0 ) { - $nl_flags->{'bgc_spinup'} = "on"; - if ( $nl_flags->{'bgc_mode'} eq "sp" ) { - $log->fatal_error("spinup_state is accelerated (=1 or 2) which is for a BGC mode of CN or BGC," . - " but the BGC mode is Satellite Phenology, change one or the other"); - } - if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) { - $log->fatal_error("spinup_state is accelerated, but clm_accelerated_spinup is off, change one or the other"); - } - } + if ( &value_is_true($nl_flags->{'use_cn'}) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, + $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{$var}, + use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'} ); + if ( $nl->get_value("spinup_state") ne 0 ) { + $nl_flags->{'bgc_spinup'} = "on"; + if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) { + $log->fatal_error("spinup_state is accelerated, but clm_accelerated_spinup is off, change one or the other"); + } } else { - $nl_flags->{'bgc_spinup'} = "off"; - $val = $defaults->get_value($var); - } - $nl_flags->{$var} = $val; - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, quote_string($val) ); - if ( ! $definition->is_valid_value( $var, $val , 'noquotes' => 1) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values"); - } - if ( $nl_flags->{'bgc_spinup'} eq "on" && (not &value_is_true( $nl_flags->{'use_cn'} )) && (not &value_is_true($nl_flags->{'use_fates'})) ) { - $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor ED is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'})."); - } - if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) { - $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" ); + $nl_flags->{'bgc_spinup'} = "off"; + $val = $defaults->get_value($var); } - if ( $nl->get_value("spinup_state") eq 1 && $nl_flags->{'bgc_spinup'} eq "off" ) { - $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" ); + } else { + if ( defined($nl->get_value("spinup_state")) ) { + $log->fatal_error("spinup_state is accelerated (=1 or 2) which is for a BGC mode of CN or BGC," . + " but the BGC mode is Satellite Phenology, change one or the other"); } } - - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - $val = $nl_flags->{'spinup'}; - } else { - $val = $nl_flags->{'bgc_spinup'}; + $nl_flags->{$var} = $val; + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, quote_string($val) ); + if ( ! $definition->is_valid_value( $var, $val , 'noquotes' => 1) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values"); } + if ( $nl_flags->{'bgc_spinup'} eq "on" && (not &value_is_true( $nl_flags->{'use_cn'} )) && (not &value_is_true($nl_flags->{'use_fates'})) ) { + $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor ED is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'})."); + } + if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) { + $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" ); + } + if ( $nl->get_value("spinup_state") eq 1 && $nl_flags->{'bgc_spinup'} eq "off" ) { + $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" ); + } + + $val = $nl_flags->{'bgc_spinup'}; $log->verbose_message("CLM CN bgc_spinup mode is $val"); } #------------------------------------------------------------------------------- sub setup_cmdl_simulation_year { - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var = "sim_year"; @@ -1293,48 +1218,43 @@ sub setup_cmdl_run_type { #------------------------------------------------------------------------------- sub setup_cmdl_dynamic_vegetation { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var = "dynamic_vegetation"; $val = $opts->{$var}; $nl_flags->{'dynamic_vegetation'} = $val; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - # not applicable - if ( $nl_flags->{'dynamic_vegetation'}eq 1) { - $log->fatal_error("** Turn dynamic_vegetation mode on with CLM_CONFIG_OPTS (-bgc cndv) for clm4_0 physics." ); - } - } else { - if ( ($nl_flags->{'dynamic_vegetation'} eq 1 ) && ($nl_flags->{'bgc_mode'} eq "sp") ) { - $log->fatal_error("** Cannot turn dynamic_vegetation mode on with bgc=sp.\n" . - "**\n" . - "** Set the bgc mode to 'cn' or 'bgc' by the following means from highest to lowest precedence:" . - "** * by the command-line options -bgc cn\n"); - } - - $var = "use_cndv"; - $nl_flags->{$var} = ".false."; - if ($nl_flags->{'dynamic_vegetation'} eq 1) { - $val = ".true."; - $nl_flags->{$var} = $val; - } - if ( defined($nl->get_value($var)) && $nl->get_value($var) ne $val ) { - $log->fatal_error("$var is inconsistent with the commandline setting of -dynamic_vegetation"); - } - if ( &value_is_true($nl_flags->{$var}) ) { - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { + if ( ($nl_flags->{'dynamic_vegetation'} eq 1 ) && ($nl_flags->{'bgc_mode'} eq "sp") ) { + $log->fatal_error("** Cannot turn dynamic_vegetation mode on with bgc=sp.\n" . + "**\n" . + "** Set the bgc mode to 'cn' or 'bgc' by the following means from highest to lowest precedence:" . + "** * by the command-line options -bgc cn\n"); + } + + $var = "use_cndv"; + $nl_flags->{$var} = ".false."; + if ($nl_flags->{'dynamic_vegetation'} eq 1) { + $val = ".true."; + $nl_flags->{$var} = $val; + } + if ( defined($nl->get_value($var)) && $nl->get_value($var) ne $val ) { + $log->fatal_error("$var is inconsistent with the commandline setting of -dynamic_vegetation"); + } + if ( &value_is_true($nl_flags->{$var}) ) { + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $val); + if ( ! $definition->is_valid_value( $var, $val ) ) { my @valid_values = $definition->get_valid_values( $var ); $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } - } + } + $log->warning("The use_cndv=T option is deprecated. We do NOT recommend using it." . + " It's known to have issues and it's not calibrated."); } } #------------------------------------------------------------------------------- sub setup_cmdl_output_reals { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = "output_reals_filename"; my $file = $opts->{$var}; @@ -1348,36 +1268,29 @@ sub setup_cmdl_output_reals { #------------------------------------------------------------------------------- sub setup_cmdl_vichydro { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; my $var = "vichydro"; $val = $opts->{$var}; $nl_flags->{'vichydro'} = $val; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - # not relevant in clm4_0 - if ( $nl_flags->{'vichydro'}eq 1) { - $log->fatal_error("** Cannot turn vichydro on with clm4_0 physics." ); - } - } else { - if ($nl_flags->{'vichydro'} eq 1) { - $log->verbose_message("Using VIC hydrology for runoff calculations."); - } + if ($nl_flags->{'vichydro'} eq 1) { + $log->verbose_message("Using VIC hydrology for runoff calculations."); + } - $var = "use_vichydro"; - $val = $nl->get_value($var); - if ($nl_flags->{'vichydro'} eq 1) { - my $group = $definition->get_group_name($var); - my $set = ".true."; - if ( defined($val) && $set ne $val ) { + $var = "use_vichydro"; + $val = $nl->get_value($var); + if ($nl_flags->{'vichydro'} eq 1) { + my $group = $definition->get_group_name($var); + my $set = ".true."; + if ( defined($val) && $set ne $val ) { $log->fatal_error("$var contradicts the command-line -vichydro option" ); - } - $nl->set_variable_value($group, $var, $set); - if ( ! $definition->is_valid_value($var, $val) ) { + } + $nl->set_variable_value($group, $var, $set); + if ( ! $definition->is_valid_value($var, $val) ) { my @valid_values = $definition->get_valid_values( $var ); $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } - } + } } } @@ -1497,7 +1410,7 @@ sub process_namelist_commandline_clm_usr_name { sub process_namelist_commandline_use_case { # Now process the -use_case arg. - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $envxml_ref, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $envxml_ref) = @_; if (defined $opts->{'use_case'}) { @@ -1513,14 +1426,11 @@ sub process_namelist_commandline_use_case { $settings{'sim_year_range'} = $nl_flags->{'sim_year_range'}; $settings{'phys'} = $nl_flags->{'phys'}; $settings{'lnd_tuning_mode'}= $nl_flags->{'lnd_tuning_mode'}; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - $settings{'use_cn'} = $nl_flags->{'use_cn'}; - $settings{'use_cndv'} = $nl_flags->{'use_cndv'}; - $settings{'use_crop'} = $nl_flags->{'use_crop'}; - $settings{'cnfireson'} = $nl_flags->{'cnfireson'}; - } else { - $settings{'bgc'} = $nl_flags->{'bgc_mode'}; - } + $settings{'use_cn'} = $nl_flags->{'use_cn'}; + $settings{'use_cndv'} = $nl_flags->{'use_cndv'}; + $settings{'use_crop'} = $nl_flags->{'use_crop'}; + $settings{'cnfireson'} = $nl_flags->{'cnfireson'}; + # Loop over the variables specified in the use case. # Add each one to the namelist. my @vars = $uc_defaults->get_variable_names(); @@ -1566,97 +1476,92 @@ sub process_namelist_commandline_clm_start_type { sub process_namelist_inline_logic { # Use the namelist default object to add default values for required # namelist variables that have not been previously set. - my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $envxml_ref, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv) = @_; ############################## # namelist group: clm_inparm # ############################## - setup_logic_site_specific($nl_flags, $definition, $nl, $physv); + setup_logic_site_specific($nl_flags, $definition, $nl); setup_logic_lnd_frac($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); setup_logic_co2_type($opts, $nl_flags, $definition, $defaults, $nl); - setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_start_type($opts, $nl_flags, $nl); setup_logic_delta_time($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_decomp_performance($opts, $nl_flags, $definition, $defaults, $nl); - setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv); + setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); setup_logic_dynamic_plant_nitrogen_alloc($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_logic_luna($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_hydrstress($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_hydrstress($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_dynamic_roots($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_params_file($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_create_crop_landunit($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_subgrid($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_fertilizer($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_params_file($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_create_crop_landunit($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_subgrid($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_fertilizer($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_grainproduct($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_soilstate($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_surface_dataset($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_soilstate($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_surface_dataset($opts, $nl_flags, $definition, $defaults, $nl); if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) { setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv); } - setup_logic_dynamic_subgrid($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_spinup($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_fates($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_dynamic_subgrid($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_spinup($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_fates($opts, $nl_flags, $definition, $defaults, $nl); ######################################### # namelist group: atm2lnd_inparm ######################################### - setup_logic_atm_forcing($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_atm_forcing($opts, $nl_flags, $definition, $defaults, $nl); ######################################### # namelist group: lnd2atm_inparm ######################################### - setup_logic_lnd2atm($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_lnd2atm($opts, $nl_flags, $definition, $defaults, $nl); ######################################### # namelist group: clm_humanindex_inparm # ######################################### - setup_logic_humanindex($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_humanindex($opts, $nl_flags, $definition, $defaults, $nl); ################################# # namelist group: cnfire_inparm # ################################# - setup_logic_cnfire($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_cnfire($opts, $nl_flags, $definition, $defaults, $nl); ###################################### # namelist group: cnprecision_inparm # ###################################### - setup_logic_cnprec($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_cnprec($opts, $nl_flags, $definition, $defaults, $nl); ############################### # namelist group: clmu_inparm # ############################### - setup_logic_urban($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_urban($opts, $nl_flags, $definition, $defaults, $nl); ############################### # namelist group: crop # ############################### - setup_logic_crop($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_crop($opts, $nl_flags, $definition, $defaults, $nl); ############################### # namelist group: ch4par_in # ############################### setup_logic_methane($opts, $nl_flags, $definition, $defaults, $nl); - setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl); ############################### # namelist group: ndepdyn_nml # ############################### - setup_logic_nitrogen_deposition($opts, $nl_flags, $definition, $defaults, $nl, $physv); - - ########################################## - # namelist group: soil_moisture_streams # - ########################################## - setup_logic_soilm_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_nitrogen_deposition($opts, $nl_flags, $definition, $defaults, $nl); ################################## # namelist group: cnmresp_inparm # ################################## - setup_logic_cnmresp($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_cnmresp($opts, $nl_flags, $definition, $defaults, $nl); ################################# # namelist group: nitrif_inparm # @@ -1666,22 +1571,22 @@ sub process_namelist_inline_logic { #################################### # namelist group: photosyns_inparm # #################################### - setup_logic_photosyns($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_photosyns($opts, $nl_flags, $definition, $defaults, $nl); ################################# # namelist group: popd_streams # ################################# - setup_logic_popd_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_popd_streams($opts, $nl_flags, $definition, $defaults, $nl); #################################### # namelist group: urbantv_streams # #################################### - setup_logic_urbantv_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_urbantv_streams($opts, $nl_flags, $definition, $defaults, $nl); ################################## # namelist group: light_streams # ################################## - setup_logic_lightning_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_lightning_streams($opts, $nl_flags, $definition, $defaults, $nl); ################################# # namelist group: drydep_inparm # @@ -1691,7 +1596,7 @@ sub process_namelist_inline_logic { ################################# # namelist group: fire_emis_nl # ################################# - setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl); ################################# # namelist group: megan_emis_nl # @@ -1701,7 +1606,12 @@ sub process_namelist_inline_logic { ################################## # namelist group: lai_streams # ################################## - setup_logic_lai_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_lai_streams($opts, $nl_flags, $definition, $defaults, $nl); + + ########################################## + # namelist group: soil_moisture_streams # + ########################################## + setup_logic_soilm_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); ################################## # namelist group: bgc_shared @@ -1711,108 +1621,119 @@ sub process_namelist_inline_logic { ############################################# # namelist group: soilwater_movement_inparm # ############################################# - setup_logic_soilwater_movement($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_soilwater_movement($opts, $nl_flags, $definition, $defaults, $nl); ############################################# # namelist group: rooting_profile_inparm # ############################################# - setup_logic_rooting_profile($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_rooting_profile($opts, $nl_flags, $definition, $defaults, $nl); ############################################# # namelist group: friction_velocity # ############################################# - setup_logic_friction_vel($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_friction_vel($opts, $nl_flags, $definition, $defaults, $nl); ################################################ # namelist group: century_soilbgcdecompcascade # ################################################ - setup_logic_century_soilbgcdecompcascade($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_century_soilbgcdecompcascade($opts, $nl_flags, $definition, $defaults, $nl); ############################# # namelist group: cngeneral # ############################# - setup_logic_cngeneral($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_cngeneral($opts, $nl_flags, $definition, $defaults, $nl); #################################### # namelist group: cnvegcarbonstate # #################################### - setup_logic_cnvegcarbonstate($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_cnvegcarbonstate($opts, $nl_flags, $definition, $defaults, $nl); ############################################# # namelist group: soil_resis_inparm # ############################################# - setup_logic_soil_resis($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_soil_resis($opts, $nl_flags, $definition, $defaults, $nl); ############################################# # namelist group: canopyfluxes_inparm # ############################################# - setup_logic_canopyfluxes($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_canopyfluxes($opts, $nl_flags, $definition, $defaults, $nl); ############################################# # namelist group: canopyhydrology_inparm # ############################################# - setup_logic_canopyhydrology($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_canopyhydrology($opts, $nl_flags, $definition, $defaults, $nl); ##################################### # namelist group: clm_canopy_inparm # ##################################### - setup_logic_canopy($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_canopy($opts, $nl_flags, $definition, $defaults, $nl); ######################################## # namelist group: soilhydrology_inparm # ######################################## - setup_logic_hydrology_params($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_hydrology_params($opts, $nl_flags, $definition, $defaults, $nl); ##################################### # namelist group: irrigation_inparm # ##################################### - setup_logic_irrigation_parameters($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_irrigation_parameters($opts, $nl_flags, $definition, $defaults, $nl); + + ######################################## + # namelist group: surfacealbedo_inparm # + ######################################## + setup_logic_surfacealbedo($opts, $nl_flags, $definition, $defaults, $nl); + + ######################################## + # namelist group: water_tracers_inparm # + ######################################## + setup_logic_water_tracers($opts, $nl_flags, $definition, $defaults, $nl); ####################################################################### # namelist groups: clm_hydrology1_inparm and clm_soilhydrology_inparm # ####################################################################### - setup_logic_hydrology_switches($nl, $physv); + setup_logic_hydrology_switches($opts, $nl_flags, $definition, $defaults, $nl); + + ####################################################################### + # namelist group: scf_swenson_lawrence_2012_inparm # + ####################################################################### + setup_logic_scf_SwensonLawrence2012($opts, $nl_flags, $definition, $defaults, $nl); ######################################### # namelist group: clm_initinterp_inparm # ######################################### - setup_logic_initinterp($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_initinterp($opts, $nl_flags, $definition, $defaults, $nl); } #------------------------------------------------------------------------------- sub setup_logic_site_specific { # site specific requirements - my ($nl_flags, $definition, $nl, $physv) = @_; - - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - # res check prevents polluting the namelist with an unnecessary - # false variable for every run - if ($nl_flags->{'res'} eq "1x1_vancouverCAN") { - my $var = "use_vancouver"; - my $val = ".true."; - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - } + my ($nl_flags, $definition, $nl) = @_; + + # res check prevents polluting the namelist with an unnecessary + # false variable for every run + if ($nl_flags->{'res'} eq "1x1_vancouverCAN") { + my $var = "use_vancouver"; + my $val = ".true."; + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $val); } - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - # res check prevents polluting the namelist with an unnecessary - # false variable for every run - if ($nl_flags->{'res'} eq "1x1_mexicocityMEX") { - my $var = "use_mexicocity"; - my $val = ".true."; - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - } + # res check prevents polluting the namelist with an unnecessary + # false variable for every run + if ($nl_flags->{'res'} eq "1x1_mexicocityMEX") { + my $var = "use_mexicocity"; + my $val = ".true."; + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $val); } - if ( $physv->as_long() >= $physv->as_long("clm4_5") && $nl_flags->{'res'} eq "1x1_smallvilleIA") { + if ($nl_flags->{'res'} eq "1x1_smallvilleIA") { if (! &value_is_true($nl_flags->{'use_cn'}) || ! &value_is_true($nl_flags->{'use_crop'})) { $log->fatal_error("1x1_smallvilleIA grids must use a compset with CN and CROP turned on."); } } - if ( $physv->as_long() >= $physv->as_long("clm4_5") && $nl_flags->{'res'} eq "1x1_numaIA") { + if ($nl_flags->{'res'} eq "1x1_numaIA") { if (! &value_is_true($nl_flags->{'use_cn'}) || ! &value_is_true($nl_flags->{'use_crop'})) { $log->fatal_error("1x1_numaIA grids must use a compset with CN and CROP turned on."); } @@ -1902,17 +1823,15 @@ sub setup_logic_co2_type { #------------------------------------------------------------------------------- sub setup_logic_irrigate { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'irrigate', - 'use_crop'=>$nl_flags->{'use_crop'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'irrigate', + 'use_crop'=>$nl_flags->{'use_crop'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, ); - if ( &value_is_true($nl->get_value('irrigate') ) ) { - $nl_flags->{'irrigate'} = ".true." - } else { - $nl_flags->{'irrigate'} = ".false." - } + if ( &value_is_true($nl->get_value('irrigate') ) ) { + $nl_flags->{'irrigate'} = ".true." + } else { + $nl_flags->{'irrigate'} = ".false." } } @@ -1924,19 +1843,6 @@ sub setup_logic_start_type { my $var = "start_type"; my $drv_start_type = $nl->get_value($var); my $my_start_type = $nl_flags->{'clm_start_type'}; - my $nsrest = $nl->get_value('override_nsrest'); - - if ( defined($nsrest) ) { - if ( $nsrest == 0 ) { $my_start_type = "startup"; } - if ( $nsrest == 1 ) { $my_start_type = "continue"; } - if ( $nsrest == 3 ) { $my_start_type = "branch"; } - if ( "$my_start_type" eq "$drv_start_type" ) { - $log->fatal_error("no need to set override_nsrest to same as start_type."); - } - if ( "$drv_start_type" !~ /startup/ ) { - $log->fatal_error("can NOT set override_nsrest if driver is NOT a startup type."); - } - } if ( $my_start_type =~ /branch/ ) { if (not defined $nl->get_value('nrevsn')) { @@ -1989,11 +1895,8 @@ sub setup_logic_decomp_performance { #------------------------------------------------------------------------------- sub setup_logic_snow { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snowveg_flag', 'phys'=>$nl_flags->{'phys'} ); - } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowaging' ); } @@ -2004,27 +1907,19 @@ sub setup_logic_glacier { # # Glacier multiple elevation class options # - my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_; my $clm_upvar = "GLC_TWO_WAY_COUPLING"; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - # glc_do_dynglacier is set via GLC_TWO_WAY_COUPLING; it cannot be set via - # user_nl_clm (this is because we might eventually want the coupler and glc - # to also respond to GLC_TWO_WAY_COUPLING, by not bothering to send / map - # these fields - so we want to ensure that CLM is truly listening to this - # shared xml variable and not overriding it) - my $var = "glc_do_dynglacier"; - my $val = logical_to_fortran($envxml_ref->{$clm_upvar}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'val'=>$val); - if (lc($nl->get_value($var)) ne lc($val)) { - $log->fatal_error("glc_do_dynglacier can only be set via the env variable $clm_upvar: it can NOT be set in user_nl_clm"); - } - - } else { - # Otherwise if CLM4.0 physics and GLC_TWO_WAY_COUPLING is TRUE -- trigger an error - if ( &value_is_true(logical_to_fortran($envxml_ref->{$clm_upvar})) ) { - $log->fatal_error( "clm4_0 physics are being used, but $clm_upvar variable is set to true. $clm_upvar can ONLY be set for physics after clm4_5" ); - } + # glc_do_dynglacier is set via GLC_TWO_WAY_COUPLING; it cannot be set via + # user_nl_clm (this is because we might eventually want the coupler and glc + # to also respond to GLC_TWO_WAY_COUPLING, by not bothering to send / map + # these fields - so we want to ensure that CLM is truly listening to this + # shared xml variable and not overriding it) + my $var = "glc_do_dynglacier"; + my $val = logical_to_fortran($envxml_ref->{$clm_upvar}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'val'=>$val); + if (lc($nl->get_value($var)) ne lc($val)) { + $log->fatal_error("glc_do_dynglacier can only be set via the env variable $clm_upvar: it can NOT be set in user_nl_clm"); } my $var = "maxpatch_glcmec"; @@ -2035,109 +1930,75 @@ sub setup_logic_glacier { $log->fatal_error("$var set to $val does NOT agree with -glc_nec argument of $nl_flags->{'glc_nec'} (set with GLC_NEC env variable)"); } - if ( $physv->as_long >= $physv->as_long("clm4_5") ) { - if ( $nl_flags->{'glc_nec'} < 1 ) { - $log->fatal_error("For clm4_5 and later, GLC_NEC must be at least 1."); - } - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glc_snow_persistence_max_days'); - - } else { - # clm4_0 - if ( $nl_flags->{'glc_nec'} > 0 ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'flndtopo' , 'hgrid'=>$nl_flags->{'res'}, 'mask'=>$nl_flags->{'mask'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fglcmask' , 'hgrid'=>$nl_flags->{'res'}); - - } else { - # glc_nec == 0 - - # Error checking for glacier multiple elevation class options when glc_mec off - # Make sure various glc_mec-specific logicals are not true, and fglcmask is not set - my $glc_dyntopo= $nl->get_value('glc_dyntopo'); - if ( defined($glc_dyntopo) ) { - if ( &value_is_true($glc_dyntopo) ) { - $log->fatal_error("glc_dyntopo is true, but glc_nec is equal to zero"); - } - } - my $fglcmask = $nl->get_value('fglcmask'); - if ( defined($fglcmask) ) { - $log->fatal_error("fglcmask is set, but glc_nec is equal to zero"); - } - } + if ( $nl_flags->{'glc_nec'} < 1 ) { + $log->fatal_error("GLC_NEC must be at least 1."); } - # Dependence of albice on glc_nec has gone away starting in CLM4_5. Thus, we - # can remove glc_nec from the following call once we ditch CLM4_0. - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'albice', 'glc_nec'=>$nl_flags->{'glc_nec'}); - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_melt_behavior'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_ice_runoff_behavior'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_rain_to_snow_behavior'); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glc_snow_persistence_max_days'); + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'albice'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_melt_behavior'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_ice_runoff_behavior'); } #------------------------------------------------------------------------------- sub setup_logic_params_file { - # get param data. For 4_0, pft-physiology, for 4_5 old - # pft-physiology was used but now now includes CN and BGC century - # parameters. - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + # get param data + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'paramfile', - 'phys'=>$nl_flags->{'phys'}, - 'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} ); - } else { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fpftcon'); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'paramfile', + 'phys'=>$nl_flags->{'phys'}, + 'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} ); } #------------------------------------------------------------------------------- sub setup_logic_create_crop_landunit { # Create crop land unit - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = 'create_crop_landunit'; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - if ( $nl_flags->{'crop'} eq "on" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var ); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'irrig'=>$nl_flags->{'irrig'} ); - } else { - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'use_fates'=>$nl_flags->{'use_fates'} ); - if ( &value_is_true($nl_flags->{'use_fates'}) && &value_is_true($nl->get_value($var)) ) { - $log->fatal_error( "$var is true and yet use_fates is being set, which contradicts that (use_fates requires $var to be .false." ); - } - if ( (! &value_is_true($nl_flags->{'use_fates'})) && (! &value_is_true($nl->get_value($var))) ) { - $log->fatal_error( "$var is false which is ONLY allowed when FATES is being used" ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'use_fates'=>$nl_flags->{'use_fates'} ); + if ( &value_is_true($nl_flags->{'use_fates'}) && &value_is_true($nl->get_value($var)) ) { + $log->fatal_error( "$var is true and yet use_fates is being set, which contradicts that (use_fates requires $var to be .false." ); + } + if ( (! &value_is_true($nl_flags->{'use_fates'})) && (! &value_is_true($nl->get_value($var))) ) { + $log->fatal_error( "$var is false which is ONLY allowed when FATES is being used" ); } } #------------------------------------------------------------------------------- sub setup_logic_subgrid { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = 'run_zero_weight_urban'; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'collapse_urban', + 'structure'=>$nl_flags->{'structure'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'n_dom_landunits', + 'structure'=>$nl_flags->{'structure'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'n_dom_pfts', + 'structure'=>$nl_flags->{'structure'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_soil'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_crop'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_glacier'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_lake'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_wetland'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_urban'); } #------------------------------------------------------------------------------- sub setup_logic_cnfire { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my @fire_consts = ( "rh_low", "rh_hgh", "bt_min", "bt_max", "cli_scale", "boreal_peatfire_c", "non_boreal_peatfire_c", "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel", "cmb_cmplt_fact" ); - if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl->get_value('use_cn')) ) { + if ( &value_is_true($nl->get_value('use_cn')) ) { foreach my $item ( @fire_consts ) { if ( ! &value_is_true($nl_flags->{'cnfireson'} ) ) { if ( defined($nl->get_value($item)) ) { @@ -2150,7 +2011,7 @@ sub setup_logic_cnfire { 'fire_method'=>$fire_method ); } } - } elsif ( $physv->as_long() >= $physv->as_long("clm4_5") ) { + } else { foreach my $item ( @fire_consts ) { if ( defined($nl->get_value($item)) ) { $log->fatal_error( "CN is off which implies that cnfire is off and yet a fire constant ($item) is being set, which contradicts that" ); @@ -2162,9 +2023,9 @@ sub setup_logic_cnfire { #------------------------------------------------------------------------------- sub setup_logic_cnprec { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl_flags->{'use_cn'}) ) { + if ( &value_is_true($nl_flags->{'use_cn'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ncrit', 'use_cn'=>$nl_flags->{'use_cn'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, @@ -2176,25 +2037,17 @@ sub setup_logic_cnprec { #------------------------------------------------------------------------------- sub setup_logic_humanindex { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'calc_human_stress_indices'); - } else { - if ( defined($nl->get_value('calc_human_stress_indices')) ) { - $log->fatal_error( "calc_human_stress_indices can NOT be set, for physics versions less than clm4_5" ); - } - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'calc_human_stress_indices'); } #------------------------------------------------------------------------------- sub setup_logic_urban { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method'); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic'); } @@ -2202,27 +2055,26 @@ sub setup_logic_urban { #------------------------------------------------------------------------------- sub setup_logic_crop { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - if ( &value_is_true($nl->get_value('use_crop')) ) { - my $maptype = 'baset_mapping'; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $maptype, - 'use_crop'=>$nl->get_value('use_crop') ); - my $baset_mapping = remove_leading_and_trailing_quotes( $nl->get_value($maptype) ); - if ( $baset_mapping eq "varytropicsbylat" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "baset_latvary_slope", - 'use_crop'=>$nl->get_value('use_crop'), $maptype=>$baset_mapping ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "baset_latvary_intercept", - 'use_crop'=>$nl->get_value('use_crop'), $maptype=>$baset_mapping ); - } else { - error_if_set( $nl, "Can only be set if $maptype == varytropicsbylat", "baset_latvary_slope", "baset_latvary_intercept" ); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting", - 'use_crop'=>$nl->get_value('use_crop') ); + if ( &value_is_true($nl->get_value('use_crop')) ) { + my $maptype = 'baset_mapping'; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $maptype, + 'use_crop'=>$nl->get_value('use_crop') ); + my $baset_mapping = remove_leading_and_trailing_quotes( $nl->get_value($maptype) ); + if ( $baset_mapping eq "varytropicsbylat" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "baset_latvary_slope", + 'use_crop'=>$nl->get_value('use_crop'), $maptype=>$baset_mapping ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "baset_latvary_intercept", + 'use_crop'=>$nl->get_value('use_crop'), $maptype=>$baset_mapping ); } else { - error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" ); + error_if_set( $nl, "Can only be set if $maptype == varytropicsbylat", "baset_latvary_slope", "baset_latvary_intercept" ); } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting", + 'use_crop'=>$nl->get_value('use_crop') ); + } else { + error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_fsat_equals_zero' ); } } @@ -2241,13 +2093,33 @@ sub error_if_set { #------------------------------------------------------------------------------- sub setup_logic_soilstate { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'organic_frac_squared' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_bedrock', + 'use_fates'=>$nl_flags->{'use_fates'}, 'vichydro'=>$nl_flags->{'vichydro'} ); - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'organic_frac_squared' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_layerstruct' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_bedrock', - 'use_fates'=>$nl_flags->{'use_fates'}, 'vichydro'=>$nl_flags->{'vichydro'} ); + my $var1 = "soil_layerstruct_predefined"; + my $var2 = "soil_layerstruct_userdefined"; + my $var3 = "soil_layerstruct_userdefined_nlevsoi"; + my $soil_layerstruct_predefined = $nl->get_value($var1); + my $soil_layerstruct_userdefined = $nl->get_value($var2); + my $soil_layerstruct_userdefined_nlevsoi = $nl->get_value($var3); + + if (defined($soil_layerstruct_userdefined)) { + if (defined($soil_layerstruct_predefined)) { + $log->fatal_error("You have set both soil_layerstruct_userdefined and soil_layerstruct_predefined in your namelist; model cannot determine which to use"); + } + if (not defined($soil_layerstruct_userdefined_nlevsoi)) { + $log->fatal_error("You have set soil_layerstruct_userdefined and NOT set soil_layerstruct_userdefined_nlevsoi in your namelist; both MUST be set"); + } + } else { + if (defined($soil_layerstruct_userdefined_nlevsoi)) { + $log->fatal_error("You have set soil_layerstruct_userdefined_nlevsoi and NOT set soil_layerstruct_userdefined in your namelist; EITHER set both OR neither; in the latter case soil_layerstruct_predefined will be assigned a default value"); + } else { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_layerstruct_predefined', + 'structure'=>$nl_flags->{'structure'}); + } } } @@ -2257,7 +2129,7 @@ sub setup_logic_demand { # # Deal with options that the user has said are required... # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my %settings; $settings{'hgrid'} = $nl_flags->{'res'}; @@ -2267,20 +2139,16 @@ sub setup_logic_demand { $settings{'crop'} = $nl_flags->{'crop'}; $settings{'ssp_rcp'} = $nl_flags->{'ssp_rcp'}; $settings{'glc_nec'} = $nl_flags->{'glc_nec'}; - if ( $physv->as_long() >= $physv->as_long("clm4_5")) { - # necessary for demand to be set correctly (flanduse_timeseries requires - # use_crop, maybe other options require other flags?)! - $settings{'irrigate'} = $nl_flags->{'irrigate'}; - $settings{'use_cn'} = $nl_flags->{'use_cn'}; - $settings{'use_cndv'} = $nl_flags->{'use_cndv'}; - $settings{'use_lch4'} = $nl_flags->{'use_lch4'}; - $settings{'use_nitrif_denitrif'} = $nl_flags->{'use_nitrif_denitrif'}; - $settings{'use_vertsoilc'} = $nl_flags->{'use_vertsoilc'}; - $settings{'use_century_decomp'} = $nl_flags->{'use_century_decomp'}; - $settings{'use_crop'} = $nl_flags->{'use_crop'}; - } elsif ( $physv->as_long() == $physv->as_long("clm4_0")) { - $settings{'irrig'} = $nl_flags->{'irrig'}; - } + # necessary for demand to be set correctly (flanduse_timeseries requires + # use_crop, maybe other options require other flags?)! + $settings{'irrigate'} = $nl_flags->{'irrigate'}; + $settings{'use_cn'} = $nl_flags->{'use_cn'}; + $settings{'use_cndv'} = $nl_flags->{'use_cndv'}; + $settings{'use_lch4'} = $nl_flags->{'use_lch4'}; + $settings{'use_nitrif_denitrif'} = $nl_flags->{'use_nitrif_denitrif'}; + $settings{'use_vertsoilc'} = $nl_flags->{'use_vertsoilc'}; + $settings{'use_century_decomp'} = $nl_flags->{'use_century_decomp'}; + $settings{'use_crop'} = $nl_flags->{'use_crop'}; my $demand = $nl->get_value('clm_demand'); if (defined($demand)) { @@ -2318,7 +2186,7 @@ sub setup_logic_surface_dataset { # consistent with it # MUST BE AFTER: setup_logic_demand which is where flanduse_timeseries is set # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; $nl_flags->{'flanduse_timeseries'} = "null"; my $flanduse_timeseries = $nl->get_value('flanduse_timeseries'); @@ -2332,27 +2200,16 @@ sub setup_logic_surface_dataset { } $flanduse_timeseries = $nl_flags->{'flanduse_timeseries'}; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - if ($flanduse_timeseries ne "null" && $nl_flags->{'bgc_mode'} eq "cndv" ) { - $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation ('-bgc cndv' in CLM_CONFIG_OPTS)." ); - } - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat', - 'hgrid'=>$nl_flags->{'res'}, - 'sim_year'=>$nl_flags->{'sim_year'}, 'irrig'=>$nl_flags->{'irrig'}, - 'crop'=>$nl_flags->{'crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}); - } else{ - if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) { - $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." ); - } - if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_fates'}) ) { - $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with ecosystem dynamics (use_fates=.true)." ); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat', - 'hgrid'=>$nl_flags->{'res'}, - 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, - 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}); + if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) { + $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." ); + } + if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_fates'}) ) { + $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with ecosystem dynamics (use_fates=.true)." ); } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat', + 'hgrid'=>$nl_flags->{'res'}, + 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, + 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}); } #------------------------------------------------------------------------------- @@ -2364,7 +2221,7 @@ sub setup_logic_initial_conditions { # or just ignore the year of the initial date via the -ignore_ic_year option. # # MUST BE AFTER: setup_logic_demand which is where flanduse_timeseries is set - # AFTER: setup_logic_irrigate which is where irrig (or irrigate) is set + # AFTER: setup_logic_irrigate which is where irrigate is set my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; my $var = "finidat"; @@ -2409,18 +2266,11 @@ sub setup_logic_initial_conditions { } else { delete( $settings{'sim_year'} ); } - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - $settings{'bgc'} = $nl_flags->{'bgc_mode'}; - foreach my $item ( "mask", "maxpft", "irrig", "glc_nec", "crop", "lnd_tuning_mode" ) { - $settings{$item} = $nl_flags->{$item}; - } - } else { - foreach my $item ( "mask", "maxpft", "irrigate", "glc_nec", "use_crop", "use_cn", "use_cndv", - "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp", "use_fates", - "lnd_tuning_mode" - ) { - $settings{$item} = $nl_flags->{$item}; - } + foreach my $item ( "mask", "maxpft", "irrigate", "glc_nec", "use_crop", "use_cn", "use_cndv", + "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp", "use_fates", + "lnd_tuning_mode" + ) { + $settings{$item} = $nl_flags->{$item}; } if ($opts->{'ignore_ic_date'}) { if ( &value_is_true($nl_flags->{'use_crop'}) ) { @@ -2447,7 +2297,7 @@ sub setup_logic_initial_conditions { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, %settings ); # If couldn't find a matching finidat file, check if can turn on interpolation and try to find one again $finidat = $nl->get_value($var); - if ( (not defined $finidat ) && ($physv->as_long() >= $physv->as_long("clm4_5")) ) { + if (not defined $finidat) { # Delete any date settings, except for crop delete( $settings{'ic_ymd'} ); delete( $settings{'ic_md'} ); @@ -2519,12 +2369,17 @@ sub setup_logic_dynamic_subgrid { # # Options controlling which parts of flanduse_timeseries to use # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - setup_logic_do_transient_pfts($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_do_transient_crops($opts, $nl_flags, $definition, $defaults, $nl, $physv); - setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_do_transient_pfts($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_do_transient_crops($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_dynbal_baselines'); + if ( &value_is_true($nl->get_value('reset_dynbal_baselines')) && + &remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) eq "branch") { + $log->fatal_error("reset_dynbal_baselines has no effect in a branch run"); + } } sub setup_logic_do_transient_pfts { @@ -2537,52 +2392,67 @@ sub setup_logic_do_transient_pfts { # - use_cndv # - use_fates # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = 'do_transient_pfts'; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - # Start by assuming a default value of '.true.'. Then check a number of - # conditions under which do_transient_pfts cannot be true. Under these - # conditions: (1) set default value to '.false.'; (2) make sure that the - # value is indeed false (e.g., that the user didn't try to set it to true). + # Start by assuming a default value of '.true.'. Then check a number of + # conditions under which do_transient_pfts cannot be true. Under these + # conditions: (1) set default value to '.false.'; (2) make sure that the + # value is indeed false (e.g., that the user didn't try to set it to true). + + my $default_val = ".true."; + + # cannot_be_true will be set to a non-empty string in any case where + # do_transient_pfts should not be true; if it turns out that + # do_transient_pfts IS true in any of these cases, a fatal error will be + # generated + my $cannot_be_true = ""; + + my $n_dom_pfts = $nl->get_value( 'n_dom_pfts' ); + my $n_dom_landunits = $nl->get_value( 'n_dom_landunits' ); + my $toosmall_soil = $nl->get_value( 'toosmall_soil' ); + my $toosmall_crop = $nl->get_value( 'toosmall_crop' ); + my $toosmall_glacier = $nl->get_value( 'toosmall_glacier' ); + my $toosmall_lake = $nl->get_value( 'toosmall_lake' ); + my $toosmall_wetland = $nl->get_value( 'toosmall_wetland' ); + my $toosmall_urban = $nl->get_value( 'toosmall_urban' ); + + if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { + $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; + } elsif (&value_is_true($nl->get_value('use_cndv'))) { + $cannot_be_true = "$var cannot be combined with use_cndv"; + } elsif (&value_is_true($nl->get_value('use_fates'))) { + $cannot_be_true = "$var cannot be combined with use_fates"; + } - my $default_val = ".true."; + if ($cannot_be_true) { + $default_val = ".false."; + } - # cannot_be_true will be set to a non-empty string in any case where - # do_transient_pfts should not be true; if it turns out that - # do_transient_pfts IS true in any of these cases, a fatal error will be - # generated - my $cannot_be_true = ""; + if (!$cannot_be_true) { + # Note that, if the variable cannot be true, we don't call add_default + # - so that we don't clutter up the namelist with variables that don't + # matter for this case + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); + } - if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { - $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; - } - elsif (&value_is_true($nl->get_value('use_cndv'))) { - $cannot_be_true = "$var cannot be combined with use_cndv"; - } - elsif (&value_is_true($nl->get_value('use_fates'))) { - $cannot_be_true = "$var cannot be combined with use_fates"; - } + # Make sure the value is false when it needs to be false - i.e., that the + # user hasn't tried to set a true value at an inappropriate time. - if ($cannot_be_true) { - $default_val = ".false."; - } + if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { + $log->fatal_error($cannot_be_true); + } - if (!$cannot_be_true) { - # Note that, if the variable cannot be true, we don't call add_default - # - so that we don't clutter up the namelist with variables that don't - # matter for this case - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); + # if do_transient_pfts is .true. and any of these (n_dom_* or toosmall_*) + # are > 0 or collapse_urban = .true., then give fatal error + if (&value_is_true($nl->get_value($var))) { + if (&value_is_true($nl->get_value('collapse_urban'))) { + $log->fatal_error("$var cannot be combined with collapse_urban"); } - - # Make sure the value is false when it needs to be false - i.e., that the - # user hasn't tried to set a true value at an inappropriate time. - - if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { - $log->fatal_error($cannot_be_true); + if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) { + $log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soi > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8"); } - } } @@ -2596,59 +2466,75 @@ sub setup_logic_do_transient_crops { # - use_crop # - use_fates # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = 'do_transient_crops'; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - # Start by assuming a default value of '.true.'. Then check a number of - # conditions under which do_transient_crops cannot be true. Under these - # conditions: (1) set default value to '.false.'; (2) make sure that the - # value is indeed false (e.g., that the user didn't try to set it to true). - - my $default_val = ".true."; - - # cannot_be_true will be set to a non-empty string in any case where - # do_transient_crops should not be true; if it turns out that - # do_transient_crops IS true in any of these cases, a fatal error will be - # generated - my $cannot_be_true = ""; + # Start by assuming a default value of '.true.'. Then check a number of + # conditions under which do_transient_crops cannot be true. Under these + # conditions: (1) set default value to '.false.'; (2) make sure that the + # value is indeed false (e.g., that the user didn't try to set it to true). + + my $default_val = ".true."; + + # cannot_be_true will be set to a non-empty string in any case where + # do_transient_crops should not be true; if it turns out that + # do_transient_crops IS true in any of these cases, a fatal error will be + # generated + my $cannot_be_true = ""; + + my $n_dom_pfts = $nl->get_value( 'n_dom_pfts' ); + my $n_dom_landunits = $nl->get_value( 'n_dom_landunits' ); + my $toosmall_soil = $nl->get_value( 'toosmall_soil' ); + my $toosmall_crop = $nl->get_value( 'toosmall_crop' ); + my $toosmall_glacier = $nl->get_value( 'toosmall_glacier' ); + my $toosmall_lake = $nl->get_value( 'toosmall_lake' ); + my $toosmall_wetland = $nl->get_value( 'toosmall_wetland' ); + my $toosmall_urban = $nl->get_value( 'toosmall_urban' ); + + if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { + $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; + } elsif (&value_is_true($nl->get_value('use_fates'))) { + # In principle, use_fates should be compatible with + # do_transient_crops. However, this hasn't been tested, so to be safe, + # we are not allowing this combination for now. + $cannot_be_true = "$var has not been tested with ED, so for now these two options cannot be combined"; + } - if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { - $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; - } - elsif (&value_is_true($nl->get_value('use_fates'))) { - # In principle, use_fates should be compatible with - # do_transient_crops. However, this hasn't been tested, so to be safe, - # we are not allowing this combination for now. - $cannot_be_true = "$var has not been tested with ED, so for now these two options cannot be combined"; - } + if ($cannot_be_true) { + $default_val = ".false."; + } - if ($cannot_be_true) { - $default_val = ".false."; - } + if (!$cannot_be_true) { + # Note that, if the variable cannot be true, we don't call add_default + # - so that we don't clutter up the namelist with variables that don't + # matter for this case + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); + } - if (!$cannot_be_true) { - # Note that, if the variable cannot be true, we don't call add_default - # - so that we don't clutter up the namelist with variables that don't - # matter for this case - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); - } + # Make sure the value is false when it needs to be false - i.e., that the + # user hasn't tried to set a true value at an inappropriate time. - # Make sure the value is false when it needs to be false - i.e., that the - # user hasn't tried to set a true value at an inappropriate time. + if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { + $log->fatal_error($cannot_be_true); + } - if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { - $log->fatal_error($cannot_be_true); + # if do_transient_crops is .true. and any of these (n_dom_* or toosmall_*) + # are > 0 or collapse_urban = .true., then give fatal error + if (&value_is_true($nl->get_value($var))) { + if (&value_is_true($nl->get_value('collapse_urban'))) { + $log->fatal_error("$var cannot be combined with collapse_urban"); } - - my $dopft = "do_transient_pfts"; - # Make sure the value agrees with the do_transient_pft flag - if ( ( &value_is_true($nl->get_value($var))) && (! &value_is_true($nl->get_value($dopft))) || - (! &value_is_true($nl->get_value($var))) && ( &value_is_true($nl->get_value($dopft))) ) { - $log->fatal_error("$var and $dopft do NOT agree and need to"); + if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) { + $log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soil > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8"); } + } + my $dopft = "do_transient_pfts"; + # Make sure the value agrees with the do_transient_pft flag + if ( ( &value_is_true($nl->get_value($var))) && (! &value_is_true($nl->get_value($dopft))) || + (! &value_is_true($nl->get_value($var))) && ( &value_is_true($nl->get_value($dopft))) ) { + $log->fatal_error("$var and $dopft do NOT agree and need to"); } } @@ -2662,63 +2548,56 @@ sub setup_logic_do_harvest { # - use_cn # - use_fates # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $var = 'do_harvest'; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - # Start by assuming a default value of '.true.'. Then check a number of - # conditions under which do_harvest cannot be true. Under these - # conditions: (1) set default value to '.false.'; (2) make sure that the - # value is indeed false (e.g., that the user didn't try to set it to true). - - my $default_val = ".true."; + # Start by assuming a default value of '.true.'. Then check a number of + # conditions under which do_harvest cannot be true. Under these + # conditions: (1) set default value to '.false.'; (2) make sure that the + # value is indeed false (e.g., that the user didn't try to set it to true). - # cannot_be_true will be set to a non-empty string in any case where - # do_harvest should not be true; if it turns out that do_harvest IS true - # in any of these cases, a fatal error will be generated - my $cannot_be_true = ""; + my $default_val = ".true."; - if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { - $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; - } - elsif (!&value_is_true($nl->get_value('use_cn'))) { - $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; - } - elsif (&value_is_true($nl->get_value('use_fates'))) { - $cannot_be_true = "$var currently doesn't work with ED"; - } + # cannot_be_true will be set to a non-empty string in any case where + # do_harvest should not be true; if it turns out that do_harvest IS true + # in any of these cases, a fatal error will be generated + my $cannot_be_true = ""; - if ($cannot_be_true) { - $default_val = ".false."; - } + if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { + $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; + } elsif (!&value_is_true($nl->get_value('use_cn'))) { + $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; + } elsif (&value_is_true($nl->get_value('use_fates'))) { + $cannot_be_true = "$var currently doesn't work with ED"; + } - if (!$cannot_be_true) { - # Note that, if the variable cannot be true, we don't call add_default - # - so that we don't clutter up the namelist with variables that don't - # matter for this case - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); - } + if ($cannot_be_true) { + $default_val = ".false."; + } - # Make sure the value is false when it needs to be false - i.e., that the - # user hasn't tried to set a true value at an inappropriate time. + if (!$cannot_be_true) { + # Note that, if the variable cannot be true, we don't call add_default + # - so that we don't clutter up the namelist with variables that don't + # matter for this case + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); + } - if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { - $log->fatal_error($cannot_be_true); - } + # Make sure the value is false when it needs to be false - i.e., that the + # user hasn't tried to set a true value at an inappropriate time. + if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { + $log->fatal_error($cannot_be_true); } } #------------------------------------------------------------------------------- sub setup_logic_spinup { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5")) { - if ( $nl_flags->{'bgc_mode'} eq "sp" && defined($nl->get_value('override_bgc_restart_mismatch_dump'))) { - $log->fatal_error("CN must be on if override_bgc_restart_mismatch_dump is set."); - } + if ( $nl_flags->{'bgc_mode'} eq "sp" && defined($nl->get_value('override_bgc_restart_mismatch_dump'))) { + $log->fatal_error("CN must be on if override_bgc_restart_mismatch_dump is set."); } if ( $nl_flags->{'clm_accelerated_spinup'} eq "on" ) { foreach my $var ( "hist_nhtfrq", "hist_fincl1", "hist_empty_htapes", "hist_mfilt" ) { @@ -2734,17 +2613,14 @@ sub setup_logic_spinup { sub setup_logic_bgc_shared { my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5")) { - if ( $nl_flags->{'bgc_mode'} ne "sp" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'constrain_stress_deciduous_onset', 'phys'=>$physv->as_string() ); - } - # FIXME(bja, 201606) the logic around fates / bgc_mode / - # use_century_decomp is confusing and messed up. This is a hack - # workaround. - if ( &value_is_true($nl_flags->{'use_century_decomp'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'decomp_depth_efolding', 'phys'=>$physv->as_string() ); - } - + if ( $nl_flags->{'bgc_mode'} ne "sp" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'constrain_stress_deciduous_onset', 'phys'=>$physv->as_string() ); + } + # FIXME(bja, 201606) the logic around fates / bgc_mode / + # use_century_decomp is confusing and messed up. This is a hack + # workaround. + if ( &value_is_true($nl_flags->{'use_century_decomp'}) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'decomp_depth_efolding', 'phys'=>$physv->as_string() ); } } @@ -2754,7 +2630,7 @@ sub setup_logic_supplemental_nitrogen { # # Supplemental Nitrogen for prognostic crop cases # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" && &value_is_true($nl_flags->{'use_crop'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, @@ -2774,11 +2650,7 @@ sub setup_logic_supplemental_nitrogen { } if ( $suplnitro =~ /ALL/i ) { - if ( $physv->as_long() == $physv->as_long("clm4_0") && $nl_flags->{'spinup'} ne "normal" ) { - $log->fatal_error("There is no need to use a spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen\n" . - "when spinup != normal you can NOT set supplemental Nitrogen (suplnitro) to ALL"); - } - if ( $physv->as_long() >= $physv->as_long("clm4_5") && $nl_flags->{'bgc_spinup'} eq "on" ) { + if ( $nl_flags->{'bgc_spinup'} eq "on" ) { $log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" ); } } @@ -2791,20 +2663,18 @@ sub setup_logic_hydrology_params { # # Logic for hydrology parameters # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5")) { - my $lower = $nl->get_value( 'lower_boundary_condition' ); - my $var = "baseflow_scalar"; - if ( $lower == 1 || $lower == 2 ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - $var, 'lower_boundary_condition' => $lower ); - } - my $val = $nl->get_value( $var ); - if ( defined($val) ) { - if ( $lower != 1 && $lower != 2 ) { - $log->fatal_error("baseflow_scalar is only used for lower_boundary_condition of flux or zero-flux"); - } + my $lower = $nl->get_value( 'lower_boundary_condition' ); + my $var = "baseflow_scalar"; + if ( $lower == 1 || $lower == 2 ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + $var, 'lower_boundary_condition' => $lower ); + } + my $val = $nl->get_value( $var ); + if ( defined($val) ) { + if ( $lower != 1 && $lower != 2 ) { + $log->fatal_error("baseflow_scalar is only used for lower_boundary_condition of flux or zero-flux"); } } } @@ -2812,29 +2682,58 @@ sub setup_logic_hydrology_params { #------------------------------------------------------------------------------- sub setup_logic_irrigation_parameters { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5")) { - my $var; - foreach $var ("irrig_min_lai", "irrig_start_time", "irrig_length", - "irrig_target_smp", "irrig_depth", "irrig_threshold_fraction", - "limit_irrigation_if_rof_enabled") { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); - } + my $var; + foreach $var ("irrig_min_lai", "irrig_start_time", "irrig_length", + "irrig_target_smp", "irrig_depth", "irrig_threshold_fraction", + "limit_irrigation_if_rof_enabled","use_groundwater_irrigation", + "irrig_method_default") { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } - $var = "irrig_river_volume_threshold"; - if ( &value_is_true($nl->get_value("limit_irrigation_if_rof_enabled")) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); - } else { - if (defined($nl->get_value($var))) { - $log->fatal_error("$var can only be set if limit_irrigation_if_rof_enabled is true"); - } + if ( &value_is_true($nl->get_value('use_groundwater_irrigation')) && + ! &value_is_true($nl->get_value('limit_irrigation_if_rof_enabled'))) { + $log->fatal_error("use_groundwater_irrigation only makes sense if limit_irrigation_if_rof_enabled is set. (If limit_irrigation_if_rof_enabled is .false., then groundwater extraction will never be invoked.)") + } + + my $lower = $nl->get_value( 'lower_boundary_condition' ); + if ( ($lower == 3 || $lower == 4) && (&value_is_true($nl->get_value( 'use_groundwater_irrigation' ))) ) { + $log->fatal_error("use_groundwater_irrigation can only be used when lower_boundary_condition is NOT 3 or 4"); + } + + $var = "irrig_river_volume_threshold"; + if ( &value_is_true($nl->get_value("limit_irrigation_if_rof_enabled")) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } else { + if (defined($nl->get_value($var))) { + $log->fatal_error("$var can only be set if limit_irrigation_if_rof_enabled is true"); } } } #------------------------------------------------------------------------------- +sub setup_logic_surfacealbedo { + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snowveg_affects_radiation' ); +} + +#------------------------------------------------------------------------------- + +sub setup_logic_water_tracers { + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + my $var; + foreach $var ("enable_water_tracer_consistency_checks", + "enable_water_isotopes") { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } +} + +#------------------------------------------------------------------------------- + sub setup_logic_nitrif_params { # # Logic for nitrification parameters @@ -2858,50 +2757,45 @@ sub setup_logic_hydrology_switches { # # Check on Switches for hydrology # - my ($nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - my $subgrid = $nl->get_value('subgridflag' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_subgrid_fluxes'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_cover_fraction_method'); + my $subgrid = $nl->get_value('use_subgrid_fluxes' ); my $origflag = $nl->get_value('origflag' ); my $h2osfcflag = $nl->get_value('h2osfcflag' ); - if ( $origflag == 1 && $subgrid == 1 ) { - $log->fatal_error("if origflag is ON, subgridflag can NOT also be on!"); - } - if ( $h2osfcflag == 1 && $subgrid != 1 ) { - $log->fatal_error("if h2osfcflag is ON, subgridflag can NOT be off!"); - } - # These should NOT be set for CLM5.0 and beyond - if ( $physv->as_long() > $physv->as_long("clm4_5") ) { - foreach my $var ( "origflag", "h2osfcflag", "oldfflag" ) { - my $val = $nl->get_value($var); - if ( defined($val) ) { - $log->fatal_error( "ERROR:: $var=$val is deprecated and can only be used with CLM4.5" ); - } - } + my $scf_method = $nl->get_value('snow_cover_fraction_method'); + if ( $origflag == 1 && &value_is_true($subgrid) ) { + $log->fatal_error("if origflag is ON, use_subgrid_fluxes can NOT also be on!"); + } + if ( $h2osfcflag == 1 && ! &value_is_true($subgrid) ) { + $log->fatal_error("if h2osfcflag is ON, use_subgrid_fluxes can NOT be off!"); + } + if ( remove_leading_and_trailing_quotes($scf_method) eq 'NiuYang2007' && &value_is_true($subgrid) ) { + $log->fatal_error("snow_cover_fraction_method NiuYang2007 is incompatible with use_subgrid_fluxes"); } # Test bad configurations - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - my $lower = $nl->get_value( 'lower_boundary_condition' ); - my $use_vic = $nl->get_value( 'use_vichydro' ); - my $use_bed = $nl->get_value( 'use_bedrock' ); - my $soilmtd = $nl->get_value( 'soilwater_movement_method' ); - if ( defined($soilmtd) && defined($lower) && $soilmtd == 0 && $lower != 4 ) { - $log->fatal_error( "If soil water movement method is zeng-decker -- lower_boundary_condition can only be aquifer" ); - } - if ( defined($soilmtd) && defined($lower) && $soilmtd == 1 && $lower == 4 ) { - $log->fatal_error( "If soil water movement method is adaptive -- lower_boundary_condition can NOT be aquifer" ); - } - if ( defined($use_bed) && defined($lower) && (&value_is_true($use_bed)) && $lower != 2 ) { - $log->fatal_error( "If use_bedrock is on -- lower_boundary_condition can only be flux" ); - } - if ( defined($use_vic) && defined($lower) && (&value_is_true($use_vic)) && $lower != 3 && $lower != 4) { - $log->fatal_error( "If use_vichydro is on -- lower_boundary_condition can only be table or aquifer" ); - } - if ( defined($origflag) && defined($use_vic) && (&value_is_true($use_vic)) && $origflag == 1 ) { - $log->fatal_error( "If use_vichydro is on -- origflag can NOT be equal to 1" ); - } - if ( defined($h2osfcflag) && defined($lower) && $h2osfcflag == 0 && $lower != 4 ) { - $log->fatal_error( "If h2osfcflag is 0 lower_boundary_condition can only be aquifer" ); - } + my $lower = $nl->get_value( 'lower_boundary_condition' ); + my $use_vic = $nl->get_value( 'use_vichydro' ); + my $use_bed = $nl->get_value( 'use_bedrock' ); + my $soilmtd = $nl->get_value( 'soilwater_movement_method' ); + if ( defined($soilmtd) && defined($lower) && $soilmtd == 0 && $lower != 4 ) { + $log->fatal_error( "If soil water movement method is zeng-decker -- lower_boundary_condition can only be aquifer" ); + } + if ( defined($soilmtd) && defined($lower) && $soilmtd == 1 && $lower == 4 ) { + $log->fatal_error( "If soil water movement method is adaptive -- lower_boundary_condition can NOT be aquifer" ); + } + if ( defined($use_bed) && defined($lower) && (&value_is_true($use_bed)) && $lower != 2 ) { + $log->fatal_error( "If use_bedrock is on -- lower_boundary_condition can only be flux" ); + } + if ( defined($use_vic) && defined($lower) && (&value_is_true($use_vic)) && $lower != 3 && $lower != 4) { + $log->fatal_error( "If use_vichydro is on -- lower_boundary_condition can only be table or aquifer" ); + } + if ( defined($origflag) && defined($use_vic) && (&value_is_true($use_vic)) && $origflag == 1 ) { + $log->fatal_error( "If use_vichydro is on -- origflag can NOT be equal to 1" ); + } + if ( defined($h2osfcflag) && defined($lower) && $h2osfcflag == 0 && $lower != 4 ) { + $log->fatal_error( "If h2osfcflag is 0 lower_boundary_condition can only be aquifer" ); } } @@ -2953,13 +2847,6 @@ sub setup_logic_methane { $log->fatal_error("lake_decomp_fact set without allowlakeprod=.true."); } } - my $anoxia = $nl->get_value('anoxia'); - if ( ! defined($anoxia) || - (defined($anoxia) && ! &value_is_true($anoxia)) ) { - if ( defined($nl->get_value('anoxia_wtsat')) ) { - $log->fatal_error("anoxia_wtsat set without anoxia=.true."); - } - } my $pftspec_rootprof = $nl->get_value('pftspecific_rootingprofile'); if ( ! defined($pftspec_rootprof) || (defined($pftspec_rootprof) && &value_is_true($pftspec_rootprof) ) ) { @@ -2968,7 +2855,7 @@ sub setup_logic_methane { } } } else { - my @vars = ( "allowlakeprod", "anoxia", "anoxia_wtsat", "pftspecific_rootingprofile" ); + my @vars = ( "allowlakeprod", "anoxia", "pftspecific_rootingprofile" ); foreach my $var ( @vars ) { if ( defined($nl->get_value($var)) ) { $log->fatal_error("$var set without methane model configuration on (use_lch4)"); @@ -2985,8 +2872,7 @@ sub setup_logic_dynamic_plant_nitrogen_alloc { # my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") && - &value_is_true($nl_flags->{'use_cn'}) ) { + if ( &value_is_true($nl_flags->{'use_cn'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_flexibleCN', 'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'} ); $nl_flags->{'use_flexibleCN'} = $nl->get_value('use_flexibleCN'); @@ -3023,7 +2909,7 @@ sub setup_logic_dynamic_plant_nitrogen_alloc { $log->fatal_error("carbon_resp_opt should NOT be set to 1 when FUN is also on"); } } - } elsif ( $physv->as_long() >= $physv->as_long("clm4_5") && ! &value_is_true($nl_flags->{'use_cn'}) ) { + } else { if ( &value_is_true($nl->get_value('use_flexibleCN')) ) { $log->fatal_error("use_flexibleCN can ONLY be set if CN is on"); } @@ -3038,37 +2924,35 @@ sub setup_logic_luna { # my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_luna', - 'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_nitrif_denitrif'=>$nl_flags->{'use_nitrif_denitrif'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_luna', + 'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_nitrif_denitrif'=>$nl_flags->{'use_nitrif_denitrif'} ); - if ( &value_is_true( $nl_flags->{'use_cn'} ) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_nguardrail', - 'use_cn'=>$nl_flags->{'use_cn'} ); - } - $nl_flags->{'use_luna'} = $nl->get_value('use_luna'); - my $vcmax_opt= $nl->get_value('vcmax_opt'); - # lnc_opt only applies if luna is on or for vcmax_opt=3/4 - if ( &value_is_true( $nl_flags->{'use_luna'} ) || $vcmax_opt == 3 || $vcmax_opt == 4 ) { - # lnc_opt can be set for both CN on and off - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lnc_opt', - 'use_cn'=>$nl_flags->{'use_cn'} ); - } - if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) { - $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" ); - } - my $var = "jmaxb1"; - if ( $physv->as_long() >= $physv->as_long("clm5_0") && &value_is_true( $nl_flags->{'use_luna'} ) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'use_luna'=>$nl_flags->{'use_luna'} ); - } - my $val = $nl->get_value($var); - if ( $physv->as_long() >= $physv->as_long("clm4_5") && ! &value_is_true( $nl_flags->{'use_luna'} ) ) { - if ( defined($val) ) { - $log->fatal_error("Cannot set $var when use_luna is NOT on" ); - } - } + if ( &value_is_true( $nl_flags->{'use_cn'} ) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_nguardrail', + 'use_cn'=>$nl_flags->{'use_cn'} ); + } + $nl_flags->{'use_luna'} = $nl->get_value('use_luna'); + my $vcmax_opt= $nl->get_value('vcmax_opt'); + # lnc_opt only applies if luna is on or for vcmax_opt=3/4 + if ( &value_is_true( $nl_flags->{'use_luna'} ) || $vcmax_opt == 3 || $vcmax_opt == 4 ) { + # lnc_opt can be set for both CN on and off + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lnc_opt', + 'use_cn'=>$nl_flags->{'use_cn'} ); + } + if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) { + $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" ); + } + my $var = "jmaxb1"; + if ( &value_is_true( $nl_flags->{'use_luna'} ) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'use_luna'=>$nl_flags->{'use_luna'} ); + } + my $val = $nl->get_value($var); + if ( ! &value_is_true( $nl_flags->{'use_luna'} ) ) { + if ( defined($val) ) { + $log->fatal_error("Cannot set $var when use_luna is NOT on" ); + } } } @@ -3078,16 +2962,13 @@ sub setup_logic_hydrstress { # # Plant hydraulic stress model # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - # TODO(kwo, 2015-09) make this depend on > clm 5.0 at some point. - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hydrstress', - 'use_fates'=>$nl_flags->{'use_fates'} ); - $nl_flags->{'use_hydrstress'} = $nl->get_value('use_hydrstress'); - if ( &value_is_true( $nl_flags->{'use_fates'} ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) { - $log->fatal_error("Cannot turn use_hydrstress on when use_fates is on" ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hydrstress', + 'configuration'=>$nl_flags->{'configuration'}, 'use_fates'=>$nl_flags->{'use_fates'} ); + $nl_flags->{'use_hydrstress'} = $nl->get_value('use_hydrstress'); + if ( &value_is_true( $nl_flags->{'use_fates'} ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) { + $log->fatal_error("Cannot turn use_hydrstress on when use_fates is on" ); } } @@ -3097,16 +2978,14 @@ sub setup_logic_fertilizer { # # Flags to control fertilizer application # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fertilizer', - 'use_crop'=>$nl_flags->{'use_crop'} ); - my $use_fert = $nl->get_value('use_fertilizer'); - if ( (! &value_is_true($nl_flags->{'use_crop'})) && &value_is_true($use_fert) ) { - $log->fatal_error("use_ferilizer can NOT be on without prognostic crop\n" ); - } - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fertilizer', + 'use_crop'=>$nl_flags->{'use_crop'} ); + my $use_fert = $nl->get_value('use_fertilizer'); + if ( (! &value_is_true($nl_flags->{'use_crop'})) && &value_is_true($use_fert) ) { + $log->fatal_error("use_ferilizer can NOT be on without prognostic crop\n" ); + } } #------------------------------------------------------------------------------- @@ -3117,13 +2996,11 @@ sub setup_logic_grainproduct { # my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_grainproduct', - 'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() ); - if ( (! &value_is_true($nl_flags->{'use_crop'})) && &value_is_true($nl->get_value('use_grainproduct') ) ) { - $log->fatal_error("use_grainproduct can NOT be on without prognostic crop\n" ); - } - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_grainproduct', + 'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() ); + if ( (! &value_is_true($nl_flags->{'use_crop'})) && &value_is_true($nl->get_value('use_grainproduct') ) ) { + $log->fatal_error("use_grainproduct can NOT be on without prognostic crop\n" ); + } } #------------------------------------------------------------------------------- @@ -3134,17 +3011,15 @@ sub setup_logic_dynamic_roots { # my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_dynroot', 'phys'=>$physv->as_string(), 'bgc_mode'=>$nl_flags->{'bgc_mode'}); - my $use_dynroot = $nl->get_value('use_dynroot'); - if ( &value_is_true($use_dynroot) && ($nl_flags->{'bgc_mode'} eq "sp") ) { - $log->fatal_error("Cannot turn dynroot mode on mode bgc=sp\n" . - "Set the bgc mode to 'cn' or 'bgc'."); - } - if ( &value_is_true( $use_dynroot ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) { - $log->fatal_error("Cannot turn use_dynroot on when use_hydrstress is on" ); - } - } # else - not relevant in clm4_0, not part of namelist definition, will not run. + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_dynroot', 'phys'=>$physv->as_string(), 'bgc_mode'=>$nl_flags->{'bgc_mode'}); + my $use_dynroot = $nl->get_value('use_dynroot'); + if ( &value_is_true($use_dynroot) && ($nl_flags->{'bgc_mode'} eq "sp") ) { + $log->fatal_error("Cannot turn dynroot mode on mode bgc=sp\n" . + "Set the bgc mode to 'cn' or 'bgc'."); + } + if ( &value_is_true( $use_dynroot ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) { + $log->fatal_error("Cannot turn use_dynroot on when use_hydrstress is on" ); + } } #------------------------------------------------------------------------------- @@ -3153,7 +3028,7 @@ sub setup_logic_c_isotope { # # Error checking for C-isotope options # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $use_c13 = $nl->get_value('use_c13'); my $use_c14 = $nl->get_value('use_c14'); @@ -3221,43 +3096,22 @@ sub setup_logic_c_isotope { #------------------------------------------------------------------------------- sub setup_logic_nitrogen_deposition { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; # # Nitrogen deposition for bgc=CN # - if ( $physv->as_long() == $physv->as_long("clm4_0") && $nl_flags->{'bgc_mode'} ne "none" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'}, - 'bgc'=>$nl_flags->{'bgc_mode'}, 'hgrid'=>$nl_flags->{'res'}, - 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'}, - 'bgc'=>$nl_flags->{'bgc_mode'}, 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_ndep', 'phys'=>$nl_flags->{'phys'}, - 'bgc'=>$nl_flags->{'bgc_mode'}, 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_ndep') != $nl->get_value('stream_year_last_ndep') ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_ndep', 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - } - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, - 'bgc'=>$nl_flags->{'bgc_mode'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, - 'hgrid'=>"1.9x2.5" ); - - } elsif ( $physv->as_long() >= $physv->as_long("clm4_5") && $nl_flags->{'bgc_mode'} =~/cn|bgc/ ) { + if ( $nl_flags->{'bgc_mode'} =~/cn|bgc/ ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); + 'use_cn'=>$nl_flags->{'use_cn'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); + 'use_cn'=>$nl_flags->{'use_cn'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); @@ -3297,14 +3151,14 @@ sub setup_logic_nitrogen_deposition { #------------------------------------------------------------------------------- sub setup_logic_cnmresp { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; # # CN Maintence respiration for bgc=CN # - if ( $physv->as_long() >= $physv->as_long("clm4_5") && $nl_flags->{'bgc_mode'} ne "sp" ) { - # When FUN is on and it's clm5_0 get a default value - if ( &value_is_true( $nl->get_value('use_fun') ) && $physv->as_long() >= $physv->as_long("clm5_0")) { + if ( $nl_flags->{'bgc_mode'} ne "sp" ) { + # When FUN is on get a default value + if ( &value_is_true( $nl->get_value('use_fun') ) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'br_root', 'phys'=>$nl_flags->{'phys'}, 'use_fun'=>$nl->get_value('use_fun'), @@ -3313,7 +3167,7 @@ sub setup_logic_cnmresp { } else { # If bgc is NOT CN/CNDV then make sure not set if ( defined($nl->get_value('br_root'))) { - $log->fatal_error("br_root can NOT be set when phys==clm4_0 or bgc_mode==sp!"); + $log->fatal_error("br_root can NOT be set when bgc_mode==sp!"); } } } @@ -3322,34 +3176,32 @@ sub setup_logic_cnmresp { sub setup_logic_photosyns { # MUST be after use_hydrstress is set - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; # - # Photo synthesis + # Photosynthesis # - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, - $nl, 'rootstem_acc', 'phys'=>$nl_flags->{'phys'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, - $nl, 'light_inhibit', 'phys'=>$nl_flags->{'phys'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, - $nl, 'leafresp_method', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, - $nl, 'modifyphoto_and_lmr_forcrop', 'phys'=>$nl_flags->{'phys'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, - $nl, 'stomatalcond_method', 'phys'=>$nl_flags->{'phys'}, - 'use_hydrstress'=>$nl_flags->{'use_hydrstress'} ); - # When CN on, must NOT be scaled by vcmax25top - if ( &value_is_true( $nl_flags->{'use_cn'} ) ) { - if ( $nl->get_value('leafresp_method') == 0 ) { - $log->fatal_error("leafresp_method can NOT be set to scaled to vcmax (0) when CN is on!"); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, + $nl, 'rootstem_acc', 'phys'=>$nl_flags->{'phys'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, + $nl, 'light_inhibit', 'phys'=>$nl_flags->{'phys'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, + $nl, 'leafresp_method', 'phys'=>$nl_flags->{'phys'}, + 'use_cn'=>$nl_flags->{'use_cn'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, + $nl, 'modifyphoto_and_lmr_forcrop', 'phys'=>$nl_flags->{'phys'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, + $nl, 'stomatalcond_method', 'phys'=>$nl_flags->{'phys'}, + 'use_hydrstress'=>$nl_flags->{'use_hydrstress'} ); + # When CN on, must NOT be scaled by vcmax25top + if ( &value_is_true( $nl_flags->{'use_cn'} ) ) { + if ( $nl->get_value('leafresp_method') == 0 ) { + $log->fatal_error("leafresp_method can NOT be set to scaled to vcmax (0) when CN is on!"); + } # And when CN off, must NOT be anything besides scaled by vxmac25top - } else { - if ( $nl->get_value('leafresp_method') != 0 ) { - $log->fatal_error("leafresp_method can NOT be set to anything besides scaled to vcmax (0) when bgc_mode==sp!"); - } + } else { + if ( $nl->get_value('leafresp_method') != 0 ) { + $log->fatal_error("leafresp_method can NOT be set to anything besides scaled to vcmax (0) when bgc_mode==sp!"); } } } @@ -3357,119 +3209,110 @@ sub setup_logic_photosyns { #------------------------------------------------------------------------------- sub setup_logic_canopy { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; # # Canopy state # - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, - $nl, 'leaf_mr_vcm', 'phys'=>$nl_flags->{'phys'} ) - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, + $nl, 'leaf_mr_vcm', 'phys'=>$nl_flags->{'phys'} ) } #------------------------------------------------------------------------------- sub setup_logic_popd_streams { - # population density streams require clm4_5/clm5_0 and CN/BGC - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + # population density streams require CN/BGC + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - if ( &value_is_true($nl_flags->{'cnfireson'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'popdensmapalgo', 'hgrid'=>$nl_flags->{'res'}, - 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'}, 'cnfireson'=>$nl_flags->{'cnfireson'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_popdens', 'phys'=>$nl_flags->{'phys'}, - 'cnfireson'=>$nl_flags->{'cnfireson'}, 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_popdens', 'phys'=>$nl_flags->{'phys'}, - 'cnfireson'=>$nl_flags->{'cnfireson'}, 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_popdens') != - $nl->get_value('stream_year_last_popdens') ) { + if ( &value_is_true($nl_flags->{'cnfireson'}) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'popdensmapalgo', 'hgrid'=>$nl_flags->{'res'}, + 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'}, 'cnfireson'=>$nl_flags->{'cnfireson'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_popdens', 'phys'=>$nl_flags->{'phys'}, + 'cnfireson'=>$nl_flags->{'cnfireson'}, 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_popdens', 'phys'=>$nl_flags->{'phys'}, + 'cnfireson'=>$nl_flags->{'cnfireson'}, 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_popdens') != + $nl->get_value('stream_year_last_popdens') ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_popdens', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, 'cnfireson'=>$nl_flags->{'cnfireson'}); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'}, - 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); - } else { - # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set - if ( defined($nl->get_value('stream_year_first_popdens')) || - defined($nl->get_value('stream_year_last_popdens')) || - defined($nl->get_value('model_year_align_popdens')) || - defined($nl->get_value('popdens_tintalgo' )) || - defined($nl->get_value('stream_fldfilename_popdens')) ) { + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'}, + 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); + } else { + # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set + if ( defined($nl->get_value('stream_year_first_popdens')) || + defined($nl->get_value('stream_year_last_popdens')) || + defined($nl->get_value('model_year_align_popdens')) || + defined($nl->get_value('popdens_tintalgo' )) || + defined($nl->get_value('stream_fldfilename_popdens')) ) { $log->fatal_error("When bgc is SP (NOT CN or BGC) or fire_method==nofire none of: stream_year_first_popdens,\n" . - "stream_year_last_popdens, model_year_align_popdens, popdens_tintalgo nor\n" . - "stream_fldfilename_popdens can be set!"); - } - } + "stream_year_last_popdens, model_year_align_popdens, popdens_tintalgo nor\n" . + "stream_fldfilename_popdens can be set!"); + } } } #------------------------------------------------------------------------------- sub setup_logic_urbantv_streams { - # urban time varying streams require clm4_5/clm5_0 - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urbantvmapalgo', - 'hgrid'=>$nl_flags->{'res'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_urbantv', 'phys'=>$nl_flags->{'phys'}, - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_urbantv', 'phys'=>$nl_flags->{'phys'}, - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_urbantv') != - $nl->get_value('stream_year_last_urbantv') ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'model_year_align_urbantv', 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'}, - 'hgrid'=>"0.9x1.25" ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urbantvmapalgo', + 'hgrid'=>$nl_flags->{'res'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_urbantv', 'phys'=>$nl_flags->{'phys'}, + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_urbantv', 'phys'=>$nl_flags->{'phys'}, + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_urbantv') != + $nl->get_value('stream_year_last_urbantv') ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'model_year_align_urbantv', 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'}, + 'hgrid'=>"0.9x1.25" ); } #------------------------------------------------------------------------------- sub setup_logic_lightning_streams { - # lightning streams require clm4_5/clm5_0 and CN/BGC - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + # lightning streams require CN/BGC + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - if ( &value_is_true($nl_flags->{'cnfireson'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lightngmapalgo', 'use_cn'=>$nl_flags->{'use_cn'}, - 'hgrid'=>$nl_flags->{'res'}, - 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_lightng') != - $nl->get_value('stream_year_last_lightng') ) { + if ( &value_is_true($nl_flags->{'cnfireson'}) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lightngmapalgo', 'use_cn'=>$nl_flags->{'use_cn'}, + 'hgrid'=>$nl_flags->{'res'}, + 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_lightng') != + $nl->get_value('stream_year_last_lightng') ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_lightng', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, - 'hgrid'=>$nl_flags->{'light_res'} ); - } else { - # If bgc is NOT CN/CNDV then make sure none of the Lightng settings are set - if ( defined($nl->get_value('stream_year_first_lightng')) || - defined($nl->get_value('stream_year_last_lightng')) || - defined($nl->get_value('model_year_align_lightng')) || - defined($nl->get_value('lightng_tintalgo' )) || - defined($nl->get_value('stream_fldfilename_lightng')) ) { + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, + 'hgrid'=>$nl_flags->{'light_res'} ); + } else { + # If bgc is NOT CN/CNDV then make sure none of the Lightng settings are set + if ( defined($nl->get_value('stream_year_first_lightng')) || + defined($nl->get_value('stream_year_last_lightng')) || + defined($nl->get_value('model_year_align_lightng')) || + defined($nl->get_value('lightng_tintalgo' )) || + defined($nl->get_value('stream_fldfilename_lightng')) ) { $log->fatal_error("When bgc is SP (NOT CN or BGC) or fire_method==nofire none of: stream_year_first_lightng,\n" . - "stream_year_last_lightng, model_year_align_lightng, lightng_tintalgo nor\n" . - "stream_fldfilename_lightng can be set!"); - } - } + "stream_year_last_lightng, model_year_align_lightng, lightng_tintalgo nor\n" . + "stream_fldfilename_lightng can be set!"); + } } } @@ -3492,12 +3335,9 @@ sub setup_logic_dry_deposition { #------------------------------------------------------------------------------- sub setup_logic_fire_emis { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; if ($opts->{'fire_emis'} ) { - if ( $physv->as_long() < $physv->as_long("clm4_5") ) { - $log->fatal_error("fire_emis option can NOT be set for CLM versions before clm4_5"); - } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier'); } else { @@ -3517,8 +3357,9 @@ sub setup_logic_megan { my $var = "megan"; if ( $opts->{$var} eq "default" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, -'megan', clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan', + 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'}, + 'configuration'=>$nl_flags->{'configuration'} ); $nl_flags->{$var} = $nl->get_value($var); } else { $nl_flags->{$var} = $opts->{$var}; @@ -3546,7 +3387,6 @@ sub setup_logic_soilm_streams { # prescribed soil moisture streams require clm4_5/clm5_0 my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_soil_moisture_streams'); if ( &value_is_true( $nl->get_value('use_soil_moisture_streams') ) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soilm_tintalgo', @@ -3568,7 +3408,7 @@ sub setup_logic_soilm_streams { } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_soilm', 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'} ); - if ( ($opts->{'use_case'} =~ /_transient$/) && + if ( ($opts->{'use_case'} =~ /_transient$/) && (remove_leading_and_trailing_quotes($nl->get_value("soilm_tintalgo")) eq "linear") ) { $log->warning("For a transient case, soil moisture streams, should NOT use soilm_tintalgo='linear'" . " since vegetated areas could go from missing to not missing or vice versa" ); @@ -3586,91 +3426,83 @@ sub setup_logic_soilm_streams { " is defined, but use_soil_moisture_streams option NOT set to true"); } } - } } #------------------------------------------------------------------------------- sub setup_logic_lai_streams { - # lai streams require clm4_5/clm5_0 - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); - - if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { - $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); - } - if ( $nl_flags->{'bgc_mode'} eq "sp" ) { + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( &value_is_true($nl->get_value('use_lai_streams')) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', - 'hgrid'=>$nl_flags->{'res'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lai', - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lai', - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_lai') != - $nl->get_value('stream_year_last_lai') ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'model_year_align_lai', 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai', - 'hgrid'=>"360x720cru" ); - } - } else { - # If bgc is CN/CNDV then make sure none of the LAI settings are set - if ( defined($nl->get_value('stream_year_first_lai')) || - defined($nl->get_value('stream_year_last_lai')) || - defined($nl->get_value('model_year_align_lai')) || - defined($nl->get_value('lai_tintalgo' )) || - defined($nl->get_value('stream_fldfilename_lai')) ) { - $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . - "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . - "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); - } - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); + + if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { + $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); + } + if ( $nl_flags->{'bgc_mode'} eq "sp" ) { + + if ( &value_is_true($nl->get_value('use_lai_streams')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', + 'hgrid'=>$nl_flags->{'res'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lai', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lai', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_lai') != + $nl->get_value('stream_year_last_lai') ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'model_year_align_lai', 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai', + 'hgrid'=>"360x720cru" ); + } + } else { + # If bgc is CN/CNDV then make sure none of the LAI settings are set + if ( defined($nl->get_value('stream_year_first_lai')) || + defined($nl->get_value('stream_year_last_lai')) || + defined($nl->get_value('model_year_align_lai')) || + defined($nl->get_value('lai_tintalgo' )) || + defined($nl->get_value('stream_fldfilename_lai')) ) { + $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . + "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . + "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); + } } } #------------------------------------------------------------------------------- sub setup_logic_soilwater_movement { - # soilwater_movement require clm4_5/clm5_0 - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soilwater_movement_method' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upper_boundary_condition' ); - - my $soilmtd = $nl->get_value("soilwater_movement_method"); - my $use_bed = $nl->get_value('use_bedrock' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'lower_boundary_condition', 'vichydro'=>$nl_flags->{'vichydro'}, - 'soilwater_movement_method'=>$soilmtd, 'use_bedrock'=>$use_bed - ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtmin' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'verySmall' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'xTolerUpper' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'xTolerLower' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'expensive' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'inexpensive' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'flux_calculation' ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soilwater_movement_method' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upper_boundary_condition' ); + + my $soilmtd = $nl->get_value("soilwater_movement_method"); + my $use_bed = $nl->get_value('use_bedrock' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'lower_boundary_condition', 'vichydro'=>$nl_flags->{'vichydro'}, + 'soilwater_movement_method'=>$soilmtd, 'use_bedrock'=>$use_bed + ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtmin' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'verySmall' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'xTolerUpper' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'xTolerLower' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'expensive' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'inexpensive' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'flux_calculation' ); } #------------------------------------------------------------------------------- sub setup_logic_century_soilbgcdecompcascade { # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") && - (&value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates'))) && + if ( (&value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates'))) && &value_is_true($nl->get_value('use_century_decomp')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_Cstocks', 'use_cn' => $nl->get_value('use_cn'), 'use_fates' => $nl->get_value('use_fates'), @@ -3685,9 +3517,9 @@ sub setup_logic_century_soilbgcdecompcascade { sub setup_logic_cnvegcarbonstate { # MUST be AFTER: setup_logic_dynamic_plant_nitrogen_alloc as depends on mm_nuptake_opt which is set there - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl->get_value('use_cn')) ) { + if ( &value_is_true($nl->get_value('use_cn')) ) { my $mmnuptake = $nl->get_value('mm_nuptake_opt'); if ( ! defined($mmnuptake) ) { $mmnuptake = ".false."; } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_vegC', @@ -3699,9 +3531,9 @@ sub setup_logic_cnvegcarbonstate { sub setup_logic_cngeneral { # Must be set after setup_logic_co2_type - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl->get_value('use_cn')) ) { + if ( &value_is_true($nl->get_value('use_cn')) ) { if ( &value_is_true($nl->get_value('use_crop')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dribble_crophrv_xsmrpool_2atm', 'co2_type' => remove_leading_and_trailing_quotes($nl->get_value('co2_type')), @@ -3725,57 +3557,49 @@ sub setup_logic_cngeneral { sub setup_logic_rooting_profile { # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'rooting_profile_method_water' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'rooting_profile_method_carbon' ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'rooting_profile_method_water' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'rooting_profile_method_carbon' ); } #------------------------------------------------------------------------------- sub setup_logic_friction_vel { # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable' ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable' ); } #------------------------------------------------------------------------------- sub setup_logic_soil_resis { # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_resis_method' ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_resis_method' ); } #------------------------------------------------------------------------------- sub setup_logic_canopyfluxes { # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_undercanopy_stability' ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_undercanopy_stability' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'itmax_canopy_fluxes', + 'structure'=>$nl_flags->{'structure'}); } #------------------------------------------------------------------------------- sub setup_logic_canopyhydrology { # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' ); } #------------------------------------------------------------------------------- @@ -3784,32 +3608,92 @@ sub setup_logic_snowpack { # # Snowpack related options # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'nlevsno'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'h2osno_max'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'int_snow_max'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'n_melt_glcmec'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fresh_snw_rds_max'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela'); - - if (remove_leading_and_trailing_quotes($nl->get_value('snow_overburden_compaction_method')) eq 'Vionnet2012') { - # overburden_compress_tfactor isn't used if we're using the Vionnet2012 - # snow overburden compaction method, so make sure the user hasn't tried - # to set it - if (defined($nl->get_value('overburden_compress_tfactor'))) { - $log->fatal_error('overburden_compress_tfactor is set, but does not apply when using snow_overburden_compaction_method=Vionnet2012'); - } - } else { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'overburden_compress_tfactor'); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'nlevsno', + 'structure'=>$nl_flags->{'structure'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'h2osno_max', + 'structure'=>$nl_flags->{'structure'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fresh_snw_rds_max'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_dzmin_1'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_dzmin_2'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_dzmax_l_1'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_dzmax_l_2'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_dzmax_u_1'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_dzmax_u_2'); + + my $dzmin1 = $nl->get_value('snow_dzmin_1'); + my $dzmin2 = $nl->get_value('snow_dzmin_2'); + my $dzmax_l1 = $nl->get_value('snow_dzmax_l_1'); + my $dzmax_l2 = $nl->get_value('snow_dzmax_l_2'); + my $dzmax_u1 = $nl->get_value('snow_dzmax_u_1'); + my $dzmax_u2 = $nl->get_value('snow_dzmax_u_2'); + + if ($dzmin1 != 0.01 || $dzmin2 != 0.015 || $dzmax_u1 != 0.02 || $dzmax_u2 != 0.05 || $dzmax_l1 != 0.03 || $dzmax_l2 != 0.07) { + $log->warning("Setting any of the following namelist variables to NON DEFAULT values remains untested as of Sep 6, 2019: snow_dzmin_1 & 2, snow_dzmax_u_1 & 2, snow_dzmax_l_1 & 2." ); + $log->warning("Leave these variables unspecified in user_nl_clm in order to use the default values." ); + } + if ($dzmin1 <= 0.0 || $dzmin2 <= 0.0 || $dzmax_u1 <= 0.0 || $dzmax_u2 <= 0.0 || $dzmax_l1 <= 0.0 || $dzmax_l2 <= 0.0) { + $log->fatal_error('One or more of the snow_dzmin_* and/or snow_dzmax_* were set incorrectly to be <= 0'); + } + if ($dzmin2 <= $dzmin1) { + $log->fatal_error('snow_dzmin_2 was set incorrectly to be <= snow_dzmin_1'); + } + if ($dzmax_l2 <= $dzmax_l1) { + $log->fatal_error('snow_dzmax_l_2 was set incorrectly to be <= snow_dzmax_l_1'); + } + if ($dzmax_u2 <= $dzmax_u1) { + $log->fatal_error('snow_dzmax_u_2 was set incorrectly to be <= snow_dzmax_u_1'); + } + if ($dzmin1 >= $dzmax_u1) { + $log->fatal_error('snow_dzmin_1 was set incorrectly to be >= snow_dzmax_u_1'); + } + if ($dzmin2 >= $dzmax_u2) { + $log->fatal_error('snow_dzmin_2 was set incorrectly to be >= snow_dzmax_u_2'); + } + if ($dzmax_u1 >= $dzmax_l1) { + $log->fatal_error('snow_dzmax_u_1 was set incorrectly to be >= snow_dzmax_l_1'); + } + if ($dzmax_u2 >= $dzmax_l2) { + $log->fatal_error('snow_dzmax_u_2 was set incorrectly to be >= snow_dzmax_l_2'); + } + + if (remove_leading_and_trailing_quotes($nl->get_value('snow_overburden_compaction_method')) eq 'Vionnet2012') { + # overburden_compress_tfactor isn't used if we're using the Vionnet2012 + # snow overburden compaction method, so make sure the user hasn't tried + # to set it + if (defined($nl->get_value('overburden_compress_tfactor'))) { + $log->fatal_error('overburden_compress_tfactor is set, but does not apply when using snow_overburden_compaction_method=Vionnet2012'); + } + } else { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'overburden_compress_tfactor'); + } +} + +#------------------------------------------------------------------------------- + +sub setup_logic_scf_SwensonLawrence2012 { + # Options related to the SwensonLawrence2012 snow cover fraction method + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'int_snow_max'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'n_melt_glcmec'); + } + else { + if (defined($nl->get_value('int_snow_max'))) { + $log->fatal_error('int_snow_max is set, but only applies for snow_cover_fraction_method=SwensonLawrence2012'); + } + if (defined($nl->get_value('n_melt_glcmec'))) { + $log->fatal_error('n_melt_glcmec is set, but only applies for snow_cover_fraction_method=SwensonLawrence2012'); + } } } @@ -3819,36 +3703,34 @@ sub setup_logic_atm_forcing { # # Options related to atmospheric forcings # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glcmec_downscale_longwave'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'repartition_rain_snow'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lapse_rate'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glcmec_downscale_longwave'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'repartition_rain_snow'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lapse_rate'); - my $var; + my $var; - foreach $var ("lapse_rate_longwave", - "longwave_downscaling_limit") { - if ( &value_is_true($nl->get_value("glcmec_downscale_longwave")) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); - } else { - if (defined($nl->get_value($var))) { - $log->fatal_error("$var can only be set if glcmec_downscale_longwave is true"); - } + foreach $var ("lapse_rate_longwave", + "longwave_downscaling_limit") { + if ( &value_is_true($nl->get_value("glcmec_downscale_longwave")) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } else { + if (defined($nl->get_value($var))) { + $log->fatal_error("$var can only be set if glcmec_downscale_longwave is true"); } } + } - foreach $var ("precip_repartition_glc_all_snow_t", - "precip_repartition_glc_all_rain_t", - "precip_repartition_nonglc_all_snow_t", - "precip_repartition_nonglc_all_rain_t") { - if ( &value_is_true($nl->get_value("repartition_rain_snow")) ){ - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); - } else { - if (defined($nl->get_value($var))) { - $log->fatal_error("$var can only be set if repartition_rain_snow is true"); - } + foreach $var ("precip_repartition_glc_all_snow_t", + "precip_repartition_glc_all_rain_t", + "precip_repartition_nonglc_all_snow_t", + "precip_repartition_nonglc_all_rain_t") { + if ( &value_is_true($nl->get_value("repartition_rain_snow")) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } else { + if (defined($nl->get_value($var))) { + $log->fatal_error("$var can only be set if repartition_rain_snow is true"); } } } @@ -3860,11 +3742,9 @@ sub setup_logic_lnd2atm { # # Options related to fields sent to atmosphere # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'melt_non_icesheet_ice_runoff'); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'melt_non_icesheet_ice_runoff'); } #------------------------------------------------------------------------------- @@ -3873,16 +3753,14 @@ sub setup_logic_initinterp { # # Options related to init_interp # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ($physv->as_long() >= $physv->as_long("clm4_5")) { - my $var = 'init_interp_method'; - if ( &value_is_true($nl->get_value("use_init_interp"))) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); - } else { - if (defined($nl->get_value($var))) { - $log->fatal_error("$var can only be set if use_init_interp is true"); - } + my $var = 'init_interp_method'; + if ( &value_is_true($nl->get_value("use_init_interp"))) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } else { + if (defined($nl->get_value($var))) { + $log->fatal_error("$var can only be set if use_init_interp is true"); } } } @@ -3893,9 +3771,9 @@ sub setup_logic_fates { # # Set some default options related to Ecosystem Demography # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ($physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true( $nl_flags->{'use_fates'}) ) { + if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" ); @@ -3920,7 +3798,7 @@ sub setup_logic_fates { #------------------------------------------------------------------------------- sub write_output_files { - my ($opts, $nl_flags, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $defaults, $nl) = @_; my $note = ""; my $var = "note"; @@ -3936,45 +3814,38 @@ sub write_output_files { # CLM component my @groups; - if ( $physv->as_long() == $physv->as_long("clm4_0") ) { - @groups = qw(clm_inparm); - # Eventually only list namelists that are actually used when CN on - #if ( $nl_flags->{'bgc_mode'} eq "cn" ) { - push @groups, "ndepdyn_nml"; - #} - } else { - - @groups = qw(clm_inparm ndepdyn_nml popd_streams urbantv_streams light_streams - soil_moisture_streams lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology - clm_soilhydrology_inparm dynamic_subgrid cnvegcarbonstate - finidat_consistency_checks dynpft_consistency_checks - clm_initinterp_inparm century_soilbgcdecompcascade - soilhydrology_inparm luna friction_velocity mineral_nitrogen_dynamics - soilwater_movement_inparm rooting_profile_inparm - soil_resis_inparm bgc_shared canopyfluxes_inparm aerosol - clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm - cnprecision_inparm clm_glacier_behavior crop irrigation_inparm); - - #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm - # finidat_consistency_checks dynpft_consistency_checks); - # Eventually only list namelists that are actually used when CN on - #if ( $nl_flags->{'bgc_mode'} eq "cn" ) { - # push @groups, qw(ndepdyn_nml popd_streams light_streams); - #} - if ( &value_is_true($nl_flags->{'use_lch4'}) ) { - push @groups, "ch4par_in"; - } - if ( $physv->as_long() >= $physv->as_long("clm4_5") ) { - push @groups, "clm_humanindex_inparm"; - push @groups, "cnmresp_inparm"; - push @groups, "photosyns_inparm"; - push @groups, "cnfire_inparm"; - push @groups, "cn_general"; - push @groups, "nitrif_inparm"; - push @groups, "lifire_inparm"; - push @groups, "ch4finundated"; - push @groups, "clm_canopy_inparm"; - } + @groups = qw(clm_inparm ndepdyn_nml popd_streams urbantv_streams light_streams + soil_moisture_streams lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology + clm_soilhydrology_inparm dynamic_subgrid cnvegcarbonstate + finidat_consistency_checks dynpft_consistency_checks + clm_initinterp_inparm century_soilbgcdecompcascade + soilhydrology_inparm luna friction_velocity mineral_nitrogen_dynamics + soilwater_movement_inparm rooting_profile_inparm + soil_resis_inparm bgc_shared canopyfluxes_inparm aerosol + clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm + cnprecision_inparm clm_glacier_behavior crop irrigation_inparm + surfacealbedo_inparm water_tracers_inparm); + + #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm + # finidat_consistency_checks dynpft_consistency_checks); + # Eventually only list namelists that are actually used when CN on + #if ( $nl_flags->{'bgc_mode'} eq "cn" ) { + # push @groups, qw(ndepdyn_nml popd_streams light_streams); + #} + if ( &value_is_true($nl_flags->{'use_lch4'}) ) { + push @groups, "ch4par_in"; + } + push @groups, "clm_humanindex_inparm"; + push @groups, "cnmresp_inparm"; + push @groups, "photosyns_inparm"; + push @groups, "cnfire_inparm"; + push @groups, "cn_general"; + push @groups, "nitrif_inparm"; + push @groups, "lifire_inparm"; + push @groups, "ch4finundated"; + push @groups, "clm_canopy_inparm"; + if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') { + push @groups, "scf_swenson_lawrence_2012_inparm"; } my $outfile; @@ -3990,7 +3861,7 @@ sub write_output_files { } sub write_output_real_parameter_file { - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; # Output real parameters if ( defined($opts->{'output_reals_filename'}) ) { @@ -4614,8 +4485,8 @@ sub main { my $cfg = read_configure_definition($cfgdir, \%opts); my $physv = config_files::clm_phys_vers->new( $cfg->get('phys') ); - my $definition = read_namelist_definition($cfgdir, \%opts, \%nl_flags, $physv); - my $defaults = read_namelist_defaults($cfgdir, \%opts, \%nl_flags, $cfg, $physv); + my $definition = read_namelist_definition($cfgdir, \%opts, \%nl_flags); + my $defaults = read_namelist_defaults($cfgdir, \%opts, \%nl_flags, $cfg); # List valid values if asked for list_options(\%opts, $definition, $defaults); @@ -4634,12 +4505,12 @@ sub main { # Process the user inputs process_namelist_user_input(\%opts, \%nl_flags, $definition, $defaults, $nl, $cfg, \%env_xml, $physv ); # Get any other defaults needed from the namelist defaults file - process_namelist_inline_logic(\%opts, \%nl_flags, $definition, $defaults, $nl, $cfg, \%env_xml, $physv); + process_namelist_inline_logic(\%opts, \%nl_flags, $definition, $defaults, $nl, \%env_xml, $physv); # Validate that the entire resultant namelist is valid $definition->validate($nl); - write_output_files(\%opts, \%nl_flags, $defaults, $nl, $physv); - write_output_real_parameter_file(\%opts, \%nl_flags, $definition, $defaults, $nl, $physv); + write_output_files(\%opts, \%nl_flags, $defaults, $nl); + write_output_real_parameter_file(\%opts, \%nl_flags, $definition, $defaults, $nl); if ($opts{'inputdata'}) { check_input_files($nl, $nl_flags{'inputdata_rootdir'}, $opts{'inputdata'}, $definition); diff --git a/bld/README b/bld/README index 9f31d22bd9..0ed6779a80 100644 --- a/bld/README +++ b/bld/README @@ -9,14 +9,8 @@ Important files/directories: --------- Configure and build scripts --------- (These scripts are also used by the cesm/cime scripts) -configure ---------------- Configure script -- sets up the CPP Macro's needed to be - defined to build CLM (only actively used for clm4_0) - ----- configure --help - Configure help mode -- sends information on all configure options config_files/clm_phys_vers.pm ------------- Perl module to handle different CLM versions -config_files/config_defaults.xml ---------- XML file of defaults for CLM -config_files/config_defaults_*.xml -------- XML file of defaults for CLM for a specific site -config_files/config_definition_clm4_0.xml - XML file definining all CLM4.0 configuration items -config_files/config_definition_clm4_5.xml - XML file definining all CLM5.5/CLM5.0 configuration items +config_files/config_definition_ctsm.xml --- XML file defining all CTSM configuration items --------- Scripts to build the namelists --------- (These scripts are also used by the cesm/cime scripts) @@ -42,16 +36,14 @@ queryDefaultXML.pm ------ Subroutines needed by queryDefaultNamelist.pl script --------- Test scripts directory unit_testers --- Directory of scripts to test scipts in this directory - (most notably build-namelist and possibly configure) + (most notably build-namelist) ---------- XML Files describing namelists in namelist_files -namelist_files/namelist_defaults_clm4_0.xml ------- List of default values for the clm4_0 namelist -namelist_files/namelist_defaults_clm4_5.xml ------- List of default values for the clm4_5 namelist -namelist_files/namelist_defaults_clm4_5_tools.xml - List of default values for the clm4_5 tools. +namelist_files/namelist_defaults_ctsm.xml --------- List of default values for the ctsm namelist +namelist_files/namelist_defaults_ctsm_tools.xml --- List of default values for the ctsm tools namelist_files/namelist_defaults_overall.xml ------ List of default values for overall settings namelist_files/namelist_defaults_usr_files.xml ---- List of default values for the user-files -namelist_files/namelist_definition_clm4_0.xml ----- Definition of all namelist items for clm4_0 -namelist_files/namelist_definition_clm4_5.xml ----- Definition of all namelist items for clm4_5 +namelist_files/namelist_definition_ctsm.xml -------- Definition of all namelist items for ctsm namelist_files/namelist_definition.xsl ------------ Describes how to view the xml file as html namelist_files/namelist_defaults_drydep.xml ------- List of default values for the dry deposition module. namelist_files/use_cases -------------------------- Specific configurations that build-namelist uses diff --git a/bld/config_files/clm_phys_vers.pm b/bld/config_files/clm_phys_vers.pm index af6d63a887..32124491a8 100755 --- a/bld/config_files/clm_phys_vers.pm +++ b/bld/config_files/clm_phys_vers.pm @@ -6,11 +6,8 @@ my $pkg_nm = 'config_files::clm_phys_vers'; # # require config_files::clm_phys_vers; # -# my $phys = config_files::clm_phys_vers->new("clm4_0"); -# print $phys->as_float(); -# print $phys->as_long(); +# my $phys = config_files::clm_phys_vers->new("clm5_0"); # print $phys->as_string(); -# print $phys->as_filename(); # # DESCRIPTION # @@ -31,10 +28,7 @@ use bigint; #use warnings; #use diagnostics; -my $major_mask = 1000000; -my $minor_mask = 1000; -my @version_strings = ( "clm4_0", "clm4_5", "clm5_0" ); -my @version_long = ( 4*$major_mask, 4*$major_mask+5*$minor_mask, 5*$major_mask ); +my @version_strings = ("clm4_5", "clm5_0"); #------------------------------------------------------------------------------- @@ -72,47 +66,6 @@ sub __validate_vers__ { #------------------------------------------------------------------------------- -sub as_long { -# Return the physics version as a long - my $self = shift; - my $vers = shift; - - if ( ! defined($vers) ) { - $vers = $self->{'vers_string'}; - } else { - $self->__validate_vers__( $vers ); - } - my $phys = undef; - for( my $i = 0; $i <= $#version_strings; $i++ ) { - if ( $vers eq $version_strings[$i] ) { - $phys = $version_long[$i]; - last; - } - } - return( $phys ); -} - -#------------------------------------------------------------------------------- - -sub as_float { -# Return the physics version as a float - my $self = shift; - - my $long = $self->as_long(); - my $major = int($long / $major_mask); - my $minor = int(($long - $major*$major_mask)/ $minor_mask); - my $rev = $long - $major*$major_mask - $minor*$minor_mask; - { - no bigint; - use bignum; - - my $phys = $major*1.0 + $minor/10.0 + $rev / 10000.0; - return( $phys ); - } -} - -#------------------------------------------------------------------------------- - sub as_string { # Return the physics version as a string my $self = shift; @@ -121,21 +74,6 @@ sub as_string { return( $phys ); } -#------------------------------------------------------------------------------- - -sub as_filename { -# Return the physics version string with clm4_5 and clm5_0 pointing to the same name - my $self = shift; - - my $phys = undef; - if ( $self->as_long() < 5*$major_mask ) { - $phys = $self->as_string(); - } else { - $phys = "clm4_5"; - } - return( $phys ); -} - #----------------------------------------------------------------------------------------------- # Unit testing of above #----------------------------------------------------------------------------------------------- @@ -145,45 +83,17 @@ if ( ! defined(caller) && $#ARGV == -1 ) { require Test::More; Test::More->import( ); - plan( tests=>13 ); + plan( tests=>2 ); sub testit { print "unit tester\n"; my %lastv; - my @vers_list = ( "clm4_0", "clm4_5", "clm5_0" ); + my @vers_list = ( "clm4_5", "clm5_0" ); foreach my $vers ( @vers_list ) { my $phys = config_files::clm_phys_vers->new($vers); isa_ok($phys, "config_files::clm_phys_vers", "created clm_phys_vers object"); - print "$vers: long: ".$phys->as_long()." float: ".$phys->as_float()." string: ".$phys->as_string()." file: ".$phys->as_filename()."\n"; - if ( exists($lastv{"long"}) ) { - is( $phys->as_long() > $lastv{'long'}, 1, "Definition of long is not increasing\n" ); - } - if ( exists($lastv{"float"}) ) { - is( $phys->as_float() > $lastv{'float'}, 1, "Definition of float is not increasing\n" ); - } - # Check that also can get results of any valid value for long - foreach my $chvers ( @vers_list ) { - my $lvalue = $phys->as_long($chvers); - print "Long value of $chvers = $lvalue\n"; - } - # Check that a bad value gives an error - eval { $phys->as_long('xxx'); }; - like( $@, qr/NOT a valid CLM version:/, "check that a bad version fails" ); - # Save last values to make sure increasing - $lastv{'long'} = $phys->as_long(); - $lastv{'float'} = $phys->as_float(); + print "$vers: string: ".$phys->as_string()."\n"; } - my $phys = config_files::clm_phys_vers->new("clm4_0"); - is( 4.0, $phys->as_float(), "Make sure clm4_0 correct float value" ); - $phys = config_files::clm_phys_vers->new("clm4_5"); - no bigint; - use bignum; - is( 4.5, $phys->as_float(), "Make sure clm4_5 correct float value" ); - no bignum; - use bigint; - $phys = config_files::clm_phys_vers->new("clm5_0"); - is( 5.0, $phys->as_float(), "Make sure clm5_0 correct float value" ); - print "\nSuccessfully ran all tests\n"; } } diff --git a/bld/config_files/config_defaults.xml b/bld/config_files/config_defaults.xml deleted file mode 100644 index 09d5634bb7..0000000000 --- a/bld/config_files/config_defaults.xml +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/bld/config_files/config_defaults_1x1_mexicocityMEX.xml b/bld/config_files/config_defaults_1x1_mexicocityMEX.xml deleted file mode 100644 index 660c16715b..0000000000 --- a/bld/config_files/config_defaults_1x1_mexicocityMEX.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - - - - - diff --git a/bld/config_files/config_defaults_1x1_numaIA.xml b/bld/config_files/config_defaults_1x1_numaIA.xml deleted file mode 100644 index b4813d0211..0000000000 --- a/bld/config_files/config_defaults_1x1_numaIA.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/bld/config_files/config_defaults_1x1_smallvilleIA.xml b/bld/config_files/config_defaults_1x1_smallvilleIA.xml deleted file mode 100644 index b4813d0211..0000000000 --- a/bld/config_files/config_defaults_1x1_smallvilleIA.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/bld/config_files/config_defaults_1x1_vancouverCAN.xml b/bld/config_files/config_defaults_1x1_vancouverCAN.xml deleted file mode 100644 index 49d9a54afb..0000000000 --- a/bld/config_files/config_defaults_1x1_vancouverCAN.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - - - - - diff --git a/bld/config_files/config_definition_clm4_0.xml b/bld/config_files/config_definition_clm4_0.xml deleted file mode 100644 index aeb78d387a..0000000000 --- a/bld/config_files/config_definition_clm4_0.xml +++ /dev/null @@ -1,115 +0,0 @@ - - - - - - - -Specifies either clm4_0, clm4_5, or clm5_0 physics - - - -CLM 4.0 Only. For CLM 4.5/5.0, spinup is controlled from build-namelist. -Spinup mode for the CN Carbon Nitrogen BGC model - AD turn on accelerated decomposition spinup for CN biogeochemistry model - exit jump from AD spinup mode to normal mode - normal no acceleration of decompositon (i.e. "final spinup") - - - -Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) radiative forcing -(SNICAR_FRC .true.is EXPERIMENTAL NOT SUPPORTED!) - - - -Flag to turn on site specific special configuration flags for supported single -point resolutions. See the specific config_defaults_*.xml file for the special -settings that are set for a particular site. - - - -CLM Biogeochemistry mode - none = Satellite Phenology (SP) - cn = Carbon Nitrogen model (CN) - (or CLM45BGC if phys=clm4_5/clm5_0, vsoilc_centbgc='on', and clm4me='on') - cndv = Carbon Nitrogen with Dynamic Global Vegetation Model (CNDV) - (or CLM45BGCDV if phys=clm4_5/clm5_0, vsoilc_centbgc='on', and clm4me='on') - - -Toggle to turn on the prognostic crop model - - - -Root directory of CLM source distribution (directory above CLM configure). - - - -Component framework interface to use -(Model Coupling Toolkit, or Earth System Modeling Framework) - - - -User source directories to prepend to the filepath. Multiple directories -are specified as a comma separated list with no embedded white space. -Normally this is SourceMods/src.clm in your case. - - - -User specified CPP defines to append to Makefile defaults. -Note: It's recommended to use configure options to set standard CPP values rather -than defining them here. - - - -Maximum number of plant function types (PFT) per gridcell -(Setting maxpft to anything other than 17 (or 25 for clm4_5/clm5_0 CROP or 21 for clm4_0 CROP) -is EXPERIMENTAL AND NOT SUPPORTED!) -(Either 17 for a standard vegetated case or -21 for prognostic clm4_0 CROP or 25 -for prognostic clm4_5/clm5_0 CROP) - - - -Toggle to make wild-fires inactive for biogeochemistry=CN mode - - - -Toggle to turn all history output completely OFF (possibly used for testing) - - - diff --git a/bld/config_files/config_definition_clm4_5.xml b/bld/config_files/config_definition_ctsm.xml similarity index 92% rename from bld/config_files/config_definition_clm4_5.xml rename to bld/config_files/config_definition_ctsm.xml index 8f57fd1844..b02510ed64 100644 --- a/bld/config_files/config_definition_clm4_5.xml +++ b/bld/config_files/config_definition_ctsm.xml @@ -5,10 +5,10 @@ -Specifies either clm4_0, clm4_5, or clm5_0 physics +Specifies either clm4_5 or clm5_0 physics ). Any value that contains - white-space must be quoted. Long option names may be supplied with either single - or double leading dashes. A consequence of this is that single letter options may - NOT be bundled. - - -bgc Build CLM with BGC package [ none | cn | cndv ] - (default is none). - -cache Name of output cache file (default: config_cache.xml). - -cachedir Name of directory where output cache file is written - (default: CLM build directory). - -cimeroot REQUIRED: Path to cime directory - -clm_root Root directory of clm source code - (default: directory above location of this script) - -cppdefs A string of user specified CPP defines. Appended to - Makefile defaults. e.g. -cppdefs '-DVAR1 -DVAR2' - -crop Toggle for prognostic crop model. [on | off] (default is off) - (can ONLY be turned on when BGC type is CN or CNDV) - -comp_intf Component interface to use (ESMF or MCT) (default MCT) - -defaults Specify full path to a configuration file which will be used - to supply defaults instead of the defaults in bld/config_files. - This file is used to specify model configuration parameters only. - Parameters relating to the build which are system dependent will - be ignored. - -help [or -h] Print usage to STDOUT. - -nofire Turn off wildfires for BGC setting of CN - (default includes fire for CN) - -noio Turn history output completely off (typically for testing). - -phys Value of clm4_0, clm4_5, or clm5_0 (default is clm4_0) - -silent [or -s] Turns on silent mode - only fatal messages issued. - -sitespf_pt Setup for the given site specific single-point resolution. - -snicar_frc Turn on SNICAR radiative forcing calculation. [on | off] - (default is off) - -spinup CLM 4.0 Only. For CLM 4.5, spinup is controlled from build-namelist. - Turn on given spinup mode for BGC setting of CN (level) - AD Turn on Accelerated Decomposition from (2) - bare-soil - exit Jump directly from AD spinup to normal mode (1) - normal Normal decomposition ("final spinup mode") (0) - (default) - The recommended sequence is 2-1-0 - -usr_src [,[,[...]]] - Directories containing user source code. - -verbose [or -v] Turn on verbose echoing of settings made by configure. - -version Echo the SVN tag name used to check out this CLM distribution. -EOF -} - -#----------------------------------------------------------------------------------------------- -# Setting autoflush (an IO::Handle method) on STDOUT helps in debugging. It forces the test -# descriptions to be printed to STDOUT before the error messages start. - -*STDOUT->autoflush(); - -#----------------------------------------------------------------------------------------------- -# Set the directory that contains the CLM configuration scripts. If the configure command was -# issued using a relative or absolute path, that path is in $ProgDir. Otherwise assume the -# command was issued from the current working directory. - -(my $ProgName = $0) =~ s!(.*)/!!; # name of this script -my $ProgDir = $1; # name of directory containing this script -- may be a - # relative or absolute path, or null if the script is in - # the user's PATH -my $cwd = getcwd(); # current working directory -my $cfgdir; # absolute pathname of directory that contains this script -if ($ProgDir) { - $cfgdir = abs_path($ProgDir); -} else { - $cfgdir = $cwd; -} - -#----------------------------------------------------------------------------------------------- -# Save commandline -my $commandline = "$cfgdir/configure @ARGV"; - -#----------------------------------------------------------------------------------------------- -# Parse command-line options. -my %opts = ( - cache => "config_cache.xml", - phys => "clm4_0", - nofire => undef, - noio => undef, - cimeroot => undef, - clm_root => undef, - spinup => "normal", - ); -GetOptions( - "spinup=s" => \$opts{'spinup'}, - "bgc=s" => \$opts{'bgc'}, - "cache=s" => \$opts{'cache'}, - "cachedir=s" => \$opts{'cachedir'}, - "snicar_frc=s" => \$opts{'snicar_frc'}, - "cimeroot=s" => \$opts{'cimeroot'}, - "clm_root=s" => \$opts{'clm_root'}, - "cppdefs=s" => \$opts{'cppdefs'}, - "comp_intf=s" => \$opts{'comp_intf'}, - "defaults=s" => \$opts{'defaults'}, - "clm4me=s" => \$opts{'clm4me'}, - "h|help" => \$opts{'help'}, - "nofire" => \$opts{'nofire'}, - "noio" => \$opts{'noio'}, - "phys=s" => \$opts{'phys'}, - "snicar_frc=s" => \$opts{'snicar_frc'}, - "s|silent" => \$opts{'silent'}, - "sitespf_pt=s" => \$opts{'sitespf_pt'}, - "usr_src=s" => \$opts{'usr_src'}, - "v|verbose" => \$opts{'verbose'}, - "version" => \$opts{'version'}, - "crop=s" => \$opts{'crop'}, -) or usage(); - -# Give usage message. -usage() if $opts{'help'}; - -# Echo version info. -version($cfgdir) if $opts{'version'}; - -# Check for unparsed arguments -if (@ARGV) { - print "ERROR: unrecognized arguments: @ARGV\n"; - usage(); -} - -# Define 3 print levels: -# 0 - only issue fatal error messages -# 1 - only informs what files are created (default) -# 2 - verbose -my $print = 1; -if ($opts{'silent'}) { $print = 0; } -if ($opts{'verbose'}) { $print = 2; } -my $eol = "\n"; - -my %cfg = (); # build configuration - -#----------------------------------------------------------------------------------------------- -# Make sure we can find required perl modules and configuration files. -# Look for them in the directory that contains the configure script. - -my $cimeroot = $opts{'cimeroot'}; -if ( ! defined($cimeroot) ) { - $cimeroot = "$cfgdir/../cime"; - if ( -d $cimeroot ) { - } elsif ( -d "$cfgdir/../../../cime" ) { - $cimeroot = "$cfgdir/../../../cime"; - } else { - die <<"EOF"; -** Cannot find the root of the cime directory enter it using the -cimeroot option - Did you run the checkout_externals scripts? -EOF - } -} -my $casecfgdir = "$cimeroot/scripts/Tools"; -my $perl5lib = "$cimeroot/utils/perl5lib/"; - -# The Build::Config module provides utilities to store and manipulate the configuration. -my $file = "$perl5lib/Build/Config.pm"; -(-f "$file") or die <<"EOF"; -** Cannot find perl module \"Build/Config.pm\" in path - \"$file\" ** -EOF -#----------------------------------------------------------------------------------------------- -# Add $cfgdir/perl5lib to the list of paths that Perl searches for modules -my @dirs = ( $cfgdir, "$perl5lib", $casecfgdir); -unshift @INC, @dirs; -require Build::Config; -require config_files::clm_phys_vers; - -# Get the physics version -my $phys = config_files::clm_phys_vers->new($opts{'phys'}); - -# Check for the physics specific configuration definition file. -my $phys_string = $phys->as_filename(); - -my $config_def_file = "config_definition_$phys_string.xml"; -(-f "$cfgdir/config_files/$config_def_file") or die <<"EOF"; -** Cannot find configuration definition file \"$config_def_file\" in directory - \"$cfgdir/config_files\" ** -EOF - -# The configuration defaults file modifies the generic defaults in the configuration -# definition file. Note that the -defaults option has precedence over all other options. -my $config_defaults_file; -my $std_config_defaults_file = "$cfgdir/config_files/config_defaults.xml"; -if ($opts{'defaults'}) { - $config_defaults_file = $opts{'defaults'}; -} elsif (defined($opts{'sitespf_pt'}) and $phys->as_long() == $phys->as_long( "clm4_0" ) ) { - $config_defaults_file = "$cfgdir/config_files/config_defaults_$opts{'sitespf_pt'}.xml"; - if ( ! -f $config_defaults_file ) { - $config_defaults_file = "$std_config_defaults_file"; - } -} else { - $config_defaults_file = "$std_config_defaults_file"; -} -(-f "$config_defaults_file") or die <<"EOF"; -** Cannot find configuration defaults file \"$config_defaults_file\" ** -EOF - -if ($print>=2) { print "Setting CLM configuration script directory to $cfgdir$eol"; } -if ($print>=2) { print "Using configuration defaults file $config_defaults_file$eol"; } - -# Initialize the configuration. The $config_def_file provides the definition of a CLM -# configuration, and the $config_defaults_file provides default values for a specific CLM -# configuration. $cfg_ref is a reference to the new configuration object. -my $cfg_ref = Build::Config->new("$cfgdir/config_files/$config_def_file", - "$config_defaults_file"); - -#----------------------------------------------------------------------------------------------- -# CLM root directory. -my $clm_root; - -if ( ! defined($opts{'clm_root'} ) ) { - $clm_root = abs_path("$cfgdir/.."); -} else { - $clm_root = $opts{'clm_root'}; -} - -if ( &is_valid_directory( "$clm_root/src", allowEnv=>0 ) ) { - $cfg_ref->set('clm_root', $clm_root); -} else { - die <<"EOF"; -** Invalid CLM root directory: $clm_root -** -** The CLM root directory must contain the subdirectory /src/. -** clm_root can be entered on the command line or it will be derived -** from the location of this script. -EOF -} - -if ($print>=2) { print "Setting CLM root directory to $clm_root$eol"; } - -#----------------------------------------------------------------------------------------------- -# CLM build directory is current directory -my $clm_bld = `pwd`; -chomp( $clm_bld ); - -# Make sure directory is valid -if ( ! &is_valid_directory( $clm_bld ) and ! mkdirp($clm_bld)) { - die <<"EOF"; -** Could not create the specified CLM build directory: $clm_bld -EOF -} - -if ($print>=2) { print "Setting CLM build directory to $clm_bld$eol"; } - -#----------------------------------------------------------------------------------------------- -# User source directories. -my $usr_src = ''; -if (defined $opts{'usr_src'}) { - my @dirs = split ',', $opts{'usr_src'}; - my @adirs; - while ( my $dir = shift @dirs ) { - if (&is_valid_directory( "$dir", allowEnv=>0 ) ) { - push @adirs, $dir; - } else { - die "** User source directory does not exist: $dir\n"; - } - } - $usr_src = join ',', @adirs; - $cfg_ref->set('usr_src', $usr_src); -} - -if ($print>=2) { print "Setting user source directories to $usr_src$eol"; } - -#----------------------------------------------------------------------------------------------- -# configuration cache directory and file. -my $config_cache_dir; -my $config_cache_file; -if (defined $opts{'cachedir'}) { - $config_cache_dir = abs_path($opts{'cachedir'}); -} -else { - $config_cache_dir = $clm_bld; -} - -if (&is_valid_directory( $config_cache_dir, allowEnv=>0 ) or mkdirp($config_cache_dir)) { - $config_cache_file = "$config_cache_dir/$opts{'cache'}"; -} else { - die <<"EOF"; -** Could not create the specified directory for configuration cache file: $config_cache_dir -EOF -} - -if ($print>=2) { print "The configuration cache file will be created in $config_cache_file$eol"; } - - -#----------------------------------------------------------------------------------------------- -# physics - -$cfg_ref->set('phys', $opts{'phys'}); -my $phys_string = $phys->as_string(); -if ($print>=2) { - if( defined($opts{'phys'}) ) { - print "Using version $phys_string physics.$eol"; - } -} - -#----------------------------------------------------------------------------------------------- -# supported single point configurations -my $sitespf_pt = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if( defined($opts{'sitespf_pt'}) ) { - $cfg_ref->set('sitespf_pt', $opts{'sitespf_pt'}); - } - $sitespf_pt = $cfg_ref->get('sitespf_pt'); - if ($print>=2) { - if( defined($opts{'sitespf_pt'}) ) { - print "Using $sitespf_pt for supported single point configuration.$eol"; - } - } -} - -#----------------------------------------------------------------------------------------------- -# NOIO option -my $noio = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if (defined $opts{'noio'}) { - $cfg_ref->set('noio', "on" ); - } - $noio = $cfg_ref->get('noio'); - if ($print>=2) { - if ( $noio eq "on") { print "ALL history output is turned OFF.$eol"; } - } -} -#----------------------------------------------------------------------------------------------- -# BGC option -my $bgc_mode = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if (defined $opts{'bgc'}) { - $cfg_ref->set('bgc', $opts{'bgc'}); - } - $bgc_mode = $cfg_ref->get('bgc'); - if ($print>=2) { print "Using $bgc_mode for bgc.$eol"; } - if ( $bgc_mode eq "casa" ) { - print "Warning:: bgc=casa is NOT validated / scientifically supported.$eol"; - } -} - -# NOFIRE option -- currently only in bgc=CN -my $nofire = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if (defined $opts{'nofire'}) { - $cfg_ref->set('nofire', "on" ); - } - $nofire = $cfg_ref->get('nofire'); - if ( ($nofire eq "on") && ($bgc_mode ne "cn") ) { - die <<"EOF"; -** Cannot turn nofire mode on -- without cn for bgc mode** -EOF - } - if ($print>=2 && $bgc_mode =~ /^cn/ ) { - if ( $nofire eq "off") { print "Wildfires are active as normal.$eol"; } - else { print "Wildfires are turned off.$eol"; } - } -} - -#----------------------------------------------------------------------------------------------- -# SPINUP option for BGC/CN mode only -my $spinup = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if (defined $opts{'spinup'}) { - $cfg_ref->set('spinup', $opts{'spinup'}); - } - $spinup = $cfg_ref->get('spinup'); - if ( ($spinup ne "normal" ) && ($bgc_mode ne "cn") ) { - die <<"EOF"; -** Cannot turn spinup mode on -- without cn for bgc mode** -** -** Set the bgc mode by the following means from highest to lowest precedence: -** * by the command-line option -bgc cn -** * by a default configuration file, specified by -defaults -EOF - } - if ($print>=2) { print "Using $spinup for spinup for cn mode.$eol"; } -} else { - if ($opts{'spinup'} ne "normal") { - die <<"EOF"; -** Spinup mode can only be controlled with configure for CLM 4.0. -** For CLM 4.5 use the bgc_spinup option to build-namelist -EOF - } -} - -#----------------------------------------------------------------------------------------------- -# comp_intf option -if (defined $opts{'comp_intf'}) { - $cfg_ref->set('comp_intf', $opts{'comp_intf'}); -} -my $comp_intf = $cfg_ref->get('comp_intf'); -if ($print>=2) { print "Using $comp_intf for comp_intf.$eol"; } - - -#----------------------------------------------------------------------------------------------- -# CROP option -my $crpmode = undef; -my $crop = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if (defined $opts{'crop'}) { - $cfg_ref->set('crop', $opts{'crop'}); - } - $crpmode = "nocrop"; - $crop = $cfg_ref->get('crop'); - if ( $crop eq "on" ) { - $crpmode = "crop"; - } - if ( ($crop eq "on" ) && ($bgc_mode ne "cn") && ($bgc_mode ne "cndv") ) { - die <<"EOF"; -** Cannot turn crop mode on -- without some form of cn for bgc mode** -** -** Set the bgc mode by the following means from highest to lowest precedence: -** * by the command-line options -bgc cn -** * by a default configuration file, specified by -defaults -EOF - } -} - -#----------------------------------------------------------------------------------------------- -# MAXPFT option - -my %maxpatchpft; -my $maxpft = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - $maxpatchpft{'crop'} = 21; - $maxpatchpft{'nocrop'} = 17; - - $cfg_ref->set('maxpft', $maxpatchpft{$crpmode} ); - $maxpft = $cfg_ref->get('maxpft'); - if ( (($bgc_mode eq "cn") || ($bgc_mode eq "cndv")) && ($maxpft != $maxpatchpft{$crpmode}) ) { - die <<"EOF"; -** For CN or CNDV BGC mode you MUST set max patch PFT's to $maxpatchpft{$crpmode} -** -** When the crop model is on then it must be set to $maxpatchpft{'crop'} otherwise to $maxpatchpft{'nocrop'} -** Set the bgc mode, crop and maxpft by the following means from highest to lowest precedence: -** * by the command-line options -bgc, -crop and -maxpft -** * by a default configuration file, specified by -defaults -** -EOF - } - if ( $maxpft > $maxpatchpft{$crpmode} ) { - die <<"EOF"; -** Max patch PFT's can NOT exceed $maxpatchpft{$crpmode} -** -** Set maxpft by the following means from highest to lowest precedence: -** * by the command-line options -maxpft -** * by a default configuration file, specified by -defaults -** -EOF - } - if ( $maxpft != $maxpatchpft{$crpmode} ) { - print "Warning:: running with maxpft NOT equal to $maxpatchpft{$crpmode} is " . - "NOT validated / scientifically supported.$eol"; - } - if ($print>=2) { print "Using $maxpft for maxpft.$eol"; } -} -#----------------------------------------------------------------------------------------------- -# SNICAR_FRC option -my $snicar_frc = undef; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - if (defined $opts{'snicar_frc'}) { - $cfg_ref->set('snicar_frc', $opts{'snicar_frc'}); - } - $snicar_frc = $cfg_ref->get('snicar_frc'); - if ($print>=2) { print "Using $snicar_frc for snicar_frc.$eol"; } -} - -#----------------------------------------------------------------------------------------------- -# Makefile configuration ####################################################################### -#----------------------------------------------------------------------------------------------- - -#----------------------------------------------------------------------------------------------- -# Name of CLM executable. -my $clm_exe = "clm"; - -if ($print>=2) { print "Name of CLM executable: $clm_exe.$eol"; } - -#----------------------------------------------------------------------------------------------- -# For the CPP tokens, start with the defaults (from defaults file) and append the specifications -# from the commandline. That way the user can override defaults since the commandline versions -# occur last. -my $usr_cppdefs = $cfg_ref->get('cppdefs'); -if (defined $opts{'cppdefs'}) { - $usr_cppdefs .= " $opts{'cppdefs'}"; - print "Warning:: running with user defined cppdefs is NOT validated / " . - "scientifically supported.$eol"; -} -$cfg_ref->set('cppdefs', $usr_cppdefs); - -if ($usr_cppdefs and $print>=2) { print "Default and user CPP definitions: \'$usr_cppdefs\'$eol";} - -# The following CPP macro definitions are used to implement the compile-time options. They are -# determined by the configuration parameters that have been set above. They will be appended to -# the CPP definitions that were explicitly set in the defaults file or by the user on the commandline. -my $cfg_cppdefs = ''; -if ($phys->as_long() == $phys->as_long("clm4_0") ) { - $cfg_cppdefs .= " -DMAXPATCH_PFT=$maxpft"; - - if ($bgc_mode eq 'cn') { - $cfg_cppdefs .= " -DCN"; - } - if ($crop eq 'on') { - $cfg_cppdefs .= " -DCROP"; - } - if ($bgc_mode eq 'cndv') { - $cfg_cppdefs .= " -DCNDV -DCN"; - } - if ($nofire eq 'on') { - $cfg_cppdefs .= " -DNOFIRE"; - } - if ($noio eq 'on') { - $cfg_cppdefs .= " -D_NOIO"; - } - if ($spinup eq 'AD') { - $cfg_cppdefs .= " -DAD_SPINUP"; - } elsif ($spinup eq 'exit') { - $cfg_cppdefs .= " -DEXIT_SPINUP"; - } - if ( $snicar_frc eq 'on' ) { - $cfg_cppdefs .= " -DSNICAR_FRC"; - } -} elsif ($phys->as_long() >= $phys->as_long("clm4_5") ) { - # clm4_5 cppdefs -- SHOULD NOT BE ANY! - if ( $cfg_cppdefs ne '' ) { - die <<"EOF"; -** CPP definitions should be empty for clm5_0 and is NOT ** -EOF - } -} elsif ($phys->as_long() == $phys->as_long("clm5_0") ) { - # clm5_0 cppdefs -- SHOULD NOT BE ANY! - if ( $cfg_cppdefs ne '' ) { - die <<"EOF"; -** CPP definitions should be empty for clm5_0 and is NOT ** -EOF - } -} else { - # this should NOT happen - die <<"EOF"; -** Bad CLM physics version ** -EOF -} -# CPP defines to put on Makefile -my $make_cppdefs = "$usr_cppdefs $cfg_cppdefs"; - -if ($print>=2) { print "CPP definitions set by configure: \'$cfg_cppdefs\'$eol"; } - -#----------------------------------------------------------------------------------------------- -# Write configuration files #################################################################### -#----------------------------------------------------------------------------------------------- - -my $fp_filename = 'Filepath'; # name of output filepath file -my $cpp_filename = 'CESM_cppdefs'; # name of output file for clm's cppdefs in cesm - -# Write the filepath file for cesm. -write_filepath_cesmbld("$clm_bld/$fp_filename", $cfg_ref, $phys, allowEnv=>0 ); -if ($print>=2) { print "creating $clm_bld/$fp_filename\n"; } - -# Write the file for clm's cppdefs needed in cesm. -write_cppdefs("$clm_bld/$cpp_filename", $make_cppdefs); -if ($print>=2) { print "creating $clm_bld/$cpp_filename\n"; } - -# Write the configuration file. -$cfg_ref->write_file($config_cache_file, $commandline); -if ($print>=2) { print "creating $config_cache_file\n"; } - -#----------------------------------------------------------------------------------------------- -# Done -chdir( $cwd ) || die <<"EOF"; -** Trouble changing directory back to $cwd -** -EOF -if ($print) { print "CLM configure done.\n"; } -exit; - -#----------------------------------------------------------------------------------------------- -# FINISHED #################################################################################### -#----------------------------------------------------------------------------------------------- - -#------------------------------------------------------------------------------- - -sub write_filepath_cesmbld -{ - my ($file, $cfg_ref, $phys, %opts) = @_; - my $fh = new IO::File; - - $fh->open(">$file") or die "** can't open filepath file: $file\n"; - - # configuration parameters used to determine paths - my $usr_src = $cfg_ref->get('usr_src'); - my $clm_root = $cfg_ref->get('clm_root'); - - # User specified source directories. - if ($usr_src =~ /\S+/) { - my @dirs = split ',', $usr_src; - while ( my $dir = shift @dirs ) { - print $fh "$dir\n"; - } - } else { - print $fh "../SourceMods/src.clm\n"; - } - - if ($phys->as_long() == $phys->as_long("clm4_0") ) { - # source root - my $srcdir = "$clm_root/src_clm40"; - if ( ! &is_valid_directory( "$srcdir", %opts ) ) { die "** source directory does not exist: $srcdir\n"; } - - # source directories under root - my @dirs = ( "main", "biogeophys", "biogeochem" ); - foreach my $dir ( @dirs ) { - if ( &is_valid_directory( "$srcdir/$dir", %opts ) ) { - print $fh "$srcdir/$dir\n"; - } else { - die "** source directory does not exist: $srcdir/$dir\n"; - } - } - } else { - # source root - my $srcdir = "$clm_root/src"; - if ( ! &is_valid_directory( "$srcdir", %opts ) ) { die "** source directory does not exist: $srcdir\n"; } - - # source directories under root - my @dirs = ( "main", - "biogeophys", - "biogeochem", - "soilbiogeochem", - "dyn_subgrid", - "init_interp", - "fates", - "fates/main", - "fates/biogeophys", - "fates/biogeochem", - "fates/fire", - "fates/parteh", - "utils", - "cpl" ); - - foreach my $dir ( @dirs ) { - if ( &is_valid_directory( "$srcdir/$dir", %opts ) ) { - print $fh "$srcdir/$dir\n"; - } else { - die "** source directory does not exist: $srcdir/$dir\n"; - } - } - } - - - $fh->close; -} -#------------------------------------------------------------------------------- - -sub write_cppdefs -{ - my ($file, $make_cppdefs) = @_; - my $fh = new IO::File; - - $fh->open(">$file") or die "** can't open cpp defs file: $file\n"; - - print $fh "$make_cppdefs\n"; - $fh->close; -} - -#------------------------------------------------------------------------------- - -sub mkdirp { - my ($dir) = @_; - my (@dirs) = split /\//, $dir; - my (@subdirs, $path); - - # if $dir is absolute pathname then @dirs will start with "" - if ($dirs[0] eq "") { push @subdirs, shift @dirs; } - - while ( @dirs ) { # check that each subdir exists and mkdir if it doesn't - push @subdirs, shift @dirs; - $path = join '/', @subdirs; - unless (-d $path or mkdir($path, 0777)) { return 0; } - } - return 1; -} - -#------------------------------------------------------------------------------- - -sub version { -# The version is found in CLM's ChangeLog file. -# $cfgdir is set by the configure script to the name of its directory. - - my ($cfgdir) = @_; - - my $logfile = "$cfgdir/../doc/ChangeLog"; - - my $fh = IO::File->new($logfile, '<') or die "** can't open ChangeLog file: $logfile\n"; - - while (my $line = <$fh>) { - - if ($line =~ /^Tag name:\s*[clm0-9_.-]*\s*[toin]*\s*([cesmclm0-9_.-]+)$/ ) { - print "$1\n"; - exit; - } - } - -} - -#------------------------------------------------------------------------------- - -sub is_valid_directory { -# -# Validate that the input is a valid existing directory. -# - my ($dir, %opts) = @_; - my $nm = "is_valid_directory"; - - my $valid = 0; - if ( -d $dir ) { $valid = 1; } - return( $valid ); - -} - diff --git a/bld/listDefaultNamelist.pl b/bld/listDefaultNamelist.pl index 063b1e6af0..dd41f00082 100755 --- a/bld/listDefaultNamelist.pl +++ b/bld/listDefaultNamelist.pl @@ -17,7 +17,7 @@ # # To then get the files from the CESM SVN repository: # -# ../../cime/scripts/Tools/check_input_data -datalistdir . -export +# ../cime/scripts/Tools/check_input_data --data-list-dir . --download # #======================================================================= @@ -44,13 +44,13 @@ #----------------------------------------------------------------------------------------------- # Add $cfgdir to the list of paths that Perl searches for modules -my @dirs = ( "$cfgdir", "../../../cime/utils/perl5lib" ); +my @dirs = ( "$cfgdir", "../cime/utils/perl5lib" ); unshift @INC, @dirs; require queryDefaultXML; # Defaults -my $cesmroot = abs_path( "$cfgdir/../../../"); +my $cesmroot = abs_path( "$cfgdir/../"); # The namelist defaults file contains default values for all required namelist variables. my @nl_defaults_files = ( "$cfgdir/namelist_files/namelist_defaults_overall.xml", @@ -84,11 +84,25 @@ sub usage { to then read the resulting clm.input_data_list file and retreive the files - ../../cime/scripts/Tools/check_input_data -datalistdir . -export + ../cime/scripts/Tools/check_input_data --data-list-dir . --download EOF } +sub make_config_cache { + # Write a config_cache.xml file to read in + my ($phys, $config_cachefile) = @_; + my $fh = IO::File->new($config_cachefile, '>') or die "can't open file: $config_cachefile"; + print $fh < + + +Specifies clm physics + +EOF + $fh->close(); +} + #----------------------------------------------------------------------------------------------- sub GetListofNeededFiles { @@ -153,7 +167,6 @@ sub GetListofNeededFiles { list => $list, usrdat => undef, help => undef, - phys => "clm4_5", ); my $cmdline = "@ARGV"; @@ -189,17 +202,15 @@ sub GetListofNeededFiles { } my %inputopts; my @nl_definition_files = ( - "$cfgdir/namelist_files/namelist_definition_$opts{'phys'}.xml" + "$cfgdir/namelist_files/namelist_definition_ctsm.xml" ); $inputopts{'nldef_files'} = \@nl_definition_files; - $inputopts{'empty_cfg_file'} = "$cfgdir/config_files/config_definition_$opts{'phys'}.xml"; + $inputopts{'empty_cfg_file'} = "config_cache.xml"; my $definition = Build::NamelistDefinition->new( $nl_definition_files[0] ); foreach my $nl_defin_file ( @nl_definition_files ) { $definition->add( "$nl_defin_file" ); } - my $cfg = Build::Config->new( $inputopts{'empty_cfg_file'} ); - # Resolutions... my @resolutions; if ( $opts{'res'} eq "all" ) { @@ -209,7 +220,8 @@ sub GetListofNeededFiles { } # Input options - push @nl_defaults_files, "$cfgdir/namelist_files/namelist_defaults_$opts{'phys'}.xml"; + &make_config_cache( "clm5_0", $inputopts{'empty_cfg_file'} ); + push @nl_defaults_files, "$cfgdir/namelist_files/namelist_defaults_ctsm.xml"; if ( defined($opts{'usrdat'}) ) { push @nl_defaults_files, "$cfgdir/namelist_files/namelist_defaults_usr_files.xml"; } @@ -249,21 +261,18 @@ sub GetListofNeededFiles { # Loop over all possible simulation year: 1890, 2000, 2100 etc. # $settings{'sim_year_range'} = "constant"; - my @rcps = $definition->get_valid_values( "rcp", 'noquotes'=>1 ); - $settings{'rcp'} = $rcps[0]; + my @ssp_rcps = $definition->get_valid_values( "ssp_rcp", 'noquotes'=>1 ); + $settings{'ssp_rcp'} = $ssp_rcps[0]; YEAR: foreach my $sim_year ( $definition->get_valid_values( "sim_year", 'noquotes'=>1 ) ) { print "sim_year = $sim_year\n" if $printing; $settings{'sim_year'} = $sim_year; if ( $sim_year ne 1850 && $sim_year ne 2000 && $sim_year > 1800 ) { next YEAR; } - my @bgcsettings = $cfg->get_valid_values( "bgc" ); - #my @glc_meclasses = $cfg->get_valid_values( "glc_nec" ); - my @glc_meclasses = ( 0, 10 ); - print "glc_nec = @glc_meclasses bgc=@bgcsettings\n" if $printing; + my @bgcsettings = $definition->get_valid_values( "bgc_mode", 'noquotes'=>1 ); + print "bgc=@bgcsettings\n" if $printing; # # Loop over all possible BGC settings # - my $phys = $opts{'phys'}; foreach my $bgc ( @bgcsettings ) { $settings{'bgc'} = $bgc; my @crop_vals; @@ -272,47 +281,29 @@ sub GetListofNeededFiles { } else { @crop_vals = ( "off" ); } + $settings{'glc_nec'} = 10; # - # Loop over all possible glc_nec settings + # Loop over all possible crop settings # - foreach my $glc_nec ( @glc_meclasses ) { - $settings{'glc_nec'} = $glc_nec; - # - # Loop over all possible crop settings - # - foreach my $crop ( @crop_vals ) { - $settings{'crop'} = $crop; - if ( $crop eq "on" ) { - $settings{'maxpft'} = 78; - } else { - $settings{'maxpft'} = 17; - } - my @irrigset; - if ( $glc_nec == 0 && $sim_year == 2000 ) { - @irrigset= ( ".true.", ".false." ); - } else { - @irrigset= ( ".false." ); - } - # - # Loop over irrigation settings - # - foreach my $irrig ( @irrigset ) { - $settings{'irrig'} = $irrig; - $inputopts{'namelist'} = "clm_inparm"; - &GetListofNeededFiles( \%inputopts, \%settings, \%files ); - if ( $printTimes >= 1 ) { - $inputopts{'printing'} = 0; - } - } + foreach my $crop ( @crop_vals ) { + $settings{'crop'} = $crop; + if ( $crop eq "on" ) { + $settings{'maxpft'} = 78; + } else { + $settings{'maxpft'} = 17; } - } - } - } + $inputopts{'namelist'} = "clm_inparm"; + &GetListofNeededFiles( \%inputopts, \%settings, \%files ); + if ( $printTimes >= 1 ) { + $inputopts{'printing'} = 0; + } + } + } + } # # Now do sim-year ranges # $settings{'bgc'} = "cn"; - $settings{'irrig'} = ".false."; $inputopts{'namelist'} = "clm_inparm"; foreach my $sim_year_range ( $definition->get_valid_values( "sim_year_range", 'noquotes'=>1 ) ) { $settings{'sim_year_range'} = $sim_year_range; @@ -320,11 +311,11 @@ sub GetListofNeededFiles { $settings{'sim_year'} = $1; } # - # Loop over all possible rcp's + # Loop over all possible ssp_rcp's # - print "sim_year_range=$sim_year_range rcp=@rcps\n" if $printing; - foreach my $rcp ( @rcps ) { - $settings{'rcp'} = $rcp; + print "sim_year_range=$sim_year_range ssp_rcp=@ssp_rcps\n" if $printing; + foreach my $ssp_rcp ( @ssp_rcps ) { + $settings{'ssp_rcp'} = $ssp_rcp; &GetListofNeededFiles( \%inputopts, \%settings, \%files ); if ( $printTimes >= 1 ) { $inputopts{'printing'} = 0; diff --git a/bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md b/bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md new file mode 100644 index 0000000000..463c3ffd65 --- /dev/null +++ b/bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md @@ -0,0 +1,58 @@ +# Steps for interpolating out-of-the-box initial conditions + +These are the steps that should be taken when interpolating (via +`init_interp`) out-of-the-box initial conditions files. This is often done +so that we'll have out-of-the-box initial conditions files that are +compatible with the current memory allocation, etc. (thus not requiring +`init_interp` to be run all the time). + +Do the following for each initial conditions file you want to +interpolate: + +1. From the latest master tag, create and run a test using the + appropriate compset and resolution for this initial conditions + file. Note that there may be other options (like carbon isotopes) + that also need to be turned on. While doing this, generate + baselines. e.g., run + `SMS_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default` or + `SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-ciso`, with + baseline generation. + + - Confirm that the test points to the desired, original finidat file, + and that `use_init_interp` is .true. by default. + +2. Rename the `finidat_interp_dest.nc` file that was generated by this + test, giving it a name that matches the original initial conditions + file, but with a new date stamp. Move this file into place + (`$CESMDATAROOT/inputdata/lnd/clm2/initdata_map/`). + +3. Add global metadata to the new file, mentioning the original file, + the test used to generate this new file, the tag used to run this + test, and a summary of what is different on this new version. For + example: + + ``` + ncatted -h -a Notes_190111,global,c,c,'Interpolated from clmi.I1850Clm50BgcCrop.1366-01-01.0.9x1.25_gx1v6_simyr1850_c171213.nc. This is the finidat_interp_dest.nc file from SMS_Ln1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel, run from ctsm1.0.dev022. Updates from the previous file are: (1) uses gx1v7 rather than gx1v6; (2) many inactive points are absent.' + ``` + +4. Using `ncdump -h`, diff the headers of the new and old files, and + make sure that there are no unexpected differences. Especially look + for missing fields on the new file, which could indicate, for + example, that carbon isotopes were turned on in the original run but + not in your new run. + +5. Update `namelist_defaults_ctsm.xml` to point to the new file. + + - Be sure to change any attributes in both the `finidat` entry and + the `init_interp_attributes` entry for this file. In particular, if + the old file had the attribute `use_init_interp=".true."`, this + should now be removed. + +6. Rerun the one-day test for which you generated baselines, comparing + against these baselines. Check the following: + + - `use_init_interp` should be .false. + + - The test should use the new `finidat` file + + - The test should pass and be bit-for-bit with the baseline diff --git a/bld/namelist_files/checkmapfiles.ncl b/bld/namelist_files/checkmapfiles.ncl index 6302615d1c..c0751adcb0 100644 --- a/bld/namelist_files/checkmapfiles.ncl +++ b/bld/namelist_files/checkmapfiles.ncl @@ -9,7 +9,7 @@ ; print( "Check that datm mapping files are consistent" ); - resolutions = (/ "128x256", "64x128", "48x96", "32x64", "8x16", "94x192", "0.23x0.31", "0.47x0.63", "0.9x1.25", "1.9x2.5", "2.5x3.33", "4x5", "10x15", "5x5_amazon", "1x1_camdenNJ", "1x1_vancouverCAN", "1x1_mexicocityMEX", "1x1_asphaltjungleNJ", "1x1_brazil", "1x1_urbanc_alpha", "1x1_numaIA", "1x1_smallvilleIA", "ne4np4", "ne16np4", "ne30np4", "ne60np4", "ne120np4", "ne240np4" /); + resolutions = (/ "128x256", "64x128", "48x96", "32x64", "8x16", "94x192", "0.23x0.31", "0.47x0.63", "0.9x1.25", "1.9x2.5", "2.5x3.33", "4x5", "10x15", "0.125nldas2", "5x5_amazon", "1x1_camdenNJ", "1x1_vancouverCAN", "1x1_mexicocityMEX", "1x1_asphaltjungleNJ", "1x1_brazil", "1x1_urbanc_alpha", "1x1_numaIA", "1x1_smallvilleIA", "ne4np4", "ne16np4", "ne30np4", "ne60np4", "ne120np4", "ne240np4" /); space = " "; badres = 0 diff --git a/bld/namelist_files/createMapEntry.pl b/bld/namelist_files/createMapEntry.pl index d767eff939..b4ea766e38 100755 --- a/bld/namelist_files/createMapEntry.pl +++ b/bld/namelist_files/createMapEntry.pl @@ -3,8 +3,8 @@ # July 18 2012 Muszala # # createMapEntry.pl - A simple script to dump a list of mappings for a specified resolution to then -# cut and paste into namelist_defaults_clm.xml. A better way is to write the output of this script -# to a file and then directly insert that file into namelist_defaults_clm.xml (using :r foo in vim for +# cut and paste into namelist_defaults_ctsm.xml. A better way is to write the output of this script +# to a file and then directly insert that file into namelist_defaults_ctsm.xml (using :r foo in vim for # example). # # Example usage:>> ./createMapEntry.pl 1x1_brazil @@ -36,7 +36,7 @@ SYNOPSIS $scriptName - is the resolution to use to dump text to paste into namelist_defaults_clm.xml + is the resolution to use to dump text to paste into namelist_defaults_ctsm.xml EOF } @@ -56,7 +56,7 @@ foreach my $foo ( @list ) { next if ($foo =~ m/^\./); #~# skip anything in the directory with a leading or stand alone 'dot' my @tokens = split(/_/, $foo); #~# split foo name by the underscore - #~# write out lines for namelist_defaults_clm.xml + #~# write out lines for namelist_defaults_ctsm.xml print "$partialPath/$foo\n"; } diff --git a/bld/namelist_files/namelist_defaults.xsl b/bld/namelist_files/namelist_defaults.xsl index bfebd0db89..6960cfbef9 100644 --- a/bld/namelist_files/namelist_defaults.xsl +++ b/bld/namelist_files/namelist_defaults.xsl @@ -27,9 +27,8 @@
  • Number of glacier multiple elevation classes (glc_nec)
  • Site specific point name (sitespf_pt)
  • Crop model (crop)
    • -
  • Irrigation model (irrig) (clm4_0 only)
  • Data model forcing source (forcing)
    • -
  • Representative concentration pathway for future scenarios (rcp)
    • +
  • Representative concentration pathway for future scenarios (SSP-rcp)
  • New good wood harvest (newwoodharv)
  • CN Spin-up mode (spinup)
  • Type of file (type)
    • @@ -134,9 +133,6 @@ crop= - - irrig= - spinup= diff --git a/bld/namelist_files/namelist_defaults_clm4_0.xml b/bld/namelist_files/namelist_defaults_clm4_0.xml deleted file mode 100644 index 4e9ddb10c9..0000000000 --- a/bld/namelist_files/namelist_defaults_clm4_0.xml +++ /dev/null @@ -1,1009 +0,0 @@ - - - - - - - - -1800 - - -379.0 -379.0 -284.7 - - -constant - - -PROG_CROP_ONLY -PROG_CROP_ONLY -NONE -NONE - - -clm4_0_CRUv7 - - -off - - -.true. -'TOTECOSYSC','TOTECOSYSN','TOTSOMC','TOTSOMN','TOTVEGC','TOTVEGN','TLAI','GPP','NPP','TWS','TSAI','HTOP','HBOT' -'TOTECOSYSC','TOTECOSYSN','TOTSOMC','TOTSOMN','TOTVEGC','TOTVEGN','TLAI','GPP','NPP','TWS' -'TLAI','TWS' --8760 - - -.false. - - -0 -1 - - -0.80,0.55 -0.60,0.40 -0.60,0.40 -0.60,0.40 -0.60,0.40 -0.60,0.40 - - -ON_WASTEHEAT - - -.false. - - - - - -lnd/clm2/pftdata/pft-physiology.clm40.c130424.nc - - -lnd/clm2/initdata/clmi.BCN.0182-01-01_0.47x0.63_g1v6_simyr1850_c120324.nc - - -lnd/clm2/initdata/clmi.BCN.0182-01-01_0.47x0.63_g1v6_simyr1850_c120324.nc - - -lnd/clm2/initdata/clmi.BCN.0182-01-01_0.47x0.63_g1v6_simyr1850_c120324.nc - - - - - -lnd/clm2/initdata_map/clmi.I1850Clm40CnGswGs.1441-01-01.0.9x1.25_gx1v6_simyr1850_c170823.nc - - -lnd/clm2/initdata_map/clmi.I1850Clm40CnGswGs.1441-01-01.0.9x1.25_gx1v6_simyr1850_c170823.nc - - -lnd/clm2/initdata_map/clmi.I1850Clm40CnCruGs.3362-01-01.0.9x1.25_gx1v6_simyr1850_c171222.nc - - -lnd/clm2/initdata_map/clmi.I1850Clm40CnCruGs.3362-01-01.0.9x1.25_gx1v6_simyr1850_c171222.nc - - - - -lnd/clm2/initdata/clmi.IQirrcr_2000-01-01_1.9x2.5_gx1v6_c101115.nc - - -ccsm4_init/b40.1850.track1.2deg.003/year_401/b40.1850.track1.2deg.003.clm2.r.0401-01-01-00000.nc - - -ccsm4_init/b40.1850.track1.2deg.003/year_401/b40.1850.track1.2deg.003.clm2.r.0401-01-01-00000.nc - - -ccsm4_init/b40.1850.track1.2deg.003/year_401/b40.1850.track1.2deg.003.clm2.r.0401-01-01-00000.nc - - -lnd/clm2/initdata/clmi.IQCNDV.0201-01-01_1.9x2.5_gx1v6_simyr2000_c100316.nc - - -ccsm4_init/b40.1850.track1.1deg.006/0863-01-01/b40.1850.track1.1deg.006.clm2.r.0863-01-01-00000.nc - 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- - - - -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_AVHRR_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_MODIS_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_USGS_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_10x10min_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_MODIS_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_USGS_to_1x1_mexicocityMEX_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_IGBP-GSDP_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_ISRIC-WISE_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_GLOBE-Gardner_to_1x1_mexicocityMEX_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_mexicocityMEX_nomask_aave_da_c120927.nc - - - - - -lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_AVHRR_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_MODIS_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_USGS_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_10x10min_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_MODIS_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_USGS_to_1x1_numaIA_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_IGBP-GSDP_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_ISRIC-WISE_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_GLOBE-Gardner_to_1x1_numaIA_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_numaIA_nomask_aave_da_c120927.nc - - - - - -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_AVHRR_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_MODIS_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_USGS_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_10x10min_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_MODIS_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_USGS_to_1x1_smallvilleIA_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_IGBP-GSDP_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_ISRIC-WISE_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_GLOBE-Gardner_to_1x1_smallvilleIA_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_smallvilleIA_nomask_aave_da_c120927.nc - - - - - -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_AVHRR_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_MODIS_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_USGS_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_10x10min_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_MODIS_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_USGS_to_1x1_urbanc_alpha_nomask_aave_da_c120928.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_IGBP-GSDP_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_ISRIC-WISE_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_GLOBE-Gardner_to_1x1_urbanc_alpha_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_urbanc_alpha_nomask_aave_da_c120927.nc - - - - - -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_AVHRR_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_MODIS_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_USGS_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_10x10min_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_MODIS_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_USGS_to_1x1_vancouverCAN_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_IGBP-GSDP_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_ISRIC-WISE_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_GLOBE-Gardner_to_1x1_vancouverCAN_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_vancouverCAN_nomask_aave_da_c120927.nc - - - -lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_landuse_to_0.9x1.25_aave_da_110307.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_lanwat_to_0.9x1.25_aave_da_110307.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_fmax_to_0.9x1.25_aave_da_110725.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_10minx10min_topo_to_0.9x1.25_aave_da_110630.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_5minx5min_soitex_to_0.9x1.25_aave_da_110722.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_5minx5min_irrig_to_0.9x1.25_aave_da_110529.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_5x5min_ISRIC-WISE_to_0.9x1.25_nomask_aave_da_c120525.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_MODIS_to_0.9x1.25_nomask_aave_da_c120523.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_USGS_to_0.9x1.25_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_LandScan2004_to_0.9x1.25_nomask_aave_da_c120522.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_GLOBE-Gardner_to_0.9x1.25_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_GLOBE-Gardner-mergeGIS_to_0.9x1.25_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_landuse_to_1.9x2.5_aave_da_110307.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_lanwat_to_1.9x2.5_aave_da_110307.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_fmax_to_1.9x2.5_aave_da_110725.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_10minx10min_topo_to_1.9x2.5_aave_da_110307.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_5minx5min_soitex_to_1.9x2.5_aave_da_110307.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_5x5min_nomask_to_1.9x2.5_nomask_aave_da_c120606.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_5x5min_ISRIC-WISE_to_1.9x2.5_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_MODIS_to_1.9x2.5_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_USGS_to_1.9x2.5_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_LandScan2004_to_1.9x2.5_nomask_aave_da_c120522.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_GLOBE-Gardner_to_1.9x2.5_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_GLOBE-Gardner-mergeGIS_to_1.9x2.5_nomask_aave_da_c120923.nc - - -lnd/clm2/mappingdata/maps/10x15/map_0.5x0.5_landuse_to_10x15_aave_da_110307.nc -lnd/clm2/mappingdata/maps/10x15/map_0.5x0.5_lanwat_to_10x15_aave_da_110307.nc -lnd/clm2/mappingdata/maps/10x15/map_0.5x0.5_fmax_to_10x15_aave_da_110725.nc -lnd/clm2/mappingdata/maps/10x15/map_10minx10min_topo_to_10x15_aave_da_110307.nc -lnd/clm2/mappingdata/maps/10x15/map_5minx5min_soitex_to_10x15_aave_da_110307.nc -lnd/clm2/mappingdata/maps/10x15/map_5x5min_nomask_to_10x15_nomask_aave_da_c120327.nc -lnd/clm2/mappingdata/maps/10x15/map_5x5min_ISRIC-WISE_to_10x15_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/10x15/map_3x3min_MODIS_to_10x15_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/10x15/map_3x3min_USGS_to_10x15_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/10x15/map_3x3min_LandScan2004_to_10x15_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/10x15/map_3x3min_GLOBE-Gardner_to_10x15_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/10x15/map_3x3min_GLOBE-Gardner-mergeGIS_to_10x15_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/360x720/map_0.5x0.5_MODIS_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_0.5x0.5_AVHRR_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_0.5x0.5_USGS_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_10x10min_nomask_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_5x5min_IGBP-GSDP_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_5x5min_nomask_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_5x5min_ISRIC-WISE_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_3x3min_MODIS_to_360x720_nomask_aave_da_c120830.nc -lnd/clm2/mappingdata/maps/360x720/map_3x3min_USGS_to_360x720_nomask_aave_da_c121128.nc -lnd/clm2/mappingdata/maps/360x720/map_3x3min_LandScan2004_to_360x720_nomask_aave_da_c121017.nc -lnd/clm2/mappingdata/maps/360x720/map_3x3min_GLOBE-Gardner_to_360x720_nomask_aave_da_c121128.nc -lnd/clm2/mappingdata/maps/360x720/map_3x3min_GLOBE-Gardner-mergeGIS_to_360x720_nomask_aave_da_c121128.nc - - -lnd/clm2/mappingdata/maps/512x1024/map_0.5x0.5_MODIS_to_512x1024_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/512x1024/map_0.5x0.5_AVHRR_to_512x1024_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/512x1024/map_0.5x0.5_USGS_to_512x1024_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/512x1024/map_10x10min_nomask_to_512x1024_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/512x1024/map_5x5min_IGBP-GSDP_to_512x1024_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/512x1024/map_5x5min_nomask_to_512x1024_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/512x1024/map_5x5min_ISRIC-WISE_to_512x1024_nomask_aave_da_c120906.nc -lnd/clm2/mappingdata/maps/512x1024/map_3x3min_MODIS_to_512x1024_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/512x1024/map_3x3min_USGS_to_512x1024_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/512x1024/map_3x3min_LandScan2004_to_512x1024_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/512x1024/map_3x3min_GLOBE-Gardner_to_512x1024_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/512x1024/map_3x3min_GLOBE-Gardner-mergeGIS_to_512x1024_nomask_aave_da_c120923.nc - - -lnd/clm2/mappingdata/maps/128x256/map_0.5x0.5_MODIS_to_128x256_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/128x256/map_0.5x0.5_AVHRR_to_128x256_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/128x256/map_0.5x0.5_USGS_to_128x256_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/128x256/map_10x10min_nomask_to_128x256_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/128x256/map_5x5min_IGBP-GSDP_to_128x256_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/128x256/map_5x5min_nomask_to_128x256_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/128x256/map_5x5min_ISRIC-WISE_to_128x256_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/128x256/map_3x3min_MODIS_to_128x256_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/128x256/map_3x3min_USGS_to_128x256_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/128x256/map_3x3min_LandScan2004_to_128x256_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/128x256/map_3x3min_GLOBE-Gardner_to_128x256_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/128x256/map_3x3min_GLOBE-Gardner-mergeGIS_to_128x256_nomask_aave_da_c120923.nc - - -lnd/clm2/mappingdata/maps/64x128/map_0.5x0.5_MODIS_to_64x128_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/64x128/map_0.5x0.5_AVHRR_to_64x128_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/64x128/map_0.5x0.5_USGS_to_64x128_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/64x128/map_10x10min_nomask_to_64x128_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/64x128/map_5x5min_IGBP-GSDP_to_64x128_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/64x128/map_5x5min_nomask_to_64x128_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/64x128/map_5x5min_ISRIC-WISE_to_64x128_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/64x128/map_3x3min_MODIS_to_64x128_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/64x128/map_3x3min_USGS_to_64x128_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/64x128/map_3x3min_LandScan2004_to_64x128_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/64x128/map_3x3min_GLOBE-Gardner_to_64x128_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/64x128/map_3x3min_GLOBE-Gardner-mergeGIS_to_64x128_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/48x96/map_0.5x0.5_MODIS_to_48x96_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/48x96/map_0.5x0.5_AVHRR_to_48x96_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/48x96/map_0.5x0.5_USGS_to_48x96_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/48x96/map_10x10min_nomask_to_48x96_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/48x96/map_5x5min_IGBP-GSDP_to_48x96_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/48x96/map_5x5min_nomask_to_48x96_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/48x96/map_5x5min_ISRIC-WISE_to_48x96_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/48x96/map_3x3min_MODIS_to_48x96_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/48x96/map_3x3min_USGS_to_48x96_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/48x96/map_3x3min_LandScan2004_to_48x96_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/48x96/map_3x3min_GLOBE-Gardner_to_48x96_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/48x96/map_3x3min_GLOBE-Gardner-mergeGIS_to_48x96_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_MODIS_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_AVHRR_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_USGS_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_10x10min_nomask_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_IGBP-GSDP_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_nomask_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_ISRIC-WISE_to_32x64_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_MODIS_to_32x64_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_USGS_to_32x64_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_LandScan2004_to_32x64_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_GLOBE-Gardner_to_32x64_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_GLOBE-Gardner-mergeGIS_to_32x64_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_MODIS_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_AVHRR_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_USGS_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_10x10min_nomask_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_IGBP-GSDP_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_nomask_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_ISRIC-WISE_to_8x16_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_MODIS_to_8x16_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_USGS_to_8x16_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_LandScan2004_to_8x16_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_GLOBE-Gardner_to_8x16_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_GLOBE-Gardner-mergeGIS_to_8x16_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/4x5/map_0.5x0.5_MODIS_to_4x5_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/4x5/map_0.5x0.5_AVHRR_to_4x5_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/4x5/map_0.5x0.5_USGS_to_4x5_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/4x5/map_10x10min_nomask_to_4x5_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/4x5/map_5x5min_IGBP-GSDP_to_4x5_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/4x5/map_5x5min_nomask_to_4x5_nomask_aave_da_c110822.nc -lnd/clm2/mappingdata/maps/4x5/map_5x5min_ISRIC-WISE_to_4x5_nomask_aave_da_c120906.nc -lnd/clm2/mappingdata/maps/4x5/map_3x3min_MODIS_to_4x5_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/4x5/map_3x3min_USGS_to_4x5_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/4x5/map_3x3min_LandScan2004_to_4x5_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/4x5/map_3x3min_GLOBE-Gardner_to_4x5_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/4x5/map_3x3min_GLOBE-Gardner-mergeGIS_to_4x5_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/0.23x0.31/map_0.5x0.5_MODIS_to_0.23x0.31_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_0.5x0.5_AVHRR_to_0.23x0.31_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_0.5x0.5_USGS_to_0.23x0.31_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_10x10min_nomask_to_0.23x0.31_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_5x5min_IGBP-GSDP_to_0.23x0.31_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_5x5min_nomask_to_0.23x0.31_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_5x5min_ISRIC-WISE_to_0.23x0.31_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_MODIS_to_0.23x0.31_nomask_aave_da_c110930.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_USGS_to_0.23x0.31_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_LandScan2004_to_0.23x0.31_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_GLOBE-Gardner_to_0.23x0.31_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_GLOBE-Gardner-mergeGIS_to_0.23x0.31_nomask_aave_da_c120923.nc - 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- - - -lnd/clm2/mappingdata/maps/ne120np4/map_0.1x0.1_nomask_to_ne120np4_nomask_aave_da_c120706.nc -lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_USGS_to_ne120np4_nomask_aave_da_c120913.nc - - - -lnd/clm2/mappingdata/maps/5x5_amazon/map_0.5x0.5_MODIS_to_5x5_amazon_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_0.5x0.5_AVHRR_to_5x5_amazon_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_0.5x0.5_USGS_to_5x5_amazon_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_10x10min_nomask_to_5x5_amazon_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_IGBP-GSDP_to_5x5_amazon_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_nomask_to_5x5_amazon_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_ISRIC-WISE_to_5x5_amazon_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_MODIS_to_5x5_amazon_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_USGS_to_5x5_amazon_nomask_aave_da_c120927.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_LandScan2004_to_5x5_amazon_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_GLOBE-Gardner_to_5x5_amazon_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_GLOBE-Gardner-mergeGIS_to_5x5_amazon_nomask_aave_da_c120923.nc - -lnd/clm2/mappingdata/maps/ne240np4/map_0.5x0.5_MODIS_to_ne240np4_nomask_aave_da_c110922.nc -lnd/clm2/mappingdata/maps/ne240np4/map_0.5x0.5_AVHRR_to_ne240np4_nomask_aave_da_c110922.nc -lnd/clm2/mappingdata/maps/ne240np4/map_0.5x0.5_USGS_to_ne240np4_nomask_aave_da_c110922.nc -lnd/clm2/mappingdata/maps/ne240np4/map_10x10min_nomask_to_ne240np4_nomask_aave_da_c110922.nc -lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_IGBP-GSDP_to_ne240np4_nomask_aave_da_c110922.nc -lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_nomask_to_ne240np4_nomask_aave_da_c110922.nc -lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_ISRIC-WISE_to_ne240np4_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_MODIS_to_ne240np4_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_USGS_to_ne240np4_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_LandScan2004_to_ne240np4_nomask_aave_da_c120521.nc -lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_GLOBE-Gardner_to_ne240np4_nomask_aave_da_c120925.nc -lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne240np4_nomask_aave_da_c120925.nc -lnd/clm2/mappingdata/maps/ne240np4/map_ne240np4_nomask_to_0.5x0.5_nomask_aave_da_c110922.nc - - - - - -. -. - - diff --git a/bld/namelist_files/namelist_defaults_clm4_0_tools.xml b/bld/namelist_files/namelist_defaults_clm4_0_tools.xml deleted file mode 100644 index 23fb007430..0000000000 --- a/bld/namelist_files/namelist_defaults_clm4_0_tools.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - - - - - diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_ctsm.xml similarity index 94% rename from bld/namelist_files/namelist_defaults_clm4_5.xml rename to bld/namelist_files/namelist_defaults_ctsm.xml index 03ef8a58a0..d64773e334 100644 --- a/bld/namelist_files/namelist_defaults_clm4_5.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -36,7 +36,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). sp -clm4_0_cam6.0 clm4_5_CRUv7 clm5_0_cam6.0 @@ -114,9 +113,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. + +.false. + +1 0 -1 +0 NONE @@ -143,8 +146,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. .false. -20SL_8.5m -10SL_3.5m +4SL_2m +20SL_8.5m +10SL_3.5m .false. .false. @@ -251,6 +255,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .true. +40 +3 + .true. 1.0 @@ -294,15 +301,30 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .false. +.false. + +drip + -OFF -ON_RAD +.true. -12 -5 -10000.0 -1000.0 +12 +5 +5 + +10000.0 +5000.0 +1000.0 + +0.010d00 +0.015d00 +0.03d00 +0.07d00 +0.02d00 +0.05d00 2000. @@ -335,6 +357,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). to .true. --> 1.e9 +SwensonLawrence2012 + 'melted','melted','remains_ice','remains_ice' -'converted_to_snow','converted_to_snow','converted_to_snow','converted_to_snow' - -lnd/clm2/paramdata/clm5_params.c171117.nc -lnd/clm2/paramdata/clm_params.c170913.nc +lnd/clm2/paramdata/clm5_params.c200402.nc +lnd/clm2/paramdata/clm_params.c200402.nc @@ -444,6 +466,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .true. + +.true. + .false. .false. @@ -464,14 +489,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -6.d+1 -.false. -.false. -.true. +.false. +.true. .true. .false. - + -1850,2000 +1850,2000,2010 .true. @@ -498,11 +522,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Or one specific file will be chosen over another. --> hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.false. irrigate=.false. glc_nec=10 +>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.false. irrigate=.true. glc_nec=10 hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.false. irrigate=.false. glc_nec=10 +>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.false. irrigate=.true. glc_nec=10 hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10 hgrid=0.9x1.25 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10 hgrid=0.9x1.25 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10 hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10 -lnd/clm2/initdata_map/clmi.I1850Clm45BgcGs.0901-01-01.0.9x1.25_gx1v6_simyr1850_c180204.nc +>lnd/clm2/initdata_map/clmi.I1850Clm45BgcGs.0901-01-01.0.9x1.25_gx1v7_simyr1850_c190718.nc -lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v6_simyr1850_c180204.nc +>lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v7_simyr1850_c190718.nc lnd/clm2/initdata_map/clmi.B1850.1171-01-01.0.9x1.25_gx1v7_simyr1850_c181029.nc +>lnd/clm2/initdata_map/clmi.B1850.0161-01-01.0.9x1.25_gx1v7_simyr1850_c190111.nc -lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v6_simyr1850_c171214.nc + ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true." + lnd_tuning_mode="clm5_0_GSWP3v1" use_init_interp=".true." +>lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v7_simyr1850_c190111.nc -lnd/clm2/initdata_map/clmi.I1850Clm50BgcCrop.1366-01-01.0.9x1.25_gx1v6_simyr1850_c171213.nc +>lnd/clm2/initdata_map/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c200428.nc -lnd/clm2/initdata_map/clmi.I1850Clm50BgcCropCru.1526-01-01.0.9x1.25_gx1v6_simyr1850_c180109b.nc + ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false." + lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true." +>lnd/clm2/initdata_map/clmi.I1850Clm50BgcCropCru-ciso.1526-01-01.0.9x1.25_gx1v7_simyr1850_c190116.nc lnd/clm2/initdata_map/clmi.B1850.1171-01-01.0.9x1.25_gx1v7_simyr1850_c181029.nc + ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false." + lnd_tuning_mode="clm5_0_cam6.0" use_init_interp=".true." +>lnd/clm2/initdata_map/clmi.B1850.0161-01-01.0.9x1.25_gx1v7_simyr1850_c190111.nc -lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v6_simyr1850_c180110.nc + ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true." + lnd_tuning_mode="clm5_0_CRUv7" use_init_interp=".true." +>lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v7_simyr1850_c190111.nc @@ -713,7 +737,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."> - lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_48x96_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc @@ -732,6 +755,9 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_16pfts_Irrig_CMIP6 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc + +lnd/clm2/surfdata_map/surfdata_0.125nldas2_hist_16pfts_Irrig_CMIP6_simyr2005_c190412.nc + lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_5x5_amazon_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc @@ -746,6 +772,8 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CM lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr2000_c190304.nc + +lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_simyr2005_c190624.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr2000_c190214.nc @@ -772,7 +800,7 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_urbanc_alpha_hist_16pfts_Ir -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_48x96_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc + lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_48x96_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc @@ -997,7 +1025,7 @@ lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr18 .true. .false. -0.83d-06 +0.83d-06 0.015d00 @@ -1098,6 +1126,17 @@ lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr18 1997 1997 +lnd/clm2/prescribed_data/LFMIP-pdLC-SST.H2OSOI.0.9x1.25.20levsoi.natveg.climo1980-2014.MONS_c190709.nc + +linear + + + +.false. +1997 +1997 +1997 + lnd/clm2/prescribed_data/LFMIP-pdLC-SST.H2OSOI.0.9x1.25.20levsoi.natveg.1980-2014.MONS_climo.c190716.nc linear @@ -1215,39 +1254,29 @@ lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr18 2106 2015 -2000 -2000 - -2000 -2000 - -1850 -1850 +2000 +2000 -1850 -1850 +1850 +1850 -2000 -2000 +2000 +2000 -2000 -2000 +2000 +2000 -2000 -2000 +2000 +2000 -2000 -2000 +1850 +2106 -2000 -2000 +lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc -2000 -2000 - -lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc - -lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc +lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc nn @@ -1265,6 +1294,22 @@ lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr18 .false. +.false. +.true. + +0 +1 + +0 +1 + +0.d00 +0.d00 +0.d00 +0.d00 +0.d00 +0.d00 + @@ -2381,6 +2426,48 @@ lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr18 + + + +lnd/clm2/mappingdata/maps/0.125nldas2/map_1km-merge-10min_HYDRO1K-merge-nomask_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_5x5min_nomask_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_0.25x0.25_MODIS_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_0.9x1.25_GRDC_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_10x10min_nomask_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_360x720cru_cruncep_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_3x3min_LandScan2004_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_10x10min_IGBPmergeICESatGIS_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_3x3min_MODIS_to_0.125nldas2_nomask_aave_da_c190412.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_3x3min_MODIS-wCsp_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_0.5x0.5_MODIS_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_3x3min_GLOBE-Gardner-mergeGIS_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_5x5min_ISRIC-WISE_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_3x3min_GLOBE-Gardner_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_0.5x0.5_AVHRR_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_3x3min_USGS_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_5x5min_IGBP-GSDP_to_0.125nldas2_nomask_aave_da_c190408.nc +lnd/clm2/mappingdata/maps/0.125nldas2/map_5x5min_ORNL-Soil_to_0.125nldas2_nomask_aave_da_c190408.nc + + + lnd/clm2/mappingdata/maps/5x5_amazon/map_0.5x0.5_MODIS_to_5x5_amazon_nomask_aave_da_c110920.nc .false. 1 + + + + + +.false. + + + + + +.false. + +.false. + diff --git a/bld/namelist_files/namelist_defaults_clm4_5_tools.xml b/bld/namelist_files/namelist_defaults_ctsm_tools.xml similarity index 99% rename from bld/namelist_files/namelist_defaults_clm4_5_tools.xml rename to bld/namelist_files/namelist_defaults_ctsm_tools.xml index a1598f3bf1..ad82dd7bf6 100644 --- a/bld/namelist_files/namelist_defaults_clm4_5_tools.xml +++ b/bld/namelist_files/namelist_defaults_ctsm_tools.xml @@ -113,6 +113,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). landmesh +lnd/clm2/mappingdata/grids/SCRIPgrid_0.125nldas2_nomask_c190328.nc lnd/clm2/mappingdata/grids/SCRIPgrid_1x1pt_camdenNJ_nomask_c110308.nc lnd/clm2/mappingdata/grids/SCRIPgrid_1x1pt_brazil_nomask_c110308.nc lnd/clm2/mappingdata/grids/SCRIPgrid_1x1pt_camdenNJ_nomask_c110308.nc @@ -217,7 +218,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_lai_histclm52deg005_earthstatmirca_2005.c190119.nc - + lnd/clm2/rawdata/pftcftlandusedynharv.0.25x0.25.MODIS.simyr1850-2015.c170412/mksrf_lai_78pfts_simyr2005.c170413.nc @@ -232,7 +233,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_soilcolor_histclm52deg005_earthstatmirca_2005.c190116.nc - + lnd/clm2/rawdata/pftcftlandusedynharv.0.25x0.25.MODIS.simyr1850-2015.c170412/mksrf_soilcolor_CMIP6_simyr2005.c170623.nc diff --git a/bld/namelist_files/namelist_defaults_drydep.xml b/bld/namelist_files/namelist_defaults_drydep.xml index 056f598d2b..e73f2987c2 100644 --- a/bld/namelist_files/namelist_defaults_drydep.xml +++ b/bld/namelist_files/namelist_defaults_drydep.xml @@ -25,6 +25,5 @@ attributes from the config_cache.xml file (with keys converted to upper-case). atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc -atm/cam/chem/trop_mozart/emis/megan21_emis_factors_c20120313.nc diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml index 44da084342..63bfb4317d 100644 --- a/bld/namelist_files/namelist_defaults_overall.xml +++ b/bld/namelist_files/namelist_defaults_overall.xml @@ -23,8 +23,7 @@ determine default values for namelists. arb_ic arb_ic arb_ic -arb_ic -cold +cold arb_ic @@ -33,7 +32,6 @@ determine default values for namelists. flanduse_timeseries flanduse_timeseries - /fs/cgd/csm/inputdata @@ -62,12 +60,9 @@ determine default values for namelists. 1 0 - + hist - -.false. - gx1v6 gx1v6 @@ -90,6 +85,7 @@ determine default values for namelists. gx1v6 gx1v6 +nldas2 navy navy navy diff --git a/bld/namelist_files/namelist_definition_clm4_0.xml b/bld/namelist_files/namelist_definition_clm4_0.xml deleted file mode 100644 index b699022f8e..0000000000 --- a/bld/namelist_files/namelist_definition_clm4_0.xml +++ /dev/null @@ -1,822 +0,0 @@ - - - - - - - - - - - -Full pathname of initial conditions file. If blank CLM will startup from -arbitrary initial conditions. - - - -Full pathname of master restart file for a branch run. (only used if RUN_TYPE=branch) -(Set with RUN_REFCASE and RUN_REFDATE) - - - -Full pathname of land fraction data file. - - - -Clumps per processor. - - - -Atmospheric CO2 molar ratio (by volume) only used when co2_type==constant (umol/mol) -(Set by CCSM_CO2_PPMV) - - - -Type of CO2 feedback. - constant = use the input co2_ppmv value - prognostic = use the prognostic value sent from the atmosphere - diagnostic = use the diagnostic value sent from the atmosphere - - - - -Supplemental Nitrogen mode and for what type of vegetation it's turned on for. -In this mode Nitrogen is unlimited rather than prognosed and in general vegetation is -over-productive. It does act as a proxy for fertilization for crops however. - NONE = No vegetation types get supplemental Nitrogen - PROG_CROP_ONLY = Supplemental Nitrogen is only active for prognostic Crops - ALL = Supplemental Nitrogen is active for all vegetation types - - - -If TRUE, separate the vegetated landunit into a crop landunit and a natural vegetation landunit - - - -Number of multiple elevation classes over glacier points. -Normally this is ONLY used when running CESM with the active glacier model. - - - -If TRUE, dynamically change topographic height over glacier points. -Only works when glc_nec is greater than zero. -(EXPERIMENTAL AND NOT FUNCTIONAL!) - - - -Visible and Near-infrared albedo's for glacier ice - - - -Time step (seconds) - - - -Override the start type from the driver: it can only be -set to 3 meaning branch. - - - -Full pathname of land-ice mask data file (on lnd grid). - - - -Full pathname of topography data file. Only required when -land-ice model is active. - - - -Full pathname datafile with plant function type (PFT) constants - - - -Full pathname of time varying PFT data file. This causes the land-use types of -the initial surface dataset to vary over time. - - - -Full pathname of surface data file. - - - -SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name - - - -SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name - - - -Per file averaging flag. - 'A' (average over history period) - 'I' (instantaneous) - 'X' (maximum over history period) - 'M' (minimum over history period) - - - -Averaging type of output for 1D vector output (when hist_dov2xy is false). - GRID means average all land-units up to the grid-point level - LAND means average all columns up to the land-unit level - COLS means average all PFT's up to the column level - PFTS means report everything on native PFT level - - - -If TRUE, implies output data on a 2D latitude/longitude grid. False means -output in 1D vector format. One setting per history tape series. - - - -If TRUE, indicates do NOT output any default history fields (requires you to use -hist_fincl* to set the exact output fields to use).. - - - -Fields to exclude from history tape series 1. - - - -Fields to exclude from history tape series 2. - - - -Fields to exclude from history tape series 3. - - - -Fields to exclude from history tape series 4. - - - -Fields to exclude from history tape series 5. - - - -Fields to exclude from history tape series 6. - - - -Fields to add to history tape series 1. - - - -Fields to add to history tape series 2. - - - -Fields to add to history tape series 3. - - - -Fields to add to history tape series 4. - - - -Fields to add to history tape series 5. - - - -Fields to add to history tape series 6. - - - -Per tape series maximum number of time samples. - - - -Per tape series history file density (i.e. output precision) - 1=double precision - 2=single precision -Default: 2,2,2,2,2,2 - - - -Per tape series history write frequency. - positive means in time steps - 0=monthly - negative means hours -(i.e. 5 means every 24 time-steps and -24 means every day -Default: 0,-24,-24,-24,-24,-24 - - - -number of segments per clump for decomposition -Default: 20 - - - -Perturbation limit when doing error growth test - - - -If FALSE, don't write any restart files. - - - -Turn urban air conditioning/heating ON or OFF and add wasteheat: - OFF = Air conditioning/heating is OFF in buildings, internal temperature allowed to float freely - ON = Air conditioning/heating is ON in buildings, internal temperature constrained - ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon - - - -If TRUE, urban traffic flux will be activated (Currently NOT implemented). - - - -If TRUE, write diagnostic of global radiative temperature written to CLM log file. - - - - - - -SCRIP format grid data file - - - -Flag to pass to the ESMF mapping utility, telling it what kind of large -file support is needed for an output file generated with this grid as -either the source or destination ('none', '64bit_offset' or 'netcdf4'). - - - -Flag to pass to the ESMF mapping utility, telling it what kind of grid -file this is (SCRIP or UGRID). - - - -For UGRID files, flag to pass to the ESMF mapping utility, telling it the -name of the dummy variable that has all of the topology information stored -in its attributes. (Only used if scripgriddata_src_type = UGRID.) - - - - - - -Filename for mksurfdata_map to remap raw data into the output surface dataset - - - -Plant Function Type dataset for mksurfdata - - - -Dataset for percent glacier land-unit for mksurfdata - - - -Dataset for topography used to define urban threshold - - - -Dataset for land topography - - - -Leaf Area Index dataset for mksurfdata - - - -Soil texture dataset for mksurfdata - - - -Soil color dataset for mksurfdata - - - -Soil max fraction dataset for mksurfdata - - - -High resolution land mask/fraction dataset for mksurfdata -(used for glacier_mec land-units) - - - -Type of grid to create for mksurfdata - - - -Grid file at the output resolution for mksurfdata - - - -Text file with filepaths (or list of XML elements) for vegetation fractions -and harvesting for each year to run over for mksurfdata to be able to model -transient land-use change - - - -High resolution topography dataset for mksurfdata -(used for glacier_mec land-units) - - - -Irrigation dataset for mksurfdata - - - -Organic soil dataset for mksurfdata - - - -Lake water dataset for mksurfdata - - - -Wetland dataset for mksurfdata - - - -Urban dataset for mksurfdata - - - -Biogenic Volatile Organic Compounds (VOC) emissions dataset for mksurfdata - - - -If TRUE, output variables in double precision for mksurfdata - - - -If TRUE, ignore other files, and set the output percentage to 100% urban and -zero for other land-use types. - - - -Number of Plant Functional Types (excluding bare-soil) - - - -Plant Function Type index to override global file with for mksurfdata - - - -Plant Function Type fraction to override global file with for mksurfdata - - - -Soil color index to override global file with for mksurfdata - - - -Soil maximum fraction to override global file with for mksurfdata - - - -Soil percent sand to override global file with for mksurfdata - - - -Soil percent clay to override global file with for mksurfdata - - - - - - - -Orography file with surface heights and land area fraction - - - -CLM grid file - - - -CESM domain file - - - -CAM file - - - -Raw topography file - - - -CAM topography file - - - -Number of longitudes to use for a regional grid (for single-point set to 1) - - - -Number of latitudes to use for a regional grid (for single-point set to 1) - - - -Northern edge of the regional grid - - - -Southern edge of the regional grid - - - -Eastern edge of the regional grid - - - -Western edge of the regional grid - - - - - - - -Historical greenhouse gas concentrations from CAM, only used -by getco2_historical.ncl - - - - - - -Aerosol deposition file name (only used for aerdepregrid.ncl) - - - -Full pathname of CLM fraction dataset (only used for mkdatadomain). - - - -Full pathname of CLM grid dataset (only used for mkdatadomain). - - - -Full pathname of output domain dataset (only used for mkdatadomain). - - - -Type of domain file to create (ocean or atmosphere) (only used for mkdatadomain) - - - - - - - -First year to loop over for Nitrogen Deposition data - - - -Last year to loop over for Nitrogen Deposition data - - - -Simulation year that aligns with stream_year_first_ndep value - - - -Filename of input stream data for Nitrogen Deposition - - - -Mapping method from Nitrogen deposition input file to the model resolution - bilinear = bilinear interpolation - nn = nearest neighbor - nnoni = nearest neighbor on the "i" (longitude) axis - nnonj = nearest neighbor on the "j" (latitude) axis - spval = set to special value - copy = copy using the same indices - - - -datm input directory - - -datm output directory - - -Datm logfile name - - - - - - - -Mapping file to go from one resolution/land-mask to another resolution/land-mask - - - -Land mask description for mksurfdata input files - - - -Horizontal grid resolutions for mksurfdata input files - - - - - - - -Check that the resolution and land-mask is valid before continuing. - - - -Shared Socioeconomic Pathway (SSP) and Representative Concentration Pathway (RCP) combination for future scenarios -The form is SSPn-m.m Where n is the SSP number and m.m is RCP radiative forcing at peak or 2100 in W/m^2 -n is just the whole number of the specific SSP scenario. The lower numbers have higher mitigation -- the higher numbers less mitigation, more than one SSP can result in the same RCP forcing -hist means do NOT use a future scenario, just use historical data. - - - -Add a note to the output namelist about the options given to build-namelist - - - -CLM run type. - 'default' use the default type of clm_start type for this configuration - 'cold' is a run from arbitrary initial conditions - 'arb_ic' is a run using initial conditions if provided, OR arbitrary initial conditions if no files can be found - 'startup' is an initial run with initial conditions provided. - 'continue' is a restart run. - 'branch' is a restart run in which properties of the output history files may be changed. - - - -Horizontal resolutions -Note: 0.1x0.1, 0.5x0.5, 5x5min, 10x10min, 3x3min and 0.33x0.33 are only used for CLM tools - - - -Land mask description - - - -Command line argument for setting up your simulation in a mode for faster -throughput. By default turns off some options, and sets up for a lower level -of output. When bgc_mode is some level of prognostic BGC (so NOT Satellite Phenology) -it also sets up for accelerated decomposition. -NOTE: THIS CORRESPONDS DIRECTLY TO THE env_run.xml VARIABLE OF THE SAME NAME. - Set the env_run variable, rather than setting this directly. - - - -General configuration of model version and atmospheric forcing to tune the model to run under. -This sets the model to run with constants that were set to run well under the configuration -of model version and atmospheric forcing. To run well constants would need to be changed -to run with a different type of atmospheric forcing. - - - -If TRUE, irrigation will be active (find surface datasets with active irrigation). - - - -If 1, turn on the MEGAN model for BVOC's (Biogenic Volitile Organic Compounds) - - - -Year to simulate and to provide datasets for (such as surface datasets, initial conditions, aerosol-deposition, Nitrogen deposition rates etc.) -A sim_year of 1000 corresponds to data used for testing only, NOT corresponding to any real datasets. -Most years are only used for clm_tools and there aren't CLM datasets that correspond to them. -CLM datasets exist for years: 1000 (for testing), 1850, and 2000 - - - -Range of years to simulate transitory datasets for (such as dynamic: land-use datasets, aerosol-deposition, Nitrogen deposition rates etc.) -Constant means simulation will be held at a constant year given in sim_year. -A sim_year_range of 1000-1002 or 1000-1004 corresponds to data used for testing only, NOT corresponding to any real datasets. -A sim_year_range that goes beyond 2005 corresponds to historical data until 2005 and then scenario data beyond that point. - - - -Namelist entries to demand be provided on the namelist. - - - -Description of the use case selected. - - - - - - - -Where dry deposition is calculated (from land, atmosphere, or from a table) - - - - -List of chemical constituents that dry deposition will be calculated for - - - - - - - -File containing MEGAN emissions factors. Includes the list of MEGAN compounds that can be -used in the Comp_Name variable on the file. - - - -MEGAN specifier. This is in the form of: Chem-compound = megan_compound(s) -where megan_compound(s) can be the sum of megan compounds with a "+" between them. -In each equation, the item to the left of the equal sign is a CAM chemistry compound, the -items to the right are compounds known to the MEGAN model (single or combinations). -For example, -megan_specifier = 'ISOP = isoprene', - 'C10H16 = pinene_a + carene_3 + thujene_a' - - - -MEGAN mapped isoprene emissions factors switch -If TRUE then use mapped MEGAN emissions factors for isoprene. - - - -List of possible MEGAN compounds to use - (the list used by the simulation is on the megan_factors_file as the Comp_Name) - - - - - -Enable C13 model - - - -Enable C14 model - - - diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_ctsm.xml similarity index 90% rename from bld/namelist_files/namelist_definition_clm4_5.xml rename to bld/namelist_files/namelist_definition_ctsm.xml index 32e247e78d..f57583b857 100644 --- a/bld/namelist_files/namelist_definition_clm4_5.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -114,12 +114,25 @@ If TRUE, square the organic fraction when it's used (as was done in CLM4.5) Otherwise use the fraction straight up (the default for CLM5.0) - + 10SL_3.5m = standard CLM4 and CLM4.5 version 23SL_3.5m = more vertical layers for permafrost simulations 49SL_10m = 49 layer soil column, 10m of soil, 5 bedrock layers 20SL_8.5m = 20 layer soil column, 8m of soil, 5 bedrock layers +4SL_2m = 4 layer soil column, 2m of soil, 0 bedrock layers + + + +User-defined vector of dzsoi. The length of this vector determines nlevgrnd. When the user sets this vector, they have to set soil_layerstruct_userdefined_nlevsoi in the namelist, too; soil_layerstruct_userdefined_nlevsoi must be less than nlevgrnd in this version of the model, even though ideally soil_layerstruct_userdefined_nlevsoi could also equal nlevgrnd. +Default: rundef + + + +User-defined number of soil layers required to be set in the namelist when the user sets soil_layerstruct_userdefined in the namelist. +Default: iundef + +Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the hardwired default value. +Default: 40 + + Fraction of intercepted precipitation @@ -437,11 +456,32 @@ Only applies if using an active runoff (ROF) model; otherwise, river storage-bas is turned off regardless of the setting of this namelist variable. + +If TRUE, supply irrigation from groundwater (in addition to surface water). + +Can only be set if limit_irrigation_if_rof_enabled is true (otherwise +groundwater extraction is never invoked). + +Cannot be combined with lower_boundary_condition = 3 or 4 + + + +Irrigation method used if not specified on surface dataset + + If TRUE, irrigation will be active. + +If TRUE, fsat will be set to zero for crop columns. + + Number of multiple elevation classes over glacier points. @@ -507,23 +547,6 @@ Allowed values are: Only applies when melt_non_icesheet_ice_runoff is .true. - -When rain-snow repartitioning / downscaling results in rain being converted to -snow, the behavior of the resulting additional snow. -First item corresponds to GLACIER_REGION with ID 0 in the surface dataset, -second to GLACIER_REGION with ID 1, etc. -Allowed values are: -'converted_to_snow': rain is converted to snow, with a corresponding sensible - heat flux correction -'runs_off': rather than being converted to snow, the excess rain runs off - immediately -IMPORTANT NOTE: Unlike other glacier_region*behavior namelist options, this -option applies to all landunit types in the given regions. -Only applies when repartition_rain_snow is .true. - - Number of days before one considers the perennially snow-covered point 'land ice' @@ -601,12 +624,6 @@ baseline proportion of nitrogen allocated for electron transport (J) Time step (seconds) - -Override the start type from the driver: it can only be -set to 3 meaning branch. - - Toggle to turn on the FATES model @@ -914,14 +931,14 @@ Human heat stress indices: If TRUE, write diagnostic of global radiative temperature written to CLM log file. - -Subgrid fluxes for snow + +Whether to use subgrid fluxes for snow - -Turn vegetation snow canopy ON, OFF, or ON with albedo influence (ON_RAD) + +Whether snow on the vegetation canopy affects the radiation/albedo calculations @@ -1082,6 +1099,62 @@ Toggle for mexico city specific logic. Max number of plant functional types in naturally vegetated landunit. + +Number of dominant pfts, so this determines the number of active pfts. Selecting the value 0 means DO NOTHING, ie all pfts in the input data are active. +Default: 0 + + + +Number of dominant landunits, so this determines the number of active landunits. Selecting the value 0 means DO NOTHING, ie all landunits in the input data are active. +Default: 0 + + + +If true, this directs the model to collapse the urban landunits to the dominant urban landunit. Selecting .false. means DO NOTHING, ie all urban landunits found in the input data are active. +Default: .false. + + +Default: 0 + + +Default: 0 + + +Default: 0 + + +Default: 0 + + +Default: 0 + + +Default: 0 + + Toggle to turn on the dynamic root model @@ -1860,7 +1933,7 @@ CLM run type. +"conus_30_x8,512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,0.125nldas2,5x5_amazon,1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.1x0.1,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4,ne60np4,ne120np4,ne240np4,1km-merge-10min"> Horizontal resolutions Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM tools @@ -1877,7 +1950,7 @@ hist means do NOT use a future scenario, just use historical data. + valid_values="USGS,gx3v7,gx1v6,gx1v7,navy,test,tx0.1v2,tx1v1,T62,cruncep,nldas2"> Land mask description @@ -2004,14 +2077,6 @@ E-folding depth over which decomposition is slowed with depth in all soils. If TRUE, reduce heterotrophic respiration according to available oxygen predicted by CH4 submodel. - -If TRUE, weight calculation of oxygen limitation by the inundated fraction and diagnostic saturated column gas -concentration profile calculated in the CH4 submodel. Only applies if anoxia = TRUE. -(EXPERIMENTAL AND NOT FUNCTIONAL!) -(deprecated -- will be removed) - - separate q10 for frozen soil respiration rates. default to same as above zero rates @@ -2242,12 +2307,6 @@ Set to alblak values (0.6, 0.4) to keep albedo constant for ice-covered lakes wi - -Use old snow cover fraction from Niu et al. 2007 -(deprecated -- will be removed) - - If surface water is active or not @@ -2354,6 +2413,52 @@ If TRUE, apply harvest from flanduse_timeseries file. (Also, only valid for use_cn = true.) + +If TRUE, reset baseline values of total column water and energy in the +first step of the run. This should typically be set when transitioning +from an offline spinup to a coupled run with transient glaciers, and +*possibly* when transitioning from the spinup to the transient portion +of a coupled run with transient glaciers; it should typically remain +unset at other times. + +These baseline values are computed only for particular columns +(currently, only for glacier columns). They provide values that are +subtracted from the current state when counting total column water and +energy. For glacier columns, these discount the water and energy +contents in the "virtual" glacier ice, while adding representative +amounts of water and energy in the non-explicitly-modeled soil beneath +the ice. Subtracting these baselines reduces the fictitious dynbal +fluxes generated when total grid cell water and energy changes as a +result of dynamic column/landunit areas. + +These baseline values are initially computed based on cold start +states. If this flag remains unset (.false.), these baseline values will +remain fixed at their cold start values. This will conserve mass and +energy, but may result in larger-than-desired dynbal energy fluxes (and, +in principle, also larger dynbal water fluxes; but currently, the mass +of glacier ice remains fixed over time, so dynbal water fluxes are +fairly small regardless of whether this flag is ever set). To further +reduce these dynbal fluxes, you can set this flag to .true. when +starting a startup or hybrid run from a partially or entirely spun-up +state. This will reset the baseline values based on the state at the +start of this run. + +Note that setting this flag can break water and energy conservation! +Specifically, any water and energy that has previously been added to or +removed from states that contribute to these baselines (currently, (a) +glacier ice and (b) soil water and energy in the vegetated landunit in +the same grid cell as glaciers) will effectively be ignored when +computing conservation corrections due to land cover change. Instead, +only the change in states from this point forward will be +considered. So, for example, this flag should NOT be set when +transitioning from a historical run to a future scenario. + +This setting only impacts startup and hybrid runs; it has no effect in a +continue run; it is an error for this to be set in a branch +run. Furthermore, this setting has no effect in a cold start run. + + If TRUE, allow area changes at times other than the year boundary. This should @@ -2420,19 +2525,48 @@ Changes in this value should possibly be accompanied by changes in: glc_snow_persistence_max_days > 0. + +Min snow thickness of layer 1 (top snow layer); values other than the default 0.01 have not been tested as of Sep 6, 2019 + + +Min snow thickness of layer 2; values other than the default 0.015 have not been tested as of Sep 6, 2019; snow_dzmin of remaining layers is generated with the following recursive formula: dzmin(j) = dzmax_u(j-1) * 0.5_r8 + + + +Max snow thickness of layer 1 (top snow layer) when no layers beneath; values other than the default 0.03 have not been tested as of Sep 6, 2019 + + +Max snow thickness of layer 2 when no layers beneath; values other than the default 0.07 have not been tested as of Sep 6, 2019; snow_dzmax_l of remaining layers is generated with the following recursive formula: dzmax_l(j) = dzmax_u(j) + dzmax_l(j-1) + + + +Max snow thickness of layer 1 (top snow layer) when layers beneath; values other than the default 0.02 have not been tested as of Sep 6, 2019 + + +Max snow thickness of layer 2 when layers beneath; values other than the default 0.05 have not been tested as of Sep 6, 2019; snow_dzmax_u of remaining layers is generated with the following recursive formula: dzmax_u(j) = 2._r8 * dzmax_u(j-1) + 0.01_r8 + + + group="scf_swenson_lawrence_2012_inparm" valid_values="" > Limit applied to integrated snowfall when determining changes in snow-covered fraction during melt (mm H2O) +Only applies when using the SwensonLawrence2012 snow cover fraction method + group="scf_swenson_lawrence_2012_inparm" valid_values="" > SCA shape parameter for glc_mec (glacier multiple elevation class) columns For most columns, n_melt is based on the standard deviation of 1km topography in the grid cell; but glc_mec columns already account for subgrid topographic variability through their use of multiple elevation classes; thus, to avoid double-accounting for topographic variability in these columns, we use a fixed value of n_melt. +Only applies when using the SwensonLawrence2012 snow cover fraction method + +Parameterization to use for snow cover fraction +NiuYang2007: Niu and Yang 2007 +SwensonLawrence2012: Swenson and Lawrence 2012 + + + + + + + +If .true., add water tracers needed to perform water tracer consistency checks. + +These consistency checks ensure that all water tracers are updated to remain in-sync with +the related bulk quantities. + + + +If .true., run with water isotopes + diff --git a/bld/namelist_files/use_cases/1850_control.xml b/bld/namelist_files/use_cases/1850_control.xml index 31d3b3eb3d..501d734129 100644 --- a/bld/namelist_files/use_cases/1850_control.xml +++ b/bld/namelist_files/use_cases/1850_control.xml @@ -11,12 +11,6 @@ .false. .false. -1850 -1850 - -1850 -1850 - 1850 1850 @@ -29,21 +23,18 @@ 1850 1850 -1850 -1850 - 1850 1850 - +1850 +1850 + lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc - + lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc cycle -NDEP_month - diff --git a/bld/namelist_files/use_cases/1850_noanthro_control.xml b/bld/namelist_files/use_cases/1850_noanthro_control.xml index 971b0cf410..cc0cc66ccf 100644 --- a/bld/namelist_files/use_cases/1850_noanthro_control.xml +++ b/bld/namelist_files/use_cases/1850_noanthro_control.xml @@ -23,7 +23,6 @@ 1850 cycle -NDEP_month 1925 1925 diff --git a/bld/namelist_files/use_cases/2000_control.xml b/bld/namelist_files/use_cases/2000_control.xml index 31a7eb1a50..f5d2cd59e9 100644 --- a/bld/namelist_files/use_cases/2000_control.xml +++ b/bld/namelist_files/use_cases/2000_control.xml @@ -12,12 +12,6 @@ .false. .false. -2000 -2000 - -2000 -2000 - 2000 2000 @@ -30,6 +24,9 @@ 2000 2000 +2000 +2000 + 2000 2000 diff --git a/bld/namelist_files/use_cases/20thC_transient.xml b/bld/namelist_files/use_cases/20thC_transient.xml index c9de2a1f58..b086337fea 100644 --- a/bld/namelist_files/use_cases/20thC_transient.xml +++ b/bld/namelist_files/use_cases/20thC_transient.xml @@ -4,7 +4,6 @@ Simulate transient land-use, and aerosol deposition changes from 1850 to 2015 Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to 2015 -Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to 2015 Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to 2015 1850 @@ -19,14 +18,6 @@ .false. .false. -1850 -2005 -1850 - -1850 -2005 -1850 - 1850 2005 1850 @@ -45,6 +36,10 @@ 2016 1850 +1850 +2106 +1850 + 1850 2106 1850 diff --git a/bld/queryDefaultNamelist.pl b/bld/queryDefaultNamelist.pl index 8c555d1f6d..920e91eb48 100755 --- a/bld/queryDefaultNamelist.pl +++ b/bld/queryDefaultNamelist.pl @@ -77,7 +77,6 @@ sub usage { -onlyfiles Only output filenames. -options "item=value,item2=value2" Set options to query for when matching. (comma delimited, with equality to set value). - -phys "CLM-version" [or -p] CLM version to use (clm4_0 or clm4_5) -res "resolution" Resolution to use for files. Use "-res list" to list all valid resolutions. Use "-res any" to use any valid resolution. @@ -111,7 +110,6 @@ sub usage { my %opts = ( namelist => $namelist, - model => "clm4_5", var => undef, hgrid => undef, config => undef, @@ -132,7 +130,6 @@ sub usage { "f|file=s" => \$opts{'file'}, "n|namelist=s" => \$opts{'namelist'}, "v|var=s" => \$opts{'var'}, - "p|phys=s" => \$opts{'model'}, "r|res=s" => \$opts{'hgrid'}, "config=s" => \$opts{'config'}, "cesm" => \$opts{'cesm'}, @@ -181,11 +178,10 @@ sub usage { # List of input options my %inputopts; # This namelist files under the cime directories are in version 2 format and can't be read by perl code EBK 11/15/2016 - my $model = $opts{'model'}; my @nl_definition_files = ("$cfgdir/namelist_files/namelist_definition_drv.xml", - "$cfgdir/namelist_files/namelist_definition_$model.xml" + "$cfgdir/namelist_files/namelist_definition_ctsm.xml" ); - $inputopts{empty_cfg_file} = "$cfgdir/config_files/config_definition_$model.xml"; + $inputopts{empty_cfg_file} = "$cfgdir/config_files/config_definition_ctsm.xml"; $inputopts{nldef_files} = \@nl_definition_files; $inputopts{namelist} = $opts{namelist}; $inputopts{printing} = $printing; @@ -249,8 +245,8 @@ sub usage { $settings{'notest'} = ! $opts{'test'}; $settings{'csmdata'} = $inputopts{csmdata}; } else { - my @files = ( "$cfgdir/namelist_files/namelist_defaults_${model}.xml", - "$cfgdir/namelist_files/namelist_defaults_${model}_tools.xml", + my @files = ( "$cfgdir/namelist_files/namelist_defaults_ctsm.xml", + "$cfgdir/namelist_files/namelist_defaults_ctsm_tools.xml", "$cfgdir/namelist_files/namelist_defaults_drv.xml", "$cfgdir/namelist_files/namelist_defaults_drydep.xml", ); diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 63407442f6..aae37e9343 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -6,6 +6,7 @@ ######################### +use lib '.'; use Test::More; use xFail::expectedFail; use IO::File; @@ -68,6 +69,20 @@ sub make_env_run { $fh->close(); } +sub make_config_cache { + # Write a config_cache.xml file to read in + my ($phys) = @_; + my $config_cachefile = "config_cache.xml"; + my $fh = IO::File->new($config_cachefile, '>') or die "can't open file: $config_cachefile"; + print $fh < + + +Specifies clm physics + +EOF + $fh->close(); +} # # Process command-line options. @@ -123,9 +138,9 @@ sub make_env_run { # # Figure out number of tests that will run # -my $ntests = 838; +my $ntests = 822; if ( defined($opts{'compare'}) ) { - $ntests += 504; + $ntests += 495; } plan( tests=>$ntests ); @@ -144,12 +159,13 @@ sub make_env_run { print "ERROR: unrecognized arguments: @ARGV\n"; usage(); } -my $mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +my $phys = "clm5_0"; +my $mode = "-phys $phys"; +&make_config_cache($phys); my $DOMFILE = "$inputdata_rootdir/atm/datm7/domain.lnd.T31_gx3v7.090928.nc"; my $real_par_file = "user_nl_clm_real_parameters"; -my $bldnml = "../build-namelist -verbose -csmdata $inputdata_rootdir -lnd_frac $DOMFILE -glc_nec 10 -no-note -output_reals $real_par_file"; +my $bldnml = "../build-namelist -verbose -csmdata $inputdata_rootdir -lnd_frac $DOMFILE -configuration clm -structure standard -glc_nec 10 -no-note -output_reals $real_par_file"; if ( $opts{'test'} ) { $bldnml .= " -test"; } @@ -244,8 +260,9 @@ sub make_env_run { print "==================================================\n"; # drydep and megan namelists -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); my @mfiles = ( "lnd_in", "drv_flds_in", $tempfile ); my $mfiles = NMLTest::CompFiles->new( $cwd, @mfiles ); foreach my $options ( "-drydep", "-megan", "-drydep -megan", "-fire_emis", "-drydep -megan -fire_emis" ) { @@ -265,16 +282,19 @@ sub make_env_run { } &cleanup(); } -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); print "\n===============================================================================\n"; -print "Test irrig, verbose, clm_demand, ssp_rcp, test, sim_year, use_case, l_ncpl\n"; +print "Test configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case, l_ncpl\n"; print "=================================================================================\n"; -# irrig, verbose, clm_demand, ssp_rcp, test, sim_year, use_case, l_ncpl +# configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case, l_ncpl my $startfile = "clmrun.clm2.r.1964-05-27-00000.nc"; -foreach my $options ( "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850", +foreach my $options ( "-configuration nwp", + "-structure fast", + "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850", "-use_case 1850_control", "-l_ncpl 1", "-clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc", "-envxml_dir . -infile myuser_nl_clm", @@ -309,8 +329,9 @@ sub make_env_run { print "\n==============================================================\n"; print "Test several use_cases and specific configurations for clm5_0\n"; print "==============================================================\n"; -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); foreach my $options ( "-bgc bgc -use_case 1850-2100_SSP1-2.6_transient -namelist '&a start_ymd=20100101/'", "-bgc sp -use_case 1850-2100_SSP2-4.5_transient -namelist '&a start_ymd=18501223/'", @@ -353,638 +374,613 @@ sub make_env_run { "coldstart but with IC file"=>{ options=>"-clm_start_type cold -envxml_dir .", namelst=>"finidat='$finidat'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "clm_demand on finidat" =>{ options=>"-clm_demand finidat -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "blank IC file, not cold" =>{ options=>"-clm_start_type startup -envxml_dir .", namelst=>"finidat=' '", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "startup without interp" =>{ options=>"-clm_start_type startup -envxml_dir . -bgc sp -sim_year 1850", namelst=>"use_init_interp=.false., start_ymd=19200901", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "l_ncpl is zero" =>{ options=>"-l_ncpl 0 -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "l_ncpl not integer" =>{ options=>"-l_ncpl 1.0 -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "both l_ncpl and dtime" =>{ options=>"-l_ncpl 24 -envxml_dir .", namelst=>"dtime=1800", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "use_crop without -crop" =>{ options=>" -envxml_dir .", namelst=>"use_crop=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", + }, + "soilm_stream wo use" =>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='missing_file'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "clm50CNDVwtransient" =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings", + namelst=>"", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", }, "reseed without CN" =>{ options=>" -envxml_dir . -bgc sp", namelst=>"reseed_dead_plants=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "dribble_crphrv w/o CN" =>{ options=>" -envxml_dir . -bgc sp", namelst=>"dribble_crophrv_xsmrpool_2atm=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "dribble_crphrv w/o crop" =>{ options=>" -envxml_dir . -bgc cn -no-crop", namelst=>"dribble_crophrv_xsmrpool_2atm=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, - "CNDV with flanduse_timeseries" =>{ options=>" -envxml_dir .", + "CNDV with flanduse_timeseries - clm4_5"=>{ options=>"-bgc bgc -dynamic_vegetation -envxml_dir . -ignore_warnings", namelst=>"flanduse_timeseries='my_flanduse_timeseries_file.nc'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-bgc cndv", + phys=>"clm4_5", }, - "soilm_stream wo use" =>{ options=>"-res 0.9x1.25 -envxml_dir .", - namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='missing_file'", + "use_cndv=T without bldnml op"=>{ options=>"-bgc cn -envxml_dir . -ignore_warnings", + namelst=>"use_cndv=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, + "use_cndv=F with dyn_veg op"=>{ options=>"-bgc cn -dynamic_vegetation -envxml_dir . -ignore_warnings", + namelst=>"use_cndv=.false.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, + "crop with use_crop false" =>{ options=>"-crop -bgc bgc -envxml_dir .", + namelst=>"use_crop=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm4_5", }, - "clm50CNDVwtransient" =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15", + "crop without CN" =>{ options=>"-crop -bgc sp -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm4_5", }, - "CNDV with flanduse_timeseries - clm4_5"=>{ options=>"-bgc bgc -dynamic_vegetation -envxml_dir .", - namelst=>"flanduse_timeseries='my_flanduse_timeseries_file.nc'", + "toosmall soil w trans" =>{ options=>"-envxml_dir .", + namelst=>"toosmall_soil=10, dyn_transient_pfts=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm5_0", }, - "use_cndv=T without bldnml op"=>{ options=>"-bgc cn -envxml_dir .", - namelst=>"use_cndv=.true.", + "toosmall lake w trans" =>{ options=>"-envxml_dir .", + namelst=>"toosmall_lake=10, dyn_transient_pfts=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm5_0", }, - "use_cndv=F with dyn_veg op"=>{ options=>"-bgc cn -dynamic_vegetation -envxml_dir .", - namelst=>"use_cndv=.false.", + "toosmall crop w trans" =>{ options=>"-bgc bgc -crop -envxml_dir .", + namelst=>"toosmall_crop=10, dyn_transient_pfts=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm5_0", }, - "crop with use_crop false" =>{ options=>"-crop -bgc bgc -envxml_dir .", - namelst=>"use_crop=.false.", + "toosmall wetl w trans" =>{ options=>"-bgc bgc -envxml_dir .", + namelst=>"toosmall_wetland=10, dyn_transient_pfts=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm5_0", }, - "crop without CN" =>{ options=>"-crop -bgc sp -envxml_dir .", - namelst=>"", + "toosmall glc w trans" =>{ options=>"-bgc sp -envxml_dir .", + namelst=>"toosmall_glacier=10, dyn_transient_pfts=T", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "toosmall urban w trans" =>{ options=>"-bgc sp -envxml_dir .", + namelst=>"toosmall_urban=10, dyn_transient_pfts=T", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "collapse_urban w trans" =>{ options=>"-bgc sp -envxml_dir .", + namelst=>"collapse_urban=T, dyn_transient_crops=T", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "n_dom_landunits w trans" =>{ options=>"-bgc sp -envxml_dir .", + namelst=>"n_dom_landunits=2, dyn_transient_crops=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm5_0", + }, + "n_dom_pfts w trans" =>{ options=>"-bgc sp -envxml_dir .", + namelst=>"n_dom_pfts=2, dyn_transient_crops=T", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", }, "baset_map without crop" =>{ options=>"-bgc bgc -envxml_dir . -no-crop", namelst=>"baset_mapping='constant'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "mapvary var w/o varymap" =>{ options=>"-crop -bgc bgc -envxml_dir . -crop", namelst=>"baset_mapping='constant', baset_latvary_slope=1.0, baset_latvary_intercept=10.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, - "-irrig with clm5_0" =>{ options=>"-bgc bgc -crop -irrig .true. -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "-irrig with -crop" =>{ options=>"-irrig .true. -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0 -bgc cn -crop on", - }, # This one should fail now, because we don't have non irrigated non-crop datasets "-irrigate=F without -crop" =>{ options=>"-bgc cn -no-crop -envxml_dir .", namelst=>"irrigate=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "grainproductWOcrop" =>{ options=>"-bgc cn -no-crop -envxml_dir .", namelst=>"use_grainproduct=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "interp without finidat" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"use_init_interp=.true. finidat=' '", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "sp and c13" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"use_c13=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "sp and c14" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"use_c14=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "bombspike no c14" =>{ options=>"-bgc bgc -envxml_dir .", namelst=>"use_c14=.false. use_c14_bombspike=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "use c13 timeseries no cn" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"use_c13_timeseries=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "use c13 timeseries no c13"=>{ options=>"-bgc bgc -envxml_dir .", namelst=>"use_c13=.false. use_c13_timeseries=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "bombspike no cn" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"use_c14_bombspike=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lightres no cn" =>{ options=>"-bgc sp -envxml_dir . -light_res 360x720", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "spno-fire" =>{ options=>"-bgc sp -envxml_dir . -use_case 2000_control", namelst=>"fire_method='nofire'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lightres no fire" =>{ options=>"-bgc cn -envxml_dir . -light_res 360x720", namelst=>"fire_method='nofire'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lightres none bgc" =>{ options=>"-bgc bgc -envxml_dir . -light_res none", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lightresnotnone-nofire" =>{ options=>"-bgc bgc -envxml_dir . -light_res 94x192", namelst=>"fire_method='nofire'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lightresnonenofirelightfil"=>{ options=>"-bgc bgc -envxml_dir . -light_res none", namelst=>"fire_method='nofire',stream_fldfilename_lightng='build-namelist_test.pl'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lightrescontradictlightfil"=>{ options=>"-bgc bgc -envxml_dir . -light_res 360x720", namelst=>"stream_fldfilename_lightng='build-namelist_test.pl'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "bgc=cn and bgc settings" =>{ options=>"-bgc cn -envxml_dir .", namelst=>"use_lch4=.true.,use_nitrif_denitrif=.true.,use_vertsoilc=.true.,use_century_decomp=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "finundated and not methane"=>{ options=>"-bgc cn -envxml_dir .", namelst=>"use_lch4=.false.,finundation_method='h2osfc'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "bgc=bgc and cn-only set" =>{ options=>"-bgc bgc -envxml_dir .", namelst=>"use_lch4=.false.,use_nitrif_denitrif=.false.,use_vertsoilc=.false.,use_century_decomp=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "use_cn=true bgc=sp" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"use_cn=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "use_cn=false bgc=cn" =>{ options=>"-bgc cn -envxml_dir .", namelst=>"use_cn=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "lower=aqu-45 with/o Zeng" =>{ options=>"-envxml_dir .", namelst=>"lower_boundary_condition=4,soilwater_movement_method=1,use_bedrock=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "Zeng w lower=flux" =>{ options=>"-envxml_dir .", namelst=>"lower_boundary_condition=1,soilwater_movement_method=0,use_bedrock=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "Zeng w lower=zeroflux" =>{ options=>"-envxml_dir .", namelst=>"lower_boundary_condition=2,soilwater_movement_method=0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "Zeng w lower=table" =>{ options=>"-envxml_dir .", namelst=>"lower_boundary_condition=3,soilwater_movement_method=0,use_bedrock=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", - }, - "vichydro without clm4_5" =>{ options=>"-vichydro -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", + phys=>"clm4_5", }, "use_vic=F with -vic op" =>{ options=>"-vichydro -envxml_dir .", namelst=>"use_vichydro=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "-vic with l_bnd=flux" =>{ options=>"-vichydro -envxml_dir .", namelst=>"lower_boundary_condition=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "-vic with l_bnd=zeroflux" =>{ options=>"-vichydro -envxml_dir .", namelst=>"lower_boundary_condition=2", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "-vic with origflag=1" =>{ options=>"-vichydro -envxml_dir .", namelst=>"origflag=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "l_bnd=flux with origflag=0"=>{ options=>"-envxml_dir .", namelst=>"origflag=0, lower_boundary_condition=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "l_bnd=zflux with origflag=0"=>{ options=>"-envxml_dir .", namelst=>"origflag=0, lower_boundary_condition=2", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "bedrock with l_bnc=flux" =>{ options=>"-envxml_dir .", namelst=>"use_bedrock=.true., lower_boundary_condition=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "bedrock with l_bnc=tabl" =>{ options=>"-envxml_dir .", namelst=>"use_bedrock=.true., lower_boundary_condition=3", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "bedrock with l_bnc=aqui" =>{ options=>"-envxml_dir .", namelst=>"use_bedrock=.true., lower_boundary_condition=4", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "zengdeck with l_bnc=flux" =>{ options=>"-envxml_dir .", namelst=>"soilwater_movement_method=0, lower_boundary_condition=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "zengdeck with l_bnc=z-flux"=>{ options=>"-envxml_dir .", namelst=>"soilwater_movement_method=0, lower_boundary_condition=2", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "zengdeck with l_bnc=tabl" =>{ options=>"-envxml_dir .", namelst=>"soilwater_movement_method=0, lower_boundary_condition=3", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "l_bnd=tabl with h2osfcfl=0"=>{ options=>"-envxml_dir .", namelst=>"h2osfcflag=0, lower_boundary_condition=3", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "l_bnd=flux with h2osfcfl=0"=>{ options=>"-envxml_dir .", namelst=>"h2osfcflag=0, lower_boundary_condition=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "l_bnd=zflux with h2osfcfl=0"=>{ options=>"-envxml_dir .", namelst=>"h2osfcflag=0, lower_boundary_condition=2", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "h2osfcfl=0 with clm5.0" =>{ options=>"-envxml_dir .", namelst=>"h2osfcflag=0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "origflag=0 with clm5.0" =>{ options=>"-envxml_dir .", - namelst=>"origflag=0", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "oldfflag=0 with clm5.0" =>{ options=>"-envxml_dir .", - namelst=>"oldfflag=0", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "bgc without clm4_5" =>{ options=>"-bgc sp -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", - }, - "spinup_state without clm4_5" =>{ options=>"-clm_accelerated_spinup on -envxml_dir .", - namelst=>"spinup_state=1", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", - }, - "40bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm4_5_CRUNCEP -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", + phys=>"clm5_0", }, "45bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm5_0_GSWP3 -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "50bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm4_5_CRUNCEP -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "DV without clm4_5" =>{ options=>"-dynamic_vegetation -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", + phys=>"clm5_0", }, "bgc_spinup without cn" =>{ options=>"-clm_accelerated_spinup on -bgc sp -envxml_dir .", namelst=>"spinup_state=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "spinup=1 without bldnml op"=>{ options=>"-clm_accelerated_spinup off -bgc bgc -envxml_dir .", namelst=>"spinup_state=1",, GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "DV without clm4_5" =>{ options=>"-dynamic_vegetation -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", + phys=>"clm5_0", }, "bgc_spinup without cn" =>{ options=>"-clm_accelerated_spinup on -bgc sp -envxml_dir .", namelst=>"spinup_state=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "baseflow w aquifer" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"baseflow_scalar=1.0, lower_boundary_condition=4,use_bedrock=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "baseflow w table" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"baseflow_scalar=1.0, lower_boundary_condition=3,use_bedrock=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "br_root and bgc=sp" =>{ options=>"-bgc sp -envxml_dir .", namelst=>"br_root=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "both co2_type and on nml" =>{ options=>"-co2_type constant -envxml_dir .", namelst=>"co2_type='prognostic'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "both lnd_frac and on nml" =>{ options=>"-lnd_frac domain.nc -envxml_dir .", namelst=>"fatmlndfrc='frac.nc'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "branch but NO nrevsn" =>{ options=>"-clm_start_type branch -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "glc_nec inconsistent" =>{ options=>"-envxml_dir .", namelst=>"maxpatch_glcmec=5", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "NoGLCMec" =>{ options=>"-envxml_dir . -glc_nec 0", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "UpdateGlcContradict" =>{ options=>"-envxml_dir .", namelst=>"glc_do_dynglacier=.false.", GLC_TWO_WAY_COUPLING=>"TRUE", - conopts=>"-phys clm4_5", - }, - "clm40andUpdateGlc" =>{ options=>"-envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"TRUE", - conopts=>"-phys clm4_0", + phys=>"clm4_5", }, "useFATESContradict" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"use_fates=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "useFATESContradict2" =>{ options=>"-envxml_dir . -no-megan", namelst=>"use_fates=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "useFATESWCN" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"use_cn=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "useFATESWcreatecrop" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"create_crop_landunit=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "createcropFalse" =>{ options=>"-bgc bgc -envxml_dir . -no-megan", namelst=>"create_crop_landunit=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "useFATESWTransient" =>{ options=>"-bgc fates -use_case 20thC_transient -envxml_dir . -no-megan -res 10x15", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "useFATESclm40" =>{ options=>"-bgc fates -envxml_dir . -no-megan", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", + phys=>"clm5_0", }, "usespitfireButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", namelst=>"use_fates_spitfire=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "useloggingButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", namelst=>"use_fates_logging=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "useinventorybutnotfile" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"use_fates_inventory_init=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "inventoryfileDNE" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"use_fates_inventory_init=.true., fates_inventory_ctrl_filename='zztop'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "useMEGANwithFATES" =>{ options=>"-bgc fates -envxml_dir . -megan", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, "useHYDSTwithFATES" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"use_hydrstress=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "useHYDSTwithdynroot" =>{ options=>"-bgc bgc -envxml_dir . -megan", namelst=>"use_hydrstress=.true., use_dynroot=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", - }, - "fireemiswith40" =>{ options=>"-envxml_dir . -fire_emis", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_0", + phys=>"clm5_0", }, "specWOfireemis" =>{ options=>"-envxml_dir . -no-fire_emis", namelst=>"fire_emis_specifier='bc_a1 = BC'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "elevWOfireemis" =>{ options=>"-envxml_dir . -no-fire_emis", namelst=>"fire_emis_elevated=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "noanthro_w_crop" =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -crop -use_case 1850_noanthro_control", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "noanthro_w_irrig" =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control", namelst=>"irrigate=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "spdotransconflict" =>{ options=>"-envxml_dir . -bgc sp -use_case 20thC_transient", namelst=>"do_transient_pfts=T,do_transient_crops=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "nocropwfert" =>{ options=>"-envxml_dir . -bgc sp -no-crop", namelst=>"use_fertilizer=T", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lmr1WOcn" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"leafresp_method=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lmr2WOcn" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"leafresp_method=2", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lmr0Wcn" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"leafresp_method=0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "nofireButSetcli_scale" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"fire_method='nofire', cli_scale=5.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "nocnButSetrh_low" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"rh_low=5.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "funWOcn" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"use_fun=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "flexCNWOcn" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"use_flexibleCN=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "flexCNFUNwcarbonresp" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_flexibleCN=.true.,use_FUN=.true.,carbon_resp_opt=1", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "funWOnitrif" =>{ options=>"-envxml_dir .", namelst=>"use_fun=.true., use_nitrif_denitrif=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "knitrmaxWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_nitrif_denitrif=.false., k_nitr_max=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "respcoefWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_nitrif_denitrif=.false., denitrif_respiration_coefficient=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "respexpWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_nitrif_denitrif=.false., denitrif_respiration_exponent=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "nitrcoefWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_nitrif_denitrif=.false., denitrif_nitrateconc_coefficient=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "nitrexpWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_nitrif_denitrif=.false., denitrif_nitrateconc_exponent=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "lunaWSPandlnctrue" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"use_luna=.true., lnc_opt=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "NOlunabutsetJmaxb1" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"use_luna=.false., jmaxb1=1.0", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "envxml_not_dir" =>{ options=>"-envxml_dir myuser_nl_clm", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, "envxml_emptydir" =>{ options=>"-envxml_dir xFail", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"", + phys=>"clm5_0", }, ); foreach my $key ( keys(%failtest) ) { print( "$key\n" ); - system( "../configure -s ".$failtest{$key}{"conopts"}); + &make_config_cache($failtest{$key}{"phys"}); my $options = $failtest{$key}{"options"}; my $namelist = $failtest{$key}{"namelst"}; &make_env_run( GLC_TWO_WAY_COUPLING=>$failtest{$key}{"GLC_TWO_WAY_COUPLING"} ); @@ -1005,42 +1001,42 @@ sub make_env_run { "coldwfinidat" =>{ options=>"-envxml_dir . -clm_start_type cold", namelst=>"finidat = 'testfile.nc'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "bgcspin_w_suplnitro" =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup on", namelst=>"suplnitro='ALL'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "use_c13_wo_bgc" =>{ options=>"-envxml_dir . -bgc cn", namelst=>"use_c13=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "use_c14_wo_bgc" =>{ options=>"-envxml_dir . -bgc cn", namelst=>"use_c14=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "maxpft_wrong" =>{ options=>"-envxml_dir . -bgc cn", namelst=>"maxpatch_pft=19", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "soilm_stream w transient" =>{ options=>"-res 0.9x1.25 -envxml_dir . -use_case 20thC_transient", namelst=>"use_soil_moisture_streams=T,soilm_tintalgo='linear'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm5_0", + phys=>"clm5_0", }, "bad_megan_spec" =>{ options=>"-envxml_dir . -bgc bgc -megan", namelst=>"megan_specifier='ZZTOP=zztop'", GLC_TWO_WAY_COUPLING=>"FALSE", - conopts=>"-phys clm4_5", + phys=>"clm4_5", }, ); foreach my $key ( keys(%warntest) ) { print( "$key\n" ); - system( "../configure -s ".$warntest{$key}{"conopts"}); + &make_config_cache($warntest{$key}{"phys"}); my $options = $warntest{$key}{"options"}; my $namelist = $warntest{$key}{"namelst"}; &make_env_run( GLC_TWO_WAY_COUPLING=>$warntest{$key}{"GLC_TWO_WAY_COUPLING"} ); @@ -1061,8 +1057,9 @@ sub make_env_run { print "==================================================\n"; # Check for ALL resolutions with CLM50SP -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); my $reslist = `../queryDefaultNamelist.pl -res list -s`; my @resolutions = split( / /, $reslist ); my @regional; @@ -1086,7 +1083,7 @@ sub make_env_run { $res eq "0.33x0.33" || $res eq "1km-merge-10min" ) { next; - # Resolutions supported in clm40 but NOT clm45/clm50 + # Resolutions that were supported in clm40 but NOT clm45/clm50 } elsif ( $res eq "ne240np4" || $res eq "ne60np4" || $res eq "ne4np4" || @@ -1129,8 +1126,9 @@ sub make_env_run { print " Test important resolutions for CLM4.5 and BGC\n"; print "==================================================\n"; -$mode = "-phys clm4_5"; -system( "../configure -s $mode" ); +$phys = "clm4_5"; +$mode = "-phys $phys"; +&make_config_cache($phys); my @resolutions = ( "4x5", "10x15", "ne30np4", "ne16np4", "1.9x2.5", "0.9x1.25" ); my @regional; my $nlbgcmode = "bgc"; @@ -1187,37 +1185,14 @@ sub make_env_run { &cleanup(); } -print "\n==================================================\n"; -print "Test single-point regional cases \n"; -print "==================================================\n"; - -# Run over single-point regional cases -foreach my $res ( @regional ) { - $mode = "-sitespf_pt $res -phys clm4_0"; - system( "../configure -s $mode" ); - &make_env_run(); - eval{ system( "$bldnml -envxml_dir . > $tempfile 2>&1 " ); }; - is( $@, '', "$res" ); - $cfiles->checkfilesexist( "$res", $mode ); - $cfiles->shownmldiff( "default", "standard" ); - if ( defined($opts{'compare'}) ) { - $cfiles->doNOTdodiffonfile( "$tempfile", "$res", $mode ); - $cfiles->dodiffonfile( "$real_par_file", "$res", $mode ); - $cfiles->comparefiles( "$res", $mode, $opts{'compare'} ); - } - if ( defined($opts{'generate'}) ) { - $cfiles->copyfiles( "$res", $mode ); - } - &cleanup(); -} - print "\n==================================================\n"; print "Test crop resolutions \n"; print "==================================================\n"; # Check for crop resolutions -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); my @crop_res = ( "1x1_numaIA", "1x1_smallvilleIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne30np4" ); foreach my $res ( @crop_res ) { $options = "-bgc bgc -crop -res $res -envxml_dir ."; @@ -1251,8 +1226,9 @@ sub make_env_run { # use cases, but I've kept these pointing to the equivalent normal use # cases; I'm not sure if it's actually important to test this with all # of the different use cases. -$mode = "-phys clm4_5"; -system( "../configure -s $mode" ); +$phys = "clm4_5"; +$mode = "-phys $phys"; +&make_config_cache($phys); my @glc_res = ( "48x96", "0.9x1.25", "1.9x2.5" ); my @use_cases = ( "1850-2100_SSP1-2.6_transient", "1850-2100_SSP2-4.5_transient", @@ -1282,8 +1258,9 @@ sub make_env_run { } } # Transient 20th Century simulations -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); my @tran_res = ( "48x96", "0.9x1.25", "1.9x2.5", "ne30np4", "10x15" ); my $usecase = "20thC_transient"; my $GLC_NEC = 10; @@ -1305,8 +1282,9 @@ sub make_env_run { &cleanup(); } # Transient ssp_rcp scenarios that work -$mode = "-phys clm5_0"; -system( "../configure -s $mode" ); +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); my @tran_res = ( "0.9x1.25", "1.9x2.5", "10x15" ); foreach my $usecase ( "1850_control", "1850-2100_SSP5-8.5_transient", "1850-2100_SSP1-2.6_transient", "1850-2100_SSP3-7.0_transient", "1850-2100_SSP2-4.5_transient" ) { @@ -1345,9 +1323,9 @@ sub make_env_run { foreach my $phys ( "clm4_5", 'clm5_0' ) { my $mode = "-phys $phys"; - system( "../configure -s $mode" ); + &make_config_cache($phys); my @clmoptions = ( "-bgc bgc -envxml_dir .", "-bgc bgc -envxml_dir . -clm_accelerated_spinup=on", "-bgc bgc -envxml_dir . -light_res 360x720", - "-bgc sp -envxml_dir . -vichydro", "-bgc bgc -dynamic_vegetation", "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000", + "-bgc sp -envxml_dir . -vichydro", "-bgc bgc -dynamic_vegetation -ignore_warnings", "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000", "-bgc bgc -envxml_dir . -namelist '&a use_c13=.true.,use_c14=.true.,use_c14_bombspike=.true./'" ); foreach my $clmopts ( @clmoptions ) { my @clmres = ( "10x15", "0.9x1.25", "1.9x2.5" ); @@ -1389,7 +1367,6 @@ sub make_env_run { &cleanup(); } } - system( "../configure -s $mode" ); my $clmopts = "-bgc cn -crop"; my $res = "1.9x2.5"; $options = "-res $res -namelist '&a irrigate=.true./' -crop -bgc cn -envxml_dir ."; @@ -1407,7 +1384,6 @@ sub make_env_run { } &cleanup(); # Run FATES mode for several resolutions and configurations - system( "../configure -s $mode" ); my $clmoptions = "-bgc fates -envxml_dir . -no-megan"; my @clmres = ( "1x1_brazil", "5x5_amazon", "10x15", "1.9x2.5" ); foreach my $res ( @clmres ) { @@ -1436,18 +1412,13 @@ sub make_env_run { my $res = "0.9x1.25"; my $mask = "gx1v6"; my $simyr = "1850"; -foreach my $phys ( "clm4_0", "clm4_5", 'clm5_0' ) { +foreach my $phys ( "clm4_5", 'clm5_0' ) { my $mode = "-phys $phys"; - system( "../configure -s $mode" ); + &make_config_cache($phys); foreach my $forc ( "CRUv7", "GSWP3v1", "cam6.0" ) { foreach my $bgc ( "sp", "bgc" ) { my $lndtuningmode = "${phys}_${forc}"; - my $clmoptions = "-res $res -mask $mask -sim_year $simyr -envxml_dir . -lnd_tuning_mod $lndtuningmode"; - if ( $phys eq "clm4_0" ) { - $clmoptions .= " -glc_nec 0"; - } else { - $clmoptions .= " -bgc $bgc"; - } + my $clmoptions = "-res $res -mask $mask -sim_year $simyr -envxml_dir . -lnd_tuning_mod $lndtuningmode -bgc $bgc"; &make_env_run( ); eval{ system( "$bldnml $clmoptions > $tempfile 2>&1 " ); }; is( $@, '', "$clmoptions" ); @@ -1489,7 +1460,7 @@ sub cleanup { system( "/bin/rm env_run.xml $real_par_file" ); if ( defined($type) ) { if ( $type eq "config" ) { - system( "/bin/rm Filepath config_cache.xml CESM_cppdefs" ); + system( "/bin/rm config_cache.xml" ); } } else { system( "/bin/rm $tempfile *_in" ); diff --git a/cime_config/SystemTests/funitctsm.py b/cime_config/SystemTests/funitctsm.py new file mode 100644 index 0000000000..8634a74c2f --- /dev/null +++ b/cime_config/SystemTests/funitctsm.py @@ -0,0 +1,24 @@ +""" +Implementation of the CTSM FUNIT test. + +This "system" test runs CTSM's Fortran unit tests. We're abusing the system test +infrastructure to run these, so that a run of the test suite can result in the unit tests +being run as well. + +Grid and compset are irrelevant for this test type. +""" + +import os +from CIME.SystemTests.funit import FUNIT +from CIME.XML.standard_module_setup import * + +logger = logging.getLogger(__name__) + +class FUNITCTSM(FUNIT): + + def __init__(self, case): + FUNIT.__init__(self, case) + + def get_test_spec_dir(self): + lnd_root = self._case.get_value("COMP_ROOT_DIR_LND") + return os.path.join(lnd_root, "src") diff --git a/cime_config/SystemTests/lciso.py b/cime_config/SystemTests/lciso.py index 214d2c4ccc..e79af2886b 100644 --- a/cime_config/SystemTests/lciso.py +++ b/cime_config/SystemTests/lciso.py @@ -1,9 +1,11 @@ """ Implementation of the CIME LCISO (Land Carbon Isotope) test. + This is a CTSM specific test: Verifies turning on carbon isotopes doesn't change answers (1) do a run with Carbon isotopes off (suffix base) (2) add C13 and C14 carbon isotopes on with their time-series (suffix cisoallon) + """ from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo @@ -19,7 +21,8 @@ def __init__(self, case): separate_builds = False, run_two_suffix = 'cisoallon', run_one_description = 'carbon isotopes off', - run_two_description = 'c13 and c14 isotopes on as well as C isotope time series') + run_two_description = 'c13 and c14 isotopes on as well as C isotope time series', + ignore_fieldlist_diffs = True) def _case_one_setup(self): append_to_user_nl_files(caseroot = self._get_caseroot(), @@ -29,9 +32,5 @@ def _case_one_setup(self): def _case_two_setup(self): append_to_user_nl_files(caseroot = self._get_caseroot(), component = "clm", - contents = "use_c13=.true.,use_c14=.true.,use_c13_timeseries=.true.,use_c14_bombspike=.true.," + \ - "hist_fexcl1='C13_AR','C13_GPP','C13_HR','C13_NBP','C13_SOILC_vr','C13_TOTECOSYSC'," + \ - "'C13_TOTLITC','C13_TOTSOMC','C13_TOTVEGC','C14_AR','C14_GPP','C14_HR','C14_NBP'," + \ - "'C14_SOILC_vr','C14_TOTECOSYSC','C14_TOTLITC','C14_TOTSOMC','C14_TOTVEGC'") - + contents = "use_c13=.true.,use_c14=.true.,use_c13_timeseries=.true.,use_c14_bombspike=.true." ) diff --git a/cime_config/SystemTests/lwiso.py b/cime_config/SystemTests/lwiso.py new file mode 100644 index 0000000000..1083e2ff36 --- /dev/null +++ b/cime_config/SystemTests/lwiso.py @@ -0,0 +1,44 @@ +""" +Implementation of the CIME LWISO (Land Water Isotope) test. + +This is a CTSM specific test: +Verifies turning on water isotopes doesn't change answers +(1) do a run with water isotopes on +(2) do a run with water isotopes off + +The reason for having water isotopes on in the first case (rather than the other way +around) is that this results in having water isotope quantities present in the baselines. + +""" + +from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo +from CIME.XML.standard_module_setup import * +from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files + +logger = logging.getLogger(__name__) + +class LWISO(SystemTestsCompareTwo): + + def __init__(self, case): + SystemTestsCompareTwo.__init__(self, case, + separate_builds = False, + run_two_suffix = 'nowiso', + run_one_description = 'water isotopes on', + run_two_description = 'water isotopes off', + ignore_fieldlist_diffs = True) + + def _case_one_setup(self): + # BUG(wjs, 2019-07-30, ESCOMP/ctsm#495) We currently can't turn on actual water + # isotopes in a multi-timestep test, so we're setting + # enable_water_tracer_consistency_checks rather than enable_water_isotopes; + # eventually, though, we should change this to the latter. (See + # .) + append_to_user_nl_files(caseroot = self._get_caseroot(), + component = "clm", + contents = "enable_water_tracer_consistency_checks=.true.") + + def _case_two_setup(self): + append_to_user_nl_files(caseroot = self._get_caseroot(), + component = "clm", + contents = "enable_water_tracer_consistency_checks=.false.") + diff --git a/cime_config/SystemTests/soilstructud.py b/cime_config/SystemTests/soilstructud.py new file mode 100644 index 0000000000..c59ab8b4f6 --- /dev/null +++ b/cime_config/SystemTests/soilstructud.py @@ -0,0 +1,37 @@ +""" +Implementation of the CIME SOILSTRUCTUD test. + +This is a CLM specific test: +Verifies that a simulation that points to user_nl_clm containing +soil_layerstruct_userdefined_nlevsoi = 4 +soil_layerstruct_userdefined = 0.1d0,0.3d0,0.6d0,1.0d0,1.0d0 +gives bfb same results as one that points to user_nl_clm containing +soil_layerstruct_predefined = '4SL_2m' + +""" + +from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo +from CIME.XML.standard_module_setup import * +from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files + +logger = logging.getLogger(__name__) + +class SOILSTRUCTUD(SystemTestsCompareTwo): + + def __init__(self, case): + SystemTestsCompareTwo.__init__(self, case, + separate_builds = False, + run_two_suffix = '4SL_2m', + run_one_description = 'soil_layerstruct_userdefined', + run_two_description = 'soil_layerstruct_predefined') + + def _case_one_setup(self): + append_to_user_nl_files(caseroot = self._get_caseroot(), + component = "clm", + contents = "soil_layerstruct_userdefined_nlevsoi = 4,soil_layerstruct_userdefined = 0.1d0,0.3d0,0.6d0,1.0d0,1.0d0") + + def _case_two_setup(self): + append_to_user_nl_files(caseroot = self._get_caseroot(), + component = "clm", + contents = "soil_layerstruct_predefined = '4SL_2m'") + diff --git a/cime_config/SystemTests/ssp.py b/cime_config/SystemTests/ssp.py index a2aacc9e43..892128ba5e 100644 --- a/cime_config/SystemTests/ssp.py +++ b/cime_config/SystemTests/ssp.py @@ -28,6 +28,10 @@ def __init__(self, case): rof = self._case.get_value("COMP_ROF") expect(rof == "mosart", "ERROR: SSP test requires that ROF component be mosart") + def build_phase(self, sharedlib_only=False, model_only=False): + self._case.set_value("MOSART_MODE", "NULL") + self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only) + def run_phase(self): caseroot = self._case.get_value("CASEROOT") orig_case = self._case @@ -41,7 +45,7 @@ def run_phase(self): # determine run lengths needed below stop_nf = self._case.get_value("STOP_N") - stop_n1 = stop_nf / 2 + stop_n1 = int(stop_nf / 2) stop_n2 = stop_nf - stop_n1 #------------------------------------------------------------------- @@ -55,10 +59,9 @@ def run_phase(self): logger.info(" writing restarts at end of run") logger.info(" short term archiving is on ") - clone.set_value("CLM_ACCELERATED_SPINUP", "on") - clone.set_value("MOSART_MODE", "NULL") - clone.set_value("STOP_N",stop_n1) - clone.flush() + with clone: + clone.set_value("CLM_ACCELERATED_SPINUP", "on") + clone.set_value("STOP_N",stop_n1) dout_sr = clone.get_value("DOUT_S_ROOT") # No history files expected, set suffix=None to avoid compare error @@ -89,7 +92,6 @@ def run_phase(self): self._case.set_value("RUN_TYPE", "hybrid") self._case.set_value("GET_REFCASE", False) self._case.set_value("RUN_REFCASE", "{}.ref1".format(orig_casevar)) - self._case.set_value("MOSART_MODE", "NULL") self._case.set_value("RUN_REFDATE", refdate) self._case.set_value("STOP_N", stop_n2) diff --git a/cime_config/buildcpp b/cime_config/buildcpp deleted file mode 100644 index 7a3bf0083e..0000000000 --- a/cime_config/buildcpp +++ /dev/null @@ -1,52 +0,0 @@ -#!/usr/bin/env python - -""" -API for clm's configure -""" - -from CIME.XML.standard_module_setup import * -from CIME.utils import run_cmd_no_fail, expect - -import glob, shutil -logger = logging.getLogger(__name__) - -def buildcpp(case): - """ - Invoke clm configure ONLY for clm4_0 - output goes in `caseroot`/Buildconf/camconf - """ - - caseroot = case.get_value("CASEROOT") - cimeroot = case.get_value("CIMEROOT") - lnd_root = case.get_value("COMP_ROOT_DIR_LND") - lnd_grid = case.get_value("LND_GRID") - mask_grid = case.get_value("MASK_GRID") - clm_usrdat_name = case.get_value("CLM_USRDAT_NAME") - clm_config_opts = case.get_value("CLM_CONFIG_OPTS") - compset = case.get_value("COMPSET") - - if mask_grid == "reg" and lnd_grid != "CLM_USRDAT": - config_opts = "-sitespf_pt $lnd_grid" - else: - config_opts = "" - - if "1PT" in compset: - config_opts = " -sitespf_pt reg" - - clmconf = os.path.join(caseroot, "Buildconf", "clmconf") - if not os.path.isdir(clmconf): - os.makedirs(clmconf) - - cmd = os.path.join(lnd_root,"bld","configure") - command = "%s -cimeroot %s %s %s -usr_src %s -comp_intf mct " \ - %(cmd, cimeroot, config_opts, clm_config_opts, os.path.join(caseroot,"SourceMods","src.clm")) - - run_cmd_no_fail(command, from_dir=clmconf) - - # determine cppdefs - caseroot/clmconf/CESM_cppdefs is created by the call to configure - with open(os.path.join(clmconf, "CESM_cppdefs"), 'r') as f: - user_cppdefs = f.readline().rstrip() - if user_cppdefs: - case.set_value("CLM_CPPDEFS", user_cppdefs) - case.flush() - - return user_cppdefs diff --git a/cime_config/buildlib b/cime_config/buildlib index b3f49f9916..13de92d236 100755 --- a/cime_config/buildlib +++ b/cime_config/buildlib @@ -3,7 +3,7 @@ """ build clm library """ -import sys, os, shutil, imp +import sys, os _CIMEROOT = os.environ.get("CIMEROOT") if _CIMEROOT is None: @@ -14,6 +14,7 @@ sys.path.append(_LIBDIR) from standard_script_setup import * from CIME.buildlib import parse_input +from CIME.build import get_standard_makefile_args from CIME.case import Case from CIME.utils import run_cmd, expect @@ -31,81 +32,43 @@ def _main_func(): lnd_root = case.get_value("COMP_ROOT_DIR_LND") gmake_j = case.get_value("GMAKE_J") gmake = case.get_value("GMAKE") - mach = case.get_value("MACH") - - clm_config_opts = case.get_value("CLM_CONFIG_OPTS") - if "clm4_5" in clm_config_opts: - clm_phys = "clm4_5" - elif "clm5_0" in clm_config_opts: - clm_phys = "clm5_0" - elif "clm4_0" in clm_config_opts: - clm_phys = "clm4_0" - else: - expect(False, "CLM_CONFIG_OPTS must support either clm4_5, clm5_0, or clm4_0 physics") - - if clm_phys == "clm4_0": - #------------------------------------------------------- - # create Filepath file and clm_cppdefs for clm4_0 - #------------------------------------------------------- - # the call to configure here creates BOTH the Filepath file and the clm_cppdefs - cmd = os.path.join(os.path.join(lnd_root,"cime_config","buildcpp")) - logger.info(" ...calling clm buildcpp to set build time options") - try: - mod = imp.load_source("buildcpp", cmd) - clm_cppdefs = mod.buildcpp(case) - except: - raise - - # the above call to buildcpp generates the Filepath file - if not os.path.isfile(os.path.join(bldroot, "Filepath")): - filesrc = os.path.join(caseroot, "Buildconf", "clmconf", "Filepath") - filedst = os.path.join(bldroot, "Filepath") - shutil.copy(filesrc,filedst) - - else: - #------------------------------------------------------- - # create Filepath file for clm4_5 or clm5_0 - #------------------------------------------------------- - filepath_file = os.path.join(bldroot,"Filepath") - if not os.path.isfile(filepath_file): - caseroot = case.get_value("CASEROOT") - paths = [os.path.join(caseroot,"SourceMods","src.clm"), - os.path.join(lnd_root,"src","main"), - os.path.join(lnd_root,"src","biogeophys"), - os.path.join(lnd_root,"src","biogeochem"), - os.path.join(lnd_root,"src","soilbiogeochem"), - os.path.join(lnd_root,"src","dyn_subgrid"), - os.path.join(lnd_root,"src","init_interp"), - os.path.join(lnd_root,"src","fates"), - os.path.join(lnd_root,"src","fates","main"), - os.path.join(lnd_root,"src","fates","biogeophys"), - os.path.join(lnd_root,"src","fates","biogeochem"), - os.path.join(lnd_root,"src","fates","fire"), - os.path.join(lnd_root,"src","fates","parteh"), - os.path.join(lnd_root,"src","utils"), - os.path.join(lnd_root,"src","cpl")] - with open(filepath_file, "w") as filepath: - filepath.write("\n".join(paths)) - filepath.write("\n") - + driver = case.get_value("COMP_INTERFACE").lower() + + #------------------------------------------------------- + # create Filepath file + #------------------------------------------------------- + filepath_file = os.path.join(bldroot,"Filepath") + if not os.path.isfile(filepath_file): + caseroot = case.get_value("CASEROOT") + paths = [os.path.join(caseroot,"SourceMods","src.clm"), + os.path.join(lnd_root,"src","main"), + os.path.join(lnd_root,"src","biogeophys"), + os.path.join(lnd_root,"src","biogeochem"), + os.path.join(lnd_root,"src","soilbiogeochem"), + os.path.join(lnd_root,"src","dyn_subgrid"), + os.path.join(lnd_root,"src","init_interp"), + os.path.join(lnd_root,"src","fates"), + os.path.join(lnd_root,"src","fates","main"), + os.path.join(lnd_root,"src","fates","biogeophys"), + os.path.join(lnd_root,"src","fates","biogeochem"), + os.path.join(lnd_root,"src","fates","fire"), + os.path.join(lnd_root,"src","fates","parteh"), + os.path.join(lnd_root,"src","utils"), + os.path.join(lnd_root,"src","cpl"), + os.path.join(lnd_root,"src","cpl",driver)] + with open(filepath_file, "w") as filepath: + filepath.write("\n".join(paths)) + filepath.write("\n") + #------------------------------------------------------- # create the library in libroot #------------------------------------------------------- - clm_config_opts = case.get_value("CLM_CONFIG_OPTS") - if clm_phys == "clm4_0": - complib = os.path.join(libroot,"liblnd.a") - else: - complib = os.path.join(libroot,"libclm.a") + complib = os.path.join(libroot,"libclm.a") makefile = os.path.join(casetools, "Makefile") - macfile = os.path.join(caseroot, "Macros.%s" % mach) - if clm_phys == "clm4_0": - cmd = "%s complib -j %d MODEL=clm COMPLIB=%s -f %s MACFILE=%s USER_CPPDEFS='%s'" \ - % (gmake, gmake_j, complib, makefile, macfile, clm_cppdefs ) - else: - cmd = "%s complib -j %d MODEL=clm COMPLIB=%s -f %s MACFILE=%s " \ - % (gmake, gmake_j, complib, makefile, macfile ) + cmd = "{} complib -j {} MODEL=clm COMPLIB={} -f {} {}" \ + .format(gmake, gmake_j, complib, makefile, get_standard_makefile_args(case)) rc, out, err = run_cmd(cmd) logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n"%(cmd,out,err)) @@ -115,4 +78,3 @@ def _main_func(): if __name__ == "__main__": _main_func() - diff --git a/cime_config/buildnml b/cime_config/buildnml index 3f5d9d3655..9940de97a3 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -3,7 +3,7 @@ """ CLM namelist creator """ -import sys, os, shutil, imp, filecmp +import sys, os, shutil _CIMEROOT = os.environ.get("CIMEROOT") if _CIMEROOT is None: @@ -38,6 +38,8 @@ def buildnml(case, caseroot, compname): lnd_root = case.get_value("COMP_ROOT_DIR_LND") din_loc_root = case.get_value("DIN_LOC_ROOT") + configuration = case.get_value("CLM_CONFIGURATION") + structure = case.get_value("CLM_STRUCTURE") ccsm_co2_ppmv = case.get_value("CCSM_CO2_PPMV") clm_co2_type = case.get_value("CLM_CO2_TYPE") clm_namelist_opts = case.get_value("CLM_NAMELIST_OPTS") @@ -76,39 +78,12 @@ def buildnml(case, caseroot, compname): # Note that build-namelist utilizes the contents of the config_cache.xml file in # the namelist_defaults.xml file to obtain namelist variables - clm_config_opts = case.get_value("CLM_CONFIG_OPTS") - if "clm4_5" in clm_config_opts: - clm_phys = "clm4_5" - elif "clm5_0" in clm_config_opts: - clm_phys = "clm5_0" - elif "clm4_0" in clm_config_opts: - clm_phys = "clm4_0" - else: - expect(False, "CLM_CONFIG_OPTS must support either clm4_5, clm5_0, or clm4_0 physics") + clm_phys = case.get_value("CLM_PHYSICS_VERSION") - if clm_phys == "clm4_0": - # call buildcpp to obtain clm_cppdefs if it is not set in env_build.xml - call_buildcpp = False - if not os.path.exists(os.path.join(caseroot,"LockedFiles","env_build.xml")): - call_buildcpp = True - else: - file1 = os.path.join(caseroot,"env_build.xml") - file2 = os.path.join(caseroot,"LockedFiles","env_build.xml") - if not filecmp.cmp(file1, file2): - call_buildcpp = True - if call_buildcpp: - cmd = os.path.join(os.path.join(lnd_root,"cime_config","buildcpp")) - logger.info(" ...calling clm buildcpp to set build time options") - try: - mod = imp.load_source("buildcpp", cmd) - mod.buildcpp(case) - except: - raise - else: - config_cache_text = _config_cache_template.format(clm_phys=clm_phys) - config_cache_path = os.path.join(caseroot, "Buildconf", "clmconf", "config_cache.xml") - with open(config_cache_path, 'w') as config_cache_file: - config_cache_file.write(config_cache_text) + config_cache_text = _config_cache_template.format(clm_phys=clm_phys) + config_cache_path = os.path.join(caseroot, "Buildconf", "clmconf", "config_cache.xml") + with open(config_cache_path, 'w') as config_cache_file: + config_cache_file.write(config_cache_text) # ----------------------------------------------------- # Determine input arguments into build-namelist @@ -217,6 +192,8 @@ def buildnml(case, caseroot, compname): clm_startfile = "%s.clm2%s.r.%s-%s.nc"%(run_refcase,inst_string,run_refdate,run_reftod) if not os.path.exists(os.path.join(rundir, clm_startfile)): clm_startfile = "%s.clm2.r.%s-%s.nc"%(run_refcase,run_refdate,run_reftod) + logger.warning( "WARNING: the start file being used for a multi-instance case is a single instance: "+clm_startfile ) + clm_icfile = "%s = \'%s\'"%(startfile_type, clm_startfile) else: clm_icfile = "" @@ -233,11 +210,13 @@ def buildnml(case, caseroot, compname): command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm start_ymd=%s %s/ \" " "%s %s -res %s %s -clm_start_type %s -envxml_dir %s -l_ncpl %s " + "-configuration %s -structure %s " "-lnd_frac %s -glc_nec %s -co2_ppmv %s -co2_type %s -config %s " "%s %s %s %s" %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts, nomeg, usecase, lnd_grid, clmusr, start_type, caseroot, lnd_ncpl, - lndfrac_file, glc_nec, ccsm_co2_ppmv, clm_co2_type, config_cache_file, + configuration, structure, + lndfrac_file, glc_nec, ccsm_co2_ppmv, clm_co2_type, config_cache_file, clm_bldnml_opts, spinup, tuning, gridmask)) rc, out, err = run_cmd(command, from_dir=clmconf) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 4a5ababeeb..cab3d0c2d2 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -14,14 +14,13 @@ - clm4.0: clm4.5: - clm5.0: + clm5.0: Satellite phenology: CN: Carbon Nitrogen model - CNDV: CN with Dynamic Vegetation + CNDV: CN with Dynamic Vegetation (deprecated) CN with prognostic crop: - CNDV with prognostic crop: + CNDV with prognostic crop: (deprecated) Satellite phenology with VIC hydrology: Satellite phenology without anthropomorphic influences @@ -33,6 +32,9 @@ BGC (vert. resol. CN and methane) with dynamic vegetation and prognostic crop: BGC (vert. resol. CN and methane) with prognostic crop, with modifications appropriate for CMIP6 DECK experiments: BGC (vert. resol. CN and methane) with prognostic crop, with modifications appropriate for CMIP6 WACCM DECK experiments: + + NWP configuration with satellite phenology: + NWP configuration with BGC and CROP: @@ -44,15 +46,6 @@ Name of land component - - char - - UNSET - build_component_cam - env_build.xml - CLM cpp definitions (if-any) (setup automatically - DO NOT EDIT) - - char run_component_clm @@ -60,12 +53,8 @@ Tuning parameters and initial conditions should be optimized for what CLM model version and what meteorlogical forcing combination? UNSET - clm4_0_CRUv7,clm4_0_GSWP3v1,clm5_0_cam6.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0 + clm5_0_cam6.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0 - clm4_0_CRUv7 - clm4_0_CRUv7 - clm4_0_CRUv7 - clm4_0_GSWP3v1 clm4_5_CRUv7 clm4_5_CRUv7 clm4_5_GSWP3v1 @@ -77,26 +66,55 @@ - + char - - - -phys clm4_0 - -bgc cn - -bgc cndv - -crop on - -phys clm4_5 - -phys clm5_0 + clm4_5,clm5_0 + + UNSET + + clm4_5 + clm5_0 - build_component_clm - env_build.xml - Provides option(s) for the CLM configure utility. - CLM_CONFIG_OPTS are normally set as compset variables (e.g., -bgc cn) - and in general should not be modified for supported compsets. - It is recommended that if you want to modify this value for your experiment, - you should use your own user-defined component sets via using create_newcase - with a compset_file argument. - This is an advanced flag and should only be used by expert users. + run_component_clm + env_run.xml + Overall physics version to use. + This sets the default values for many different namelist options. + This is typically set by the compset. + + + + char + clm,nwp + clm + + nwp + + run_component_clm + env_run.xml + Sets CLM default namelist options related to model configuration. + clm: Configuration used for climate applications (CLM) + nwp: Configuration used for numerical weather prediction applications + + + + + char + standard,fast + standard + + fast + + run_component_clm + env_run.xml + Sets CLM default namelist options related to model structure. + standard: Standard model structure, allowing for more subgrid heterogeneity, + deeper soil, etc., at the cost of slower speeds. + fast: Simplified model structure, achieving faster speeds at the cost of less + subgrid heterogeneity, shallower soil, etc. + @@ -104,11 +122,11 @@ UNSET - 2010_control - 2000_control - 1850_control + 2010_control + 2000_control + 1850_control 1850_noanthro_control - 20thC_transient + 20thC_transient 1850-2100_SSP5-8.5_transient 1850-2100_SSP1-2.6_transient 1850-2100_SSP3-7.0_transient @@ -118,7 +136,7 @@ 1850-2100_SSP4-3.4_transient 1850-2100_SSP4-6.0_transient 1850-2100_SSP5-8.5_transient - 20thC_transient + 20thC_transient 1850-2100_SSP5-8.5_transient run_component_clm @@ -174,9 +192,6 @@ prognostic diagnostic diagnostic - run_component_clm env_run.xml diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index cff59f02fa..d559c8192b 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -14,7 +14,7 @@ Where for the CAM specific compsets below the following is supported TIME = Time period (e.g. 2000, HIST, SSP585...) ATM = [CAM40, CAM50, CAM55] - LND = [CLM40, CLM45, CLM50, SLND] + LND = [CLM45, CLM50, SLND] ICE = [CICE, DICE, SICE] OCN = [DOCN, ,AQUAP, SOCN] ROF = [RTM, SROF] @@ -37,13 +37,13 @@ - I1PtClm50SpGs - 2000_DATM%1PT_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV + I1PtClm50SpRsGs + 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV - I1PtClm45SpGs - 2000_DATM%1PT_CLM45%SP_SICE_SOCN_RTM_SGLC_SWAV + I1PtClm45SpRsGs + 2000_DATM%1PT_CLM45%SP_SICE_SOCN_SROF_SGLC_SWAV @@ -53,6 +53,18 @@ 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + I2000Clm50SpRsGs + 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV + + + + + I2000Clm50SpRtmGs + 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_RTM_SGLC_SWAV + + I2010Clm50Sp 2010_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV @@ -69,6 +81,12 @@ 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + + + I2000Clm50BgcCropRtmGs + 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV + + I2000Clm50BgcCrop 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV @@ -140,6 +158,28 @@ 2000_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + I2000Clm50BgcCropQianRsGs + 2000_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV + + + I2000Clm45BgcCropQianRsGs + 2000_DATM%QIA_CLM45%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV + + + + + I2000Clm50BgcCropQianGs + 2000_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + I2000Clm50BgcCruGs 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV @@ -167,6 +207,11 @@ 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV + + I2000Clm50FatesRsGs + 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV + + I1850Clm50Bgc 1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV @@ -217,6 +262,47 @@ HIST_DATM%QIA_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV + + + ISSP585Clm50BgcCrop + SSP585_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP126Clm50BgcCrop + SSP126_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP119Clm50BgcCrop + SSP119_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP245Clm50BgcCrop + SSP245_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP370Clm50BgcCrop + SSP370_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP434Clm50BgcCrop + SSP434_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP460Clm50BgcCrop + SSP460_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + ISSP534Clm50BgcCrop + SSP534_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + + + + IHistClm50BgcCropQianGs + HIST_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + I2000Clm50BgcDvCrop @@ -254,48 +349,33 @@ 1850_DATM%CPLHIST_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - - - ISSP585Clm50BgcCrop - SSP585_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - + + - ISSP126Clm50BgcCrop - SSP126_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + I2000Ctsm50NwpSpGswpGs + 2000_DATM%GSWP3v1_CLM50%NWP-SP_SICE_SOCN_MOSART_SGLC_SWAV - ISSP119Clm50BgcCrop - SSP119_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + I2000Ctsm50NwpBgcCropGswpGs + 2000_DATM%GSWP3v1_CLM50%NWP-BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + - ISSP245Clm50BgcCrop - SSP245_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + I2000Ctsm50NwpSpNldasGs + 2000_DATM%NLDAS2_CLM50%NWP-SP_SICE_SOCN_MOSART_SGLC_SWAV + - ISSP370Clm50BgcCrop - SSP370_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + I2000Ctsm50NwpSpNldasRsGs + 2000_DATM%NLDAS2_CLM50%NWP-SP_SICE_SOCN_SROF_SGLC_SWAV - - ISSP434Clm50BgcCrop - SSP434_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - - - - ISSP460Clm50BgcCrop - SSP460_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - - - - ISSP534Clm50BgcCrop - SSP534_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - - - @@ -339,7 +419,12 @@ 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV - + + + I2000Clm45FatesRsGs + 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_SROF_SGLC_SWAV + + I2000Clm45FatesGs 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_SGLC_SWAV @@ -420,38 +505,6 @@ 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV - - IHistClm50BgcCropG - HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV - - - - - I2000Clm40SpCruGs - 2000_DATM%CRUv7_CLM40%SP_SICE_SOCN_RTM_SGLC_SWAV - - - - I1850Clm40SpCruGs - 1850_DATM%CRUv7_CLM40%SP_SICE_SOCN_RTM_SGLC_SWAV - - - - - - I1850Clm40SpGswGs - 1850_DATM%GSWP3v1_CLM40%SP_SICE_SOCN_RTM_SGLC_SWAV - - - - - - I1850Clm40CnGswGs - 1850_DATM%GSWP3v1_CLM40%CN_SICE_SOCN_RTM_SGLC_SWAV - - - - IHistClm40SpGswGs HIST_DATM%GSWP3v1_CLM40%SP_SICE_SOCN_RTM_SGLC_SWAV @@ -460,34 +513,19 @@ - IHistClm40SpCruGs - HIST_DATM%CRUv7_CLM40%SP_SICE_SOCN_RTM_SGLC_SWAV - - - - IHistClm40CnGswGs - HIST_DATM%GSWP3v1_CLM40%CN_SICE_SOCN_RTM_SGLC_SWAV - - - - - - IHistClm40CnCruGs - HIST_DATM%CRUv7_CLM40%CN_SICE_SOCN_RTM_SGLC_SWAV - - + IHistClm50BgcCropG + HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV - - - 1850-01-01 - 2015-01-01 + 2000-01-01 + 2010-01-01 + 2015-01-01 1980-01-15 1997-12-31 1993-12-01 diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 4de8baaa1d..9467994e62 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -671,6 +671,80 @@ + + + + none + + -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -50 + -50 + -50 + -50 + -50 + -50 + -50 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index 911afe014b..8a40ea9183 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -18,6 +18,15 @@ SSP smoke CLM spinup test (only valid for CLM compsets with CLM45) + + Run CTSM's Fortran unit tests. Grid and compset (and most case settings) are ignored. + 1 + ndays + 11 + FALSE + FALSE + + CLM initial condition interpolation test (requires configuration with non-blank finidat) 1 @@ -66,8 +75,18 @@ SSP smoke CLM spinup test (only valid for CLM compsets with CLM45) $STOP_N + + CTSM Land model test to ensure Water isotopes on or off does NOT change answers + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + - smoke CLM spinup test (only valid for CLM45 or CLM50 compsets) + smoke CLM spinup test 1 ndays startup @@ -78,4 +97,14 @@ SSP smoke CLM spinup test (only valid for CLM compsets with CLM45) $STOP_N + + CLM user-defined soil structure test + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 9f41cc2e52..4b9b0ca8b0 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -1,22 +1,133 @@ - - - FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianGs.cheyenne_gnu.clm-monthly RUN - FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianGs.cheyenne_intel.clm-monthly RUN - FAIL SMS.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN - FAIL SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN - FAIL SMS.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop RUN - FAIL SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop RUN - FAIL PEPEM_Ld1.f10_f10_musgs.I2000Clm50BgcCrop.hobart_intel.clm-crop RUN - - - FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro RUN - FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro COMPARE_base_rest - FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro RUN - FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro RUN - FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro MEMLEAK - FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro RUN - FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro RUN - + + + + + + + + + + FAIL + #158 + + + + + + FAIL + #550 + + + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#510 + + + + + + FAIL + NGEET/fates#508 + + + + + + FAIL + NGEET/fates#508 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + + + + FAIL + NGEET/fates#315 + + + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 0f1af44769..bc68ad1088 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -26,12 +26,13 @@ - + + @@ -59,20 +60,22 @@ - + + - + + @@ -91,7 +94,7 @@ - + @@ -107,10 +110,10 @@ - + - + @@ -121,13 +124,12 @@ - - + @@ -135,9 +137,9 @@ - + - + @@ -202,14 +204,6 @@ - - - - - - - - @@ -354,15 +348,6 @@ - - - - - - - - - @@ -453,12 +438,19 @@ - + + + + + + + + @@ -487,7 +479,7 @@ - + @@ -518,7 +510,7 @@ - + @@ -575,14 +567,22 @@ - + - - + + + + + + + + + + @@ -683,14 +683,6 @@ - - - - - - - - @@ -708,12 +700,13 @@ - + + @@ -734,14 +727,6 @@ - - - - - - - - @@ -761,7 +746,17 @@ - + + + + + + + + + + + @@ -769,60 +764,62 @@ - + - + - + - + - + + - + + - + - - - - + + + + - + @@ -849,14 +846,6 @@ - - - - - - - - @@ -865,7 +854,7 @@ - + @@ -891,14 +880,6 @@ - - - - - - - - @@ -907,23 +888,7 @@ - - - - - - - - - - - - - - - - - + @@ -932,7 +897,7 @@ - + @@ -942,17 +907,15 @@ - - + - @@ -965,17 +928,18 @@ - + - + - + + @@ -987,18 +951,9 @@ - - - - - - - - - @@ -1014,12 +969,12 @@ - + - + @@ -1036,7 +991,7 @@ - + @@ -1045,7 +1000,7 @@ - + @@ -1059,13 +1014,13 @@ - + - + @@ -1083,8 +1038,8 @@ - - + + @@ -1117,8 +1072,6 @@ - - @@ -1136,7 +1089,7 @@ - + @@ -1182,15 +1135,7 @@ - - - - - - - - - + @@ -1198,7 +1143,7 @@ - + @@ -1206,7 +1151,7 @@ - + @@ -1237,17 +1182,19 @@ - + - + + + + + + - - - - + - + @@ -1264,26 +1211,11 @@ - - - - - - - - - - - - - - - - + @@ -1300,15 +1232,7 @@ - - - - - - - - - + @@ -1323,16 +1247,17 @@ - + + - + @@ -1342,23 +1267,13 @@ - - - - - - - - - - + - - - + + @@ -1380,22 +1295,6 @@ - - - - - - - - - - - - - - - - @@ -1420,15 +1319,7 @@ - - - - - - - - - + @@ -1462,15 +1353,6 @@ - - - - - - - - - @@ -1481,14 +1363,6 @@ - - - - - - - - @@ -1497,22 +1371,13 @@ - + - - - - - - - - - - + @@ -1521,6 +1386,7 @@ + @@ -1534,7 +1400,7 @@ - + @@ -1544,7 +1410,6 @@ - @@ -1560,14 +1425,6 @@ - - - - - - - - @@ -1597,26 +1454,29 @@ + - + - + + - + + @@ -1673,14 +1533,6 @@ - - - - - - - - @@ -1690,12 +1542,13 @@ - + + @@ -1704,7 +1557,7 @@ - + @@ -1765,6 +1618,7 @@ + @@ -1789,6 +1643,7 @@ + @@ -1835,7 +1690,87 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2006,6 +1941,7 @@ + @@ -2021,6 +1957,7 @@ + @@ -2059,7 +1996,7 @@ - + @@ -2069,4 +2006,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/cime_config/testdefs/testlist_clm_nuopc.xml b/cime_config/testdefs/testlist_clm_nuopc.xml new file mode 100644 index 0000000000..fe8f121f4a --- /dev/null +++ b/cime_config/testdefs/testlist_clm_nuopc.xml @@ -0,0 +1,1911 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/40crop/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/40crop/include_user_mods deleted file mode 100644 index e009e9a25a..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40crop/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../40default diff --git a/cime_config/testdefs/testmods_dirs/clm/40crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/40crop/user_nl_clm deleted file mode 100644 index 7ba5b8685b..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40crop/user_nl_clm +++ /dev/null @@ -1,3 +0,0 @@ - hist_fincl1 += 'GDD0', 'GDD8', 'GDD10', - 'GDD020', 'GDD820', 'GDD1020', - 'GDDPLANT', 'GDDTSOI', 'A5TMIN', 'A10TMIN' diff --git a/cime_config/testdefs/testmods_dirs/clm/40default/shell_commands b/cime_config/testdefs/testmods_dirs/clm/40default/shell_commands deleted file mode 100644 index c931cba688..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40default/shell_commands +++ /dev/null @@ -1,3 +0,0 @@ -# Turn fire emission driver namelist off in case clm4_0 is being used -./xmlchange CLM_BLDNML_OPTS="-no-fire_emis" --append - diff --git a/cime_config/testdefs/testmods_dirs/clm/40default/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/40default/user_nl_clm deleted file mode 100644 index 4018165f31..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40default/user_nl_clm +++ /dev/null @@ -1,25 +0,0 @@ - wrtdia = .true. - hist_dov2xy = .true.,.false. -! Even though only 2 history tapes are defined here, set ndens to 1 for up to 6 history -! tapes, for the sake of mods that extend these default mods and may add other history tapes - hist_ndens = 1,1,1,1,1,1 - hist_nhtfrq =-24,-8 - hist_mfilt = 1,1 - hist_fincl1 = 'TRAFFICFLUX', 'SNOWLIQ:A','SNOWICE:A' - hist_fincl2 = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS', - 'FSR','FSA','FGEV','FSH','FGR','TSOI', - 'ERRSOI','SABV','SABG', - 'FSDSVD','FSDSND','FSDSVI','FSDSNI', - 'FSRVD','FSRND','FSRVI','FSRNI', - 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', - 'H2OSNO','SOILLIQ','SOILICE', - 'TSA_U', 'TSA_R', - 'TREFMNAV_U', 'TREFMNAV_R', - 'TREFMXAV_U', 'TREFMXAV_R', - 'TG_U', 'TG_R', - 'RH2M_U', 'RH2M_R', - 'QRUNOFF_U', 'QRUNOFF_R', - 'SoilAlpha_U', - 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT' - - diff --git a/cime_config/testdefs/testmods_dirs/clm/40pts/README b/cime_config/testdefs/testmods_dirs/clm/40pts/README deleted file mode 100644 index 30d71a7c8b..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40pts/README +++ /dev/null @@ -1,5 +0,0 @@ -This testmods directory should not be used directly. Instead, it should be -extended (i.e., included) by a mods directory that defines the point to run -over - something like: - -./xmlchange PTS_LAT=42,PTS_LON=260 diff --git a/cime_config/testdefs/testmods_dirs/clm/40pts/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/40pts/include_user_mods deleted file mode 100644 index e009e9a25a..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40pts/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../40default diff --git a/cime_config/testdefs/testmods_dirs/clm/40pts/shell_commands b/cime_config/testdefs/testmods_dirs/clm/40pts/shell_commands deleted file mode 100644 index ad140e45e1..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40pts/shell_commands +++ /dev/null @@ -1,24 +0,0 @@ -./xmlchange PTS_MODE=TRUE -./xmlchange ATM_NX=0 -./xmlchange ATM_NY=0 -./xmlchange LND_NX=0 -./xmlchange LND_NY=0 -./xmlchange ICE_NX=0 -./xmlchange ICE_NY=0 -./xmlchange OCN_NX=0 -./xmlchange OCN_NY=0 -./xmlchange ROF_NX=0 -./xmlchange ROF_NY=0 -./xmlchange GLC_NX=0 -./xmlchange GLC_NY=0 -./xmlchange WAV_NX=0 -./xmlchange WAV_NY=0 -./xmlchange NTASKS_ATM=1 -./xmlchange NTASKS_LND=1 -./xmlchange NTASKS_ICE=1 -./xmlchange NTASKS_OCN=1 -./xmlchange NTASKS_CPL=1 -./xmlchange NTASKS_GLC=1 -./xmlchange NTASKS_ROF=1 -./xmlchange NTASKS_WAV=1 -./xmlchange NTASKS_ESP=1 diff --git a/cime_config/testdefs/testmods_dirs/clm/40ptsRLA/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/40ptsRLA/include_user_mods deleted file mode 100644 index 85ea433e18..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40ptsRLA/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../40pts diff --git a/cime_config/testdefs/testmods_dirs/clm/40ptsRLA/shell_commands b/cime_config/testdefs/testmods_dirs/clm/40ptsRLA/shell_commands deleted file mode 100644 index 48287a2998..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40ptsRLA/shell_commands +++ /dev/null @@ -1,2 +0,0 @@ -./xmlchange PTS_LAT=42,PTS_LON=260 -./xmlchange --force CLM_FORCE_COLDSTART=on diff --git a/cime_config/testdefs/testmods_dirs/clm/40ptsRLB/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/40ptsRLB/include_user_mods deleted file mode 100644 index 85ea433e18..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40ptsRLB/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../40pts diff --git a/cime_config/testdefs/testmods_dirs/clm/40ptsRLB/shell_commands b/cime_config/testdefs/testmods_dirs/clm/40ptsRLB/shell_commands deleted file mode 100644 index 15fd1cced4..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40ptsRLB/shell_commands +++ /dev/null @@ -1,2 +0,0 @@ -./xmlchange PTS_LAT=-5,PTS_LON=290 -./xmlchange --force CLM_FORCE_COLDSTART=on diff --git a/cime_config/testdefs/testmods_dirs/clm/40ptsROA/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/40ptsROA/include_user_mods deleted file mode 100644 index 85ea433e18..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40ptsROA/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../40pts diff --git a/cime_config/testdefs/testmods_dirs/clm/40ptsROA/shell_commands b/cime_config/testdefs/testmods_dirs/clm/40ptsROA/shell_commands deleted file mode 100644 index d5be09e860..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40ptsROA/shell_commands +++ /dev/null @@ -1,2 +0,0 @@ -./xmlchange PTS_LAT=30,PTS_LON=315 -./xmlchange --force CLM_FORCE_COLDSTART=on diff --git a/cime_config/testdefs/testmods_dirs/clm/40reduceOutput/shell_commands b/cime_config/testdefs/testmods_dirs/clm/40reduceOutput/shell_commands deleted file mode 100644 index e075bf29fd..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40reduceOutput/shell_commands +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -# Turn fire emission driver namelist off in case clm4_0 is being used -./xmlchange CLM_BLDNML_OPTS="-no-fire_emis" --append - diff --git a/cime_config/testdefs/testmods_dirs/clm/40reduceOutput/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/40reduceOutput/user_nl_clm deleted file mode 100644 index 3d94564c47..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/40reduceOutput/user_nl_clm +++ /dev/null @@ -1,12 +0,0 @@ -hist_empty_htapes = .true. -hist_fincl1 = 'SNOWLIQ','SNOWICE' , - 'TG','TBOT','FIRE','FIRA','FLDS','FSDS', - 'FSR','FSA','FGEV','FSH','FGR','TSOI', - 'ERRSOI','SABV','SABG', - 'FSDSVD','FSDSND','FSDSVI','FSDSNI', - 'FSRVD','FSRND','FSRVI','FSRNI', - 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', - 'H2OSNO','SOILLIQ','SOILICE', - 'TG', - 'RH2M_U', 'RH2M_R', - 'QRUNOFF' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/include_user_mods new file mode 100644 index 0000000000..4c7aa0f2b4 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/include_user_mods @@ -0,0 +1 @@ +../Fates diff --git a/cime_config/testdefs/testmods_dirs/clm/_includes/README b/cime_config/testdefs/testmods_dirs/clm/_includes/README new file mode 100644 index 0000000000..3eaf50affa --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/_includes/README @@ -0,0 +1,9 @@ +This directory contains testmods directories that are meant to be +included in other testmods directories, not used directly. + +One reason for doing this is so that we can have testmods here that +apply science settings without including one of the testmods that is +typically included for setting output frequency (e.g., 'default' or +'monthly'). Then the testmods here can be included in other testmods +that use different output frequencies (e.g., daily vs. monthly) while +having the same science options. diff --git a/cime_config/testdefs/testmods_dirs/clm/_includes/ignore_warnings/shell_commands b/cime_config/testdefs/testmods_dirs/clm/_includes/ignore_warnings/shell_commands new file mode 100644 index 0000000000..109b06a0b1 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/_includes/ignore_warnings/shell_commands @@ -0,0 +1 @@ +./xmlchange --append CLM_BLDNML_OPTS="-ignore_warnings" diff --git a/cime_config/testdefs/testmods_dirs/clm/_includes/irrig_alternate/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/_includes/irrig_alternate/user_nl_clm new file mode 100644 index 0000000000..a5b850669b --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/_includes/irrig_alternate/user_nl_clm @@ -0,0 +1,6 @@ + +! Settings from irrig_alternate: test some non-default irrigation options +limit_irrigation_if_rof_enabled = .true. +use_groundwater_irrigation = .true. +irrig_method_default = 'sprinkler' +hist_fincl1 += 'QIRRIG_DEMAND','QIRRIG_DRIP','QIRRIG_SPRINKLER' diff --git a/cime_config/testdefs/testmods_dirs/clm/basic_interp/README b/cime_config/testdefs/testmods_dirs/clm/basic_interp/README new file mode 100644 index 0000000000..7aecd6e723 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/basic_interp/README @@ -0,0 +1,2 @@ +This testmod directory is for tests that want to use the 'basic' +testmod, but also need use_init_interp = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/basic_interp/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/basic_interp/include_user_mods new file mode 100644 index 0000000000..068a5b784e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/basic_interp/include_user_mods @@ -0,0 +1 @@ +../basic diff --git a/cime_config/testdefs/testmods_dirs/clm/basic_interp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/basic_interp/user_nl_clm new file mode 100644 index 0000000000..05c8a39983 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/basic_interp/user_nl_clm @@ -0,0 +1 @@ +use_init_interp = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/shell_commands b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/shell_commands deleted file mode 100755 index fdc79af2de..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/shell_commands +++ /dev/null @@ -1 +0,0 @@ -./xmlchange RUN_STARTDATE=1963-01-01 diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/user_nl_clm deleted file mode 100644 index 37b7c1ac3d..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/user_nl_clm +++ /dev/null @@ -1,6 +0,0 @@ -use_c14_bombspike=.true. -use_c13_timeseries = .true. - -! This testmod is used in a long test, so change output frequency -hist_nhtfrq = 0,-240 -hist_mfilt = 1,1 diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/shell_commands b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/shell_commands new file mode 100755 index 0000000000..19c5e78e3a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/shell_commands @@ -0,0 +1,4 @@ +./xmlchange RUN_STARTDATE=1963-12-30 + +# This is done for the decStart testmod, so doing it here, too +./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/user_nl_clm new file mode 100644 index 0000000000..d0d9106e48 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_bombspike1963DecStart/user_nl_clm @@ -0,0 +1,2 @@ +use_c14_bombspike=.true. +use_c13_timeseries = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50KSinkMOut/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm50KSinkMOut/include_user_mods deleted file mode 100644 index 0a64f1e6cc..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/clm50KSinkMOut/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../clm50KitchenSink diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50KitchenSink/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/coldStart/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/clm50KitchenSink/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/coldStart/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/coldStart/shell_commands b/cime_config/testdefs/testmods_dirs/clm/coldStart/shell_commands new file mode 100644 index 0000000000..a66f52f6fd --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/coldStart/shell_commands @@ -0,0 +1,3 @@ +#!/bin/bash +./xmlchange CLM_FORCE_COLDSTART="on" + diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README new file mode 100644 index 0000000000..81fb991ed0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README @@ -0,0 +1,26 @@ +This test reads 78-pft datasets (glcMEC_decrease happens to be similar but +reads 16-pft datasets). In this way, it tests the +new combination do_transient_crops = .true. and use_crop = .false. while +exercising the collapse2gencrop branch ability to collapse the full crop data +to clm's generic crops. + +According to the file +/glade/work/slevis/git/collapse_pfts/bld/namelist_files/namelist_defaults_clm4_5.xml +the following two files used in this test +are default files for the following options: + +fsurdat = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc' +hgrid="10x15" sim_year="1850" use_crop=".true." + +flanduse_timeseries = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc' +hgrid="10x15" sim_year_range="1850-2000" use_crop=".true." +hgrid="10x15" rcp="8.5" sim_year_range="1850-2100" use_crop=".true." +hgrid="10x15" rcp="6" sim_year_range="1850-2100" use_crop=".true." +hgrid="10x15" rcp="4.5" sim_year_range="1850-2100" use_crop=".true." +hgrid="10x15" rcp="2.6" sim_year_range="1850-2100" use_crop=".true." + +This test includes the settings of the decStart test so as to also test the +end-of-year transition since it's an IHist case and transient vegetation gets +updated every new year. + +NB: This test is testing the 10x15 resolution only. diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/include_user_mods new file mode 100644 index 0000000000..acdaa462fc --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/include_user_mods @@ -0,0 +1 @@ +../decStart diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm new file mode 100644 index 0000000000..ff78e0122c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm @@ -0,0 +1,2 @@ +fsurdat = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc' +flanduse_timeseries = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/compatible_finidat_f09/README b/cime_config/testdefs/testmods_dirs/clm/compatible_finidat_f09/README deleted file mode 100644 index 566826ac8e..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/compatible_finidat_f09/README +++ /dev/null @@ -1,23 +0,0 @@ -This testmod provides an finidat file compatible with the current model -configuration, at f09 resolution. - -This testmods directory is for running LII tests which compare the answers for a case where -initial condition interpolation is on (use_init_interp=T) to a case with it's off and ensures -they are exact. For the interpolated result to match uninterpolation, it needs to be a case that -essentially needs no interpolation so it's at the same resolution as the initial condition -file (finidat file). When surface datasets are changed, or the land-mask is changed, or an -important change is made to model physics (for example where new fields are added to the restart -file) -- you'll need to update the initial conditions file in this test (finidat file in -the user_nl_clm file). - -To update the initial conditions (finidat) file for this test: - -(1) Run the LII test; the 'base' case should run to completion even if the -no_interp test fails. - -(2) Copy the finidat_interp_dest.nc file from the 'base' case to the inputdata -space. Rename this to be similar to the name of the file pointed to in this -test's user_nl_clm file, but with a new creation date. - -(3) Update this the user_nl_clm file in this directory to point to the new -finidat file. diff --git a/cime_config/testdefs/testmods_dirs/clm/deepsoil_bedrock/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/deepsoil_bedrock/user_nl_clm index 0c98d81ff0..daaf704226 100644 --- a/cime_config/testdefs/testmods_dirs/clm/deepsoil_bedrock/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/deepsoil_bedrock/user_nl_clm @@ -1,3 +1,3 @@ lower_boundary_condition = 2 -soil_layerstruct = '49SL_10m' +soil_layerstruct_predefined = '49SL_10m' use_bedrock = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README new file mode 100644 index 0000000000..83fad7964a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README @@ -0,0 +1 @@ +This test mod turns on extra diagnostic fields diff --git a/cime_config/testdefs/testmods_dirs/clm/compatible_finidat_f09/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/compatible_finidat_f09/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/extra_outputs/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm new file mode 100644 index 0000000000..512a426909 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm @@ -0,0 +1 @@ +calc_human_stress_indices = 'ALL' diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_decrease/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/glcMEC_decrease/user_nl_clm index c2bebaabd5..7980fe129c 100644 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_decrease/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/glcMEC_decrease/user_nl_clm @@ -1 +1,7 @@ for_testing_allow_non_annual_changes = .true. + +! Also test the reset_dynbal_baselines flag. We want at least one restart test that uses +! this flag; for this test to have power, it should have some change in glacier area +! after the restart. (So, in this decrease test, the glacier decrease should be slow +! enough that there is some decrease after the restart.) +reset_dynbal_baselines = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_increase/README b/cime_config/testdefs/testmods_dirs/clm/glcMEC_increase/README index 1833bf6a8c..a520765d84 100644 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_increase/README +++ b/cime_config/testdefs/testmods_dirs/clm/glcMEC_increase/README @@ -1,2 +1,2 @@ This testmods directory is like the standard glcMEC testmods directory, except -it forces a quick increas in glacier area. +it forces a quick increase in glacier area. diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm index ad22edcfb8..44014d43e0 100644 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm @@ -2,4 +2,4 @@ ! ! Initial condition file at the desired configuration to run, so can verify that interpolating from it gives the same result ! Note that this was generated with GLC_TWO_WAY_COUPLING=FALSE -finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.I2000Clm50BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_dynglc_c190311.nc' +finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.I2000Clm50BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c200428.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutput/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutput/include_user_mods new file mode 100644 index 0000000000..6aed6a8eea --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutput/include_user_mods @@ -0,0 +1,2 @@ +../_includes/ignore_warnings +../cropMonthOutput diff --git a/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutputColdStart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutputColdStart/include_user_mods new file mode 100644 index 0000000000..5c73adaa4a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutputColdStart/include_user_mods @@ -0,0 +1,3 @@ +../_includes/ignore_warnings +../coldStart +../cropMonthOutput diff --git a/cime_config/testdefs/testmods_dirs/clm/irrigOn_reduceOutput/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/irrigOn_reduceOutput/user_nl_clm index ee85bb983a..5356104bd8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/irrigOn_reduceOutput/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/irrigOn_reduceOutput/user_nl_clm @@ -1,5 +1,4 @@ -hist_fincl1 += 'QIRRIG','QIRRIG_DEMAND' -hist_fincl2 += 'QIRRIG' +hist_fincl1 += 'QIRRIG_FROM_SURFACE','QIRRIG_FROM_GW_UNCONFINED','QIRRIG_FROM_GW_CONFINED','QIRRIG_DRIP','QIRRIG_SPRINKLER','QIRRIG_DEMAND' hist_dov2xy = .true.,.false. hist_nhtfrq = 0, -8760 hist_mfilt = 1,1 diff --git a/cime_config/testdefs/testmods_dirs/clm/irrig_alternate/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/irrig_alternate/include_user_mods new file mode 100644 index 0000000000..224c74adfc --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/irrig_alternate/include_user_mods @@ -0,0 +1,2 @@ +../_includes/irrig_alternate +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/irrig_alternate_monthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/irrig_alternate_monthly/include_user_mods new file mode 100644 index 0000000000..a2d9575131 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/irrig_alternate_monthly/include_user_mods @@ -0,0 +1,2 @@ +../_includes/irrig_alternate +../monthly diff --git a/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/README b/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/README new file mode 100644 index 0000000000..97bae04376 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/README @@ -0,0 +1,8 @@ +The purpose of this testmod is to exercise the newer snow cover fraction +method along with having use_subgrid_fluxes = .false. + +Note that we also need h2osfcflag = 0 in this testmod, because +h2osfcflag = 1 is incompatible with use_subgrid_fluxes = .false. Also, +this needs to be used in a clm45 configuration for compatibility with +other options (or else would need to set some other flags: +lower_boundary_condition and possibly others) diff --git a/cime_config/testdefs/testmods_dirs/clm/rain_to_snow_runs_off/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/rain_to_snow_runs_off/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/user_nl_clm new file mode 100644 index 0000000000..efbd30d380 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/no_subgrid_fluxes/user_nl_clm @@ -0,0 +1,2 @@ + h2osfcflag = 0 + use_subgrid_fluxes = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README new file mode 100644 index 0000000000..aefd8adee7 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README @@ -0,0 +1,10 @@ +This testmod directory currently isn't used in any tests, but is useful +for the following reason: + +According to Mariana Vertenstein: At least at one point, you could get +bit-for-bit answers when comparing the mct and nuopc versions of CTSM in +an I compset with SROF and SGLC, if using the changes in this testmod in +both the mct and nuopc runs. + +So we are keeping this around in case someone wants to reproduce that +comparison. diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl new file mode 100644 index 0000000000..6bfefec90b --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl @@ -0,0 +1,4 @@ +orb_eccen = 0. +orb_mvelp = 0. +orb_obliq = 0. +orb_mode = "fixed_parameters" diff --git a/cime_config/testdefs/testmods_dirs/clm/oldhyd/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/oldhyd/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/oldhyd/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/oldhyd/shell_commands b/cime_config/testdefs/testmods_dirs/clm/oldhyd/shell_commands deleted file mode 100644 index e2a2ce67e3..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/oldhyd/shell_commands +++ /dev/null @@ -1,2 +0,0 @@ -./xmlchange BFBFLAG="TRUE" - diff --git a/cime_config/testdefs/testmods_dirs/clm/oldhyd/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/oldhyd/user_nl_clm index 8e8f3b73fc..351bce0a82 100644 --- a/cime_config/testdefs/testmods_dirs/clm/oldhyd/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/oldhyd/user_nl_clm @@ -1,5 +1,4 @@ - hist_ndens = 1,1 - oldfflag = 1 + snow_cover_fraction_method = 'NiuYang2007' h2osfcflag = 0 origflag = 1 - subgridflag = 0 + use_subgrid_fluxes = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/rain_to_snow_runs_off/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/rain_to_snow_runs_off/user_nl_clm deleted file mode 100644 index ac152ceb5c..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/rain_to_snow_runs_off/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ - glacier_region_rain_to_snow_behavior = 'converted_to_snow','converted_to_snow','runs_off','converted_to_snow' - diff --git a/cime_config/testdefs/testmods_dirs/clm/reduceOutput/shell_commands b/cime_config/testdefs/testmods_dirs/clm/reduceOutput/shell_commands index 350466ae70..070b7ba1a8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/reduceOutput/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/reduceOutput/shell_commands @@ -1,8 +1,3 @@ #!/bin/bash -# -# # Use SUBSET rearranger on hobart -if [ `hostname` == "hobart" ]; then - ./xmlchange LND_PIO_REARRANGER=2 -fi ./xmlchange BFBFLAG="TRUE" diff --git a/cime_config/testdefs/testmods_dirs/clm/snowveg_norad/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/snowveg_norad/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/snowveg_norad/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/snowveg_norad/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/snowveg_norad/user_nl_clm new file mode 100644 index 0000000000..4db404f7d1 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/snowveg_norad/user_nl_clm @@ -0,0 +1 @@ +snowveg_affects_radiation = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/README b/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/README new file mode 100644 index 0000000000..9a0139fc31 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/README @@ -0,0 +1,6 @@ +This test turns on water tracer consistency checks. This ensures that +water tracers are updated to stay in sync with bulk quantities. + +As of now (2018-09-05), water tracers are not yet initialized properly +when starting from a restart file that did not itself have water tracers +on it. So we use cold start for this test. diff --git a/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/include_user_mods new file mode 100644 index 0000000000..3dbc936366 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/include_user_mods @@ -0,0 +1 @@ +../coldStart diff --git a/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/user_nl_clm new file mode 100644 index 0000000000..94704a2547 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/tracer_consistency/user_nl_clm @@ -0,0 +1 @@ +enable_water_tracer_consistency_checks = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/vrtlay/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/vrtlay/user_nl_clm index cccaf2abf2..15a92be2d7 100644 --- a/cime_config/testdefs/testmods_dirs/clm/vrtlay/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/vrtlay/user_nl_clm @@ -1 +1 @@ -soil_layerstruct = '23SL_3.5m' +soil_layerstruct_predefined = '23SL_3.5m' diff --git a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/user_nl_clm index 841e8b2a4c..678fbebeb5 100644 --- a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/user_nl_clm @@ -1,5 +1,5 @@ ! Add in an initial condition file that isn't in equilibrium and will need to be brought into equilibrium. ! We purposely want to add a shock to ensure the model can properly respond to it, skipping balance checks ! at the beginning and then coming into balance after enough time. - finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.IG1850CLM45SP.1850-01-01.1.9x2.5_gx1v7_gl4_simyr1850_c170608.nc' + finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.I1850Clm45BgcGs.0901-01-01.0.9x1.25_gx1v7_simyr1850_c190718.nc' use_init_interp = .true. diff --git a/cime_config/user_nl_clm b/cime_config/user_nl_clm index a4cfe51182..cfc5c71308 100644 --- a/cime_config/user_nl_clm +++ b/cime_config/user_nl_clm @@ -8,7 +8,6 @@ ! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting ! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting ! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting -! Set irrigate by the CLM_BLDNML_OPTS -irrig .true. setting ! Set co2_ppmv with CCSM_CO2_PPMV option ! Set dtime with L_NCPL option ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options diff --git a/cime_config/usermods_dirs/_includes/output_base/user_nl_clm b/cime_config/usermods_dirs/_includes/output_base/user_nl_clm index 8ed36a1fa3..52254161ef 100644 --- a/cime_config/usermods_dirs/_includes/output_base/user_nl_clm +++ b/cime_config/usermods_dirs/_includes/output_base/user_nl_clm @@ -8,7 +8,6 @@ ! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting ! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting ! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting -! Set irrigate by the CLM_BLDNML_OPTS -irrig setting ! Set co2_ppmv with CCSM_CO2_PPMV option ! Set dtime with L_NCPL option ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options @@ -30,7 +29,7 @@ hist_dov2xy(1) = .true. hist_nhtfrq(1) = 0 hist_type1d_pertape(1) = ' ' hist_fexcl1 += 'PCT_GLC_MEC','PCT_NAT_PFT' -hist_fincl1 += 'EFLX_LH_TOT_ICE', 'FIRE_ICE', 'FLDS_ICE', 'FSH_ICE', 'FSNO_ICE', 'FSR_ICE', 'QFLX_SUB_SNOW_ICE', 'QRUNOFF_ICE', 'QSNOFRZ_ICE', 'QSNOMELT_ICE', 'RAIN_ICE', 'SNOW_ICE', 'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE' +hist_fincl1 += 'EFLX_LH_TOT_ICE', 'FIRE_ICE', 'FLDS_ICE', 'FSH_ICE', 'FSNO_ICE', 'FSR_ICE', 'QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE', 'QRUNOFF_ICE', 'QSNOFRZ_ICE', 'QSNOMELT_ICE', 'RAIN_ICE', 'SNOW_ICE', 'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE' ! h1 stream (monthly average, finest sub-grid) ! Emon, Lmon @@ -46,7 +45,7 @@ hist_mfilt(3) = 1 hist_dov2xy(3) = .false. hist_nhtfrq(3) = 0 hist_type1d_pertape(3) = 'LAND' -hist_fincl3 += 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', 'EFLX_LH_TOT', 'RH2M', 'TLAI', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'U10', 'TSOI_10CM', 'QIRRIG', 'URBAN_HEAT', 'WASTEHEAT', 'TSKIN' +hist_fincl3 += 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', 'EFLX_LH_TOT', 'RH2M', 'TLAI', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'U10', 'TSOI_10CM', 'QIRRIG_FROM_SURFACE', 'URBAN_HEAT', 'WASTEHEAT', 'TSKIN' ! h3 stream (yearly average, gridcell-level) ! Eyr diff --git a/cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm b/cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm index 0972d19bb5..0e1ceeb4a5 100644 --- a/cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm +++ b/cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm @@ -8,7 +8,7 @@ hist_mfilt(6) = 365 hist_dov2xy(6) = .true. hist_nhtfrq(6) = -24 hist_type1d_pertape(6) = ' ' -hist_fincl6 += 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'EFLX_LH_TOT', 'FSH', 'FGR12', 'FSM', 'QSNOEVAP', 'TLAI', 'QDRAI', 'QDRAI_PERCH', 'QOVER', 'QFLX_SUB_SNOW', 'FSA', 'FIRA', 'H2OSNO', 'SNOCAN', 'QSNOFRZ', 'QFLX_SNOW_DRAIN', 'SNOWDP', 'H2OSFC', 'TV', 'TG', 'TAUX', 'TAUY', 'QVEGT', 'TWS', 'H2OCAN', 'QVEGE', 'QSOIL', 'TSKIN', 'FSDS','FSNO','SNOFSRVD','SNOFSRVI','SNOFSRND','SNOFSRNI','FSDSVD','FSDSVI','FSDSND','FSDSNI','SNOWLIQ','SOILICE','SOILLIQ','QINTR','SNOBCMSL','TSOI','SNOTXMASS','SNOWICE','SNOWLIQ','QRUNOFF','RAIN','SNOW' +hist_fincl6 += 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'EFLX_LH_TOT', 'FSH', 'FGR12', 'FSM', 'QSNOEVAP', 'TLAI', 'QDRAI', 'QDRAI_PERCH', 'QOVER', 'QFLX_SOLIDEVAP_FROM_TOP_LAYER', 'FSA', 'FIRA', 'H2OSNO', 'SNOCAN', 'QSNOFRZ', 'QFLX_SNOW_DRAIN', 'SNOWDP', 'H2OSFC', 'TV', 'TG', 'TAUX', 'TAUY', 'QVEGT', 'TWS', 'H2OCAN', 'QVEGE', 'QSOIL', 'TSKIN', 'FSDS','FSNO','SNOFSRVD','SNOFSRVI','SNOFSRND','SNOFSRNI','FSDSVD','FSDSVI','FSDSND','FSDSNI','SNOWLIQ','SOILICE','SOILLIQ','QINTR','SNOBCMSL','TSOI','SNOTXMASS','SNOWICE','SNOWLIQ','QRUNOFF','RAIN','SNOW' ! h6 stream (daily average, landunit-level) ! Eday @@ -21,10 +21,10 @@ hist_fincl7 += 'TREFMXAV','TREFMNAV' ! h7 stream (3-hourly average, gridcell-level) ! 3hr, E3hr, CF3hr ! 3hr requires QRUNOFF for time mean, and SOILWATER_10CM, TSKIN for time point (I) -! CF3hr requires QFLX_SUB_SNOW for time point (I) +! CF3hr requires QFLX_SOLIDEVAP_FROM_TOP_LAYER for time point (I) hist_mfilt(8) = 2920 hist_dov2xy(8) = .true. hist_nhtfrq(8) = -3 hist_type1d_pertape(8) = ' ' -hist_fincl8 += 'TSA','RH2M','SOILWATER_10CM:I','FSH','EFLX_LH_TOT','FSDS','QRUNOFF','QFLX_SUB_SNOW:I','TSKIN:I' +hist_fincl8 += 'TSA','RH2M','SOILWATER_10CM:I','FSH','EFLX_LH_TOT','FSDS','QRUNOFF','QFLX_SOLIDEVAP_FROM_TOP_LAYER:I','TSKIN:I' diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/output_bgc/user_nl_clm index de136ad4b4..0c0bcd52ff 100644 --- a/cime_config/usermods_dirs/output_bgc/user_nl_clm +++ b/cime_config/usermods_dirs/output_bgc/user_nl_clm @@ -11,7 +11,7 @@ hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTO ! h2 stream (monthly average, landunit-level) ! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level -hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP' +hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'FROOTC:I', 'HTOP' ! h3 stream (yearly average, gridcell-level) hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I' diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index bfe250c85c..20c803ca21 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -31,9 +31,9 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -46,11 +46,11 @@ Changes made to namelist defaults (e.g., changed parameter values): Changes to the datasets (e.g., parameter, surface or initial files): -Substantial timing or memory changes: +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): @@ -79,25 +79,25 @@ CTSM testing: cheyenne - - unit-tests (components/clm/src): + tools-tests (test/tools): cheyenne - - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - + (any machine) - regular tests (aux_clm): - cheyenne_intel ---- - cheyenne_gnu ------ - izumi_nag --------- - izumi_pgi --------- - izumi_intel ------- + cheyenne ---- + izumi ------- + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + Answer changes -------------- diff --git a/doc/.release-ChangeLog_template b/doc/.release-ChangeLog_template deleted file mode 100644 index 19c997d86d..0000000000 --- a/doc/.release-ChangeLog_template +++ /dev/null @@ -1,101 +0,0 @@ -=============================================================== -Tag name: -Originator(s): -Date: -One-line Summary: - -Purpose of this version: ------------------------- - -[Fill this in with details] - - -CTSM Master Tag This Corresponds To: - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): [If none, remove this line] -CIME Issues fixed (include issue #): [If none, remove this line] - -Science changes since: - -Software changes since: - -Changes to User Interface since: - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - - - unit-tests (components/clm/src): - - cheyenne - - hobart --- - - tools-tests (components/clm/test/tools): - - cheyenne - - hobart --- - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - - hobart --- - - regular tests (aux_clm): - - cheyenne_intel ---- - cheyenne_gnu ------ - hobart_nag -------- - hobart_pgi -------- - hobart_intel ------ - - regular tests (prealpha): - - cheyenne_intel - - cheyenne_gnu --- - hobart_nag ----- - - regular tests (prebeta): - - cheyenne_intel - - cheyenne_gnu --- - hobart_nag ----- - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: - - what platforms/compilers: - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - URL for LMWG diagnostics output for new climate: - - Will new REFCASES need to be made for cesm and/or CAM?: No - (This will likely be true if the LII tests failed) - -Detailed list of changes: ------------------------- - -Externals being used: - -CTSM Tag versions pulled over from master development branch: - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - -=============================================================== diff --git a/doc/ChangeLog b/doc/ChangeLog index 52fef26586..983563f718 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,9483 @@ =============================================================== +Tag name: ctsm1.0.dev093 +Originator(s): erik (Erik Kluzek) +Date: Fri May 1 22:27:16 MDT 2020 +One-line Summary: Bring in changes from release-clm5.0 branch to master + +Purpose of changes +------------------ + +Move changes from release-clm5.0.12.13/14/16/17/18/20/21/22/23/24/25/26/27/28/29/30 to master +(note excludes release-clm5.0.15, release-clm5.0.19) + +Answer changing! +Updates FATES with PARTEH option. + +Remove CRUNCEP half degree, ne120np4, f05 surface datasets +Landuse-timeseries files for just: f09, f19, f10, ne30np4, 1x1_numaIA, 1x1_smallvilleIA, 1x1_brazil +Add datasets needed for SSP scenarios (only Tier I for ndep). Add ZWT_inversion dataset for methane. + +Add new ability to use prescribed soil moisture data (from streams files based on an earlier CTSM simulation). + +Add new MODISv2 mapping files for mksurfdata_map. Remove T5 and T21 mapping files. Add conus_30_x8 mapping files, +and T62 mapping files + +Add contrib directory to tools with contributed tools and scripts. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 31 issues.... + #873 -- Release clm5.0.12 changes + #871 -- don't check for valid resolution for CESM cases by default + #836 -- add izumi as a place that can run tools tests + #831 -- add namelist tint_algo settings for input streams + #817 -- Have clm4_5 use the same ndep file as clm5_0 for 1850 + #809 -- mkmapdata using an old version of intel + #804 -- mksurfdata option + #791 -- fix threading for prescribed LAI and soil-moisture + #786 -- allow use_init_interp for a branch + #746 -- Some CLM45 configurations use CLM50 initial conditions files + #741 -- C13_HR, C13_NBP, FPI values result in numeric conversion not representable error (changes answers) + #734 -- Isotope historical files off of NetCDF-4 + #716 -- 2 degree CMIP6WACCMDECK needs Carbon isotopes off + #707 -- Missing mapping files for hirespft + #673 -- Ice shelf wetland fix in mksurfdata_map can lead to glacier+lake > 100% on surface datasets (changes surface dataset creation) + #653 -- To save disk on fsurdat files use zwt0 on finindated file + #629 -- Remove unused fields from surface datasets + #624 -- QSNOEVAP history output incorrect + #621 -- Fully remove rcp in place of only ssp_rcp + #608 -- Odd (blocky) spatial patterns in generic crop leafc for BGC simulation when initialized from BGC-Crop (changes answers) + #589 -- Existence of content in the lai_streams namelist makes it confusing to users + #557 -- no-anthro compset and options + #553 -- More robust mksurfdata_map logic for determining where to put wetlands + #547 -- Add conus_30_x8 grid as valid option for CTSM and mksurfdata_map + #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers + #544 -- Transient cases are matching wrong IC file + #533 -- Add -no-anthro option to mksurfdata + #276 -- Tests for pre_alpha/pre_beta + #262 -- hirespft option to mksurfdata.pl + #175 -- Set stream_year_first_urbantv/last for CLM4.5 + #150 -- mksurfdata code cleanup + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): New surface datasets do mean initial conditions + will need to be interpolated + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Add 2010 compset option + New namelist items: ndep_tintalgo, lai_tintalgo, lightng_tintalgo, urbantv_tintalgo, dribble_crophrv_xsmrpool_2atm + New soil moisture namelist items: use_soil_moisture_streams, stream_year_first_soilm, stream_year_last_soilm, model_year_align_soilm, + model_year_align_soilm, soilm_tintalgo, soilm_offset, soilm_ignore_data_if_missing + New namelist items for FATES: fates_parteh_mode + New 2010, no-anthro, SSP use cases + New compsets: I2010Clm50Sp, I2000Clm50BgcCropQianGs, I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro, IHistClm50SpCru, IHistClm50SpCru, + IHistClm45SpGs, IHistClm45SpGs + New SSP compsets: ISSP585Clm50BgcCrop, ISSP126Clm50BgcCrop, ISSP126Clm50BgcCrop, ISSP245Clm50BgcCrop, ISSP370Clm50BgcCrop, + ISSP434Clm50BgcCrop, ISSP460Clm50BgcCrop, ISSP460Clm50BgcCrop + LAI streams options don't show up in the namelist unless you ask for them + finundation comes from streams files, no longer from the surface dataset + FATES adds a list of new history variables and dimension types + +Changes made to namelist defaults (e.g., changed parameter values): New fsurdat files, SSP C13/C14 files + Add PtVg surface dataset + most finidat files now need to be interpolated, a few added in to get testing to work + New ndep datasets + +Changes to the datasets (e.g., parameter, surface or initial files): + New fsurdat files, finidat files need to be interpolated from now + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Threshold to reseed dead vegetation increased from zero to 1.0 as a hard coded parameter. + Reseeding also happens for generic crop types and not just natural vegetation now. + The ability to read in 3D streams was added (input files have to be at the same resolution as the model) + +Changes to tests or testing: + Add no-anthro, 2010, f19 waccm and SSP tests + Make sure prealpha/prebeta tests are also run by aux_clm + Add prescribed soil moisture test + Lengthen waccm_offline test + Remove hcru_hcru and edison tests + Add some aux_cime_baseline tests + +Code reviewed by: self + + +CTSM testing: regular, tools + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (345 are different than baseline) + + tools-tests (test/tools): + + cheyenne - OK + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - OK + + python testing (see instructions in python/README.md; document testing done): + + cheyennne -- PASS (when ncar_pylib run) + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes + + Updates in all fsurdat files leads to changes in answers + Also there are updated finidat files as they had to be interpolated + to work with the new fsurdat files + Reseeding change can effect answers on startup if activated + Extra call to SoilBiogeochemPrecisionControl can cause a small answer change + + Summarize any changes to answers, i.e., + - what code configurations: all global + - what platforms/compilers: all + - nature of change: Main change is around Antarctica + + CMIP6 simulations and release branch simulations were run with these surface datasets + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates, PTCLM + + fates to sci.1.30.0_api.8.0.0 + PTCLM to PTCLM2_20200121 + + FATES now points to the NGEET repository rather than the NCAR fates-release + +Pull Requests that document the changes (include PR ids): #998, #883, #849, #567, #564, #561 +(https://github.com/ESCOMP/ctsm/pull) + #998 -- Remove Copyright file + #883 -- Bring changes on release-clm5.0 branch to master PR status: ready priority: high type: enhancement + #849 -- Fix link to new forums + #567 -- Ignore patterns for vim + #564 -- Update mksurfdata_map to include glaciers outside of pft landmask + #561 -- Add list of checks that should be done when making new surface datasets + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev092 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Mon Apr 27 14:51:21 MDT 2020 +One-line Summary: Update cime to version in cesm2_2_beta04 + +Purpose of changes +------------------ + +Update cime to latest in cesm2.2 beta tag (cesm2_2_beta04) +Fix two small issues that had gone on the release-clm5.0 branch. +Update manage_externals (to manic-v1.1.8) + +NOTE: Part of the reason for updating cime, was because of some problems +Mike Mills was having on cheyenne with inputdata files being deleted out +from under him before setting up his cases. We think system issues were +interacting with issues with cime putting in place zero length +missing files for the version of cime he was using. Those issues went +away with a cime update, so we hope updating to a newer cime version here +will help prevent those issues for CTSM users. + +cime updates: + +some cleanup from the last maint-5.6 update +Add ne5np4.pg4 grid. +case.setup: Add --keep option +Add omip as option to DATM_CO2_TSERIES + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #974 #966 + Fixes #974 -- python 3 problem in ssp test + Fixes #966 -- a few history fields need to be made CF compliant +CIME Issues fixed (include issue #): 3459 3466 + 3459 -- case.setup refuses to fix corrupted env_mach_specfic.xml + 3466 -- fix for aquap + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + ./case.setup now has a --keep option + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - OK + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - OK + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: None bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime + cime to cime5.8.19 + (NOTE: CMEPS is pointing to a newer hash than used in the beta tag) + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #996 -- Update cime to latest cesm2.2 beta tag + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev091 +Originator(s): sacks (Bill Sacks) +Date: Fri Apr 24 07:43:46 MDT 2020 +One-line Summary: Increase tolerance on near-zero truncation for a snow state update + +Purpose of changes +------------------ + +In UpdateState_TopLayerFluxes, the tolerance of 1.e-13 was occasionally +exceeded. Although I haven't done a careful analysis, it seems okay to +me to increase this tolerance slightly. Here I increase it to 1.e-12. + +Previously, if top-layer h2osoi_ice or h2osoi_liq were reduced to less +than 1e-13 times the original value (in an absolute value sense), these +masses were set to 0; now we set these masses to 0 if they are reduced +to less than 1e-12 times the original. So we can now occasionally set a +value to exactly 0 when before it was left at slightly different from +zero. If the previous code led to a small positive value, between 1e-13 +and 1e-12 times the original, this tag will change answers slightly. If +the previous code led to a small negative number, it would cause the +model to abort, leading to the issue reported in ESCOMP/CTSM#988; this +change should fix those occasional aborts. + +This tag also introduces the general ability to set tolerances to a +custom value in calls to truncate_small_values. + +See ESCOMP/CTSM#988 for details. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#988 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, in theory (but none in test suite) + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: potentially all, but very rarely + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Roundoff + + Potentially changes answers by roundoff (see notes above), but no + changes were observed in any test in the test suite + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/989 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev090 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Thu Apr 23 09:21:18 MDT 2020 +One-line Summary: Refactoring banded diagonal matrix and solve system in SoilTemperature module + +Purpose of changes +------------------ + +Previously, the SoilTemperature module has a high level of nested subroutine +calls, which hurt its performance and readability. There were many +redundancies, logical issues, and nested conditionals in the modular code +as discussed in issue #323. In this PR, SoilTemperature module is optimized +and rewritten for better readability and performance while maintaining bfb +compatibility. + + +This PR addresses issue ESCOMP/ctsm#323 + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + -ESCOMP/ctsm#323 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: The revised code improved the +performance of the previous code by ~1.5-2x. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +Externals used for the testing: + [cism] + tag = cism2_1_68 + [rtm] + tag = rtm1_0_70 + [mosart] + tag = mosart1_0_35 + [cime] + tag = branch_tags/cime5.8.15_a01 + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/CTSM/pull/979) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev089 +Originator(s): sacks (Bill Sacks) +Date: Tue Apr 7 12:01:59 MDT 2020 +One-line Summary: Bring documentation source to master + +Purpose of changes +------------------ + +1. Bring documentation source to master: Pulls in the source from + https://github.com/escomp/ctsm-docs. This is important so that + documentation can remain in sync with changes in the model + code. Images are stored here using git-lfs (Git Large File + Storage). I also made some minor fixes to get the pdf build of the + tech note working. + +2. Use a different documentation theme that supports a version dropdown + menu, and add the code needed to support this versioning on the + documentation web pages. At a high level, the way the versioned + documentation works is to have separate subdirectories in the + gh-pages branch of the ctsm-docs repository for each version of the + documentation we want to support. There is then a bit of JavaScript + code which uses a json file in the gh-pages branch to determine which + versions exist and how these should be named in the dropdown + menu. Most of these changes were borrowed from ESMCI/cime#3439, which + in turn borrowed from ESCOMP/CISM-wrapper#23, which in turn was a + slight modification of an implementation provided by @mnlevy1981 for + the MARBL documentation, which in turn borrowed from an + implementation put together by Unidata (credit where credit is due). + + I am not aware of out-of-the-box support for a version pull-down in + out-of-the-box sphinx themes (though the last time I looked was in + Fall, 2018, so there may be something available now). However, + support for a version dropdown exists in an open PR in the sphinx + readthedocs theme repository: readthedocs/sphinx_rtd_theme#438. I + have pushed this branch to a new repository in ESMCI + (https://github.com/ESMCI/sphinx_rtd_theme) to facilitate long-term + maintenance of this branch in case it disappears from the official + sphinx_rtd_theme repository. I have also cherry-picked a commit onto + that branch, which is needed to fix search functionality in sphinx1.8 + (from readthedocs/sphinx_rtd_theme#672) (which is another reason for + maintaining our own copy of this branch). The branch in this + repository is now named version-dropdown-with-fixes (branching off of + the version-dropdown branch in the sphinx_rtd_theme repository). In + the long-term, I am a little concerned about using this theme that + isn't showing any signs of being merged to the main branch of the + readthedocs theme, but this has been working for us in other projects + for the last 2 years, so I feel this is a reasonable approach in the + short-medium term. + +The new process for building the documentation is given here: +https://github.com/ESCOMP/CTSM/wiki/Directions-for-editing-CLM-documentation-on-github-and-sphinx + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#239 (Move documentation source to master) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- not run! + izumi ------- not run! + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/954 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev088 +Originator(s): sacks (Bill Sacks) +Date: Tue Apr 7 10:43:03 MDT 2020 +One-line Summary: Fix bug in snow aerosol numerics (causes occasional HUGE aerosol values) + +Purpose of changes +------------------ + +Multiplications / divisions by dtime were missing in a few places, in +some code that ensures that aerosol mass fluxes between the snow layers +don't exceed the total mass. This bug was introduced in ctsm1.0.dev065, +when a term was changed from a mass to a flux (per unit time), but some +of the code wasn't changed correspondingly. + +In one case this bug caused a crash, but in other cases it just causes +incorrect answers. The issue can be seen by examining the history +variables SNOBCMCL, SNOOCMCL and SNODSTMCL. In the case that led to the +crash, SNOBCMCL and SNOOCMCL became huge in one grid cell (~ 10^12) for +a long period before the crash. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#965 (Bug in snow aerosol numerics can cause + aerosol masses to blow up, starting with ctsm1.0.dev065) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none (not checked, but none expected) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek, Keith Oleson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + ok means tests pass, some answer changes as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff/same climate + + Answer changes arise due to a bug fix for a condition that only + appears infrequently. When it does appear, answer changes can + potentially be enormous (e.g., snow aerosol concentrations 20 + orders of magnitude too large), though answer changes observed in + the test suite all appear relatively small. + + Answer changes just appeared for the following tests: + + FAIL ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_Ld1.nldas2_rnldas2_mnldas2.I2000Ctsm50NwpSpNldasGs.cheyenne_gnu.clm-default BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_Ld1.nldas2_rnldas2_mnldas2.I2000Ctsm50NwpSpNldasRsGs.cheyenne_gnu.clm-default BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_D_Ld9.ne30_g16.I2000Clm50BgcCruGs.cheyenne_intel.clm-vrtlay BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_D_Ld9.T31_g37.I2000Clm50Sp.cheyenne_intel.clm-SNICARFRC BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_Ld9.f45_g37.I2000Clm50BgcCruGs.cheyenne_intel.clm-nofire BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_N2_Ld9.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-default BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_D_Lm6.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-FatesColdDef BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_D_Lm6_P144x1.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-FatesColdDef BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput BASELINE ctsm1.0.dev087: DIFF + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/971 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev087 +Originator(s): sacks (Bill Sacks) +Date: Mon Apr 6 11:23:51 MDT 2020 +One-line Summary: Change hard-coded soil layers in phenology to use a target depth + +Purpose of changes +------------------ + +Adds infrastructure for finding the soil layer containing a given depth +(covered by unit tests). + +In phenology code, replaces hard-coded level 3 with a target soil +depth. This value is read from the parameter file. The default value is +set in a way that is bit-for-bit for standard CLM45 and CLM50 +configurations, but this will change answers for non-SP configurations +using the NWP soil layer structure or non-standard soil layer +structures. + +This is important for the sake of supporting flexible soil layers, as in +the NWP configuration. + +Also, some cleanup of the CNPhenology parameter reading code. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#952 (Change hard coded soil layers in phenology + to use a target depth) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[X] ctsm5_0-nwp -- only for non-SP cases + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- New parameter added to NetCDF parameter file: phenology_soil_depth + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + ok means tests pass, a few answer changes as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Non-SP cases with NWP or non-standard + soil layer structures + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff; same vs. new climate not investigated + + Differences in non-SP cases with soil layer structure different + from that of standard clm45 or clm50. Differences observed in + tests + ERS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_intel.clm-deepsoil_bedrock + and + SOILSTRUCTUD_Ld5.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-default. + + ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Ctsm50NwpBgcCropGswpGs.cheyenne_intel.clm-default + had no differences; I'm guessing this is just because there didn't + happen to be the appropriate PFTs present to show differences in + this short, coarse-resolution test. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/963 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev086 +Originator(s): mvertens (Mariana Vertenstein) +Date: Thu Mar 19 16:03:26 MDT 2020 +One-line Summary: Updates to NUOPC cap and minor fixes to ncdio_pio + +Purpose of changes +------------------ + +This tag has updates to the NUOPC cap that are needed for the latest +version of CMEPS. + +Now each component NUOPC cap needs to compute possibly time varying +orbital parameters. Before, in cpl7, this was done in the driver and +passed to the components via seq_infodata. However, now the driver is +really just a simple ascii file - so those calculations needed to +migrate to the component caps. + +In addition, this tag contains changes to ncdio_pio.F90 that improve +performance in some situations. + +This also updates MOSART and RTM tags to include fixes for the NUOPC cap +for MOSART and implementation of an initial NUOPC cap for RTM. + +Also, I1Pt compsets now use SROF rather than using an active runoff +model in 'null' mode. This leads to differences in namelists, but not in +results. + +Mariana Vertenstein implemented most of the changes in this tag; Jim +Edwards implemented the ncdio_pio changes; Bill Sacks did final testing +and integration. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#943 (NUOPC tests will fail in ctsm1.0.dev085) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- I1Pt tests and cases now use SROF rather than an active runoff model + with a null grid (only impacts namelists, not results) +- Changed nuopc test to use MOSART rather than SROF +- Changed finidat file used by LII test to solve a problem that was + uncovered with the ncdio_pio changes in this tag + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (just for NUOPC configurations) + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Just some NUOPC configurations + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Not investigated carefully, but likely to be larger than roundoff + / same climate (due to introduction of time-varying orbital parameters) + + Differences are expected in NUOPC configurations using time-varying + orbital parameters. Note that no differences showed up in the test + suite, however, because the only nuopc test in the test suite is + new in this tag (so did not have baselines). + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- mosart: mosart1_0_35 -> mosart1_0_36 +- rtm: rtm1_0_70 -> rtm1_0_71 +- cmeps + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/issues/943 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev085 +Originator(s): sacks (Bill Sacks) +Date: Mon Mar 16 09:19:57 MDT 2020 +One-line Summary: Update cime + +Purpose of changes +------------------ + +Update to latest version of cime master + +Bugs fixed or introduced +------------------------ + +Known bugs introduced in this tag (include github issue ID): +- https://github.com/ESCOMP/CTSM/issues/943 - NUOPC tests will fail in ctsm1.0.dev085 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- NUOPC cases will fail from a standalone checkout + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + Two test failures: + + PEND SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default SHAREDLIB_BUILD + I have added this to the expected fails list for now + FAIL SMS_P720x1_Ln6.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStart BASELINE ctsm1.0.dev084: ERROR BFAIL baseline directory '/glade/p/cgd/tss/ctsm_baselines/ctsm1.0.dev084/SMS_P720x1_Ln6.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStart' does not exist + This test was added in the previous tag, but apparently wasn't run from there + + Note: I did testing using cime hash + 4f1880756a66ff12d304937d3c166d451ea50cf9, then updated to the tag + (cime5.8.17). The two are identical except for the cime ChangeLog. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +cime: branch_tags/cime5.8.15_a01 -> cime5.8.17 + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev084 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Wed Feb 19 15:05:03 MST 2020 +One-line Summary: Bounds assertion for C isotopes when threading is on + +Purpose of changes +------------------ + +Previously, the bounds of c13 and c14 in subroutines TruncateCStates and +TruncateCandNStates were not checked when threading was on. This PR allows us +to handle c13 and c14 arrays like everything else in CTSM including (bounds +checking). + +This PR resolves issue ESCOMP/ctsm#811 + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + -ESCOMP/ctsm#811 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + - There was an issue (wrong wallclock time ) for one of the tests in the test + definitions which got fixed: (SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs..) + - Also, I tried making the wallclocktime for all tests in + cime_config/testdefs/testlist_clm.xml consistent in the format of hh:mm:ss. + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/CTSM/pull/923) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev083 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Thu Feb 6 12:12:26 MST 2020 +One-line Summary: Some BFB Fixes: Resolve issues #683, # 874, #878, # 885, # 745, #838 + +Purpose of changes +------------------ + +Resolved issues: + +ESCOMP/ctsm#683 : Writing out FATES parameters only on masterproc. +ESCOMP/ctsm#874 : Changing the number of timesteps to run for + SMS_P720x1_Ln3.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStar + to prevent failing with CMEPS. +ESCOMP/ctsm#878 : Removing the unused atm2lnd field. +ESCOMP/ctsm#885 : Changing the defaults for br_root in namelist_defaults to + enable FUN with CLM4.5. +ESCOMP/ctsm#745 : Removing ReadNL private subroutine from initVerticalMod.F90. +ESCOMP/ctsm#838 : Clarifying ZISNO in the variable long name. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +Resolves : + - ESCOMP/ctsm#683 + - ESCOMP/ctsm#874 + - ESCOMP/ctsm#878 + - ESCOMP/ctsm#885 + - ESCOMP/ctsm#745 + - ESCOMP/ctsm#838 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): + Not any changes in parameter values. + changing the default for br_root in namelist_defaults to enable FUN with + CLM4.5. + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + Changed the number of timesteps from Ln3 to Ln6 for + SMS_P720x1_Ln3.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStar + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/897 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev082 +Originator(s): oleson (Keith Oleson) +Date: Sat Feb 1 09:28:41 MST 2020 +One-line Summary: Rename variables to avoid confusion; fix QSNOEVAP diagnostic + +Purpose of changes +------------------ + +Renamed variables as discussed in ESCOMP/ctsm#118 throughout the code. + +Also made a couple of minor changes to fix a couple of potential +problems with these variables as described in the branch commit logs. + +Tested for bfb before changing the history field variables +themselves. These changes are all bfb (with the exception of QSNOEVAP) +for a 1 month global 2deg simulation, but may not be bfb under all +conditions. QSNOEVAP is not bfb because I've added in qflx_ev_snow for +lakes. + +Also, update cime slightly with a fix for izumi machine updates + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#118 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok: tests pass, answer changes in QSNOEVAP but nothing else (as expected) + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Larger than roundoff, but only in the diagnostic field QSNOEVAP + + Possibility of other answer changes in rare circumstances, not + observed in testing. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.15 -> branch_tags/cime5.8.15_a01 + Minor update for izumi machine changes + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/893 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev081 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Mon Jan 13 15:37:07 MST 2020 +One-line Summary: Speed up restart writes + +Purpose of changes +------------------ + + E3SM#3163 made some changes to speed up restart writes. I use E3SM#3163 + function GetGlobalIndexArray in place of GetGlobalIndex so as to get + global indices by array rather than looping over every element. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #801 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: Limited testing did not show substantial timing changes + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: + @billsacks + @bishtgautam + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + No + + @billsacks recommended running a global test in the branch vs. in master (i.e. + with vs. without the code mods) to compare restart files because the test suite + does not compare restart files and an error in the subgrid indices on the + restart file might go undetected. I ran this test: + ERS_D_Ld6.f10_f10_musgs.I1850Clm45BgcCrop.cheyenne_intel.clm-clm50CMIP6frc + and got identical values for all variables in the two restart files. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/880 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev080 +Originator(s): sacks (Bill Sacks) +Date: Mon Dec 2 12:23:22 MST 2019 +One-line Summary: Update externals, minor fixes to work with latest cime, get nuopc cap working + +Purpose of changes +------------------ + +(1) Update to latest version of externals. This includes a significant + cime update. + +(2) Minor fixes to get things working with the latest version of cime. + +(3) Fix from Mariana Vertenstein to get NUOPC cap working, fixes to + externals cfg files to allow running NUOPC cases out of the box, and + add a NUOPC test. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +CIME update brings in some changes, e.g., in mapping files; otherwise, none. + +Substantial timing or memory changes: not investigated + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Added NUOPC test: + SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests passed, some baseline comparisons failed as expected + + Note: Most testing was done on ad1ad752; then, from the latest + version, I ran a 2-test test list of: + - SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default + - SMS_D.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default + + In addition to verifying that the above tests passed, I also + inspected the sharedlib build area to verify that separate builds of + the clm library were done for mct and nuopc. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: +- cheyenne tests compared against ctsm1.0.dev078, since cheyenne testing +was not run on ctsm1.0.dev079. + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Cases at f10 resolution + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff, but probably same climate + + Answer changes are due to https://github.com/esmci/cime/pull/3186 + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: branch_tags/cime5.8.3_chint17-05 -> cime5.8.15 +- rtm: rtm1_0_68 -> rtm1_0_70 +- mosart: mosart1_0_34 -> mosart1_0_35 +- cmeps: 471ac52 -> 181ff1ed9dfb279e619e8a2173f43baf7bf1dce3 + Also, note that cmeps is now checked out automatically + + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/845 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev079 +Originator(s): sacks (Bill Sacks) +Date: Mon Nov 4 14:41:41 MST 2019 +One-line Summary: Change a few uses of shr_kind + +Purpose of changes +------------------ + +Change a few uses of shr_kind to work with latest cime. These changes +are from Mariana Vertenstein. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- NOT RUN! + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev078 +Originator(s): oleson (Keith Oleson) +Date: Thu Oct 31 12:30:00 MDT 2019 +One-line Summary: Fix rootr calculation with use_hydrstress true + +Purpose of changes +------------------ + +In cases with use_hydrstress=.true., both rootr_patch and rootr_col had +problems. This affected the diagnostic fields ROOTR and ROOTR_COLUMN, +and (in BGC cases) fed back on other parts of the system via affecting +the methane code. See https://github.com/ESCOMP/CTSM/issues/812 for more +details. + +This tag fixes this issue via these specific changes: + +1. Calculate btran in SoilMoistStressMod.F90 regardless of + use_hydrstress + +2. Comment on the applicability of this calculation and that of rootr in + SoilMoistStressMod.F90 + +3. Add the following comment to uses of rootr and rootr_col throughout + the code: "SMS method only" + +4. Allow ROOTR_COL history field only if use_hydrstress = .false. + +5. Remove the calculation of rootr_col in subroutine + Compute_EffecRootFrac_And_VertTranSink_HydStress within module + SoilWaterPlantSinkMod.F90 since that calculation is invalid for PHS. + +6. Normalize root resistances for pervious road over nlevgrnd, not + nlevsoi + +Note that the rootr calculation is done using the non-PHS (i.e., SMS) +method. So rootr is not really consistent with PHS; this is something +that should probably be revisited later. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#812 (Problems with rootr when use_hydrstress=.true.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: not checked; none expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Clm50Bgc (cases with both use_hydrstress=.true. and methane active) + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff / same climate + + For details on differences, see + https://github.com/ESCOMP/CTSM/issues/812#issuecomment-547924289 + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: + http://webext.cgd.ucar.edu/I20TR/clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist/lnd/clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist.1995_2014-clm50_ctsm10d074_2deg_GSWP3V1_hist.1995_2014/setsIndex.html + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev077 +Originator(s): sacks (Bill Sacks) +Date: Sun Oct 27 16:23:39 MDT 2019 +One-line Summary: Consistently use frac_sno_eff rather than frac_sno in qg calculations + +Purpose of changes +------------------ + +Consistently use frac_sno_eff rather than frac_sno in qg calculations + +The change here only changes answers for (1) urban pervious road, and +(2) more broadly with use_subgrid_fluxes = .false. + +Previously, code in CalculateSurfaceHumidity was inconsistent regarding +the use of frac_sno vs. frac_sno_eff. I wanted to make this consistent +to facilitate upcoming cleanup of CalculateSurfaceHumidity. I went back +and forth as to which one we should use here. (See also +https://github.com/ESCOMP/CTSM/issues/822). + +Argument for frac_sno_eff: This is consistent with the use of +frac_sno_eff elsewhere in the calculation of surface fluxes. + +Argument for frac_sno: Even in CLM4.0 (prior to the introduction of +frac_sno_eff and frac_h2osfc), frac_sno was used to calculate surface +relative humidity. That makes me think that the parameterizations were +improved by using frac_sno here, even though frac_sno at that point was +mainly just used for albedo / radiation calculations. So sticking with +frac_sno would be more consistent with what has been done for a long +time, and would presumably be a bit better scientifically. + +However, when I tried changing this to use frac_sno rather than +frac_sno_eff: + + qg(c) = frac_sno_eff(c)*qg_snow(c) + (1._r8 - frac_sno_eff(c) - frac_h2osfc(c))*qg_soil(c) & + + frac_h2osfc(c) * qg_h2osfc(c) + +I got a crash with use_subgrid_fluxes false (test +SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm45BgcCropQianRsGs.bishorn_gnu.clm-no_subgrid_fluxes), +due to a check I put in relatively recently to ensure that the top-layer +soil liquid never goes significantly negative: + +WJS 218: frac_sno, frac_sno_eff, frac_h2osfc, snl = 6.6447358408778726E-005 1.0000000000000000 0.0000000000000000 -1 + qg_snow, qg_soil, qg_h2osfc, qg = 3.8414454029812475E-003 3.6634834595404343E-003 3.6635176705822736E-003 3.6634952846414733E-003 + ERROR: In UpdateState_TopLayerFluxes, h2osoi_liq has gone significantly negative + Bulk/tracer name = bulk + c, lev_top(c) = 218 0 + h2osoi_liq_top_orig = 6.6448689668604415E-004 + h2osoi_liq = -2.6754040213948407E-004 + frac_sno_eff = 1.0000000000000000 + qflx_liq_grnd*dtime = 0.0000000000000000 + qflx_dew_grnd*dtime = 0.0000000000000000 + qflx_evap_grnd*dtime = 9.3202729882552822E-004 + ENDRUN: + ERROR: In UpdateState_TopLayerFluxes, h2osoi_liq has gone significantly negative + +What seems to be going on is: With a little bit of snow present, when I +use frac_sno rather than frac_sno_eff, we end up with a qg value very +close to that of soil. But I think the later evaporation happens from +the snow, at which point I guess the dryer air above leads to there +being too large evaporation from the snow. + +So in the end, I decided to consistently use frac_sno_eff, even though +this might be a small step backwards in terms of the accuracy of surface +humidity for urban pervious road and with use_subgrid_fluxes = .false. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self (but approved conceptually by Sean Swenson and +Keith Oleson) + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Expected to be larger than roundoff/same climate, but not + investigated carefully + + For the default configuration with use_subgrid_fluxes = .true., + differences are restricted to urban pervious road. I spot-checked + a few tests to ensure that we only saw differences in FSH for + urban landunits; this was generally true, with the exception of + ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput, + which also had differences over crop and natural veg + landunits. This spillover effect seems to be related to the + non-local interactions that arise from methane's dependence on + TWS, though I don't understand why I only saw this in a transient + case, and not in similar non-transient cases. See + https://github.com/ESCOMP/CTSM/issues/658#issuecomment-546740771 + for more details. + + For the non-default use_subgrid_fluxes = .false., there + differences in the natural vegetation and crop landunits, too. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev076 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 25 16:04:20 MDT 2019 +One-line Summary: Set frac_sno_eff=0 if frac_sno is 0; avoid unnecessary calls to QSat + +Purpose of changes +------------------ + +Two changes that are bit-for-bit except for changes in the FSNO_EFF +diagnostic field, both with an eye towards cleaning up +SurfaceHumidityMod in preparation for adding water tracers to that +module: + +(1) Set frac_sno_eff to 0 if frac_sno is 0. Previously, for cases where + frac_sno_eff was a binary 0/1 rather than being set equal to + frac_sno, frac_sno_eff was always being set to 1, even if there was + no snow. Sean Swenson thinks that didn't matter, but I found it + confusing, and it could be more problematic with some upcoming + changes I plan to make (where I'm going to use frac_sno_eff as a + weighting factor in calculating qg terms, including for landunits + that use a binary 0/1 frac_sno_eff.) + +(2) Avoid unnecessary calls to QSat, since this function is relatively + expensive. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: No substantial changes; from a +single run of PFS_Ld20.f09_g17.I2000Clm50BgcCrop.cheyenne_intel, max +timing of the main changed section (bgp1) decreased by about 10%; this +may be within machine variability, though. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answer changes as expected just for FSNO_EFF + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but just for the diagnostic field FSNO_EFF + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + diagnostic only: just changes FSNO_EFF + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev075 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 25 15:44:52 MDT 2019 +One-line Summary: Lakes: Adjust frac_sno after updating 0-layer snow pack for dew & sublimation + +Purpose of changes +------------------ + +Main change is: for lakes, possibly adjust frac_sno after updating +0-layer snow pack for dew & sub, ensuring that zero vs. non-zero values +of frac_sno agree with whether the snow pack has zero or non-zero +amounts of snow. The main motivation for this is to ensure that, if we +have any snow, then frac_sno should be non-zero. Along with this, I'm +also ensuring that, if we go down to 0 snow, then we also go down to 0 +frac_sno. + +A related change was to move the code ensuring that h2osno_no_layers +doesn't go negative: I have moved this to before h2osno_no_layers is +referenced, to assure we don't get a slightly negative snow depth. (I +haven't noticed any problems due to the old placement, but it seems +safer to put the limiting before the reference to h2osno_no_layers.) + +Also, an unrelated change in run_sys_tests: Add option for rerunning +existing failed tests. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#827 (Lake frac_sno can remain 0 even when there + is some snow addition from frost) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: None expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - pass (on my mac: 'make test' with python2 & python3 and 'make lint') + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Expected to be larger than roundoff/same climate + + Changes are introduced only over lake columns, and these changes + should be small, since they only relate to the setting of frac_sno + when there is dew or sublimation on a very thin snow + pack. + + Although the direct changes should only affect lakes, I did + observe changes in crop columns in a transient test that I + spot-checked + (ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput) + - maybe due to some of the non-local interactions in + https://github.com/ESCOMP/CTSM/wiki/Parameterizations-that-can-cause-nonlocal-interactions, + or maybe due to some other non-local interaction, either known or + buggy. (In non-transient tests that I spot checked + (ERP_P72x2_Lm36.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-clm50cropIrrigMonth_interp + and + SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput): + diffs in FSH in h1 file are just over lake landunits, as + expected.) + + Update: it seems that these changes in crop columns arise from + the nonlocal interactions caused by the dependence of methane + on TWS, though I don't understand why I only saw this in a + transient case, and not in similar non-transient cases. See + https://github.com/ESCOMP/CTSM/issues/658#issuecomment-546740771 + for more details. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev074 +Originator(s): sacks (Bill Sacks) +Date: Wed Oct 23 19:25:21 MDT 2019 +One-line Summary: For lakes: when reading finidat, set frac_sno=1 if h2osno_total > 0 + +Purpose of changes +------------------ + +Due to ESCOMP/ctsm#783, frac_sno used to be 0 for all lake points. That +was mostly fixed, but the issue is still present on initial conditions +files that were generated prior to that fix (which includes most or all +of our out-of-the-box restart files). This causes frac_sno to be 0 for +lake points at the start of the simulation, even if there is a snow pack +present. Currently this doesn't cause significant problems, but I'd like +to change the calculation of frac_sno_eff so that it is 0 if frac_sno is +0 - and then this frac_sno problem becomes an issue (causing divide by 0 +in at least one place). + +However, further problems were introduced if I tried to always apply +this correction: It appears that sometimes the restart file legitimately +has frac_sno == 0 for lake columns with non-zero snow cover. To avoid +changing answers for newer restart files, I am writing metadata to the +restart file documenting whether the fix has already been applied on +that restart file, and if so, we avoid reapplying the fix. + +Getting this restart metadata correct was tricky, especially when +running init_interp. I have introduced a new module to encapsulate this +complexity. This can be used in general for writing / reading metadata +on which issues have been fixed on a given restart file. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): [If none, remove this line] +- Resolves ESCOMP/ctsm#783 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- The setting of initial lake frac_sno to 1 isn't exactly correct, but + it's better than the old value of 0. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +- I didn't check the PFS test, but the only change that could have + likely led to performance changes was the addition of a metadata copy + in init_interp. I checked the timing of this piece, and found it to be + a negligible portion of the total init_interp time + (https://github.com/ESCOMP/CTSM/pull/825#issuecomment-545219601). + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek gave this an initial look and gave general +approval for the restart file metadata mechanism I have added. He may +give it a more careful look, possibly accompanied by a further cleanup +tag addressing any issues he finds. + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests passed, baselines fail as expected. + + Note that the FUNIT test failed initially; I got it passing on my + Mac, but didn't rerun it on cheyenne. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + The only change is in initial lake frac_sno. This should only + affect the start of the simulation, and only over lake points. I + verified that changes are only over lake points via: For both + SMS_D_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default (which + doesn't use init_interp) and + SMS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_gnu.clm-default + (which uses init_interp): I checked which points have differences + in FSH in the h1 (vector) history file. Diffs were only over lake + points. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/825 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev073 +Originator(s): sacks (Bill Sacks) +Date: Tue Oct 22 06:14:24 MDT 2019 +One-line Summary: Fix bug in calculation of dqgdT + +Purpose of changes +------------------ + +The calculation of dqgdT, which gives the derivative, d(qg)/dT, was +incorrect for soil/crop landunits when there is no snow. This tag fixes +that bug. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#824 (dqgdT incorrect when there is no snow) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: not checked, but none expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson reviewed and approved my plan, though not the final code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + I checked the impact from one-day averages in test + SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm50BgcCropQianRsGs.bishorn_gnu.clm-default, + by looking at differences in EFLX_LH_TOT. The impact is small: + daily-average differences in that variable are typically 0.01 W + m-2 or less; most grid cells have significantly less difference + than that; only one or a few f10 grid cells have significantly + greater differences, with the biggest difference being about 0.1 W + m-2. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev072 +Originator(s): mvertens (Mariana Vertenstein) +Date: Tue Oct 15 09:41:50 MDT 2019 +One-line Summary: Add NUOPC cap + +Purpose of changes +------------------ + +Add NUOPC cap in order to run with the new NUOPC driver/mediator. There +was some code movement / refactoring of existing code to support this, +with the biggest change being the introduction of a new subdirectory +under src/cpl. + +Most changes are from Mariana Vertenstein and Jim Edwards. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- NUOPC cap currently does not have any tests in the aux_clm test suite +- There are currently no tests ensuring that the nuopc and mct caps give + bit-for-bit answers, though the nuopc_cap_bfb testmod could be used to + support such a test + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- mosart: mosart1_0_33 -> mosart1_0_34 (supports nuopc cap) + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev071 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 11 07:03:40 MDT 2019 +One-line Summary: Split CanopyTemperature into separate pieces + +Purpose of changes +------------------ + +CanopyTemperature was doing a few unrelated things, none of which +actually had anything to do with calculating canopy temperature. At the +driver level, I have split CanopyTemperature into BiogeophysPreFluxCalcs +and CalculateSurfaceHumidity. BiogeophysPreFluxCalcs calls out to a +number of separate routines, some in that same module and some +elsewhere, including a new routine in FrictionVelocityMod. + +Also some minor related cleanup, including + +- Made FrictionVelocityMod object-oriented + +- A bit of rework of how qflx_evap_veg and qflx_tran_veg are set. This + changes answers for the (default inactive) QFLX_EVAP_VEG history field + (see also ESCOMP/ctsm#816). + +- Removed qsat conditionals that should never be invoked + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#816 (QFLX_EVAP_VEG should be 0 over lakes) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but only for the +(default-inactive) field QFLX_EVAP_VEG + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff, but only for the default-inactive field QFLX_EVAP_VEG + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev070 +Originator(s): sacks (Bill Sacks) +Date: Wed Oct 9 06:16:39 MDT 2019 +One-line Summary: Fix for writing 0-d variables with PIO2 + +Purpose of changes +------------------ + +Previously, there were problems when writing 0-d (scalar) variables with +PIO2 in DEBUG mode. This change fixes that issue. + +Jim Edwards put in place an initial fix; I put in place the final fix +based on changes Mariana Vertenstein made in MOSART. I have not tested +this with PIO2, but am hopeful that it fixes the PIO2 problem since the +similar MOSART changes fixed that problem. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self; earlier version reviewed by Erik Kluzek and Mariana Vertenstein + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/810 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev069 +Originator(s): sacks (Bill Sacks) +Date: Mon Oct 7 10:22:22 MDT 2019 +One-line Summary: Misc. code cleanup and minor bug fixes + +Purpose of changes +------------------ + +Resolve a variety of "simple bfb" issues. Note that some of these result +in answer changes for select diagnostic fields. See specific notes below +for details, under "Issues fixed" and answer changes. + +The fix for ESCOMP/ctsm#27 changes answers for some diagnostic fields, +as noted below. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#27 (BTRAN should be spval over all special + landunits) + - Also fixed some related fields, as noted below, under answer changes + +- Resolves ESCOMP/ctsm#31 (some CLM history fields don't restart + properly) + - This was mostly resolved previously; here I just did some final + cleanup and fixing of NFIRE + +- Resolves ESCOMP/ctsm#48 (code for initializing some isotope carbon + state variables looks wrong) + - Removed the incorrect code, which was never being exercised + +- Resolves ESCOMP/ctsm#58 (Change SHR_ASSERT calls to avoid using + errMsg) + - Purpose was to speed up DEBUG runs on some machines/compilers + +- Resolves ESCOMP/ctsm#111 (Precision of constants in + SoilTemperature.F90 is not double) + - No answer changes, because 1 (single prec) = 1 (double prec) + +- Resolves ESCOMP/ctsm#334 (Introduce a new activelayer_type) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: potentially speeds up debug runs on some machines/compilers + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, some baseline comparisons fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but just for select diagnostic fields + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Greater than roundoff, but only in select diagnostic field - no impact on climate + + There were changes in the following diagnostic fields, which are + now averaged over only vegetated landunits (see ESCOMP/ctsm#27): + - BTRAN + - BTRANMN + - RSSHA + - RSSUN + - ROOTR (inactive by default) + - ROOTR_COLUMN (inactive by default) + - RRESIS (inactive by default) + + Changes are also possible in rare circumstances for the NFIRE + diagnostic field, in transient cases, although no differences were + observed for this field in the test suite (see ESCOMP/ctsm#31). + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev068 +Originator(s): sacks (Bill Sacks) +Date: Mon Sep 30 09:57:04 MDT 2019 +One-line Summary: Add water tracers to CombineSnowLayers, DivideSnowLayers, ZeroEmptySnowLayers + +Purpose of changes +------------------ + +Add water tracers to CombineSnowLayers, DivideSnowLayers and +ZeroEmptySnowLayers. This completes the tracerization of the core snow +code: most or all of the code in SnowHydrologyMod is now tracerized. + +In contrast to most routines that I have tracerized, the tracerization +of these routines is done by embedding loops over tracers inside +existing code structures, rather than splitting out separate routines +that operate on bulk or tracer quantities. This is because (1) it didn't +make sense to introduce explicit fluxes for the state updates done here, +so we didn't have the extra need of having separate routines for flux +calculations vs. state updates; (2) the state updates were embedded in +loops over levels and conditionals in a way that would have been awkward +and messy to try to separately update bulk-and-tracer quantities +(h2osoi_liq, h2osoi_ice, etc.) from bulk-only quantities (dz, etc.). + +Also, a bit of reordering of LakeHydrologyMod in order to keep the snow +code more together. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#778 (Implement water tracers for combining and + dividing snow layers) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: I don't think so + Based on the changes introduced, I expect *very* small increases in + runtime of the modified routines (which would show up in the + hydro_without_drainage timer), even for cases without water tracers, + but I wouldn't expect this to have a significant impact. From PFS + test, and specifically looking at the timing of + hydro_without_drainage in that test, I see a possible small increase + (a few percent) in the timing of that section, though the differences + are within typical machine variability, so don't seem necessarily + significant. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev067 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Thu Sep 26 15:02:39 MDT 2019 +One-line Summary: Add config_archive.xml to CTSM cime_config -- no testing + +Purpose of changes +------------------ + +Add config_archive.xml to cime_config for CTSM. Update the CODE_OF_CONDUCT +to the August/2019 UCAR version. + +No testing done. + +Bugs fixed or introduced +------------------------ + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self + + +CTSM testing: doc (no standard testing done) + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + src unit-tests: + + cheyenne - PASS + + regular tests (aux_clm): None + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: No! + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): None +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev066 +Originator(s): sacks (Bill Sacks) +Date: Fri Sep 20 09:07:23 MDT 2019 +One-line Summary: Add water tracers to SnowCapping + +Purpose of changes +------------------ + +Update water tracer terms in SnowCapping. As I have done elsewhere, this +has involved splitting each piece of SnowCapping into its own subroutine, +which operates either on bulk, tracers, or bulk + tracers. + +This is supported by calls to ResetCheckedTracers prior to the call to +SnowCapping, since some intervening code is not yet tracerized. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#777 (Implement water tracers for SnowCapping) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + Small increase in total runtime of PFS test, but the relevant timing + section, hydro_without_drainage, took slightly *less* time compared + with the last tag. + + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev065 +Originator(s): sacks (Bill Sacks) +Date: Sat Sep 14 12:52:42 MDT 2019 +One-line Summary: Add water tracers to SnowWater + +Purpose of changes +------------------ + +Update water tracer terms in SnowWater. As I have done elsewhere, this +has involved splitting each piece of SnowWater into its own subroutine, +which operates either on bulk, tracers, or bulk + tracers. + +This is supported by calls to ResetCheckedTracers prior to the call to +SnowWater, since some intervening code is not yet tracerized. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#776 (Implement water tracers for SnowWater) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, baselines fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Roundoff level: answer changes just arise because I have made + qflx_snow_percolation_col a true flux, with units of + per-unit-time; this involved dividing by dtime, and later + multiplying by dtime when it is applied to states. Previously, the + corresponding variable (qout / qin) was not per-unit-time. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I ran comparisons against a version off of master that had the + minimal changes to exhibit these roundoff-level changes. Diffs for + this are below. My branch is bit-for-bit with this version. + + diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 + index cad47e28..0abcc49f 100644 + --- a/src/biogeophys/SnowHydrologyMod.F90 + +++ b/src/biogeophys/SnowHydrologyMod.F90 + @@ -1140,17 +1140,17 @@ subroutine SnowWater(bounds, & + c = filter_snowc(fc) + if (j >= snl(c)+1) then + + - h2osoi_liq(c,j) = h2osoi_liq(c,j) + qin(c) + + h2osoi_liq(c,j) = h2osoi_liq(c,j) + qin(c)*dtime + + - mss_bcphi(c,j) = mss_bcphi(c,j) + qin_bc_phi(c) + - mss_bcpho(c,j) = mss_bcpho(c,j) + qin_bc_pho(c) + - mss_ocphi(c,j) = mss_ocphi(c,j) + qin_oc_phi(c) + - mss_ocpho(c,j) = mss_ocpho(c,j) + qin_oc_pho(c) + + mss_bcphi(c,j) = mss_bcphi(c,j) + qin_bc_phi(c)*dtime + + mss_bcpho(c,j) = mss_bcpho(c,j) + qin_bc_pho(c)*dtime + + mss_ocphi(c,j) = mss_ocphi(c,j) + qin_oc_phi(c)*dtime + + mss_ocpho(c,j) = mss_ocpho(c,j) + qin_oc_pho(c)*dtime + + - mss_dst1(c,j) = mss_dst1(c,j) + qin_dst1(c) + - mss_dst2(c,j) = mss_dst2(c,j) + qin_dst2(c) + - mss_dst3(c,j) = mss_dst3(c,j) + qin_dst3(c) + - mss_dst4(c,j) = mss_dst4(c,j) + qin_dst4(c) + + mss_dst1(c,j) = mss_dst1(c,j) + qin_dst1(c)*dtime + + mss_dst2(c,j) = mss_dst2(c,j) + qin_dst2(c)*dtime + + mss_dst3(c,j) = mss_dst3(c,j) + qin_dst3(c)*dtime + + mss_dst4(c,j) = mss_dst4(c,j) + qin_dst4(c)*dtime + + if (j <= -1) then + ! No runoff over snow surface, just ponding on surface + @@ -1167,8 +1167,8 @@ subroutine SnowWater(bounds, & + qout(c) = max(0._r8,(vol_liq(c,j) & + - ssi*eff_porosity(c,j))*dz(c,j)*frac_sno_eff(c)) + end if + - qout(c) = qout(c)*1000._r8 + - h2osoi_liq(c,j) = h2osoi_liq(c,j) - qout(c) + + qout(c) = (qout(c)*1000._r8)/dtime + + h2osoi_liq(c,j) = h2osoi_liq(c,j) - qout(c)*dtime + qin(c) = qout(c) + + ! mass of ice+water: in extremely rare circumstances, this can + @@ -1187,7 +1187,7 @@ subroutine SnowWater(bounds, & + if (qout_bc_phi(c) > mss_bcphi(c,j)) then + qout_bc_phi(c) = mss_bcphi(c,j) + endif + - mss_bcphi(c,j) = mss_bcphi(c,j) - qout_bc_phi(c) + + mss_bcphi(c,j) = mss_bcphi(c,j) - qout_bc_phi(c)*dtime + qin_bc_phi(c) = qout_bc_phi(c) + + ! BCPHO: + @@ -1196,7 +1196,7 @@ subroutine SnowWater(bounds, & + if (qout_bc_pho(c) > mss_bcpho(c,j)) then + qout_bc_pho(c) = mss_bcpho(c,j) + endif + - mss_bcpho(c,j) = mss_bcpho(c,j) - qout_bc_pho(c) + + mss_bcpho(c,j) = mss_bcpho(c,j) - qout_bc_pho(c)*dtime + qin_bc_pho(c) = qout_bc_pho(c) + + ! OCPHI: + @@ -1205,7 +1205,7 @@ subroutine SnowWater(bounds, & + if (qout_oc_phi(c) > mss_ocphi(c,j)) then + qout_oc_phi(c) = mss_ocphi(c,j) + endif + - mss_ocphi(c,j) = mss_ocphi(c,j) - qout_oc_phi(c) + + mss_ocphi(c,j) = mss_ocphi(c,j) - qout_oc_phi(c)*dtime + qin_oc_phi(c) = qout_oc_phi(c) + + ! OCPHO: + @@ -1214,7 +1214,7 @@ subroutine SnowWater(bounds, & + if (qout_oc_pho(c) > mss_ocpho(c,j)) then + qout_oc_pho(c) = mss_ocpho(c,j) + endif + - mss_ocpho(c,j) = mss_ocpho(c,j) - qout_oc_pho(c) + + mss_ocpho(c,j) = mss_ocpho(c,j) - qout_oc_pho(c)*dtime + qin_oc_pho(c) = qout_oc_pho(c) + + ! DUST 1: + @@ -1223,7 +1223,7 @@ subroutine SnowWater(bounds, & + if (qout_dst1(c) > mss_dst1(c,j)) then + qout_dst1(c) = mss_dst1(c,j) + endif + - mss_dst1(c,j) = mss_dst1(c,j) - qout_dst1(c) + + mss_dst1(c,j) = mss_dst1(c,j) - qout_dst1(c)*dtime + qin_dst1(c) = qout_dst1(c) + + ! DUST 2: + @@ -1232,7 +1232,7 @@ subroutine SnowWater(bounds, & + if (qout_dst2(c) > mss_dst2(c,j)) then + qout_dst2(c) = mss_dst2(c,j) + endif + - mss_dst2(c,j) = mss_dst2(c,j) - qout_dst2(c) + + mss_dst2(c,j) = mss_dst2(c,j) - qout_dst2(c)*dtime + qin_dst2(c) = qout_dst2(c) + + ! DUST 3: + @@ -1241,7 +1241,7 @@ subroutine SnowWater(bounds, & + if (qout_dst3(c) > mss_dst3(c,j)) then + qout_dst3(c) = mss_dst3(c,j) + endif + - mss_dst3(c,j) = mss_dst3(c,j) - qout_dst3(c) + + mss_dst3(c,j) = mss_dst3(c,j) - qout_dst3(c)*dtime + qin_dst3(c) = qout_dst3(c) + + ! DUST 4: + @@ -1250,7 +1250,7 @@ subroutine SnowWater(bounds, & + if (qout_dst4(c) > mss_dst4(c,j)) then + qout_dst4(c) = mss_dst4(c,j) + endif + - mss_dst4(c,j) = mss_dst4(c,j) - qout_dst4(c) + + mss_dst4(c,j) = mss_dst4(c,j) - qout_dst4(c)*dtime + qin_dst4(c) = qout_dst4(c) + + end if + @@ -1280,9 +1280,9 @@ subroutine SnowWater(bounds, & + do fc = 1, num_snowc + c = filter_snowc(fc) + ! Qout from snow bottom + - qflx_snow_drain(c) = qflx_snow_drain(c) + (qout(c) / dtime) + + qflx_snow_drain(c) = qflx_snow_drain(c) + qout(c) + + - qflx_rain_plus_snomelt(c) = (qout(c) / dtime) & + + qflx_rain_plus_snomelt(c) = qout(c) & + + (1.0_r8 - frac_sno_eff(c)) * qflx_liq_grnd(c) + int_snow(c) = int_snow(c) + frac_sno_eff(c) & + * (qflx_dew_snow(c) + qflx_dew_grnd(c) + qflx_liq_grnd(c)) * dtime + + + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev064 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Mon Sep 9 13:14:51 MDT 2019 +One-line Summary: User defined top-two snow layers + +Purpose of changes +------------------ + + Instead of hardcoding, we now set: + + dzmin(1) = snow_dzmin_1 + dzmax_l(1) = snow_dzmax_l_1 + dzmax_u(1) = snow_dzmax_u_1 + dzmin(2) = snow_dzmin_2 + dzmax_l(2) = snow_dzmax_l_2 + dzmax_u(2) = snow_dzmax_u_2 + + where the right-hand-side variables get namelist-defined values and the + model calculates dzmin and dzmax_* for the remaining snow layers using + recursive formulas. The calculation is intended to match the previously + hardcoded values, except for the bottom snow layer when nlevsno < 12. + The bottom layer now always gets dzmax_* = huge(1._r8). The formulas + appear in a document titled "A firn model for CLM" that is linked to + #729. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #729 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist parameters for specifying the top-two snow layers: + snow_dzmin_1, snow_dzmax_l_1, snow_dzmax_u_1 + snow_dzmin_2, snow_dzmax_l_2, snow_dzmax_u_2 + +Changes made to namelist defaults (e.g., changed parameter values): + Introduced default values for the new parameters so as to maintain + same answers to within roundoff + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change: roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + Introduced temporary code to overwrite dzmin(j), dzmax_l(j), and + dzmax_u(j) with their original values when different by less than + 1e-13 from their original values for all but the bottom snow layer. + The bottom layer was left as dzmax_l = dzmax_u(j) = huge(1._8), i.e. + the new value. The test resulted in bit-for-bit same answers. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/792 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev063 +Originator(s): erik (Erik Kluzek) +Date: Thu Sep 5 21:28:02 MDT 2019 +One-line Summary: Two answer changing fixes (fire, DWT_SLASH) and fix for urban streams for Clm45 + +Purpose of changes +------------------ + +Fire bug fix and DWT_SLASH change and fix urban stream years for clm4_5. +The latitude used in an expression for Bgc-Fire model Li2016 (used in Clm50) +had latitude in degrees rather than in radians as it should have been. The +term is used for ignition and the cosine was being taken in degrees rather +than radians, hence the spatial pattern for ignition with latitude was incorrect. + +The history field DWT_SLASH_CFLUX was being calculated on the column, but +really should have been a patch level variable. In the same way other fields +were handled we made DWT_SLASH_CFLUX a grid-cell variable, and added +DWT_SLASH_CFLUX_PATCH on the patch level that could be added to output. The same +is true of the C13_ and C14_ versions of it. + +Clm45 was setting urbantv to year 2000, rather than 1850 or historical as it should +have. The urbantv file for Clm45 doesn't actually change, so this doesn't actually +make a difference. But, it does make the namelist look wrong. + +Note, that SP cases, Vic cases and Fates cases do NOT change answers. Or if fire is +off, or certain single-point cases. Some cold-start cases don't seem to be sensitive +to it either. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #175, #787, #780 + fixes #175 urban stream years for clm4_5 + fixes #787 DWT_SLASH field + fixes #780 Bug in CN Fire Li 2016 which used latitude in degrees rather than radians + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): Defaults for urbantv for clm4_5 + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self, @olywon + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (62 compare fail due to namelist changes) + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! + + Summarize any changes to answers, i.e., + - what code configurations: Clm50Bgc and some Clm45Bgc cases + - what platforms/compilers: All + - nature of change: similar climate (but fire ignition pattern changes by latitude) + DWT_SLASH_* history fields change because moved to gridcell quantity (so change is relatively minor) + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: + oleson/clm50_cesm20R_2deg_GSWP3V1_issue780_hist (for the fire change) + + URL for LMWG diagnostics output used to validate new climate: +http://webext.cgd.ucar.edu/I20TR/clm50_cesm20R_2deg_GSWP3V1_issue780_hist/lnd/clm50_cesm20R_2deg_GSWP3V1_issue780_hist.1995_2014-clm50_cesm20R_2deg_GSWP3V1_hist.1995_2014/setsIndex.html + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #802 +(https://github.com/ESCOMP/ctsm/pull) + #802 -- Three answer changing fixes (fire, DWT_SLASH, urban streams for clm4_5) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev062 +Originator(s): sacks (Bill Sacks) +Date: Tue Sep 3 16:04:28 MDT 2019 +One-line Summary: Move hobart tests to izumi + +Purpose of changes +------------------ + +Move all hobart testing to izumi. + + +Bugs fixed or introduced +------------------------ + +Known bugs introduced in this tag (include github issue ID): +- Recurrence of ESCOMP/ctsm#174 (ne30 case fails on hobart_nag due to floating overflow) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Testing should now be run on izumi, not hobart + +Changes to tests or testing: +- All hobart tests moved to izumi + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- not run + izumi ------- pass + + Also ran prealpha and prebeta tests that I moved from hobart to izumi. These passed except: + - ERP_D_Ld5.ne30_g16.I1850Clm50BgcCrop.izumi_nag.clm-default (#174) + - ERP_Ld5.f19_g17.I2000Clm50SpRtmFl.izumi_pgi.clm-default + - SMS_D_Ld1.f19_g17.I1850Clm45Cn.izumi_pgi.clm-default + + The last two failed with errors like: + + i011.unified.ucar.edu.44619hfi_userinit: mmap of status page (dabbad0008040000) failed: Operation not permitted + + I wonder if the issue is that multi-node pgi cases don't work on izumi? + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.3_chint17-04 -> cime5.8.3_chint17-05 + Minor change on izumi to allow using run_sys_tests + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev061 +Originator(s): erik (Erik Kluzek) +Date: Sun Sep 1 22:37:07 MDT 2019 +One-line Summary: Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated + +Purpose of changes +------------------ + +New clm5 paramsfile that has the bad date of 631 changed to 701. Along with some simple bit for +bit changes. Removing some problematic options. Making Dynamic Vegetation a deprecated option +that requires you to use -ignore_warnings with it. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #463 #79 #97 #98 #104 #122 #173 #794 #795 #796 + + Fixes #463 bad date on params file that didn't allow using ESMF library with Crop + Fixes #79 correct documentation of qflx_evap_tot + Fixes #97 remove override_nsrest + Fixes #98 add warning when using single instance of a startup file for multi-instance cases + Fixes #104 use get_step_size_real when putting into a real variable + Fixes #122 decomp pool arrays should not start at 0 but 1 + Fixes #173 remove psi_soil_ref as not used + Fixes #794 remove anoxia_wtsat + Fixes #795 Correct documentation of -light_res + Fixes #796 Deprecate Dynamic Vegetation + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Remove namelist items + Remove namelist items: anoxia_wtsat, override_nsrest + Turning dynamic Vegetation on, now displays a warning, and requires using -ignore_warnings in CLM_BLDNML_OPTS + +Changes made to namelist defaults (e.g., changed parameter values): New paramdata files + +Changes to the datasets (e.g., parameter, surface or initial files): + clm5 paramdata file has correct date for crop of 701 (rather than incorrect 631) + clm5 and clm4_5 paramdata file removed an unused variable + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: DV tests removed or changed + +Code reviewed by: self + +CTSM testing: regular + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (compare shows changes becausse of paramdata files) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +An additional fail is ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Clm50Cn.cheyenne_gnu.clm-default, because +of #798. Because it's an issue with cime, I'm not marking it as an expected error. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #797 +(https://github.com/ESCOMP/ctsm/pull) + + #797 -- Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev060 +Originator(s): sacks (Bill Sacks) +Date: Thu Aug 29 11:18:20 MDT 2019 +One-line Summary: In SnowWater, truncate small h2osoi residuals + +Purpose of changes +------------------ + +Previously, in the handling of sublimation and evaporation from the snow +pack, if these fluxes led to negative h2osoi_ice or h2osoi_liq, these +negative values would be passed down the snow pack until they found a +layer with a large enough positive state to absorb them. This logic was +going to be a challenge for adding water tracers. + +I have done some tests to verify that these negative values never exceed +roundoff-level in either an absolute or relative sense (with tolerance +of 1.e-13). Specifically, I ran the full aux_clm test suite with the +diffs below and verified that the endrun calls were never triggered. + +So here, I simplify this logic: After truncating any near-zero states to +exactly zero, I check to confirm that the states are never negative. I +then removed the code that passed these negative values down the snow +pack: if they are only roundoff-level negative, then it seems safe to +just throw them away rather than trying to handle them. + +Here were the diffs used to verify that the negative values are never +greater than roundoff-level; these endrun calls were never triggered in +a run of the full aux_clm test suite: + + diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 + index 3dd555cc..07776123 100644 + --- a/src/biogeophys/SnowHydrologyMod.F90 + +++ b/src/biogeophys/SnowHydrologyMod.F90 + @@ -970,6 +970,8 @@ subroutine SnowWater(bounds, & + real(r8) :: vol_ice(bounds%begc:bounds%endc,-nlevsno+1:0) ! partial volume of ice lens in layer + real(r8) :: eff_porosity(bounds%begc:bounds%endc,-nlevsno+1:0) ! effective porosity = porosity - vol_ice + real(r8) :: mss_liqice(bounds%begc:bounds%endc,-nlevsno+1:0) ! mass of liquid+ice in a layer + + real(r8) :: h2osoi_ice_orig + + real(r8) :: h2osoi_liq_orig + !----------------------------------------------------------------------- + + associate( & + @@ -1017,10 +1019,23 @@ subroutine SnowWater(bounds, & + c = filter_snowc(fc) + l=col%landunit(c) + + + h2osoi_ice_orig = h2osoi_ice(c,snl(c)+1) + + h2osoi_liq_orig = h2osoi_liq(c,snl(c)+1) + + + wgdif = h2osoi_ice(c,snl(c)+1) & + + frac_sno_eff(c) * (qflx_dew_snow(c) - qflx_sub_snow(c)) * dtime + h2osoi_ice(c,snl(c)+1) = wgdif + if (wgdif < 0._r8) then + + if (wgdif < -1.e-13_r8) then + + write(iulog,*) 'WJS: big abs wgdif ice: ', c, wgdif, h2osoi_ice_orig + + call endrun('WJS: big abs wgdif ice') + + end if + + if (h2osoi_ice_orig > 0._r8) then + + if (abs(wgdif / h2osoi_ice_orig) > 1.e-13_r8) then + + write(iulog,*) 'WJS: big rel wgdif ice: ', c, wgdif, h2osoi_ice_orig + + call endrun('WJS: big rel wgdif ice') + + end if + + end if + h2osoi_ice(c,snl(c)+1) = 0._r8 + h2osoi_liq(c,snl(c)+1) = h2osoi_liq(c,snl(c)+1) + wgdif + end if + @@ -1030,6 +1045,16 @@ subroutine SnowWater(bounds, & + + ! if negative, reduce deeper layer's liquid water content sequentially + if(h2osoi_liq(c,snl(c)+1) < 0._r8) then + + if (h2osoi_liq(c,snl(c)+1) < -1.e-13_r8) then + + write(iulog,*) 'WJS: big abs wgdif liq: ', c, h2osoi_liq(c,snl(c)+1), h2osoi_liq_orig + + call endrun('WJS: big abs wgdif liq') + + end if + + if (h2osoi_liq_orig > 0._r8) then + + if (abs(h2osoi_liq(c,snl(c)+1) / h2osoi_liq_orig) > 1.e-13_r8) then + + write(iulog,*) 'WJS: big rel wgdif liq: ', c, h2osoi_liq(c,snl(c)+1), h2osoi_liq_orig + + call endrun('WJS: big rel wgdif liq') + + end if + + end if + do j = snl(c)+1, 1 + wgdif=h2osoi_liq(c,j) + if (wgdif >= 0._r8) exit + +Bugs fixed or introduced +------------------------ + +None + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- It's possible that the extra error checks I have added (to ensure we + don't have greater-than-roundoff-level negative residuals) will be + triggered in rare circumstances in a production run, even though they + were never triggered in the test suite. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +Although there was a very small increase in total lnd run time, the +timing of hydro_without_drainage actually decreased slightly in the PFS +test relative to the last tag. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- It's possible that the extra error checks I have added (to ensure we + don't have greater-than-roundoff-level negative residuals) will be + triggered in rare circumstances in a production run, even though they + were never triggered in the test suite. + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests passed, some answer changes as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: potentially all, though only show up in + a few tests + - what platforms/compilers: potentially all, though only show up in + a few tests + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + First, I did some preliminary analyses as documented above, to + ensure that any negative residuals were no greater than roundoff. + + Second, note that the use of truncate_small_values can only + introduce roundoff-level changes (by truncating values that are + roundoff-level different from zero to exactly zero). + + Third, only a few tests showed answer changes, and these were only + in limited fields, and were fairly small RMS differences: + + ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput + ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic + ERS_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput + ERS_Ly5_P144x1.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput + + I actually expected more tests to show differences, but most tests + were bit-for-bit. I'm guessing this is because the code added a + roundoff-level term to a larger term, and this ended up not + changing the larger term. + + Finally, as an extra precaution, I ran the test suite twice, on + two different implementations of the truncation: the final one + (which uses truncate_small_values), and one in which I did the + truncation using custom, inline code (commit 0d21ccb5). These two + were bit-for-bit with each other, giving me more confidence that I + didn't make a mistake with either implementation. + + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev059 +Originator(s): sacks (Bill Sacks) +Date: Sat Aug 24 15:14:06 MDT 2019 +One-line Summary: Continue adding water tracers to LakeHydrology + +Purpose of changes +------------------ + +Finish implementing water tracers for initial snow-related code in +LakeHydrology. This involved refactoring code in order to reuse existing +code in SnowHydrology rather than having near-duplicates of that code in +LakeHydrology. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#775 (Implement water tracers for initial + snow-related code in LakeHydrology) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +Many tests took longer, including the PFS test. However, by looking at +more detailed timing numbers in the PFS test, the main increases in time +were in initialization and atm run: lnd run only showed a very small +increase. This suggests that glade slowness was probably primarily +responsible for the increased time. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: Increased allowed wallclock time for a few tests +These tests took longer, likely due to machine variability. Increasing +their wallclock time to prevent them from timing out. + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev058 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Thu Aug 22 10:02:49 MDT 2019 +One-line Summary: Soil texture interpolation bug-fix + +Purpose of changes +------------------ + + When assigning soil texture values from dataset soil levels to model + soil levels, we should be comparing zsoi (NOT zisoi) in the model with + zisoi on the file, i.e. we should be asking whether the node + center (NOT interface) of a given model level falls between two + interface depths on the file. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #772 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + Unexpected failure of test + SMS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency + Bill Sacks did some follow-up testing and concluded that this may be a + compiler-specific issue, so he changed the test from "nag" to "intel" + and generated the new test's corresponding baseline + +Code reviewed by: @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + Summarize any changes to answers, i.e., + - what code configurations: not clm45 + - what platforms/compilers: all + - nature of change: larger than roundoff/same climate + based on the assumption that shifting soil texture assignments by + one level in model soil levels below the top-most level should not + generate climate-changing differences. + +Detailed list of changes +------------------------ + 1. Changed zisoi to zsoi as described in the Purpose section above. + This caused the larger than roundoff changes. Before the fix some + model soil levels were getting assigned soil textures from a deeper + soil level in the dataset than they should. + 2. In the same section of code I completed the if-block to address all + zsoi vs. zisoifl comparisons. This ensures explicit assignment of + soil textures for all model soil levels and avoids leaving some + model soil levels with the texture assignment of the previous model + soil level. + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull/788) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev057 +Originator(s): sacks (Bill Sacks) +Date: Tue Aug 20 13:17:39 MDT 2019 +One-line Summary: Fix frac_sno bugs + +Purpose of changes +------------------ + +Two bug fixes related to frac_sno, and a third change involving +replacing a frac_sno calculation with a simpler equation that is +algebraically equivalent: + +(1) Fix lake frac_sno always being 0 + (https://github.com/ESCOMP/ctsm/issues/783). This fixes the albedo + calculation (and possibly others) over snow-covered lake surfaces. + +(2) Fix threshold for explicit snow pack initiation to use frac_sno_eff, + not frac_sno (https://github.com/ESCOMP/ctsm/issues/785). For + standard runs (which have use_subgrid_fluxes = .true.), this just + changes answers for urban columns. This also changes answers more + widely for runs with use_subgrid_fluxes = .false. + +(3) Rewrite Swenson & Lawrence 2012 frac_sno equation to be more + straightforward and less sensitive to roundoff errors + (https://github.com/ESCOMP/ctsm/issues/784) + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#783 (frac_sno is always 0 for lake points) +- Resolves ESCOMP/ctsm#785 (Threshold for explicit snow pack initiation + should use frac_sno_eff, not frac_sno) +- Resolves ESCOMP/ctsm#784 (Suggested algebraic rework of frac_sno + calculation) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + + Ran most testing on 95dad328 (before 8f1263a7, which removes a + temporary endrun error check). Just reran + SMS_Ld5_D_P48x1.f10_f10_musgs.IHistClm50Bgc.hobart_nag.clm-decStart + on the final version. + + There was a memleak for this test: + + FAIL SMS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency MEMLEAK memleak detected, memory went from 1250.830000 to 1518.500000 in 8 days + + I have had memleak issues for this test before + (https://github.com/ESCOMP/ctsm/issues/763), which I have chalked up + to a compiler-specific issue. I have simply increased the tolerance + for memleaks for this test moving forward. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff; expected to be same climate in general, + because the only impacts are on urban and lake points, which + represent a small fraction of most grid cells. However, this needs + further investigation. + + See above (under "Purpose of changes") for a description of the + different answer changes in this tag. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I verified that change (3) is no greater than roundoff by + temporarily putting in an endrun if the new frac_sno differs from + the old by more than 1e-13; this was not triggered for any test in + the aux_clm test suite. + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A (Keith Oleson will run this) + + URL for LMWG diagnostics output used to validate new climate: N/A (Keith Oleson will run this) + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev056 +Originator(s): sacks (Bill Sacks) +Date: Fri Aug 16 11:44:43 MDT 2019 +One-line Summary: Start adding water tracers to LakeHydrology, and related refactoring + +Purpose of changes +------------------ + +Start adding water tracers to LakeHydrology, beginning with some initial +things done for snow. + +This also includes some significant refactoring to allow LakeHydrology +to reuse some of the same snow code used for non-lake columns. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses ESCOMP/ctsm#775 (Implement water tracers for + initial snow-related code in LakeHydrology) + +Known bugs found since the previous tag (include github issue ID): +The following will be fixed in an upcoming tag: +- ESCOMP/ctsm#783 (frac_sno is always 0 for lake points) +- ESCOMP/ctsm#784 (Suggested algebraic rework of frac_sno calculation) +- ESCOMP/ctsm#785 (Threshold for explicit snow pack initiation should + use frac_sno_eff, not frac_sno) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + + Note: Did most testing on 054dc95b (before the small change in + 7e4e52a9); just ran + LWISO_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_gnu.clm-coldStart + on the final commit + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff + + There are two answer-changes here: + + (1) Roundoff-level changes due to changing some order of operations + for the updating of snow_depth and dz for lakes: The previous + code effectively used (qflx_snow_grnd(c)/bifall(c))*dtime, + whereas the new code uses (qflx_snow_grnd(c)*dtime)/bifall(c); + similarly, the dz update differs. + + (2) A change in FSNO_EFF for lakes: previously, this was set to 0 + when there was no snow. Now this is set consistently with other + landunits, for which it is 1 even if there is no snow. Note that + this only affects the FSNO_EFF diagnostic field, and nothing + else. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I confirmed that the order-of-operations change is the only + answer-changing part of this tag by comparing against a one-off + from master with the following diffs; this comparison was + bit-for-bit except for changes in the FSNO_EFF diagnostic field: + + diff --git a/src/biogeophys/LakeHydrologyMod.F90 b/src/biogeophys/LakeHydrologyMod.F90 + index 91ddfc79..9711dad7 100644 + --- a/src/biogeophys/LakeHydrologyMod.F90 + +++ b/src/biogeophys/LakeHydrologyMod.F90 + @@ -126,6 +126,8 @@ subroutine LakeHydrology(bounds, & + real(r8) :: heatsum(bounds%begc:bounds%endc) ! used in case above [J/m^2] + real(r8) :: snowmass ! liquid+ice snow mass in a layer [kg/m2] + real(r8) :: snowcap_scl_fct ! temporary factor used to correct for snow capping + + real(r8) :: temp_snow_depth + + real(r8) :: newsnow + real(r8), parameter :: snow_bd = 250._r8 ! assumed snow bulk density (for lakes w/out resolved snow layers) [kg/m^3] + ! Should only be used for frost below. + !----------------------------------------------------------------------- + @@ -246,8 +248,10 @@ subroutine LakeHydrology(bounds, & + ! U.S.Department of Agriculture Forest Service, Project F, + ! Progress Rep. 1, Alta Avalanche Study Center:Snow Layer Densification. + + - dz_snowf = qflx_snow_grnd(c)/bifall(c) + - snow_depth(c) = snow_depth(c) + dz_snowf*dtime + + temp_snow_depth = snow_depth(c) + + newsnow = qflx_snow_grnd(c)*dtime + + snow_depth(c) = snow_depth(c) + newsnow/bifall(c) + + dz_snowf = (snow_depth(c) - temp_snow_depth)/dtime + if (snl(c) == 0) then + h2osno_no_layers(c) = h2osno_no_layers(c) + qflx_snow_grnd(c)*dtime ! snow water equivalent (mm) + else + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev055 +Originator(s): sacks (Bill Sacks) +Date: Tue Aug 6 14:06:50 MDT 2019 +One-line Summary: Modularize snow cover fraction method + +Purpose of changes +------------------ + +This tag moves the calculation of frac_sno - and the related updates of +snow_depth - into a new set of classes, with one class for each +parameterization (Niu & Yang 2007 and Swenson & Lawrence 2012). + +Previously, the code always calculated frac_sno the new way, but then +possibly overwrote it if using the older Niu & Yang method. The new code +cleans this up, only doing the calculations that are needed for each +method. + +In addition, other code that is specific to one of the two methods is +now moved to a home that makes this dependence on method explicit. This +includes the addition of newsnow to int_snow: previously, int_snow was +always updated using an equation specific to the newer CLM5 +parameterization of frac_sno, which was not appropriate if using the Niu +& Yang parameterization; this doesn't make a difference currently, since +int_snow is only referenced if using the Swenson & Lawrence +parameterization, but this clears up some confusion. Also, time-constant +parameters read from namelist or the netCDF parameter file now reside in +the appropriate class rather than being more global. + +This tag also renames two namelist options to increase clarity: +- subgridflag is renamed to use_subgrid_fluxes, and is now a logical +- oldfflag is renamed to snow_cover_fraction_method, and is now a string + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#502 (oldfflag can NOT be used with + subgridflag==1, and rename subgridflag) +- Resolves ESCOMP/ctsm#503 (Clean up CanopyHydrology) + - This tag does the last piece of cleanup called for in that issue +- Resolves ESCOMP/ctsm#571 (Add a system test: turning on water isotopes + shouldn't change answers) + - This is unrelated to the other changes in this tag + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +This tag renames two namelist options to increase clarity: +- subgridflag is renamed to use_subgrid_fluxes, and is now a logical +- oldfflag is renamed to snow_cover_fraction_method, and is now a string + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Added a LWISO test, which confirms that turning on water isotopes + doesn't change answers for bulk +- Added a test with the newer snow cover fraction method but + use_subgrid_fluxes false (testmod no_subgrid_fluxes) + +Code reviewed by: Sean Swenson, Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + Tests pass; baseline comparisons not done (baseline comparisons + expected to differ) + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + + Additional tests: Compared both of these against ctsm1.0.dev052 (which + should be bit-for-bit with ctsm1.0.dev054): Both were bit-for-bit: + + ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes + This is a new test, so did not have baselines; I created baselines + from ctsm1.0.dev052 and compared against those + SMS_Ly3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_intel.clm-oldhyd_monthly + This was a temporary test for the sake of running a longer test with + the oldhyd testmod. This testmod was created as a one-off by + changing the current oldhyd testmod to inherit from monthly rather + than default. I ran baselines like this from ctsm1.0.dev052 then ran + this test from this branch and compared against those baselines. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/769 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev054 +Originator(s): sacks (Bill Sacks) +Date: Fri Aug 2 07:57:51 MDT 2019 +One-line Summary: Fix interpolation of surfdat soil layers so we can use interpolation for 10SL case + +Purpose of changes +------------------ + +Previously, on master, there was special-purpose code for the 10SL case +that avoided doing interpolation from the surface dataset to the soil +variables in the model. It would be cleaner - especially now that we +allow user-defined soil layer structures - if we could use the general +interpolation code always, rather than sometimes having special-purpose +code that avoids doing the interpolation. + +This tag accomplishes that generality. In order to preserve answers for +clm45 cases, I needed to make three changes: + +1. The constant 0.025 needed an _r8 appended to it; otherwise, zisoifl + could differ by roundoff from zisoi. + +2. I changed which level is used when zisoi(lev) is exactly equal to + zisoifl(j) for some j: I changed the conditional in the following: + + if (zisoi(lev) >= zisoifl(j) .AND. zisoi(lev) < zisoifl(j+1)) then + clay = clay3d(g,j+1) + sand = sand3d(g,j+1) + om_frac = organic3d(g,j+1)/organic_max + endif + + to: + + if (zisoi(lev) > zisoifl(j) .AND. zisoi(lev) <= zisoifl(j+1)) then + + Previously, when the zisoi values in the model exactly lined up with + the zisoi values in the file, we would set clay in model level j + equal to the value from level j+1 from the surface dataset (and + similarly for sand and om_frac); in the new code, we use level j from + the surface dataset for model level j in this case. + +3. I changed the way zisoifl is calculated for the lowest layer, so that + it matches zisoi(nlevsoi) when running with 10SL_3.5m. Previously, we + had: + + zisoi(10) = 0.38018819123227207690E+01 + zisoifl(10) = 0.34330930154359391437E+01 + + This tag changes zisoifl(10) to match zisoi(10). + +Bugs fixed or introduced +------------------------ + +Known bugs found since the previous tag (include github issue ID): +- #772: Interpolation of clay, sand and om_frac can use the wrong layer + (points out more fundamental issues with this interpolation of layers + from the surface dataset) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sam Levis + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (but see note below) + + In principle, the changes in this tag could change answers for some + soil layer structures, but there were no answer changes for any of + the cases covered by the test suite. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/771 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev053 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Thu Aug 1 16:56:09 MDT 2019 +One-line Summary: Soil layer definition clean-up and user-defined option + +Purpose of changes +------------------ + + Code clean-up clarifes that there are two types of soil layer + definition: the node-based and the thickness-based. + + User-defined option allows user to specify a soil layer profile in the + form of a dzsoi vector (values in meters) in the thickness-based + approach. + + Default nlevsoi for NWP configurations had to change from 5 to 4 for + consistency with the new error check described in known bugs below. + + Other code clean-up removes a couple of sections of repeating code. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #279 #728 + +Known bugs found since the previous tag (include github issue ID): + #759 (this PR) bug causes model to abort when nlevsoi = nlevgrnd; + bug has been corrected with an error check + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[X] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + if neither soil_layerstruct_predefined nor soil_layerstruct_userdefined + get specified in the namelist, then the model sets + soil_layerstruct_predefined to the old default setting for + soil_layerstruct (clm5: 20SL_8.5m, clm4.5: 10SL_3.5m) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + renamed soil_layerstruct to soil_layerstruct_predefined and added + soil_layerstruct_userdefined + +Changes made to namelist defaults (e.g., changed parameter values): + Default nlevsoi for NWP configurations had to change from 5 to 4 for + consistency with the new error check described in known bugs below + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers +-------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + 1) New test... + ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Ctsm50NwpBgcCropGswpGs.cheyenne_intel.clm-default + replaces existing test + ERS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-rm_indiv_lunits_and_collapse_to_dom + to check the correction described in known bugs above; the new test + together with existing unit tests cover what the old test was testing + + 2) New test and new test type... + SOILSTRUCTUD_Ld5.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-default + ensures that soil_layerstruct_userdefined gives bfb same answers as + soil_layerstruct_predefined = '4SL_2m' when set with the same dzsoi + values. The new test type was put together by: + - listing the test in (1) testlist_clm.xml (as all tests) and (2) config_tests.xml + - creating the file .../cime_config/SystemTests/soilstructud.py named after the test in lower case + +Code reviewed by: @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (just for NWP configurations) + + Summarize any changes to answers, i.e., + - what code configurations: nwp + - what platforms/compilers: all + - nature of change: larger than roundoff/same climate + This is due to the change of nlevsoi from 5 to 4 (more info above). + I confirmed that nwp does return bfb same answers when I revert this + change. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/759 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev052 +Originator(s): sacks (Bill Sacks) +Date: Mon Jul 22 14:02:43 MDT 2019 +One-line Summary: Fix rare soil color bug in mksurfdata_map + +Purpose of changes +------------------ + +Under rare conditions, mksurfdata_map could put the default soil color +in an output cell where there is actually more information. This tag +fixes that issue. None of the out-of-the-box surface datasets are +impacted by this bug, so I have not recreated any surface datasets. (I +checked all out-of-the-box surface datasets except for +surfdata_0.125x0.125_mp24_simyr2000_c150114.nc, because it doesn't get +remade cleanly out of the box.) + +Also: + +- Add some unit tests for the creation of soil color in mksurfdata_map + +- Point to correct (existing) surface dataset for year-1850 at f05 + resolution + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#4 (Minor bug in creation of soil color in + mksurfdata_map: points can be given the default soil color, when they + should have a real color) +- Resolves ESCOMP/ctsm#765 (Year-1850 f05 surface dataset missing from + inputdata repository) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- Year-1850 f05 surface dataset now points to a file that actually exists + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - ok + + Most tests pass, including baseline comparisons. The following tests fail, but also failed for me on master: + + 019 smiS4 TSMscript_tools.sh ncl_scripts getregional_datasets.pl getregional ....................\c + rc=6 FAIL + 020 bliS4 TBLscript_tools.sh ncl_scripts getregional_datasets.pl getregional ....................\c + rc=4 FAIL + 027 smf84 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c + rc=6 FAIL + 028 blf84 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c + rc=4 FAIL + 029 smfc4 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c + rc=6 FAIL + 030 blfc4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c + rc=4 FAIL + 031 smfg4 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Global_clm4_5^buildtools .............\c + rc=6 FAIL + 032 blfg4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Global_clm4_5^buildtools .............\c + rc=4 FAIL + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- not run + hobart ------ not run + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev051 +Originator(s): sacks (Bill Sacks) +Date: Fri Jul 19 13:26:25 MDT 2019 +One-line Summary: Update water tracers for remainder of first stage of hydrology + +Purpose of changes +------------------ + +Main change is to do tracer updates for final pieces of first stage of +hydrology: HandleNewSnow and UpdateFracH2oSfc. Along with this, I have +introduced greater modularity into these routines (breaking the +operations down into more granular steps). + +Other changes included here (somewhat related to the main changes) are: + +- Added a routine that resets checked tracers to bulk*ratio to allow + running the tracer consistency check for more than one time step; we + now run it for 10 days + +- Change logic for rain-snow conversion terms: Use rain diff in rain to + snow, snow diff in snow to rain. This is less sensitive to roundoff + errors, and was needed in order to get the 10-day tracer consistency + test to pass. + +- Setting of qflx_snow_h2osfc moved to CanopyInterceptionAndThroughfall + +- Add col%lun_itype. col%lun_itype(ci) is the same as + lun%itype(col%landunit(ci)), but is often a more convenient way to + access this type. I got tired of having to get the landunit index just + for the sake of getting the landunit's type of a given column. I have + NOT gone through the code and replaced lun%itype(l) with + col%lun_itype(c) where applicable, but this will be useful for the + future. + +- Removed unnecessary code for backwards compatibility of FH2OSFC from + restart files + +- Point to slightly modified initial conditions files for two CLm45 + initial conditions files. These two had FH2OSFC > 0 for some glc_mec + points. I'm not sure how that came to be, but Sean Swenson and I think + that shouldn't be the case. This caused soil balance errors in these + tests: + + ERS_Ly5_P72x1.f10_f10_musgs.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput + SMS_D_Ld1.f09_g17.I1850Clm45BgcCruGs.cheyenne_intel.clm-default + + I'm fixing the problem by pointing to updated files with FH2OSFC set + to 0 for special landunits, using the following python: + + ctypel = dat.variables['cols1d_ityplun'][:] + dat.variables['FH2OSFC'][ctypel > 2] = 0 + +- Small cime update to fix the SHAREDLIBBUILD phase of + ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#718 (Implement water tracers for HandleNewSnow + and FracH2oSfc) +- Resolves ESCOMP/ctsm#498 (Do tracer consistency checks every time + step, not just first) + +CIME Issues fixed (include issue #): +- ESCMI/cime#3717 (Cheyenne ESMF missing for WACCM X) + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/ctsm#762 (Water tracers: Make sure calls to ResetCheckedTracers + are removed) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- If you have an initial conditions file with non-zero FH2OSFC for + glacier (this was the case for some out-of-the-box clm45 files, which + are now fixed), may run into soil balance errors. To fix this, set + FH2OSFC to 0 in your restart file for all special landunits. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- Point to slightly modified initial conditions files for two CLm45 + initial conditions files: see above for details. + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Changed tracer consistency test to 10 days rather than a single time step + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, some roundoff-level diffs in baseline + comparisons, as noted below + + Also, in order to have a more powerful test of the changes in + SurfaceWaterMod (since the relevant code isn't triggered very often), + I introduced the following diffs: + + diff --git a/src/biogeophys/SurfaceWaterMod.F90 b/src/biogeophys/SurfaceWaterMod.F90 + index 1bc03cae..be656a15 100644 + --- a/src/biogeophys/SurfaceWaterMod.F90 + +++ b/src/biogeophys/SurfaceWaterMod.F90 + @@ -12,6 +12,7 @@ module SurfaceWaterMod + use shr_spfn_mod , only : erf => shr_spfn_erf + use clm_varcon , only : denh2o, denice, roverg, wimp, tfrz, pc, mu, rpi + use clm_varpar , only : nlevsno, nlevgrnd + + use clm_varctl , only : iulog + use clm_time_manager , only : get_step_size + use column_varcon , only : icol_roof, icol_road_imperv, icol_sunwall, icol_shadewall, icol_road_perv + use decompMod , only : bounds_type + @@ -201,7 +202,7 @@ subroutine BulkDiag_FracH2oSfc(bounds, num_soilc, filter_soilc, & + SHR_ASSERT_FL((ubound(qflx_too_small_h2osfc_to_soil, 1) == bounds%endc), sourcefile, __LINE__) + + ! arbitrary lower limit on h2osfc for safer numerics... + - min_h2osfc=1.e-8_r8 + + min_h2osfc=1.e0_r8 + + do f = 1, num_soilc + c = filter_soilc(f) + @@ -230,6 +231,9 @@ subroutine BulkDiag_FracH2oSfc(bounds, num_soilc, filter_soilc, & + + else + frac_h2osfc(c) = 0._r8 + + if (h2osfc(c) > 0._r8) then + + write(iulog,*) 'WJS: in else' + + end if + qflx_too_small_h2osfc_to_soil(c) = h2osfc(c) / dtime + ! The update of h2osfc is deferred to later, keeping with our standard + ! separation of flux calculations from state updates, and because the state + + With those diffs, I ran the tracer consistency test; it passed. In + addition, I ran + SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm50BgcCropQianRsGs.bishorn_gnu.clm-default + with comparison against master, with the following diffs on master + (the first change changes behavior to force the relevant code to be + triggered, and is the same on master and on the branch; the second + change on master divides then multiplies by dtime to avoid + roundoff-level diffs): + + diff --git a/src/biogeophys/SurfaceWaterMod.F90 b/src/biogeophys/SurfaceWaterMod.F90 + index 959d539b..4a4a4824 100644 + --- a/src/biogeophys/SurfaceWaterMod.F90 + +++ b/src/biogeophys/SurfaceWaterMod.F90 + @@ -77,7 +77,7 @@ subroutine FracH2oSfc(bounds, num_nolakec, filter_nolakec, & + ) + + ! arbitrary lower limit on h2osfc for safer numerics... + - min_h2osfc=1.e-8_r8 + + min_h2osfc=1.e0_r8 + + call waterstatebulk_inst%CalculateTotalH2osno(bounds, num_nolakec, filter_nolakec, & + caller = 'FracH2oSfc', & + @@ -112,7 +112,7 @@ subroutine FracH2oSfc(bounds, num_nolakec, filter_nolakec, & + + else + frac_h2osfc(c) = 0._r8 + - h2osoi_liq(c,1) = h2osoi_liq(c,1) + h2osfc(c) + + h2osoi_liq(c,1) = h2osoi_liq(c,1) + (h2osfc(c) / get_step_size()) * get_step_size() + h2osfc(c)=0._r8 + endif + + This test passed and was bit-for-bit with master with the above changes. + + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Many/all + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Roundoff: just roundoff-level changes in FSH_PRECIP_CONVERSION, + FSH_TO_COUPLER, l2x_Fall_sen due to refactored calculation of + FSH_PRECIP_CONVERSION + + If bitwise differences were observed, how did you show they were no worse + than roundoff? via summarize_cprnc_diffs + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: branch_tags/cime5.8.3_chint17-03 -> branch_tags/cime5.8.3_chint17-04 + Fixes ESMCI/cime#3171 + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev050 +Originator(s): slevis (Samuel Levis,SLevisConsulting LLC,303-665-1310) +Date: Mon Jul 15 11:40:09 MDT 2019 +One-line Summary: dz --> dz_lake bug-fix in LakeTemperatureMod.F90 line 960 + +Purpose of changes +------------------ + + Bug-fix to prevent the model from aborting when running with fewer soil + layers than lake layers; not to imply that this was not a bug when the + model wasn't aborting. It was. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #760 + +Known bugs found since the previous tag (include github issue ID): #759 bug causing model to abort when nlevsoi = nlevgrnd + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers +-------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: @dlawrenncar @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + Summarize any changes to answers, i.e., + - what code configurations: use_lch4 = .true. + - what platforms/compilers: all + - nature of change: diagnostic variable WTGQ only + Confirmed this on cheynne and hobart by running + ./summarize_cprnc_diffs -baseline .../tests_0712... -testid '*' + and inspecting the file cprnc.summary.*.by_varname + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/761 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev049 +Originator(s): erik (Erik Kluzek) +Date: Sun Jun 23 20:56:55 MDT 2019 +One-line Summary: Update mosart and intel to intel-19 on cheyenne + +Purpose of changes +------------------ + +Update mosart to trunk tag (that has a roundoff change to history file +output). And update intel compiler on cheyenne to intel-19. + +Bugs fixed or introduced None +------------------------ + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes + + Summarize any changes to answers, i.e., + - what code configurations: some compsets with mosart + - what platforms/compilers: cheyenne/intel + - nature of change: roundoff + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, and mosart + mosart to mosart1_0_33 + cime to branch_tags/cime5.8.3_chint17-03 + +Pull Requests that document the changes (include PR ids): #753 +(https://github.com/ESCOMP/ctsm/pull) + #753 -- Update cheyenne to intel/19 and update mosart + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev048 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Sun Jun 23 15:16:01 MDT 2019 +One-line Summary: Updates for buildlib changes and cime and externals updates + +Purpose of changes +------------------ + +Update of most externals: cime, mosart, rtm, cism. The cime update also includes a required CESM-wide +change in buildlib. Uses a function to get the Macros filename "get_standard_makefile_args". +The cime update brought in some answer chagnes, with an update of the intel compiler (but we backed those +out by using a cime branch). There is also a roundoff change by going to the trunk version of RTM. + +Bugs fixed or introduced None +------------------------ + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: @jedwards, self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - PASS + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - PASS + + python testing (see instructions in python/README.md; document testing done): + + cheyenne - PASS (for python3) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, but only for a few cases (compsets with RTM) + + Summarize any changes to answers, i.e., + - what code configurations: With RTM + - what platforms/compilers: All + - nature of change: roundoff + fieldlist is different for CISM in some cases + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, mosart, rtm, cism + cime to branch_tags/cime5.8.3_chint17-02 + cism to cism2_0_68 + rtm to rtm1_0_68 + mosart to nldas-grid.n02_mosart1_0_31 + +Pull Requests that document the changes (include PR ids): #752 +(https://github.com/ESCOMP/ctsm/pull) + + #752 -- buildlib, cime and externals update + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev047 +Originator(s): sacks (Bill Sacks) +Date: Sun Jun 16 13:04:38 MDT 2019 +One-line Summary: Fix negative snow compaction during snow melt + +Purpose of changes +------------------ + +Fix an issue reported by @kjetilaas: In the presence of surface water, +the old and new snow cover fractions are inconsistently calculated in +subroutine "SnowCompaction". This can result in significant negative +compaction (snow depth increase) during snow melt. + +More details from @kjetilaas (copied from +https://github.com/escomp/ctsm/issues/573): + +There is an inconsistency in the calculation of snow cover fraction +(FSNO) in the SnowCompaction subroutine when there is surface water +present. The actual snow cover is limited to 0.99 when surface water is +present (and the surface water fraction is set to 0.01). However, +SnowCompaction recalculates the old FSNO without accounting for this +limitation. This results in an apparent decrease in FSNO, and +corresponding negative snow compaction from snow melt (ddz3). + +This can result in substantial, artificial increase in snow depth during +summer (can be more than 0.5 m during a single season). + +The problem might be masked in monthly output, but could be significant +whenever snow cover is close to 1 and surface water present. Snow mass +is indirectly affected by this as radiation and temperature fluxes in +the snow pack will be affected by artificially thick snow layers. + +This tag fixes this issue. The fix was implemented and tested by +@swensosc (Sean Swenson). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#573 (Snow depth increase due to inconsistent snow + cover fraction calculation) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson, @kjetilaas, Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + Sean Swenson ran the LMWG diagnostics package and looked at the + results with Keith Oleson. Their main findings were: + + - Snow depth is a bit smaller over Greenland and polar regions on + average, as expected (up to 5-10% decrease in average snow depth + averaged over the Canadian Arctic) + + - There is a small increase in h2osno over Greenland: about 30 mm + averaged over Greenland; it looks like the main changes are + around the coasts (which makes sense given that this bug only + affects vegetated landunits) + + - There are small changes in runoff over Greenland + + - Changes in snow cover fraction are tiny + + - Overall, this doesn't look climate changing, but could + potentially have a significant impact on select grid cells, and + on some variables in polar regions + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev046 +Originator(s): sacks (Bill Sacks) +Date: Sat Jun 15 15:54:44 MDT 2019 +One-line Summary: Separate the two uses of h2osno + +Purpose of changes +------------------ + +Until now, h2osno has been used in two ways: + +1. When there are explicit snow layers, h2osno is the sum of snow + (liquid + ice) in all layers + +2. When there is a little bit of snow, but not enough to create a snow + layer, h2osno gives the amount of this very thin snow pack (assumed + to be all ice) + +This is confusing and complicates the addition of water tracers to the +code. This tag separates h2osno into two different variables: + +1. h2osno_no_layers is a fundamental state variable that gives the + amount of snow in the case where we don't have explicit snow layers + +2. h2osno_total is purely a diagnostic variable that is the sum of snow + in all explicit layers, plus h2osno_unresolved. This exists in + waterdiagnosticbulk_type, but the version there is just set once at + the end of the time step, so that version is only meant for + diagnostic (history) output. Code that needs the current sum of + h2osno at a given point now computes it locally, via a new method on + waterstate_type: CalculateTotalH2osno. If running in debug mode, that + routine also performs some consistency checks. + +Also, an unrelated change to prevent user from trying to interpolate a +file onto itself. + +Also, add a compset for testing, which is good for use on my mac. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#733 (Make h2osno purely a diagnostic variable) +- Resolves ESCOMP/ctsm#749 (h2osno inconsistent when interpolating from + initial conditions with different snow layers) +- Resolves ESCOMP/ctsm#750 (Prevent user from trying to use the same + filename for init_interp source and destination files) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none (possibly a small improvement +in timing based on PFS run time) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass; baseline comparisons fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Mostly roundoff; greater than roundoff/same climate for cases for + which number of snow layers is less in the case than in its + initial conditions file, due to fixing #749 + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + There was one point where h2osno_total differed from the old h2osno + by roundoff, as verified by a run of the test suite (where I verified + that (a) it only differed by 1e-11 or less, and (b) if I reset it, + there were just roundoff-level changes in a few diagnostic + fields). That one place with roundoff-level diffs can lead to + propagation of diffs, causing differences in many fields in the final + run of the test suite. In particular: I ran the test suite on + 69823de4 (which had this temporary check and reset of h2osno_total + vs. old h2osno). For nearly all tests, there were only roundoff-level + changes in a few diagnostic fields. I then removed the temporary + check and reset and ran the test suite on the result + (4353cc90). Finally, I ran the test suite on the final, cleaned-up + code, with comparison against 4353cc90 and verified bfb. + + In my testing on 69823de4: There were a few tests with greater than + roundoff-level changes due just to differences in the initial value + of h2osno_total (which was incorrect in the old due to #749). I + verified that these only had roundoff-level changes in a few + diagnostic fields if I used the following diffs in both the baseline + and my branch, indicating that the diffs just arose due to the fix of + #749: + + diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 + index 793b36ac..f10ee5e1 100644 + --- a/src/main/clm_initializeMod.F90 + +++ b/src/main/clm_initializeMod.F90 + @@ -762,6 +762,18 @@ subroutine initialize2( ) + !$OMP END PARALLEL DO + end if + + do c = bounds_proc%begc, bounds_proc%endc + + if (col%snl(c) < 0) then + + water_inst%waterstatebulk_inst%h2osno_col(c) = 0._r8 + + do j = col%snl(c)+1, 0 + + water_inst%waterstatebulk_inst%h2osno_col(c) = & + + water_inst%waterstatebulk_inst%h2osno_col(c) + & + + water_inst%waterstatebulk_inst%h2osoi_ice_col(c,j) + & + + water_inst%waterstatebulk_inst%h2osoi_liq_col(c,j) + + end do + + end if + + end do + + + end subroutine initialize2 + end module clm_initializeMod + + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: n/a + + URL for LMWG diagnostics output used to validate new climate: n/a + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev045 +Originator(s): sacks (Bill Sacks) +Date: Thu Jun 6 12:26:57 MDT 2019 +One-line Summary: Recalculate h2osno for the sake of SnowCapping + +Purpose of changes +------------------ + +SnowCapping decides whether to remove excess snow based on +h2osno. However, at the point where this is called,h2osno is out of sync +with (h2osoi_liq + h2osoi_ice): Those variables can be changed slightly +in SnowWater (which is called before SnowCapping), yet h2osno isn't +recalculated based on those changes. + +I don't think this causes a big problem in practice, but it seems like +it would improve code understandability if we had the general rule that +any code that references h2osno is using a version of h2osno that is in +sync with (h2osoi_liq + h2osoi_ice). This is also needed to prevent +answer changes in an upcoming major refactor. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#736 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson signed off on the change, but didn't +review the final code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + Answer changes are expected to be small, since this should just + change the timing of snow capping a bit, but I haven't looked + closely at the magnitude of the answer changes. + + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev044 +Originator(s): sacks (Bill Sacks) +Date: Thu Jun 6 12:14:39 MDT 2019 +One-line Summary: Make wetland snow resetting behavior more explicit + +Purpose of changes +------------------ + +There is some code that zeroes out h2osno over thawed wetlands. It seems +like the intended behavior here is to zero out the entire snow +pack. Currently, however, this only zeros out a very thin (zero-layer) +snow pack. For now, I'm adding an snl==0 conditional to make this +behavior explicit; long-term, we'd like to change this to actually zero +out the whole snow pack. (At that time, this code block should probably +be moved to a more appropriate home, as noted in comments in issue +ESCOMP/ctsm#735.) + +Also, unrelated change in run_sys_tests: support machine-specific +baseline directory, in order to support new default location for CTSM +baselines on cheyenne. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses, but does NOT fix, ESCOMP/ctsm#735 + +Known bugs introduced in this tag (include github issue ID): +- Partially addresses, but does NOT fix, ESCOMP/ctsm#735 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson and Keith Oleson approved this change, +though didn't actually review the final code. + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - pass on cgdm-bishorn + make python=python2 test + make pyhton=python3 test + make lint + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + + Also ran SMS_Ly1.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-monthly + with comparison against baselines: passed and bit-for-bit. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (but see notes below) + + It seems theoretically possible for this to change answers, but no + answer changes were observed in the aux_clm test suite or + SMS_Ly1.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-monthly. + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev043 +Originator(s): erik (Erik Kluzek) +Date: Wed Jun 5 10:17:06 MDT 2019 +One-line Summary: Fix FUN bug (frac_ideal_C_use was backwards in regard to delta_CN), and replace Ball-Berry mbbopt with the CLM4.5 version + +Purpose of changes +------------------ + +Carbon allocation to uptake responds to CN(uptake-cost) and CN(actual). The intended implementation is: For C:N +less than the target C:N, C allocation is reduced with cost. For C:N greater than the target C:N, C allocation +is increased with high C:N. However, the actual implementation is reversed. This change fixes that problem. + +Also the Ball-Berry mbbopt values had been changed in the creation of CLM5.0, as part of the tuning, but the new +values don't work well (as our final tuning uses Medlyn photosynshesis rather than Ball-Berry). This brings the values +for Ball-Berry for CLM5.0 back to the CLM4.5 values. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #704 #705 + + Fixes #705 -- Ball-Berry parameters in CLM5.0 should go back to the previous values in CLM4.5 + Fixes #704 -- FUN code logic to reduce or increase carbon allocation used for uptake is reversed + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): New clm5.0 paramdata file + +Changes to the datasets (e.g., parameter, surface or initial files): mbbopt now use the clm4_5 values + rather than the pretuned clm5_0 values (before Medlyn was being used) + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self, olyson + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (134 tests are different from baseline as expected) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! + + Summarize any changes to answers, i.e., + - what code configurations: Anything with use_FUN=T (so Clm50Bgc compsets) + Also with Clm5.0 and Ball-Berry (stomatalcond_method='Ball-Berry1987') (so Clm50Nwp compsets) + - what platforms/compilers: All + - nature of change: climate is similar + + "Our assessment is that the impact is relatively small, but would affect climate; + however it doesn’t appear to strongly affect transient C response." + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + Experiments were done on the release branch + - casename: oleson/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850 + oleson/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist + + URL for LMWG diagnostics output used to validate new climate: + +http://webext.cgd.ucar.edu/I1850/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850/lnd/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850.21_40-clm50_release-clm5.0.15_2deg_GSWP3V1_1850.21_40/setsIndex.html + +We've also completed a historical run. Diagnostics are here: + +http://webext.cgd.ucar.edu/I20TR/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist/lnd/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist.1995_2014-clm50_release-clm5.0.15_2deg_GSWP3V1_hist.1995_2014/setsIndex.html + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #727 +(https://github.com/ESCOMP/ctsm/pull) + + #727 -- Fix the FUN bug, where an if statement was backwards + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev042 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Tue May 21 23:29:31 MDT 2019 +One-line Summary: Rename, correct, and simplify parameters dewmx and sno_stor_max + +Purpose of changes +------------------ + + To rename + dewmx to liq_canopy_storage_scalar + sno_stor_max to sno_canopy_storage_scalar + in the code and in the clm45 and clm50 param files. + + To change snocanmx, liqcanmx, and fcansno to... + snocanmx = params_inst%snow_canopy_storage_scalar(p) * (elai(p) + esai(p)) + liqcanmx = params_inst%liq_canopy_storage_scalar(p) * (elai(p) + esai(p)) + fcansno(p) = (snocan(p) / (vegt * params_inst%sno_stor_max))**0.15_r8 + + Rewrote fwet(p) to follow the same format as fcansno(p). + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #710 + Fixes #710 -- rename dewmx + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): New default parameter file + +Changes to the datasets (e.g., parameter, surface or initial files): + Pointing to new clm45 and clm50 param files containing the two renamed + parameters listed above. + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: + @billsacks + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (196 different because of new param file) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + Roundoff changes were expected. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + The code modifications causing the change were of the order-of-calculations + type in two lines of code. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/719 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev041 +Originator(s): sacks (Bill Sacks) +Date: Fri May 17 06:02:38 MDT 2019 +One-line Summary: Add water tracers to CanopyHydrologyMod + +Purpose of changes +------------------ + +Major overhaul of CanopyHydrologyMod in order to support water tracers. + +The part of CanopyHydrology that was actually dealing with canopy +hydrology has now been broken out into a number of small routines in +order to separate flux calculations from state updates. This is needed +in order to calculate tracer versions of the relevant variables, which +is now done here. + +The parts of CanopyHydrology that were NOT dealing with canopy hydrology +have been moved to more appropriate homes. They have not yet been +tracerized, but will be soon. + +This also makes some minor changes to diagnostic fields related to +canopy hydrology. Of particular note: QDRIP now has a different meaning: +it now corresponds to the excess liquid water that runs off from the +canopy (and is inactive by default). + +The design of this broken-out code was developed in consultation with +Mike Barlage, Erik Kluzek, Negin Sobhani, Sean Swenson and Mariana +Vertenstein. We plan to apply this design moving forward to other parts +of the code that need tracerization. See also +. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#360 - Implement water isotopes for + CanopyHydrology +- Resolves ESCOMP/ctsm#709 - QDRIP diagnostic field misleadingly named +- Partially addresses ESCOMP/ctsm#503 - Clean up CanopyHydrology + (We still need to clean up / tracerize the parts that have now been + moved elsewhere.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Changed meaning of QDRIP diagnostic field: it now corresponds to + qflx_liqcanfall rather than qflx_prec_grnd_patch, and is default + inactive. (There is no longer a diagnostic field corresponding to + qflx_prec_grnd_patch, but there are separate diagnostic fields for the + rain and snow portions of this, both default inactive.) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +- checked timing of hydro1 timer vs. previous canhydro timer from my + dev039 testing: differences are negligible + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: +- Design reviewed by Mike Barlage, Erik Kluzek, Negin Sobhani, Sean + Swenson and Mariana Vertenstein +- Final code reviewed only by self + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, baseline comparisons fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + Ensured no-greater-than-roundoff-level by: + + First, generated baselines using code with these diffs (note extra + parentheses in multiplication): + + diff --git a/src/biogeophys/CanopyHydrologyMod.F90 b/src/biogeophys/CanopyHydrologyMod.F90 + index f848f520..31c8c550 100644 + --- a/src/biogeophys/CanopyHydrologyMod.F90 + +++ b/src/biogeophys/CanopyHydrologyMod.F90 + @@ -338,8 +338,8 @@ subroutine CanopyHydrology(bounds, & + ! Intercepted precipitation [mm/s] + qflx_prec_intr(p) = forc_snow(c)*fpisnow + qflx_liq_above_canopy(p)*fpi + ! storage of intercepted snowfall, rain, and dew + - snocan(p) = max(0._r8, snocan(p) + dtime*forc_snow(c)*fpisnow) + - liqcan(p) = max(0._r8, liqcan(p) + dtime*qflx_liq_above_canopy(p)*fpi) + + snocan(p) = max(0._r8, snocan(p) + dtime*(forc_snow(c)*fpisnow)) + + liqcan(p) = max(0._r8, liqcan(p) + dtime*(qflx_liq_above_canopy(p)*fpi)) + + ! Initialize rate of canopy runoff and snow falling off canopy + qflx_snocanfall(p) = 0._r8 + + + Then ran test suite on 1cc9d38a. This is very close to the final + branch, but had a few small tweaks in place to get bit-for-bit: + + 1. Under some conditions, the final branch code resets slightly + negative snocan and liqcan to 0, where master did not. This + commit puts in place temporary code to maintain the slightly + negative values under these conditions, along with a check to + ensure that the values are really always only slightly negative + in this situation. + + 2. When snocan > snocanmx, master reset snocan to exactly snocanmx, + whereas the final branch code can result in snocan being + roundoff-level different from snocanmx, and similar for + liqcan. This commit puts in place temporary code to set snocan + to snocanmx under appropriate circumstances, and liqcan to + liqcanmx, along with a check to ensure that this is only leading + to roundoff-level changes in these state variables. + + 3. Multiplies then divides a flux by dtime in one place + + 4. Has parentheses around a partial sum to ensure same order of + operations as before + + This was bfb with the baselines generated with the diff noted + above, except for roundoff-level changes in SNOCAN in one grid cell + in just one test + (SMS_D_Ld1.f19_g17.I1850Clm45Cn.hobart_gnu.clm-default; old: + -8.15e-322, new: -2e-323). + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +None. But see +https://github.com/billsacks/prototypes-ctsm-canopyhydrology_tracers, +which was the source of our design discussions and contains notes from +these discussions. + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev040 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Fri May 03 10:34:46 MDT 2019 +One-line Summary: Move some hard-coded parameters from code to params.nc file + +Purpose of changes +------------------ + + Reduce the number of parameters that get hardwired directly in the code + by placing in the params.nc file where they become visible and easier + to modify. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #680 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users: + None + +Changes to CTSM's user interface: + Parameters that were hardwired in the code can now be seen and changed + in the params.nc file. + +Changes made to namelist defaults (e.g., changed parameter values): + None + +Changes to the datasets (e.g., parameter, surface or initial files): + Various parameters have moved out of the code and into the params.nc file. + +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] + +Notes of particular relevance for developers: + None +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + None + +Changes to tests or testing: + None + +Code reviewed by: + @ekluzek + @billsacks + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + Answers change as expected. + +CTSM tag used for the baseline comparisons: + ctsm1.0.dev039 + +Answer changes +-------------- + +Changes answers relative to baseline: YES + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: single-precision roundoff + Changes are due to four parameters: + accum_factor + ko25_coef + kc25_coef + frac_sat_soil_dsl_init + that were not declared "_r8" when hardwired in the code, + while now they are declared "double" in the params.nc files. I + showed that the change was no greater than single-precision roundoff + by writing the new and old values to the lnd and cesm log files and + confirming differences smaller than 1.e-6. + +Detailed list of changes +------------------------ + + - Updated the clm5 and clm4.5 params.nc files to contain the previously + hard-coded parameters that Katie Dagon recommended moving out of the + code (listed here: https://docs.google.com/spreadsheets/d/1cRmcB0xz7CjVP6ljUoCehJx49Usxsore5ma4mWcvQwM/edit#gid=0) + - Now read the parameters in the modules that use them + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/684 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev039 +Originator(s): sacks (Bill Sacks) +Date: Wed May 1 11:12:34 MDT 2019 +One-line Summary: Remove excess canopy liquid/snow regardless of temperature + +Purpose of changes +------------------ + +Previously: if it was above freezing, snow was allowed to accumulate on +the canopy beyond the specified capacity, and if it was below freezing, +liquid was allowed to accumulate beyond the specified capacity. Sean +Swenson, Keith Oleson and Dave Lawrence agreed that this seems wrong. + +This tag changes the behavior so that both liquid and snow canopy +capacities are enforced regardless of temperature. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#699 (Canopy liquid and snow capacities not + enforced consistently?) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Keith Oleson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev038 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff; likely same climate, but this still requires + investigation + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A (Keith Oleson will run this soon) + + URL for LMWG diagnostics output used to validate new climate: N/A + (Keith Oleson will run this soon) + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/703 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev038 +Originator(s): sacks (Bill Sacks) +Date: Wed May 1 10:53:02 MDT 2019 +One-line Summary: Support for NWP configuration, NLDAS grid and NLDAS datm forcing + +Purpose of changes +------------------ + +This tag includes a set of changes that, together, provide support for +running an initial Numerical Weather Prediction version of CTSM over the +Continental U.S. + +(1) NWP configuration: The changes in this configuration relative to the + climate (CLM5) configuration mainly target decreasing runtime by + removing features that are expensive and not as important for NWP + time scales (days to months rather than many years) and space scales + (high resolution): + + - Single dominant landunit; if vegetated, single dominant PFT + + - Only 5 soil layers, down to 3 m + + - Only 5 snow layers + + - Plant hydraulic stress off + + - Ball-Berry rather than Medlyn stomatal conductance method (this is + a side-effect of turning plant hydraulic stress off, and is not + itself a critical aspect of the NWP configuration) + + - Maximum of 3 iterations to compute canopy fluxes + + - MEGAN is off + + Note that the NWP compset triggers changes in two new xml variables: + CLM_CONFIGURATION ('clm' vs. 'nwp'; this controls things of a more + scientific nature, like whether plant hydraulic stress is on or + off), and CLM_STRUCTURE ('standard' vs. 'fast'; this controls + structural things like the maximum number of landunits per grid cell + and the soil layer structure). Thus, you can create a case that is a + hybrid between the CLM and NWP configurations by changing these two + xml variables independently. + +(2) NLDAS2 regional grid: 0.125 deg grid over the Continental U.S. + +(3) Updated version of MOSART with support for the same NLDAS2 regional + grid + +(4) NLDAS2 data atmosphere forcing: over the same regional grid; forcing + data are available from 1980 - 2018. (We have excluded 1979 because + a small amount of data were missing for that year, and we didn't + have a good way to handle those missing data.) + +These changes can be used independently or all together. However, note +that you will get garbage if you try to use the new NLDAS2 datm forcing +for a run that extends beyond the boundaries of the NLDAS2 domain. + +There are three new NWP compsets: +- I2000Ctsm50NwpSpGswpGs: GSWP3 datm forcing; meant for global runs or + regional runs outside the NLDAS domain +- I2000Ctsm50NwpSpNldasGs: NLDAS2 datm forcing; meant for regional runs + over the NLDAS domain or some portion of it +- I2000Ctsm50NwpSpNldasRsGs: Same as above, but with a stub runoff model + in place of MOSART, for runs that aren't interested in having a runoff + model and for which you want improved throughput + +The alias for the new grid is: nldas2_rnldas2_mnldas2 (indicating that +we're using the nldas2 grid for land/atmosphere, runoff ('r') and the +ocean mask ('m'). + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#451 (Add NWP physics option) +- Resolves ESCOMP/ctsm#452 (Add an NWP compset) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- The NWP configuration is still a work in progress +- The NLDAS surface data set is still a work in progress (will soon + update this to use high-res PFTs) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New xml variables: + - CLM_CONFIGURATION (will eventually be renamed to CTSM_CONFIGURATION) + - CLM_STRUCTURE (will eventually be renamed to CTSM_STRUCTURE) +- New namelist variable: + - itmax_canopy_fluxes + +Changes made to namelist defaults (e.g., changed parameter values): +No changes for existing CLM compsets; new defaults for NWP compsets + +Changes to the datasets (e.g., parameter, surface or initial files): +No changes for existing grids; new surface dataset for nldas2 grid + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- New tests covering NWP compsets, nldas grid and nldas datm forcing + +Code reviewed by: Mike Barlage, Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + tests pass; namelists change as expected + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev037 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- MOSART: release-cesm2.0.00 -> nldas-grid.n01_mosart1_0_31 +- CIME: ctsm/ctsm1.0/cime5.7.9/n04 -> ctsm/ctsm1.0/cime5.7.9/n05 + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/682 +- https://github.com/ESCOMP/ctsm/pull/685 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev037 +Originator(s): sacks (Bill Sacks) +Date: Mon Apr 29 16:11:47 MDT 2019 +One-line Summary: Change year alignment for present-day I compsets + +Purpose of changes +------------------ + +Change year alignment for present-day I compsets (typically, these +compsets have aliases beginning with "I2000"), in order to work better +for cases that are meant to replicate particular years. + +(1) Start the model in year 2000 rather than year 1 + +(2) Change datm's year alignment so that model year 2000 uses +observations from year 2000, model year 2001 uses observations from year +2001, etc. + +(This change was requested by Sean Swenson and supported by Dave +Lawrence.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Year-2000 compsets now start in model year 2000 rather than 1 + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: cime changes reviewed by Erik Kluzek and others + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, year-2000 cases change answers as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev036 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Present-day compsets (I2000, I1Pt; also I2010 once those compsets are added) + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff/same climate + + This changes the year alignment of datm. Climatological averages + should be the same as before, but the alignment of model year to + datm year changes. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: ctsm/ctsm1.0/cime5.7.9/n03 -> ctsm/ctsm1.0/cime5.7.9/n04 + +Pull Requests that document the changes (include PR ids): +- cime changes documented in https://github.com/ESMCI/cime/pull/3093 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev036 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Fri Apr 26 01:20:57 MDT 2019 +One-line Summary: Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change + +Purpose of changes +------------------ + +We currently have a bug so that for transient land-use change cases answers are different starting in soil +carbon when Carbon isotopes (use_c13, or use_c14) are on versus off. Answers are identical if there is no +land-use change. The bug does cause bulk Carbon (C12) to be slightly different, but qualitatively the same. +There is a significant impact to the Carbon isotope simulation however. The bug was causing changes in isotopic +pools to be directed to the bulk Carbon. Because, isotopes are so much smaller than bulk Carbon, this doesn't +cause a marked difference in the bulk Carbon simulation. But, the lack of the change in the isotopic pool +does have a meaningful impact on the simulation of the Carbon isotopic fields. + +Also added a general test for this and specific one to catch this case. And did some updates on documentation +files, and a small bug fix for run_sys_tests. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #692 #675 #686 + #675 -- Answers differ when carbon isotopes are on under transient cases + #686 -- Add a system test to make sure turning on carbon isotopes doesn't change answers + #692 -- run_sys_test issue + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: Added LCISO test type and a 13 month Hist test to make sure carbon isotopes + don't cause a change to answers + +Code reviewed by: dlawren, billsacks, klindsey, bishtgautum + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - PASS + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - PASS (compare tests fail, because of namelist updates) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +CTSM tag used for the baseline comparisons: ctsm1.0.dev035 + + +Answer changes +-------------- + +Changes answers relative to baseline: Only for Carbon isotopes on under transient land-use change! + + Summarize any changes to answers, i.e., + - what code configurations: Bgc with use_c13 or use_c14 T and with a transient land-use change after each year boundary + - what platforms/compilers: All + - nature of change: same climate for bulk Carbon, isotopic Carbon is quite different for regions with land-use change + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: + + URL for LMWG diagnostics output used to validate new climate: + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime + cime from -- ctsm/ctsm1.0/cime5.7.9/n01 to ctsm/ctsm1.0/cime5.7.9/n03 + cime update allows the new test to work and starts adding NLDAS grid in + +Pull Requests that document the changes (include PR ids): #696 #694 +(https://github.com/ESCOMP/ctsm/pull) + #696 -- run_sys_test small fix + #694 -- Carbon isotope fix + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev035 +Originator(s): sacks (Bill Sacks) +Date: Mon Apr 22 20:17:40 MDT 2019 +One-line Summary: Change h2ocan to a purely diagnostic variable + +Purpose of changes +------------------ + +Previously, h2ocan_patch was maintained through the driver loop as the +sum of liqcan_patch and snocan_patch. However, there were places where +it was updated separately (though consistently) - i.e., it was not +simply a matter of 'h2ocan = liqcan + snocan'. This made the code +more complex, especially for the upcoming addition of water tracers. + +This tag changes h2ocan_patch to be a purely diagnostic variable, set +once at the end of the driver loop. Prognostic equations that used to +use h2ocan now use liqcan and snocan, either directly or indirectly via +a temporary variable set equal to the current value of liqcan+snocan. + +This tag also completely removes support for snowveg_flag = 'OFF' in +order to clean up the code. + +In addition, this tag renames the namelist variable snowveg_flag to +snowveg_affects_radiation (now a logical). + +Finally, this tag includes a minor change to always compute fcansno, +even if snowveg_affects_radiation is false, in order to simplify the +code. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#199 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- snowveg_flag renamed to snowveg_affects_radiation, and changed to a + logical flag + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: +- Answer-changing portion of these changes reviewed by Keith Oleson and + (at least to some extent) Sean Swenson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev034 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I split these changes into two pieces: (1) an answer-changing piece + where I made minimal changes to replace uses of h2ocan_patch with + liqcan+snocan (via temporary h2ocan variables holding this sum), + and (2) non-answer-changing code cleanup. (1) consisted of the + first two commits on this branch (461cafea and f195c105). With the + changes in (1), I added checks near each change to ensure that the + new expression differed by no more than roundoff from the old + (using an absolute cutoff of 1e-13). I ran the full test suite with + these checks in place, and generated new baselines. I then compared + the changes in (2) with the baselines from (1); this cleanup step + was bit-for-bit except for roundoff-level changes in the + now-diagnostic-only field H2OCAN. + + As noted in ESCOMP/ctsm#689, the changes in (1) were larger than I + expected, presumably because initially roundoff-level differences + can lead to divergent code behavior. The most obvious example of + this is in the check of h2ocan > 0 in subroutine FracWet. I have + found that, due to roundoff errors, it is possible for h2ocan_patch + > 0 by roundoff, while (liqcan_patch + snocan_patch) <= 0 by + roundoff. (Presumably the reverse could also be true, though I + haven't seen that – but I haven't spent much time looking for it.) + + Soon, we plan to do a more rigorous test to double check that this + change is not climate-changing. + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- First part of changes in https://github.com/ESCOMP/ctsm/pull/689 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev034 +Originator(s): sacks (Bill Sacks) +Date: Sat Apr 20 06:11:23 MDT 2019 +One-line Summary: Change clm4_5: Use Justin Perket snow on vegetation + +Purpose of changes +------------------ + +This tag changes the behavior of clm4_5, making it now use Justin +Perket's snow on vegetation parameterization. This parameterization was +originally introduced in clm4_5_1_r112. At the time it was only used for +clm5_0 cases. This tag uses that parameterization for clm4_5 cases, too, +so that (like clm5_0) they use snowveg_flag = 'ON_RAD' (i.e., vegetation +snow canopy on with albedo influence). + +This changes climate for clm4_5, mainly through albedo changes, +particularly in the shoulder seasons. + +The reason for this change is to allow an upcoming cleanup of the +relationship between h2ocan, snocan and liqcan. (See +https://github.com/escomp/ctsm/issues/199 for details.) + +This tag also no longer allows snowveg_flag = 'OFF'. However, code +cleanup is deferred to a follow-on tag, in order to separate the answer +changes in this tag from the no-greater-than-roundoff-level changes in +the follow-on tag. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- First step towards addressing ESCOMP/ctsm#199 (Clean up relationship + between h2ocan, snocan and liqcan) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Changes the scientific configuration of clm4_5 cases, as noted above + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): +- For clm4_5: snowveg_flag = 'ON_RAD' rather than 'OFF' + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Need to clean up code involving snowveg_flag, liqcan, snocan and + h2ocan. I will do this in a follow-on tag. + +Changes to tests or testing: +- Added a test with snowveg_flag = 'ON'. (At least some of the code + paths triggered by this setting were previously covered by clm45 + cases. Now that both clm45 and clm50 use snowveg_flag = 'ON_RAD', + there was some uncovered code. This new test covers this code.) +- Changed long single-point tests to use Qian forcing: With the default + GSWP3 forcing, the vast majority of the runtime was being spent in + datm. In addition, I was getting repeated failures of + ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropGs.cheyenne_intel.clm-cropMonthOutput, + I think due to memory issues; I'm hopeful that changing the datm + forcing will help with that. + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass; NLCOMP and BASELINE failures for Clm45 cases, + as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev033 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Clm45 compsets + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + New climate (as in clm4_5_1_r112 for clm5_0); the main impact is + through albedo changes, particularly in the shoulder seasons. + + Changes in clm4_5 cases are due to: + + (1) Using snowveg_flag = 'ON_RAD' rather than 'OFF' + + (2) Changed initial conditions for canopy water: Rather than using + H2OCAN, which is the meaningful state variable on previous + clm4_5 initial conditions files, now we use LIQCAN and + SNOCAN. These may be 0, although at least some clm4_5 initial + conditions files (including the two non-Fates out-of-the-box + clm4_5 initial conditions files) have non-zero (though still + reasonable) LIQCAN for reasons I can't understand. + + (Also changes answers for + ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline, + which uses a clm45 initial file.) + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev033 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) +Date: Thu Apr 11 10:51:29 MDT 2019 +One-line Summary: Limit landunit presence with thresholds set in the namelist + +Purpose of changes +------------------ + + Faster simulations. Motivated by NWP applications: + - Introduce user-defined namelist parameters to use as thresholds + above which landunit areas are kept and + below which landunit areas are removed. + - Introduce user-defined logical namelist parameter to collapse the up to + three urban landunits to the dominant urban landunit. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #581 + Fixes #581 -- Allow zeroing out special landunits if their area is below some threshold + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + - New namelist variables with valid real values from 0._r8 to 100._r8, where + 0 means "do nothing" and other values determine the threshold above + which to keep the landunit in a gridcell. The new variables are: + toosmall_soil + toosmall_crop + toosmall_glacier + toosmall_lake + toosmall_wetland + toosmall_urban + - New logical namelist variable collapse_urban. If .true. then the up to + three urban landunits collapse to the dominant urban landunit. + +--------------------------------------------- +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + There's a typo in the name for n_dom_landunits (missing the s) in bld/CLMBuildNamelist.pm + build-namelist doesn't check for toosmall_* below 0 or above 100, but the code does + +Changes to tests or testing: Yes + New unit tests subroutine test_collapse_individual_lunits and + test_collapse_all_lunit_opts_active in test_surfrdUtils.pf + Modified standard suite test + ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_to_dominant_decStart + to + ERS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-rm_indiv_lunits_and_collapse_to_dom + and introduced fatal error message when namelist parameters toosmall_* > 0 or + n_dom_* > 0 in transient simulations + +Code reviewed by: Erik Kluzek, Bill Sacks + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (384 differences because of new namelist items) + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + +CTSM tag used for the baseline comparisons: + cheyenne ctsm1.0.dev031 + hobart ctsm1.0.dev032 + + +Answer changes +-------------- + +Changes answers relative to baseline: No + Note: Comparison to baseline gives NLCOMP failures because the new namelist + parameters always appear in the namelist now, even when they have not been + changed from their default value by the user. + +Detailed list of changes +------------------------ + - Introduced call to new subroutine collapse_individual_lunits that uses + the user-defined namelist variables listed above to determine whether + a landunit gets kept or removed from a gridcell. + - Introduced new call to collapse_to_dominant for when collapse_urban = .true. + - Introduced error checks that do not allow coexistence of transient + simulations and the toosmall_* variables OR the n_dom_pfts/n_dom_landunits + variables OR the collapse_urban parameter. + +Pull Requests that document the changes (include PR ids): #641 + https://github.com/ESCOMP/ctsm/pull/641 + #641 -- Ability to remove individual landunits for faster runs + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev032 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Mon Apr 8 08:26:57 MDT 2019 +One-line Summary: Fixing the balance check to check for possible errors over all columns/patches + +Purpose of changes +------------------ +Up until now, the BalanceCheckMod code in biogeophysics did not check all +the possible errors over all columns or patches with the error threshold for +aborting clm and it merely compared the last column/patch found (where +warning threshold is met) with the error threshold. +Therefore, there was always a possibility that the abort is not triggered +when it should have been. This issue was first mentioned in ctsm issue #55 +for soil energy balance check, but a similar issue is also present for +other balance checks in BalanceCheckMod.F90 . + +Below is the list of the balance checks with a similar issue: +1. Water balance check +2. Snow balance check +3. Solar radiation energy balance check +4. Longwave radiation energy balance check +5. Surface energy balance check +6. Soil energy balance check (Issue #55) + +For remediating this issue, we used MAXVAL and MAXLOC Fortran intrinsic functions +to compare the largest error with the warning and error thresholds instead +of checking the last column or looping over all columns. + + +In addition, this PR also makes slight changes to ./run_sys_tests outputi/case +directory structure. Previously for each case in a test suite, there were +two set of directories created by run_sys_tests as follows: + * one directory which included run/ and bld/ and named as $SCRATCH/[case-name].... + * The case directory which included logs , timings, CaseDocs/, and misc. scripts + for ./case.build, ./case.submit... under $SCRATCH/tests-[testID]/[case-name].... + +This made debugging confusing and populated many folders in user's scratch. +Now, for every case in a test, all directories related to that case +including bld/ and run/ directories are nested under the case directory under $SCRATCH/tests-[testID]/[case-name].... +This is now similar to ./create_test output folder structure. + + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm issue#55 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + - ./run_sys_test is changed so that it nests bld/ and run/ directories under the case directory as $SCRATCH/tests-[testID]/[case-name]... + The output folder structure now is similar to ./create_test for each case in a test. + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + +CTSM tag used for the baseline comparisons: ctsm1.0.dev031 + + +Answer changes +-------------- + +Changes answers relative to baseline: No + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/670 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev031 +Originator(s): sacks (Bill Sacks) +Date: Wed Mar 13 15:03:42 MDT 2019 +One-line Summary: Subtract virtual states to reduce dynbal fluxes for transient glaciers + +Purpose of changes +------------------ + +Up until now, when computing the dynbal correction (conservation) fluxes +for transient glacier columns, we have been (1) counting the mass and +energy in the ice column as if that is a real state, but on the other +hand (2) NOT accounting for the fact that glacier columns don't +represent the soil under glacier. These two issues work in opposite +directions, but (1) dominates, because there is much more ice (and +energy, I think) in the roughly 50 m of glacial ice than there is in a +typical 50 m soil column. + +In discussing this issue with Bill Lipscomb, we came up with the idea of +subtracting some baseline value from each glacier column. I think that, +as long as we subtract the same baseline value throughout an entire +simulation for a given column, we will still conserve mass and energy +through dynamic landunit transitions. + +So, here we subtract baseline values from glacier columns, accounting +for the two issues mentioned above: (1) we subtract the water and energy +in the glacier ice, because this is a virtual state in CTSM, and (2) we +add the water and energy from the vegetated column(s), to account for +the fact that we don't have an explicit representation of +soil-under-glacier (this carries the assumption that the +soil-under-glacier has the same state as the initial vegetated state in +that grid cell). We set these baselines in initialization, so they begin +equal to the cold start state. Water and ice in the glacial ice stay +fixed over the course of a simulation, so the cold start values should +be the same as the current values at any point in time. The heat content +of the glacial ice does change over time, but by subtracting this +baseline value, we can potentially reduce the dynbal sensible heat +fluxes (however, note that it's also possible that these sensible heat +fluxes could increase when subtracting the cold start value, if ice +temperatures are closer to 0 deg C than to the cold start value, +currently 250 K). + +In addition, this introduces a new namelist flag, +reset_dynbal_baselines, which allows the user to reset these baselines +at some desired point in the simulation. I think that, in general, this +resetting would break conservation. But as long as it is done before the +onset of transient glaciers, I think this should be okay. In this way, +the user can minimize dynbal fluxes even further, by resetting the +baselines after the system has spun up. If the states haven't changed +much from this point to the point when glacier dynamics occur, then the +dynbal fluxes should now be very small. (See the documentation of this +flag in namelist_definition_ctsm.xml for more details.) + +Without this change, dynbal fluxes for a grid cell that undergoes 100% +glaciation / deglaciation in a single year are around 50 m ice, 1 m +liquid water, and a few tens of W m-2 (where those quantities of ice and +water are dribbled throughout the year, so we end up with an ice flux of +about 1.5e-6 mm/s throughout the year; and the energy flux is applied +evenly throughout the year - i.e., tens of W m-2 every time step for a +year). With this change, and with reset_dynbal_baselines set at an +appropriate time, these fluxes can be reduced to close to zero. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses ESCOMP/ctsm#274 (Dynamic landunits: improve water + and energy conservation) + +CIME Issues fixed (include issue #): +- Fixes three issues related to inputdata checksum: + - ESCMI/cime#3033 + - ESCMI/cime#3034 + - ESCMI/cime#3036 + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/ctsm#659 (Subtract dynbal baselines from begwb and endwb) + - This can't be fixed until we're okay having this answer change on + master + +Known bugs found since the previous tag (include github issue ID): +- ESCOMP/ctsm#658 (Methane should not depend on gridcell-level TWS) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] clm4_5 + +Significant answer changes for runs with transient glaciers. + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- For runs with transient glaciers, careful thought should be given to + when to set reset_dynbal_baselines +- Inconsistency between begwb/endwb and liq1/liq2/ice1/ice2 (see ESCOMP/ctsm#659) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variable: reset_dynbal_baselines + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Inconsistency between begwb/endwb and liq1/liq2/ice1/ice2 (see ESCOMP/ctsm#659) + +Changes to tests or testing: +- Tweaked a test with transient glacier areas, including adding this new + flag to the test + +Code reviewed by: Bill Lipscomb reviewed the conceptual ideas, but +nobody has reviewed the actual code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev030 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: ALL, but different configurations show + different levels of changes, as noted below + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + - new climate (at least regionally) for some configurations; + roundoff for others: see below + + There are three levels of changes here: + + (1) For runs with transient glaciers, there are large answer changes + in regions with changing glacier area. These answer changes are + in the various dynbal fluxes - for liquid water and ice runoff, + and for the dynbal sensible heat flux. + + (2) For runs with transient vegetation (Hist, Dv and Fates), there + are roundoff-level changes in the dynbal fluxes. For liquid + water and ice, these changes appear to only occur in grid cells + where there is some glacier area (because now both the before + and after gridcell water contents have changed by the same fixed + amount, which changes the difference at the roundoff level). For + heat, there are roundoff-level changes everywhere (because of + changes in the order of operations). + + (3) All runs have large changes in the diagnostic variables, + ICE_CONTENT1, LIQUID_CONTENT1 and HEAT_CONTENT1, over grid cells + containing some glacier area. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.7.9 -> ctsm/ctsm1.0/cime5.7.9/n01 + - Fixes issues related to inputdata checksum + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/650 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev030 +Originator(s): sacks (Bill Sacks) +Date: Fri Mar 8 15:08:34 MST 2019 +One-line Summary: Update CIME; hookup expected test fails + +Purpose of changes +------------------ + +Two main changes: + +(1) Update to latest cime (from ctsm/ctsm1.0/cime5.7.5/n01 to + cime5.7.9). Some of the important changes are: + - Fix for recent cheyenne system changes + - New domain file for f19_g17 (changes answers at the roundoff + level) + - New domain file for T31_g37 (changes answers by greater than + roundoff) + +(2) In system tests: Annotate cs.status output with expected failures + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#654 + +CIME Issues fixed (include issue #): (Many) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none? + The PFS test showed a significant speedup (170s in the previous tag, + 124s in this tag). However, some other tests showed either a slowdown + or not much change. So I'm not sure there is a consistent pattern of + speedup in this tag. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, some baselines failed as noted below + + Most testing done with cime at eb2eb704f - excluded PR #3030, which + updated support for CAM-SE grids (but the changes in this PR were + very limited). Ran SSP tests with the final version of cime (so I'd + have a few tests covering the latest cime). + +CTSM tag used for the baseline comparisons: ctsm1.0.dev029 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: f19_g17, T31_g37 + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + - f19_g17: roundoff-level, presumably due to new domain file (some + diffs grew to greater than roundoff-level: some methane + variables in a long test - + SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput; + and many variables in test with flooding - + ERP_P180x2_D.f19_g17.I2000Clm50SpRtmFl.cheyenne_intel.clm-default) + + - T31_g37: greater than roundoff-level, presumably due to new + domain file from cime commit 4fcf592ee + + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: ctsm/ctsm1.0/cime5.7.5/n01 -> cime5.7.9 + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/602 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev029 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) +Date: Tue Feb 26 23:42:39 MST 2019 +One-line Summary: Collapse landunits to the N most dominant + +Purpose of changes +------------------ + + Allows the collapse to fewer landunits using the concept of + N most dominant for the purpose of faster runs, eg in the context + of NWP (Numerical Weather Prediction). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #581 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist variable n_dom_landunits with valid integer values from 0 to + max_lunit currently equal to 9, where 0 means “do nothing” and other + values determine the number of active landunits when running the model. + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + There is a question left in on whether the collapse call needs to also + be moved to inside dynamic landunits reading. + +Changes to tests or testing: Yes + ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_to_dominant_decStart + now replaces (by combining with) this test introduced in ctsm1.0.dev026 + ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_nat_pfts_decStart + I added subroutine test_collapse_to_dom_landunits to test_surfrdUtils.pf + to include new Unit Tests. In same file I renamed + subroutine test_collapse_nat_pfts to test_collapse_to_dom_pfts + to accurately describe the contents of the subroutine. + +Code reviewed by: Erik Kluzek + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +CTSM tag used for the baseline comparisons: + ctsm1.0.dev028 + + +Answer changes +-------------- + +Changes answers relative to baseline: No + +Detailed list of changes +------------------------ + + Replaced existing subroutine collapse_nat_pfts with + subroutine collapse_to_dominant which can collapse to the + N dominant landunits or N dominant pfts by performing the + same actions on the data. + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #639 + https://github.com/ESCOMP/ctsm/pull/639 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev028 +Originator(s): sacks (Bill Sacks) +Date: Tue Feb 26 14:35:01 MST 2019 +One-line Summary: Interpolate out-of-the-box initial conditions and remove expensive tests + +Purpose of changes +------------------ + +Two main changes (plus some small additional changes): + +1. Removed / reworked some expensive tests + +2. Interpolated all out-of-the-box initial conditions, so that the + out-of-the-box version is now compatible with our current + configuration. The changes from before were (a) our standard + configuration now uses the gx1v7 rather than gx1v6 land mask; (b) + many inactive points are now absent in memory. + +See https://github.com/ESCOMP/ctsm/pull/622 for details. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#312 +- Partially addresses ESCOMP/ctsm#275 (just a bit) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- New finidat files + +Substantial timing or memory changes: +- Faster initialization times for cases that no longer need to interpolate initial conditions + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Removed or reworked expensive tests: see details in https://github.com/ESCOMP/ctsm/pull/622 + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok: tests pass, baselines fail as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev027 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: all configurations that still need use_init_interp = .true. + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Not investigated carefully, but expected to be larger than roundoff/same climate + + Answers change for cases that still need to do interpolation from + these out-of-the-box finidat files. + + I first confirmed that the new finidat files are good via: + + - Compared `ncdump -h` of old vs. new initial conditions files + + - Ran the following tests, with comparison against master; verified that + these all pass and are bit-for-bit, that they use the new initial + conditions files, and that they now have `use_init_interp` unset + (whereas they used to have `use_init_interp` set to `.true.`); note + that these cover 6 of the 7 new initial conditions files: + + ``` + SMS_Ld1.f09_g17.I1850Clm45BgcGs.cheyenne_intel.clm-default + SMS_Ld1.f09_g17.I1850Clm45BgcCruGs.cheyenne_intel.clm-default + SMS_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default + SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-ciso + SMS_Ld1.f09_g17.I1850Clm50BgcCropCru.cheyenne_intel.clm-ciso + SMS_Ld1.f09_g17.I1850Clm50SpCru.cheyenne_intel.clm-default + ``` + + - To cover the last new initial conditions file, ran the following test + (with the same checks as above: passes and bit-for-bit, checked + finidat, and checked `use_init_interp`), with `./xmlchange + LND_TUNING_MODE=clm5_0_cam6.0` (for the baseline for this test, I set + `init_interp_method = 'use_finidat_areas'`, which I also used in + interpolating this initial conditions file): + + ``` + SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel + ``` + + Details on answer changes: + + As noted above, these changes are bit-for-bit for configurations + that can now use the out-of-the-box initial conditions without + interpolation. However, answers change for configurations that still + require interpolation of the out-of-the-box initial conditions + (e.g., because they are at a different resolution than the finidat + file). + + I expected these answer changes around the Caspian Sea, due to the + fact that we are now effectively interpolating twice from the + original file: once to produce the new out-of-the-box file (which + includes an interpolation from `gx1v6` to `gx1v7`, and so + interpolates onto the Caspian Sea region) and once to go from + `f09_g17` to the target resolution (rather than interpolating + directly from `f09_g16` to the target resolution). + + However, when I ran a test with comparison to baselines - + `ERP_Ld5.f19_g17.I1850Clm50Bgc.cheyenne_intel.clm-default` - I saw + changes in regions further afield than simply around the Caspian + Sea. See images in https://github.com/ESCOMP/ctsm/pull/622 for + details. It's possible that the other differences are also due to + the Caspian Sea change, but it's also possible that there is some + other cause here that I don't understand. But Erik Kluzek and I + agreed that it isn't worth trying to understand these other + (isolated) differences. + + Also note: While most f09_g17 tests are bit-for-bit with the earlier + tag (because now use_init_interp is .false. for those tests), + `SMS_Ld2_D.f09_g17.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic_interp` + differs in some glc forcing fields for a few grid cells in + Antarctica. This is perhaps not surprising, since this test needs to + use interpolation to get fields for the Antarctica virtual columns; + so, while I don't completely understand the cause of these answer + changes, I suspect the root cause is similar to the isolated answer + changes I saw sprinkled around the world for + `ERP_Ld5.f19_g17.I1850Clm50Bgc.cheyenne_intel.clm-default`. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/622 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev027 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Tue Feb 19 12:57:12 MST 2019 +One-line Summary: Non-constant time initialization for soil hydrology types are moved to SoilHydrologyType.F90. + +Purpose of changes +------------------ + +Initalization of time-varying `zwt`, `zwt_perched`, and `frost_table` are moved to `InitCold` in `SoilHydrologyType.F90`. + +Previously, `zwt`, `zwt_perched`, and `frost_table` were initialized in `SoilHydrologyInitTimeConstMod.F90`, which caused confusions. + +Bugs fixed or introduced +------------------------ +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#575 ("Some variables initialized in SoilHydrologyInitTimeConstMod are not time-constant") + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: Updated a test. The test added in previous tag included decStart with transient glaciers, which would not work. Hence, this test is modified so the compset does not include G. +Test IHistClm50SpG is updated to IHistClm50Sp. + +Code reviewed by: +Bill Sacks +Erik Kluzek + +CTSM testing: + + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, except for the expected failures. + +CTSM tag used for the baseline comparisons: +ctsm1.0.dev026 + +Answer changes +------------- + +Changes answers relative to baseline: no + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +PR #631 Soil hydrology initialization of time-constant variables moved to SoilHydrologyType +https://github.com/ESCOMP/ctsm/pull/631 + + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev026 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) +Date: Tue Feb 5 17:08:48 MST 2019 +One-line Summary: Collapse unmanaged PFTs to the N most dominant + +Purpose of changes +------------------ + +To run simulations fast for applications such as NWP (Numerical Weather +Prediction), allow collapsing natural PFT's to the number the user wants. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 457 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +New namelist parameter n_dom_pfts with valid integer values from 0 to +14, where 0 means “do nothing” and other values determine the number +of active pfts when running the model + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None (unless new option invoked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: updated tests, added new test +Updated standard testing test to include decStart +(December start). Confirmed that answers were bit-for-bit same with +baseline before introducing the change. +Added standard testing test to test n_dom_pfts = 2 in a +transient vegetation case with December start. +Added subroutine test_collapse_nat_pfts to test_surfrdUtils.pf to +include new Unit Tests. + +Code reviewed by: +Erik Kluzek +Bill Sacks + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +CTSM tag used for the baseline comparisons: +ctsm1.0.dev025 + +Answer changes +-------------- + +Changes answers relative to baseline: No (bit-for-bit) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/588 -- NWP collapse pfts to the N most dominant +https://github.com/ESCOMP/ctsm/pull/583 -- Add routine to find indices of max k values in data + +Added new subroutines collapse_nat_pfts and collapse_crop_var and called +them from surfrdMod.F90. The second of these subroutines is not needed +when collapsing unmanaged PFTs; however, I created it early in the PR +and decided to keep it for use soon with crop-related variables like +irrigation water and fertilizer. + +Bill Sacks made changes to include subroutine find_k_max_indices for the +benefit of this PR (#583) + +=============================================================== +=============================================================== Tag name: ctsm1.0.dev025 Originator(s): Keith Oleson, Bill Sacks Date: Wed Jan 23 10:48:01 MST 2019 @@ -7,25 +9486,1258 @@ One-line Summary: History fields for vertically-resolved sums of soil C and N, a Purpose of changes ------------------ -Main change is from Keith Oleson: Add history fields for -vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, -C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and -C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, -including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', -'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output -'SOILC_vr', 'SOILN_vr', and similarly for C isotopes. +Main change is from Keith Oleson: Add history fields for +vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, +C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and +C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, +including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', +'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output +'SOILC_vr', 'SOILN_vr', and similarly for C isotopes. + +Also minor fixes: +- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61) +- Remove FATES-related commented-out code in OzoneMod (this has been + moved to https://github.com/ESCOMP/ctsm/issues/618) +- Minor tweak to run_sys_tests + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#61 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): +- For runs that use the output_bgc usermods, including cmip6 runs, we no + longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', + 'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr', + and similarly for C isotopes. + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks; Erik Kluzek reviewed the changes to the SSP test + + +CTSM testing: + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev024 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/551 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev024 +Originator(s): slevis (Samuel Levis,SLevis Consulting, LLC, 303-665-1310) +Date: Mon Jan 14 11:07:04 MST 2019 +One-line Summary: Remove unnecessary restart variables + +Purpose of changes +------------------ + +Remove unnecessary restart variables to conserve on computing resources +and disk space + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 285 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: + +Notes of particular relevance for developers: +Code reviewed by Bill Sacks. +Standard testing (cheyenne and hobart) OK +Unit testing PASS +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + +Code reviewed by: Bill Sacks + +CTSM testing: +Regular testing (cheyenne and hobart) OK +Unit testing PASS + +CTSM tag used for the baseline comparisons: +ctsm1.0.dev023 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (bfb) + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/598 + +Variables removed from restart: +plant_nalloc +pot_f_nit_vr* +f_nit_vr* +root_depth +qflx_floodg +snounload +qflx_snofrz_lyr +sminn_to_plant_fun_patch + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev023 +Originator(s): sacks (Bill Sacks) +Date: Thu Jan 10 13:00:42 MST 2019 +One-line Summary: Remove CLM4.0 + +Purpose of changes +------------------ + +Remove CLM4.0. This consists of removing code and other files that are +specific to CLM4.0, and doing some resulting cleanup of code that was +shared between CLM4.0 and later versions (primarily in build-namelist). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves #455 (Remove CLM4.0) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Can no longer run CLM4.0 cases + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- CLM4.0 compsets no longer supported + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: Removed CLM4.0 tests + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + build-namelist tests: + + cheyenne - pass + + tools-tests (test/tools): + + cheyenne - pass + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - ok + + Total number of tests = 52 + Number of tests that PASS = 51 + Number of tests that Fail = 1 + Number of compare tests that PASS = 37 + Number of compare tests that Fail = 4 + Number of tests without compare = 11 + + The one failing test is: + FAIL fail-no_towerdata.-d+/glade/p/cesmdata/cseg/inputdata++-s+RF-Bra+--debug+--pftgrid+--soilgrid. + + These same failures occurred in ctsm1.0.dev022 (including the + compare tests that Fail). Erik Kluzek says these failures are + okay. + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + + Notes on testing: + + - Most testing done on b5380c7e8. Since then, updated to a version of + cime that fixes cime's configure tool (but this isn't invoked in + system tests, so I didn't rerun the system tests) and pointed cime + to a tag rather than a hash. + + - For tools tests: In baseline, cherry-picked commit 148bc2158 into + cime + +CTSM tag used for the baseline comparisons: ctsm1.0.dev022 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: points to branch tag off of cime5.7.5 + (ctsm/ctsm1.0/cime5.7.5/n01), with changes for: + (1) Removal of support for CLM4.0 (equivalent to the changes in + https://github.com/ESMCI/cime/pull/2968) + + (2) Fix for cime configure (cherry-picked 148bc2158) + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/609 (Remove CLM4.0) +- https://github.com/ESCOMP/ctsm/pull/601 (Print git status and related + info when running run_sys_tests) + + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev022 +Originator(s): sacks (Bill Sacks) +Date: Tue Jan 8 11:01:38 MST 2019 +One-line Summary: Set tracer version of irrigation fluxes + +Purpose of changes +------------------ + +Set tracer version of irrigation fluxes. + +This required a substantial rewrite of ApplyIrrigation (now renamed to +CalcIrrigationFluxes). The problem was that the code was written to +compute the total irrigation withdrawal from groundwater, then use this +to compute the application fluxes (drip/sprinkler), then later divide +this total withdrawal by layer. But for tracer fluxes to be computed +correctly, we needed to reorder this, so that the per-layer withdrawals +are determined before determining the application fluxes. This is +because the application flux needs to know the tracer concentrations of +the source, which requires knowing which layers the source is drawing +from. This was made more challenging because of the mix of patch-level +and column-level variables at play: irrigation demand is patch-level, +groundwater availability and extraction is column-level, but application +is back to patch-level. + +In a somewhat-related change, I also reworked the passing of information +between soil hydrology (groundwater availability) and irrigation: +Previously, there was some near-duplicate code in +CalcAvailableUnconfinedAquifer (which was called prior to +ApplyIrrigation) and WithdrawGroundwaterIrrigation (which was called +after ApplyIrrigation). I have reworked the code to remove this +duplication, calling the new CalcIrrigWithdrawals in the midst of +CalcIrrigationFluxes. In doing so, I reconciled an accidental +discrepancy between the two original routines (see +https://github.com/escomp/ctsm/issues/595). + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#521 (Set tracer versions of fluxes set by + ApplyIrrigation) +- Resolves ESCOMP/ctsm#593 (Generalize groundwater irrigation availability to + handle multiple patches per column) +- Resolves ESCOMP/ctsm#595 (Inconsistency between CalcAvailableUnconfinedAquifer + and WithdrawGroundwaterIrrigation) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: + +- Sean Swenson reviewed the initial parts of the rework of + ApplyIrrigation and the passing of information between soil hydrology + and irrigation + +CTSM testing: + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, expected baseline failures as noted below + + Additional manual testing: + + - Out of the box, the one-timestep tracer consistency test + (SMS_D_Ln1.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency) + passed when the new check was inserted after the irrigation call, + even without the changes in this tag. Presumably this is because no + irrigation was being done in the first time step of this test. To + confirm that the changes here were both necessary and effective, I + hacked the code to force irrigation of all types (surface and + groundwater) on the first time step (see + https://github.com/billsacks/ctsm/commit/d28a03145). I confirmed + that this test, with those code hacks, failed before the changes in + this tag, and passed with these changes in place. + + - I used a multi-step process to confirm that these changes are only + roundoff-level different for groundwater irrigation (because + feedbacks in the system result in + SMS_D_Ld5.f10_f10_musgs.I2000Clm50BgcCrop.hobart_nag.clm-irrig_alternate + looking greater-than-roundoff-level different from the baseline): + + (1) Confirmed that e507fe603 is only roundoff-level different from + baseline using cprnc output from this test. + + (2) Confirmed that a4a1a626c is only roundoff-level different from + e507fe603. This was the tricky part. I did this by introducing + some temporary code that (a) computed some fluxes in both the + old and new ways, (b) compared the old and new methods for each + point and time step, confirming that they were no more than + roundoff-level different, then (c) set the fluxes to the old + method. I confirmed that this was bit-for-bit with e507fe603, + and the checks for greater-than-roundoff-level differences + between the old and new methods were never triggered. (See + https://github.com/billsacks/ctsm/commit/7d23e9e and the earlier + commits on that branch.) + + (3) Confirmed that remaining changes an the branch are bit-for-bit + with a4a1a626c. + +CTSM tag used for the baseline comparisons: ctsm1.0.dev021 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: + + - Small answer changes when groundwater irrigation is enabled. In + principle, could change answers by greater than roundoff due to + fix of #595, but I didn't see any answer changes in my 7-month + test due to that change. Other than that, just roundoff-level + changes. + + - Answer changes when tracers are enabled. + + - Roundoff-level changes in the diagnostic field, + QIRRIG_FROM_SURFACE, for many tests + + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + See notes under "what code configurations" for details. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/600 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev021 +Originator(s): mvr (Mathew Rothstein,UCAR/CSEG,303-497-1304) +Date: Wed Dec 26 16:29:06 MST 2018 +One-line Summary: Added tracer ratio capability and included it in consistency checks + +Purpose of changes +------------------ + +These changes are needed to support the implementation of water isotopes by ensuring +that isotope-related variables are being updated consistently throughout the model. +The consistency checks include the testing of a bulk tracer that should always be +equal to the bulk, and also test tracers that maintain a fixed ratio (other than +one) to the bulk. This commit includes fixes to the cold start initialization for +the water tracers with ratios other than one. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): [If none, remove this line] +#541 Only do water tracer consistency checks on tracers that are + supposed to maintain a fixed ratio +#459 Fix cold start initialization of water tracers +#508 Remove unused variables in new Water types +#357 Put in place Water isotope consistency checks + + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: added unit tests + +Code reviewed by: bill sacks + + +CTSM testing: + + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- PASS + hobart ------ PASS + +CTSM tag used for the baseline comparisons: ctsm1.0.dev020 + + +Answer changes +-------------- + +Changes answers relative to baseline: no, b4b + + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): #599 Adding isotope + tracer ratios +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev020 +Originator(s): Sean Swenson, Bill Sacks +Date: Mon Dec 3 11:51:24 MST 2018 +One-line Summary: New options for irrigation and crop fsat + +Purpose of changes +------------------ + +Introduce three new options: + +(1) Ability to withdraw irrigation water from groundwater if not enough + water is available from rivers. This is controlled via new namelist + flag, use_groundwater_irrigation. Water can be withdrawn from both + the unconfined (from the soil column) and confined (from wa) + aquifers. + +(2) Irrigation method: sprinkler (above canopy) vs. drip (below + canopy). This can be set on a per-crop and per-gridcell basis on the + surface dataset, but out-of-the-box support for creating the + necessary surface dataset field is not yet in place (see + ESCOMP/ctsm#565). For now, it can be controlled globally via a new + namelist flag, irrig_method_default. The default is drip, which was + what we were previously using implicitly. + +(3) Set crop fsat to zero. This is controlled by a new namelist option, + crop_fsat_equals_zero. + +Default behavior is the same as before for all three options. + +Also: + +- If use_aquifer_layer is false (which is the default for CLM50), no + longer reset wa_col every time step + +- Adds indices to vector history files giving column, landunit and + gridcell indices for each patch, etc. (Resolves ESCOMP/ctsm#81: + "Restart files are different for CLM when run over different number of + tasks" (issue name is a misnomer of the remaining to-dos in that + issue.) + +- Writes 3d time-constant fields on first history file for all tapes, + not just the first + +- Small performance improvements to irrigation + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#81 ("Restart files are different for CLM when run + over different number of tasks", but that name was a misnomer for the + remaining work needed on the issue) + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/ctsm#565: Surface dataset enhancements needed for irrigation method + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variables: + - use_groundwater_irrigation + - irrig_method_default + - crop_fsat_equals_zero +- Partial support for new surface dataset field: irrigation_method + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: +- Added two tests of the new irrigation options +- Added an _includes directory to hold things that should be included by + testmods (not used directly) + + +Code reviewed by: Bill Sacks and Sean Swenson reviewed each other's code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + Tests pass, namelists differ as expected + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ pass + + ok: tests pass, some answers change as noted below + +CTSM tag used for the baseline comparisons: ctsm1.0.dev019 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Some CLM50 cases that are either cold start + or (unusually) use a CLM45 initial conditions file; it's possible + that non-cold-start configurations would see differences rarely. + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff, same climate + + Differences arise due to no longer resetting wa_col to + aquifer_water_baseline every time step in BeginWaterBalanceSingle + if use_aquifer_layer is false (which is the default for + CLM50). (This change is needed to conserve water properly with the + new groundwater-based irrigation.) For the most part, wa_col + wasn't being changed when use_aquifer_layer is false (so no longer + resetting it has no effect if groundwater irrigation isn't being + used), but the one exception is the "work around of the negative + liquid water" added by Jinyun Tang in subroutine SoilWater (dated + Jan 14, 2015), which can be exercised when use_flexibleCN is + true. Sean Swenson did some experimentation, and found that the + code that updates wa_col is only exercised in the first time step + of a cold start run, and that finding is borne out in the test + suite results. However, it's possible that there are rare cases + when this is exercised later in a run. + + I have confirmed that this branch is bit-for-bit with the baseline + if I revert the addition of the use_aquifer_layer conditional + around the wa_col resetting in + BeginWaterBalanceSingle. Alternatively, nearly all tests are + bit-for-bit with the baseline if I remove the one line updating + wa_col in subroutine SoilWater (and also remove the endrun for + water balance errors from BalanceCheck); the one exception is the + waccmx_offline test, which uses a CLM45 initial conditions file in + a CLM50 configuration. + + The following tests had baseline failures: + + Cold start tests: + + ERP_D_Ld5.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-allActive + ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-cropColdStart + ERP_P180x2_D_Ld5.f19_g17.I2000Clm50BgcDvCrop.cheyenne_intel.clm-crop + ERP_P36x2_Lm25.f10_f10_musgs.I2000Clm50BgcDvCrop.cheyenne_intel.clm-monthly + ERP_P72x2_Lm25.f10_f10_musgs.I2000Clm50BgcDvCrop.cheyenne_intel.clm-monthly + + Test that uses a CLM45 initial conditions file in a CLM50 + configuration: + + ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/523 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev019 +Originator(s): sacks (Bill Sacks) +Date: Fri Nov 30 13:36:57 MST 2018 +One-line Summary: Rework cold start initialization of wa and zwt + +Purpose of changes +------------------ + +Rework cold start initialization of wa and zwt when use_aquifer_layer is +false to reduce answer changes in upcoming groundwater_irrigation +branch. + +In the groundwater_irrigation branch +(https://github.com/ESCOMP/ctsm/pull/523), Sean Swenson has stopped +resetting wa_col each time step if use_aquifer_layer is false. However, +this leads to having a substantially different value of wa_col when +use_aquifer_layer is false: previously, it was reset to +aquifer_water_baseline each time step, but with Sean's changes, it stays +close to its initial values, which have been 4000 in most places. This +tag changes the initial values to match the value it was being reset to, +so it simply starts at aquifer_water_baseline - so the +every-time-step-resetting to aquifer_water_baseline can be removed +without massively changing the value of wa_col. + +In addition to changing the cold start initialization of wa_col, we are +also changing the cold start initialization of zwt in this case where +use_aquifer_layer is false: The old initialization of zwt wouldn't work +as intended now that we have changed the initial value of wa_col; Sean +Swenson suggested this new initialization method instead. This +initialization to zi(c,nbedrock(c)) is correct if there are no saturated +layers, and close enough for a decent cold start even if there are. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected for some cases + +CTSM tag used for the baseline comparisons: ctsm1.0.dev018 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: CLM50 cold start or transient (Hist) cases + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Larger than roundoff, same climate (not investigated completely + rigorously through long simulations, but Sean Swenson and Bill + Sacks are both pretty confident that the resulting changes will be + small, partly based on difference statistics from the test suite, + and partly based on the fact that the only change in this tag is + in cold start initialization of some values). + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/577 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev018 +Originator(s): sacks (Bill Sacks) +Date: Thu Nov 29 16:03:50 MST 2018 +One-line Summary: Water tracer updates for initial things in driver loop + +Purpose of changes +------------------ + +Update water tracers for initial stuff done in driver loop. This includes +atm2lnd forcings (non-downscaled and downscaled), balance check initialization, +and dyn subgrid updates. + +Broadly speaking, the changes here are: + +(1) Reworked WaterType to make it easier / more robust for other code to loop + over tracers or bulk+tracers + +(2) The most interesting changes are probably the code to update the atm2lnd + water tracers (in Wateratm2lndType.F90 and WaterTracerUtils.F90) + +(3) In various other places, do some infrastructurey stuff (initializing water + balance, doing dyn subgrid stuff) for tracers as well as bulk + +(4) Supporting unit tests and unit test infrastructure + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +Resolves ESCOMP/ctsm#487 +Resolves ESCOMP/ctsm#488 +Resolves ESCOMP/ctsm#489 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- We have chosen not to set all water tracers as soon as possible, but instead + to do these tracer settings later in the driver loop. This keeps the driver + loop cleaner, but means that you cannot arbitrarily sprinkle calls to + TracerConsistencyCheck throughout the driver. Specifically for this tag: the + non-downscaled, gridcell-level atm2lnd water tracers are not updated until + after the call to downscale_forcings, so tracer consistency checks before that + point would fail. + +Changes to tests or testing: +- Added a PFS test + +Code reviewed by: Portions of the design (and possibly code) have been reviewed +by Mat Rothstein, David Noone and Mariana Vertenstein + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, some answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev017 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: many + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + roundoff-level changes in sensible heat flux from precip conversion due to + refactoring this calculation; everything else bit-for-bit + + If bitwise differences were observed, how did you show they were no worse + than roundoff? via summarize_cprnc_diffs to see differences in the test suite + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/572 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev017 +Originator(s): slevis (Samuel Levis, Slevis Consulting LLC,303-665-1310) +Date: Wed Nov 28 14:27:50 MST 2018 +One-line Summary: Merge the collapse2gencrop branch + +Purpose of changes +------------------ + +These changes allow the model to not need to read 16-pft +datasets and rather read 78-pft datasets. The 78-pft datasets were +developed for use with prognostic crops originally. The current changes +allow the model to use the 78-pft datasets in 16-pft runs by +collapsing the crop pfts (cfts) from specific types to the model's +generic crop types. The changes are generic so that the model may still +read 16-pft datasets for 16-pft runs. Ultimately these changes will +permit users to run with any number of pfts, while the ctsm group +maintains a single set of input pft data. -Also minor fixes: -- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61) -- Remove FATES-related commented-out code in OzoneMod (this has been - moved to https://github.com/ESCOMP/ctsm/issues/618) -- Minor tweak to run_sys_tests +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): Fixes #509 (partial) + #509 -- irrigate in 1850 is off for runs with use_crop but on for those without + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Changes made to namelist defaults (e.g., changed parameter values): +- maxpatch_pft made obsolete +- nnegcrit was increased because of failure in the TRENDY simulations. +This was done in the source, rather than the namelist but does have an +effect on user behavior. + +Substantial timing or memory changes: No + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + + The "irrigate" attribute should now be removed from all fsurdat files for namelist generation. + Thus irrigate on or off is now an option for non-crop cases. + + +Renamed parameters: +maxpatch_pft is obsolete; remove from namelist-related scripts in future PR +numpft + 1 ---> maxsoil_patches +maxpatch_pft ---> maxsoil_patches in CNDV +numpft ---> maxveg +numpft_ed ---> maxveg_fates + +Several modules were made default private. The list of variables in them +that are public are explicitly listed now: +LakeCon.F90 +clm_initializeMod.F90 +clm_instMod.F90 +clm_varpar.F90 +pftconMod.F90 +subgridAveMod.F90 + +Changes to tests or testing: +New test +New unit tests in test_surfrdUtils.pf, all containing the prefix +test_collapse_crop_types_* + +Code reviewed by: +Erik Kluzek and Bill Sacks + +CTSM testing: +Regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- PASS + hobart_pgi -------- OK + hobart_intel ------ PASS + +CTSM tag used for the baseline comparisons: ctsm1.0.dev016 + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #483 + +Sam Levis cloned Erik Kluzek's collapse2gencrop branch and then +tested, corrected errors, resolved conflicts, added unit tests, while +updating to newer tags as needed. + + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev016 +Originator(s): sacks (Bill Sacks) +Date: Thu Nov 1 07:27:48 MDT 2018 +One-line Summary: Update cime, fix FATES DEBUG token, add script to easily run system tests + +Purpose of changes +------------------ + +(1) Update to latest version of cime master + +(2) Update FATES with a minor change: change DEBUG to debug, to allow + working with a preprocessor-defined DEBUG token + +(3) Add a script (run_sys_tests) that allows easily running all system + tests (see + https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide#running-test-suites-with-the-run-sys-tests-wrapper + for details) + +(4) As part of (3), start work on a CTSM python library and associated + test infrastructure. Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#61 +- Fixes ESCOMP/ctsm#535 (Run Fortran unit tests as part of create_test) + +CIME Issues fixed (include issue #): +- Various - see CIME ChangeLog for details + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -35,9 +10747,11 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 +[X] clm5_0 -[ ] clm4_5 +[X] clm4_5 + +[X] clm4_0 Notes of particular relevance for users --------------------------------------- @@ -46,11 +10760,7 @@ Caveats for users (e.g., need to interpolate initial conditions): none Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): -- For runs that use the output_bgc usermods, including cmip6 runs, we no - longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', - 'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr', - and similarly for C isotopes. +Changes made to namelist defaults (e.g., changed parameter values): none Changes to the datasets (e.g., parameter, surface or initial files): none @@ -62,13 +10772,17 @@ NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the codin Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Changes to tests or testing: none +Changes to tests or testing: +- New run_sys_tests wrapper +- Fortran unit tests now run as part of aux_clm -Code reviewed by: Bill Sacks; Erik Kluzek reviewed the changes to the SSP test +Code reviewed by: Erik Kluzek CTSM testing: + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + build-namelist tests: cheyenne - not run @@ -83,25 +10797,52 @@ CTSM testing: regular tests (aux_clm): - cheyenne ---- pass - hobart ------ pass + cheyenne ---- ok + hobart ------ ok -CTSM tag used for the baseline comparisons: ctsm1.0.dev024 + ok means tests pass, baselines fail as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev015 Answer changes -------------- -Changes answers relative to baseline: NO +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: All I compsets (except spinup test that uses cplhist datm forcing) + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Potentially new climate + + Changes answers for I compsets due to datm update as part of the cime + update: new presaero and CO2 datasets + (https://github.com/esmci/cime/pull/2828) + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + URL for LMWG diagnostics output used to validate new climate: N/A + Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.7.3 -> cime5.7.5 +- fates: fates_s1.8.1_a3.0.0 -> fates_s1.8.1_a3.0.0_rev2 Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/551 +- https://github.com/escomp/ctsm/pull/493 (Wrapper to system tests, and + start of a ctsm python library) =============================================================== =============================================================== @@ -718,17 +11459,131 @@ Purpose of changes 5. Add a system test that exercises the water tracer consistency checks -6. Add a 'ratio' variable for each water tracer +6. Add a 'ratio' variable for each water tracer + +7. Add some unit tests of the new water tracer infrastructure + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses #357 +- Resolves #479 +- Resolves #492 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Don't be fooled by the new namelist variable, enable_water_isotopes: + This is just a place-holder for now, not implying that water isotopes + are actually working. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variables: enable_water_tracer_consistency_checks and + enable_water_isotopes. The latter is just a place-holder for now. + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: New test that runs the water tracer consistency check + I ran this test on cheyenne_gnu and cheyenne_intel along with the + out-of-the-box hobart_nag version + +Code reviewed by: Mat Rothstein and I have worked together on many of +these changes, but not all code has been reviewed by the other. + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok (tests pass, clm4_5 and clm5_0 namelists differ from + baseline as expected) + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev010 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/497 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev010 +Originator(s): sacks (Bill Sacks) +Date: Thu Aug 30 17:14:28 MDT 2018 +One-line Summary: Update cime to cime5.7.3 + +Purpose of changes +------------------ -7. Add some unit tests of the new water tracer infrastructure +Update cime from cime5.6.10 to cime5.7.3. To support this change, there +are also minor code changes related to the pause-resume implementation +(from Erik Kluzek). Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Partially addresses #357 -- Resolves #479 -- Resolves #492 +- ESCOMP/ctsm#384 (VIC test is failing at f09 resolution with signal) + (I'm not sure what fixed this, but it's passing now) + +CIME Issues fixed (include issue #): many + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -747,14 +11602,9 @@ Does this tag change answers significantly for any of the following physics conf Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): -- Don't be fooled by the new namelist variable, enable_water_isotopes: - This is just a place-holder for now, not implying that water isotopes - are actually working. +Caveats for users (e.g., need to interpolate initial conditions): none -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- New namelist variables: enable_water_tracer_consistency_checks and - enable_water_isotopes. The latter is just a place-holder for now. +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none Changes made to namelist defaults (e.g., changed parameter values): none @@ -768,12 +11618,10 @@ NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding s Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Changes to tests or testing: New test that runs the water tracer consistency check - I ran this test on cheyenne_gnu and cheyenne_intel along with the - out-of-the-box hobart_nag version +Changes to tests or testing: none + +Code reviewed by: self -Code reviewed by: Mat Rothstein and I have worked together on many of -these changes, but not all code has been reviewed by the other. CTSM testing: @@ -781,8 +11629,7 @@ CTSM testing: build-namelist tests: - cheyenne - ok (tests pass, clm4_5 and clm5_0 namelists differ from - baseline as expected) + cheyenne - not run unit-tests (components/clm/src): @@ -804,21 +11651,21 @@ CTSM testing: hobart_pgi -------- pass hobart_intel ------ pass -CTSM tag used for the baseline comparisons: ctsm1.0.dev010 +CTSM tag used for the baseline comparisons: ctsm1.0.dev009 Answer changes -------------- -Changes answers relative to baseline: NO +Changes answers relative to baseline: NO - bit-for-bit Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +cime: cime5.6.10 -> cime5.7.3 -Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/497 +Pull Requests that document the changes (include PR ids): none =============================================================== =============================================================== @@ -1312,6 +12159,165 @@ Pull Requests that document the changes (include PR ids): - #392 (Remove old code for snw_rds restart that looks no longer needed) - (Other changes not documented in PRs) +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev005 +Originator(s): sacks (Bill Sacks), mvr (Mathew Rothstein) +Date: Fri Aug 3 07:54:59 MDT 2018 +One-line Summary: Rework water data types to accommodate isotopes and other tracers + +Purpose of changes +------------------ + +This tag reworks the various water data types to allow having multiple +instances of variables that are needed for isotopes and other water +tracers. + +Specific changes include: + +(1) Separated "water state" variables into state, diagnostic and balance + check-related variables. This separation was not essential for the + work here, but was desired by Martyn Clark and others. + +(2) For each of water state, diagnostic and flux variables, separated + variables into those needed for both bulk and tracers vs. those only + needed for bulk. This way, we can have multiple instances of the + variables needed by tracers, but only a single instance of variables + that only apply to bulk water. This follows the design laid out in + https://github.com/escomp/ctsm/pull/395. The separation was based + largely on what was done in the old water isotope branch; we didn't + put a lot of thought into this, because the new design allows us to + easily migrate variables between bulk-only and bulk-and-tracer as + needed. + +(3) Moved water fluxes that were defined in science modules back into + waterflux_type or waterfluxbulk_type. This was needed for (2); there + is more discussion on this in + https://github.com/escomp/ctsm/pull/395 and the log message for + commit 711e5cd7. + +(4) Introduced a top-level water_type that holds instances of all of the + other water-related objects. This follows the design laid out in + https://github.com/escomp/ctsm/pull/395. This is particularly + valuable for the tracer instances: the logic related to number of + tracers can be encapsulated in water_type, rather than infiltrating + clm_instMod. + +(5) Added placeholders for water tracer instances + +(6) Added infrastructure to generate history / restart field names for + the tracer instances. Eventually, the isotope class can also hold + information specific to each isotope. + +This work was a joint effort between Mathew Rothstein and myself; Mat +gets much of the credit for the actual refactoring done here. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #358 (Separate WaterStateType into multiple types) +- Fixes #434 (Separate WaterFluxType into a base class and a class that just applies to bulk) +- Fixes #359 (Set up infrastructure for multiple instances of WaterState and WaterFlux types) +- Fixes #458 (Implement handling of history and restart variables for water tracers) + +Known bugs introduced in this tag (include github issue ID): +- #464 (Some lines longer than 132 characters) +- #456 (Remove backwards compatibility check for snw_rds) (not a + newly-introduced issue, but it's more important to fix this with the + separation of waterstate_type) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Water tracers are not yet functional - they are just placeholders +- Whether to use water tracers and which water tracers to use are + currently hard-coded; eventually, this should be namelist-controlled + +Changes to tests or testing: none + +Code reviewed by: Mathew Rothstein and Bill Sacks worked together on +these changes and reviewed each other's changes to some extent. The +high-level design was also reviewed and co-developed by Mariana +Vertenstein. Martyn Clark contributed substantially to the breakout of +water state into state, diagnostic and balance check-related variables. + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev004 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO - bit-for-bit + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/escomp/ctsm/pull/395 (documents the high-level design) + =============================================================== =============================================================== Tag name: ctsm1.0.dev004 @@ -1662,3 +12668,227 @@ Pull Requests that document the changes (include PR ids): =============================================================== =============================================================== +Tag name: ctsm1.0.dev001 +Originator(s): sacks (Bill Sacks) +Date: Fri Jun 22 07:31:43 MDT 2018 +One-line Summary: Begin separating SoilHydrology flux calculations + +Note the new tag naming: Starting with this tag, we are naming tags +"ctsm..." rather than "clm...". We are starting with ctsm version 1, +which for now is nearly the same as clm version 5. We are moving to this +new tag naming now because: + +(1) The changes in this tag represent the first step towards + implementing the CTSM vision (separating the biogeophysics flux + calculations from state updates, making it easier to plug in + alternative parameterizations, etc.). + +(2) This tag changes answers relative to the CLM5 release. (We expect + the climate to be the same, but we haven't tested this carefully + yet.) + +Purpose of changes +------------------ + +First steps toward separating various flux calculations in the soil +hydrology code. The focus here is on saturated surface runoff and +infiltration excess runoff. The changes here separate flux calculations +from state updates and extract various calculations into their own +subroutines to facilitate swapping in alternative parameterizations. + +Most of the changes here are refactorings that are either bit-for-bit or +just introduce roundoff-level differences. However, there are also a few +larger answer changes, as described below. + +These are the greater-than-roundoff-level answer changes: + +(A1) Use full qflx_surf in BGC code. Previously, the subroutines ch4 and + SoilBiogeochemNLeaching had been using a flux that excluded surface + water runoff (qflx_h2osfc_surf). That was deemed to be incorrect + (by Dave Lawrence and others), so these BGC subroutines have been + changed to use the full surface runoff (saturated excess runoff + + infiltration excess runoff + h2osfc runoff). + + Configurations affected: BGC compsets + + Magnitude of change: Larger than roundoff; expected to be same + climate, but not investigated carefully + +(A2) VIC: Don't ever use the TOPModel formulation for SurfaceRunoff + + The code was using the TOPModel-based formulation for SurfaceRunoff + if frost_table > zwt_perched. Sean Swenson felt this shouldn't be + done, and refactoring will be easier if VIC always uses the + vic-looking formulation, so I'm stopping applying this formulation + when using VIC. + + Configurations affected: VIC compsets + + Magnitude of change: Larger than roundoff; not investigated carefully + +(A3) VIC: Remove infiltration excess runoff + + Martyn Clark reviewed the VIC implementation, and felt that the + current implementation of infiltration excess runoff is + inconsistent with the standard VIC implementation. It appears that + what was being called VIC's infiltration excess runoff was actually + just an attempt to give a better numerical approximation to the + solution for saturated surface excess runoff. So deleting this + leaves only a first-order approximation to VIC's saturated surface + excess runoff. + + Eventually we may want to put in place a more accurate solution for + VIC's saturated surface excess runoff. But Martyn's feeling is that + this can come in with other changes we want to make regarding + numerical solutions in CTSM. + + Configurations affected: VIC compsets + + Magnitude of change: Larger than roundoff; expected to be same + climate, but not investigated carefully + +(A4) Change in QOVER diagnostic field: now includes QH2OSFC. + +These are the major refactorings (either bit-for-bit or just +roundoff-level differences): + +(R1) Extract surface runoff to its own module, and other modularization + related to what used to be subroutine SurfaceRunoff: extract a + subroutine for each fsat method, move urban surface runoff code + into different routines. + +(R2) Extract infiltration excess runoff to its own module, and other + modularization related to what used to be subroutine Infiltration. + +NOTE: For a detailed breakdown of changes, including documentation of +which changed changed answers, see the file ChangeLog_branch which was +deleted from this branch shortly before it was merged to master. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #424 (decStart testmod is missing an `--append` in an xmlchange command) + + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: +- Shortened a 25-month f19 test to 13-months + (SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput): + This test took a long time to run, and we already have long tests of + this configuration at coarse-resolution. I suggested removing this + test entirely, but Erik Kluzek wanted to maintain a shortened version + of it. Erik's comments were: + + How about either flip it to f45 (because Rosie is using that + resolution for science) -- or leave it at f19 and have it run for 9 + months? The 25 months was to take it just past the 2-year spinup + time. From spunup initial conditions 9-months pretty much does a + full harvest cycle. f19 and f09 are the main configurations for + science and it would be good to have something longer than just + really short tests. + + I decided on Lm13, because this still completes in significantly less + than 2-hours, and if we're running for 9 months anyway, it seems + valuable to finish out the year and run a bit into the next year, + since some crop stuff triggers at the end of the year. + +Code reviewed by: Various code reviews done last Fall, when these +changes were first implemented. + +CLM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- OK + hobart_intel ------ OK + + OK means tests pass, answers change as expected. + +CLM tag used for the baseline comparisons: clm5.0.dev013 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: Essentially all (except CLM4) + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Roundoff-level changes for nearly all configurations (except CLM4). + + Greater-than-roundoff-level changes for the following + configurations: + - BGC: see (A1) note above (expected to be same climate, but not + investigated carefully) + - VIC: see (A2) and (A3) notes above (magnitude of change not + investigated carefully) + - QOVER diagnostic field: see (A4) note above + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/244 +- https://github.com/ESCOMP/ctsm/pull/190 +- Other PRs that existed on the old NCAR/clm-ctsm repository (which has + been deleted), which were not migrated to the new repository + +=============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index b377f166a2..6285bf6bc9 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,563 +1,630 @@ Tag Who Date Summary ============================================================================================================================ -release-clm5.0.30 erik 01/21/2020 Update FATES to sci.1.30.0_api.8.0.0 -release-clm5.0.29 erik 11/19/2019 Some answer changes needed for prescribed soil-moisture and clm4_5 defaults (1850-ndep, and urbantv settings) -release-clm5.0.28 erik 11/14/2019 Several bit-for-bit fixes especially around soil-moisture streams -release-clm5.0.27 erik 08/13/2019 Add presoribed soil moisture streams as an option, and a few fixes -release-clm5.0.26 sacks 07/29/2019 Add a CN precision control call to fix problems related to small negative values -release-clm5.0.25 erik 05/29/2019 Change two files from NetCDF-4 format to NetCDF-3 (because some machines have trouble with NetCDF-4 in pnetcdf) -release-clm5.0.24 erik 05/22/2019 Correct ndep end year for SSPs, 2-degree CMIP6WACCMDECK with C-isotopes off, fixes mksurfdata for high resolution -release-clm5.0.23 erik 05/15/2019 Update cime to bring in CO2 transient files for the CMIP6 SSP's as well as presaero for three of them -release-clm5.0.22 erik 05/08/2019 Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change -release-clm5.0.21 erik 05/03/2019 New ndep files, update fates, fix some issues -release-clm5.0.20 erik 03/12/2019 Update all fsurdat files and bring in files for future scenarios, remove CMIP5 rcp options, bring in some bug fixes -release-clm5.0.19 erik 03/08/2019 Update cime version to one with updates for cheyenne after the Mar/5th/2019 downtime that resulting in mpt2.16 not being able to be used -release-clm5.0.18 erik 02/13/2019 Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory -release-clm5.0.17 sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes - ctsm1.0.dev025 sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes -release-clm5.0.16 erik 01/15/2019 PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere -release-clm5.0.15 sacks 12/06/2018 Option for rain-to-snow to immediately run off in some regions -release-clm5.0.14 erik 11/29/2018 Update cime and fix surface dataset for f05 1850 non-crop case -release-clm5.0.13 erik 11/14/2018 Update externals with new CO2/presearo/rtm/mosart, add science_support, change testing -release-clm5.0.12 erik 11/03/2018 New IC files for clm45/clm50 coupled cases, add 2010 compset -release-clm5.0.11 erik 10/30/2018 Bring fix for transient Bgc/Sp to release branch (from ctsm1.0.dev013) -release-clm5.0.10 sacks 10/29/2018 Bring in CMIP6 compset modifiers, output usermods and bit-for-bit fixes from dev014 and dev015 + ctsm1.0.dev093 erik 05/01/2020 Bring in changes from release-clm5.0 branch to master +release-clm5.0.30 erik 01/21/2020 Update FATES to sci.1.30.0_api.8.0.0 +release-clm5.0.29 erik 11/19/2019 Some answer changes needed for prescribed soil-moisture and clm4_5 defaults (1850-ndep, and urbantv settings) +release-clm5.0.28 erik 11/14/2019 Several bit-for-bit fixes especially around soil-moisture streams +release-clm5.0.27 erik 08/13/2019 Add presoribed soil moisture streams as an option, and a few fixes +release-clm5.0.26 sacks 07/29/2019 Add a CN precision control call to fix problems related to small negative values +release-clm5.0.25 erik 05/29/2019 Change two files from NetCDF-4 format to NetCDF-3 (because some machines have trouble with NetCDF-4 in pnetcdf) +release-clm5.0.24 erik 05/22/2019 Correct ndep end year for SSPs, 2-degree CMIP6WACCMDECK with C-isotopes off, fixes mksurfdata for high resolution +release-clm5.0.23 erik 05/15/2019 Update cime to bring in CO2 transient files for the CMIP6 SSP's as well as presaero for three of them +release-clm5.0.22 erik 05/08/2019 Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change +release-clm5.0.21 erik 05/03/2019 New ndep files, update fates, fix some issues +release-clm5.0.20 erik 03/12/2019 Update all fsurdat files and bring in files for future scenarios, remove CMIP5 rcp options, bring in some bug fixes +release-clm5.0.19 erik 03/08/2019 SKIPPED ON MASTER -- Update cime version +release-clm5.0.18 erik 02/13/2019 Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory +release-clm5.0.17 sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes +release-clm5.0.16 erik 01/15/2019 PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere +release-clm5.0.15 sacks 12/06/2018 SKIPPED ON MASTER -- Option for rain-to-snow +release-clm5.0.14 erik 11/29/2018 Update cime and fix surface dataset for f05 1850 non-crop case +release-clm5.0.13 erik 11/14/2018 Update externals with new CO2/presearo/rtm/mosart, add science_support, change testing +release-clm5.0.12 erik 11/03/2018 New IC files for clm45/clm50 coupled cases, add 2010 compset (IC FILES UPDATE SKIPPED ON MASTER) + ctsm1.0.dev092 erik 04/27/2020 Update cime to version in cesm2_2_beta04 + ctsm1.0.dev091 sacks 04/24/2020 Increase tolerance on near-zero truncation for a snow state update + ctsm1.0.dev090 negins 04/23/2020 Refactoring banded diagonal matrix code in SoilTemperature module + ctsm1.0.dev089 sacks 04/07/2020 Bring documentation source to master + ctsm1.0.dev088 sacks 04/07/2020 Fix bug in snow aerosol numerics (causes occasional HUGE aerosol values) + ctsm1.0.dev087 sacks 04/06/2020 Change hard-coded soil layers in phenology to use a target depth + ctsm1.0.dev086 mvertens 03/19/2020 Updates to NUOPC cap and minor fixes to ncdio_pio + ctsm1.0.dev085 sacks 03/16/2020 Update cime + ctsm1.0.dev084 negins 02/19/2020 Bounds assertion for C isotopes when threading is on + ctsm1.0.dev083 negins 02/06/2020 Some BFB Fixes: Resolve issues #683, # 874, #878, # 885, # 745, #838 + ctsm1.0.dev082 oleson 02/01/2020 Rename variables to avoid confusion; fix QSNOEVAP diagnostic + ctsm1.0.dev081 slevis 01/13/2020 Speed up restart writes + ctsm1.0.dev080 sacks 12/02/2019 Update externals, minor fixes to work with latest cime, get nuopc cap working + ctsm1.0.dev079 sacks 11/04/2019 Change a few uses of shr_kind + ctsm1.0.dev078 oleson 10/31/2019 Fix rootr calculation with use_hydrstress true + ctsm1.0.dev077 sacks 10/27/2019 Consistently use frac_sno_eff rather than frac_sno in qg calculations + ctsm1.0.dev076 sacks 10/25/2019 Set frac_sno_eff=0 if frac_sno is 0; avoid unnecessary calls to QSat + ctsm1.0.dev075 sacks 10/25/2019 Lakes: Adjust frac_sno after updating 0-layer snow pack for dew & sublimation + ctsm1.0.dev074 sacks 10/23/2019 For lakes: when reading finidat, set frac_sno=1 if h2osno_total > 0 + ctsm1.0.dev073 sacks 10/22/2019 Fix bug in calculation of dqgdT + ctsm1.0.dev072 mvertens 10/15/2019 Add NUOPC cap + ctsm1.0.dev071 sacks 10/11/2019 Split CanopyTemperature into separate pieces + ctsm1.0.dev070 sacks 10/09/2019 Fix for writing 0-d variables with PIO2 + ctsm1.0.dev069 sacks 10/07/2019 Misc. code cleanup and minor bug fixes + ctsm1.0.dev068 sacks 09/30/2019 Add water tracers to CombineSnowLayers, DivideSnowLayers, ZeroEmptySnowLayers + ctsm1.0.dev067 erik 09/26/2019 Add config_archive.xml to CTSM cime_config -- no testing + ctsm1.0.dev066 sacks 09/20/2019 Add water tracers to SnowCapping + ctsm1.0.dev065 sacks 09/14/2019 Add water tracers to SnowWater + ctsm1.0.dev064 slevis 09/09/2019 User defined top-two snow layers + ctsm1.0.dev063 erik 09/05/2019 Two answer changing fixes (fire, DWT_SLASH) and fix for urban streams for Clm45 + ctsm1.0.dev062 sacks 09/03/2019 Move hobart tests to izumi + ctsm1.0.dev061 erik 09/01/2019 Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated + ctsm1.0.dev060 sacks 08/29/2019 In SnowWater, truncate small h2osoi residuals + ctsm1.0.dev059 sacks 08/24/2019 Continue adding water tracers to LakeHydrology + ctsm1.0.dev058 slevis 08/22/2019 Soil texture interpolation bug-fix + ctsm1.0.dev057 sacks 08/20/2019 Fix frac_sno bugs + ctsm1.0.dev056 sacks 08/16/2019 Start adding water tracers to LakeHydrology, and related refactoring + ctsm1.0.dev055 sacks 08/06/2019 Modularize snow cover fraction method + ctsm1.0.dev054 sacks 08/02/2019 Fix interpolation of surfdat soil layers so we can use interpolation for 10SL case + ctsm1.0.dev053 slevis 08/01/2019 Soil layer definition clean-up and user-defined option + ctsm1.0.dev052 sacks 07/22/2019 Fix rare soil color bug in mksurfdata_map + ctsm1.0.dev051 sacks 07/19/2019 Update water tracers for remainder of first stage of hydrology + ctsm1.0.dev050 slevis 07/15/2019 dz --> dz_lake bug-fix in LakeTemperatureMod.F90 line 960 + ctsm1.0.dev049 erik 06/23/2019 Update mosart and intel to intel-19 on cheyenne + ctsm1.0.dev048 erik 06/23/2019 Updates for buildlib changes and cime and externals updates + ctsm1.0.dev047 sacks 06/16/2019 Fix negative snow compaction during snow melt + ctsm1.0.dev046 sacks 06/15/2019 Separate the two uses of h2osno + ctsm1.0.dev045 sacks 06/06/2019 Recalculate h2osno for the sake of SnowCapping + ctsm1.0.dev044 sacks 06/06/2019 Make wetland snow resetting behavior more explicit + ctsm1.0.dev043 erik 06/05/2019 Fix FUN bug (frac_ideal_C_use was backwards in regard to delta_CN), + and replace Ball-Berry mbbopt with the CLM4.5 version + ctsm1.0.dev042 slevis 05/21/2019 Rename, correct, and simplify parameters dewmx and sno_stor_max + ctsm1.0.dev041 sacks 05/17/2019 Add water tracers to CanopyHydrologyMod + ctsm1.0.dev040 slevis 05/03/2019 Move some hard-coded parameters from code to params.nc file + ctsm1.0.dev039 sacks 05/01/2019 Remove excess canopy liquid/snow regardless of temperature + ctsm1.0.dev038 sacks 05/01/2019 Support for NWP configuration, NLDAS grid and NLDAS datm forcing + ctsm1.0.dev037 sacks 04/29/2019 Change year alignment for present-day I compsets + ctsm1.0.dev036 erik 04/26/2019 Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change + ctsm1.0.dev035 sacks 04/22/2019 Change h2ocan to a purely diagnostic variable + ctsm1.0.dev034 sacks 04/20/2019 Change clm4_5: Use Justin Perket snow on vegetation + ctsm1.0.dev033 slevis 04/11/2019 Limit landunit presence with thresholds set in the namelist + ctsm1.0.dev032 negins 04/08/2019 Fixing the balance check to check for possible errors over all columns/patches + ctsm1.0.dev031 sacks 03/13/2019 Subtract virtual states to reduce dynbal fluxes for transient glaciers + ctsm1.0.dev030 sacks 03/08/2019 Update CIME; hookup expected test fails + ctsm1.0.dev029 slevis 02/26/2019 Collapse landunits to the N most dominant + ctsm1.0.dev028 sacks 02/26/2019 Interpolate out-of-the-box initial conditions and remove expensive tests + ctsm1.0.dev027 negins 02/19/2019 non-constant time init for soil hydrology types are moved to SoilHydrologyType.F90 + ctsm1.0.dev026 slevis 02/05/2019 Collapse unmanaged PFTs to the N most dominant + ctsm1.0.dev025 sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes + ctsm1.0.dev024 slevis 01/14/2019 Remove unnecessary restart variables + ctsm1.0.dev023 sacks 01/10/2019 Remove CLM4.0 + ctsm1.0.dev022 sacks 01/08/2019 Set tracer version of irrigation fluxes + ctsm1.0.dev021 mvr 12/26/2018 Added tracer ratio capability and included it in consistency checks + ctsm1.0.dev020 sacks 12/03/2018 New options for irrigation and crop fsat + ctsm1.0.dev019 sacks 11/30/2018 Rework cold start initialization of wa and zwt + ctsm1.0.dev018 sacks 11/29/2018 Water tracer updates for initial things in driver loop + ctsm1.0.dev017 slevis 11/28/2018 Merge the collapse2gencrop branch + ctsm1.0.dev016 sacks 11/01/2018 Update cime, fix FATES DEBUG token, add script to easily run system tests ctsm1.0.dev015 sacks 10/28/2018 CMIP6 compset modifiers, usermods for typical output, and other output enhancements ctsm1.0.dev014 sacks 10/26/2018 Miscellaneous minor, bit-for-bit bug fixes ctsm1.0.dev013 erik 10/25/2018 Fix the fact that transient Bgc and SP cases had constant crop area in time -release-clm5.0.09 erik 10/23/2018 Bring in bit-for-bit changes from master up to ctsm1.0.dev012: AnnEt init, snowmip fields ctsm1.0.dev012 erik 09/29/2018 Add snow-free fields for snowmip, fix several issues - ctsm1.0.dev011 sacks 09/12/2018 SKIPPED ON RELEASE BRANCH -- water tracer consistency checks - ctsm1.0.dev010 sacks 08/30/2018 SKIPPED ON RELEASE BRANCH -- cime update + ctsm1.0.dev011 sacks 09/12/2018 Add water tracer consistency checks, and other water tracer work + ctsm1.0.dev010 sacks 08/30/2018 Update cime to cime5.7.3 ctsm1.0.dev009 sacks 08/22/2018 Fix initialization of AnnET in InitAccVars -release-clm5.0.08 erik 09/28/2018 Updated CMIP6 ndep file for historical transient Bgc cases, 1850_control same as before -release-clm5.0.07 erik 08/08/2018 Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007 -release-clm5.0.06 erik 08/07/2018 Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007 - ctsm1.0.dev008 erik 08/14/2018 Update 1850 ndep file and last year for streams for Historical transient cases (same as release-clm5.0.05) -release-clm5.0.05 erik 08/05/2018 Update 1850 ndep file, and last year for transient streams + ctsm1.0.dev008 erik 08/14/2018 Update 1850 ndep file and last year for streams for Historical transient cases (corresponds to release-clm5.0.05) ctsm1.0.dev007 sacks 08/05/2018 Avoid glacier dynamic landunit adjustments in first time step ctsm1.0.dev006 sacks 08/04/2018 Minor bug fixes, cleanup, documentation and enhancements -release-clm5.0.04 erik 07/18/2018 Fix some NFIX variables, update cime/cism for upgraded hobart new glade, new diagnostic fields, update cmip6 output - ctsm1.0.dev005 sacks 08/03/2018 SKIPPED ON RELEASE BRANCH -- water types refactor - ctsm1.0.dev004 erik 07/18/2018 Add some new diagnostic fields, fix a few issues, update cmip6 output + ctsm1.0.dev005 sacks 08/03/2018 Rework water data types to accommodate isotopes and other tracers (skipped on release-clm5.0) + ctsm1.0.dev004 erik 07/18/2018 Add some new diagnostic fields, fix a few issues, update cmip6 output (corresponds to release-clm5.0.04) ctsm1.0.dev003 erik 07/15/2018 Update cime/cism to work on upgraded hobart and with glade changes on cheyenne ctsm1.0.dev002 erik 07/06/2018 Fix NFIX flux variables so special land-units are zeroed out, tools update, add some *_MAX fields on mksurfdata_map for transient cases - ctsm1.0.dev001 sacks 06/22/2018 SKIPPED ON RELEASE BRANCH -- SoilHydrology -release-clm5.0.03 erik 06/12/2018 Second release branch tag for CESM2.0 release, fixing DA and tools and README files, identical to clm5.0.dev013 -release-clm5.0.02 erik 06/12/2018 Mistake tag identical to previous version - clm5.0.dev013 erik 06/12/2018 cleanup and update cime and cism -release-clm5.0.01 erik 05/22/2018 First release branch tag for CESM2.0 release, identical to clm5.0.dev012 - clm5.0.dev012 sacks 05/17/2018 Fixes for variable_year orbital mode - clm5.0.dev011 erik 05/16/2018 1850 ndep update, cism update, PE layouts, turn BFBFLAG for testing - clm5.0.dev010 erik 05/15/2018 Update cime version to version in cesm2.0.beta10, changes answers for 1850 compsets because of orbit - clm5.0.dev009 sacks 05/10/2018 New init_interp method - clm5.0.dev008 erik 04/27/2018 With FUN subtract out soil nitrification flux of plant uptake of soil NH3 and NO3 - clm5.0.dev007 erik 04/24/2018 Bring in a few answer changing things: FATES, cism updates, IC file fix, - testing 1850 compset use 1850 orbit - clm5.0.dev006 sacks 04/12/2018 Don't allocate memory for zero-weight natveg patches and urban - clm5.0.dev005 sacks 04/10/2018 Two fixes for init_interp - clm5.0.dev004 erik 04/09/2018 List of important bug fixes - clm5.0.dev003 erik 03/09/2018 Bug fixes for energy imbalance associated with surface water and lakes - clm5.0.dev002 sacks 02/25/2018 Add some land ice diagnostic vars needed for CMIP6 - clm5.0.dev001 erik 02/14/2018 Fix LND_TUNING_MODE for fully coupled case, update some README files/PTCLM - clm5.0.dev000 erik 02/05/2018 Double tag of clm5.0.000 with new naming convention, some updated documentation - clm5.0.000 erik 02/05/2018 Double tag of clm4_5_18_r275 for clm5.0 release - clm4_5_18_r275 erik 02/05/2018 Update initial condition files, update fates, new CMIP6 pop-dens, more lnd_tuning_mod options, updated ndep for fully coupled - clm4_5_18_r274 sacks 01/30/2018 Fix auto-detection of CIME_MODEL in a standalone checkout - clm4_5_18_r273 sacks 01/26/2018 Support a standalone checkout from git - clm4_5_18_r272 erik 01/25/2018 Bring in latest FATES release version to CLM trunk: fates_s1.4.1_a3.0.0_rev2 - clm4_5_18_r271 erik 01/20/2018 Update testlist to v2 and remove yellowstone - clm4_5_18_r270 sacks 12/20/2017 Always use multiple elevation classes for glacier, even with stub glc - clm4_5_18_r269 erik 12/16/2017 Move externals to version in github - clm4_5_18_r268 erik 12/11/2017 Fix calculation of stomatal resistence used in dry-deposition, increase threshold of totvegc for soil decomposition to 0.1 - clm4_5_18_r267 sacks 12/07/2017 Fixes to accumulator fields - clm4_5_17_r266 sacks 11/27/2017 Avoid negative snow densities - clm4_5_17_r265 erik 11/18/2017 Update the clm50 parameter file for better behavior with prognostic crop, and fix a bug in clm50 urban model - clm4_5_17_r264 erik 11/16/2017 Changes from Dave Lawrenece on resetting soil carbon for spinup - clm4_5_17_r263 erik 11/08/2017 Drydep vel. for SO2 doubled, influence of organic mater in soil calmed, max daylength not hardwired to present day - clm4_5_16_r262 sacks 10/27/2017 Rename atm2lnd history fields for downscaled fields, properly turn on vic for clm45, and other minor fixes - clm4_5_16_r261 sacks 10/25/2017 Add option to reset snow over glacier columns - clm4_5_16_r260 erik 10/24/2017 Update paramater file for CLM50 as well as fates, fix a few issues - clm4_5_16_r259 erik 10/17/2017 Update to latest cime from cesm2_0_beta07 and config_components version 3 - clm4_5_16_r258 erik 10/06/2017 Revert change to fire, set n_melt_glcmec=10, update mosart to version that doesn't accumulate water in short rivers - clm4_5_16_r257 erik 09/29/2017 Fix two bugs found by Hui Tang, one for Carbon isotopes and one in the fire model - clm4_5_16_r256 erik 09/20/2017 Fresh snow grain radius is temperature dependent - clm4_5_16_r255 erik 09/18/2017 Changes to crop and enabling Carbon isotopes for crop and some miscellaneous small changes - clm4_5_16_r254 erik 09/01/2017 Update surface datasets, and point to new CMIP6 population density dataset - clm4_5_16_r253 erik 08/04/2017 Check on reasonable import/export from CLM, check ndep units from input file - clm4_5_16_r252 erik 07/24/2017 Update parameter file for some crop albedo issues, and fix a bug in urban albedo for nightime - clm4_5_16_r251 erik 07/14/2017 Update mksurfdata_map for soil depth/color, add new mapping files - clm4_5_16_r250 erik 07/13/2017 Update finundation dataset, new fsurdat files with updated soil color and soil depth, - update mosart areas, fix cheyenne_gnu - clm4_5_16_r249 sacks 07/06/2017 All new compsets, reworked test lists, and related fixes - clm4_5_16_r248 sacks 06/28/2017 Melt most ice runoff - clm4_5_16_r247 sacks 06/26/2017 New GLACIER_REGION field with CISM domain split in two - clm4_5_16_r246 sacks 06/14/2017 Update to latest cime - clm4_5_16_r245 sacks 06/14/2017 Only adjust glc_mec topographic heights if glc_do_dynglacier is true - clm4_5_16_r244 erik 06/09/2017 Update cime and cism externals, changes answers for IG compsets, test g17 grids, fix a few - issues, update mksurfdata_map - clm4_5_16_r243 andre 05/23/2017 History output cleanup from Dave Lawrence - clm4_5_16_r242 erik 05/21/2017 Use finundated streams for CLM50, and use ndep if it comes from cpl - clm4_5_16_r241 sacks 05/16/2017 Fix ch4 subtle dependence on processor count - clm4_5_16_r240 sacks 05/15/2017 Make glc_dyn_runoff_routing real-valued - clm4_5_16_r239 sacks 05/13/2017 Avoid division by zero in snow WindDriftCompaction - clm4_5_16_r238 andre 05/13/2017 ED is now an external library 'fates' - clm4_5_16_r237 erik 05/09/2017 Latest parameter file and some changes for CLM50, CLM45-transient changes answers also - clm4_5_15_r236 erik 05/01/2017 New surface datasets, and landuse.timeseries files, as well as interpolating initial conditions for - almost all cases - clm4_5_15_r235 sacks 04/27/2017 Zero dynbal fluxes if namelist variable is set - clm4_5_15_r234 andre 04/14/2017 Update rtm and mosart externals - clm4_5_15_r233 erik 04/11/2017 Pull out some constants and options to namelist - clm4_5_15_r232 erik 04/05/2017 Some small changes that affect both clm4_5 and clm5_0 answers (can be considered bug fixes to clm4_5) - clm4_5_14_r231 sacks 04/02/2017 Add option to reset snow pack over non-glacier columns - clm4_5_14_r230 sacks 03/31/2017 Fix dynamic landunits water and energy conservation - clm4_5_14_r229 erik 03/10/2017 Update cime and make some changes to drv_flds_in namelist, fix some minor bugs - clm4_5_14_r228 erik 03/07/2017 Bring in changes that were accidentally dropped as part of the clm4_5_14_r226 tag - clm4_5_14_r227 sacks 03/06/2017 Improve performance of dynamic landunits code - clm4_5_14_r226 erik 03/02/2017 Update cime, mosart and ccism to a version that is cesm2_0_beta05 or part of beta06 - clm4_5_14_r225 sacks 02/19/2017 Fix GDD accumulation in new crop columns - clm4_5_14_r224 sacks 02/10/2017 Tweaks for glaciers and snow - clm4_5_14_r223 sacks 02/03/2017 Handle patch-level C&N variables correctly with dynamic landunits - clm4_5_14_r222 sacks 01/27/2017 Fix energy budget bug with fractional snow on glacier and wetland columns - clm4_5_14_r221 sacks 01/24/2017 Change rain-snow partitioning and ice albedo for glacier columns - clm4_5_14_r220 sacks 01/22/2017 Fix crop seeding - clm4_5_14_r219 erik 01/21/2017 Answer changes for CLM50 for several issues that lead to dead crops - clm4_5_14_r218 sacks 01/13/2017 For newly initiating columns: do not copy snow state - clm4_5_14_r217 sacks 01/13/2017 Bug fix for snow radiation absorption - clm4_5_14_r216 erik 01/12/2017 Fix previous broken tag - clm4_5_14_r215 erik 01/12/2017 Update mksurfdata_map to work with new updated datasets from Peter, and use hand-edited - surfdata/landuse.timeseries datasets for f09/f19 - clm4_5_14_r214 sacks 01/03/2017 Update column states based on dwt terms between dyn_cnbal_patch and dyn_cnbal_col, and minor fixes - clm4_5_14_r213 sacks 12/30/2016 Convert buildnml to python - clm4_5_14_r212 sacks 12/22/2016 Bump science version number due to changes in clm4_5_13_r211 - clm4_5_13_r211 sacks 12/22/2016 Apply transient land cover and harvest all at once in first time step of year - clm4_5_13_r210 sacks 12/17/2016 Update cime to cesm2_0_beta04 version - clm4_5_13_r209 sacks 12/11/2016 Change definition of NBP; bring back some r205 changes that were lost in r207 - clm4_5_13_r208 sacks 12/10/2016 Rework irrigation; remove glc_smb logical - clm4_5_13_r207 andre 12/08/2016 PHS - Calculate separate root water uptake resistances for soil and root pathways - clm4_5_13_r206 andre 11/29/2016 Bugfix for Luna causing arctic to die - clm4_5_13_r205 sacks 11/16/2016 Add diagnostics for snow and glacier; fix crash in Megan - clm4_5_13_r204 erik 11/15/2016 A few answer changing bug fixes - clm4_5_12_r203 sacks 11/10/2016 Bug fixes for snow-on-lake - clm4_5_12_r202 sacks 11/09/2016 Update to cime version used in cesm2_0_beta03 - clm4_5_12_r201 sacks 11/09/2016 Rework initialization of transient weights - important with use_init_interp - clm4_5_12_r200 erik 11/08/2016 Latest parameter updates from simulations, ignore surface soil layer for plant hydraulic stress - for greater variability in surface soil moisture - clm4_5_12_r199 sacks 10/29/2016 Use CISM2 by default - clm4_5_12_r198 sacks 10/20/2016 Rework mapping of irrigation from CLM to ROF - clm4_5_12_r197 erik 10/14/2016 Some cleanup for plant hydraulic stress and adding more namelist parameters - clm4_5_12_r196 erik 09/27/2016 Bring new cime5 to clm trunk - clm4_5_12_r195 sacks 09/18/2016 Remove dependence on column weights in fire code - clm4_5_12_r194 sacks 09/01/2016 Dribble annual dyn landunit adjustment fluxes; initialize water state for new crop columns - clm4_5_12_r193 andre 08/30/2016 Bugfix in BalanceCheckMod: revert tolerance change and removal of endrun call introduced in r192 - clm4_5_12_r192 andre 08/27/2016 ED bugfixes and initial refactoring for a standalone library - clm4_5_12_r191 sacks 08/21/2016 New parameterizations for snow overburden compaction and wind drift compaction - clm4_5_12_r190 sacks 08/20/2016 Fix snow capping bug - clm4_5_11_r189 erik 08/18/2016 Bring in time varying streams for urban data (currently triggers AC use) - clm4_5_11_r188 erik 08/05/2016 A set of small answer changing issues for both clm45 and clm50 - clm4_5_10_r187 erik 07/26/2016 CLM45/50 changes: seperate carbon and water root profile, turn off undercanopystability, - really turn PHS on, LUNA predict sunlit fraction N fractionation - clm4_5_9_r186 sacks 07/13/2016 Initialize biogeochem balance checks AFTER column area updates - clm4_5_9_r185 sacks 07/07/2016 Revert glacial melt behavior to the old treatment for mountain glaciers - clm4_5_9_r184 erik 07/06/2016 CLM50 changes: Atkin form of lmr changed, new parameters and files, turn PHS on by default, - new cold snow density, reseed at exit AD spinup, fix fire bug, fix npool and cpool errors - clm4_5_9_r183 erik 07/02/2016 Decomposition is not water limited after reaching a field capacity parameter (maxpsi_hr) - rather than only at soil saturation - clm4_5_8_r182 erik 06/24/2016 Bring in option for plant hydraulic stress for clm50 - clm4_5_8_r181 erik 06/17/2016 Update cime version which fixes several issues and changes answers - clm4_5_8_r180 sacks 06/06/2016 Refactor dyn_cnbal_patch - clm4_5_8_r179 sacks 05/27/2016 Update column-level BGC state variables with dynamic landunits - clm4_5_8_r178 sacks 04/17/2016 Remove some consistency checks, and merge crop_prog with use_crop in code - clm4_5_8_r177 sacks 04/14/2016 Move CN product pools to gridcell level - clm4_5_8_r176 sacks 04/13/2016 Calculate active flags and filters earlier in initialization - clm4_5_8_r175 sacks 04/09/2016 For glc_mec, change downscaling and where SMB is computed - clm4_5_8_r174 erik 03/25/2016 Bring Rosie's respiration changes to the trunk - clm4_5_8_r173 sacks 03/17/2016 Major refactor of CN Products - clm4_5_8_r172 sacks 03/08/2016 Exclude land use and product pools / fluxes from CN summary diagnostics - clm4_5_8_r171 erik 03/02/2016 Backout COMP_RUN_BARRIERS setting, and remove all ED tests from testlist (as they all fail) - clm4_5_8_r170 sacks 02/28/2016 Add a wrapper for CN Vegetation - clm4_5_8_r169 erik 02/23/2016 Add fire several fire constants to namelist, add some new clm45/50 surface datasets - clm4_5_8_r168 sacks 02/20/2016 Fix zero methane production - clm4_5_7_r167 sacks 02/20/2016 Fix carbon isotopes in transient runs - clm4_5_7_r166 sacks 02/02/2016 Infrastructure for carbon and nitrogen conservation with dynamic landunits - clm4_5_7_r165 sacks 01/29/2016 Remove fglcmask, recreate all surface datasets - clm4_5_7_r164 erik 01/12/2016 Update CIME and MOSART - clm4_5_7_r163 sacks 12/23/2015 Improve crop performance by allocating less memory - clm4_5_7_r162 andre 12/18/2015 negative runoff updates. - clm4_5_6_r161 sacks 12/17/2015 Collapse mountain glaciers to a single elevation class - clm4_5_6_r160 sacks 12/11/2015 For glc_mec, get gridcell topographic height from atm - clm4_5_6_r159 erik 12/10/2015 Update CIME version - clm4_5_6_r158 andre 12/04/2015 misc clm 5.0 bugfixes - clm4_5_6_r157 sacks 11/27/2015 Reduce memory use for init_interp - clm4_5_6_r156 sacks 11/24/2015 Fix QSNWCPICE and glacial inception - clm4_5_6_r155 erik 11/23/2015 Bring FUN (Fixation and Uptake of Nitrogen) code option to trunk - from Mingjie, as well as latitude varying spinup from Charlie, - and a fix for crop with dynamic roots from Beth - clm4_5_6_r154 andre 11/18/2015 one year grain product pool - clm4_5_6_r153 sacks 11/17/2015 Fix snow cover fraction bug - clm4_5_5_r152 sacks 11/17/2015 Fix glc_mec energy conservation bug - clm4_5_4_r151 erik 11/13/2015 Fix broken r150 tag, with bgc_spinup issue in it - clm4_5_4_r150 erik 11/13/2015 Some needed answer changing fixes for: fire, disallow - negative photosynthis, and reduce LAI of DBT in evergreen state - clm4_5_3_r149 sacks 11/08/2015 Change cold start initialization of snow pack - clm4_5_3_r148 sacks 11/07/2015 For CLM5, increase max snow depth to 20 m - clm4_5_3_r147 andre 11/05/2015 swenson bedrock and coupler runoff bugfixes - clm4_5_3_r146 sacks 11/04/2015 Implement vertical interpolation in init_interp - clm4_5_3_r145 andre 11/03/2015 update clm50 defaults, enable clm50 crop compsets - clm4_5_3_r144 sacks 10/27/2015 Better fix for bug that leads to infinite growth in snow depth - clm4_5_3_r143 andre 10/22/2015 flexibleCN and luna bugfixes. - clm4_5_3_r142 sacks 10/19/2015 Fix bug in initialization of 12-layer snow pack - clm4_5_3_r141 sacks 10/19/2015 Fix bug that leads to infinite growth in snow depth - clm4_5_3_r140 andre 10/15/2015 mosart direct to ocean runoff - clm4_5_3_r139 andre 10/13/2015 dynamic roots from Beth Drewniak - clm4_5_3_r138 andre 10/11/2015 new accelerated spinup and soil vertical structure - clm4_5_3_r137 erik 10/09/2015 Bring in changes for fire-emissions as well tuning changes to the fire model to be used with clm5_0 - clm4_5_3_r136 andre 10/08/2015 coupler field prep for mosart and externals update - clm4_5_3_r135 sacks 10/06/2015 Substantial reduction in memory allocation for prognostic crops - clm4_5_3_r134 sacks 10/04/2015 Fixes for transient and preindustrial crop cases - clm4_5_3_r133 andre 10/02/2015 Bugfix for mksurfdata_map - add file missed by clm4_5_2_r125. - clm4_5_3_r132 andre 10/02/2015 Modify soil BGC diffusion and cryoturbation code to allow for spatially variable soil thickness. - clm4_5_3_r131 sacks 09/30/2015 Bring in cime3 - clm4_5_3_r130 andre 09/28/2015 add namelist option to reduce lake evaporation and irrigation when river water storage falls below a threshold value, and add an additional constraint on stress deciduous leaf onset. - clm4_5_3_r129 andre 09/25/2015 bump tag revision number because clm4_5_2_r128 was climate changing. - clm4_5_2_r128 andre 09/24/2015 science bugfixes (not bfb) for root fraction and bedrock thermal properties - clm4_5_2_r127 sacks 09/18/2015 Fix interpolation of initial conditions for glc_mec and crop <-> non-crop - clm4_5_2_r126 andre 09/17/2015 New decomp_depth_efolding value for clm5.0, set as a namelist parameter instead of netcdf params file. - clm4_5_2_r125 andre 09/15/2015 clm 50 hydrology updates. - clm4_5_2_r124 sacks 09/13/2015 Wind-dependent snow density - clm4_5_2_r123 sacks 09/10/2015 Fix some problems with pgi and nag compilers - clm4_5_2_r122 sacks 09/09/2015 Update to latest cime - clm4_5_2_r121 sacks 09/04/2015 Rework snow capping - clm4_5_1_r120 andre 08/29/2015 CLM 5 nitrogen models Flexible CN and LUNA - clm4_5_1_r119 erik 08/26/2015 Bring hobart/nag bug fixes to trunk, and fix a few bugs - clm4_5_1_r118 sacks 08/05/2015 Minor rework of glc coupling fields - clm4_5_1_r117 sacks 07/28/2015 Repartition rain vs. snow from atmosphere - clm4_5_1_r116 sacks 07/22/2015 Rename some history fields - clm4_5_1_r115 sacks 07/15/2015 Remove redundant code, rename a variable - clm4_5_1_r114 sacks 07/10/2015 Update cime external, remove genf90-generated files - clm4_5_1_r113 sacks 07/09/2015 Support backwards compatibility of restart variable names - clm4_5_1_r112 oleson 07/01/2015 Justin Perket snow on vegetation - clm4_5_1_r111 sacks 06/12/2015 Remove temporary hack to get bfb results in InitSnowLayers - clm4_5_1_r110 sacks 06/12/2015 Add flexibility to have more snow layers - clm4_5_1_r109 sacks 06/06/2015 Fix bug in DivideSnowLayers - clm4_5_1_r108 andre 05/29/2015 Crop changes from Sam Levis - clm4_5_1_r107 andre 05/19/2015 Update externals to use github version of cime1.0.7. - clm4_5_1_r106 erik 05/14/2015 Fix CO2 forcing for MEGAN - clm4_5_1_r105 erik 04/16/2015 Move test lists to beneath active components, change build scripts from cshell to perl, move to new cime directory structure - clm4_5_1_r104 erik 01/27/2015 Update externals to latest cesm beta tag + bring in shared build for clm4_5/clm5_0 for testing - clm4_5_1_r103 sacks 01/01/2015 enable transient crops - clm4_5_1_r102 sacks 12/27/2014 make new input datasets to support transient crops - clm4_5_1_r101 sacks 12/09/2014 rework cold start initialization for transient runs - clm4_5_1_r100 sacks 12/03/2014 update pio calls to pio2 API - clm4_5_1_r099 sacks 12/02/2014 add ozone stress code from Danica Lombardozzi - clm4_5_1_r098 sacks 11/29/2014 update externals to cesm1_3_beta14 or beyond - clm4_5_1_r097 mvertens 11/24/2014 major refactorization to introduce new soilbiogeochem data types and routines that are independent of either ED or CN datatypes - clm4_5_1_r096 erik 11/19/2014 Several answer changing bug-fixes: snow grain size, lake hydrology, default settings, organic soil - clm4_5_1_r095 andre 11/10/2014 N comp refactoring by Jinyun Tang (LBL) and transpiration sink isolation by Gautam Bisht (LBL) - clm4_5_1_r094 sacks 11/07/2014 misc. glacier-related updates - clm4_5_1_r093 sacks 11/07/2014 change cold-start snow initialization, update cism external - clm4_5_1_r092 muszala 11/04/2014 bug fixes from santos that address valgrind problems. update rtm external - clm4_5_1_r091 muszala 10/27/2014 update externals. fix bug so CLM runs with Intel 14x. - clm4_5_1_r090 sacks 10/16/2014 modularize irrigation; do some unit test rework - clm4_5_1_r089 erik 10/13/2014 Bring new urban building temperature to trunk as a clm5.0 feature as well as human-stress index calculations - clm4_5_1_r088 muszala 10/01/2014 pull out ED deps. in TemperatureTypeMod, can now compile with pgi 14.7 - clm4_5_1_r087 erik 09/30/2014 Fix two balance check errors, and turn abort for balance check back on to appropriate levels - clm4_5_1_r086 muszala 09/25/2014 critical ED modifications from r fisher, fix bug 2043 - clm4_5_1_r085 sacks 09/19/2014 replace conditionals with polymorphism for soil water retention curve - clm4_5_1_r084 sacks 09/18/2014 make glc_dyn_runoff_routing spatially-varying, based on input from glc - clm4_5_1_r083 muszala 09/17/2014 only update scripts and run new baselines. this due to an error in yellowstone pgi test naming (clm_aux45 changed to aux_clm45) - clm4_5_1_r082 muszala 09/11/2014 Merge in a number of ED changes to address science bugs and infrastructure (partiulararly restarts) - clm4_5_1_r081 mvertens 08/24/2014 major infrastructure changes and directory reorganization under src - clm4_5_1_r080 erik 08/16/2014 Update externals to trunk version, allow eighth degree as a valid resolution - clm4_5_1_r079 andre 07/31/2014 G. Bisht (LBL) soil temperature refactor; machines update for goldbach-intel - clm4_5_1_r078 muszala 07/23/2014 add lai stream capability and the ability to run with V5 cruncep data - clm4_5_1_r077 andre 07/10/2014 Refactor from Jinyun Tang (LBL) to make hydrology more modular. - clm4_5_1_r076 erik 07/07/2014 Answer changes for fire code from Fang Li - clm4_5_75 muszala 05/30/2014 update externals to rtm1_0_38 and esmf_wrf_timemgr_140523 - clm4_5_74 sacks 05/28/2014 misc. bfb changes - see detailed summary below - clm4_5_73 erik 05/28/2014 Add the stub ability for clm5_0 physics to CLM build system - clm4_5_72 muszala 05/05/2014 Introduce code for Ecosystem Demography (CLM(ED)) Model - clm4_5_71 sacks 05/02/2014 2-way feedbacks for glacier, veg columns compute glacier SMB, and related changes - clm4_5_70 muszala 04/18/2014 bring in SHR_ASSERT macros - clm4_5_69 andre 03/18/2014 start unit testing build-namelist - clm4_5_68 erik 03/07/2014 Update scripts to version that turns on transient CO2 streams for transient compsets, and update CISM (changes answers) - clm4_5_67 mvertens 03/06/2014 removed initSurfAlb as part of the initialization - clm4_5_66 mvertens 03/03/2014 refactoring of initialization and introduction of run-time finidat interpolation - clm4_5_65 mvertens 02/25/2014 Turn off MEGAN vocs when crops is running - clm4_5_64 muszala 02/19/2014 fix and clean ncdio_pio.F90.in. clean clm_time_manager. update externals. - clm4_5_63 sacks 02/14/2014 add some code needed for dynamic landunits; activate 0-weight veg landunit sometimes - clm4_5_62 erik 02/10/2014 Get PTCLM working robustly, US-UMB test working, add CO2 streams to datm, add more consistency testing between compsets and user settings - clm4_5_61 sacks 02/04/2014 add 3-d snow history fields; continue harvest past end of pftdyn timeseries - clm4_5_60 andre 01/30/2014 refactor build-namelist - clm4_5_59 sacks 01/22/2014 use new get_curr_yearfrac function in clm_time_manager - clm4_5_58 sacks 01/22/2014 major refactor of transient pft code, in prep for dynamic landunits - clm4_5_57 sacks 01/07/2014 change CNDV water conservation to use the pftdyn method - clm4_5_56 sacks 01/02/2014 update scripts external to fix I20TRCLM45BGC compset - clm4_5_55 sacks 12/27/2013 add hooks to Sean Santos's unit test frameworks, and begin to add CLM unit tests - clm4_5_54 sacks 12/27/2013 update externals to cesm1_3_beta06 - clm4_5_53 muszala 12/19/2013 refactor restart interfaces - clm4_5_52 sacks 11/26/2013 turn on longwave radiation downscaling for glc_mec by default - clm4_5_51 sacks 11/26/2013 rework downscaling of atm fields for glc_mec - clm4_5_50 erik 11/24/2013 Bring in a bunch of b4b bugfixes, fix getregional script, start move of PTCLM to PTCLMmkdata tool - clm4_5_49 muszala 11/16/2013 swenson anomaly forcing - part 1 - clm4_5_48 muszala 11/14/2013 bug fixes for CLM dry deposition and MEGAN VOC emissions - clm4_5_47 muszala 11/12/2013 fix Bug 1858 - AGDD now reset annually - clm4_5_46 sacks 11/08/2013 remove zeroing out of slope for special landunits - clm4_5_45 sacks 11/08/2013 refactor daylength calculation, and other minor changes - clm4_5_44 sacks 11/08/2013 temporary hack to daylength initialization to provide baselines for the next tag - clm4_5_43 sacks 11/06/2013 allocate memory for most landunits in every grid cell (needed for dynamic landunits) - clm4_5_42 sacks 11/04/2013 fix bug 1857 for CLM4.5 - CNDV running temperature means are incorrect - clm4_5_41 andre 10/30/2013 update scripts to convert clm4_5 CPP flags to namelist variables. - clm4_5_40 muszala 10/24/2013 fix Bug 1752 - urban conductances depend on weights in an undesirable way - clm4_5_39 muszala 10/23/2013 bug fix from santos - h2osoi_vol not passed to atmosphere model on restart - clm4_5_38 sacks 10/18/2013 change irrigation variables to be pft-level - clm4_5_37 muszala 10/10/2013 Modifications to bring clm up to date with major driver refactoring in drvseq5_0_01 - clm4_5_36 sacks 10/04/2013 new surface datasets, and other minor fixes - clm4_5_35 sacks 10/01/2013 get CLM running on edison - clm4_5_34 erik 09/30/2013 Get PTCLM working, fix a few small bugs - clm4_5_33 muszala 09/26/2013 clean up from mistakes in previous tag - clm4_5_32 muszala 09/26/2013 bug fix tag - 1798, 1810 - clm4_5_31 sacks 09/25/2013 fix bug 1820: incomplete conditional in CNSoyfix leads to buggy results and decomposition dependence - clm4_5_30 sacks 09/24/2013 fix performance bug in decomposition initialization - clm4_5_29 sacks 09/24/2013 fix threading in CLM4.5, and other misc fixes - clm4_5_28 sacks 09/20/2013 fix FracH2oSfc bug - clm4_5_27 sacks 09/20/2013 fix crop nyrs bug - clm4_5_26 muszala 09/19/2013 water balance and SMS_Ly1.f19_g16.ICLM45BGCCROP fix - clm4_5_25 erik 09/13/2013 Bring in Tony's changes to kick sno all the way up to the coupler layer, makes all - CESM components more similar to each other - clm4_5_24 sacks 09/03/2013 update externals to cesm1_3_beta02 or later - clm4_5_23 muszala 08/22/2013 refactor to allow CH4 params. to be read from netcdf file and clean up clm4_5_20 - clm4_5_22 muszala 07/30/2013 aux_clm testlist reorganization - clm4_5_21 muszala 07/24/2013 ifdef and bounds refactor - clm4_5_20 muszala 07/20/2013 refactor to allow CN and BGC params. to be read from netcdf file - clm4_5_19 sacks 07/17/2013 fix setting of bd in iniTimeConst - clm4_5_18 sacks 07/09/2013 rework urban indexing - clm4_5_17 sacks 07/03/2013 misc cleanup and bug fixes - clm4_5_16 sacks 07/02/2013 only run filters over 'active' points - clm4_5_15 muszala 07/01/2013 complete associate refactor for pointers in clm4_5 source - clm4_5_14 muszala 06/20/2013 preparation for associate refactor in clm4_5_15 - clm4_5_13 andre 06/14/2013 hydrology reordering from Jinyun Tang - clm4_5_12 muszala 06/13/2013 NoVS test, NAG mods and remove TWS from restart file - clm4_5_11 sacks 06/11/2013 Change pct_pft and related surface dataset variables to be % of landunit - clm4_5_10 muszala 06/10/2013 refactor clmtype - clm4_5_09 muszala 06/04/2013 volr and vic fix, update mct and rtm - clm4_5_08 muszala 06/03/2013 port for NAG compiler - clm4_5_07 erik 05/31/2013 New spinup files for CLM45 AND RTM, work on PTCLM, turn drydep off by default, update externals - clm4_5_06 erik 05/15/2013 A few small bug fixes, more updates to README files - clm4_5_05 muszala 05/14/2013 hcru bug fixes - clm4_5_04 erik 05/13/2013 Fix the previous broken tag - clm4_5_03 erik 05/10/2013 Several bug fixes for release, urban and test single point surface datasets - clm4_5_02 sacks 05/07/2013 make 'shared' tools directory, and other minor tools fixes - clm4_5_01 muszala 05/06/2013 update externals - clm4_5_00 erik 05/02/2013 Official end to CLM4.5 development for CLM offline - clm4_0_81 bandre 04/29/2013 Charlie Koven's variable consolidation, cryoturbation and BSW CPP changes - clm4_0_80 erik 04/26/2013 Bring Fang Li. Fire model into CLM4.5 science, update ALL CLM4.5 surface datasets, - provide a working initial condition file for CLM45BGC@f19_g16-1850 - clm4_0_79 muszala 04/24/2013 pftdyn, pft-phys*.nc and datm8 update - clm4_0_78 muszala 04/23/2013 MEGAN fixes - clm4_0_77 sacks 04/23/2013 fix carbon balance bug in transient runs with VERTSOI, and fix Soil Hydrology bug - clm4_0_76 muszala 04/22/2013 spinup changes from Charlie Koven (part 1) - clm4_0_75 muszala 04/19/2013 run propset - clm4_0_74 muszala 04/17/2013 snow_depth changes, major scripts overhaul, bug fix for tools - clm4_0_73 sacks 04/15/2013 update mksurfdata_map for CLM4.5, and other misc. updates, mainly to tools - clm4_0_72 muszala 04/11/2013 maoyi bug fix for vic hydro - clm4_0_71 muszala 04/10/2013 compsets refactoring by mvertens - clm4_0_70 muszala 04/01/2013 bring in vic hydrology - clm4_0_69 muszala 03/26/2013 remove hydro reorder, volr and esmf mods - clm4_0_68 erik 03/16/2013 Fix some issues in mksurfdata_map for generation of ne120np surface data file. - Put error back in CLM if weights don't sum to 100. Add in Keith's photosynthesis change for CLM45. - clm4_0_67 muszala 03/12/2013 Jinyun photosynthesis and hydrology reorder - clm4_0_66 sacks 03/07/2013 turn off subgrid topography snow parameterization for glc_mec landunits - clm4_0_65 sacks 03/07/2013 back out Machines external to get more tests to pass, especially IG - clm4_0_64 muszala 03/06/2013 update externals. fixes 40/45 intial condition problem - clm4_0_63 muszala 03/04/2013 bug 1635 fix - 4_0 CN bug - clm4_0_62 sacks 02/24/2013 add active flags, change subgrid weighting convention, other misc fixes - clm4_0_61 muszala 02/20/2013 rtm, drv and clm mods: tws, olr, r01 rdric file and SoilHydroMod - clm4_0_60 erik 02/11/2013 Bring CLM4.5 code from clm45sci branch to trunk as an option set at configure time - clm4_0_59 mvertens 12/20/2012 restructure clmtype and all pointer references, new directory structure - clm4_0_58 erik 12/14/2012 Uncomment us20 and wus12 datasets, more testing to: bluefire, yellowstone, frankfurt - clm4_0_57 muszala 11/30/2012 update trunk with release mods, some rtm fixes - clm4_0_56 sacks 11/27/2012 fix s2x tsrf, add s2x diagnostics - clm4_0_55 muszala 11/14/2012 bring in flooding capability - clm4_0_54 erik 10/09/2012 Fix esmf for carma field, fix some CLM_USRDAT issues - clm4_0_53 erik 10/03/2012 Update to fsurdat, fpftdyn, finidat datasets, new high resolution organic/fmax/glacier raw datasets - clm4_0_52 sacks 09/27/2012 new pct_glacier raw data file - clm4_0_51 muszala 09/26/2012 bug fixes, pio performance and SCRIP files - clm4_0_50 muszala 09/21/2012 testing of clm and new rof component - clm4_0_49 erik 09/16/2012 Move clm testing to use CESM test framework - clm4_0_48 muszala 09/11/2012 bug fixes, xFail to tests and normalize test output for CLM - clm4_0_47 muszala 08/23/2012 bug fixes - clm4_0_46 muszala 08/08/2012 R01 support and update externals - clm4_0_45 sacks 07/20/2012 fix virtual columns; new urban mksurfdata_map - clm4_0_44 erik 07/09/2012 Add wrf resolutions, update externals to cesm1_1_beta15, all components use build-namelist now - clm4_0_43 sacks 04/06/2012 Add diagnostic fields, modify some existing history fields - clm4_0_42 erik 03/27/2012 Bring in Francis Vitt's MEGAN changes. - clm4_0_41 erik 03/13/2012 Bring rmfmesh/rtmmap branches to trunk - clm4_0_40 erik 02/16/2012 Back out update to new T31 surface datasets - clm4_0_39 erik 02/01/2012 Bring newgrid branch to trunk - clm4_0_38 erik 01/23/2012 Fix f09 surface datasets - clm4_0_37 erik 09/26/2011 Fix unstructured grids history files - clm4_0_36 erik 09/22/2011 Comment out RTM mapping files for f09 and f19 - clm4_0_35 erik 09/13/2011 Bring in Mariana's non2D grid branch to trunk, enabling HOMME grids: ne30np4/ne120np4 - clm4_0_34 erik 08/18/2011 Bring tcens branch to trunk, fix a few issues - clm4_0_33 erik 07/25/2011 Move changes on release branch over to trunk - clm4_0_32 erik 05/19/2011 Make I1850SPINUPCN compset use MOAR data, various bug fixes, work on test lists - clm4_0_31 erik 05/13/2011 Fix answers for transient_CN, fix interpinic - clm4_0_30 erik 05/11/2011 New finidat/fsurdat files for T31 - clm4_0_29 erik 05/05/2011 Backout interpinic changes to one that works - clm4_0_28 erik 05/03/2011 Remove DUST/PROGSSLT in land coupler layer, update driver and scripts - clm4_0_27 erik 05/02/2011 Move crop branch over to trunk - clm4_0_26 erik 03/23/2011 Update externals, driver update changes answers, drydep changes from fvitt, fix bugs - clm4_0_25 erik 03/22/2011 Always output restart-history files add more meta-data to them, fix urbanc_alpha and 2.5x3.33 datasets, Changes from Keith O on SNOWLIQ/SNOWICE - clm4_0_24 erik 02/09/2011 Fix mksurfdata and add ability to override soil_fmax - clm4_0_23 erik 02/03/2011 Add in new glacier-MEC use-cases - clm4_0_22 erik 01/20/2011 Move coupler field indicies to clm, move cpl_* directories up a level, add the cpl_share directory - clm4_0_21 jedwards 01/12/2011 Remove includes, finish PIO transition - clm4_0_20 erik 01/11/2011 Update for ESMF metadata, update doc. from release branch, bug fixes (doc of qflx_evap_tot, threading CNDV, aer/ndepregrid) - clm4_0_19 erik 12/08/2010 Bring irrigation branch to the trunk - clm4_0_18 erik 11/21/2010 Fix a problem with the clm template, update scripts version to fix bug with linking with ESMF - clm4_0_17 erik 11/20/2010 Update to externals that change answers to roundoff, use drv pio namelist, add in T341 datasets - clm4_0_16 erik/mverten 10/27/2010 Fix downscaling roundoff difference for same-grids by copying scale factor when needed - clm4_0_15 erik/mverten 10/24/2010 Move pio branch to trunk - clm4_0_14 erik 10/19/2010 Fix finidat file for T31 sim_year=2000 cases - clm4_0_13 erik 10/16/2010 Bring in PTCLM branch, add in T31 finidat file and turn off ice_runoff for T31 - clm4_0_12 erik 09/10/2010 Add U10 to history, cesm1_0_rel06 updates, PTCLM02 updates (except mksurfdata), remove ndepdat/dyn/faerdep - clm4_0_11 erik 08/27/2010 New files for rcp6, fix MPI bug, update externals - clm4_0_10 erik 08/04/2010 Update doc to cesm_rel05, bug-fixes, fix issues for single-point, mksurfdata/getregional scripts - clm4_0_09 erik 06/14/2010 Fix some small issues, update documentation, and externals - clm4_0_08 erik 06/04/2010 Snow hydrology bug fix from Keith and Dave - clm4_0_07 erik 06/03/2010 Some cleanup/fix bugs, add RTM var, add albice to namelist, allow last-millenium in mksurfdata, allow setting of datm_presaero in clm test-suite - clm4_0_06 erik 05/26/2010 Update gglc to cism - clm4_0_05 erik 05/25/2010 Move Nitrogen deposition stream branch to trunk - clm4_0_04 erik 05/20/2010 New namelist items: ice_runoff, scaled_harvest, carbon_only, - new RTM hist vars, new finidat files, update esmf interface, turn off aerosol read quicker - clm4_0_03 erik 05/17/2010 Changes from Francis for VOC and drydep - clm4_0_02 erik 05/13/2010 Make sure dtime is initialized, so that answers are consistently the same as clm4_0_00 - clm4_0_01 erik 05/11/2010 Move glacier multiple elevation class branch to the trunk so that we can work with the active glacier model - clm4_0_00 erik 05/04/2010 Update to datm8, redirect aquifer overflow - to drainage, add gx3v7 masks, script to extract regional - datasets, add harvesting for CN, modify shrubs, include urban - model, ice stream for snowcapping, new build-namelist system, - scale solar by solar zenith angle in datm, deep soil with - bedrock at bottom, organic matter in soils, SNICAR for snow - radiation, sparce dense aero, snow cover changes - clm3_8_00 erik 05/04/2010 Get future scenarios working, finalize - documentation, bring in MEGAN VOC and CNDV, simplify, - mksurfdata optimization, fix bugs: snow enthalpy, BMOZ, pergro, - use pft weights from fsurdat NOT finidat - clm3_7_15 erik 04/27/2010 Finish User's Guide, surfdata files for urban-1pt, fix mksurfdata ifort bugs, work with testing - clm3_7_14 erik 04/08/2010 Fix rcp=2.6/4.5 1-degree fndepdyn filenames - clm3_7_13 erik 04/08/2010 Add in missing rcp=2.6/6 use-cases, and fix syntax errors in the namelist_defaults file - clm3_7_12 erik 04/08/2010 rcp=2.6/4.5 datasets for fndepdyn and aerdepdat, fix some minor issues, new 1pt urban surfdata files - clm3_7_11 erik 04/07/2010 qtr-degree and T85 surfdata, rcp=2.6/4.5 datasets, doc updates - clm3_7_10 erik 03/22/2010 Fix drydep so that BMOZ case will work - clm3_7_09 erik 03/21/2010 Fix snow enthalpy bug, cndv datasets, various fixes - clm3_7_08 mvertens 03/12/2010 Removal of check for weights if dynamic land use is - used - clm3_7_07 erik 03/10/2010 New finidat datasets for 1-deg, 2-deg, and abort if weights from finidat/fsurdat files are too different, and use fsurdat files as truth - clm3_7_06 erik 03/10/2010 Bring cndv branch to trunk - clm3_7_05 erik 02/24/2010 Bring VOC branch source code to trunk - clm3_7_04 erik 02/17/2010 Bring VOC branch (vocemis-drydep18_clm3_7_03) tools, testing, and build to trunk (everything other than VOC code changes) - clm3_7_03 erik 02/10/2010 Add in more future scenario datasets, new history fields from Keith - clm3_7_02 erik 02/06/2010 Start adding in new rcp=8.5 datasets, remove some junk, change some env_conf variables, add user_nl_clm - clm3_7_01 erik 01/29/2010 OpenMP fix for pftdyn, start adding in rcp's, update ndeplintInterp.ncl script - clm3_7_00 erik 01/22/2010 Update to datm8, redirect aquifer overflow to drainage, add gx3v7 masks, script to extract regional datasets, add harvesting for CN, modify shrubs, include urban model, ice stream for snowcapping, new build-namelist system, scale solar by solar zenith angle in datm, deep soil with bedrock at bottom, organic matter in soils, SNICAR for snow radiation, sparce dense aero, snow cover changes - clm3_6_64 erik 01/22/2010 Update documentation and README/Quickstart files, set NetCDF large-file format on by default in template, update pio, update some fsurdat files to vocemis-drydep versions, add 2.5x3.33_gx3v7 frac file, make gx3v7 default for 4x5 res - clm3_6_63 erik 01/09/2010 Get answers to be identical with ccsm4_0_beta38 for 1 and 2 degree transient cases - clm3_6_62 erik 01/08/2010 Fix startup of PFT transient cases so properly use data from pftdyn file rather than finidat file - clm3_6_61 erik 01/07/2010 Comment out endrun on finidat and fsurdat weights being incomptable, and go back to using finidat weights - clm3_6_60 erik 01/05/2010 Fix clm template - clm3_6_59 erik 01/05/2010 Update to datm8, fix so wts used are from fsurdat file NOT finidat file - clm3_6_58 erik 12/08/2009 Fix rpointer, correct units for export of nee, start adding testing for intrepid - clm3_6_57 erik 11/20/2009 Redirect aquifer overflow to drainage, so doesn't end up in ocean - clm3_6_56 erik 11/10/2009 New ndepdat and ndepdyn datasets - clm3_6_55 erik 11/05/2009 Fix tool to create Nitrogen deposition datasets, and change configure to use CCSM Makefile as source for TopLevel Makefile - clm3_6_54 erik 10/28/2009 Allow comp_intf to change on ccsm build, reduce default hist fields, start adding 2.5x3.33, start adding VOC fsurdat datasets, new finidat files for f09 and f19 - clm3_6_53 erik 09/22/2009 Fix so that T31_gx3v7 file is actually included - clm3_6_52 erik 09/17/2009 Add T31_gx3v7 support, remove forganic, read from fsurdat, add script to extract regional datasets, work with CN output, add more urban/rural fields - clm3_6_51 erik 09/01/2009 Update fndepdyn and aerdep datasets (f02,f05,f09,f10) (1850,2000) and f09, f10 transient (1850-2000) - clm3_6_50 erik 08/28/2009 Fix ncl regridding scripts so that NO missing values are allowed for aerosol and nitrogen deposition - clm3_6_49 erik 08/25/2009 Fix ncl interpolation scripts, update externals, turn on CLM_CCSM_BLD for bluefire,jaguar, ESMF3 compliance - clm3_6_48 erik 08/12/2009 New aerosol/nitrogen deposition datasets, mksurfdata work, scm work, clm_usr_name option to build-namelist - clm3_6_47 erik 08/03/2009 Fix hybrid bug for dynpft case, update externals - clm3_6_46 erik 07/22/2009 Get more tests to work/document them, add use cases for 1850_control, 2000_control, and - 20thC_transient, straighten out single-point grids, Listen to LND_CDF64 env variable from - template, remove CLM_ARB_IC. - clm3_6_45 erik 07/10/2009 Remove inconsistent finidat file in clm3_6_44 - clm3_6_44 erik 07/09/2009 Fix C13 bug, update scripts, drv, datm. Add domain files for idmap atm-ocn grids for datm. Remove SEQ_MCT, add new ESMF env vars to template. Work with ndeplintInterp - clm3_6_43 erik 06/10/2009 Fix pftdyn bug, enable 1D primary hist files, fix time-const3D output, fix template bug, enable cpl_esmf/cpl_mct - clm3_6_42 erik 06/02/2009 Bring CN Harvest branch to trunk - clm3_6_41 kauff 05/29/2009 shrub mods, abort if nthreads > 1 (temporary, wrt bugz #965) - clm3_6_40 erik 05/28/2009 Fix openMP bug, add fndepdyn ncl script, fix interpinic for urban, add mkharvest to mksurfdata, new spinups, turn CLAMP on for CASA or CN - clm3_6_39 erik 05/07/2009 Bug fix for script version and maxpatchpft back to numpft+1 - clm3_6_38 erik 05/06/2009 New fsurdat for other resolutions, bug-fixes, deep wetlands to bedrock, new spinups for 1.9x2.5 1850, 2000 - clm3_6_37 erik 04/27/2009 Update faerdep dataset for 1.9x2.5 to point to version cice is using for 1850 and 2000 - clm3_6_36 erik 04/27/2009 Handle transient aersol, make maxpatchpft=numpft+1 default, new datasets for 1.9x2.5 and 0.9x1.25, change doalb - clm3_6_35 erik 04/20/2009 Fix major logic bug in mksurfdata - clm3_6_34 oleson 04/19/2009 Fix bangkok urban bug - clm3_6_33 erik 04/16/2009 Bring in dynpft changes from cbgc branch - clm3_6_32 erik 04/15/2009 Add irrigation area to mksrfdata, fix high-res and pftdyn problems - clm3_6_31 erik 04/01/2009 New surface datasets for 1850,2000, support for 0.9x1.25_gx1v6, urban always on. New pft-physiology file. Update scripts so remove some CLM_ env_conf vars. Fix CN for urban/pftdyn. - clm3_6_30 oleson 03/19/2009 Fix urban roof/wall layers - clm3_6_29 oleson 03/19/2009 CN SAI, CN testing fix, rad step size fix - clm3_6_28 oleson 03/17/2009 Fix permission denied error when reading surface dataset - clm3_6_27 oleson 03/16/2009 Urban model changes and FGR12 fix - clm3_6_25 dlawren 03/13/2009 Daylength control on Vcmax, 1%Lake,wetland,glacier in mksrfdat, remove ELEVATION in surface data file - clm3_6_24 oleson 03/09/2009 Fix urban testing and some history field changes - clm3_6_23 oleson 03/08/2009 Prune history fields and change to snowdp threshold for solar radiation penetration into snow - clm3_6_21 oleson 03/04/2009 History file changes and finish testing on tags clm3_6_19 and clm3_6_20 - clm3_6_19 oleson 02/27/2009 Changes to urban model and urban surface data - clm3_6_17 oleson 02/26/2009 Urban model changes and mksurfdata changes to incorporate urban data - clm3_6_16 erik 02/12/2009 Multiple elevation classes on surface dataset, urban fixes, mpi-serial and testing fixes - clm3_6_15 erik 01/19/2009 Bring clm36sci branch to the trunk - clm3_6_14 erik 10/10/2008 Fix some global urban issues, fix pftdyn, really get compile-only option - working in testing - clm3_6_13 erik 10/01/2008 Update to new version of cpl7 scripts and build, update externals for versions - needed for clm36sci branch, add new CASA tests - clm3_6_12 erik 09/21/2008 Fix restarts for urban, add capability to do global urban experiments, - add in new forcing height changes - clm3_6_11 dlawren 08/26/2008 Ice stream for snow capped regions - clm3_6_10 tcraig 08/15/2008 extend rtm tracer, ascale for tri-grids, AIX O3 to O2 - clm3_6_09 erik 08/11/2008 Fix clm.cpl7.template to run hybrid and branch cases - clm3_6_08 erik 08/06/2008 Fix bugs, and build changes for inputdata repo - clm3_6_07 erik 07/08/2008 Implement new build namelist system from Vertenstein/Eaton, bluefire, and BGP updates - clm3_6_06 erik 05/30/2008 Small fix needed for ccsm4_alpha30 - (use gx1v5 for some resolutions when OCN_GRID==ATM_GRID) - clm3_6_05 erik 05/27/2008 Fix to compile with PGI-6, update scripts, fix cpl7.template for new scripts LND_GRID, - fix 2.65x3.33 frac dataset. - clm3_6_04 erik 05/20/2008 Remove all MCT permutes, fix cpl7 script issues, remove offline mode, - add ability to run over a range of years - clm3_6_03 erik 05/08/2008 Fix so listen to next_swcday to calculate albedo rather than using irad - clm3_6_02 erik 03/25/2008 Minor fix in configure remove perl5lib version under models/lnd/clm/bld - clm3_6_01 erik 03/20/2008 40 m forcing height changes for clm - clm3_6_00 erik 03/20/2008 Fully implement sequential-ccsm mode, upgrade configure, build-namelist and testing, - upgrade interpolation tool, add mkdatadomain, write to iulog rather than 6 explicitly, - SCAM update, Update datasets, add archiving, and build-streams, add in point version - of Urban model, change directory structure to mimic CCSM - clm3_5_20 erik 03/17/2008 Bug fixes before spinning off clm3_6_00, put in changes from ccsm4a01_clm3_5_18 - to ccsm4a04_clm3_5_18 - clm3_5_19 erik 03/06/2008 Change directory structure to mimic CCSM, fix so no NaNS on BGC interpinic output, - new half degree CN clmi dataset - clm3_5_18 erik 02/21/2008 Update to latest seq-ccsm4.alpha tag - clm3_5_17 erik 02/06/2008 Merge Tony Craig's FMI branch fmi12_clm3_5_16 to the clm trunk - clm3_5_16 erik 01/28/2008 Get point version of Urban code onto trunk (urban code can not restart) - clm3_5_15 erik 12/10/2007 Fix interpinic for half degree grid, add in large-file support, - allow configure to work with ccsm directory structure - clm3_5_14 erik 11/27/2007 Use build-streams, and archiving, multiple bug-fixes - clm3_5_13 erik 11/16/2007 Update xml file with file needed for ccsm3_5_beta18 - clm3_5_12 erik 11/08/2007 Tag with new files needed for ccsm3_5_beta17 - clm3_5_11 erik 09/28/2007 Update datasets in the DefaultCLM file for 0.23x0.31, 0.47x0.63, 0.9x1.25 and - add fndepdyn file for 1.9x2.5 - clm3_5_10 jet 09/18/2007 SCAM update - clm3_5_09 erik 08/31/2007 Change configure to NOT have csm_share code for ccsm_con option, and add in 1x1.25 file, - and update datm7 and csm_share - clm3_5_08 tcraig 08/20/2007 convert 6 to iulog in logfile, updates for I/O - clm3_5_07 erik 08/17/2007 Add mkdatadomain tool, add cprnc and perl5lib as externals - clm3_5_06 erik 08/10/2007 Update: interpolation, testing, script namelist build, and scripts. Fix bugs, - and fix possible - clm3_5_05 tcraig 07/11/2007 seq clm mods and first hist refactor mods - clm3_5_04 mvertens 06/05/2007 lnd_comp_mct.F90 change to work with sequential diagnostics - clm3_5_03 tcraig 05/23/2007 reduce memory, partial I/O refactor, downscaling implementation - clm3_5_02 mvertens 05/22/2007 put in hourly coupling with sequential driver - clm3_5_01 erik 05/16/2007 Move newcn06 branch to trunk - clm3_5_00 erik 05/03/2007 New surface datasets, improved canopy integration, and various improvements to Hydrology + ctsm1.0.dev001 sacks 06/22/2018 Begin separating SoilHydrology flux calculations (this was skipped on release branch) + clm5.0.dev013 erik 06/12/2018 cleanup and update cime and cism (corresponds to release-clm5.0.03) + clm5.0.dev012 sacks 05/17/2018 Fixes for variable_year orbital mode (corresponds to release-clm5.0.01 and release-clm5.0.02) + clm5.0.dev011 erik 05/16/2018 1850 ndep update, cism update, PE layouts, turn BFBFLAG for testing + clm5.0.dev010 erik 05/15/2018 Update cime version to version in cesm2.0.beta10, changes answers for 1850 compsets because of orbit + clm5.0.dev009 sacks 05/10/2018 New init_interp method + clm5.0.dev008 erik 04/27/2018 With FUN subtract out soil nitrification flux of plant uptake of soil NH3 and NO3 + clm5.0.dev007 erik 04/24/2018 Bring in a few answer changing things: FATES, cism updates, IC file fix, + testing 1850 compset use 1850 orbit + clm5.0.dev006 sacks 04/12/2018 Don't allocate memory for zero-weight natveg patches and urban + clm5.0.dev005 sacks 04/10/2018 Two fixes for init_interp + clm5.0.dev004 erik 04/09/2018 List of important bug fixes + clm5.0.dev003 erik 03/09/2018 Bug fixes for energy imbalance associated with surface water and lakes + clm5.0.dev002 sacks 02/25/2018 Add some land ice diagnostic vars needed for CMIP6 + clm5.0.dev001 erik 02/14/2018 Fix LND_TUNING_MODE for fully coupled case, update some README files/PTCLM + clm5.0.dev000 erik 02/05/2018 Double tag of clm5.0.000 with new naming convention, some updated documentation + clm5.0.000 erik 02/05/2018 Double tag of clm4_5_18_r275 for clm5.0 release + clm4_5_18_r275 erik 02/05/2018 Update initial condition files, update fates, new CMIP6 pop-dens, more lnd_tuning_mod options, updated ndep for fully coupled + clm4_5_18_r274 sacks 01/30/2018 Fix auto-detection of CIME_MODEL in a standalone checkout + clm4_5_18_r273 sacks 01/26/2018 Support a standalone checkout from git + clm4_5_18_r272 erik 01/25/2018 Bring in latest FATES release version to CLM trunk: fates_s1.4.1_a3.0.0_rev2 + clm4_5_18_r271 erik 01/20/2018 Update testlist to v2 and remove yellowstone + clm4_5_18_r270 sacks 12/20/2017 Always use multiple elevation classes for glacier, even with stub glc + clm4_5_18_r269 erik 12/16/2017 Move externals to version in github + clm4_5_18_r268 erik 12/11/2017 Fix calculation of stomatal resistence used in dry-deposition, increase threshold of totvegc for soil decomposition to 0.1 + clm4_5_18_r267 sacks 12/07/2017 Fixes to accumulator fields + clm4_5_17_r266 sacks 11/27/2017 Avoid negative snow densities + clm4_5_17_r265 erik 11/18/2017 Update the clm50 parameter file for better behavior with prognostic crop, and fix a bug in clm50 urban model + clm4_5_17_r264 erik 11/16/2017 Changes from Dave Lawrenece on resetting soil carbon for spinup + clm4_5_17_r263 erik 11/08/2017 Drydep vel. for SO2 doubled, influence of organic mater in soil calmed, max daylength not hardwired to present day + clm4_5_16_r262 sacks 10/27/2017 Rename atm2lnd history fields for downscaled fields, properly turn on vic for clm45, and other minor fixes + clm4_5_16_r261 sacks 10/25/2017 Add option to reset snow over glacier columns + clm4_5_16_r260 erik 10/24/2017 Update paramater file for CLM50 as well as fates, fix a few issues + clm4_5_16_r259 erik 10/17/2017 Update to latest cime from cesm2_0_beta07 and config_components version 3 + clm4_5_16_r258 erik 10/06/2017 Revert change to fire, set n_melt_glcmec=10, update mosart to version that doesn't accumulate water in short rivers + clm4_5_16_r257 erik 09/29/2017 Fix two bugs found by Hui Tang, one for Carbon isotopes and one in the fire model + clm4_5_16_r256 erik 09/20/2017 Fresh snow grain radius is temperature dependent + clm4_5_16_r255 erik 09/18/2017 Changes to crop and enabling Carbon isotopes for crop and some miscellaneous small changes + clm4_5_16_r254 erik 09/01/2017 Update surface datasets, and point to new CMIP6 population density dataset + clm4_5_16_r253 erik 08/04/2017 Check on reasonable import/export from CLM, check ndep units from input file + clm4_5_16_r252 erik 07/24/2017 Update parameter file for some crop albedo issues, and fix a bug in urban albedo for nightime + clm4_5_16_r251 erik 07/14/2017 Update mksurfdata_map for soil depth/color, add new mapping files + clm4_5_16_r250 erik 07/13/2017 Update finundation dataset, new fsurdat files with updated soil color and soil depth, + update mosart areas, fix cheyenne_gnu + clm4_5_16_r249 sacks 07/06/2017 All new compsets, reworked test lists, and related fixes + clm4_5_16_r248 sacks 06/28/2017 Melt most ice runoff + clm4_5_16_r247 sacks 06/26/2017 New GLACIER_REGION field with CISM domain split in two + clm4_5_16_r246 sacks 06/14/2017 Update to latest cime + clm4_5_16_r245 sacks 06/14/2017 Only adjust glc_mec topographic heights if glc_do_dynglacier is true + clm4_5_16_r244 erik 06/09/2017 Update cime and cism externals, changes answers for IG compsets, test g17 grids, fix a few + issues, update mksurfdata_map + clm4_5_16_r243 andre 05/23/2017 History output cleanup from Dave Lawrence + clm4_5_16_r242 erik 05/21/2017 Use finundated streams for CLM50, and use ndep if it comes from cpl + clm4_5_16_r241 sacks 05/16/2017 Fix ch4 subtle dependence on processor count + clm4_5_16_r240 sacks 05/15/2017 Make glc_dyn_runoff_routing real-valued + clm4_5_16_r239 sacks 05/13/2017 Avoid division by zero in snow WindDriftCompaction + clm4_5_16_r238 andre 05/13/2017 ED is now an external library 'fates' + clm4_5_16_r237 erik 05/09/2017 Latest parameter file and some changes for CLM50, CLM45-transient changes answers also + clm4_5_15_r236 erik 05/01/2017 New surface datasets, and landuse.timeseries files, as well as interpolating initial conditions for + almost all cases + clm4_5_15_r235 sacks 04/27/2017 Zero dynbal fluxes if namelist variable is set + clm4_5_15_r234 andre 04/14/2017 Update rtm and mosart externals + clm4_5_15_r233 erik 04/11/2017 Pull out some constants and options to namelist + clm4_5_15_r232 erik 04/05/2017 Some small changes that affect both clm4_5 and clm5_0 answers (can be considered bug fixes to clm4_5) + clm4_5_14_r231 sacks 04/02/2017 Add option to reset snow pack over non-glacier columns + clm4_5_14_r230 sacks 03/31/2017 Fix dynamic landunits water and energy conservation + clm4_5_14_r229 erik 03/10/2017 Update cime and make some changes to drv_flds_in namelist, fix some minor bugs + clm4_5_14_r228 erik 03/07/2017 Bring in changes that were accidentally dropped as part of the clm4_5_14_r226 tag + clm4_5_14_r227 sacks 03/06/2017 Improve performance of dynamic landunits code + clm4_5_14_r226 erik 03/02/2017 Update cime, mosart and ccism to a version that is cesm2_0_beta05 or part of beta06 + clm4_5_14_r225 sacks 02/19/2017 Fix GDD accumulation in new crop columns + clm4_5_14_r224 sacks 02/10/2017 Tweaks for glaciers and snow + clm4_5_14_r223 sacks 02/03/2017 Handle patch-level C&N variables correctly with dynamic landunits + clm4_5_14_r222 sacks 01/27/2017 Fix energy budget bug with fractional snow on glacier and wetland columns + clm4_5_14_r221 sacks 01/24/2017 Change rain-snow partitioning and ice albedo for glacier columns + clm4_5_14_r220 sacks 01/22/2017 Fix crop seeding + clm4_5_14_r219 erik 01/21/2017 Answer changes for CLM50 for several issues that lead to dead crops + clm4_5_14_r218 sacks 01/13/2017 For newly initiating columns: do not copy snow state + clm4_5_14_r217 sacks 01/13/2017 Bug fix for snow radiation absorption + clm4_5_14_r216 erik 01/12/2017 Fix previous broken tag + clm4_5_14_r215 erik 01/12/2017 Update mksurfdata_map to work with new updated datasets from Peter, and use hand-edited + surfdata/landuse.timeseries datasets for f09/f19 + clm4_5_14_r214 sacks 01/03/2017 Update column states based on dwt terms between dyn_cnbal_patch and dyn_cnbal_col, and minor fixes + clm4_5_14_r213 sacks 12/30/2016 Convert buildnml to python + clm4_5_14_r212 sacks 12/22/2016 Bump science version number due to changes in clm4_5_13_r211 + clm4_5_13_r211 sacks 12/22/2016 Apply transient land cover and harvest all at once in first time step of year + clm4_5_13_r210 sacks 12/17/2016 Update cime to cesm2_0_beta04 version + clm4_5_13_r209 sacks 12/11/2016 Change definition of NBP; bring back some r205 changes that were lost in r207 + clm4_5_13_r208 sacks 12/10/2016 Rework irrigation; remove glc_smb logical + clm4_5_13_r207 andre 12/08/2016 PHS - Calculate separate root water uptake resistances for soil and root pathways + clm4_5_13_r206 andre 11/29/2016 Bugfix for Luna causing arctic to die + clm4_5_13_r205 sacks 11/16/2016 Add diagnostics for snow and glacier; fix crash in Megan + clm4_5_13_r204 erik 11/15/2016 A few answer changing bug fixes + clm4_5_12_r203 sacks 11/10/2016 Bug fixes for snow-on-lake + clm4_5_12_r202 sacks 11/09/2016 Update to cime version used in cesm2_0_beta03 + clm4_5_12_r201 sacks 11/09/2016 Rework initialization of transient weights - important with use_init_interp + clm4_5_12_r200 erik 11/08/2016 Latest parameter updates from simulations, ignore surface soil layer for plant hydraulic stress + for greater variability in surface soil moisture + clm4_5_12_r199 sacks 10/29/2016 Use CISM2 by default + clm4_5_12_r198 sacks 10/20/2016 Rework mapping of irrigation from CLM to ROF + clm4_5_12_r197 erik 10/14/2016 Some cleanup for plant hydraulic stress and adding more namelist parameters + clm4_5_12_r196 erik 09/27/2016 Bring new cime5 to clm trunk + clm4_5_12_r195 sacks 09/18/2016 Remove dependence on column weights in fire code + clm4_5_12_r194 sacks 09/01/2016 Dribble annual dyn landunit adjustment fluxes; initialize water state for new crop columns + clm4_5_12_r193 andre 08/30/2016 Bugfix in BalanceCheckMod: revert tolerance change and removal of endrun call introduced in r192 + clm4_5_12_r192 andre 08/27/2016 ED bugfixes and initial refactoring for a standalone library + clm4_5_12_r191 sacks 08/21/2016 New parameterizations for snow overburden compaction and wind drift compaction + clm4_5_12_r190 sacks 08/20/2016 Fix snow capping bug + clm4_5_11_r189 erik 08/18/2016 Bring in time varying streams for urban data (currently triggers AC use) + clm4_5_11_r188 erik 08/05/2016 A set of small answer changing issues for both clm45 and clm50 + clm4_5_10_r187 erik 07/26/2016 CLM45/50 changes: seperate carbon and water root profile, turn off undercanopystability, + really turn PHS on, LUNA predict sunlit fraction N fractionation + clm4_5_9_r186 sacks 07/13/2016 Initialize biogeochem balance checks AFTER column area updates + clm4_5_9_r185 sacks 07/07/2016 Revert glacial melt behavior to the old treatment for mountain glaciers + clm4_5_9_r184 erik 07/06/2016 CLM50 changes: Atkin form of lmr changed, new parameters and files, turn PHS on by default, + new cold snow density, reseed at exit AD spinup, fix fire bug, fix npool and cpool errors + clm4_5_9_r183 erik 07/02/2016 Decomposition is not water limited after reaching a field capacity parameter (maxpsi_hr) + rather than only at soil saturation + clm4_5_8_r182 erik 06/24/2016 Bring in option for plant hydraulic stress for clm50 + clm4_5_8_r181 erik 06/17/2016 Update cime version which fixes several issues and changes answers + clm4_5_8_r180 sacks 06/06/2016 Refactor dyn_cnbal_patch + clm4_5_8_r179 sacks 05/27/2016 Update column-level BGC state variables with dynamic landunits + clm4_5_8_r178 sacks 04/17/2016 Remove some consistency checks, and merge crop_prog with use_crop in code + clm4_5_8_r177 sacks 04/14/2016 Move CN product pools to gridcell level + clm4_5_8_r176 sacks 04/13/2016 Calculate active flags and filters earlier in initialization + clm4_5_8_r175 sacks 04/09/2016 For glc_mec, change downscaling and where SMB is computed + clm4_5_8_r174 erik 03/25/2016 Bring Rosie's respiration changes to the trunk + clm4_5_8_r173 sacks 03/17/2016 Major refactor of CN Products + clm4_5_8_r172 sacks 03/08/2016 Exclude land use and product pools / fluxes from CN summary diagnostics + clm4_5_8_r171 erik 03/02/2016 Backout COMP_RUN_BARRIERS setting, and remove all ED tests from testlist (as they all fail) + clm4_5_8_r170 sacks 02/28/2016 Add a wrapper for CN Vegetation + clm4_5_8_r169 erik 02/23/2016 Add fire several fire constants to namelist, add some new clm45/50 surface datasets + clm4_5_8_r168 sacks 02/20/2016 Fix zero methane production + clm4_5_7_r167 sacks 02/20/2016 Fix carbon isotopes in transient runs + clm4_5_7_r166 sacks 02/02/2016 Infrastructure for carbon and nitrogen conservation with dynamic landunits + clm4_5_7_r165 sacks 01/29/2016 Remove fglcmask, recreate all surface datasets + clm4_5_7_r164 erik 01/12/2016 Update CIME and MOSART + clm4_5_7_r163 sacks 12/23/2015 Improve crop performance by allocating less memory + clm4_5_7_r162 andre 12/18/2015 negative runoff updates. + clm4_5_6_r161 sacks 12/17/2015 Collapse mountain glaciers to a single elevation class + clm4_5_6_r160 sacks 12/11/2015 For glc_mec, get gridcell topographic height from atm + clm4_5_6_r159 erik 12/10/2015 Update CIME version + clm4_5_6_r158 andre 12/04/2015 misc clm 5.0 bugfixes + clm4_5_6_r157 sacks 11/27/2015 Reduce memory use for init_interp + clm4_5_6_r156 sacks 11/24/2015 Fix QSNWCPICE and glacial inception + clm4_5_6_r155 erik 11/23/2015 Bring FUN (Fixation and Uptake of Nitrogen) code option to trunk + from Mingjie, as well as latitude varying spinup from Charlie, + and a fix for crop with dynamic roots from Beth + clm4_5_6_r154 andre 11/18/2015 one year grain product pool + clm4_5_6_r153 sacks 11/17/2015 Fix snow cover fraction bug + clm4_5_5_r152 sacks 11/17/2015 Fix glc_mec energy conservation bug + clm4_5_4_r151 erik 11/13/2015 Fix broken r150 tag, with bgc_spinup issue in it + clm4_5_4_r150 erik 11/13/2015 Some needed answer changing fixes for: fire, disallow + negative photosynthis, and reduce LAI of DBT in evergreen state + clm4_5_3_r149 sacks 11/08/2015 Change cold start initialization of snow pack + clm4_5_3_r148 sacks 11/07/2015 For CLM5, increase max snow depth to 20 m + clm4_5_3_r147 andre 11/05/2015 swenson bedrock and coupler runoff bugfixes + clm4_5_3_r146 sacks 11/04/2015 Implement vertical interpolation in init_interp + clm4_5_3_r145 andre 11/03/2015 update clm50 defaults, enable clm50 crop compsets + clm4_5_3_r144 sacks 10/27/2015 Better fix for bug that leads to infinite growth in snow depth + clm4_5_3_r143 andre 10/22/2015 flexibleCN and luna bugfixes. + clm4_5_3_r142 sacks 10/19/2015 Fix bug in initialization of 12-layer snow pack + clm4_5_3_r141 sacks 10/19/2015 Fix bug that leads to infinite growth in snow depth + clm4_5_3_r140 andre 10/15/2015 mosart direct to ocean runoff + clm4_5_3_r139 andre 10/13/2015 dynamic roots from Beth Drewniak + clm4_5_3_r138 andre 10/11/2015 new accelerated spinup and soil vertical structure + clm4_5_3_r137 erik 10/09/2015 Bring in changes for fire-emissions as well tuning changes to the fire model to be used with clm5_0 + clm4_5_3_r136 andre 10/08/2015 coupler field prep for mosart and externals update + clm4_5_3_r135 sacks 10/06/2015 Substantial reduction in memory allocation for prognostic crops + clm4_5_3_r134 sacks 10/04/2015 Fixes for transient and preindustrial crop cases + clm4_5_3_r133 andre 10/02/2015 Bugfix for mksurfdata_map - add file missed by clm4_5_2_r125. + clm4_5_3_r132 andre 10/02/2015 Modify soil BGC diffusion and cryoturbation code to allow for spatially variable soil thickness. + clm4_5_3_r131 sacks 09/30/2015 Bring in cime3 + clm4_5_3_r130 andre 09/28/2015 add namelist option to reduce lake evaporation and irrigation when river water storage falls below a threshold value, and add an additional constraint on stress deciduous leaf onset. + clm4_5_3_r129 andre 09/25/2015 bump tag revision number because clm4_5_2_r128 was climate changing. + clm4_5_2_r128 andre 09/24/2015 science bugfixes (not bfb) for root fraction and bedrock thermal properties + clm4_5_2_r127 sacks 09/18/2015 Fix interpolation of initial conditions for glc_mec and crop <-> non-crop + clm4_5_2_r126 andre 09/17/2015 New decomp_depth_efolding value for clm5.0, set as a namelist parameter instead of netcdf params file. + clm4_5_2_r125 andre 09/15/2015 clm 50 hydrology updates. + clm4_5_2_r124 sacks 09/13/2015 Wind-dependent snow density + clm4_5_2_r123 sacks 09/10/2015 Fix some problems with pgi and nag compilers + clm4_5_2_r122 sacks 09/09/2015 Update to latest cime + clm4_5_2_r121 sacks 09/04/2015 Rework snow capping + clm4_5_1_r120 andre 08/29/2015 CLM 5 nitrogen models Flexible CN and LUNA + clm4_5_1_r119 erik 08/26/2015 Bring hobart/nag bug fixes to trunk, and fix a few bugs + clm4_5_1_r118 sacks 08/05/2015 Minor rework of glc coupling fields + clm4_5_1_r117 sacks 07/28/2015 Repartition rain vs. snow from atmosphere + clm4_5_1_r116 sacks 07/22/2015 Rename some history fields + clm4_5_1_r115 sacks 07/15/2015 Remove redundant code, rename a variable + clm4_5_1_r114 sacks 07/10/2015 Update cime external, remove genf90-generated files + clm4_5_1_r113 sacks 07/09/2015 Support backwards compatibility of restart variable names + clm4_5_1_r112 oleson 07/01/2015 Justin Perket snow on vegetation + clm4_5_1_r111 sacks 06/12/2015 Remove temporary hack to get bfb results in InitSnowLayers + clm4_5_1_r110 sacks 06/12/2015 Add flexibility to have more snow layers + clm4_5_1_r109 sacks 06/06/2015 Fix bug in DivideSnowLayers + clm4_5_1_r108 andre 05/29/2015 Crop changes from Sam Levis + clm4_5_1_r107 andre 05/19/2015 Update externals to use github version of cime1.0.7. + clm4_5_1_r106 erik 05/14/2015 Fix CO2 forcing for MEGAN + clm4_5_1_r105 erik 04/16/2015 Move test lists to beneath active components, change build scripts from cshell to perl, move to new cime directory structure + clm4_5_1_r104 erik 01/27/2015 Update externals to latest cesm beta tag + bring in shared build for clm4_5/clm5_0 for testing + clm4_5_1_r103 sacks 01/01/2015 enable transient crops + clm4_5_1_r102 sacks 12/27/2014 make new input datasets to support transient crops + clm4_5_1_r101 sacks 12/09/2014 rework cold start initialization for transient runs + clm4_5_1_r100 sacks 12/03/2014 update pio calls to pio2 API + clm4_5_1_r099 sacks 12/02/2014 add ozone stress code from Danica Lombardozzi + clm4_5_1_r098 sacks 11/29/2014 update externals to cesm1_3_beta14 or beyond + clm4_5_1_r097 mvertens 11/24/2014 major refactorization to introduce new soilbiogeochem data types and routines that are independent of either ED or CN datatypes + clm4_5_1_r096 erik 11/19/2014 Several answer changing bug-fixes: snow grain size, lake hydrology, default settings, organic soil + clm4_5_1_r095 andre 11/10/2014 N comp refactoring by Jinyun Tang (LBL) and transpiration sink isolation by Gautam Bisht (LBL) + clm4_5_1_r094 sacks 11/07/2014 misc. glacier-related updates + clm4_5_1_r093 sacks 11/07/2014 change cold-start snow initialization, update cism external + clm4_5_1_r092 muszala 11/04/2014 bug fixes from santos that address valgrind problems. update rtm external + clm4_5_1_r091 muszala 10/27/2014 update externals. fix bug so CLM runs with Intel 14x. + clm4_5_1_r090 sacks 10/16/2014 modularize irrigation; do some unit test rework + clm4_5_1_r089 erik 10/13/2014 Bring new urban building temperature to trunk as a clm5.0 feature as well as human-stress index calculations + clm4_5_1_r088 muszala 10/01/2014 pull out ED deps. in TemperatureTypeMod, can now compile with pgi 14.7 + clm4_5_1_r087 erik 09/30/2014 Fix two balance check errors, and turn abort for balance check back on to appropriate levels + clm4_5_1_r086 muszala 09/25/2014 critical ED modifications from r fisher, fix bug 2043 + clm4_5_1_r085 sacks 09/19/2014 replace conditionals with polymorphism for soil water retention curve + clm4_5_1_r084 sacks 09/18/2014 make glc_dyn_runoff_routing spatially-varying, based on input from glc + clm4_5_1_r083 muszala 09/17/2014 only update scripts and run new baselines. this due to an error in yellowstone pgi test naming (clm_aux45 changed to aux_clm45) + clm4_5_1_r082 muszala 09/11/2014 Merge in a number of ED changes to address science bugs and infrastructure (partiulararly restarts) + clm4_5_1_r081 mvertens 08/24/2014 major infrastructure changes and directory reorganization under src + clm4_5_1_r080 erik 08/16/2014 Update externals to trunk version, allow eighth degree as a valid resolution + clm4_5_1_r079 andre 07/31/2014 G. Bisht (LBL) soil temperature refactor; machines update for goldbach-intel + clm4_5_1_r078 muszala 07/23/2014 add lai stream capability and the ability to run with V5 cruncep data + clm4_5_1_r077 andre 07/10/2014 Refactor from Jinyun Tang (LBL) to make hydrology more modular. + clm4_5_1_r076 erik 07/07/2014 Answer changes for fire code from Fang Li + clm4_5_75 muszala 05/30/2014 update externals to rtm1_0_38 and esmf_wrf_timemgr_140523 + clm4_5_74 sacks 05/28/2014 misc. bfb changes - see detailed summary below + clm4_5_73 erik 05/28/2014 Add the stub ability for clm5_0 physics to CLM build system + clm4_5_72 muszala 05/05/2014 Introduce code for Ecosystem Demography (CLM(ED)) Model + clm4_5_71 sacks 05/02/2014 2-way feedbacks for glacier, veg columns compute glacier SMB, and related changes + clm4_5_70 muszala 04/18/2014 bring in SHR_ASSERT macros + clm4_5_69 andre 03/18/2014 start unit testing build-namelist + clm4_5_68 erik 03/07/2014 Update scripts to version that turns on transient CO2 streams for transient compsets, and update CISM (changes answers) + clm4_5_67 mvertens 03/06/2014 removed initSurfAlb as part of the initialization + clm4_5_66 mvertens 03/03/2014 refactoring of initialization and introduction of run-time finidat interpolation + clm4_5_65 mvertens 02/25/2014 Turn off MEGAN vocs when crops is running + clm4_5_64 muszala 02/19/2014 fix and clean ncdio_pio.F90.in. clean clm_time_manager. update externals. + clm4_5_63 sacks 02/14/2014 add some code needed for dynamic landunits; activate 0-weight veg landunit sometimes + clm4_5_62 erik 02/10/2014 Get PTCLM working robustly, US-UMB test working, add CO2 streams to datm, add more consistency testing between compsets and user settings + clm4_5_61 sacks 02/04/2014 add 3-d snow history fields; continue harvest past end of pftdyn timeseries + clm4_5_60 andre 01/30/2014 refactor build-namelist + clm4_5_59 sacks 01/22/2014 use new get_curr_yearfrac function in clm_time_manager + clm4_5_58 sacks 01/22/2014 major refactor of transient pft code, in prep for dynamic landunits + clm4_5_57 sacks 01/07/2014 change CNDV water conservation to use the pftdyn method + clm4_5_56 sacks 01/02/2014 update scripts external to fix I20TRCLM45BGC compset + clm4_5_55 sacks 12/27/2013 add hooks to Sean Santos's unit test frameworks, and begin to add CLM unit tests + clm4_5_54 sacks 12/27/2013 update externals to cesm1_3_beta06 + clm4_5_53 muszala 12/19/2013 refactor restart interfaces + clm4_5_52 sacks 11/26/2013 turn on longwave radiation downscaling for glc_mec by default + clm4_5_51 sacks 11/26/2013 rework downscaling of atm fields for glc_mec + clm4_5_50 erik 11/24/2013 Bring in a bunch of b4b bugfixes, fix getregional script, start move of PTCLM to PTCLMmkdata tool + clm4_5_49 muszala 11/16/2013 swenson anomaly forcing - part 1 + clm4_5_48 muszala 11/14/2013 bug fixes for CLM dry deposition and MEGAN VOC emissions + clm4_5_47 muszala 11/12/2013 fix Bug 1858 - AGDD now reset annually + clm4_5_46 sacks 11/08/2013 remove zeroing out of slope for special landunits + clm4_5_45 sacks 11/08/2013 refactor daylength calculation, and other minor changes + clm4_5_44 sacks 11/08/2013 temporary hack to daylength initialization to provide baselines for the next tag + clm4_5_43 sacks 11/06/2013 allocate memory for most landunits in every grid cell (needed for dynamic landunits) + clm4_5_42 sacks 11/04/2013 fix bug 1857 for CLM4.5 - CNDV running temperature means are incorrect + clm4_5_41 andre 10/30/2013 update scripts to convert clm4_5 CPP flags to namelist variables. + clm4_5_40 muszala 10/24/2013 fix Bug 1752 - urban conductances depend on weights in an undesirable way + clm4_5_39 muszala 10/23/2013 bug fix from santos - h2osoi_vol not passed to atmosphere model on restart + clm4_5_38 sacks 10/18/2013 change irrigation variables to be pft-level + clm4_5_37 muszala 10/10/2013 Modifications to bring clm up to date with major driver refactoring in drvseq5_0_01 + clm4_5_36 sacks 10/04/2013 new surface datasets, and other minor fixes + clm4_5_35 sacks 10/01/2013 get CLM running on edison + clm4_5_34 erik 09/30/2013 Get PTCLM working, fix a few small bugs + clm4_5_33 muszala 09/26/2013 clean up from mistakes in previous tag + clm4_5_32 muszala 09/26/2013 bug fix tag - 1798, 1810 + clm4_5_31 sacks 09/25/2013 fix bug 1820: incomplete conditional in CNSoyfix leads to buggy results and decomposition dependence + clm4_5_30 sacks 09/24/2013 fix performance bug in decomposition initialization + clm4_5_29 sacks 09/24/2013 fix threading in CLM4.5, and other misc fixes + clm4_5_28 sacks 09/20/2013 fix FracH2oSfc bug + clm4_5_27 sacks 09/20/2013 fix crop nyrs bug + clm4_5_26 muszala 09/19/2013 water balance and SMS_Ly1.f19_g16.ICLM45BGCCROP fix + clm4_5_25 erik 09/13/2013 Bring in Tony's changes to kick sno all the way up to the coupler layer, makes all + CESM components more similar to each other + clm4_5_24 sacks 09/03/2013 update externals to cesm1_3_beta02 or later + clm4_5_23 muszala 08/22/2013 refactor to allow CH4 params. to be read from netcdf file and clean up clm4_5_20 + clm4_5_22 muszala 07/30/2013 aux_clm testlist reorganization + clm4_5_21 muszala 07/24/2013 ifdef and bounds refactor + clm4_5_20 muszala 07/20/2013 refactor to allow CN and BGC params. to be read from netcdf file + clm4_5_19 sacks 07/17/2013 fix setting of bd in iniTimeConst + clm4_5_18 sacks 07/09/2013 rework urban indexing + clm4_5_17 sacks 07/03/2013 misc cleanup and bug fixes + clm4_5_16 sacks 07/02/2013 only run filters over 'active' points + clm4_5_15 muszala 07/01/2013 complete associate refactor for pointers in clm4_5 source + clm4_5_14 muszala 06/20/2013 preparation for associate refactor in clm4_5_15 + clm4_5_13 andre 06/14/2013 hydrology reordering from Jinyun Tang + clm4_5_12 muszala 06/13/2013 NoVS test, NAG mods and remove TWS from restart file + clm4_5_11 sacks 06/11/2013 Change pct_pft and related surface dataset variables to be % of landunit + clm4_5_10 muszala 06/10/2013 refactor clmtype + clm4_5_09 muszala 06/04/2013 volr and vic fix, update mct and rtm + clm4_5_08 muszala 06/03/2013 port for NAG compiler + clm4_5_07 erik 05/31/2013 New spinup files for CLM45 AND RTM, work on PTCLM, turn drydep off by default, update externals + clm4_5_06 erik 05/15/2013 A few small bug fixes, more updates to README files + clm4_5_05 muszala 05/14/2013 hcru bug fixes + clm4_5_04 erik 05/13/2013 Fix the previous broken tag + clm4_5_03 erik 05/10/2013 Several bug fixes for release, urban and test single point surface datasets + clm4_5_02 sacks 05/07/2013 make 'shared' tools directory, and other minor tools fixes + clm4_5_01 muszala 05/06/2013 update externals + clm4_5_00 erik 05/02/2013 Official end to CLM4.5 development for CLM offline + clm4_0_81 bandre 04/29/2013 Charlie Koven's variable consolidation, cryoturbation and BSW CPP changes + clm4_0_80 erik 04/26/2013 Bring Fang Li. Fire model into CLM4.5 science, update ALL CLM4.5 surface datasets, + provide a working initial condition file for CLM45BGC@f19_g16-1850 + clm4_0_79 muszala 04/24/2013 pftdyn, pft-phys*.nc and datm8 update + clm4_0_78 muszala 04/23/2013 MEGAN fixes + clm4_0_77 sacks 04/23/2013 fix carbon balance bug in transient runs with VERTSOI, and fix Soil Hydrology bug + clm4_0_76 muszala 04/22/2013 spinup changes from Charlie Koven (part 1) + clm4_0_75 muszala 04/19/2013 run propset + clm4_0_74 muszala 04/17/2013 snow_depth changes, major scripts overhaul, bug fix for tools + clm4_0_73 sacks 04/15/2013 update mksurfdata_map for CLM4.5, and other misc. updates, mainly to tools + clm4_0_72 muszala 04/11/2013 maoyi bug fix for vic hydro + clm4_0_71 muszala 04/10/2013 compsets refactoring by mvertens + clm4_0_70 muszala 04/01/2013 bring in vic hydrology + clm4_0_69 muszala 03/26/2013 remove hydro reorder, volr and esmf mods + clm4_0_68 erik 03/16/2013 Fix some issues in mksurfdata_map for generation of ne120np surface data file. + Put error back in CLM if weights don't sum to 100. Add in Keith's photosynthesis change for CLM45. + clm4_0_67 muszala 03/12/2013 Jinyun photosynthesis and hydrology reorder + clm4_0_66 sacks 03/07/2013 turn off subgrid topography snow parameterization for glc_mec landunits + clm4_0_65 sacks 03/07/2013 back out Machines external to get more tests to pass, especially IG + clm4_0_64 muszala 03/06/2013 update externals. fixes 40/45 intial condition problem + clm4_0_63 muszala 03/04/2013 bug 1635 fix - 4_0 CN bug + clm4_0_62 sacks 02/24/2013 add active flags, change subgrid weighting convention, other misc fixes + clm4_0_61 muszala 02/20/2013 rtm, drv and clm mods: tws, olr, r01 rdric file and SoilHydroMod + clm4_0_60 erik 02/11/2013 Bring CLM4.5 code from clm45sci branch to trunk as an option set at configure time + clm4_0_59 mvertens 12/20/2012 restructure clmtype and all pointer references, new directory structure + clm4_0_58 erik 12/14/2012 Uncomment us20 and wus12 datasets, more testing to: bluefire, yellowstone, frankfurt + clm4_0_57 muszala 11/30/2012 update trunk with release mods, some rtm fixes + clm4_0_56 sacks 11/27/2012 fix s2x tsrf, add s2x diagnostics + clm4_0_55 muszala 11/14/2012 bring in flooding capability + clm4_0_54 erik 10/09/2012 Fix esmf for carma field, fix some CLM_USRDAT issues + clm4_0_53 erik 10/03/2012 Update to fsurdat, fpftdyn, finidat datasets, new high resolution organic/fmax/glacier raw datasets + clm4_0_52 sacks 09/27/2012 new pct_glacier raw data file + clm4_0_51 muszala 09/26/2012 bug fixes, pio performance and SCRIP files + clm4_0_50 muszala 09/21/2012 testing of clm and new rof component + clm4_0_49 erik 09/16/2012 Move clm testing to use CESM test framework + clm4_0_48 muszala 09/11/2012 bug fixes, xFail to tests and normalize test output for CLM + clm4_0_47 muszala 08/23/2012 bug fixes + clm4_0_46 muszala 08/08/2012 R01 support and update externals + clm4_0_45 sacks 07/20/2012 fix virtual columns; new urban mksurfdata_map + clm4_0_44 erik 07/09/2012 Add wrf resolutions, update externals to cesm1_1_beta15, all components use build-namelist now + clm4_0_43 sacks 04/06/2012 Add diagnostic fields, modify some existing history fields + clm4_0_42 erik 03/27/2012 Bring in Francis Vitt's MEGAN changes. + clm4_0_41 erik 03/13/2012 Bring rmfmesh/rtmmap branches to trunk + clm4_0_40 erik 02/16/2012 Back out update to new T31 surface datasets + clm4_0_39 erik 02/01/2012 Bring newgrid branch to trunk + clm4_0_38 erik 01/23/2012 Fix f09 surface datasets + clm4_0_37 erik 09/26/2011 Fix unstructured grids history files + clm4_0_36 erik 09/22/2011 Comment out RTM mapping files for f09 and f19 + clm4_0_35 erik 09/13/2011 Bring in Mariana's non2D grid branch to trunk, enabling HOMME grids: ne30np4/ne120np4 + clm4_0_34 erik 08/18/2011 Bring tcens branch to trunk, fix a few issues + clm4_0_33 erik 07/25/2011 Move changes on release branch over to trunk + clm4_0_32 erik 05/19/2011 Make I1850SPINUPCN compset use MOAR data, various bug fixes, work on test lists + clm4_0_31 erik 05/13/2011 Fix answers for transient_CN, fix interpinic + clm4_0_30 erik 05/11/2011 New finidat/fsurdat files for T31 + clm4_0_29 erik 05/05/2011 Backout interpinic changes to one that works + clm4_0_28 erik 05/03/2011 Remove DUST/PROGSSLT in land coupler layer, update driver and scripts + clm4_0_27 erik 05/02/2011 Move crop branch over to trunk + clm4_0_26 erik 03/23/2011 Update externals, driver update changes answers, drydep changes from fvitt, fix bugs + clm4_0_25 erik 03/22/2011 Always output restart-history files add more meta-data to them, fix urbanc_alpha and 2.5x3.33 datasets, Changes from Keith O on SNOWLIQ/SNOWICE + clm4_0_24 erik 02/09/2011 Fix mksurfdata and add ability to override soil_fmax + clm4_0_23 erik 02/03/2011 Add in new glacier-MEC use-cases + clm4_0_22 erik 01/20/2011 Move coupler field indicies to clm, move cpl_* directories up a level, add the cpl_share directory + clm4_0_21 jedwards 01/12/2011 Remove includes, finish PIO transition + clm4_0_20 erik 01/11/2011 Update for ESMF metadata, update doc. from release branch, bug fixes (doc of qflx_evap_tot, threading CNDV, aer/ndepregrid) + clm4_0_19 erik 12/08/2010 Bring irrigation branch to the trunk + clm4_0_18 erik 11/21/2010 Fix a problem with the clm template, update scripts version to fix bug with linking with ESMF + clm4_0_17 erik 11/20/2010 Update to externals that change answers to roundoff, use drv pio namelist, add in T341 datasets + clm4_0_16 erik/mverten 10/27/2010 Fix downscaling roundoff difference for same-grids by copying scale factor when needed + clm4_0_15 erik/mverten 10/24/2010 Move pio branch to trunk + clm4_0_14 erik 10/19/2010 Fix finidat file for T31 sim_year=2000 cases + clm4_0_13 erik 10/16/2010 Bring in PTCLM branch, add in T31 finidat file and turn off ice_runoff for T31 + clm4_0_12 erik 09/10/2010 Add U10 to history, cesm1_0_rel06 updates, PTCLM02 updates (except mksurfdata), remove ndepdat/dyn/faerdep + clm4_0_11 erik 08/27/2010 New files for rcp6, fix MPI bug, update externals + clm4_0_10 erik 08/04/2010 Update doc to cesm_rel05, bug-fixes, fix issues for single-point, mksurfdata/getregional scripts + clm4_0_09 erik 06/14/2010 Fix some small issues, update documentation, and externals + clm4_0_08 erik 06/04/2010 Snow hydrology bug fix from Keith and Dave + clm4_0_07 erik 06/03/2010 Some cleanup/fix bugs, add RTM var, add albice to namelist, allow last-millenium in mksurfdata, allow setting of datm_presaero in clm test-suite + clm4_0_06 erik 05/26/2010 Update gglc to cism + clm4_0_05 erik 05/25/2010 Move Nitrogen deposition stream branch to trunk + clm4_0_04 erik 05/20/2010 New namelist items: ice_runoff, scaled_harvest, carbon_only, + new RTM hist vars, new finidat files, update esmf interface, turn off aerosol read quicker + clm4_0_03 erik 05/17/2010 Changes from Francis for VOC and drydep + clm4_0_02 erik 05/13/2010 Make sure dtime is initialized, so that answers are consistently the same as clm4_0_00 + clm4_0_01 erik 05/11/2010 Move glacier multiple elevation class branch to the trunk so that we can work with the active glacier model + clm4_0_00 erik 05/04/2010 Update to datm8, redirect aquifer overflow + to drainage, add gx3v7 masks, script to extract regional + datasets, add harvesting for CN, modify shrubs, include urban + model, ice stream for snowcapping, new build-namelist system, + scale solar by solar zenith angle in datm, deep soil with + bedrock at bottom, organic matter in soils, SNICAR for snow + radiation, sparce dense aero, snow cover changes + clm3_8_00 erik 05/04/2010 Get future scenarios working, finalize + documentation, bring in MEGAN VOC and CNDV, simplify, + mksurfdata optimization, fix bugs: snow enthalpy, BMOZ, pergro, + use pft weights from fsurdat NOT finidat + clm3_7_15 erik 04/27/2010 Finish User's Guide, surfdata files for urban-1pt, fix mksurfdata ifort bugs, work with testing + clm3_7_14 erik 04/08/2010 Fix rcp=2.6/4.5 1-degree fndepdyn filenames + clm3_7_13 erik 04/08/2010 Add in missing rcp=2.6/6 use-cases, and fix syntax errors in the namelist_defaults file + clm3_7_12 erik 04/08/2010 rcp=2.6/4.5 datasets for fndepdyn and aerdepdat, fix some minor issues, new 1pt urban surfdata files + clm3_7_11 erik 04/07/2010 qtr-degree and T85 surfdata, rcp=2.6/4.5 datasets, doc updates + clm3_7_10 erik 03/22/2010 Fix drydep so that BMOZ case will work + clm3_7_09 erik 03/21/2010 Fix snow enthalpy bug, cndv datasets, various fixes + clm3_7_08 mvertens 03/12/2010 Removal of check for weights if dynamic land use is +used + clm3_7_07 erik 03/10/2010 New finidat datasets for 1-deg, 2-deg, and abort if weights from finidat/fsurdat files are too different, and use fsurdat files as truth + clm3_7_06 erik 03/10/2010 Bring cndv branch to trunk + clm3_7_05 erik 02/24/2010 Bring VOC branch source code to trunk + clm3_7_04 erik 02/17/2010 Bring VOC branch (vocemis-drydep18_clm3_7_03) tools, testing, and build to trunk (everything other than VOC code changes) + clm3_7_03 erik 02/10/2010 Add in more future scenario datasets, new history fields from Keith + clm3_7_02 erik 02/06/2010 Start adding in new rcp=8.5 datasets, remove some junk, change some env_conf variables, add user_nl_clm + clm3_7_01 erik 01/29/2010 OpenMP fix for pftdyn, start adding in rcp's, update ndeplintInterp.ncl script + clm3_7_00 erik 01/22/2010 Update to datm8, redirect aquifer overflow to drainage, add gx3v7 masks, script to extract regional datasets, add harvesting for CN, modify shrubs, include urban model, ice stream for snowcapping, new build-namelist system, scale solar by solar zenith angle in datm, deep soil with bedrock at bottom, organic matter in soils, SNICAR for snow radiation, sparce dense aero, snow cover changes + clm3_6_64 erik 01/22/2010 Update documentation and README/Quickstart files, set NetCDF large-file format on by default in template, update pio, update some fsurdat files to vocemis-drydep versions, add 2.5x3.33_gx3v7 frac file, make gx3v7 default for 4x5 res + clm3_6_63 erik 01/09/2010 Get answers to be identical with ccsm4_0_beta38 for 1 and 2 degree transient cases + clm3_6_62 erik 01/08/2010 Fix startup of PFT transient cases so properly use data from pftdyn file rather than finidat file + clm3_6_61 erik 01/07/2010 Comment out endrun on finidat and fsurdat weights being incomptable, and go back to using finidat weights + clm3_6_60 erik 01/05/2010 Fix clm template + clm3_6_59 erik 01/05/2010 Update to datm8, fix so wts used are from fsurdat file NOT finidat file + clm3_6_58 erik 12/08/2009 Fix rpointer, correct units for export of nee, start adding testing for intrepid + clm3_6_57 erik 11/20/2009 Redirect aquifer overflow to drainage, so doesn't end up in ocean + clm3_6_56 erik 11/10/2009 New ndepdat and ndepdyn datasets + clm3_6_55 erik 11/05/2009 Fix tool to create Nitrogen deposition datasets, and change configure to use CCSM Makefile as source for TopLevel Makefile + clm3_6_54 erik 10/28/2009 Allow comp_intf to change on ccsm build, reduce default hist fields, start adding 2.5x3.33, start adding VOC fsurdat datasets, new finidat files for f09 and f19 + clm3_6_53 erik 09/22/2009 Fix so that T31_gx3v7 file is actually included + clm3_6_52 erik 09/17/2009 Add T31_gx3v7 support, remove forganic, read from fsurdat, add script to extract regional datasets, work with CN output, add more urban/rural fields + clm3_6_51 erik 09/01/2009 Update fndepdyn and aerdep datasets (f02,f05,f09,f10) (1850,2000) and f09, f10 transient (1850-2000) + clm3_6_50 erik 08/28/2009 Fix ncl regridding scripts so that NO missing values are allowed for aerosol and nitrogen deposition + clm3_6_49 erik 08/25/2009 Fix ncl interpolation scripts, update externals, turn on CLM_CCSM_BLD for bluefire,jaguar, ESMF3 compliance + clm3_6_48 erik 08/12/2009 New aerosol/nitrogen deposition datasets, mksurfdata work, scm work, clm_usr_name option to build-namelist + clm3_6_47 erik 08/03/2009 Fix hybrid bug for dynpft case, update externals + clm3_6_46 erik 07/22/2009 Get more tests to work/document them, add use cases for 1850_control, 2000_control, and + 20thC_transient, straighten out single-point grids, Listen to LND_CDF64 env variable from + template, remove CLM_ARB_IC. + clm3_6_45 erik 07/10/2009 Remove inconsistent finidat file in clm3_6_44 + clm3_6_44 erik 07/09/2009 Fix C13 bug, update scripts, drv, datm. Add domain files for idmap atm-ocn grids for datm. Remove SEQ_MCT, add new ESMF env vars to template. Work with ndeplintInterp + clm3_6_43 erik 06/10/2009 Fix pftdyn bug, enable 1D primary hist files, fix time-const3D output, fix template bug, enable cpl_esmf/cpl_mct + clm3_6_42 erik 06/02/2009 Bring CN Harvest branch to trunk + clm3_6_41 kauff 05/29/2009 shrub mods, abort if nthreads > 1 (temporary, wrt bugz #965) + clm3_6_40 erik 05/28/2009 Fix openMP bug, add fndepdyn ncl script, fix interpinic for urban, add mkharvest to mksurfdata, new spinups, turn CLAMP on for CASA or CN + clm3_6_39 erik 05/07/2009 Bug fix for script version and maxpatchpft back to numpft+1 + clm3_6_38 erik 05/06/2009 New fsurdat for other resolutions, bug-fixes, deep wetlands to bedrock, new spinups for 1.9x2.5 1850, 2000 + clm3_6_37 erik 04/27/2009 Update faerdep dataset for 1.9x2.5 to point to version cice is using for 1850 and 2000 + clm3_6_36 erik 04/27/2009 Handle transient aersol, make maxpatchpft=numpft+1 default, new datasets for 1.9x2.5 and 0.9x1.25, change doalb + clm3_6_35 erik 04/20/2009 Fix major logic bug in mksurfdata + clm3_6_34 oleson 04/19/2009 Fix bangkok urban bug + clm3_6_33 erik 04/16/2009 Bring in dynpft changes from cbgc branch + clm3_6_32 erik 04/15/2009 Add irrigation area to mksrfdata, fix high-res and pftdyn problems + clm3_6_31 erik 04/01/2009 New surface datasets for 1850,2000, support for 0.9x1.25_gx1v6, urban always on. New pft-physiology file. Update scripts so remove some CLM_ env_conf vars. Fix CN for urban/pftdyn. + clm3_6_30 oleson 03/19/2009 Fix urban roof/wall layers + clm3_6_29 oleson 03/19/2009 CN SAI, CN testing fix, rad step size fix + clm3_6_28 oleson 03/17/2009 Fix permission denied error when reading surface dataset + clm3_6_27 oleson 03/16/2009 Urban model changes and FGR12 fix + clm3_6_25 dlawren 03/13/2009 Daylength control on Vcmax, 1%Lake,wetland,glacier in mksrfdat, remove ELEVATION in surface data file + clm3_6_24 oleson 03/09/2009 Fix urban testing and some history field changes + clm3_6_23 oleson 03/08/2009 Prune history fields and change to snowdp threshold for solar radiation penetration into snow + clm3_6_21 oleson 03/04/2009 History file changes and finish testing on tags clm3_6_19 and clm3_6_20 + clm3_6_19 oleson 02/27/2009 Changes to urban model and urban surface data + clm3_6_17 oleson 02/26/2009 Urban model changes and mksurfdata changes to incorporate urban data + clm3_6_16 erik 02/12/2009 Multiple elevation classes on surface dataset, urban fixes, mpi-serial and testing fixes + clm3_6_15 erik 01/19/2009 Bring clm36sci branch to the trunk + clm3_6_14 erik 10/10/2008 Fix some global urban issues, fix pftdyn, really get compile-only option + working in testing + clm3_6_13 erik 10/01/2008 Update to new version of cpl7 scripts and build, update externals for versions + needed for clm36sci branch, add new CASA tests + clm3_6_12 erik 09/21/2008 Fix restarts for urban, add capability to do global urban experiments, + add in new forcing height changes + clm3_6_11 dlawren 08/26/2008 Ice stream for snow capped regions + clm3_6_10 tcraig 08/15/2008 extend rtm tracer, ascale for tri-grids, AIX O3 to O2 + clm3_6_09 erik 08/11/2008 Fix clm.cpl7.template to run hybrid and branch cases + clm3_6_08 erik 08/06/2008 Fix bugs, and build changes for inputdata repo + clm3_6_07 erik 07/08/2008 Implement new build namelist system from Vertenstein/Eaton, bluefire, and BGP updates + clm3_6_06 erik 05/30/2008 Small fix needed for ccsm4_alpha30 + (use gx1v5 for some resolutions when OCN_GRID==ATM_GRID) + clm3_6_05 erik 05/27/2008 Fix to compile with PGI-6, update scripts, fix cpl7.template for new scripts LND_GRID, + fix 2.65x3.33 frac dataset. + clm3_6_04 erik 05/20/2008 Remove all MCT permutes, fix cpl7 script issues, remove offline mode, + add ability to run over a range of years + clm3_6_03 erik 05/08/2008 Fix so listen to next_swcday to calculate albedo rather than using irad + clm3_6_02 erik 03/25/2008 Minor fix in configure remove perl5lib version under models/lnd/clm/bld + clm3_6_01 erik 03/20/2008 40 m forcing height changes for clm + clm3_6_00 erik 03/20/2008 Fully implement sequential-ccsm mode, upgrade configure, build-namelist and testing, + upgrade interpolation tool, add mkdatadomain, write to iulog rather than 6 explicitly, + SCAM update, Update datasets, add archiving, and build-streams, add in point version + of Urban model, change directory structure to mimic CCSM + clm3_5_20 erik 03/17/2008 Bug fixes before spinning off clm3_6_00, put in changes from ccsm4a01_clm3_5_18 + to ccsm4a04_clm3_5_18 + clm3_5_19 erik 03/06/2008 Change directory structure to mimic CCSM, fix so no NaNS on BGC interpinic output, + new half degree CN clmi dataset + clm3_5_18 erik 02/21/2008 Update to latest seq-ccsm4.alpha tag + clm3_5_17 erik 02/06/2008 Merge Tony Craig's FMI branch fmi12_clm3_5_16 to the clm trunk + clm3_5_16 erik 01/28/2008 Get point version of Urban code onto trunk (urban code can not restart) + clm3_5_15 erik 12/10/2007 Fix interpinic for half degree grid, add in large-file support, + allow configure to work with ccsm directory structure + clm3_5_14 erik 11/27/2007 Use build-streams, and archiving, multiple bug-fixes + clm3_5_13 erik 11/16/2007 Update xml file with file needed for ccsm3_5_beta18 + clm3_5_12 erik 11/08/2007 Tag with new files needed for ccsm3_5_beta17 + clm3_5_11 erik 09/28/2007 Update datasets in the DefaultCLM file for 0.23x0.31, 0.47x0.63, 0.9x1.25 and + add fndepdyn file for 1.9x2.5 + clm3_5_10 jet 09/18/2007 SCAM update + clm3_5_09 erik 08/31/2007 Change configure to NOT have csm_share code for ccsm_con option, and add in 1x1.25 file, + and update datm7 and csm_share + clm3_5_08 tcraig 08/20/2007 convert 6 to iulog in logfile, updates for I/O + clm3_5_07 erik 08/17/2007 Add mkdatadomain tool, add cprnc and perl5lib as externals + clm3_5_06 erik 08/10/2007 Update: interpolation, testing, script namelist build, and scripts. Fix bugs, + and fix possible + clm3_5_05 tcraig 07/11/2007 seq clm mods and first hist refactor mods + clm3_5_04 mvertens 06/05/2007 lnd_comp_mct.F90 change to work with sequential diagnostics + clm3_5_03 tcraig 05/23/2007 reduce memory, partial I/O refactor, downscaling implementation + clm3_5_02 mvertens 05/22/2007 put in hourly coupling with sequential driver + clm3_5_01 erik 05/16/2007 Move newcn06 branch to trunk + clm3_5_00 erik 05/03/2007 New surface datasets, improved canopy integration, and various improvements to Hydrology diff --git a/doc/IMPORTANT_NOTES b/doc/IMPORTANT_NOTES index 1ff8949139..573bdb0484 100644 --- a/doc/IMPORTANT_NOTES +++ b/doc/IMPORTANT_NOTES @@ -1,30 +1,11 @@ $CTSMROOT/doc/IMPORTANT_NOTES Jun/08/2018 Erik Kluzek -I.) For clm4_0: - -Configure Modes NOT scientifically validated, documented, supported or even advised to be used: -(options to CLM_CONFIG_OPTS) - - SNICAR_FRC (-snicar_frc) - This mode is tested and functional, but is NOT constantly scientifcally validated, and should be - considered experimental. - -Namelist items that should NOT be exercised: - - glc_dyntopo Change topographic height over glacier MEC (Not functional) - suplnitro='ALL' (suplnitro='ALL' with -bgc cn) - The suplemental Nitrogen mode of the CN model is known - to be too productive. - urban_traffic: Not currently functional - -II.) For clm4_5/clm5_0: - Namelist items that are not regularly tested or used. Some aren't even implemented. See - ../bld/namelist_files/namelist_definition_clm4_5.xml -- for definitions + ../bld/namelist_files/namelist_definition_ctsm.xml -- for definitions CN_evergreen_phenology_opt CN_partition_opt @@ -32,7 +13,6 @@ Namelist items that are not regularly tested or used. Some aren't even implement CNratio_floating all_active allowlakeprod - anoxia_wtsat carbon_resp_opt ch4offline downreg_opt @@ -50,6 +30,7 @@ Namelist items that are not regularly tested or used. Some aren't even implement urban_traffic use_extralakelayers use_lai_streams + use_cndv use_snicar_frc use_vichydro usefrootc diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000000..47304542de --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,42 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = clmdoc +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +# Before building html or pdf, obtain all of the images. This is needed +# because we have configured this repository (via an .lfsconfig file at +# the top level) to NOT automatically fetch any of the large files when +# cloning / fetching. +html: fetch-images +latexpdf: fetch-images +fetch-images: + git lfs pull --exclude="" + +.PHONY: help fetch-images Makefile + +# For the pdf, we only build the tech note, but use the conf.py file in +# the top-level source directory (the -c option says where to find +# conf.py). Note that we also override the setting of +# numfig_secnum_depth in order to have figure numbering as desired in +# the pdf, given that the pdf just contains the tech note, so doesn't +# have the top-level numbering present in the web documentation (where +# top-level section 1 is the User's Guide and section 2 is the Tech +# Note). +# +# The use of $(0) is as in the catch-all target. +latexpdf: + $(SPHINXBUILD) -M $@ "$(SOURCEDIR)/tech_note" "$(BUILDDIR)" -c "$(SOURCEDIR)" -D numfig_secnum_depth=1 $(SPHINXOPTS) $(O) + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/CTSMMasterChecklist b/doc/README.CHECKLIST.master_tags similarity index 87% rename from CTSMMasterChecklist rename to doc/README.CHECKLIST.master_tags index 793146c2a1..31c09895be 100644 --- a/CTSMMasterChecklist +++ b/doc/README.CHECKLIST.master_tags @@ -25,6 +25,8 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow 3b -- update the ExpectedFails list if expected fails changes in 1a $EDITOR cime_config/testdefs/ExpectedTestFails.xml 3c -- make sure you understand any changes to the baselines -- to document in ChangeLog + 3d -- Check the log file for run_sys_tests (../run_sys_test.log), to make sure that + externals are correct (see 2c above) (4) Use diff and status to make sure any new files are in the repo and only the correct changes are on the branch @@ -43,6 +45,7 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow 5c -- Update date stamp on ChangeLog ./UpDateChangeLog.pl -update 5d -- Commit new change files + 5e -- Push all the changes on your local branches to the branch on your fork (6) Submit a pull request (PR) for the changes Have someone review it if you are able. At minimum review it youself. The PR mechanism @@ -64,6 +67,12 @@ This should show no diffs (10) Push master and tag to ESCOMP/ctsm +(11) Update the CTSM upcoming tags project, if necessary + (https://github.com/ESCOMP/ctsm/projects/6) + +(12) Add tag to the CESM test database + (https://csegweb.cgd.ucar.edu/testdb) + ---- NOTES ---- (3) -- Always test on your fork with a feature-branch so that we can change tag order if needed. Put diff --git a/doc/UpdateChangelog.pl b/doc/UpdateChangelog.pl index 78a3afe42d..88f8331d03 100755 --- a/doc/UpdateChangelog.pl +++ b/doc/UpdateChangelog.pl @@ -41,7 +41,7 @@ sub usage { To document a new tag - $ProgName release-elm5.0.09 "Description of this tag" + $ProgName ctsm1.0.dev012 "Description of this tag" EOF } @@ -67,7 +67,7 @@ sub usage { $tag = $ARGV[0]; $sum = $ARGV[1]; - if ( $tag !~ /release-clm[0-9]\.[0-9]\.([0-9][0-9])/ ) { + if ( $tag !~ /ctsm[0-9]\.[0-9]\.(dev[0-9][0-9][0-9]|[0-9][0-9])/ ) { print "ERROR: bad tagname: $tag\n"; usage(); } @@ -84,8 +84,8 @@ sub usage { } -my $template = ".release-ChangeLog_template"; -my $changelog = "release-clm5.0.ChangeLog"; +my $template = ".ChangeLog_template"; +my $changelog = "ChangeLog"; my $changesum = "ChangeSum"; my $changelog_tmp = "ChangeLog.tmp"; my $changesum_tmp = "ChangeSum.tmp"; @@ -137,7 +137,7 @@ sub usage { my $oldTag = ""; while( $_ = ) { # If adding a new tag check that new tag name does NOT match any old tag - if ( $_ =~ /Tag name:[ ]*(release-clm.+)/ ) { + if ( $_ =~ /Tag name:[ ]*(ctsm.+)/ ) { $oldTag = $1; if ( (! $opts{'update'}) && ($tag eq $oldTag) ) { close( CL ); @@ -177,10 +177,10 @@ sub usage { # Find header line if ( $_ =~ /=====================/ ) { print FH $_; - my $format = "%17.17s %8.8s %10.10s %s\n"; + my $format = "%16.16s %8.8s %10.10s %s\n"; if ( $update ) { $_ = ; - if ( /^(.{17}) (.{8}) (.{10}) (.+)$/ ) { + if ( /^(.{16}) (.{8}) (.{10}) (.+)$/ ) { $tag = $1; $user = $2; $sum = $4; diff --git a/doc/UsersGuide/Makefile b/doc/UsersGuide/Makefile deleted file mode 100644 index 1c76bc75bd..0000000000 --- a/doc/UsersGuide/Makefile +++ /dev/null @@ -1,193 +0,0 @@ -# -# Makefile to convert DocBook CLM Users-Guide into html and/or pdf -# (rtf, txt, ps, tex, man, dvi, and texi are also valid docbook formats) -# -VPATH := ../../tools/cprnc . .. ../../bld ../../tools/ncl_scripts \ - ../../tools/mksurfdata ../../test/system ../../bld/namelist_files \ - ../../bld/config_files ../../tools ../../../../../scripts/ccsm_utils/Tools \ - ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM/ ../../src/main - -PDFUG := clm_ug.pdf -HTMLUG := book1.html -DOCBKUG := clm_ug.xml -CFGLOG := config_help -CPRLOG := cprnc_readme -BNMLOG := buildnml_help -BSTLOG := build_streams_help -RESLOG := buildnml_resolutions -USCLOG := buildnml_usecases -QCKLOG := quickstart_guide -COPLOG := filecopies -MKSLOG := mksurfdata.pl -USRLOG := quickstart_usrdat -PTCLOG := ptclm_help -PTCLST := ptclm_list -TDRLOG := test_driver.sh -GETREG := getregional_datasets -CO2DIF := addco2_datm.buildnml -DATLOG := build_date -NMLDFTBL := namelist_definition_table -NMLDLTBL := namelist_defaults_clm_table -HSFLDTBL := history_fields_table -CFGDFTBL := config_definition_table -COMPLIST := compsets_list_ofIcases.xml -SOURCES := $(DOCBKUG) $(COMPLIST) $(CFGLOG).xml $(PTCLOG).xml $(BNMLOG).xml \ - $(RESLOG).xml $(USCLOG).xml $(QCKLOG).xml $(COPLOG).xml $(PTCLST).xml \ - $(USRLOG).xml $(GETREG).xml preface.xml custom.xml special_cases.xml \ - tools.xml adding_files.xml single_point.xml addco2_datm.buildnml.xml \ - appendix.xml trouble_shooting.xml ptclm.xml $(BSTLOG).xml \ - $(MKSLOG).xml $(TDRLOG).xml $(DATLOG).xml $(CPRLOG).xml \ - $(NMLDFTBL).xml $(NMLDLTBL).xml $(CFGDFTBL).xml $(HSFLDTBL).xml - -CONVAMP := sed 's/\&/\&/g' -CONVSIGNS := sed 's/>/\>/g' | sed 's/ tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -$(NMLDLTBL).xhtml: namelist_defaults_clm.xml namelist_defaults.xsl - xsltproc ../../bld/namelist_files/namelist_defaults.xsl $< > tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -$(CFGDFTBL).xhtml: config_definition.xml config_definition.xsl - xsltproc ../../bld/config_files/config_definition.xsl $< > tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -history_fields.xml: findHistFields.pl - cd ../../src/main; ./findHistFields.pl >& tmpFile.txt - $(RM) tmpFile.txt - -$(HSFLDTBL).xhtml: history_fields.xml history_fields.xsl - xsltproc ../../bld/namelist_files/history_fields.xsl $< > tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -.xhtml.xml: - xsltproc stylesheethtml2docbook.xsl $< > $@ - -.tlog.xml: - $(CONVAMP) $< | $(CONVSIGNS) > tempFile.txt - limitLineLen.pl tempFile.txt > $@ - $(RM) tempFile.txt - -.diff.xml: - $(CONVAMP) $< | $(CONVSIGNS) > $@ - -debug: - @echo "SOURCES: $(SOURCES)" - @echo "CONVAMP: $(CONVAMP)" - @echo "CONVSIGNS: $(CONVSIGNS)" - -$(COMPLIST): - ./get_Icaselist.pl > $@ - -$(HTMLUG): $(SOURCES) - docbook2html --dsl clm_stylesheet.dsl#html $< - -$(PDFUG): $(SOURCES) - docbook2pdf --dsl clm_stylesheet.dsl#print $< - -$(BNMLOG).tlog: build-namelist - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/build-namelist -help >& $@ - -$(BSTLOG).tlog: build_streams - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../../../../scripts/ccsm_utils/Tools/build_streams --help >& $@ - -$(DATLOG).tlog: - @echo "Get current build date" - date +%b-%d-%Y >& $@ - -$(RESLOG).tlog: build-namelist - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/build-namelist -res list >& $@ - -$(USCLOG).tlog: build-namelist - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/build-namelist -use_case list >& $@ - -$(CFGLOG).tlog: configure - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/configure -help >& $@ - -$(PTCLOG).tlog: PTCLM.py - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM/PTCLM.py --help >& $@ - -$(PTCLST).tlog: PTCLM.py - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - cd ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM; \ - PTCLM.py --list >& $(CURDIR)/$@ - -$(MKSLOG).tlog: mksurfdata.pl - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../tools/mksurfdata/mksurfdata.pl -help >& $@ - -$(TDRLOG).tlog: test_driver.sh - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../test/system/test_driver.sh -help >& $@ - -$(QCKLOG).tlog: Quickstart.GUIDE - cp $< $@ - -$(COPLOG).tlog: README.filecopies - cp $< $@ - -$(CPRLOG).tlog: README - cp $< $@ - -$(USRLOG).tlog: Quickstart.userdatasets - cp $< $@ - -$(GETREG).tlog: getregional_datasets.pl - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $(GETREG) is good and redo your make" - ../../tools/ncl_scripts/getregional_datasets.pl -help >& $@ - -clean: - $(RM) -f $(HTMLUG) $(PDFUG) *.tlog $(DATLOG).xml *.xhtml *.tex - -realclean: clean - $(RM) -f f*.html c*.html x*.html a*.html i*.html $(COMPLIST) $(CFGLOG).xml \ - $(BNMLOG).xml $(BSTLOG).xml $(PTCLOG).xml $(PTCLST).xml \ - $(RESLOG).xml $(USCLOG).xml $(USRLOG).xml $(GETREG).xml $(QCKLOG).xml \ - $(CO2DIF).xml *.tlog $(MKSLOG).xml $(TDRLOG).xml $(DATLOG).xml \ - $(NMLDFTBL).xml $(NMLDLTBL).xml $(CFGDFTBL).xml $(CPRLOG).xml \ - $(COPLOG).xml diff --git a/doc/UsersGuide/addco2_datm.buildnml.diff b/doc/UsersGuide/addco2_datm.buildnml.diff deleted file mode 100644 index b8fbf34e36..0000000000 --- a/doc/UsersGuide/addco2_datm.buildnml.diff +++ /dev/null @@ -1,59 +0,0 @@ -*** datm.buildnml.csh.orig 2010-06-11 10:59:29.246523532 -0600 ---- datm.buildnml.csh 2010-06-11 11:06:30.710784206 -0600 -*************** -*** 34,48 **** - streams = 'clm_qian.T62.stream.Solar.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.Precip.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.TPQW.txt 1895 1948 1972 ', -! 'presaero.stream.txt 1849 1849 2006' - vectors = 'null' - mapmask = 'nomask', - 'nomask', - 'nomask', - 'nomask' - tintalgo = 'coszen', - 'nearest', - 'linear', - 'linear' - / - EOF1 ---- 34,56 ---- - streams = 'clm_qian.T62.stream.Solar.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.Precip.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.TPQW.txt 1895 1948 1972 ', -! 'presaero.stream.txt 1849 1849 2006', -! 'datm.global1val.stream.CO2.txt 1766 1766 2005 ' - vectors = 'null' - mapmask = 'nomask', - 'nomask', - 'nomask', -+ 'nomask', - 'nomask' -+ mapalgo = 'bilinear', -+ 'bilinear', -+ 'bilinear', -+ 'bilinear', -+ 'nn' - tintalgo = 'coszen', - 'nearest', - 'linear', -+ 'linear', - 'linear' - / - EOF1 -*************** -*** 1112,1121 **** ---- 1120,1132 ---- - - EOF1 - -+ cp $CASEBUILD/co2_streams.txt datm.global1val.stream.CO2.txt -+ - - $CASETOOLS/listfilesin_streams -input_data_list -t clm_qian.T62.stream.Solar.txt >> $CASEBUILD/datm.input_data_list - $CASETOOLS/listfilesin_streams -input_data_list -t clm_qian.T62.stream.Precip.txt >> $CASEBUILD/datm.input_data_list - $CASETOOLS/listfilesin_streams -input_data_list -t clm_qian.T62.stream.TPQW.txt >> $CASEBUILD/datm.input_data_list -+ $CASETOOLS/listfilesin_streams -input_data_list -t datm.global1val.stream.CO2.txt >> $CASEBUILD/datm.input_data_list - - cat >! presaero.stream.txt << EOF1 - diff --git a/doc/UsersGuide/adding_files.xml b/doc/UsersGuide/adding_files.xml deleted file mode 100644 index 18c034cbbb..0000000000 --- a/doc/UsersGuide/adding_files.xml +++ /dev/null @@ -1,357 +0,0 @@ - - -Adding New Resolutions or New Files to the build-namelist Database - -In the last chapter we gave the details on how to create new files for input into -CLM. These files could be either global resolutions, regional-grids or even a single -grid point. If you want to easily have these files available for continued use in your -development you will then want to include them in the build-namelist database so -that build-namelist can easily find them for you. You can deal with them, just by -editing your namelist by hand (or using a &usernlclm; namelist file), or by using -&CLMUSRDAT;. Another way to deal with them is to enter them into -the database for build-namelist, so that build-namelist can find them for you. -This keeps one central database for all your files, rather than having multiple locations -to keep track of files. If you have a LOT of files to keep track of it also might -be easier than keeping track by hand, especially if you have to periodically update -your files. If you just have a few quick experiments to try, for a short time period -you might be best off using the other methods mentioned above. - - -There are two parts to adding files to the build-namelist database. The first part -is adding new resolution names which is done in the -models/lnd/clm/bld/namelist_files/namelist_definition.xml file -(and in the -models/lnd/clm/bld/config_files/config_definition.xml file -when adding supported single-point datasets). -The second part is actually adding the new filenames which is done in the -models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml file -(models/lnd/clm/bld/namelist_files/namelist_defaults_clm_tools.xml -file for CLM tools). -If you aren't adding any new resolutions, and you are just changing the files for existing -resolutions, you don't need to edit the namelist_definition file. - - - -Managing Your Own Data-files - -If you are running on a supported machine (such as bluefire or jaguar) the standard -input datasets will already be available and you won't have to check them out of the -subversion inputdata server. However, you also will NOT be able to add your own datafiles -to these standard inputdata directories -- because most likely you won't have permissions -to do so. In order to add files to the XML database or to use &CLMUSRDAT; you need -to put data in the standard locations so that they can be found. The recommended -way to do this is to use the link_dirtree tool in the &cesm; scripts. -Some information on link_dirtree is available in the -&cesmrel; Scripts User's Guide. We also have -some examples of it's use here and in other sections of this User's Guide. - - -Using link_dirtree is quite simple, you give the directory where -data exists and then the directory that you want to create where datasets will point -to the original source files. In the example below we use "$HOME/inputdata", but -MYCSMDATA could be any directory you have access to where you want to -put your data. - -> cd scripts -# First make sure you have a inputdata location that you can write to -# You only need to do this step once, so you won't need to do this in the future -# (except to bring in any updated files in the original $CSMDATA location). -> setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data -> ./link_dirtree $CSMDATA $MYCSMDATA - -Then when you create a case you will change DIN_LOC_ROOT_CSMDATA to -point to the location you linked to rather than the default location. - -> ./xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA - - - -In order to list the files that you have created you merely need to use the UNIX -command find to find the files that are NOT softlinks. So for -example executing the following command: - -> find $MYCSMDATA -type f -print - -for me gives the following list of &CLMUSRDAT; files that I have created. - -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1849-2006_1x1pt_US-Ha1.nc -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1849-2006_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp8.5_monthly_1850-2100_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1850-2100_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/atm/datm7/domain.clm/domain.lnd.1x1pt_US-Ha1_USGS.nc -/blhome/erik/inputdata/atm/datm7/domain.clm/domain.lnd.13x12pt_f19_alaskaUSA_gx1v6.nc -/blhome/erik/inputdata/lnd/clm2/griddata/fracdata_13x12pt_f19_alaskaUSA_gx1v6.nc -/blhome/erik/inputdata/lnd/clm2/griddata/fracdata_1x1pt_US-Ha1_USGS.nc -/blhome/erik/inputdata/lnd/clm2/griddata/topodata_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/lnd/clm2/griddata/griddata_1x1pt_US-Ha1.nc -/blhome/erik/inputdata/lnd/clm2/griddata/griddata_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_13x12pt_f19_alaskaUSA_simyr1850.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_1x1pt_US-Ha1_simyr2000.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_rcp4.5_13x12pt_f19_alaskaUSA_simyr1850-2100.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_1x1pt_US-Ha1_simyr1850.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_13x12pt_f19_alaskaUSA_simyr2000.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_1x1pt_US-Ha1_simyr1849-2006.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_13x12pt_f19_alaskaUSA_simyr1850-2100.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_rcp8.5_13x12pt_f19_alaskaUSA_simyr1850-2100.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_13x12pt_f19_alaskaUSA_simyr1849-2006.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_1x1pt_US-Ha1_simyr1850-2100.nc - -You can also use find to list files that have a particular pattern -in the name as well (using the -name option with wildcards). Also you can always rerun the -link_dirtree command if any new files are added that you need to be -linked into your directory tree. Since, the files are soft-links -- it doesn't take up -much space other than the files that you add there. This way all of the files are kept -in one place, they are organized by usage according to &cesm; standards, and you can -easily find your own files, and &clm; can find them as well. - - - - -Adding Resolution Names - -If you are adding files for new resolutions which aren't covered in the -namelist_definition file -- you'll need to add them in. The list of valid resolutions -is in the id="res" entry in the -models/lnd/clm/bld/namelist_files/namelist_definition.xml file. -You need to choose a name for your new resolution and simply add it to the comma -delimited -list of valid_values for the id="res" entry. The convention for global Gaussian grids -is number_of_latitudes x number_of_longitudes. The convention for global finite -volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude -is measured in degrees. For regional or single-point datasets the names have a grid size -number_of_latitudes x number_of_longitudes followed by an underscore and then a -descriptive name such as a City name followed by an abbreviation for the Country in caps. -The only hard requirement is that names be unique for different grid files. -Here's what the entry for resolutions looks like in the file: - -<entry id="res" type="char*30" category="default_settings" - group="default_settings" - valid_values= -"128x256,64x128,48x96,32x64,8x16,94x192,0.23x0.31,0.47x0.63, -0.9x1.25,1.9x2.5,2.65x3.33,4x5,10x15,5x5_amazon, -1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ, -1x1_brazil,1x1_urbanc_alpha,0.5x0.5"> -Horizontal resolutions -</entry> - -As you can see you just add your new resolution names to the end of the valid_values -list. - - -When using &ptclm; and adding supported single-point resolutions, you'll also want to -add these resolutions to the -models/lnd/clm/bld/config_files/config_definition.xml under -the sitespf_pt name. The entry in that file looks like: - -<entry id="sitespf_pt" -valid_values="none,1x1_brazil,5x5_amazon, -1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ, -1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA" -value="none" category="physics"> -Flag to turn on site specific special configuration flags for supported single -point resolutions. -Currently the only special settings are for MEXICOCITY and VANCOUVER, which make -changes to urban parameters. -</entry> - -&ptclm; assumes that any supported single-point resolutions are valid settings for -sitespf_pt. - - - - -Adding or Changing Default Filenames - -To add or change the default filenames you edit the -models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml -and either change an existing filename or add a new one. Most entries in the -default namelist files, include different attributes that describe the different -properties that describe the differences in the datasets. Attributes include -the: resolution, year to simulation, range of years to simulate for transient -datafiles, the land-mask, the representative concentration pathway (rcp) for future -scenarios, and the type of biogeochemistry (bgc) model used. For example the -fatmgrid for the 1.9x2.5 resolution is as follows: - -<fatmgrid hgrid="1.9x2.5" >lnd/clm2/griddata/griddata_1.9x2.5_060404.nc -</fatmgrid> - -Other fatmgrid files are distinguished from this one by -their resolution (hgrid) attribute. - - -To add or change the default filenames for &clm; tools edit the -models/lnd/clm/bld/namelist_files/namelist_defaults_clm_tools.xml -and either change an existing filename or add a new one. Editing this file is -similar to the namelist_defaults_clm.xml talked about above. - - -What are the required files? - -Different types of simulations and different types of configurations for &clm; require -different lists of files. The Carbon Nitrogen (cn) Biogeochemistry model for example -requires stream_fldfilename_ndep files, which are NOT required by -other bgc modes. Transient simulations also require transient datasets, and the names -of these datasets are sometimes different from the static versions (sometimes both are -required as in the dynamic PFT cases). - - -In the following table we list the different files used by CLM, they are listed -in order of importance, dependencies, and customizing. So the required files -are all near the top, and the files used only under different conditions are listed -later, and files with the fewest dependencies are near the top, as are the files -that are least likely to be customized. - - -Required Files for Different Configurations and Simulation Types - - - - - - - Filename - Config. type - Simulation type - Resol. Dependent? - Other Dependencies? - - - Notes - - - - - - fpftcon - ALL - ALL - No - No - - - Not usually customized, as describes plant function -type properties. &ptclm; copies the file for you so that you can customize it if you -like, see . - - - fsnowoptics - ALL - ALL - No - No - - - Not usually customized as describes global snow optical properties. - - - fsnowaging - ALL - ALL - No - No - - - Not usually customized as describes global snow aging properties. - - - fatmgrid - ALL - ALL - Yes - No - - - Creating, using mkgriddata -usually gives you the amount of customization -you need, as it just describes the grid and grid extents. - - - fatmlndfrc - ALL - ALL - Yes - land-mask - - - Describes the land-mask for points with active land, as well as the fraction -of each grid-cell covered by land. You might customize it to make sure the land-fraction -of your grid-cell matches the expected values for your site. But, usually you will just -use what mkgriddata gives you. - - - fsurdat - ALL - ALL - Yes - simulation-year - - - Describes percentages of different land-units, columns and -vegetation types within each grid-cell. To customize for a specific point -or region you may want to use custom input datasets to mksurfdata when -creating the file. mksurfdata also allows you to customize the PFT, -and soil types to it see . &ptclm; takes -advantage of this to create customized datasets as well, see the chapter on &ptclm; -at . - - - flanduse_timeseries - ALL - transient land-use land-cover change - Yes - Simulation year range, and representative concentration pathway (rcp) - - - See notes on fsurdat files. - - - frivinp_rtm - RTM only - ALL - No - No - - - We only provide a half-degree global river routing file. If you want -to model river flow for a smaller scale, or a basin regional scale, you would -need to create your own custom file to do that. Normally, we turn river-routing -OFF for regional or single point simulations. - - - finidat - ALL - RUN_TYPE="startup", CLM_FORCE_COLDSTART="off" - Yes - mask, maxpft, bgc, simulation-year, start-date - - - Used for starting the model from a spun-up state. -Create these files by running the model -for multiple years and saving the restart file from the end of a spin-up -simulation. - - - - stream_fldfilename_ndep - bgc=cn/cndv - Yes - No - simulation-year - - - -You may customize this file to get the Nitrogen deposition characteristics -of your site if available. This file will be interpolated while the model is -running from it's resolution to the resolution that &clm; is running at. - - - - - -
    -     - -     - -     - diff --git a/doc/UsersGuide/addxhtmlhead.pl b/doc/UsersGuide/addxhtmlhead.pl deleted file mode 100755 index d5f9615c58..0000000000 --- a/doc/UsersGuide/addxhtmlhead.pl +++ /dev/null @@ -1,78 +0,0 @@ -#!/usr/bin/env perl -# -use strict; -use Cwd; -use English; -use IO::File; -use Getopt::Long; -use IO::Handle; -#----------------------------------------------------------------------------------------------- - -# Get the directory name and filename of this script. If the command was -# issued using a relative or absolute path, that path is in $ProgDir. Otherwise assume -# the -# command was issued from the current working directory. - -(my $ProgName = $0) =~ s!(.*)/!!; # name of this script -my $ProgDir = $1; # name of directory containing this script -- may be a - # relative or absolute path, or null if the script - # is in - # the user's PATH -my $nm = "$ProgName::"; # name to use if script dies -my $scrdir; -if ($ProgDir) { - $scrdir = $ProgDir; -} else { - $scrdir = getcwd() -} - -sub usage { - my $msg = shift; - - print "ERROR:: $msg\n"; - die < -OPTIONS - NONE -EOF -} - -my %opts = ( ); - -GetOptions( -) or usage(); - -if ( $#ARGV != 0 ) { - &usage( "Wrong number of command line arguments" ); -} - -my $inputFile = $ARGV[0]; - -if ( ! -f $inputFile ) { - &usage( "Input file does NOT exist : $inputFile" ); -} - -my $fh = IO::File->new($inputFile, '<') or die "** $nm - can't open input file: -$inputFile\n"; - -# -# Add in XML XHTML headers -# -print <<"EOF"; - - - -EOF -while (my $line = <$fh>) { - if ( $line =~ /^$/ ) { - print "
    \n"; - } elsif ( $line =~ /^'."\n"; - } else { - print $line; - } -} -$fh->close(); diff --git a/doc/UsersGuide/appendix.xml b/doc/UsersGuide/appendix.xml deleted file mode 100644 index 058e67d577..0000000000 --- a/doc/UsersGuide/appendix.xml +++ /dev/null @@ -1,305 +0,0 @@ - -Editing Template Files Before Configure - -The last kind of customization that you can do for a case, before configure is run -is to edit the templates. The &clm; template is in -models/lnd/clm/bld/clm.cpl7.template, the &datm; template is -in models/atm/datm/bld/datm.cpl7.template, and the driver templates -are in the models/drv/bld directory and are named: -ccsm.template and cpl.template. When a case is -created they are also copied to the Tools/Templates directory -underneath your case. If you want to make changes that will impact all your cases, you -should edit the template files under the models directory, but -if you want to make a change ONLY for a particular case you should edit the template -under that specific case. - - - -Editing the template files is NOT for the faint of heart! We recommend this ONLY for -experts! It's difficult to do because the template is a script that actually creates -another script. So part of the script is echoing the script to be created and part of -it is a script that is run when "configure -case" is run. As a result any variables -in the part of the script that is being echoed have to be escaped like this: - -\$VARIABLE - -But, in other parts of the script that is run, you can NOT escape variables. So you -need to understand if you are in a part of the script that is echoing the script to -be created, or in the part of the script that is actually run. - - - -If you can customize your case using: compsets, env_*.xml variables, -or a user namelist, as outlined in you should do so. -The main reason to actually edit the template files, is if you are in a situation where -the template aborts when you try it run it when "configure -case" is run. The other -reason to edit the template is if you are &clm; developer and need to make adjustments -to the template because of code or script updates. An example of modifying the &datm; -template is in where sed is used to modify the path -for &CPLHIST; data. - - -Outline of the &clm; template - -The outline of the &clm; template is as follows: - -# set up options for clm configure and then run clm configure -$CODEROOT/lnd/clm*/bld/configure <options> -# set up options for clm build-namelist and then run clm build-namelist -$CODEROOT/lnd/clm*/bld/build-namelist <options> -# echo the $CASEBUILD/clm.buildnml.csh script out -cat >! $CASEBUILD/clm.buildnml.csh << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -# Remove temporary namelist files - -# echo the $CASEBUILD/clm.buildexe.csh script out -cat > $CASEBUILD/clm.buildexe.csh <<EOF2 -# NOTE: variables in this section must be escaped -EOF2 -# Remove temporary configure files - - - - - -Outline of the &datm; template - -The outline of the &datm; template is as follows: - -# Check $GRID to set the $DOMAINFILE and $DOMAINPATH - -# Check DATM_PRESAERO to set the prescribed aerosol option -# If &CLMUSRDAT; is set and $DOMAINFILE is NOT -- set it by &CLMUSRDAT; -# Ensure $DOMAINFILE is set or else abort - -#============================================================================== -# Create resolved prestage data script -#============================================================================== -cat >! $CASEBUILD/datm.buildnml.csh << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -# Major if blocks look at DATM_MODE: -# the if blocks setup streams and run Tools/build_streams to create stream files -#----- CLM_QIAN mode ---------------------------------------------------------- -else if ($DATM_MODE == "&CLMQIAN;" ) then -. - # Customize &CLMQIAN; options here - - # A.) Setup datm_atm_in namelist -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_atm_in << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -EOF - - # B.) Setup options to build_streams -. -. -. -#----- CLM1PT mode ---------------------------------------------------------- -else if ($DATM_MODE == "CLM1PT" ) then -. - # Customize CLM1PT options here - - # A.) Setup datm_atm_in namelist -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_atm_in << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -EOF - - # B.) Setup options to build_streams -. -. -. -. -#----- CPLHIST 3-hourly time-averaging mode ----------------------------------------------------------- -else if ($DATM_MODE == "&CPLHIST;" ) then -. - # Customize &CPLHIST; options here - - # A.) Setup datm_atm_in namelist -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_atm_in << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -EOF - - # B.) Setup options to build_streams -. -. -. -. - -#----- INVALID mode -----------------------------------------------------------else - echo "ERROR: unrecognized DATM_MODE = \$DATM_MODE " - exit -1 -endif - -#============================================================================== -# Create prescribed aero streams if appropriate -#============================================================================== -. -. -. -#============================================================================== -# Create remaining resolved namelist -#============================================================================== - -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_in << EOF1 -# NOTE: variables in this section must be escaped -. -. -. -EOF1 - -EOF - -#============================================================================== -# Create script to build executable -#============================================================================== - -cat > $CASEBUILD/datm.buildexe.csh <<EOF -#! /bin/csh -f -# NOTE: variables in this section must be escaped -EOF - -#============================================================================== -# end of script -#============================================================================== - - - - - -Adding a new DATM_MODE to the &datm; template - - The steps to adding a new DATM_MODE - -Add a new "if" block to the &datm; template - -As you can see from above -there are major "if" blocks for the different DATM_MODE's. So adding a new -DATM_MODE means adding a new "if" block. The two major parts of each DATM_MODE -block are: - -Setup datm_atm_in namelist -Setup options to build_streams - - - - -In the "if" block create the <filename>datm_atm_in</filename> namelist - -See for some notes about the -&datm; namelist and streams files. That and the - -&datm; User's Guide should give you guidance on how to -setup the namelist for your case. - - - -In the "if" block create options to and call <command>build_streams</command> - -The next part of the "if" block in the &datm; template file to work with is the -call to build_streams. You may need to add additional options -to it. You may also need to call it multiple times for multiple streams. You will -also likely need to add a new source option to it with the "-s" option. For more -information on build_streams do the following. - -Getting help with <command>build_streams</command> for &datm; - -> scripts/ccsm_utils/Tools/build_streams -help - - -The output of the above command is: - - -&build_streams_help; - - - - - -Add new streams templates to the &datm; -<filename>datm.template.streams.xml</filename> file - -As part of modifying the behavior of build_streams you will also -have to edit the models/atm/datm7/bld/datm.template.streams.xml -file as well (or the local version in your -$CASENAME/Tools/Templates directory for a particular case). -The template is an XML file much like the output streams file, but there are attributes -to distinguish which fields will be used based on things like: RESOLUTION or datasource. -And there are filename indicators (starting with a "%") that get translated into various -things such as: - -%c = Case (from above -case command line option) -%do = Use domain file -%y = Year (through range given from begyear to endyear) -%ym = Year-Month (all 12 months through year range) -%6ym = Like %ym but 6 digit year (ie. %YYYYYY-MM). (can replace the 6 with any digit 1-9) - - - - -Add a new valid_value to the <filename>config_definition.xml</filename> file in -scripts. - -Adding a new DATM_MODE also requires adding a new valid_value to -scripts/ccsm_utils/Case.template/config_definition.xml. This -enables the scripts to recognize the new value as a valid option to DATM_MODE -in the &envconf; file. - - - - - - - -Building the Users-Guide Documentation for &clm; - -All of the documentation for &clm; can be built using GNU Makefiles that are -available in the appropriate directories. The Makefiles require the following -utilities: docbook2html, docbook2pdf, -protex, and latex2html. - - -To build the Users Guide for &clm; (requires docbook). - -> cd models/lnd/clm/doc/UsersGuide -> gmake - -Note, that when the Users-Guide is built it will get output from other &clm; -utilities that by nature abort, and hence stop the make from continuing. However, -this is expected so you should simply run gmake again until -it either completes or comes upon a legitimate issue. Here is what a sample -warning looks like when gmake is run. - -The following line will fail in the make as it calls die -- but that is expected -Check that the output config_help.tlog is good and redo your make -../../bld/configure -help >&` config_help.tlog -make: *** [config_help.tlog] Error 255 - -To build the Code Reference Guide for &clm; (requires protex and -latex2html). The make here uses a Filepath -file that points to the list of directories that you want protex -to run over. You should examine this file and make sure it is appropriate for what -you need to do, before running the make. - -> cd models/lnd/clm/doc/CodeReference -> gmake - -To build the table of tests for the &clm; test suite. The make here runs a UNIX -shell script to create a html table of the list of tests run on the different machines -from the &clm; test suite. - -> cd models/lnd/clm/test/system -> gmake - - - - - diff --git a/doc/UsersGuide/badpergro.jpg b/doc/UsersGuide/badpergro.jpg deleted file mode 100644 index 4a378cf52d..0000000000 Binary files a/doc/UsersGuide/badpergro.jpg and /dev/null differ diff --git a/doc/UsersGuide/clm_stylesheet.dsl b/doc/UsersGuide/clm_stylesheet.dsl deleted file mode 100644 index 7bc3ed0036..0000000000 --- a/doc/UsersGuide/clm_stylesheet.dsl +++ /dev/null @@ -1,154 +0,0 @@ - - -]> - - - - - - - - - -;;Default extension for filenames -(define %html-ext% ".html") -;;What font would you like for the body? -(define %body-font-family% - "Arial") - -(element emphasis -(if (equal? (normalize "bold") (attribute-string (normalize "role"))) - ($bold-seq$) - ($italic-seq$))) - -(element tgroup - (let* ((wrapper (parent (current-node))) - (frameattr (attribute-string (normalize "frame") wrapper)) - (pgwide (attribute-string (normalize "pgwide") wrapper)) - (footnotes (select-elements (descendants (current-node)) - (normalize "footnote"))) - (border (if (equal? frameattr (normalize "none")) - '(("BORDER" "0")) - '(("BORDER" "1")))) - (bgcolor '(("BGCOLOR" "#E0E0E0"))) - (width (if (equal? pgwide "1") - (list (list "WIDTH" ($table-width$))) - '())) - (head (select-elements (children (current-node)) (normalize "thead"))) - (body (select-elements (children (current-node)) (normalize "tbody"))) - (feet (select-elements (children (current-node)) (normalize "tfoot")))) - (make element gi: "TABLE" - attributes: (append - border - width - bgcolor - '(("CELLSPACING" "0")) - '(("CELLPADDING" "4")) - (if %cals-table-class% - (list (list "CLASS" %cals-table-class%)) - '())) - (process-node-list head) - (process-node-list body) - (process-node-list feet) - (make-table-endnotes)))) - - -;;Should verbatim items be 'shaded' with a table? -(define %shade-verbatim% - #t) - -;;Define shade-verbatim attributes -(define ($shade-verbatim-attr$) - (list - (list "BORDER" "0") - (list "BGCOLOR" "#E0E0E0") - (list "WIDTH" ($table-width$)))) - -;;Index -(define (generate-index) - ("1")) - -;;======================== -;;Title Pages for Books -;;======================= - -(define (book-titlepage-recto-elements) - (list (normalize "title") - (normalize "subtitle") - (normalize "authorgroup") - (normalize "author") - (normalize "date") - (normalize "releaseinfo") - (normalize "orgname") - (normalize "graphic") - (normalize "copyright") - (normalize "legalnotice"))) - - - - - - - - - -;;Index -(define ($insert.xref.page.number$) - ("yes")) - -;;Index -(define ($generate-index$) - ("1")) - -;;Tex Backend off -(define tex-backend - #f) - -;;What elements should have a LOT? -(define ($generate-book-lot-list$) - (list (normalize "example") - (normalize "table") - (normalize "figure") - (normalize "equation"))) - -;;======================== -;;Title Pages for Books -;;======================= - -(define (book-titlepage-recto-elements) - (list (normalize "title") - (normalize "subtitle") - (normalize "authorgroup") - (normalize "author") - (normalize "date") - (normalize "orgname") - (normalize "graphic") - (normalize "copyright") - (normalize "legalnotice") - (normalize "releaseinfo"))) - -(define %show-ulinks% - ;; Display URLs after ULinks? - #t) - -(define %indent-screen-lines% - ;; Indent lines in a 'Screen'? - " ") - - - - - - - - diff --git a/doc/UsersGuide/clm_ug.xml b/doc/UsersGuide/clm_ug.xml deleted file mode 100644 index 68aa69b1d6..0000000000 --- a/doc/UsersGuide/clm_ug.xml +++ /dev/null @@ -1,191 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - build-namelist"> - configure"> - NCAR"> - CCSM"> - CCSM4.0"> - CESM"> - CESM1.0"> - CESM1.0.1"> - CESM1.0.2"> - CESM1.0.3"> - - PTCLM"> - PTCLM1"> - PTCLM1.110504"> - CLM"> - CLMCN"> - CLMSP"> - CLMU"> - CLM3.0"> - CLM3.5"> - CLM4"> - CLM4.0.00"> - - - - - - - - DATM"> - models/lnd/clm/doc/KnownBugs"> - NetCDF"> - FORTRAN"> - FORTRAN-90"> - MPI"> - PIO"> - OpenMP"> - NCL"> - Perl"> - XML"> - xmlchange"> - 2"> - - - - env_run.xml"> - env_build.xml"> - env_conf.xml"> - user_nl_clm"> - - - PTS_MODE"> - CSMDATA"> - CLM_FORCE_COLDSTART"> - CLM_CONFIG_OPTS"> - CLM_BLDNML_OPTS"> - CLM_NML_USE_CASE"> - CLM_NAMELIST_OPTS"> - CLM_PT1_NAME"> - CLM_QIAN"> - CPLHIST3HrWx"> - CLM_USRDAT_NAME"> - CLM_CO2_TYPE"> - DIN_LOC_ROOT"> - - - CLM_QIAN"> - - - - %ISOamsa; - ]]> - - - - %ISOgrk1; - ]]> - -]> - - - - -&cesm; Research Tools: &clmrel; User's Guide Documentation - - - CESM - CLM - community earth system model - climate - climate model - earth system model - land surface model - hydrology - biogeochemistry - urban model - documentation - - - - - - Erik - Kluzek - - NCAR - - - - - - - -The user's guide to &clmrel; which is the active land surface model component of &cesmrel;. -The purpose of this guide is to instruct both the novice and experienced user, as well as -&clm; developers in the use of &clm4; for land-surface climate modeling. - - - -$URL$ - -&build_date; - - - - - -Dedicated to the Land Model Working Group, winners of the 2008 &ccsm; Distinguished Achievement Award. -May you continue to collaborate together well, and continue to drive -the science of land surface modeling forward with your diligent and persistent efforts. - - - - -&preface; -&custom; -&tools; -&adding_files; -&special_cases; -&single_point; -&ptclmdoc; -&trouble; -&testing; -&appendix; - - diff --git a/doc/UsersGuide/co2_streams.txt b/doc/UsersGuide/co2_streams.txt deleted file mode 100644 index 4d38c6d06e..0000000000 --- a/doc/UsersGuide/co2_streams.txt +++ /dev/null @@ -1,50 +0,0 @@ - - - This is a streams file to pass historical CO2 from datm8 to the other - surface models. It reads in a historical dataset derived from data used - by CAM. The getco2_historical.ncl script in components/clm/tools/ncl_scripts - was used to convert the CAM file to a streams compatible format (adding domain - information and making CO2 have latitude/longitude even if only for a single - point. - - - - Input stream description file for historical CO2 reconstruction data - - 04 March 2010: Converted to form that can be used by datm8 by Erik Kluzek - 18 December 2009: Prepared by B. Eaton using data provided by - Jean-Francois Lamarque. All variables except f11 are directly from - PRE2005_MIDYR_CONC.DAT. Data from 1765 to 2007 with 2006/2007 just - a repeat of 2005. - - - CLMNCEP - - - - time time - lonc lon - latc lat - area area - mask mask - - - /fis/cgd/cseg/csm/inputdata/atm/datm7/CO2 - - - fco2_datm_1765-2007_c100614.nc - - - - - CO2 co2diag - - - /fis/cgd/cseg/csm/inputdata/atm/datm7/CO2 - - - fco2_datm_1765-2007_c100614.nc - - - - diff --git a/doc/UsersGuide/custom.xml b/doc/UsersGuide/custom.xml deleted file mode 100644 index d6a60a28f7..0000000000 --- a/doc/UsersGuide/custom.xml +++ /dev/null @@ -1,1615 +0,0 @@ - - - - - - - component set - compset - "I" compsets - "B" compsets - "E" compsets - "F" compsets - &CLMCONFIG; - &CLMNAMELIST; - &CLMFORCECOLD; - &CLMUSECASE; - &CLM1PT; - &CLMUSRDAT; - &CLMCO2; - - -How to customize the configuration for a case with &clm; - - -The -&cesm; User's Guide gives you the details on how to setup, &configure;, build, and run -a case. That is the document to give you the details on using the &cesm; scripts. The purpose -of this document is to give you the details when using &cesm; with &clm; on how to customize -and use advanced features in &clm;. You should be familiar with the &cesm; User's Guide and -how to setup cases with &cesmrel; before referring to this document. - - -In this chapter we deal with three different ways of customizing a case: Choosing a compset, -Customizing Configuration options, and customizing the &clm; Namelist. There are many different -compsets that use &clm; and many are setup to enable special features of &clm; from the start. So -the first thing you want to be familiar with are the different options in the compsets. The -next section shows the different options for customizing the configuration options for -&clm;. -Here we introduce the &clm; &configure; and &buildnml; scripts and how using the options in -&envconf; you can customize the configuration and the initial -namelist. The final section tells you about the &clm; namelist and how you can customize the -namelist once you have run "&configure; -case" and have an initial namelist in -BuildConf/clm.buildnml.csh. You can also -use &envconf; options to change your namelist as well, before "&configure; -case" is -run. - - - -Choosing a compset using &clm; - - -When setting up a new case one of the first choices to make is which "component -set" (or compset) to use. The -compset refers to which component models are used as well as specific settings for them. We label the different -types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). -The compsets of interest when working with &clm; are the "I" compsets (which contain -&clm; with a data atmosphere model -and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain &clm; -with the active atmosphere model (CAM), -prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. Below we -go into details on the "I" compsets which emphasize &clm; as the only active model, and just mention the two other categories. - - -When working with &clm; you usually want to start with a relevant "I" compset before moving to the more -complex cases that involve other active model components. The "I" compsets can exercise -&clm; in a way that -is similar to the coupled modes, but with much lower computational cost and faster turnaround times. - - -Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) -&compsets_list; - - - - Compsets coupled to active atmosphere with data ocean - - CAM compsets are compsets that start with "E" or "F" in the name. They are - described more fully in the scripts documentation or the CAM documentation. "E" compsets have -a slab ocean model while "F" compsets have a data ocean model. - - - - -Fully coupled compsets with fully active ocean, sea-ice, and atmosphere - - Fully coupled compsets are compsets that start with "B" in the name. They are - described more fully in the scripts documentation. - - - - -Conclusion to choosing a compset - -We've introduced the basic type of compsets that use &clm; and given some further details -for the "standalone &clm;" (or "I" compsets). The - -config_compsets.xml lists all of the compsets and gives a full description -of each of them. In the next section we look into customizing the &configure; time options -for compsets using &clm;. - - - - - - - -Customizing the &clm; configuration - -The "Creating a Case" section of the -&cesm1; Scripts -User's-Guide -gives instructions on creating a case. What is of interest here is how to customize your -use of &clm; -for the case that you created. In this section we discuss how to customize your case before the first -step -- the "&configure; -case" step is done. In the next section we will discuss how to customize your -&clm; namelist after "&configure; -case" has already been done. - - -For &clm; when "&configure; -case" is called there are two steps that take place: - - -The &clm; "&configure;" script is called to setup the build-time -configuration for &clm; (more information on &configure; is given in -). -The &clm; "&buildnml;" script is called to generate the initial -run-time namelist for &clm; (more information on &buildnml; is given below in -. - - -When customizing your case at the &configure; step you are able to modify the process by effecting either one -or both of these steps. The &clm; "&configure;" and "&buildnml;" scripts are both available in the "models/lnd/clm/bld" -directory in the distribution. Both of these scripts have a "-help" option that is useful to examine to see what -types of options you can give either of them. - - -There are five different types of customization for the configuration that we will -discuss: &cesm1; &clm; configuration items, Configure time User Namelist, -other noteworthy &cesm; configuration items, the &clm; &configure; script options, and -the &clm; &buildnml; script options. - - -Information on all of the script, configuration, build and run items is found under -scripts/ccsm_utils/Case.template -in the -config_definition.xml - file. - - - -&clm; Script configuration items - -Below we list each of the &cesm; configuration items that are specific to &clm;. All -of these are available in your: &envconf; file. - - - - &CLMCONFIG; - &CLMBLDNML; - &CLMNAMELIST; - &CLMFORCECOLD; - &CLMUSECASE; - &CLM1PT; - &CLMUSRDAT; - &CLMCO2; - -For the precedence of the different options to &buildnml; see the section on -precedence below. - - -The first item &CLMCONFIG; has to do with customizing the &clm; configuration options for your case, the rest -all have to do with generating the initial namelist. - - - -&CLMCONFIG; - - -The option &CLMCONFIG; is all about passing command line arguments to the &clm; &configure; script. It is important -to note that some compsets, may already put a value into the &CLMCONFIG; variable. You can still add more -options to your &CLMCONFIG; but make sure you add to what is already there rather than replacing it. Hence, -we recommend using the "-append" option to the xmlchange script. In - -below we will go into more details on options that can be customized in the &clm; "&configure;" script. It's -also important to note that the &clm; template may already invoke certain &clm; &configure; options and as such those -command line options are NOT going to be available to change at this step (nor would you want to change them). -The options to &configure; are given with the "-help" option which is given in -. - - - - - -&CLMUSECASE; - - -&CLMUSECASE; is used to set a particular set of conditions that set multiple namelist items, all centering around -a particular usage of the model. -To list the valid options do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -use_case list - - -The output of the above command is: - - -&usecases_list; - - - -See the section for the precedence of this -option relative to the others. - - - - - - -&CLMBLDNML; - - -The option &CLMBLDNML; is for passing options to the &clm; "&buildnml;" script. As with the "&configure;" -script the &clm; template may already invoke certain options and as such those options will NOT be available to be -set here. The best way to see what options can be sent to the "&buildnml;" script is to do - - -> cd models/lnd/clm/bld -> ./&buildnml; -help - - -Here is the output from the above. - - -./&buildnml_help; - - -The &clm; template already sets the resolution and mask as well as the &configure; file, -the start-type, the co2_ppmv, rtm_tstep, and rtm_res, and defines an input -namelist and namelist input file, and it normally sets either "-ignore_ic_year" or -"-ignore_ic_date". Also many -of the options are designed solely for &clm; stand-alone testing and hence should NOT -be used (any of the options starting -with a "datm_" or "drv_" prefix. Hence there are then only five different options that could be set: - - - --lnd_res --sim_year --rcp --clm_demand --verbose - - - -"-lnd_res" is used to run &clm; in fine-mesh mode at a higher resolution than the atmospheric model. This can -be useful to get higher resolution from the land model, but saving computer time -by running the more expensive atmospheric model at a lower resolution. -To get a list of valid resolutions to run at do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -lnd_res list - - - -The fine-mesh mode is considered experimental, and you may run into problems when you use -it. Another option is to use the CESM level "tri-grid" capability to run the land model -on a different grid than the atmospheric model. Read the CESM User's-Guide to learn how -to do this. - - - - - -See the section for the precedence of this -option relative to the others. - - - - -"-clm_demand" asks the &buildnml; step to require that the list of variables -entered be set. Typically, this is used to require that optional filenames be used and ensure -they are set before continuing. For example, you may want to require that -flanduse_timeseries be set to get dynamically changing vegetation types. To do this -you would do the following. - -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val "-clm_demand flanduse_timeseries" - -To see a list of valid variables that you could set do this: - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -clm_demand list - - - - -Using a 20th-Century transient compset or the 20thC_transient use-case -using &CLMUSECASE; would set this as well, but would also use -dynamic nitrogen and aerosol deposition files, so using -clm_demand would be a way -to get just dynamic vegetation types and NOT the other files as well. - - - -"-sim_year" is used to set the simulation year you want the data-sets to simulate conditions for in the input -datasets. The simulation "year" can also be a range of years in order to do simulations -with changes in the dataset values as the simulation progresses. To list the valid -options do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -sim_year list - - -"-rcp" is used to set the representative concentration pathway for the future scenarios -you want the data-sets to simulate conditions for, in the input -datasets. To list the valid options do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -rcp list - - - - - -&CLMNAMELIST; - - -The option &CLMNAMELIST; is for passing namelist items into the "clm_inparm" namelist. -Any items that are set in &CLMNAMELIST; will be set in your namelist after "&configure; --case" is done. - - - -For character namelist items you need to use "&apos;" as quotes for strings so that the -scripts don't get confused with other quotes they use. - - - -Example, you want to set hist_dov2xy to .false. -so that you get vector output to your history files. To do so edit -&envconf; and add a setting for hist_dov2xy. -So do the following: - -> ./xmlchange -file env_conf.xml -id &CLMNAMELIST; -val hist_dov2xy=.false. - - - -Example, you want to set hist_fincl1 to add the variable 'HK' -to your history files. To do so edit -&envconf; and add a setting for hist_fincl1. -So do the following: - -> ./xmlchange -file env_conf.xml -id &CLMNAMELIST; -val "hist_fincl1=&apos;HK&apos;" - -For a list of the history fields available see -&clm; History Fields. - - - -See the section for the precedence of this -option relative to the others. - - - - - - -&CLMCO2; - - -&CLMCO2; sets the type of input &CO2; for either "constant", "diagnostic" or prognostic". -If "constant" the value from CCSM_CO2_PPMV will be used. If "diagnostic" -or "prognostic" the values MUST be sent from the atmosphere model. For more information on how -to send &CO2; from the data atmosphere model see . - - - - - -&CLMFORCECOLD; - - -&CLMFORCECOLD; when set to on, requires that -your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it -will use an initial condition file if it can find an appropriate one, and otherwise do a cold -start. &CLMFORCECOLD; is a good way to ensure that you are doing a cold -start if that is what you want to do. - - - - - -&CLM1PT; - - -&CLM1PT; is used ONLY for a pt1_pt1 -resolution simulation to set the name of the single-point files to use. -To see a list of the valid resolutions do this: - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -res list - - - -The output of the above command is: - - -&res_list; - - -the valid resolutions that can be used with &CLM1PT; are the ones that -have city or nation names such as: 5x5_amazon, 1x1_vancouverCAN 1x1_mexicocityMEX, or -1x1_brazil. The "1x1_" prefix means the file is for a single-point, while "5x5_" prefix means -it's for a region of five points in latitude by five points in longitude. Both regional -and single point datasets can be used for &CLM1PT;. If you create your own datasets -you can also use &CLM1PT; along with &CLMUSRDAT; (documented below), setting &CLM1PT; to -the value in &CLMUSRDAT; so that your datasets are used rather than the standard ones.o - - - - - -&CLMUSRDAT; - - -&CLMUSRDAT; provides a way to enter your own datasets into the initial -namelist setup at "&configure; -case". The files you create must be named with -specific naming conventions outlined in: . -To see what the expected names of the files are, use the -queryDefaultNamelist.pl to see -what the names will need to be. For example if your &CLMUSRDAT; will -be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, -the following will list what your filenames should be: - -> cd models/lnd/clm/bld -> queryDefaultNamelist.pl -usrname "1x1_boulderCO" -options \ -mask=navy,sim_year=1850,sim_year_range="constant" -csmdata $CSMDATA - -An example of using &CLMUSRDAT; for a simulation is given in -. - - - -See the section for the precedence of this -option relative to the others. - - - - - - - - - -Configure time User Namelist - -&CLMNAMELIST; as described above allows you to set any -extra namelist items you would like to appear in your namelist after first &configure;d. -However, it only allows you a single line to enter namelist items, and strings must -be quoted with &apos; which is a bit awkward. If you have a long list of namelist -items you want to set (such as a long list of history fields) a convenient way to do it -is to create a &usernlclm; that contains just the list of namelist -variables you want to add to your initial namelist. The &usernlclm; -will only be used when &configure; is run, so if you change it after &configure; -- it won't -change anything. The file needs to be in valid FORTRAN namelist format, and the &configure; -step will abort if there are syntax errors. It merely needs to be named correctly -&usernlclm; and placed in your case directory (where your other -env_*.xml files are). The namelist name actually doesn't have to be -valid, but all the variable names must be. Here's an example &usernlclm; -namelist that sets a bunch of history file related items, to create output history files -monthly, daily, every six and 1 hours. - -Example &usernlclm; namelist file - -&clmexp - hist_fincl2 = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS', - 'FSR','FSA','FGEV','FSH','FGR','TSOI', - 'ERRSOI','BUILDHEAT','SABV','SABG', - 'FSDSVD','FSDSND','FSDSVI','FSDSNI', - 'FSRVD','FSRND','FSRVI','FSRNI', - 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', - 'H2OSNO','SOILLIQ','SOILICE', - 'TSA_U', 'TSA_R', - 'TREFMNAV_U', 'TREFMNAV_R', - 'TREFMXAV_U', 'TREFMXAV_R', - 'TG_U', 'TG_R', - 'RH2M_U', 'RH2M_R', - 'QRUNOFF_U', 'QRUNOFF_R', - 'SoilAlpha_U', - 'Qanth', 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT' - hist_fincl3 = 'TG:I', 'FSA:I', 'SWup:I', 'URBAN_AC:I', 'URBAN_HEAT:I', - 'TG_U:I', 'TG_R:I', - hist_fincl4 = 'TG', 'FSA', 'SWup', 'URBAN_AC', 'URBAN_HEAT' - hist_mfilt = 1, 30, 28, 24 - hist_nhtfrq = 0, -24, -6, -1 -/ - - - - -See the section for the precedence of this -option relative to the others. - - - - -In the above example we use an invalid namelist name &clmexp -- but it works anyway -because the &clm; &buildnml; knows the namelist that specific variable names belong to, and -it puts them there. - - -Obviously, all of this would be difficult to put in the &CLMNAMELIST; -variable, especially having to put &apos; around all the character strings. For -more information on the namelist variables being set here and what they mean, see -the section on &clm; namelists below, as well as the namelist definition that gives -details on each variable. - - - - -Precedence of Options - -Note: The precedence for setting the values of namelist variables with the -different env_conf options is (highest to lowest): - -Namelist values set by specific command-line options, like, -d, -sim_year -(i.e. &CLMBLDNML; env_conf variable) -Values set on the command-line using the -namelist option, -(i.e. &CLMNAMELIST; env_conf variable) -Values read from the file specified by -infile, -(i.e. &usernlclm; file) -Datasets from the -clm_usr_name option, -(i.e. &CLMUSRDAT; env_conf variable) -Values set from a use-case scenario, e.g., -use_case -(i.e. &CLMUSECASE;env_conf variable) -Values from the namelist defaults file. - -Thus a setting in &CLMBLDNML; will override a setting for the same thing given in -a use case with &CLMUSECASE;. Likewise, a setting in &CLMNAMELIST; will override a -setting in &usernlclm;. - - - - -Setting Your Initial Conditions File - -Especially with &clmcn; starting from initial conditions is very important. Even -with &clmsp; it takes many simulation years to get the model fully spunup. There -are a couple different ways to provide an initial condition file. - - - - - - - - -Your initial condition file MUST agree with the surface dataset you are using -to run the simulation. If the two files do NOT agree you will get a -run-time about a mis-match in PFT weights, or in the number of PFT's or -columns. To get around this you'll need to use -to interpolate your initial condition dataset. - - - - - -Doing a hybrid simulation to provide initial conditions - -The first option is to setup a hybrid simulation and give a -RUN_REFCASE and RUN_REFDATE to specify the -reference case simulation name to use. -When you setup most cases, at the standard resolutions of "f09" or "f19" it -will already do this for you. For example, if you run an "I2000CN" compset -at "f09_g16" resolution the following settings will already be done for you. - -./xmlchange -file env_conf.xml -id RUN_TYPE -val hybrid -./xmlchange -file env_conf.xml -id RUN_REFCASE -val I2000CN_f09_g16_c100503 -./xmlchange -file env_conf.xml -id RUN_REFDATE -val 0001-01-01 -./xmlchange -file env_conf.xml -id GET_REFCASE -val TRUE - -Setting the GET_REFCASE option to TRUE means it -will copy the files from the: -$DIN_LOC_ROOT/ccsm4_init/I2000CN_f09_g16_c100503/0001-01-01 -directory. Note, that the RUN_REFCASE and -RUN_REFDATE variables are expanded to get the directory name -above. If you do NOT set GET_REFCASE to TRUE then -you will need to have placed the file in your run directory yourself. In either -case, the file is expected to be named: -$RUN_REFCASE.clm2.r.$RUN_REFDATE-00000.nc with the variables -expanded of course. - - - - -Doing a branch simulation to provide initial conditions - -The setup for running a branch simulation is essentially the same as for a hybrid. -With the exception of setting RUN_TYPE to branch -rather than hybrid. A branch simulation runs the case essentially -as restarting from it's place before to exactly reproduce it. While a hybrid simulation -allows you to change namelist items, and use a different code base that may have -fewer fields on it than a full restart file. The GET_REFCASE works -similarily for a branch case as for a hybrid. - - - - -Providing a finidat file in your &usernlclm; file - -Setting up a branch or hybrid simulation requires the initial condition file -to follow a standard naming convention, and a standard input directory if you -use the GET_REFCASE option. If you want to name your file willy -nilly and place it anywhere, you can set it in your &usernlclm; file as in this -example. - -&clm_inparm - finidat = '/glade/home/$USER/myinitdata/clmi_I1850CN_f09_g16_0182-01-01.c120329.nc' -/ - -Note, if you provide an initial condition file -- you can NOT set &CLMFORCECOLD; to -TRUE. - - - - -Adding a finidat file to the XML database - -Like other datasets, if you want to use a given initial condition file to -be used for all (or most of) your cases you'll want to put it in the XML -database so it will be used by default. The initial condition files, are -resolution dependent, and dependent on the number of PFT's and other variables -such as GLC_NEC or if irrigation is on or off. -See for more information on this. - - - - - -Other noteworthy configuration items - -For running "I" cases there are several other noteworthy configuration items that -you may want to work with. Most of these involve settings for the &datm;, but one -CCSM_CO2_PPMV applies to all models. If you are running an B, E, -or F case that doesn't use the &datm; obviously the DATM_* settings will not be used. -All of the settings below are in your &envconf; file - - CCSM_CO2_PPMV - CCSM_VOC - DATM_MODE - DATM_PRESAERO - DATM_CLMNCEP_YR_ALIGN - DATM_CLMNCEP_YR_START - DATM_CLMNCEP_YR_END - DATM_CPL_CASE - DATM_CPL_YR_ALIGN - DATM_CPL_YR_START - DATM_CPL_YR_END - - - - - -CCSM_CO2_PPMV - -CCSM_CO2_PPMV sets the mixing ratio of &CO2; in -parts per million by volume for ALL &cesm; components to use. Note that most compsets -already set this value to something reasonable. Also note that some compsets may -tell the atmosphere model to override this value with either historic or ramped -values. If the CCSM_BGC variable is set to something other than "none" -the atmosphere model will determine &CO2;, and &clm; will listen -and use what the atmosphere sends it. On the &clm; side the namelist item -co2_type tells &clm; to use the value sent from the atmosphere rather than -a value set on it's own namelist. - - - - -CCSM_VOC - -CCSM_VOC enables passing of the Volatile Organic Compounds (VOC) from -&clm; to the atmospheric model. This of course is only important if the atmosphere -model is a fully active model that can use these fields in it's chemistry calculations. - - - - -DATM_MODE - -DATM_MODE sets the mode that the &datm; model should run in this determines -how data is handled as well as what the source of the data will be. Many of the modes -are setup specifically to be used for ocean and/or sea-ice modeling. The modes -that are designed for use by &clm; are: - -&CLMQIAN; -CLM1PT -&CPLHIST; - - - -&CLMQIAN; is for the standard mode of using global atmospheric data -that was developed by Qian et. al. for &clm; using NCEP data from 1948 to 2004. -See for more information on -the &datm; settings for &CLMQIAN; mode. -CLM1PT is for the special cases where we have single-point tower -data for particular sites. Right now we only have data for three urban locations: -MexicoCity Mexico, Vancouver Canada, and the urban-c alpha site. -See for more information on -the &datm; settings for CLM1PT mode. -&CPLHIST; is for running with atmospheric forcing from a previous &cesm; simulation. -See for more information on -the &datm; settings for &CPLHIST; mode. - - -There is a problem with running simulations for the CLM1PT mode -that are greater than one data cycle, where the atm forcing will be held constant. -This will result in useless -results as all atmosphere forcing fields will be held constant at the last value. -See bug 1377 in the &KnownBugs; file on how to fix this problem. - - - - - - - -DATM_PRESAERO - -DATM_PRESAERO sets the prescribed aerosol mode for the data atmosphere -model. The list of valid options include: - -clim_1850 = constant year 1850 conditions -clim_2000 = constant year 2000 conditions -trans_1850-2000 = transient 1850 to year 2000 conditions -rcp2.6 = transient conditions for the rcp=2.6 -W/m2 future -scenario -rcp4.5 = transient conditions for the rcp=4.5 -W/m2 future -scenario -rcp6.0 = transient conditions for the rcp=6.0 -W/m2 future -scenario -rcp8.5 = transient conditions for the rcp=8.5 -W/m2 future -scenario -pt1_pt1 = read in single-point or regional datasets - - - - - -DATM_CLMNCEP_YR_START - -DATM_CLMNCEP_YR_START sets the beginning year to cycle the atmospheric -data over for the &CLMQIAN; mode. - - - - -DATM_CLMNCEP_YR_END - -DATM_CLMNCEP_YR_END sets the ending year to cycle the atmospheric -data over for the &CLMQIAN; mode. - - - - -DATM_CLMNCEP_YR_ALIGN - -DATM_CLMNCEP_YR_START and DATM_CLMNCEP_YR_END determine -the range of years to cycle the atmospheric data over, and DATM_CLMNCEP_YR_ALIGN -determines which year in that range of years the simulation will start with. - - - - -DATM_CPL_CASE - -DATM_CPL_CASE sets the casename to use for the &CPLHIST; mode. - - - - -DATM_CPL_YR_START - -DATM_CPL_YR_START sets the beginning year to cycle the atmospheric -data over for the &CPLHIST; mode. - - - - -DATM_CPL_YR_END - -DATM_CPL_YR_END sets the ending year to cycle the atmospheric -data over for the &CPLHIST; mode. - - - - -DATM_CPL_YR_ALIGN - -DATM_CPL_YR_START and DATM_CPL_YR_END determine -the range of years to cycle the atmospheric data over, and DATM_CPL_YR_ALIGN -determines which year in that range of years the simulation will start with. - - - - - - - - -Downloading DATM Forcing Data - -In Chapter One of the -&cesm; User's Guide -there is a section on "Downloading input data". The normal process of setting up -cases will use the "scripts/ccsm_utils/Tools/check_input_data" script to retrieve -data from the &cesm; subversion inputdata repository. However, the DATM forcing data -is unique -- because it is large compared to the rest of the input data (56 Gbytes). Most of the -data is stored in the directory set by the &envrun; variable -DIN_LOC_ROOT_CSMDATA. The &CLMQIAN; forcing data is in a (possibly) -separate directory using the &envrun; variable DIN_LOC_ROOT_CLMQIAN. -In most cases this directory will be in the directory: -atm/datm7/atm_forcing.datm7.Qian.T62.c080727 under -DIN_LOC_ROOT_CSMDATA. On bluefire there is a separate path for -the &CLMQIAN; forcing data. We have the full set of data available on a few of -the machines we use: bluefire, jaguarpf, and edinburgh. As of October, 18th, 2011 -we've uploaded the entire set of forcing data into the input data repository so -now it can be treated like other input datasets and the check_input_data script -can retreive it for you. Previously only two years of data was available. -You can also download the data from the -Earth System Grid for other machines. See the -Model Forcing Data -link under the -&clm; Documentation Page - - - - -Customizing via the template files - -The final thing that the user may wish to do before &configure; is run is to edit -the template files which determine the configuration and initial namelist. The -variables in &envconf; typically mean you will NOT have -to edit the template. But, there are rare instances where it is useful to do so. - gives the details on how to do this. -The template files are copied to your case directory and are available under -Tools/Templates. -The list of template files you might wish to edit are: - - clm.cpl7.template - datm.cpl7.template - cpl.template - - - - - - -More information on the &clm; &configure; script - -The &configure; script defines the details of a clm configuration and summarizes it into a -config_cache.xml file. The config_cache.xml -will be placed in your case directory under Buildconf/clmconf. -The config_definition.xml -in models/lnd/clm/bld/config_files -gives a definition of each &clm; configuration item, it is viewable in a web-browser. -Many of these items are things that you would NOT change, but looking through the -list gives you the valid options, and a good description of each. Below we repeat -the config_definition.xml files contents: - - - - - -Help on &clm; &configure; - -Coupling this with looking at the options to &configure; with -"-help" as below will enable you to understand how to set the different options. - -> cd models/lnd/clm/bld -> &configure; -help - - - -The output to the above command is as follows: - - -&config_help; - - -We've given details on how to use the options in &envconf; to -interact with the &clm; "&configure;" and "&buildnml;" scripts, as well as giving a good -understanding of how these scripts work and the options to them. In the next section we -give further details on the &clm; namelist. You could customize the namelist for these -options after "&configure; -case" is run. - - - - - - - - - - Customizing the &clm; namelist - -Once a case is &configure;d, we can then customize the case further, by editing the -run-time namelist for &clm;. First let's list the definition of each namelist -item and their valid values, and then we'll list the default values for them. -Next for some of the most used or tricky namelist items we'll give examples of their -use, and give you example namelists that highlight these features. - - - - -Definition of Namelist items and their default values - -Here we point to you where you can find the definition of each namelist item and -separately the default values for them. The default values may change depending on -the resolution, land-mask, simulation-year and other attributes. Both of these -files are viewable in your web browser. Below we provide the link for them, and -then expand each in turn. - - - -Definition of each Namelist Item - - -Default values of each -&clm; Namelist Item - - - -One set of the namelist items allows you to add fields to the output history files: -hist_fincl1, hist_fincl2, -hist_fincl3, hist_fincl4, -hist_fincl5, and hist_fincl6. The link -&clm; History Fields -documents all of the history fields available and gives the long-name and units -for each. - - - - - -&hisfldtbl; - - - - - - - -Examples of using different namelist features - -Below we will give examples of user namelists that activate different commonly used -namelist features. We will discuss the namelist features in different examples and then -show a user namelist that includes an example of the use of these features. First we -will show the default namelist that doesn't activate any user options. - - - -The default namelist - -Here we give the default namelist as it would be created for a I1850CN compset at 0.9x1.25 -resolution with a gx1v6 land-mask. To edit the namelist you would edit the -BuildConf/clm.buildnml.csh under your case (or before &configure; -include a user namelist with just the items you want to change). For simplicity we will -just show the namelist and NOT the entire file. In the sections below, for simplicity - we will just show the user namelist (&usernlclm;) that will add (or modify existing) -namelist items to the namelist. Again, just adding the &usernlclm; file to your case -directory, before "&configure; -case" is invoked will cause the given namelist items to -appear in your &clm; namelist. - -Default &clm; Namelist - -&clm_inparm - co2_ppmv = 284.7 - co2_type = 'constant' - create_crop_landunit = .false. - dtime = 1800 - fatmgrid = '$DIN_LOC_ROOT/lnd/clm2/griddata/griddata_0.9x1.25_070212.nc' - fatmlndfrc = -'$DIN_LOC_ROOT/lnd/clm2/griddata/fracdata_0.9x1.25_gx1v6_c090317.nc' - finidat = 'I1850CN_f09_g16_c100503.clm2.r.0001-01-01-00000.nc' - fpftcon = '$DIN_LOC_ROOT/lnd/clm2/pftdata/pft-physiology.c110425.nc' - frivinp_rtm = '$DIN_LOC_ROOT/lnd/clm2/rtmdata/rdirc_0.5x0.5_simyr2000_slpmxvl_c120717.nc' - fsnowaging = -'$DIN_LOC_ROOT/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc' - fsnowoptics = -'$DIN_LOC_ROOT/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc' - fsurdat = -'$DIN_LOC_ROOT/lnd/clm2/surfdata/surfdata_0.9x1.25_simyr1850_c091006.nc' - ice_runoff = .true. - outnc_large_files = .true. - rtm_nsteps = 6 - urban_hac = 'ON_WASTEHEAT' - urban_traffic = .false. -/ -&ndepdyn_nml - stream_fldfilename_ndep = -'$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_hist_simyr1849-2006_1.9x2.5_c100428.nc' - stream_year_first_ndep = 1850 - stream_year_last_ndep = 1850 -/ - - -Note that the namelist introduces some of the history namelist options that will be -talked about in further detail below (hist_mfilt and -hist_nhtfrq). - - - - -Adding/removing fields on your primary history file - -The primary history files are output monthly, and contain an extensive list of -fieldnames, but the list of fieldnames can be added to using hist_fincl1 -or removed from by adding fieldnames to hist_fexcl1. -A sample user namelist &usernlclm; adding few new fields -(cosine of solar zenith angle, and solar declination) and excluding a few -standard fields is (ground temperature, vegetation temperature, soil temperature and soil water).: - -Example &usernlclm; namelist adding and removing fields on primary history file - -&clm_inparm - hist_fincl1 = 'COSZEN', 'DECL' - hist_fexcl1 = 'TG', 'TV', 'TSOI', 'H2OSOI' -/ - - - - - - -Adding auxiliary history files and changing output -frequency - -The hist_fincl2 through hist_fincl6 set of -namelist variables add given history fieldnames to auxiliary history file "streams", and -hist_fexcl2 through hist_fexcl6 set of -namelist variables remove given history fieldnames from history file auxiliary "streams". -A history "stream" is a set of history files that are produced at a given frequency. -By default there is only one stream of monthly data files. To add more streams you -add history fieldnames to hist_fincl2 through -hist_fincl6. The output frequency and the way averaging is done -can be different for each history file stream. By default the primary history files -are monthly and any others are daily. You can have up to six active history streams, but you need -to activate them in order. So if you activate stream "6" by setting -hist_fincl6, but if any of hist_fincl2 through -hist_fincl5 are unset, only the history streams up to the first blank one -will be activated. - - -The frequency of the history file streams is given by the namelist variable -hist_nhtfrq which is an array of rank six for each history stream. -The values of the array hist_nhtfrq must be integers, where the -following values have the given meaning: - -Positive value means the output frequency is the number of -model steps between output. - -Negative value means the output frequency is the absolute -value in hours given (i.e -1 would mean an hour and -24 would mean a full day). Daily -(-24) is the default value for all auxiliary files. - -Zero means the output frequency is monthly. This is the -default for the primary history files. - - - - -The number of samples on each history file stream is given by the namelist variable -hist_mfilt which is an array of rank six for each history stream. -The values of the array hist_mfilt must be positive integers. By -default the primary history file stream has one time sample on it (i.e. output is -to separate monthly files), and all other streams have thirty time samples on them. - - -A sample user namelist &usernlclm; turning on four extra file -streams for output: daily, six-hourly, hourly, and every time-step, -leaving the primary history files as monthly, and changing the number -of samples on the streams to: yearly (12), thirty, weekly (28), daily (24), and daily -(48) is: - -Example &usernlclm; namelist adding auxiliary history files and changing output frequency - -&clm_inparm - hist_fincl2 = 'TG', 'TV' - hist_fincl3 = 'TG', 'TV' - hist_fincl4 = 'TG', 'TV' - hist_fincl5 = 'TG', 'TV' - hist_nhtfrq = 0, -24, -6, -1, 1 - hist_mfilt = 12, 30, 28, 24, 48 -/ - - - - - - -Removing all history fields - -Sometimes for various reasons you want to remove all the history fields either -because you want to do testing without any output, or you only want a very small -custom list of output fields rather than the default extensive list of fields. -By default only the primary history files are active, so technically using -hist_fexcl1 explained in the first example, you could list -ALL of the history fields that are output in -hist_fexcl1 and then you wouldn't get any output. However, as -the list is very extensive this would be a cumbersome thing to do. So to facilitate -this hist_empty_htapes allows you to turn off all default output. -You can still use hist_fincl1 to turn your own list of fields -on, but you then start from a clean slate. -A sample user namelist &usernlclm; turning off all history -fields and then activating just a few selected fields (ground and vegetation temperatures -and absorbed solar radiation) is: - -Example &usernlclm; namelist removing all history fields - -&clm_inparm - hist_empty_htapes = .true. - hist_fincl1 = 'TG', 'TV', 'FSA' -/ - - -Note, you could also build adding the "-noio" option to &CLMCONFIG;. But, this would -build the model without history output and you wouldn't be able to add that in later. - - - - -Various ways to change history output averaging flags - -There are two ways to change the averaging of output history fields. The first is using -hist_avgflag_pertape which gives a default value for each history -stream, the second is when you add fields using hist_fincl*, you add -an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would -output the maximum of TSOI). -The types of averaging that can be done are: - -A Average, over the output interval. -I Instantaneous, output the value at the output interval. -X Maximum, over the output interval. -M Minimum, over the output interval. - - -The default averaging depends on the specific fields, but for most fields is an average. -A sample user namelist &usernlclm; making the monthly output -fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), -and adding auxiliary file streams for instantaneous (6-hourly), -maximum (daily), minimum (daily), and average (daily). For some of the fields we -diverge from the per-tape value given and customize to some different type of -optimization. - -Example &usernlclm; namelist with various ways to average history fields - -&clm_inparm - hist_empty_htapes = .true. - hist_fincl1 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl2 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl3 = 'TSOI', 'TG:I', 'TV', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl4 = 'TSOI', 'TG', 'TV:I', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl5 = 'TSOI', 'TG', 'TV', 'FIRE:I', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_avgflag_pertape = 'A', 'I', 'X', 'M', 'A' - hist_nhtfrq = 0, -6, -24, -24, -24 -/ - - - - - -In the example we put the same list of fields on each of the tapes: soil-temperature, -ground temperature, vegetation temperature, emitted longwave radiation, reflected -solar radiation, sensible heat, total latent-heat, and total water storage. We also -modify the soil-temperature for the primary and secondary auxiliary tapes by outputting -them for a maximum instead of the prescribed per-tape of average and instantaneous -respectively. For the tertiary auxiliary tape we output ground temperature instantaneous -instead of as a maximum, and for the fourth auxiliary tape we output vegetation -temperature instantaneous instead of as a minimum. Finally, for the fifth auxiliary -tapes we output FIRE instantaneously instead of as an average. - - - - -We also use hist_empty_htapes as in the previous example, -so we can list ONLY the fields that we want on the primary history tapes. - - - - - -Outputting history files as a vector in order to analyze -the plant function types within gridcells - -By default the output to history files are the grid-cell average of all land-units, and -vegetation types within that grid-cell, and output is on the -full 2D latitude/longitude grid with ocean masked out. Sometimes it's important to -understand how different land-units or vegetation types are acting within a grid-cell. -The way to do this is to output history files as a 1D-vector of all land-units and vegetation -types. In order to display this, you'll need to do extensive post-processing to make sense -of the output. Often you may only be interested in a few points, so once you figure out the -1D indices for the grid-cells of interest, you can easily view that data. 1D vector output -can also be useful for single point datasets, since it's then obvious that all data is for the -same grid cell. - - -To do this you use hist_dov2xy which is an array of rank six for -each history stream. Set it to -.false. if you want one of the history streams to be a 1D vector. -You can also use hist_type1d_pertape if you want to average over all the: -Plant-Function-Types, columns, land-units, or grid-cells. -A sample user namelist &usernlclm; leaving the primary monthly -files as 2D, and then doing grid-cell (GRID), column (COLS), -and no averaging over auxiliary tapes output daily for a single field -(ground temperature) is: - -Example &usernlclm; namelist outputting some files in 1D Vector format - -&clm_inparm - hist_fincl2 = 'TG' - hist_fincl3 = 'TG' - hist_fincl4 = 'TG' - hist_fincl5 = 'TG' - hist_fincl6 = 'TG' - hist_dov2xy = .true., .false., .false., .false. - hist_type2d_pertape = ' ', 'GRID', 'COLS', ' ' - hist_nhtfrq = 0, -24, -24, -24 -/ - - - - -LAND and COLS are also options to the pertape averaging, but currently there is a bug -with them and they fail to work. - - - - - -Technically the default for hist_nhtfrq is for primary files -output monthly and the other auxiliary tapes for daily, so we don't actually have -to include hist_nhtfrq, we could use the default for it. Here -we specify it for clarity. - - - - -Visualizing global 1D vector files will take effort. You'll probably want -to do some post-processing and possibly just extract out single points of interest -to see what is going on. Since, the output is a 1D vector, of only land-points -traditional plots won't be helpful. The number of points per grid-cell will also -vary for anything, but grid-cell averaging. You'll need to use the output fields -pfts1d_ixy, and pfts1d_jxy, to get the mapping -of the fields to the global 2D array. pfts1d_itype_veg gives you -the PFT number for each PFT. Most likely you'll want to do this analysis in a -data processing tool (such as NCL, Matlab, Mathmatica, IDL, etcetera that is able -to read and process &netcdf; data files). - - - - - -Outputting multi-layer snow history fields - -A number of history fields provide information about individual snow layers: -SNO_ABS, SNO_T, SNO_GS, -SNO_Z, SNO_LIQH2O, -SNO_ICE, SNO_TK, and -SNO_BW; there is also an auxiliary field to aid -interpretation: SNO_EXISTENCE (described below). These fields -are inactive by default, but can be enabled like other history fields. If the -maximum number of snow layers is 5 (for example), then the layers of these -fields are arranged on the history file so that layer 1 is at the top of the -snow pack, and layer 5 only exists if the snow is deep enough to support all -layers. - - -Because snow layers can come into and out of existence, these fields can be -challenging to interpret. It is easiest to analyze these fields if you do output -every time step, and do not average to the grid cell (i.e., dov2xy = -.false.). Otherwise, a few principles should be kept in mind when -working with these fields: - -Temporal averages are taken only over times when a given snow layer exists -Grid cell averages are taken only over columns in which a given snow layer exists -SNO_EXISTENCE gives the fraction of the averaging -period in which a given snow layer existed. For grid cell averages, this gives -the weighted spatial fraction of the columns in which a snow layer existed for -this averaging period. This is most useful for subsetting grid cells for -analysis. For example, grid cells that have SNO_EXISTENCE = 1 -for all snow layers can be analyzed most easily. - - - -Here is a simple example illustrating this averaging; this considers a given -snow layer, L: - - -Assume a grid cell with 2 columns, with averaging done over 4 time steps. Column -#1 has subgrid weight 0.2, and no snow in layer L in any time -step. Column #2 has subgrid weight 0.8, and has snow in layer -L in time steps 3 and 4; the snow field of interest has -values 1.0 and 2.0 in these two time steps, for this layer. - - -SNO_EXISTENCE is then 0.8*(2/4) = 0.4. The snow field's value -would be 1.5 (note that times and columns with no snow in this layer are simply -ignored). - - -Finally, note that the SNOABS field is not computed for urban -columns, so it will have a missing value if snow only exists over urban columns -for a given snow layer. - - - - -Conclusion to namelist examples - -We've given various examples of namelists that feature the use of different namelist options -to customize a case for particular uses. Most the examples revolve around how to customize the -output history fields. This should give you a good basis for setting up your own &clm; namelist. - - - - - - - - - -Customizing the &datm; Namelist and Streams files - -When running "I" compsets with &clm; you use the &datm; model to give atmospheric -forcing data to &clm;. There are four ways to customize &datm;: - - -&datm; Main Namelist (datm_in) - - -&datm; Stream Namelist (datm_atm_in) - - -&datm; stream files - - -&datm; template file -(Tools/Templates.datm.cpl7.template) - - -The -Data Model Documentation gives the details of all the options for the data -models and for &datm; specifically. It goes into detail on all namelist items both for -&datm; -and for &datm; streams. It shows examples of stream files and talks about their use. In - we talk about editing the CLM and &datm; -template files. So here we won't talk about the &datm; template file, and we won't list -ALL of the &datm; namelist options, nor go into great details about stream files. But, -we will talk about a few of the different options that are relevant for running with -&clm;. All of the options for changing the namelists or stream files is done by editing -the Buildconf/datm.buildnml.csh file. - - -Because, they aren't useful for work with &clm; we will NOT discuss any of the options -for the main &datm; namelist. Use the &datm; Users Guide at the link above to find -details of that. For the streams namelist we will discuss three items: - - -mapalgo - - -taxmode - - -tintalgo - - -And for the streams file itself we will discuss: - - offset - -Again everything else (and including the above items) are discussed in the Data Model -User's Guide. Of the above the last three: offset, taxmode and tintalgo are all closely -related and have to do with the time interpolation of the &datm; data. - - - - -mapalgo - -mapalgo sets the spatial interpolation method to go from the -&datm; input data to the output &datm; model grid. The default is -bilinear. For CLM1PT we set it to nn to just -select the nearest neighbor. This saves time and we also had problems running the -interpolation for single-point mode. - - - - -taxmode - -taxmode is the time axis mode. For &clm; we usually have it -set to cycle which means that once the end of the data is reached -it will start over at the beginning. The extend modes is used -have it use the last time-step of the forcing data once it reaches the end of forcing -data (or use the first time-step before it reaches where the forcing data starts). -See the warning below about the extend mode. - - -THE extend OPTION NEEDS TO BE USED WITH CAUTION! -It is only invoked by default for the CLM1PT mode and is only intended for the -supported urban datasets to extend the data for a single time-step. If you have the -model run extensively through periods in this mode you will effectively -be repeating that last time-step over that entire period. This means the -output of your simulation will be worthless. See bug 1377 in the &KnownBugs; file for -more information on this issue. - - - - - - -offset (in the stream file) - -offset is the time offset in seconds to give to each stream -of data. Normally it is NOT used because the time-stamps for data is set correctly -for each stream of data. Note, the offset may NEED to be -adjusted depending on the taxmode described above, or it may -need to be adjusted to account for data that is time-stamped at the END of an -interval rather than the middle or beginning of interval. The -offset can is set in the stream file rather than on the -stream namelist. For data with a taxmode method of -coszen the time-stamp needs to be for the beginning of the interval, -while for other data it should be the midpoint. The offset can be -used to adjust the time-stamps to get the data to line up correctly. - - - - -tintalgo - -tintalgo is the time interpolation algorithm. For &clm; we usually -use one of three modes: coszen, nearest, or -linear. We use coszen for solar data, -nearest for precipitation data, and linear -for everything else. If your data is half-hourly or hourly, nearest -will work fine for everything. The coszen scaling is useful for -longer periods (three hours or more) to try to get the solar to match the cosine of -the solar zenith angle over that longer period of time. If you use -linear for longer intervals, the solar will cut out at night-time -anyway, and the straight line will be a poor approximation of the cosine of the -solar zenith angle of actual solar data. nearest likewise would -be bad for longer periods where it would be much higher than the actual values. - - -For coszen the time-stamps of the data should correspond to the -beginning of the interval the data is measured for. Either make sure the time-stamps -on the datafiles is set this way, or use the offset described above -to set it. - - - - -For nearest and linear the time-stamps of the -data should correspond to the middle of the interval the data is measured for. Either -make sure the time-stamps on the datafiles is set this way, or use the -offset described above to set it. - - - - - - -In the sections below we go over each of the relevant DATM_MODE -options and what the above &datm; settings are for each. This gives you examples -of actual usage for the settings. We also describe in what ways you might want -to customize them for your own case. - - - -&CLMQIAN; mode and it's &datm; settings - -In &CLMQIAN; mode the Qian dataset is used which has 6-hourly -solar and precipitation data, and 3-hourly for everything else. -The dataset is divided into those three data streams: solar, precipitation, -and everything else (temperature, pressure, humidity and wind). The time-stamps -of the data were also adjusted so that they are the beginning of the interval -for solar, and the middle for the other two. Because, of this the -offset is set to zero, and the tintalgo -is: coszen, nearest, and -linear for the solar, precipitation and other data -respectively. taxmode is set to cycle -and mapalgo is set to bilinear so that -the data is spatially interpolated from the input T62 grid to the grid the atmosphere -model is being run at. - - -Normally you wouldn't customize the &CLMQIAN; settings, but you might replicate -it's use for your own global data that had similar temporal characteristics. - - - - -CLM1PT mode and it's &datm; settings - -In CLM1PT mode the model is assumed to have half-hourly or hourly data -for a single-point. For the supported datasets that is exactly what it has. -But, if you add your own data you may need to make adjustments accordingly. -Using the &CLMUSRDAT; option you can easily extend this mode for your own -datasets that may be regional or even global and could be at different temporal -frequencies. If you do so you'll need to make adjustments to your &datm; settings. -The dataset has all data in a single stream file. The time-stamps -of the data were also adjusted so that they are at the middle of the interval. -Because, of this the offset is set to zero, and the -tintalgo is set to nearest. -taxmode is set to extend -and mapalgo is set to nn so that -simply the nearest point is used. - - -If you are using your own data for this mode and it's not at least hourly -you'll want to adjust the &datm; settings for it. If the data is three or -six hourly, you'll need to divide it up into separate streams like in -&CLMQIAN; mode which will require fairly extensive changes to the &datm; -namelist and streams files. For an example of doing this see -. - - - - -&CPLHIST; mode and it's &datm; settings - -In &CPLHIST; mode the model is assumed to have 3-hourly for a global grid from -a previous &cesm; simulation. Like &CLMQIAN; mode the data is divided into -three streams: one for precipitation, one for solar, and one for everything else. -The time-stamps for Coupler history files for &cesm; is at the end of the interval, -so the offset needs to be set in order to adjust the time-stamps to what it needs -to be for the tintalgo settings. For precipitation -taxmode is set to nearest so the -offset is set to -5400 seconds so that -the ending time-step is adjusted by an hour and half to the middle of the interval. -For solar taxmode is set to coszen so the -offset is set to -10800 seconds so that -the ending time-step is adjust by three hours to the beginning of the interval. -For everything else taxmode is set to -linear so the offset is set to --5400 seconds so that the ending time-step is adjusted by an -hour and half to the middle of the interval. - - -Normally you wouldn't modify the &datm; settings for this mode. However, if you -had data at a different frequency than 3-hours you would need to modify the -offset and possibly the taxmode. The other -two things that you might modify would be the path to the data (which you can -change in the &datm; template see ) or -the domain file for the resolution (which is currently hardwired to f09). For -data at a different input resolution you would need to change the domain file -in the streams file to use a domain file to the resolution that the data comes in -on. - - - - - - - -Conclusion to customizing chapter - -We've given extensive details on customizing cases with &clm;, by choosing compsets, by changing -&configure; options and interacting with the &clm; "&configure;" and "&buildnml;" scripts, -we've given details on all of the &clm; namelist items, and finally given some -instruction in customizing the &datm; namelist and streams files. In the next chapter we talk -about further ways to customize cases with &clm; by creating your own datasets using the tools -provided in &clm;. - - - - diff --git a/doc/UsersGuide/get_Icaselist.pl b/doc/UsersGuide/get_Icaselist.pl deleted file mode 100755 index 6aefc26159..0000000000 --- a/doc/UsersGuide/get_Icaselist.pl +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env perl -#----------------------------------------------------------------------------------------------- -# -# get_Icaselist.pl -# -# This utility gets a list of the I cases from the CCSM compset database. -# -#----------------------------------------------------------------------------------------------- - -use strict; -use Cwd; -use English; -use Getopt::Long; -use IO::File; -use IO::Handle; -#----------------------------------------------------------------------------------------------- - -sub usage { - die <autoflush(); - -#----------------------------------------------------------------------------------------------- -my $cwd = getcwd(); # current working directory -my $cfgdir; # absolute pathname of directory that contains this script -$cfgdir = $cwd; - -#----------------------------------------------------------------------------------------------- -# Parse command-line options. -my %opts = ( - ); -GetOptions( - "h|help" => \$opts{'help'}, -) or usage(); - -# Give usage message. -usage() if $opts{'help'}; - -# Check for unparsed argumentss -if (@ARGV) { - print "ERROR: unrecognized arguments: @ARGV\n"; - usage(); -} - -# Check for manditory case input if not just listing valid values - -my %cfg = (); # build configuration - -#----------------------------------------------------------------------------------------------- - -# Check for the configuration definition file. -my $config_def_file = "config_definition.xml"; -my $case_def_dir = "$cfgdir/../../../../../scripts/ccsm_utils/Case.template"; -(-f "$case_def_dir/$config_def_file") or die <<"EOF"; -** Cannot find configuration definition file \"$config_def_file\" in directory - \"$case_def_dir\" ** -EOF - -# Compset definition file. -my $compset_file = 'config_compsets.xml'; -(-f "$case_def_dir/$compset_file") or die <<"EOF"; -** Cannot find compset parameters file \"$compset_file\" in directory - \"$case_def_dir\" ** -EOF - -my $xml_dir = "$cfgdir/../../../../../scripts/ccsm_utils/Tools/perl5lib"; -# The XML::Lite module is required to parse the XML configuration files. -(-f "$xml_dir/XML/Lite.pm") or die <<"EOF"; -** Cannot find perl module \"XML/Lite.pm\" in directory - \"$xml_dir\" ** -EOF - - -#----------------------------------------------------------------------------------------------- -my @dirs = ( $cfgdir, $xml_dir, $case_def_dir ); -unshift @INC, @dirs; -require XML::Lite; -require ConfigCase; - -#----------------------------------------------------------------------------------------------- -my $cfg_ref = ConfigCase->new("$case_def_dir/$config_def_file"); -print_compsets( "$case_def_dir/$compset_file" ); - -#----------------------------------------------------------------------------------------------- -# FINNISHED #################################################################################### -#----------------------------------------------------------------------------------------------- - -#------------------------------------------------------------------------------- - -sub print_compsets -{ - # Print all currently supported valid compsets - - my ($compset_file) = @_; - my $xml = XML::Lite->new( $compset_file ); - my $root = $xml->root_element(); - - # Check for valid root node - my $name = $root->get_name(); - $name eq "config_compset" or die - "file $compset_file is not a compset parameters file\n"; - - # Read the compset parameters from $compset_file. - my @e = $xml->elements_by_name( "compset" ); - my %a = (); - my %data; - while ( my $e = shift @e ) { - %a = $e->get_attributes(); - my $sname = $a{'SHORTNAME'}; - if ($a{GRID_MATCH} && exists($data{$sname}) && defined($data{$sname}{'DESC'} && defined($a{'DESC'}) ) ) { - if ( $data{$sname}{'DESC'} =~ /^INVALID:/ ) { - $data{$sname}{'DESC'} = $a{'DESC'}; - } - } elsif ( $a{'SHORTNAME'} =~ /^I/ ) { - $data{$sname}{'NAME'} = $a{'NAME'}; - $data{$sname}{'DESC'} = $a{'DESC'}; - } - } - print "\n"; - foreach my $sname ( sort(keys(%data)) ) { - print "$data{$sname}{'NAME'}" . - "($sname)\n"; - print "$data{$sname}{'DESC'}\n"; - } - print "\n"; -} - diff --git a/doc/UsersGuide/limitLineLen.pl b/doc/UsersGuide/limitLineLen.pl deleted file mode 100755 index 25f1216d06..0000000000 --- a/doc/UsersGuide/limitLineLen.pl +++ /dev/null @@ -1,104 +0,0 @@ -#!/usr/bin/env perl -# -# Limit the line length for output designed to go into the document. -# -use strict; -use Cwd; -use English; -use IO::File; -use Getopt::Long; -use IO::Handle; -#----------------------------------------------------------------------------------------------- - -# Get the directory name and filename of this script. If the command was -# issued using a relative or absolute path, that path is in $ProgDir. Otherwise assume the -# command was issued from the current working directory. - -(my $ProgName = $0) =~ s!(.*)/!!; # name of this script -my $ProgDir = $1; # name of directory containing this script -- may be a - # relative or absolute path, or null if the script - # is in - # the user's PATH -my $nm = "$ProgName::"; # name to use if script dies -my $scrdir; -if ($ProgDir) { - $scrdir = $ProgDir; -} else { - $scrdir = getcwd() -} -my $limitLen = 99; - -sub usage { - my $msg = shift; - - print "ERROR:: $msg\n"; - die < -OPTIONS - -l = Limit line length to this value (default $limitLen) -EOF -} - -sub LengthofwhiteSpaceNearLength { - my $line = shift; - my $leng = shift; - - my $l = $leng; - while( substr( $line, $l, 1 ) !~ /\s|:|,|\// ) { - # First search for white-space before desired length -- and then after - if ( $l <= $leng ) { - $l--; - } else { - $l++; - } - # Once reach beginning of line, go to the desired length+1 and increment - if ( $l < 0 ) { $l = $leng+1; } - # Once reach the very end of the line die as couldn't break it - if ( $l >= length($line) ) { - die "ERROR : went through entire line and did NOT find a place to break it\n"; - } - } - return( $l ); -} - -my %opts = ( limitLen => $limitLen ); - -GetOptions( - "l=s" => \$opts{'limitLen'}, -) or usage(); - -if ( $#ARGV != 0 ) { - &usage( "Wrong number of command line arguments" ); -} - -$limitLen = $opts{'limitLen'}; - -my $inputFile = $ARGV[0]; - -if ( ! -f $inputFile ) { - &usage( "Input file does NOT exist : $inputFile" ); -} - -my $fh = IO::File->new($inputFile, '<') or die "** $nm - can't open input file: $inputFile\n"; - -while (my $line = <$fh>) { - - while( length($line) > $limitLen ) { - print STDERR "Line length over $limitLen\n"; - my $lenlim = &LengthofwhiteSpaceNearLength( $line, $limitLen ); - if ( ($lenlim == length($line)) || $lenlim < 0 ) { - print "Can NOT truncate long line: $line\n"; - die "ERROR : Having trouble breaking a long line\n"; - } - my $substring = substr( $line, 0, $lenlim+1 ); - print "$substring \\ \n"; - my $newline = " " . substr( $line, $lenlim+1, length($line) ); - $line = $newline; - } - print $line; - -} -$fh->close; - - diff --git a/doc/UsersGuide/modelnl/Makefile b/doc/UsersGuide/modelnl/Makefile deleted file mode 100644 index 595a1b3a3e..0000000000 --- a/doc/UsersGuide/modelnl/Makefile +++ /dev/null @@ -1,85 +0,0 @@ -# -# Makefile to create HTML documentation of namelists -# -SCRNLDIR := ../../../../../../scripts/doc/modelnl -VPATH := . $(SCRNLDIR) ../../../../../drv/bld/namelist_files ../../../../../glc/cism/bld/namelist_files \ - ../../../../../atm/datm/bld/namelist_files ../../../../../../scripts/ccsm_utils/Case.template \ - ../../../../../../scripts/ccsm_utils/Machines ../../../../../rof/rtm/bld/namelist_files \ - ../../../bld/namelist_files ../.. -SOURCES := namelist_definition_drv.xml namelist_definition_cism.xml namelist_definition.xml \ - namelist_definition_rtm.xm namelist_definition_datm.xml config_definition.xml \ - config_grid.xml config_machines.xml config_compsets.xml ChangeSum -TAGFILE := clmtag.txt - -CWD := $(shell pwd ) -ALLOUT := $(CWD)/clm_nl_drv.html $(CWD)/clm_nl_cism.html $(CWD)/clm_nl_clm.html $(CWD)/clm_nl_rtm.html \ - $(CWD)/clm_nl_datm.html $(CWD)/clm_env_case.html $(CWD)/clm_env_build.html $(CWD)/clm_env_pesetup.html \ - $(CWD)/clm_env_run.html $(CWD)/clm_grid.html $(CWD)/clm_machines.html $(CWD)/clm_compsets.html \ - $(TAGFILE) $(CWD)/index.html - -all: $(ALLOUT) - -debug: - @echo "SOURCES = $(SOURCES)" - @echo "VPATH = $(VPATH)" - @echo "ALLOUT = $(ALLOUT)" - @echo "SCRNLDIR = $(SCRNLDIR)" - @echo "CWD = $(CWD)" - @echo "TAGFILE = $(TAGFILE)" - -.SUFFIXES: -.SUFFIXES: .xml .html .txt - -RM := /bin/rm - -CTAGNAME = $(shell cat $(TAGFILE) ) - - -$(TAGFILE): ChangeSum - head -3 $< | tail -1 | awk '{print $$1}' > $@ - -$(CWD)/index.html: $(TAGFILE) index.cpp - sed 's/CLMTAGNAME/$(CTAGNAME)/' index.cpp > $@ - -$(CWD)/clm_nl_drv.html: namelist_definition_drv.xml - cd $(SCRNLDIR) ; ./nldef2html_drv > $@ - -$(CWD)/clm_nl_cism.html: namelist_definition_cism.xml - cd $(SCRNLDIR) ; ./nldef2html_cism > $@ - -$(CWD)/clm_nl_clm.html: namelist_definition.xml - cd $(SCRNLDIR) ; ./nldef2html_clm > $@ - -$(CWD)/clm_nl_rtm.html: namelist_definition_rtm.xml - cd $(SCRNLDIR) ; ./nldef2html_rtm > $@ - -$(CWD)/clm_nl_datm.html: namelist_definition_datm.xml - cd $(SCRNLDIR) ; ./nldef2html_datm > $@ - -$(CWD)/clm_env_case.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_case > $@ - -$(CWD)/clm_env_build.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_build > $@ - -$(CWD)/clm_env_pesetup.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_pesetup > $@ - -$(CWD)/clm_env_run.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_run > $@ - -$(CWD)/clm_grid.html: config_grid.xml - cd $(SCRNLDIR) ; ./xmldef2html_grid > $@ - -$(CWD)/clm_machines.html: config_machines.xml - cd $(SCRNLDIR) ; ./xmldef2html_machines > $@ - -$(CWD)/clm_compsets.html: config_compsets.xml - cd $(SCRNLDIR) ; ./xmldef2html_compsets > $@ - -clean: - $(RM) -f $(ALLOUT) - -realclean: clean - $(RM) -f $(TAGFILE) - diff --git a/doc/UsersGuide/modelnl/index.cpp b/doc/UsersGuide/modelnl/index.cpp deleted file mode 100644 index c55aa64159..0000000000 --- a/doc/UsersGuide/modelnl/index.cpp +++ /dev/null @@ -1,45 +0,0 @@ - - - - - -CLM Namelist Definitions (CLMTAGNAME) - - - - - - -
    - - -

    CLM Tag: CLMTAGNAME

    - -

    Component Namelist Definitions

    - - -

    create_newcase files (supported machines, grids, compsets)

    - - -

    $CASEROOT xml files

    - - - - - - diff --git a/doc/UsersGuide/modelnl/showinfo.js b/doc/UsersGuide/modelnl/showinfo.js deleted file mode 100644 index fd8a608472..0000000000 --- a/doc/UsersGuide/modelnl/showinfo.js +++ /dev/null @@ -1,193 +0,0 @@ - function applyFilter(filter_text) { - - // applying a filter hides all standard names not matching filter_text - // if filter_text contains no spaces, it is treated as a regexp - // otherwise, all substrings must occur somewhere - - var is_match = false; - var search_type = 'regexp'; - var search_help_text = false; - var num_matches = 0; - var is_boolean_and = true; - - search_help_text = (document.getElementById('search_help_text').checked); - is_boolean_and = (document.getElementById('logical_operator_and').checked); - - if (filter_text.indexOf(' ') == -1) { - search_type = 'regexp'; - var re = new RegExp(filter_text, 'i') - } - else { - search_type = 'string'; - var string_parts = filter_text.split(' '); - } - - allTRs = document.getElementsByTagName('tr'); - - for (var i = 0; i < allTRs.length; i++) { - curTR = allTRs[i]; - - if (curTR.id != '') { - - if (search_type == 'regexp') { - - is_match = curTR.id.substring(0, curTR.id.length - 3).match(re); - - if (search_help_text) { - - var helpText = document.getElementById(curTR.id.substring(0,curTR.id.length - 3) + '_help').innerHTML; - is_match = is_match || helpText.match(re); - } - } - else { - - if (is_boolean_and) { - var is_name_match = true; - for (var j = 0; j < string_parts.length && is_name_match; j++) { - - if (!curTR.id.match(new RegExp(string_parts[j], 'i'))) { - is_name_match = false; - } - } - } - else { - - var is_name_match = false; - for (var j = 0; j < string_parts.length && !is_name_match; j++) { - - if (curTR.id.substring(0, curTR.id.length - 3).match(new RegExp(string_parts[j], 'i'))) { - is_name_match = true; - } - } - } - - is_match = is_name_match; - - if (search_help_text) { - var helpText = document.getElementById(curTR.id.substring(0,curTR.id.length - 3) + '_help').innerHTML; - - if (is_boolean_and) { - var is_help_match = true; - - for (var j = 0; j < string_parts.length && is_help_match; j++) { - - if (!helpText.match(new RegExp(string_parts[j], 'i'))) { - is_help_match = false; - } - } - } - else { - - var is_help_match = false; - - for (var j = 0; j < string_parts.length && !is_help_match; j++) { - - if (helpText.match(new RegExp(string_parts[j], 'i'))) { - is_help_match = true; - } - } - } - - is_match = is_match || is_help_match; - - } - } - - if (!is_match) { - curTR.style.display = 'none'; - } - else { - num_matches++; - curTR.style.display = ''; - if (search_help_text) { - showHelp(curTR.id.substring(0,curTR.id.length - 3)); - } - else { - hideHelp(curTR.id.substring(0,curTR.id.length - 3)); - } - } - } - } - - var filter_matches = document.getElementById('filter_matches'); - var filter_matches_num = document.getElementById('filter_matches_num'); - var filter_matches_query = document.getElementById('filter_matches_query'); - - if (filter_text != '') { - filter_matches.style.visibility = 'visible'; - filter_matches_num.innerHTML = num_matches; - filter_matches_query.innerHTML = filter_text; - } - else { - filter_matches.style.visibility = 'hidden'; - } - - } // end function applyFilter() - - function clearFilter() { - - allTRs = document.getElementsByTagName('tr'); - - for (var i = 0; i < allTRs.length; i++) { - curTR = allTRs[i]; - if (curTR.id != '') { - curTR.style.display = ''; - hideHelp(curTR.id.substring(0,curTR.id.length - 3)); - - } - } - - var filter_matches = document.getElementById('filter_matches'); - filter_matches.style.visibility = 'hidden'; - - document.getElementById('filter_text').value = ''; - } - - function toggleHelp(standard_name) { - - // check for the existence of the help "tr" object for this standard_name - - var helpDiv = document.getElementById(standard_name + '_help'); - - if (helpDiv) { - - if (helpDiv.style.display != 'none') { - - helpDiv.style.display = 'none'; - - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_right.gif"; - } - else { - helpDiv.style.display = ''; - - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_down.gif"; - } - } - } - - - function showHelp(standard_name) { - - var helpDiv = document.getElementById(standard_name + '_help'); - - if (helpDiv) { - - helpDiv.style.display = ''; - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_down.gif"; - } - } - - function hideHelp(standard_name) { - - var helpDiv = document.getElementById(standard_name + '_help'); - - if (helpDiv) { - helpDiv.style.display = 'none'; - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_right.gif"; - } - } - diff --git a/doc/UsersGuide/modelnl/xmldef2html_compsets b/doc/UsersGuide/modelnl/xmldef2html_compsets deleted file mode 100755 index 2659beed17..0000000000 --- a/doc/UsersGuide/modelnl/xmldef2html_compsets +++ /dev/null @@ -1,162 +0,0 @@ -#!/usr/bin/env perl - -use strict; - -if ( $#ARGV != 0 ) { - die "Wrong number of input arguments -- should just enter one filename\n"; -} -my $infilename = $ARGV[0]; -if ( ! -f $infilename ) { - die "Input file: $infilename does NOT exist\n"; -} - -my @dirs = ('../../../../../../scripts/ccsm_utils/Tools/per5lib', '../../../../../../scripts//ccsm_utils/Tools/perl5lib/Build'); -unshift @INC, @dirs; -require XML::Lite; -use lib "../../../../../../scripts/ccsm_utils/Tools/perl5lib"; - -my $image_dir = "./images"; - -print <<"END_of_Start"; - - - - - - - CESM Component Models Namelist Definitions - - - - - - -

    Search or Browse supported component sets

    -

    -This page contains the complete list of config_grid.xml variables available. They are grouped -by categories designed to aid browsing. Clicking on the name of a variable will display descriptive -information. If search terms are entered in the text box below, the list will be condensed to contain -only matched variables. -

    - -
    - - - - - - -
    - - - -
    - - - (separate search terms with spaces) -
    - -
    -
    - - - -END_of_Start - -my $xml = XML::Lite->new( $infilename ); -my $root = $xml->root_element(); - -# Check for valid root node -my $name = $root->get_name(); -$name eq "config_compset" or die - "file $infilename is not a compset definition file\n"; - -# Print table -print_start_table("config_compsets.xml variables"); -my @e = $xml->elements_by_name( "compset" ); -my %a = (); -while ( my $e = shift @e ) { - %a = $e->get_attributes(); - - if ($a{'NAME'} =~ /I_/ ) { - my $var = $a{'NAME'}; - my $doc = "Description: $a{DESC} \n"; - my $grp = "$a{SHORTNAME}"; - print_row($var, $doc, $grp); - } -} -print_end_table(); - -# Finish -print <<"END_of_html"; - - -END_of_html - -#-------------------------------------------------------------------------------------------- - -sub print_start_table { - my $hdr = shift; - -print <<"START_table"; -

    $hdr

    - - - -START_table -} - -#-------------------------------------------------------------------------------------------- - -sub print_row { - - my $name = shift; - my $doc = shift; - my $grp = shift; - -print <<"END_of_row"; - - - - -END_of_row -} - -#-------------------------------------------------------------------------------------------- - -sub print_end_table { - -print <<"END_table"; -
    Compset NameShort Name
    - - - $name - - - $grp
    -END_table -} - -#-------------------------------------------------------------------------------------------- - diff --git a/doc/UsersGuide/pergro.jpg b/doc/UsersGuide/pergro.jpg deleted file mode 100644 index a0cb81e046..0000000000 Binary files a/doc/UsersGuide/pergro.jpg and /dev/null differ diff --git a/doc/UsersGuide/preface.xml b/doc/UsersGuide/preface.xml deleted file mode 100644 index ed063ce774..0000000000 --- a/doc/UsersGuide/preface.xml +++ /dev/null @@ -1,1419 +0,0 @@ - - - -$Id$ - -Acknowledgments - -I want to acknowledge all of the people that helped review or edit the model -documentation: David Lawrence, Samuel Levis, Keith Oleson, and Sean Swenson. -Thank you for your help in catching errors, and making the document more -understandable and readable. Our readers thank you as well, as now it is much -easier for them to digest. Any mistakes, or errors are all mine. If you run -across one of those errors, please let us know, by following -. -I also want to thank Sheri -Mickelson, for her work in doing perturbation analysis on bluefire and intrepid, -which was used in our initial versions of this User's Guide. We also want to -thank the original authors of &ptclm;: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, -Wilfred M. Post, and R. Quinn Thomas for providing a nice addition to the &cesm; -effort. We also want to thank the folks at University of Michigan Biological Stations -(US-UMB) who allowed us to use their Fluxnet station data and import it into our -inputdata repository, especially Gil Bohrer the PI on record for this site -(see for permission information on using this -data). - - - - -Introduction - - -The Community Land Model (&clmrel;) is the latest in a series of -global land models developed by the &cesm; Land Model Working Group -(LMWG) and maintained at the National Center for -Atmospheric Research (&ncar;). This guide is intended to instruct both -the novice and experienced user on running &clm;. This guide pertains to the -latest version &clmrel; available for download from the public release -subversion repository as a part of &cesmrel;. Documentation may be different if you are using an -older version, you should either update to the latest version, or use the -documentation inside your own source tree. There is information in the -ChangeLog file and in the -regarding the changes from previous versions of &cesm;. - - - -The novice user should read - in detail before beginning work, while the -expert user should read and - chapters, and then use the more detailed -chapters as reference. Before novice users go onto more technical problems covered -in , , , or they -should know the material covered in and be able -to replicate some of the examples given there. - - -All users should read the - -and sections to understand the document conventions -and the various ways of getting help on using &clm4;. Users should also read -the section to see if their planned use of the -model is something that has been scientifically validated and well tested. Users -that are NOT using &ncar; machines or our list of well tested machines should also -read the section to make sure they have -all the required UNIX utilities on the system they want to do their work. - - - - - -Introduction to the &clm4; User's Guide -What is in here anyway? - - -Here in the introduction we first give a simple guide to understand the document -conventions in . The next section -describes the differences between &clmrel; and &clm40; (for each &cesm; release version -up to &cesmrel;) as well as between -&clm40; and &clm35;, both from a scientific -as well as a software engineering point of view. It also talks about differences in the -configuration, namelist, and history fields. The next section -is for users that are already experts in using &clm; and gives a quickstart guide to the -bare details on how to use &clm4;. The next tells -you about what has been extensively tested and scientifically validated (and maybe more -importantly) what has NOT. lists the UNIX utilities -required to use &clm4; and is important if you are running on non-&ncar; machines, generic -local machines, or machines NOT as well tested by us at &ncar;. Next we -have to detail some of the best practices for using -&clm4; for science. The last introductory section is which lists -different resources for getting help with &cesm1; and &clm4;. - - - - goes into detail on how to setup and run simulations with -&clm4; and especially how to customize cases. Details of &configure; -modes and &buildnml; options as well as namelist options are given in this chapter. - - - - gives instructions on the &clm4; tools for creating input datasets -for use by &clm;, for the expert user. There's an overview of what each tool does, and some general notes on how to build -the FORTRAN tools. Then each tool is described in detail along with different ways in -which the tool might be used. -A final section -on how to customize datasets for observational sites for very savvy expert users is given as the last section of this chapter. - - - -As a followup to the tools chapter, tells how to add files to the -XML database for &buildnml; to use. This is important if you want to use the XML database to automatically select -user-created input files that you have created when you setup new cases with &clm;. - - - -In , again for the expert user, we give details on how to do some particularly -difficult special cases. For example, we give the protocol for spinning up both the &clmcn; model and &clm; with dynamic -vegetation active (CNDV). We give instructions to do a spinup case -from a previous case with Coupler history output for atmospheric forcing. We also give -instructions on running the prognostic crop model and its irrigation option. We also review -how to validate a port to a new machine using the Perturbation error -growth technique. Lastly we tell the user how to use the DATM model to send historical &CO2; data to &clm;. - - - - outlines how to do single-point or -regional simulations using &clm4;. -This is useful to either compare &clm; simulations with point observational stations, -such as tower sites (which might include your own atmospheric forcing), or -to do quick simulations with &clm; for example to test a new parameterization. There are -several different ways given on how to perform -single-point simulations which range from simple &PTSMODE; to more complex where you create all your own datasets, tying into - and also to add the -files into the &buildnml; XML database. After this chapter - chapter outlines how to use the &ptclm; python script to -help you run single-point simulations. - - - -Finally, gives some guidance on trouble-shooting -problems when using &clm4;. It doesn't cover all possible problems with &clm;, but gives -you some guidelines for things that can be done for some common problems. - - - -In the appendices we talk about some issues that are useful for advanced users and -developers of &clm;. -In we give some basic background to the &clm; -developer on how to edit the models/lnd/clm/bld/clm.cpl7.template. -This is a very difficult exercise and we don't recommend it for any, but the most -advanced users of &clm; who are also experts in UNIX and UNIX scripting. - - -In we go over how to run the script -runinit_ibm.csh" that will interpolate standard resolution -initial condition dataset to several other resolutions at once. It also runs &clm; -to create template files as well as doing the interpolation using -interpinic. In general this is only something that a developer -would want to do. Most users will only want to interpolate for a few specific -resolutions. - - -In we go over the automated testing scripts for -validating that the &clm; is working correctly. The test scripts run many different -configurations and options with &clm; making sure that they work, as well as doing -automated testing to verify restarts are working correctly, and testing at many -different resolutions. In general this is an activity important only for a developer -of &clm;, but could also be used by users who are doing extensive code modifications -and want to ensure that the model continues to work correctly. - - -Finally in we give instructions on how to build -the documentation associated with &clm; (i.e. how to build this document). This -document is included in every &clm; distribution and can be built so that you can -view a local copy rather than having to go to the &cesm; website. This also could -be useful for developers who need to update the documentation due to changes they -have made. - - - - - - - - - -Important Notes and Best Practices for Usage of &clm4; - - - -When running with CN, it is critical to begin with initial conditions -hat are provided with the release or to spin the model up following the CN spinup -procedure before conducting scientific runs (see . -Simulations without a proper spinup will effectively be starting from an unvegetated -world. See for information on how to -provide initial conditions for your simulation. - - -Initial condition files are provided for fully coupled BCN and offline -ICN cases for 1850 and 2000 at 1deg, 2deg, and T31 resolutions. There's also an -initial condition file for ICN with the prognostic crop model for 2000 at 2deg -resolution, and one with &clmsp; for 2000 at 2deg resolution. We also have initial -conditions for offline CNDV for 1850. And there are interpolated datasets for 4x5 and -10x15 resolution for 1850. The 1850 initial condition -files are in 'reasonable' equilibrium. The 2000 initial condition files represent -the model state for the year 2000, and have been taken from transient simulations. -Therefore, by design the year 2000 initial condition files do not represent an -equilibrium state. Note also that spinning the 2000 initial conditions out to -equilibrium will not reflect the best estimate of the real carbon/nitrogen state -for the year 2000. - - -Users can generate initial condition files at different resolutions by -using the &clm; tool interpinic to interpolate from one of the -provided resolutions to the resolution of interest. Interpolated initial condition -files may no longer be in 'reasonable' equilibrium. - - -Aerosol deposition is a required field to &clm4; sent from the -atmosphere model. Simulations without aerosol deposition will exhibit unreasonably -high snow albedos. The model sends aerosol deposition from the atmospheric model (either -CAM or &datm;). When running with prescribed aerosol the atmosphere -model will interpolate the aerosols from 2-degree resolution to the resolution the -atmosphere model is running at. - - - - - - - - - - - - - $EDITOR - - - -How to Use This Document -Conventions used in the document for code and commands - - -This section provides the details in using &clm; with the &cesm; modeling -system. Links to descriptions and definitions have been provided in the code below. -We use the same conventions used in the &cesm; documentation as outlined below. - - - -Throughout the document this style is used to indicate shell -commands and options, fragments of code, namelist variables, etc. -Where examples from an interactive shell session are presented, lines -starting with > indicate the shell prompt. A backslash "\" at the end -of a line means the line continues onto the next one (as it does in -standard UNIX shell). Note that $EDITOR" is used to refer to the -text editor of your choice. $EDITOR is a standard UNIX environment -variable and should be set on most UNIX systems. Comment lines are -signaled with a "#" sign, which is the standard UNIX comment sign as well. -$CSMDATA is used to denote the path to the inputdata directory for -your &cesm; data. - -> This is a shell prompt with commands \ -that continues to the following line. -> $EDITOR filename # means you are using a text editor to edit "filename" -# This is a comment line - - - - - - - - - - - &clmcn; - &clmsp; - - -What is new with &clmrel; since previous public releases? - -In this section we list the updates that have occurred to &clm4; since previous -public releases. In the first sections we describe changes in &clmrel; since the &ccsm4; release, -and in the last one we describe changes from &clm35; to &clm40; release. Note, that -the changes in the last section do NOT include the more recent changes given in the -first section, but only list the changes from &clm35; to the &clm40; release that -was part of the &ccsm4; public release. We will describe both the -changes in the science in the model as the software engineering changes. Software -engineering changes includes the configure and namelist changes, as well as the new -history fields. - - -What is new with &clmrel; since the December 8th, 2010 &cesm102; release? - - - -What is new with &clmrel; Science since &clmcesm102;? - -A prognostic crop model option was added in (based on Agro-IBIS) from work by -Samuel Levis. The crop model adds in four new vegetation types for: soybean, -winter and spring temperate cereals, and corn on their own separate columns. Winter -cereal was added as a PFT type, but doesn't exist in the input datasets, only -spring cereal is used. Winter cereal also has NOT been scientifically validated -or tested. The model manages these by modeling both planting and harvesting. See for an example of running with it. - - -An irrigation model was added from work by Samuel Levis and Bill Sacks. This -model takes water from runoff and adds it to the crop pfts for areas equipped -for irrigation. See for an example of running with it. -Please note that the irrigation model only works with the crop model active. - - - - -What is new with &clmrel; Software since &clmcesm102;? - -Since &clmcesm102; all Input/Output uses &pio; (Parallel Input/Output package). -Restart history files are now &netcdf;. Input and output files can be read/written -in parallel using PIO. We removed a list of old CPP defines and removed the -old misc/preproc.h files. Also a new tool for working with single-point sites was -added into the &cesm; scripts the Python tool &ptclm;. We have a complete chapter on it's use. - - -New configuration options: - --crop --noio - - - -Configuration options removed: - --dust --progsslt - - - -New build-namelist options: - --co2_ppmv --rtm_res --rtm_tstep - - - -New precedence for build-namelist options is... - -Values set on the command-line using the -namelist option -(&CLMNAMELIST;). -Values read from the file specified by -infile (&usernlclm; file). -Datasets from the -clm_usr_name option (&CLMUSRDAT;). -Values set from a use-case scenario, e.g., -use_case (&CLMUSECASE;). -Values from the namelist defaults file. - - - -Namelist options renamed: - -carbon_only => suplnitro (can be set to NONE or ALL) - - - -namelist options removed: - -carbon_only => suplnitro -scaled_harvest -hist_crtinic -hist_pioflag -ncd_lowmem2d -ncd_pio_def -ncd_pio_UseRearranger -ncd_pio_UseBoxRearr -ncd_pio_SerialCDF -ncd_pio_IODOF_rootonly -ncd_pio_DebugLevel -ncd_pio_num_iotasks - - - -New history fields: - -A5TMIN 5-day running mean of min 2-m temperature -(K) -A10TMIN 10-day running mean of min 2-m temperature -(K) -GDD0 Growing degree days base 0C from planting -(ddays) -GDD8 Growing degree days base 8C from planting -(ddays) -GDD10 Growing degree days base 10C from planting -(ddays) -GDD020 Twenty year average of growing degree days base 0C from planting -(ddays) -GDD820 Twenty year average of growing degree days base 8C from planting -(ddays) -GDD1020 Twenty year average of growing degree days base 10C from planting -(ddays) -GDDPLANT Accumulated growing degree days past planting date for crop -(ddays) -GDDHARV Growing degree days (gdd) needed to harvest -(ddays) -GDDTSOI Growing degree-days from planting (top two soil layers) -(ddays) -QIRRIG water added through irrigation -(mm/s) - - - -SNOWLIQ and SNOWICE changed from average to instantaneous output. - - - - -What was new with &clm4014; (in &cesm102;) since the September 17th, 2010 &cesm101; release? - -Since, &clm4010; in the &cesm101; release there were several developments made -to &clmrel;. Several new namelist items were added -a few new history fields. There were also some updates for -running the model with single-point mode. - - -Configuration options that were renamed: - -prog_seasalt => progsslt - - - -Namelist items removed: - -prog_seasalt => progsslt - - - -What was new with &clm4014; Science since &clm4010;? - -A long simulation at the course resolution of T31 (typically used for Paleo-climate -studies) was done and an spun-up initial condition file was provided for this -resolution (also by default the namelist variable ice_runoff was -turned off for T31). Also a new surface dataset and transient land-cover dataset was -provided for half-degree resolution. - - - -What was new with &clm4014; Software since &clm4010;? - -New configuration options - -sitespf_pt - - - -sitespf_pt is used for single-point/regional mode and is set to the site-name -that will be used (see the config_definition.xml for the -list of valid options). - - -Configuration options that were renamed: - -prog_seasalt => progsslt - - - -Namelist items removed: - -faerdep -fndepdat -fndepdyn -use_ndepstream - - - -Nitrogen deposition datasets are now only entered through the -ndepdyn_nml namelist (removing fndepdat, fndepdyn, and -use_ndepstream). Aerosol deposition is now a required input from -the atmosphere model, hence faerdep is removed. - - -New history fields: - -U10 10-m wind (m/s) -U10_DUST 10-m wind for dust model (m/s) -VA atmospheric wind speed plus convective velocity (m/s) -VOLR RTM storage: LIQ (m3) -VOLR_ICE RTM storage: ICE (m3) - - - - - - -What was new with &clm4010; (in &cesm101;) since the April 1st, 2010 &ccsm4; release? - -From, &clm40; in the &ccsm4; release to &clm4010; there were several developments made -to &clm;. A glacier multiple elevation class option was added that allows the -use of &clm4; with a glacier land ice model the Community Ice Sheet Model (CISM). -A bug-fix for the snow hydrology was added. Several new namelist items were added -a few new history fields. Also the capability of reading aerosol and nitrogen -deposition from stream files at one resolution and regridded on the fly rather than -with datasets at the model resolution was added in. This was important for higher -resolutions so that large datasets do not have to be created before running the model, -nor are datasets for every resolution required. - - -What was new with &clm4010; Science since &ccsm4;? - -In general, snow layers should not be thinner than - -dzmin = wice/rhoice + wliq/rholiq - -If dz < dzmin, then the value of "void" computed in subroutine -SnowCompaction is negative, which is unphysical. This doesn't cause -problems with the compaction itself, but results in unrealistic values -of vol_ice, vol_liq, and eff_porosity in subroutine SnowWater. We can -have vol_ice = 1 and vol_liq = 0 even when liquid is present, which cuts -off the runoff (qout) from the lowest snow layer. Liquid water then -accumulates in the snow column without draining, which leads to further -problems and eventually a code crash. - - -The solution to this problem was to adjust layer thickness dz for any water+ice content -changes in excess of previous layer thickness, e.g., - -dz(c,j) = max(dz(c,j),h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice) - -at appropriate steps in the snow hydrology subroutines. - - - -Snow hydrology bug fix. -Add multiple elevation class option for glaciers so can interact with -the land ice sheet model. - - - - -What was new with &clm4010; Software since &ccsm4;? - -New configuration options - -glc_nec - - - -glc_nec can be 1,3,5, or 10 and MUST match the number on the input surface dataset -the elevation classes themselves are read from the surface dataset - - -New namelist items: - -carbon_only -create_glacier_mec_landunit -glc_dyntopo -ice_runoff -ndepmapalgo -scaled_harvest - - - -carbon_only = If true, and CLMCN carbon-nitrogen model is on, Nitrogen is unlimited - rather than prognosed and vegetation will be over-productive (replaces the supplemental Nitrogen #ifdef) - - - create_glacier_mec_landunit (= T when these landunits are created; F by default) - - - glc_dyntopo (= T if &clm; topography changes dynamically; currently F) - (NOT fully implemented yet) - - -ice_runoff = If true, river runoff will be split up into liquid and ice streams, - otherwise ice runoff will be zero and all runoff directed to liquid stream - - - ndepmapalgo = Mapping method from Nitrogen deposition input file to the model - resolution (can be bilinear,nn,nnoni,nnonj,spval,copy, bilinear by default) - - -scaled_harvest = If true, harvesting will be scaled according to coefficients - determined by Johann Feddema, 2009 - - -New history fields: - -aais_area Antarctic ice area (km^2) -aais_mask Antarctic mask (unitless) -gris_area Greenland ice area (km^2) -gris_mask Greenland mask (unitless) -QICE ice growth/melt (mm/s) -QICEYR ice growth/melt (mm/s) -QTOPSOIL water input to surface (mm/s) -VOLR RTM storage: LIQ (m3) -VOLR_ICE RTM storage: ICE (m3) - - - - - - - -What was new with &clm40; since &clm35;? - - -From &clm35; to &clm40; there were advances in both the science and the software infrastructure. -There were also new configure and namelist options as well as new history fields. In this -section we will describe each of these changes in turn. - - - -What was new with &clm40; Science? - -The following aspects are changes to the science in &clm40; since &clm35;. - - -Biogeophysics and Hydrology - -Changes to &clm40; beyond &clm35; (Oleson et al., 2008a; Stockli et al., 2008) include -updates throughout the model. The hydrology scheme has been modified with a revised -numerical solution of the Richards equation (Zeng and Decker, 2009; Decker and Zeng, -2009); a revised soil evaporation parameterization that removes the soil resistance term -introduced in &clm35; and replaces it with a so-called &Bgr; formulation, as well as accounts for the role of litter and within- -canopy stability (Sakaguchi and Zeng, 2009). -&clm4; also includes a representation of the thermal and hydraulic properties of organic -soil that operates in conjunction with the mineral soil properties (Lawrence and Slater, -2008). The ground column has been extended to ~50-m depth by adding five additional -hydrologically inactive ground layers (making a total of 15 ground layers, 10 soil -layers and 5 bedrock layers; Lawrence et al., 2008). An urban landunit and associated -urban canyon model (&clmu;) has been added which permits the study of urban climate -and urban heat island effects (Oleson et al., 2008b). - - - - -Snow Model - -The snow model is significantly modified via incorporation of SNICAR (SNow and Ice Aerosol Radiation) which represents the effect of aerosol deposition (e.g. black and organic carbon and dust) on albedo, introduces a grain-size dependent snow aging parameterization, and permits vertically resolved snowpack heating (Flanner and Zender, 2005; Flanner and Zender, 2006; Flanner et al., 2007). The new snow model also includes a new density-dependent snow cover fraction parameterization (Niu and Yang, 2007), a revised snow burial fraction over short vegetation (Wang and Zeng, 2009) and corrections to snow compaction (Lawrence and Slater, 2009). - - - - -Surface Datasets - -The PFT distribution is as in Lawrence and -Chase (2007) except that a new cropping dataset is used (Ramankutty et al., 2008) and -a grass PFT restriction has been put in place to reduce a high grass PFT bias in -forested regions by replacing the herbaceous fraction with low trees rather than grass. -Grass and crop PFT optical properties have been adjusted according to values presented -in Asner et al. (1998), resulting in significantly reduced albedo biases. Soil colors -have been re-derived according to the new PFT distribution. - - - - -Biogeochemistry - -The model is extended with a carbon-nitrogen biogeochemical model (Thornton et al., 2007; -Thornton et al., 2009; Randerson et al., 2009) which is referred to as &clmcn;. CN is -based on the terrestrial biogeochemistry Biome-BGC model with prognostic carbon and -nitrogen cycle (Thornton et al., 2002; Thornton and Rosenbloom, 2005). &clmcn; is -prognostic with respect to carbon and nitrogen state variables in the vegetation, litter, -and soil organic matter. Vegetation phenology and canopy heights are also prognostic. A -detailed description of the biogeochemical component can be found in Thornton et al. -(2007). Note that &clm40; can be run with either prescribed satellite phenology -(&clmsp;) or with prognostic phenology provided by the carbon- nitrogen cycle model -(&clmcn;). Additionally, a transient land cover and land use change, including wood harvest, -capability has been introduced that enables the evaluation of the impact of historic and -future land cover and land use change on energy, water, and momentum fluxes as well as -carbon and nitrogen fluxes. The dynamic global vegetation model in &clm3; has been -revised such that the carbon dynamics (e.g. productivity, decomposition, phenology, -allocation, etc.) are controlled by CN and only the dynamic vegetation biogeography -(competition) aspect of the &clm3; DGVM is retained. -The biogenic volatile organic compounds model (BVOC) that was available in &clm3; has -been replaced with the MEGAN BVOC model (Heald et al. 2008). - - - - -Miscellaneous Changes - -Several other minor changes have been incorporated including a change to the atmospheric reference height so that it is the height above zo+d for all surface types. The convergence of -canopy roughness length zo and displacement height d to bare soil values as the -above-ground biomass, or the sum of leaf and stem area indices, goes to zero is ensured -(Zeng and Wang, 2007). Several corrections have been made to the way the offline forcing -data is interpreted. The main change is a vastly improved and smooth diurnal cycle of -incoming solar radiation that conserves the total incoming solar radiation from the -forcing dataset. Additionally, in offline mode rather than partitioning incoming solar -radiation into a constant 70%/30% direct vs diffuse split, it is partitioned according to -empirical equations that are a function of total solar radiation. Finally, to improve -global energy conservation in fully coupled simulations, runoff is split into separate -liquid and ice water streams that are passed separately to the ocean. Input to the ice -water comes from excess snowfall in snow-capped regions. - - - - -Summary of Science Changes - -Taken together, these augmentations to &clm35; in &clm40; result in improved soil moisture dynamics -that lead to higher soil moisture variability and drier soils. Excessively wet and -unvarying soil moisture was recognized as a deficiency in &clm35; (Oleson et al. 2008a, -Decker and Zeng, 2009). The revised model also simulates, on average, higher snow cover, -cooler soil temperatures in organic-rich soils, greater global river discharge, lower -albedos over forests and grasslands, and higher transition-season albedos in snow covered -regions, all of which are improvements compared to &clm35;. - - - - - -What is new with &clm40; Software Infrastructure? - -The following aspects are changes to the software infrastructure in &clm40; since &clm35;. - - - - Update to cpl7 and scripts. - Remove offline and cpl6 modes. - Remove support for CASA model. - Update to datm8 atmospheric data model. - Add gx3v7 land mask for T31 and fv-4x5 horizontal resolutions. - Add gx1v6 land mask for f05, f09, and f19 horizontal resolutions. - Add tx1v1 land mask and 1.9x2.5_tx1v1 horizontal resolution. - Add in 2.5x3.33 horizontal resolution. - Add in T62 horizontal resolution so can run at same resolution as input &datm; -data. - Allow first history tape to be 1D. - Add ability to use own version of input datasets with &CLMUSRDAT; -variable. - Add a script to extract out regional datasets. - New &buildnml; system with XML file describing all namelist -items. - Add glacier_mec use-case and stub glacier model. - Make default of maxpatch_pft=numpft+1 instead of 4. - Only output static 3D fields on first h0 history file to save space. - Add new fields for VOC (Volatile Organic Compounds) on surface datasets, - needed for the new MEGAN VOC model. - Add multiple elevation class option for glaciers in mksurfdata tool (NOT used -in &clm; yet). - Add ascale field to land model in support of model running on it's own -grid. - - - - - -What are The New Configuration Options in &clm40;? - -Describe any changes made to build system: - - - -Change directory structure to match &ccsm;. -Add BGP target. -Add choice between ESMF and MCT frameworks. -Start removing #ifdef and directives that supported Cray-X1 Phoenix as now -decommissioned. -Make default of maxpatch_pft=numpft+1 instead of 4 for all -configurations. -By default turn on CLAMP when either CN or CASA is enabled -New SNICAR_FRC, CARBON_AERO, and C13 CPP ifdef tokens. - - - - -New options added to &configure;: -More information on options to &clm; &configure; are given in . - - - - -OptionDescription --comp_intf <name>Component interface to use (ESMF or MCT) (default -MCT) --nofireTurn off wildfires for bgc setting of CN (default includes -fire for CN) --pio <name>Switch enables building with Parallel I/O library. [on -| off] (default is on) --snicar_frc <name>Turn on SNICAR radiative forcing calculation. [on | -off] (default is off) - -More information on options to &clm; &configure; are given in . - - - - -What are The New Namelist Options in &clm40;? - -&buildnml; now checks the validity of your namelist you generate by looking at data in -the namelist_definition.xml file. In order to add new namelist items you need to -change the code and also edit this file (e.g. a namelist option required for your -research project that is not currently an option in &clm40;). To view information -on the namelist view the -file: models/lnd/clm/bld/namelist_files/namelist_definition.xml -in a browser and you'll see the names, type, description and valid_values for all -namelist variables. - - -Changes to &buildnml;: - -Allow simulation year entered to include ranges of years (i.e. 1850-2000) -Remove cam_hist_case option. -Make sure options ONLY used for stand-alone testing have a "drv_" or "datm_" - prefix in them and list these options all together and last when asking for - help from &buildnml;. - - - - New option to &buildnml;: - - -clm_usr_name "name" Dataset resolution/descriptor for personal datasets. - Default: not used - Example: 1x1pt_boulderCO_c090722 to describe location, - number of pts, and date files created - - - - New list options to &buildnml; - - cd models/lnd/clm/bld - ./&buildnml; -res list # List valid resolutions - ./&buildnml; -mask list # List valid land-masks - ./&buildnml; -sim_year list # List valid simulation years and simulation year ranges - ./&buildnml; -clm_demand list # List namelist variables including those you could - # demand to be set. - ./&buildnml; -use_case list # List valid use-cases - - - - -New use-cases for &buildnml;: - - 1850_control = Conditions to simulate 1850 land-use - 2000_control = Conditions to simulate 2000 land-use -20thC_transient = Simulate transient land-use, aerosol and Nitrogen deposition - from 1850 to 2005 - - - - - New namelist items: - - urban_hac = OFF, ON or ON_WASTEHEAT (default OFF) Flag for urban Heating - and Air-Conditioning - OFF = Building internal temperature is un-regulated. - ON = Building internal temperature is bounded to reasonable range. - ON_WASTEHEAT = Building internal temperature is bounded and resultant waste - heat is given off. - urban_traffic = .true. or .false. Flag to include additional multiplicative - factor of urban traffic to sensible heat flux. - (default .false.) - fsnowoptics = filename file for snow/aerosol optical properties (required) - fsnowaging = filename file for snow aging parameters (required) - -More information on the &buildnml; options are given in -. -and in -&CLMBLDNML;. - - -More information on the &buildnml; options are given in in . - - - - -What are The New History Fields? - -New history variables: (note watt vs. W in units, 26 vs. 76) - - - - -NameLong-nameUnitsActive/Inactive -BCDEPtotal BC deposition (dry+wet) from -atmospherekg/m^2/s -BIOGENCObiogenic CO -fluxuGC/M2/H -C13_PRODUCT_CLOSSC13 total carbon loss from wood product -poolsgC13/m^2/s -DSTDEPtotal dust deposition (dry+wet) from -atmospherekg/m^2/s -EFLX_DYNBALdynamic land cover change conversion energy -fluxW/m^2 -FGR12heat flux between soil layers 1 and -2watt/m^2 -FSATfractional area with water table at -surfaceunitless -FSH_NODYNLNDUSEsensible heat flux not including correction for land use change - watt/m^2 -GC_HEAT1initial gridcell total heat -contentJ/m^2 -GC_HEAT2post land cover change total heat -contentJ/m^2inactive -GC_ICE1initial gridcell total ice -contentmm/s -GC_ICE2post land cover change total ice -contentmm/sinactive -GC_LIQ1initial gridcell total liq -contentmm -GC_LIQ2initial gridcell total liq content -mminactive -H2OSNO_TOPmass of snow in top snow -layerkg - HEAT_FROM_ACsensible heat flux put into canyon due to heat -removed from air conditioningwatt/m^2 -HKhydraulic -conductivitymm/sinactive -ISOPRENEisoprene fluxuGC/M2/H -LAND_USE_FLUXtotal C emitted from land cover conversion and -wood product poolsgC/m^2/s -LAND_UPTAKENEE minus LAND_USE_FLUX, negative for -updategC/m^2/s -LWupupwelling longwave -radiationwatt/m^2inactive -MONOTERPmonoterpene -fluxuGC/M2/H -NBPnet biome production, includes fire, landuse, and harvest -flux, positive for sinkgC/m^2/s -OCDEPtotal OC deposition (dry+wet) from -atmospherekg/m^2/s -OVOCother VOC fluxuGC/M2/H -ORVOCother reactive VOC -fluxuGC/M2/H -PBOTatmospheric pressurePa -PCO2atmospheric partial pressure of -&CO2;Pa -PRODUCT_CLOSStotal carbon loss from wood product -poolsgC/m^2/s -PRODUCT_NLOSStotal N loss from wood product -poolsgN/m^2/s -Qairatmospheric specific -humiditykg/kginactive -Qanthanthropogenic heat -fluxwatt/m^2inactive -Qtaumomentum fluxkg/m/s^2 -QFLX_LIQ_DYNBALliq dynamic land cover change conversion -runoff fluxmm/s -QFLX_ICE_DYNBALice dynamic land cover change conversion -runoff fluxmm/s -QRUNOFF_NODYNLNDUSEtotal liquid runoff not including correction for land use change (does not include QSNWCPICE) -mm/s -QSNWCPICEexcess snowfall due to snow -cappingmm/s -QSNWCPICE_NODYNLNDUSEexcess snowfall due to snow capping not including correction for land use change -mm/s -QSNWCPLIQexcess rainfall due to snow -cappingmm/sinactive -SMPsoil matric -potentialmminactive -SNOAERFRC2Lsurface forcing of all aerosols in snow, averaged only when snow is present (land) -watt/m^2 -SNOAERFRCLsurface forcing of all aerosols in snow -(land)watt/m^2 -SNOBCFRCLsurface forcing of BC in snow -(land)watt/m^2 -SNOBCMCLmass of BC in snow -columnkg/m2 -SNOBCMSLmass of BC in top snow -layerkg/m2 -SNOdTdzLtop snow layer temperature gradient -(land)K/m -SNODSTFRC2Lsurface forcing of dust in snow, averaged only when snow is present (land) -watt/m^2 -SNODSTFRCLsurface forcing of dust in snow -(land)watt/m^2 -SNODSTMCLmass of dust in snow -columnkg/m2 -SNODSTMSLmass of dust in top snow -layerkg/m2 -SNOFSRNDdirect nir reflected solar radiation from -snowwatt/m^2inactive -SNOFSRNIdiffuse nir reflected solar radiation from -snowwatt/m^2inactive -SNOFSRVDdirect vis reflected solar radiation from -snowwatt/m^2inactive -SNOFSRVIdiffuse vis reflected solar radiation from -snowwatt/m^2inactive -SNOFSDSNDdirect nir incident solar radiation on -snowwatt/m^2inactive -SNOFSDSNIdiffuse nir incident solar radiation on -snowwatt/m^2inactive -SNOFSDSVDdirect vis incident solar radiation on -snowwatt/m^2inactive -SNOFSDSVIdiffuse vis incident solar radiation on -snowwatt/m^2inactive -SNOLIQFLtop snow layer liquid water fraction -(land)fractioninactive -SNOOCMCLmass of OC in snow -columnkg/m2 -SNOOCMSLmass of OC in top snow -layerKg/m2 -SNOOCFRC2Lsurface forcing of OC in snow, averaged only when snow is present (land) -watt/m^2 -SNOOCFRCLsurface forcing of OC in snow -(land)watt/m^2 -SNORDSLtop snow layer effective grain -radiusm^-6inactive -SNOTTOPLsnow temperature (top -layer)K/minactive -SWupupwelling shortwave -radiationwatt/m^2inactive -TSOI_10CMsoil temperature in top 10cm of -soilK -URBAN_ACurban air conditioning -fluxwatt/m^2 -URBAN_HEATurban heating -fluxwatt/m^2 -VOCFLXTtotal VOC flux into -atmosphereuGC/M2/H -Windatmospheric wind velocity -magnitudem/sinactive -WOOD_HARVESTCwood harvest (to product -pools)gC/m^2/s -WOOD_HARVESTwood harvest (to product -pools)gN/m^2/s - - - - - History field name changes: - - -OldNew -ANNSUM_PLANT_NDEMAND= -ANNSUM_POTENTIAL_GPP -ANNSUM_RETRANSN= ANNMAX_RETRANSN -C13_DWT_PROD10C_LOSS= C13_PROD10C_LOSS -C13_DWT_PROD100C_LOSS= C13_PROD100C_LOSS -C13_DWT_PROD10N_LOSS= C13_PROD10N_LOSS -C13_DWT_PROD100C_LOSS= C13_PROD100C_LOSS -DWT_PROD100N_LOSS= PROD10N_LOSS -DWT_PROD100N_LOSS= PROD100N_LOSS -DWT_PROD100C_LOSS= PROD10C_LOSS -DWT_PROD100C_LOSS= PROD100C_LOSS -HCSOISNO= HC -TEMPSUM_PLANT_NDEMAND= -TEMPSUM_POTENTIAL_GPP -TEMPSUM_RETRANSN= TEMPMAX_RETRANSN - - - -History field names deleted include: SNOWAGE, TSNOW, FMICR, FCO2, DMI, QFLX_SNOWCAP - - - -Add new urban oriented _U, and _R (Urban and Rural) for the following history variables: -EFLX_LH_TOT, FGR, FIRA, FSH, FSM, Q2M, QRUNOFF, RH2M, SoilAlpha, TG, TREFMNAV, -TREFMXAV, and TSA (missing _R for SoilAlpha as the regular SoilAlpha is only defined -for rural areas anyway) - - - -We are missing the Rural soil-alpha variable: SoilAlpha_R on purpose. -SoilAlpha_U is only defined over pervious road, and missing everywhere else. -SoilAlpha is defined only for rural areas. - - - - - - - - - - - -Quickstart to using &clm4; - -Before working with &clm4; read the QuickStart Guide in the -&cesmrel; -Scripts User's Guide. Once you are familiar with how to setup cases for -any type of simulation with &cesm; you will want to direct your attention to the specifics -of using &clm;. - - -For some of the details of setting up cases for &clm4; read the README and text files available -from the "models/lnd/clm/doc" directory (see the "&clm; Web pages" section for a link to the list -of these files). Here are the important ones that you should be familiar with. - -README file describing the directory structure. -Quickstart.userdatasets file describing how to -use your own datasets in the model (also see ). -&KnownBugs; file describing known -problems in &clm4; (that we expect to eventually fix). -KnownLimitations file -describing known limitations in &clm4; and workarounds that we do NOT expect to -fix. - - -The IMPORTANT_NOTES file is given in the next chapter on what -is functional/validated in &clm4;? - -The ChangeLog/ChangeSum files are largely explained in the previous chapter on "What is new with -&clm4;?" - -Note other directories have README files that explain different components and tools used -when running &clm; and are useful in -understanding how those parts of the model work and should be consulted when using tools in those directories. -For more details on configuring and customizing a case with &clm; see . - -The Quickstart.GUIDE (which can be found in -models/lnd/clm/doc) is repeated here. - -&quickstart_guide; - - - - -What is scientifically validated and functional in &clm4;? - -In this section we go over what has been extensively tested and scientifically validated -with &clm4;, and maybe more importantly what has NOT been tested and may NOT be -scientifically validated. You can use all features of &clm;, but need to realize that -some things haven't been tested extensively or validated scientifically. When you use -these features you may run into trouble doing so, and will need to do your own work to -make sure the science is reasonable. - - - -Standard Configuration and Namelist Options that are Validated - -The standard version of the model is &clmcn; at 1-degree horizontal resolution (0.9x1.25). This version has been scientifically -validated with long simulations for: fully coupled simulations ("B" cases), coupled to -atmosphere model CAM ("F" cases), and stand-alone &clm; -cases ("I" cases). We've also done both long simulations for 1850 conditions, and transient 20th century simulations from 1850 to 2005 (with -transient land-use, Nitrogen and Aerosol deposition). There have also been transient -future scenario simulations done for fully coupled cases for different "representative -concentration pathway" (RCP) scenarios (RCP2.6, RCP4.5, RCP6.0, and RCP8.5). -To a lesser extent there have also -been simulations done at T31 and 2-degree horizontal -resolution (1.9x2.5), and with &clmsp; for these resolutions. As such we have provided -appropriate 1-degree, 2-degree, and T31 initial condition -datasets for these configurations. The irrigation and prognostic crop models were both -validated at 2-degree resolution. The irrigation model for &clmsp; for present day -conditions for an "I" compset, and the prognostic crop model for present day conditions -for a case coupled to the active land model, but using a data ocean model (an "F" -compset). Other resolutions, configurations, and namelist options are less well tested or scientifically validated. -The further you get away from the standard configurations and resolutions, the more likely you are to run into trouble, and/or need to -scientifically validate your work. - - -In the sections below we go through configuration and/or namelist options or modes that the user should be especially wary of using. You -are of course free to use these options, and you may find that they work functionally. Although in some cases you will find issues even -with functionality of using them. If so you will need to test, debug and find solutions for these issues on your own. But in every case -you will need to go through more extensive work to validate these options from a scientific standpoint. - - - - -Configure Modes NOT scientifically validated, documented, supported or, in some -cases, even advised to be used: - - - - - C13(-c13) -The C13 mode for bgc=cn is NOT scientifically validated or documented and is NOT -recommended for use. - - - - - - CASA(-bgc casa) -The bgc=casa mode is NOT scientifically validated or documented and is NOT -recommended for use. - - - - - - SNICAR_FRC(-snicar_frc) - This mode is tested and functional, but is NOT constantly scientifically validated, and should be - considered experimental. - - - - - - - -Namelist options that should NOT be exercised: - -Build-Namelist options that should NOT be exercised: - - --irrig with -bgc cn -We have only run the irrigation model with &clmsp; (i.e. without the CN model). We -recommend that if you want to run the irrigation model with CN, that you do a spinup. -But, more than that you may need to make adjustments to -irrig_factor in -models/lnd/clm/src/biogeophys/CanopyFluxesMod.F90. See the -notes on this in the description of the irrigation model in the - -Technical Descriptions of the Interactive Crop Management and Interactive -Irrigation Models. - - --irrig with -crop on -Irrigation doesn't work with the prognostic crop model. Irrigation is only applied to -generic crop currently, which negates it's practical usage. We also have a known -problem when both are on (see bug 1326 in the &KnownBugs; file). -If you try to run in this mode, the &clm; &buildnml; will return with an error. - - --lnd_res: Fine-mesh mode, functional, but experimental - --rcp: Representative Concentration Pathway (RCP) -for future scenarios, functional for limited resolutions, but experimental - --datm_*: All options that start with "datm_" they are -only used for &clm; stand-alone testing. - --drv_*: All options that start with "drv_" they are -only used for &clm; stand-alone testing. - - - - - - -Namelist items that should NOT be exercised: - - -casa namelist options: lnpp, lalloc, q10, spunup, and fcpool - - CASA has NOT been scientifically validated in &clm4;. - - - - suplnitro='ALL' - The suplnitro namelist option to the CN Biogeochemistry model supplies -unlimited nitrogen and therefore vegetation is over-productive in this mode. - - - -urban_traffic: Not currently functional - - - - - - - - - -What are the UNIX utilities required to use &clm;? - -Running the &clm; requires a suite of UNIX utilities and programs and you should -make sure you have all of these available before trying to go forward with using -it. If you are missing one of these you should contact the systems administrator -for the machine you wish to run on and make sure they are installed. - -&FORTRAN90; compiler -"C" compiler -GNU make -UNIX csh and tcsh shells -UNIX sh shell -UNIX bash shell -UNIX awk -UNIX sed -&netcdf; library -MPI Library -"C" pre-processor -&perl; -Autoconf -m4 macro processor -Parallel &netcdf; (optional) -&ncl; (for some of the offline tools for creating/modifying &clm; input -datasets see for more information on &ncl;) -Python (optional, needed for &ptclm;) -xsltproc, docbook and docbook utilities (optional, needed to build the Users-Guide) -protex and latex2html (optional, needed to build the Code-Reference Guide) - - - - - - - - - &cesm; Online Bulletin Board - &cesmrel; Scripts User's Guide - - -Other resources to get help from - - -In addition to this users-guide there are several other resources that are available -to help you use &clm4;. The first one is the &cesm; User's-Guide, which documents the entire -process of creating cases with &cesm;. The next is the &cesm; bulletin board which is -a web-site for exchanging information between users of &cesm;. There are also &clm; -web-pages specific for &clm;, and finally there is an email address to report bugs that -you find in &cesm1;. - - - -The &cesm; User's-Guide - -&clmrel; is always run from within the standard &cesmrel; build and run scripts. Therefore, the -user of &clm4; -should familiarize themselves with the &cesmrel; scripts and understand how to work with them. -User's-Guide documentation on the &cesmrel; scripts are available from the following web-page. The purpose -of this &clmrel; User's Guide is to give the &clm4; user more complete details on how to work -with &clm; and the set of tools that support &clm;, as well as to give examples that are unique to the use -of &clm;. However, the &cesmrel; Scripts User's-Guide remains the primary source to get detailed -information on how to build and run the &cesm; system. - -&cesm1; Scripts -User's-Guide - - - - - -The &cesm; Bulletin Board - -There is a rich and diverse set of people that use the &cesm;, and often it is useful to be in contact with -others to get help in solving problems or trying something new. To facilitate this we have an online -Bulletin Board for questions on the &cesm;. There are also different sections in the Bulletin Board for -the different component models or for different topics. - -&cesm; Online Bulletin Board - - - - - -The &clm; web pages - -The main &clm; web page contains information on the &clm;, it's history, developers, as well as -downloads for previous model versions. There are also documentation text files in the -models/lnd/clm/doc directory that give some quick information on using &clm;. - -&clm; web page -&clm; Documentation Text Files - -Also note that several of the XML database files can be viewed in a web browser to get -a nice table of namelist options, namelist defaults, or compsets. Simply view them -as a local file and bring up one of the following files: - -models/lnd/clm/bld/namelist_files/namelist_definition.xml --- definition of &clm; namelist items. -models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml --- default values for &clm; namelist items. -scripts/ccsm_utils/Case.template/config_definition.xml --- definition of all env_*.xml items. -scripts/ccsm_utils/Case.template/config_compsets.xml --- definition of all the compsets. -models/lnd/clm/bld/namelist_files/history_fields.xml --- definition of &clm; history fields. - - - - - -Reporting bugs in &clm4; - -If you have any problems, additional questions, bug reports, or any other feedback, please send an email to -cesmhelp@cgd.ucar.edu. If you find bad, wrong, or misleading information - in this users guide send an email to erik@ucar.edu. The current list of -known issues for &clmrel; is in the &KnownBugs; file, and the list of issues for -&cesmrel; is at... - -&cesmwebmodelrel;/tags/cesm1_0_3/#PROBLEMS -. - - - - - - - - diff --git a/doc/UsersGuide/ptclm.xml b/doc/UsersGuide/ptclm.xml deleted file mode 100644 index 6c0ef2aec8..0000000000 --- a/doc/UsersGuide/ptclm.xml +++ /dev/null @@ -1,992 +0,0 @@ - - -How to run &ptclm; - -&ptclm; (pronounced point clime) is a Python script to help you set up PoinT CLM -simulations. It runs the &clm; tools for you to get datasets set up, and copies them -to a location you can use them according to the &CLMUSRDAT; naming convention. Then -it runs create_newcase for you and modifies the env settings and -namelist appropriately. &ptclm; has a simple ASCII text file for storing basic -information for your sites. We also have complete lists for AmeriFlux and Fluxnet-Canada -sites, although we only have the meteorology data for one site. For other sites you -will need to obtain the meteorology data and translate it to a format that the &cesm; -datm model can use. But, even without meteorology data &ptclm; is useful to setup -datasets to run with standard &CLMQIAN; data. - - - -The original authors of &ptclm; are: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, -Wilfred M. Post all at Environmental Sciences Division, Oak Ridge National Laboratory -(ORNL) and R. Quinn Thomas at Cornell University. It was then modified -fairly extensively by Erik Kluzek at &ncar;. We want to thank all of these individuals -for this contribution to the &cesm; effort. We also want to thank the folks at -University of Michigan Biological Stations (US-UMB) who allowed us to use their Fluxnet -station data and import it into our inputdata repository, especially Gil Bohrer the -PI on record for this site. - - - -Introduction to PTCLM - -To get help on &ptclm; use the "--help" option as follows. - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py --help - - - -The output to the above command is as follows: - - - -&ptclm_help; - - - - -Here we give a simple example of using &ptclm; for a straightforward case of running -at the US-UMB Fluxnet site on bluefire where we already have the meteorology data on -the machine. Note, see for permission information -to use this data. - -Example of running &ptclm; for US-UMB on bluefire - -setenv CSMDATA /fis/cgd/cseg/csm/inputdata -setenv MYCSMDATA $HOME/inputdata -setenv SITE US-UMB -setenv MYMACH bluefire -setenv MYCASE testPTCLM - -# First link the standard input files to a location you have write access -cd scripts -./link_dirtree $CSMDATA $MYCSMDATA - -# Next build all of the clm tools you will need -cd ../models/lnd/clm/tools/mksurfdata -gmake -gmake clean -cd ../mkdatadomain -gmake -gmake clean -cd ../mkgriddata -gmake -gmake clean -# next run PTCLM (NOTE -- MAKE SURE python IS IN YOUR PATH) -cd ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM -./PTCLM.py -m $MYMACH --case=$MYCASE --site=$SITE --csmdata=$MYCSMDATA \ - --aerdepgrid --ndepgrid -# NOTE: we use --aerdepgrid --ndepgrid so that you use the global -# aerosol and Nitrogen deposition files rather than site-specific ones. -cd ../../../../../$MYCASE -# Finally configure, build, and run the case as normal - - - - - - -Guide to the options of &ptclm; - -There are three types of options to &ptclm;: required, configure/run-time, and -dataset generation options. The three required options are the three settings that -MUST be specified for &ptclm; to work at all. The other settings have default -values that will default to something useful. The configure/run-time options control -how the simulation will be setup and run. The dataset generation options control -the generation of datasets needed when &ptclm; is run. Most options use a double -dash "--" "longname" such as "--list", but the most common options also have a short-name -with a single dash (such as -m instead of --machine). - - -The required options to &ptclm; are: inputdata directory (-d), machine (-m) and -site-name (-s). Inputdata directory is the directory where you have the &cesm; -inputdata files, you need to have write access to this directory, so if you are -running on a machine that you do NOT have write access to the standard inputdata -location (such as &ncar; bluefire or ORNL jaguar) you need -to link the standard files to a location you do have control over. We recommend -using the scripts/link_dirtree tool to do that. "machine" is -the scripts name for the machine/compiler you will be using for your case. And -finally site-name is the name of the site that you want to run for. Site-name -can either be a valid &CLM1PT; supported dataset name or a Fluxnet site name -from the list of sites you are running on (see the --sitegroupname for more information -about the site lists). - - -After &ptclm; is run a case directory where you can then configure, build and run -your &cesm; case as normal. It also creates a README.PTCLM -in that directory that documents the commandline options to &ptclm; that were used -to create it. - - -After "help" the "list" option is one of the most useful options for getting -help on using &ptclm;. This option gives you information about some of the other -options to &ptclm;. To get a list of the machine, sites, and compsets that can be -used for &ptclm; use the "--list" option as follows. - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py --list - - - -The output to the above command is as follows: - - - -&ptclm_list; - - - - -Overview on using &ptclm; - -Steps in running &ptclm; - -Setup Inputdata directory with write access (use -<command>link_dirtree</command> script) - -You need to setup an inputdata directory where you have write access to it. -Normally, for &ncar; machines the data is on an inputdata where the user -does NOT have write access to it. A way that you can get around this is -to use the link_dirtree script to create softlinks from -the normal location to a location you have write access to. So for example -on bluefire: - -> setenv CSMDATA /fs/cgd/csm/inputdata -> setenv MYCSMDATA $HOME/inputdata -> mkdir $MYCSMDATA -> cd scripts -> ./link_dirtree $CSMDATA $MYCSMDATA - -See for more information on this. - - - -Build the &clm; tools - -Next you need to make sure all the &clm; &FORTRAN; tools are built. - -> cd models/lnd/clm/tools/mkgriddata -> gmake -> gmake clean -> cd ../mkdatadomain -> gmake -> gmake clean -> cd ../mksurfdata -> gmake -> gmake clean - - - - -Run &ptclm; - -Next you actually run &ptclm; which does the different things listed below: - - - -&ptclm; names your case based on your input - -&ptclm; names you case based on the input you give to it. - -[Prefix_]SiteCode_Compset[_QIAN][_spinuptype] -Where: - Prefix is from the caseidprefix option (or blank if not used). - SiteCode is the site name you entered with the -s option. - Compset is the compset name you entered with the -c option. - _QIAN is part of the name only if the useQIAN is used. - _spinuptype is part of the name if one of: ad_spinup, exit_spinup, or - final_spinup is used, and the exact spinup name chosen is used. - -For example, the casename for the following will be: - -> cd scripts -> ./PTCLM.py -m bluefire -s US-UMB -d $MYCSMDATA -c I_2000_CN --ad_spinup --useQIAN - -"US-UMB_I_2000_CN_QIAN_ad_spinup". - - - -&ptclm; creates datasets for you - -It will populate $MYCSMDATA with new datasets it creates using the -&clm; tools. - - - -If a transient compset and &ptclm; finds a <filename>_dynpftdata.txt</filename> -file - -If you are running a transient compset (such as the "I_1850-2000_CN" compset) -AND you there is a file in the PTCLM_sitedata directory under -the &ptclm; directory called $SITE_dynpftdata.txt it will use -this file for the land-use changes. Otherwise it will leave land-use constant, unless -you use the pftgrid option so it uses the global dataset for landuse changes. -See for more information on this. There -is a sample transient dataset called US-Ha1_dynpftdata.txt. -Transient compsets, are compsets that create transient land-use change and -forcing conditions such as: -'I_1850-2000', 'I_1850-2000_CN', 'I_RCP8.5_CN', 'I_RCP6.0_CN', 'I_RCP4.5_CN', -or 'I_RCP2.6_CN'. - - - -&ptclm; creates a <filename>pft-physiology</filename> for you - -&ptclm; will create a local copy of the pft-physiology -specific for your site that you could then customize with changes specific -for that site. - - - -&ptclm; creates a <filename>README.PTCLM</filename> for you - -&ptclm; will create a simple text file with the command line for it in a file -called README.PTCLM in the case directory it creates for you. - - - - - - -Customize, configure, build and run case as normal - -You then customize your case as you would normally. See the chapter for more information on doing this. - - - - - - - -Details on the options of &ptclm; - -Next we discuss the configure and run-time options, dividing them up into -configure, spinup, and run-time options. - - -Configure options include: - --c MYCOMPSET, --compset=MYCOMPSET ---caseidprefix=MYCASEID ---cesm_root=BASE_CESM ---namelist=NAMELIST ---rmold ---scratchroot=SCRATCHROOT ---sitegroupname=SITEGROUP ---QIAN_tower_yrs ---useQIAN - - - - - ---compset - -The "-c" option is the most commonly used option after the required options, as it -specifies the &cesm; scripts component set to use with &ptclm;. The default compset -is the "ICN" compset with CN on for present day conditions. - - - - - ---caseidprefix - -This option gives a prefix to include in the casename when the case is created, in -case you want to customize your casenames a bit. By default, casenames are figured -out based on the other options. The argument to this option can either be a name to -prefix casenames with and/or a pathname to include. Hence, if you want cases to -appear in a specific directory you can give the pathname to that directory with this -option. - - - - - ---cesm_root - -This option is for running &ptclm; with a different root directory to &cesm; than the -version &ptclm; exists in. Normally you do NOT need to use this option. - - - - - ---namelist - -This option adds any items given into the &clm; &usernlclm; namelist. This allows you to -add customizations to the namelist before the clm.buildnml.csh file -is created for the case. - - - - - ---rmold - -This option will remove an old case directory of the same name if one exists. Otherwise, -if an old case directory already exists and you try to run &ptclm; it will return with -an error. - - - - - ---scratchroot - -This option is ONLY valid when using one of the generic machines (the -m option). -This passed onto create_newcase and gives the location where cases -will be built and run. - - - - - ---sitegroupname - -In the &ptclm; directory there is a subdirectory "PTCLM_sitedata" that contains -files with the site, PFT and soil data information for groups of sites. These site groups -are all separate ASCII files with the same prefix followed by a "_*data.txt" name. -See for more information on these files. -By default we have provided three different valid group names: - -EXAMPLE -AmeriFlux -Fluxnet-Canada - -The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that -is the only site we have data provided for. The other two site groups include the -site information for all of both the AmeriFlux and Fluxnet-Canada sites. You can use -the "sitegroupname" option to use one of the other lists, or you can create your own -lists using the EXAMPLE file as an example. Your list of sites could be real world -locations or could be theoretical "virtual" sites given to exercise &clm; on -differing biomes for example. Note, see with -permission information to use the US-UMB data. - - - - - ---useQIAN - -This option says to use the standard &clm; global Qian T62 atmospheric forcing rather -than any tower site forcing data available. Otherwise, &ptclm; will try to find tower -forcing data for the specific site entered. - - - - - ---QIAN_tower_yrs - -This option is used with the "useQIAN" option to set the years to cycle over for -the Qian data. In this case Qian atmospheric forcing will be used, but the -simulation will run over the same years that tower site is available for this site. - - - - - - -Spinup options include: - ---coldstart ---ad_spinup ---exit_spinup ---final_spinup ---finidat=FINIDAT - - - - -The spinup options enable the different CN spinup modes, but also set the run -length. The coldstart option says to startup with OUT an initial condition file, while -the finidat option explicitly gives the initial condition file to use. Obviously, -the different spinup options can NOT be used together, nor can the coldstart and -finidat options be either. - - ---coldstart - -This option ensures that a cold-start will be done with arbitrary initial conditions. - - - - - ---ad_spinup - -This option enables the accelerated decomposition mode when a CN compset is used. It -also sets the run-length as given in the example for running exit spinup in -. - - - - - ---exit_spinup - -This option enables the exit spinup mode when a CN compset is used. It also sets the -run-length to a year just as given in the example for running exit spinup in -. - - - - - ---final_spinup - -This option sets the run length as given in the example for a final spinup in -. This option can be used for any compset. - - -There is a bug in the final_spinup mode for setting the run length. Because of the -bug, final_spinup mode only runs for a very short time, you'll need to edit -the run length by hand to be 50 years. See bug 1367 in the &KnownBugs; file. - - - - - - - ---finidat - -This option sets the initial condition file to startup the simulation from. - - - - - - - - - -Run-time options include: - ---debug ---run_n=MYRUN_N ---run_units=MYRUN_UNITS ---stdurbpt - - - - - - - ---debug - -This option tells &ptclm; to echo what it would do if it were run, but NOT actually -run anything. So it will show you the dataset creation commands it would use. -It does however, run create_newcase, but then it only displays -the xmlchange commands and changes that it would do. Also note -that if you give the "--rmold" option it won't delete the case directory beforehand. -Primarily this is intended for debugging the operation of &ptclm;. - - - - - ---run_n - -This option along with run_units is used to set the length for the simulation. "run_n" -is the number of units to use. -The default run length depends on the site, compset, -and configuration and for example if a "spinup" option is selected. - - - - - ---run_units - -This option is the units of time to use for the length of the simulation. It is used -along with "run_n" to set the length of the simulation. -The default run length depends on the site, compset, -and configuration and for example if a "spinup" option is selected. - - - - - ---stdurbpt - -This option turns on the "stdurbpt_pd" use-case for &CLMUSECASE;. This option -can NOT be used for compsets that set the use-case to something besides present-day. - - - - - - - - -Lastly we discuss the dataset generation options. The dataset generation options are: - ---aerdepgrid ---ndepgrid ---pftgrid ---soilgrid ---nopointdata ---owritesrfaer - - - - -The options that with a "grid" suffix all mean to create datasets using the global -gridded information rather than using the site specific point data. By default the -site specific point data is used. The "nopointdata" and "owritesrfaer" options have to -do with file creation. - - -Because supported single-point datasets already have the data created for them, you -MUST use the "nopointdata" and "ndepgrid" options when you are using a supported -single-point site. You must use "ndepgrid" even for a compset without CN. You also -can NOT use the options: "soilgrid", "pftgrid", "aerdepgrid", or "owritesrfaer". - - - - - ---aerdepgrid - -This option says to use the aerosol deposition files from the global dataset rather -than creating an interpolated version. - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - ---ndepgrid - -This option says to use the Nitrogen deposition files from the global dataset rather -than creating an interpolated version. This is only needed for compsets with CN. - - - -This option is required when you you are using a site that -is a supported single point dataset. This is true even when you are NOT using a -compset with CN. - - - - - - ---pftgrid - -This option says to use the PFT values provided on the global dataset rather than -using the specific site based values from the -PTCLM_sitedata/*_pftdata.txt file when creating the surface dataset. - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - ---soilgrid - -This option says to use the soil values provided on the global dataset rather than -using the specific site based values from the -PTCLM_sitedata/*_soildata.txt file when creating the surface dataset. - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - ---nopointdata - -This option says to NOT create any input datasets -- assume this step has already been -done. If datasets weren't already created, your case will fail when you try to run it. -In general the first time you run &ptclm; for a new site you want it to generate new -datasets, but the next time and future times you want to use this option so that it -doesn't waste a lot of time rebuilding datasets over again. - - - -This option is required when you you are using a site that -is a supported single point dataset. - - - - - - ---owritesrfaer - -This option says to overwrite any surface and/or aerosol deposition datasets that -were already created. Otherwise, the creation of these files will be skipped if a file -is already found (but it WILL create files if they don't exist). - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - - - - -Note on the aerosol and Nitrogen deposition files. When the "aerdepgrid" and "ndepgrid" -options are NOT used -- aerosol and Nitrogen deposition files will be created by -interpolating from the global datasets. However, after these interpolated files -are created you could customize them for your site with data that you provide. You -could then write protect the files and use the "nopointdata" option so that &ptclm; -doesn't try to overwrite them in the future. - - - - - - -Examples using &ptclm; - -Now let's give a few more complex examples using some of the options we have -discussed above. - - -In this first example, we'll demonstrate using a supported single point dataset, -which then requires using the "nopointdata" and "ndepgrid" options. We'll also -demonstrate the compset option, "stdurbpt" and "caseidprefix" options. - -Example of running &ptclm; for the Mexicocity supported single point -dataset - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py -m bluefire -s 1x1_mexicocityMEX -d $CSMDATA --nopointdata --ndepgrid \ ---stdurbpt -c I --caseidprefix `pwd`/myPTCLMcases/site -> cd myPTCLMcases/site_1x1_mexicocityMEX_I -> ./configure -case -# Now build and run normally -> ./site_1x1_mexicocityMEX_I.bluefire.build -# Here we show running interactively -> ./site_1x1_mexicocityMEX_I.bluefire.run - - - - - -Now, let's demonstrate using a different group list, doing a spinup, running with Qian -global forcing data, but using tower years to set the years to run over. This uses -the options: sitegroupname, ad_spinup, useQIAN, and QIANtower_years. - -Example of running &ptclm; for a spinup simulation with Qian data for tower years. - - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py -m bluefire -s US-Ha1 -d $CSMDATA --sitegroupname AmeriFlux \ ---ad_spinup --useQIAN --QIAN_tower_yrs -> cd ../../../../../US-Ha1_ICN_QIAN_ad_spinup -> ./configure -case -# Now build and run normally -> ./US-Ha1_ICN_QIAN_ad_spinup.bluefire.build -# Here we show running interactively -> ./US-Ha1_ICN_QIAN_ad_spinup.bluefire.run - - - - - -Finally, let's demonstrate using a generic machine (which then requires the scratchroot -option), using the global grid for PFT and soil types, and setting the run length -to two months. - -Example of running &ptclm; on a generic machine with global PFT and soil types -dataset - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -# Note, see the with permission information -# to use the US-UMB data. -> ./PTCLM.py -m generic_darwin_intel -s US-UMB -d $CSMDATA --pftgrid --soilgrid \ ---scratchroot $HOME --run_n 2 --run_units nmonths -> cd ../../../../../US-UMB_ICN -> ./configure -case -# Now build -> ./US-UMB_ICN.generic_darwin_intel.build -# To get the files from the svn server... -# First list the files from the streams text file -> ../ccsm_utils/Tools/listfilesin_streams \ --t $HOME/US-UMB_ICN/run/clm1PT.1x1pt_US-UMB.stream.txt -l \ -> Buildconf/datm.input_data_list -# And now run the script to export data to your machine -> ../ccsm_utils/Tools/check_input_data -export -# Here we show running interactively -> ./US-UMB_ICN.generic_darwin_intel.run - - - - -Because of Bug 1364, when running this case as above we get a floating point -error after reaching time-step 124 for the example exactly as above. Other -machines or compilers probably won't have this problem. See the &KnownBugs; file -for more information on this problem. - - - - -As documented in Bug 1368, spinning up the US-UMB site for a I2000CN compset gives -zero Gross Primary Production (GPP). If the user wishes to use this site for &clmcn;, -they'll need to address this issue. -See the &KnownBugs; file for more information on this problem. - - - - - - -Adding data for use by &ptclm; - -&ptclm; Group Site Lists - -The "sitegroupname" option to &ptclm; looks for groups of sites in the -files in the PTCLM_sitedata directory under the &ptclm; directory. -You can add new names available for this option including your own lists of sites, by -adding more files in this directory. There are three files for each "sitegroupname": -$SITEGROUP_sitedata.txt, -$SITEGROUP_soildata.txt -and $SITEGROUP_pftdata.txt (where $SITEGROUP is the name that would -be entered as "sitegroupname" to &ptclm;). Each file needs to have the same list of sites, -but gives different information: site data, PFT data, and soil data respectively. -Although the site codes need to be the same between the three files, the files do NOT -have to be in the same order. Each file has a one-line header that lists the contents -of each column which are separated by commas. The first column for each of the files -is the "site_code" which must be consistent between the three files. The site code -can be any unique character string, but in general we use the AmeriFlux site code. - - -Site data file: $SITEGROUP_sitedata.txt): The header for -this file is: - -site_code,name,state,lon,lat,elev,startyear,endyear,alignyear - -The columns: name, state, and elevation are informational only. Name is a longer -descriptive name of the site, and state is the state for U.S. sites or country -for non U.S. sites. The columns: lon and lat are the longitude and latitude of -the location in decimal degrees. The last three columns are the start and ending -year for the data and the align year for an 1850 case for the data. The align year -is currently unused. - - -Soil data file: $SITEGROUP_soildata.txt): The header for this -file is: - -site_code,soil_depth,n_layers,layer_depth,layer_sand%,layer_clay% - -The first three fields after "site_code" are currently unused. The only two that -are used are the percent sand and clay columns to set the soil texture. - - -PFT data file: $SITEGROUP_pftdata.txt): The header for this -file is: - -site_code,pft_f1,pft_c1,pft_f2,pft_c2,pft_f3,pft_c3,pft_f4,pft_c4,pft_f5,pft_c5 - -This file gives the vegetation coverage for the different vegetation types for the site. -The file only supports up to five PFT's at the same time. The columns with "pft_f" are -the fractions for each PFT, and the columns with "pft_c" is the integer index of the -given PFT. Look at the pft-physiology file to see what the PFT index for each PFT type -is. - - - - -Dynamic Land-Use Change Files for use by &ptclm; - -There is a mechanism for giving site-specific land-use change in &ptclm;. Adding -site specific files to the PTCLM_sitedata directory under -&ptclm; allows you to specify the change in vegetation and change in harvesting -(for the CN model) for that site. Files are named: -$SITE_dynpftdata.txt. There is a sample file for the US-Ha1 -site called: US-Ha1_dynpftdata.txt. The file has a one-line -header with the information that the file has, and then one-line for each year -with a transition. The header line is as follows: - -trans_year,pft_f1,pft_c1,pft_f2,pft_c2,pft_f3,pft_c3,pft_f4,pft_c4,pft_f5,pft_c5,har_vh1,har_vh2,har_sh1,har_sh2,har_sh3,graze,hold_harv,hold_graze - -This file only requires a line for each year where a transition or harvest happens. As -in the "pftdata" file above "pft_f" refers to the fraction and "pft_c" refers to the -PFT index, and only up to five vegetation types are allowed to co-exist. The last -eight columns have to do with harvesting and grazing. The last two columns are whether -to hold harvesting and/or grazing constant until the next transition year and will -just be either 1 or 0. This file will be converted by the -PTCLM_sitedata/cnvrt_trnsyrs2_landuse_timeseries_txtfile.pl script in the &ptclm; -directory to a format that mksurfdata can read that has an entry -for each year for the range of years valid for the compset in question. - - - - -Converting AmeriFlux Data for use by &ptclm; - -AmeriFlux data comes in comma separated format and is available from: - -http://public.ornl.gov/ameriflux/dataproducts.shtml. Before you -download the data you need to agree to the usage terms. - - -Here is a copy of the usage terms from the web-site on June/13/2011. - - -"The AmeriFlux data provided on this site are freely available and were furnished by -individual AmeriFlux scientists who encourage their use. Please kindly inform the -appropriate AmeriFlux scientist(s) of how you are using the data and of any publication -plans. Please acknowledge the data source as a citation or in the acknowledgments if the -data are not yet published. If the AmeriFlux Principal Investigators (PIs) feel that they -should be acknowledged or offered participation as authors, they will let you know and we -assume that an agreement on such matters will be reached before publishing and/or use of -the data for publication. If your work directly competes with the PI's analysis they may -ask that they have the opportunity to submit a manuscript before you submit one that uses -unpublished data. In addition, when publishing, please acknowledge the agency that -supported the research. Lastly, we kindly request that those publishing papers using -AmeriFlux data provide preprints to the PIs providing the data and to the data archive at -the Carbon Dioxide Information Analysis Center (CDIAC)." - - -The above agreement applies to the "US-UMB" dataset imported into our repository as -well, and Gil Bohrer is the PI on record for that dataset. - - -The &cesm; can NOT handle missing data, so we recommend using the "Level 4" Gap filled -datasets. -The fields will also need to be renamed. The "WS" column becomes "WIND", "PREC" becomes -"PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes -"FLDS", "PRESS" becomes "PSRF". "ZBOT" can just be set to the constant of "30" (m). -The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the -value in SHR_CONST_TKFRZ in the file -models/csm_share/shr/shr_const.F90 of 273.15. -The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and -LONGXY should also be set to the latitude and longitude of the site. - - - -&ptclm; transient example over a shorter time period - - -Example of running &ptclm; for transient land-use 1991-2006 for US-Ha1 on bluefire - -This is an example of using &ptclm; for Harvard Forest (AmeriFlux site code US-Ha1). In -order to do this we would've needed to have converted the AmeriFlux data into &netcdf; -format as show in the section above. Also note -that this site has a site-specific dynamic land-use change file for it -PTCLM_sitedata/US-Ha1_dynpftdata.txt in the &ptclm; directory -and this file will be used for land-use change and harvesting rather than the -global dataset. - - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -# We are going to use forcing data over 1991 to 2006, but we need to start with -# a transient compset to do so, so we use the 20th Century transient: 1850-2000 -# Note: When creating the flanduse_timeseries dataset for this site it will use the -# PTCLM_sitedata/US-Ha1_dynpftdata.txt -# file for land-use change and harvesting -> ./PTCLM.py -m bluefire -s US-Ha1 -d $MYCSMDATA --sitegroupname AmeriFlux \ --c I_1850-2000_CN -> mkdir $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1 -> cd $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1 -# Copy data in &netcdf; format to this directory, filenames should be YYYY-MM.nc -# The fieldnames on the file should be: -# FLDS,FSDS,LATIXY, LONGXY, PRECTmms,PSRF,RH,TBOT,WIND,ZBOT -# With units -# W/m2,W/m2,degrees_N,degrees_E,mm/s, Pa, %, K, m/s, m -# The time coordinate units should be: days since YYYY-MM-DD 00:00:00 -> cd ../../../../../US-Ha1_I_1850-2000_CN -# We need to turn cold-start on, so it doesn't expect an initial condition file -# preferably, you would generate your own initial condition file and then use -# the --finidat option to &ptclm; to enter it -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -# Now we need to set the start date to 1991, and have it cycle forcing data -# over 1991 to 2006 -> ./xmlchange -file env_conf.xml -id RUN_STARTDATE -val 1991-01-01 -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_ALIGN -val 1991 -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_END -val 2006 -> ./xmlchange -file env_conf.xml -id CLM_NAMELIST_OPTS -val \ -# Similarly for Nitrogen deposition data we cycle over: 1991 to 2006 -"model_year_align_ndep=1991,stream_year_first_ndep=1991,stream_year_last_ndep=2006" -# Now configure the case, and we'll edit the datm namelist for prescribed aerosols -> ./configure -case -# We also need to change the datm to run with aerosols over the 1991-2006 period -cat << EOF > patch.diff -*** datm.buildnml.csh.orig 2011-06-14 09:28:20.000000000 -0600 ---- datm.buildnml.csh 2011-06-14 09:28:57.000000000 -0600 -*************** -*** 32,38 **** - dataMode = 'CLMNCEP' - domainFile = '$DOMAINFILE' - streams = 'clm1PT.1x1pt_US-Ha1.stream.txt 1991 1991 2006 ', -! 'presaero.stream.txt 1849 1849 2006' - vectors = 'null','null' - mapmask = 'nomask','nomask' - mapalgo = 'nn','nn' ---- 32,38 ---- - dataMode = 'CLMNCEP' - domainFile = '$DOMAINFILE' - streams = 'clm1PT.1x1pt_US-Ha1.stream.txt 1991 1991 2006 ', -! 'presaero.stream.txt 1991 1991 2006' - vectors = 'null','null' - mapmask = 'nomask','nomask' - mapalgo = 'nn','nn' -EOF -# Apply the above patch to the datm build namelist file -> patch Buildconf/datm.buildnml.csh patch.diff - - - - - - -Because of bug 1361, this won't work out of the box. You'll need to add the change -to PTCLM.py given in the KnownBugs file on this issue. - - - - - - - - -A bit about the structure of &ptclm;, what it does, and how it works - -A large part of &ptclm; just sets up the different options and does error checking -on the options given. &ptclm; then uses the options provided to use -create_newcase to create a new case. It then queries both the -case directory and/or the XML database (using -queryDefaultNamelist.pl in models/lnd/clm/bld -and does other settings for the case. It then runs the different &clm; tools in turn to -create the necessary datasets and points to them in the case with the &CLMUSRDAT; option. -It runs mkgriddata, mksurfdata.pl, and -mkdatadomain as well as the aerdepregrid.ncl and -ndepregrid.ncl &ncl; scripts. mkgriddata and -mkdatadomain have template namelist files in the -scripts/ccsm_utils/Tools/lnd/clm/PTCLM/usr_files directory. -When running mksurfdata.pl if it finds a -$SITE_dynpftdata.txt in the -scripts/ccsm_utils/Tools/lnd/clm/PTCLM/PTCLM_sitedata directory -it will use that file for transient landuse changes (there's a sample file for -"US-Ha1" called US-Ha1_dynpftdata.txt). -It modifies the different env*.xml using -xmlchange and creates an initial &usernlclm; filename. After -&ptclm; is run you can then make changes to the case by hand, and configure, build -and run as normal. - - -There is a simple test script to test &ptclm;. See -for more information on using it. - - - - - diff --git a/doc/UsersGuide/single_point.xml b/doc/UsersGuide/single_point.xml deleted file mode 100644 index b07f76ecb6..0000000000 --- a/doc/UsersGuide/single_point.xml +++ /dev/null @@ -1,930 +0,0 @@ - - - -How to run Single-Point/Regional cases - -The &clm; also allows you to set up and run cases with a single-point or a local region as well -as global resolutions. This is often useful for running quick cases for testing, evaluating -specific vegetation types, or land-units, or running with observed data for a specific site. -There are four different ways to do this: &PTSMODE;, -&CLM1PT;, &CLMUSRDAT;, and with &ptclm;. - -&PTSMODE; -- to run for a single point -using global datasets. -&CLM1PT; -- to run for a supported single-point -or regional dataset. -&CLMUSRDAT; -- to run using your own datasets (single-point -or regional). -&ptclm; -- to easily setup simulations to run for -tower sites.. - - - - -&PTSMODE; and &ptclm; only work for a single point, while the other two options can -also work for regional datasets as well. - - - -Which Single Point Option Should I choose? - -In general is the quick and dirty method -that gets you started without having to create datasets -- but has limitations. It's -good for an initial attempt at seeing results for a point of interest, but since you -can NOT restart with it, it's usage is limited. It is the quickest method as you can -create a case for it directly from create_newcase. Although you -can't restart, running a single point is very fast, and you can run for long -simulation times even without restarts. If you need restarts a good solution is to use -getregional_datasets.pl and &CLMUSRDAT; -which can get you running almost as quickly as well as -&PTSMODE;. Like -&PTSMODE; - only runs for points that exist within -a global dataset. - - -Running &CLM1PT; is a great solution, if one of the supported -single-point/regional datasets, is your region of interest (see -). All the datasets are -created for you, and you can easily select one and run, pretty much, out of the box -with it. The problem is that there is a very limited set of supported datasets. You -can also use this method for your own datasets, but you have to create the datasets, -and add them to the XML database and to the &datm;. This is worthwhile if you want to -repeat many multiple cases for a given point or region. - - -Next, &CLMUSRDAT; is the best way to setup cases quickly -where you have to create your own datasets (see -). With this method you don't have to -change &datm; or add files to the XML database -- but you have to follow a strict -naming convention for files. However, once the files are named and in the proper -location, you can easily setup new cases that use these datasets. This is good -for treating all the required datasets as a "group" and for a particular -model version. For advanced &clm; developers who need to track dataset changes with -different model versions you would be best off adding these datasets as supported -datasets with the &CLM1PT; method. - - -Lastly &ptclm; is a great way to easily create datasets, -setup simulations and run simulations for tower sites. It takes advantage of both -&CLM1PT; and &CLMUSRDAT; internally. A big advantage to it, is that it's one-stop -shopping, it runs tools to create datasets, and runs create_newcase -and sets the appropriate env variables for you. So you only have to learn how to run -one tool, rather than work with many different ones. &ptclm; is described in the next -chapter . - - -Finally, if you also have meteorology data that you want to force your &clm; simulations -with you'll need to setup cases as described in . -You'll need to create &clm; datasets either according to &CLM1PT; -or &CLMUSRDAT;, but you'll also need to modify &datm; to use -your forcing data. And you'll need to change your forcing data to be in a format that -&datm; can use. In the &ptclm; chapter the -section tells you how to use AmeriFlux data for atmospheric forcing. - - - - -Running &PTSMODE; configurations - -&PTSMODE; enables you to run the model using global datasets, but just picking a -single point from those datasets and operating on it. It can be a very quick way to do fast -simulations and get a quick turnaround. - - -To setup a &PTSMODE; simulation you use the "-pts_lat" and "-pts_lon" -arguments to create_newcase to give the latitude and longitude of the point you want to -simulate for (the code will pick the point on the global grid nearest to the point you -give. Here's an example to setup a simulation for the nearest point at 2-degree resolution -to Boulder Colorado. - -> cd scripts -> ./create_newcase -case testPTS_MODE -res f19_g16 -compset I -mach bluefire \ --pts_lat 40.0 -pts_lon -105 -> cd testPTS_MODE -# We make sure the model will start up cold rather than using initial conditions -> ./xmlchange -file env_conf.xml -id &CLMFORCECOLD; -val on -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup - -Then configure, build and run as normal. We make sure initial conditions are NOT used -since &PTSMODE; currently CAN NOT run with initial conditions. - - - -By default it sets up to run with -USE_MPISERIAL (in the env_build.xml file) turned on, -which allows you to run the model interactively. On some machines this mode is NOT -supported and you may need to change it to FALSE before you are able to build. - - - - -&PTSMODE; currently does NOT restart nor -is it able to startup from global initial condition files. See bugs "1017 and 1025" -in the KnownLimitations file. - - - - -You can change the point you are simulating for at run-time by changing the values of -PTS_LAT and PTS_LON in the env_run.xml file. - - - - -Note, that when running with &PTSMODE; the number of processors -is automatically set to one. When running a single grid point you can only use a single -processor. You might also want to set the "env_conf" variable: USE_MPISERIAL to -TRUE so that you can also run interactively without having to use -&mpi; to start up your job. - - - - -Warning about Running with a Single-Processor on a Batch Machine - -This problem always comes up when running for a single point, because you can only use -a single-processor, but may come up in other instances when you are running with -one processor. This applies to all the different ways of running in single-point mode. - - - -A warning for submitting single-point simulations to the batch que when only using -one processor. On many machines this will mean using up at least an entire node, and -being charged for all the CPU's on that node even if you aren't using them. For example, -on the &ncar; machine bluefire, there are 32 processors for each node -and the batch scripts are setup to have exclusive use of that node (and hence be charged -for all 32 processors). There are similar issues on other machines, below we show you -what to do when running on bluefire. - - -To change this on bluefire -- change the following: - -#BSUB -q regular -#BSUB -N -#BSUB -x - -to... - -#BSUB -q share -#BSUB -N - -so remove the "#BSUB -x" which gives you the entire node exclusively, and change to the -share que. One other machines you may have to do something similar, but the particulars -depend on the given machine, hence you will need to consult with the system -administrators for the given machine you are running on. - - - - -Another similar problem on many machines is that some batch ques have a minimum number -of nodes or processors that can be used. On these machine you may have to change the -queue (in some way similar to the above for bluefire) and possibly the time-limits of -the job, to get it to run in the batch que. - - - -Another way to get around this problem is to run the job interactively using -USE_MPISERIAL so that you don't submit the job to the batch que. -For single point mode you also may want to consider using a smaller workstation or -cluster, rather than a super-computer, because you can't take advantage of the -multi-processing power of the super-computer anyway. - - - - -Running Supported Single-point/Regional Datasets - -In addition to &PTSMODE; the &clm; supports running using single-point or -regional datasets that are customized to a particular region. In the section below we -tell the user how to create their own dataset, but we also support a small number of -single-point and regional datasets that are ready to setup and run in the CESM modeling -system. - - -To get the list of supported dataset resolutions see the method�given in the -section on use of &CLM1PT;, which results in the following: - -&res_list; - -The resolution names that have an underscore in them ("_") are all single-point or -regional resolutions. -To run with the supported single-point and regional datasets, you setup a simulation for the -"pt1_pt1" resolution and give the short-name for the file to use in the -env_conf.xml file. - - -To run for the Brazil test site -do the following: - -Example of running &clm; over a single-point test site in Brazil -with the default Qian atmosphere data forcing. - - -> cd scripts -> ./create_newcase -case testSPDATASET -res pt1_pt1 -compset I \ --mach bluefire -> cd testSPDATASET -# Configure to run for the test site -> set SITE=1x1_brazil -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-sitespf_pt $SITE" -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $SITE - - - - -Then configure, build and run normally. - - -Then to run for the urban Mexico City Mexico test site that also has atmosphere -forcing data, but to run it with the Qian forcing data, but over the period for -which it's own forcing data is provided do the following: - -Example of running &clm; over the single-point of Mexicocity Mexico -with the default Qian atmosphere data forcing. - - -> cd scripts -> ./create_newcase -case testSPDATASET -res pt1_pt1 -compset I \ --mach bluefire -> cd testSPDATASET -# Set a variable to the site you want to use (as it's used several times below) -> set SITE=1x1_mexicocityMEX -# Configure to run for the urban test site -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-sitespf_pt $SITE" -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $SITE -# Set &datm; prescribed aerosols to single-point dataset -# Will then use the dataset with just the point for this $SITE -> ./xmlchange -file env_conf.xml -id DATM_PRESAERO -val pt1_pt1 -# -# Set some of the settings that are particular to this site, by values contained -# in the XML database. For some sites, or for new sites this information won't be -# stored. And the queryDefaultNamelist.pl command will abort. -# -# Set &datm; start and end range (optional just to run over the same years that -# atmospheric forcing data is available for this site) -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_START -val \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_beg_year -justvalue` -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_END -val \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_end_year -justvalue` - - - - -Then configure, build and run normally. - - - -Just like &PTSMODE; above, By default it sets up to run with -USE_MPISERIAL (in the env_build.xml file) turned on, -which allows you to run the model interactively. On some machines this mode is NOT -supported and you may need to change it to FALSE before you are able to build. - - - - -See for a warning about running single-point jobs -on batch machines. - - - - -Note, that when running a pt1_pt1 resolution the number of processors -is automatically set to one. When running a single grid point you can only use a single -processor. You might also want to set the "env_conf" variable: USE_MPISERIAL to -TRUE so that you can also run interactively without having to use -mpi to start up your job. - - - -Running Supported Single-point Datasets that have their own Atmospheric Forcing - -Of the supported single-point datasets we have three that also have atmospheric forcing data -that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and -urbanc_alpha (test data for an Urban inter-comparison project). Mexico city and Vancouver -also have "#ifdef" in the source code for them to work with modified urban data -parameters that are particular to these locations. They can be turned on by using -the &CLMCONFIG; &envconf; variable to set the "-sitespf_pt" option in the &clm; -&configure;. To turn on the atmospheric forcing for these datasets, you set the -&envconf; DATM_MODE variable to "CLM1PT", and then the atmospheric -forcing datasets will be used for the point picked. - - -When running with datasets that have their own atmospheric forcing you need to be careful -to run over the period that data is available. If you have at least one year of forcing -it will cycle over the available data over and over again no matter how long of a simulation -you run. However, if you have less than a years worth of data (or if the start date doesn't -start at the beginning of the year, or the end date doesn't end at the end of the year) then -you won't be able to run over anything but the data extent. In this case you will need to -carefully set the RUN_STARTDATE, START_TOD and -STOP_N/STOP_OPTION variables for your case to run over the entire time extent -of your data. For the supported data points, these values are in the XML database -and you can use the queryDefaultNamelist.pl script to query the values -and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and -urbanc_alpha). - - -In the example below we will show how to do this for the Vancouver, Canada point. - - -Example of running &clm; over the single-point of Vancouver Canada with -supplied atmospheric forcing data for Vancouver. - - -> cd scripts -# Create a case at the single-point resolutions -> ./create_newcase -case testSPDATASETnAtmForcing -res pt1_pt1 -compset I \ --mach bluefire -> cd testSPDATASETnAtmForcing -# Set a variable to the site you want to use (as it's used several times below) -> set SITE=1x1_vancouverCAN -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-sitespf_pt $SITE" -# Now set the CLM single-point variable to the site name -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $SITE -# Set the aerosols to use the single-point dataset for 2000 conditions -# You could also use the default global dataset, but running would be a bit slower -> ./xmlchange -file env_conf.xml -id DATM_MODE -val CLM1PT -# Set the coupling frequency to once an hour -> ./xmlchange -file env_conf.xml -id ATM_NCPL -val 24 -# Set the standard namelist options for an urban test site -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val stdurbpt -# Set many of the settings that are particular to this site, by values contained -# in the XML database. For some sites, or for new sites this information won't be -# stored. And the queryDefaultNamelist.pl command will abort. -# -# Set the start date -> setenv RUN_STARTDATE \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var run_startdate -justvalue` -> setenv STARTDATE `echo $RUN_STARTDATE | sed s/-//g` -> @ START_YEAR = $STARTDATE / 10000 -> ./xmlchange -file env_conf.xml -id RUN_STARTDATE -val $RUN_STARTDATE -# Set the run length and start time of day -> ./xmlchange -file env_run.xml -id STOP_OPTION \ --val `../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist seq_timemgr_inparm -silent -var stop_option -justvalue` -> setenv STOP_N \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist seq_timemgr_inparm -silent -var stop_n -justvalue` -> ./xmlchange -file env_run.xml -id STOP_N -val $STOP_N -> ./xmlchange -file env_run.xml -id START_TOD \ --val `../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist seq_timemgr_inparm -silent -var start_tod -justvalue` -# Set &datm; start and end range... -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_START -val -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_beg_year -justvalue` -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_END -val -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_end_year -justvalue` -# Set the User namelist to set the output frequencies of the history files -# Setting the stdurbpt use-case option create three history file streams -# The frequencies and number of time-samples needs to be set -> cat << EOF > &usernlclm; -&clm_inparm - hist_mfilt = $STOP_N,$STOP_N,$STOP_N - hist_nhtfrq = -1,-1,-1 -/ -EOF -# Set align year to start year as defined above -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_ALIGN -val $START_YEAR -# Set &datm; prescribed aerosols to single-point dataset -# Will then use the dataset with just the point for this site -> ./xmlchange -file env_conf.xml -id DATM_PRESAERO -val pt1_pt1 -> ./configure -case - - - - -If you don't set the start-year and run-length carefully as shown above the -model will abort with a "dtlimit error" in the atmosphere model (see bug 1110 in -the KnownLimitations file for documentation on this). Since, the forcing data for -this site (and the MexicoCity site) is less than a year, the model won't be able to -run for a full year. The 1x1_urbanc_alpha site has data for more -than a full year, but neither year is complete hence, it has the same problem (see the -problem for this site above). - - - - -Just like &PTSMODE; above, By default it sets up to run with -USE_MPISERIAL (in the env_build.xml file) turned on, -which allows you to run the model interactively. On some machines this mode is NOT -supported and you may need to change it to FALSE before you are able to build. - - - - -See for a warning about running single-point jobs -on batch machines. - - - - -Note, that when running a pt1_pt1 resolution the number of processors -is automatically set to one. When running a single grid point you can only use a single -processor. You might also want to set the "env_conf" variable: USE_MPISERIAL to -TRUE so that you can also run interactively without having to use -mpi to start up your job. - - - - - - -Creating your own single-point/regional surface datasets - -The file: -Quickstart.userdatasets in the -models/lnd/clm/doc directory gives guidelines on how to create and run -with your own single-point or regional datasets. Below we reprint the above guide. - -&quickstart_userdata; - - - - -Using getregional_datasets.pl to get a complete suite of single-point/regional -surface datasets from global ones - -Use the regional extraction script to get regional datasets from the global ones -The getregional_datasets.pl script to extract out regional datasets of interest. -Note, the script works on all files other than the "finidat" file as it's a 1D vector file. -The script will extract out a block of gridpoints from all the input global datasets, -and create the full suite of input datasets to run over that block. The input datasets -will be named according to the input "id" you give them and the id can then be used -as input to &CLMUSRDAT; to create a case that uses it. See -the section on &clm; Script Configuration Items for -more information on setting &CLMUSRDAT; (in ). The list of files extracted by -their name used in the namelists are: -fatmgrid, fatmlndfrc, -fsurdat, flanduse_timeseries, -stream_fldfilename_ndep, and the &datm; files -domainfile, and faerdep. -For more information on these files see the Table on required files. - - -The alternatives to using this script are to use &PTSMODE;, -discussed earlier, to use &ptclm; discussed in the next chapter, or creating the files -individually using the different file creation tools (given in the -Tools Chapter). Creating -all the files individually takes quite a bit of effort and time. &PTSMODE; -has some limitations as discussed earlier, but also as it uses global files, is -a bit slower when running simulations than using files that just have the set -of points you want to run over. Another advantage is that once you've created the -files using this script you can customize them if you have data on this specific -location that you can replace with what's already in these files. - - -The script requires the use of both "Perl" and "NCL". See the NCL Script section in the Tools Chapter -on getting and using NCL and NCL scripts. The main script to use is a &perl; script -which will then in turn call the NCL script that actually creates the output files. -The ncl script gets it's settings from environment variables set by the perl script. -To get help with the script use "-help" as follows: - -> cd models/lnd/clm/tools/ncl_scripts -> ./getregional_datasets.pl -help - -The output of the above is: - -&getreg_datasets; - - - -The required options are: -id, --ne, and -se, for the output identifier -name to use in the filenames, latitude and longitude of the Northeast corner, and -latitude and longitude of the SouthEast corner (in degrees). Options that specify -which files will be used are: -mask, -res, --rcp, -sim_year, and -sim_yr_rng -for the land-mask to use, global resolution name, representative concentration pathway -for future scenarios, simulation year, and simulation year range. The location of the -input and output files will be determined by the option -mycsmdata -(can also be set by using the environment variable $CSMDATA). If -you are running on a machine like at &ncar; where you do NOT have write permission -to the CESM inputdata files, you should use the scripts/link_dirtree -script to create soft-links of the original files to a location that you can write -to. This way you can use both your new files you created as well as the original -files and use them from the same location. - - -The remaining options to the script are -debug, -and -verbose. -debug is used to show what -would happen if the script was run, without creating the actual files. --verbose adds extra log output while creating the files so you -can more easily see what the script is doing. - - -For example, Run the extraction for data from 52-73 North latitude, 190-220 longitude -that creates 13x12 gridcell region from the f19 (1.9x2.5) global resolution over Alaska. - -Example of running <command>getregional_datasets.pl</command> to get -datasets for a specific region over Alaska - -> cd scripts -# First make sure you have a inputdata location that you can write to -# You only need to do this step once, so you won't need to do this in the future -> setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data -> ./link_dirtree $CSMDATA $MYCSMDATA -> cd ../models/lnd/clm/tools/ncl_scripts -> ./getregional_datasets.pl -sw 52,190 -ne 73,220 -id 13x12pt_f19_alaskaUSA -mycsmdata $MYCSMDATA - - -Repeat this process if you need files for multiple sim_year, resolutions, land-masks, -and sim_year_range values. - - - -See for a warning about running single-point jobs -on batch machines. - - - - -See for notes about managing your data -when using link_dirtree. - - - -Now to run a simulation with the datasets created above, you create a single-point -case, and set &CLMUSRDAT; to the identifier used above. Note that in the example below -we set the number of processors to use to one (-pecount 1). For a single point, you -should only use a single processor, but for a regional grid, such as the example below -you could use up to the number of grid points (12x13=156 processors. - - -Example of using &CLMUSRDAT; to run a simulation using user datasets for a -specific region over Alaska - -> cd scripts -# Create the case and set it to only use one processor -> ./create_newcase -case my_userdataset_test -res pt1_pt1 -compset I1850 \ --mach bluefire -> cd my_userdataset_test/ -> ./xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA -> ./xmlchange -file env_conf.xml -id &CLMUSRDAT; -val 13x12pt_f19_alaskaUSA -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val '-mask gx1v6' -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val 13x12pt_f19_alaskaUSA -> ./configure -case - - - - - - - -Running with your own atmosphere forcing - -Here we want to run with our own customized datasets for &clm; as well as -running with our own supplied atmosphere forcing datasets. Thus we effectively -combine the information from with -. First we need to follow -the procedures in to come up with &clm; -datasets that are customized for our point or region in question. This includes -running link_dirtree to create a directory location where you -can add your own files to it. Next, set -DATM_MODE to "CLM1PT" and &CLM1PT; and &CLMUSRDAT; to the -id of the data you created. To see a list of what the filenames need to be -see the section on setting &CLMUSRDAT;. - - -Next we need to setup the atmosphere forcing data in &netcdf; format that can be -read by &datm;. There is a list of eight variables that are expected to be on the input -files with the names and units on the following table (in the table TDEW and SHUM -are optional fields that can be used in place of RH). In the table we also list -which of the fields are required and if not required what the code will do to -replace them. If the names of the fields are different or the list is changed -from the standard list of eight fields: FLDS, FSDS, PRECTmms, -PSRF, RH, TBOT, WIND, and ZBOT, the resulting streams file will need to be modified -to take this into account (see an example streams file for this in below). - -Atmosphere Forcing Fields - - - - Short-name - Description - Units - Required? - If NOT required how replaced - - - - - FLDSincident longwave -(FLDS)W/m2No -calculates based on Temperature, Pressure and Humidity - - - FSDSincident solar -(FSDS)W/m2Yes- - - - FSDSdifincident solar (FSDS) -diffuseW/m2Nobased on FSDS - - - FSDSdirincident solar (FSDS) -directW/m2Nobased on FSDS - - - PRECTmmsprecipitation -(PRECTmms)mm/sYes- - - - PSRFpressure at the lowest atm level -(PSRF)PaNoassumes standard-pressure - - - RHrelative humidity at the lowest atm level -(RH)%Nocan be replaced with SHUM or TDEW - - - SHUMspecific humidity at the lowest atm level -kg/kgOptional in place of RHcan be replaced with RH or TDEW - - - TBOTtemperature at the lowest atm level -(TBOT)K (or can be C)Yes- - - - TDEWdew point temperature -K (or can be C)Optional in place of RHcan be replaced with RH or SHUM - - - WINDwind at the lowest atm level -(WIND)m/sYes- - - - ZBOTobservational heightmNo -assumes 30 meters - - - -
    -All of the variables should be dimensioned: time, lat, lon, with time being the unlimited -dimension. The coordinate variable "time" is also required with CF-compliant units in -days, hours, minutes, or seconds. It can also have a calendar attribute that can -be "noleap" or "gregorian". Normally the files will be placed in the: -$MYCSMDATA/atm/datm7/CLM1PT_data/$MYUSRDAT directory with separate files per -month called YYYY-MM.nc where YYYY-MM corresponds to the four -digit year and two digit month with a dash in-between. You also need a domain file that -gives the coordinate information for the data that should be placed in: -$MYCSMDATA/atm/datm7/domain.lnd.$MYUSRDAT_USGS.nc. - -Example of setting up a case with your own atmosphere forcing - -> cd scripts -# First make sure you have a inputdata location that you can write to -# You only need to do this step once, so you won't need to do this in the future -> setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data -> ./link_dirtree $CSMDATA $MYCSMDATA -# Next create and move all your datasets into $MYCSMDATA with id $MYUSRDAT -# See above for naming conventions - -# Now create a single-point case -> ./create_newcase -case my_atmforc_test -res pt1_pt1 -compset I1850 \ --mach bluefire -> cd my_atmforc_test -# Set the data root to your inputdata directory, and set &CLM1PT; and &CLMUSRDAT; -# to the user id you created for your datasets above -> ./xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $MYUSRDAT -> ./xmlchange -file env_conf.xml -id &CLMUSRDAT; -val $MYUSRDAT -# Set the land-mask to USGS, so both clm and &datm; can find files -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val '-mask USGS' -# Then set DATM_MODE to single-point mode so &datm; will use your forcing datasets -# Put your forcing datasets into $MYCSMDATA/atm/datm7/CLM1PT_data/$MYUSRDAT -> ./xmlchange -file env_conf.xml -id DATM_MODE -val CLM1PT -> ./configure -case -# If the list of fields, or filenames, filepaths, or fieldnames are different -# you'll need to edit the &datm; namelist streams file to make it consistent -> $EDITOR Buildconf/datm.buildnml.csh - - -     - - -See for a warning about running single-point jobs -on batch machines. - - - - -See for notes about managing your data -when using link_dirtree. - - - - -Now, we'll show an example of what the &datm; streams file might look like for a case -with your own forcing data with 3-hourly forcing. In this example, we'll leave off the -fields: ZBOT, and FLDS so they'll be calculated as given in the - table above. We'll also include: -FSDSdif and FSDSdir which aren't required, and we'll use TDEW in place of RH. In this -example the datafiles are in &netcdf; format and contain the fields: TA, Tdew, WS, -PREC, Rg, Rgdir, Rgdif, and PRESS which are translated into the &datm; internal names -in this streams file. There is also a domain file that has the position information -for this location. The normal assumption for CLM1PT mode in the &datm; is that data is -hourly or half-hourly and as such is often enough that using the data on the nearest -time-stamp is reasonable and as such the data is in a single streams file (see - for more information on -the default settings for &datm; and how to change them. If the data is less often three to six hours -- see -below, where you will need to modify the time-interpolation method as well as the -time stamp offsets. In the example below we also have to divide the single -stream file into three files to manage the time-stamps and time interpolation -algorithm for the different types of data differently. - -Example of &datm; streams files with your own forcing for 3-hourly data - -Precipitation streams file -(clm1PT.1x1pt_lapazMEX.precip.stream.txt file) . - - -<streamstemplate> -<stream> - <dataSource> - CLMNCEP - </dataSource> - <domainInfo> - <variableNames> - time time - xc lon - yc lat - area area - mask mask - </variableNames> - <filePath> - $DIN_LOC_ROOT/atm/datm7/domain.clm - </filePath> - <fileNames> - domain.lnd.1x1pt_lapazMEX_navy.nc - </fileNames> - </domainInfo> - <fieldInfo> - <variableNames> - PRECTmms PREC - </variableNames> - <offset> - -5400 - </offset> - <filePath> - $DIN_LOC_ROOT/atm/datm7/CLM1PT_data/1x1pt_lapazMEX - </filePath> - <fileNames> - 2004-01.nc - 2004-02.nc - 2004-03.nc -. -. -. - 2009-12.nc - </fileNames> - </fieldInfo> -</stream> -</streamstemplate> - - -Solar streams file (clm1PT.1x1pt_lapazMEX.solar.stream.txt file). - - -<streamstemplate> -<stream> - <dataSource> - CLMNCEP - </dataSource> - <domainInfo> - <variableNames> - time time - xc lon - yc lat - area area - mask mask - </variableNames> - <filePath> - $DIN_LOC_ROOT/atm/datm7/domain.clm - </filePath> - <fileNames> - domain.lnd.1x1pt_lapazMEX_navy.nc - </fileNames> - </domainInfo> - <fieldInfo> - <variableNames> - FSDS Rg - FSDSdir Rgdir - FSDSdif Rgdif - </variableNames> - <offset> - -10800 - </offset> - <filePath> - $DIN_LOC_ROOT/atm/datm7/CLM1PT_data/1x1pt_lapazMEX - </filePath> - <fileNames> - 2004-01.nc - 2004-02.nc - 2004-03.nc -. -. -. - 2009-12.nc - </fileNames> - </fieldInfo> -</stream> -</streamstemplate> - - -Other fields streams file. -(clm1PT.1x1pt_lapazMEX.other.stream.txt file) . - - -<streamstemplate> -<stream> - <dataSource> - CLMNCEP - </dataSource> - <domainInfo> - <variableNames> - time time - xc lon - yc lat - area area - mask mask - </variableNames> - <filePath> - $DIN_LOC_ROOT/atm/datm7/domain.clm - </filePath> - <fileNames> - domain.lnd.1x1pt_lapazMEX_navy.nc - </fileNames> - </domainInfo> - <fieldInfo> - <variableNames> - TBOT TA - TDEW Tdew - WIND WS - PSRF PRESS - </variableNames> - <offset> - -5400 - </offset> - <filePath> - $DIN_LOC_ROOT/atm/datm7/CLM1PT_data/1x1pt_lapazMEX - </filePath> - <fileNames> - 2004-01.nc - 2004-02.nc - 2004-03.nc -. -. -. - 2009-12.nc - </fileNames> - </fieldInfo> -</stream> -</streamstemplate> - - -Example streams namelist for the above streams files: - - - &shr_strdata_nml - dataMode = 'CLMNCEP' - domainFile = '$DOMAINFILE' - streams = 'clm1PT.1x1pt_lapazMEX.solar.stream.txt 1 2004 2009 ', - 'clm1PT.1x1pt_lapazMEX.precip.stream.txt 1 2004 2009 ', - 'clm1PT.1x1pt_lapazMEX.other.stream.txt 1 2004 2009 ', - 'presaero.stream.txt 1 2000 2000' - vectors = 'null','null','null','null' - mapmask = 'nomask','nomask','nomask','nomask' - mapalgo = 'nn','nn','nn','nn' - tintalgo = 'coszen','nearest','linear','linear' - taxmode = 'cycle','cycle','cycle','cycle' - / - - - - - -The example above shows the resolved namelist and streams file after &configure; -has been run. In order to save this configuration for future use, you would need -to edit the &datm; template adding new DATM_MODE see - for more information on how to do this. - - - - -We've outlined and given a few examples of using your own atmosphere -forcing. In the next chapter we go into the details of using &ptclm;. - - -     - -     - diff --git a/doc/UsersGuide/special_cases.xml b/doc/UsersGuide/special_cases.xml deleted file mode 100644 index ac5c7fef3b..0000000000 --- a/doc/UsersGuide/special_cases.xml +++ /dev/null @@ -1,916 +0,0 @@ - - -How to run some special cases - -In this chapter we describe how to run some special cases that take more than one step -to do. The straightforward cases have compsets and/or build-namelist use-cases setup for -them or require simple editing of a single-case. All of the cases here require you -to do at least two simulations with different configurations, or require more complex -editing of the case (changing the streams files). - - -The nine cases we will describe are: - - - -Running with the prognostic crop model on - - - - -Running with the irrigation model on - - - - -Spinning up the Satellite Phenology Model (&clmsp; spinup) - - - - -Spinning up the biogeochemistry Carbon-Nitrogen Model (CN spinup) - - - - -Spinning up the Carbon-Nitrogen Dynamic Global Vegetation Model (CNDV spinup) - - - - -Running with MOAR data as atmospheric forcing to spinup the model - - - - -Running with your own previous simulation as atmospheric forcing to spinup the model - - - - -Doing perturbation error growth tests - - - - -Running stand-alone &clm; with transient historical &CO2; -concentration - - - - - - -The cases in this chapter are more sophisticated and require more technical knowledge -and skill than cases in previous chapters. The user should be very familiar with doing -simple cases before moving onto the cases described here. - - - -Running with the prognostic crop model on - - -In &clmcesm103; a prognostic crop model was added to &clm4;. The prognostic crop -model is setup to work with CN for present day conditions and we have surface -and initial condition datasets at f19 resolution. In order to use the initial condition -file, we need to set the RUN_TYPE to startup rather -than hybrid since the compset for f19 sets up to use an initial -condition file without crop active. To activate the crop model we simply add "-crop on" -to &CLMCONFIG;. - -Example Crop Simulation - -> cd scripts -> ./create_newcase -case CROP -res f19_g16 -compset ICN -mach bluefire -> cd CROP -# Append "-crop on" to &CLMCONFIG; in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-crop on" -append -# Change to startup type so uses spunup initial conditions file for crop if it exists -# By default the model will do a hybrid startup with an initial condition file -# incompatible with the crop surface dataset. -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -> ./configure -case -# Now build and run normally -> ./CROP.bluefire.build -> ./CROP.bluefire.submit - - - - - - -Running with the irrigation model on - - -In &clmcesm103; an irrigation model for generic crop was added to &clm4;. Currently, -irrigation and crop can NOT be used together see bug number 1326 in the -&KnownBugs; file. -The irrigation model is tuned to work only with &clmsp; see the caution below for -for more information on this. To turn on -irrigation we simply add "-irrig on" to &CLMBLDNML;. Just as in the crop example we -also change RUN_TYPE to startup so that we don't use -an initial condition file that is incompatible with irrigation. - -Example Irrigation Simulation - -> cd scripts -# Note here we do a &clmsp; simulation as that is what has been validated -> ./create_newcase -case IRRIG -res f19_g16 -compset I -mach bluefire -> cd IRRIG -# Append "-irrig on" to &CLMBLDNML; in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val "-irrig" -append -# Change to startup type so uses spunup initial conditions file for irrigation if it exists -# By default the model will do a hybrid startup with an initial condition file -# incompatible with the irrigation surface dataset. -> xmlchange -file env_conf.xml -id RUN_TYPE -val startup -> ./configure -case -# Now build and run normally -> ./IRRIG.bluefire.build -> ./IRRIG.bluefire.submit - - - - -We have only run the irrigation model with &clmsp; (i.e. without the CN model). We -recommend that if you want to run the irrigation model with CN, that you do a spinup -as outlined in the examples below. But, more than that you may need to make -the adjustments we discuss in . - - - - - - -Spinning up the Satellite Phenology Model (&clmsp; spinup) - - -To spin-up the &clmsp; model you merely need to run &clmsp; for 50 simulation -years starting from arbitrary initial conditions. You then use the final -restart file for initial conditions in other simulations. -Because, this is a straight forward operation we will NOT give -the details on how to do that here, but leave it as an exercise for the reader. -See the as an example of doing this -as the last step for &clmcn;. - - - - -Spinning up the biogeochemistry Carbon-Nitrogen Model (CN spinup) - -To get the &clmcn; model to a steady state, you first run it from arbitrary initial conditions -using the "accelerated decomposition spinup" (-ad_spinup in configure) mode for 600 simulation years. After -this you branch from this mode in the "exit spinup" (-exit_spinup in configure), run -for a simulation year, and then save a restart from that and use it as initial conditions -for further spinup of CN (at least 50 simulation years). - - -Spinup of &clmcn; - -AD_SPINUP - -For the first step of running 600 years in "-ad_spinup" mode, you will setup -a case, and then edit the values in env_conf.xml and -env_run.xml so that the right configuration is turned on and -the simulation is setup to run for the required length of simulation time. -So do the following: - -Example AD_SPINUP Simulation - -> cd scripts -> ./create_newcase -case CN_spinup -res f19_g16 -compset ICN -mach bluefire -> cd CN_spinup -# Append "-ad_spinup on" to &CLMCONFIG; in env_conf.xml -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-ad_spinup on" -append -# The following sets &CLMFORCECOLD; to "on" in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMFORCECOLD; -val on -# Make the output history files only annual, by adding the following to the &usernlclm; namelist -> echo '&clm_inparm hist_nhtfrq = -8760 /' > &usernlclm; -# Now configure -> ./configure -case -> ./xmlchange -file env_run.xml -id STOP_DATE -val 6010101 -# Now build -> ./CN_spinup.bluefire.build -# The following sets RESUBMIT to 30 times in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 30 -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -# The following sets STOP_N to 20 years in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_N -val 20 -# The following sets STOP_DATE to Jan/1 of year 601 in env_run.xml (you could also use an editor) -# Now run normally -> ./CN_spinup.bluefire.submit - - -Afterwards save the last restart file from this simulation to use in the next step. - - - - -EXIT_SPINIP - - -Example EXIT_SPINUP Simulation - -> cd scripts -> ./create_newcase -case CN_exitspinup -res f19_g16 -compset ICN -mach bluefire -> cd CN_exitspinup -# Append "-exit_spinup on" to &CLMCONFIG; in env_conf.xml -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-exit_spinup on" -append -# Change run type to branch and branch from the last year of the last simulation -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val branch -> ./xmlchange -file env_conf.xml -id RUN_REFCASE -val CN_spinup -> ./xmlchange -file env_conf.xml -id RUN_REFDATE -val 0601-01-01 -> ./xmlchange -file env_conf.xml -id GET_REFCASE -val FALSE -> ./configure -case -# Go ahead and build, so that the run directory is created -> ./CN_exitspinup.bluefire.build -# Now, Copy the last restart files from the earlier case into your run directory -> cp /ptmp/$LOGIN/archive/CN_spinup/rest/CN_spinup.*.r*.0601-01-01-00000* /ptmp/$LOGIN/CN_exitspinup -# And copy the rpointer files for datm and drv from the earlier case -> cp /ptmp/$LOGIN/archive/CN_spinup/rest/rpointer.atm /ptmp/$LOGIN/CN_exitspinup -> cp /ptmp/$LOGIN/archive/CN_spinup/rest/rpointer.drv /ptmp/$LOGIN/CN_exitspinup -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -> ./xmlchange -file env_run.xml -id STOP_N -val 1 -# Now run normally -> ./CN_exitspinup.bluefire.submit - - - - - - -Final spinup - -Next save the last restart file from this step and use it as the "finidat" file to -use for one more spinup for at least 50 years in normal mode. -So do the following: - -Example Final CN Spinup Simulation - -> cd scripts -> ./create_newcase -case CN_finalspinup -res f19_g16 -compset ICN -mach bluefire -> cd CN_finalspinup -# The following sets &CLMFORCECOLD; to "on" in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMFORCECOLD; -val on -# Now, Copy the last &clm; restart file from the earlier case into your run directory -> cp /ptmp/$LOGIN/archive/CN_exitspinup/rest/CN_exitspinup.clm*.r*.0602-01-01-00000.nc \ -/ptmp/$LOGIN/CN_finalspinup -# And copy the rpointer files for datm and drv from the earlier case -> cp /ptmp/$LOGIN/archive/CN_exitspinup/rest/rpointer.atm /ptmp/$LOGIN/CN_finalspinup -> cp /ptmp/$LOGIN/archive/CN_exitspinup/rest/rpointer.drv /ptmp/$LOGIN/CN_finalspinup -# Set the finidat file to the last restart file saved in previous step -> echo '&clm_inparm finidat = "CN_exitspinup.clm2.r.0602-01-01-00000.nc" /' > &usernlclm; -# Now configure -> ./configure -case -> $EDITOR Buildconf/clm.buildnml.csh -> Now build -> .CN_finalspinup.bluefire.build -# The following sets RESUBMIT to 5 times in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 5 -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -# The following sets STOP_N to 10 years in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_N -val 10 -> Now run as normal -> .CN_finalspinup.bluefire.submit - - - - -To assess if the model is spunup plot trends of CN variables of interest. If you see -a trend, you may need to run the simulation longer. -Finally save the restart file from the end of this simulation to use as an "finidat" file for future -simulations. - - - - - - -Spinning up the Carbon-Nitrogen Dynamic Global Vegetation Model (CNDV spinup) - -To spinup the &clm; CNDV model -- you first follow the procedures above to spinup the CN model. -Then you take the CN initial state file you created for the spinup with just CN, and -run CNDV for 200 more years. -We've provided such spunup files for two resolutions (f09 and f19) and two time-periods -(1850 and 2000), so in this example we will use the files provided to start from. -We've also provided a spinup file at f19 resolution for CNDV, hence the following is -NOT required when running at f19. -If you were to start from your own &clmcn; spunup files -- the procedure would require -some modification. -There are no compsets using CNDV, so in -env_conf.xml change CLM_CONFIG_OPTS to --bgc cndv. - -Example CNDV Spinup Simulation - -> cd scripts -> ./create_newcase -case CNDV_spinup -res f09_g16 -compset ICN -mach bluefire -> cd CNDV_spinup -# Set run type to startup and do a cold start -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -# The following sets CLM_CONFIG_OPTS to "-bgc cndv" in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val "-bgc cndv" -# Make the default primary history file annual and add an annual 1D vector auxiliary file -# By putting the following in a &usernlclm; file. -> cat << EOF > &usernlclm; -&clm_inparm - hist_nhtfrq = -8760, -8760 - hist_mfilt = 1, 1 - hist_fincl2 = 'TLAI', 'TSAI', 'HTOP', 'HBOT', 'NPP' - hist_dov2xy = .true., .false. -/ -> ./configure -case -# NOTE: If you were using your own CN spinup files you would edit the namelist to use it -# $EDITOR Buildconf/clm.buildnml.csh -# -# Now build and run as normal -> ./CNDV_spinup.bluefire.build -# The following sets RESUBMIT to 10 times in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 10 -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -# The following sets STOP_N to 20 years in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_N -val 20 -# Make sure you turn archiving on, so you save your files to long term archival -> ./xmlchange -file env_run.xml -id DOUT_L_MS -val TRUE -> ./CNDV_spinup.bluefire.submit - - - - - -There is a build bug with &clmcesm103; see bug 1370 in the &KnownBugs; on -how to address this. - - - - - -In a data analysis tool you should examine the auxiliary file and examine the -pfts1d_wtgcell to see where and what types of vegetation have -been established. See the caution in for more -information on visualizing and analyzing 1D vector fields. - - - -CNDV also writes out two vector fields to "hv" auxiliary files, on an annual basis by -default. - - - - -We've provided a spinup file for CNDV at f19 resolution, you could also use -interpinic to interpolate this file to other resolutions. - - - - - -Running with MOAR data as atmospheric forcing to spinup the model - -Because it takes so long to spinup the CN model (as we just saw previously), if you -are doing fully coupled simulations with active atmosphere and ocean, you will want -to do the spinup portion of this "offline". So instead of doing expensive fully -coupled simulations for the spinup duration, you run &clm; in a very cheap "I" -compset using atmospheric forcing from a shorter fully coupled simulation -(or a simulation run previously by someone else). - - -In this example we will use the I1850SPINUPCN compset to setup -&clm; to run with atmospheric forcing from a previous fully coupled simulation with -data that is already stored on disk on bluefire. There are several simulations that -have high frequency data for which we can do this. You can also do this on a machine -other than bluefire, but would need to download the data from the Earth System Grid and -change the datapath similar to . -This compset is designed for constant -1850 conditions, but unfortunately (because of bug 1354 see the &KnownBugs; file) by -default it points to a transient simulation instead of an 1850 simulation. Here we -point to an 1850 simulation and setup the forcing years to run over. - -Example Simulation with MOAR Data on bluefire - -> cd scripts -> ./create_newcase -case MOARforce1850 -res f19_g16 -compset I1850SPINUPCN -mach bluefire -> cd MOARforce1850 -# The following sets the casename to point to for atm forcing (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_CASE -val b40.1850.track1.1deg.006a -# The following sets the align year and years to run over for atm forcing -# (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_ALIGN -val 1 -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_START -val 960 -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_END -val 1030 -> ./configure -case -# Now build and run as normal -> ./MOARforce1850.bluefire.build -> ./MOARforce1850.bluefire.submit - - - - -Because of bug 1339 (see the &KnownBugs; file on this) -you can't run with 83 or more years of forcing. If you do need to run with more years of -forcing, you'll need to address the issue as outlined in the &KnownBugs; file. - - - - - - -Running with your own previous simulation as atmospheric forcing to spinup the model - -Another way that you might want to spinup the model is to run your own simulation -for a relatively short period (either a B, E, or F compset) and then use it as forcing -for your "I" case later. By only running 20 to 50 years for the fully coupled case, -you'll save a substantial amount of computer time rather than running the entire spinup -period with a fully coupled model. - - -The first thing we need to do is to run a fully coupled case and save the atmospheric -coupling fields on a three hourly basis. In this example, we will run on bluefire -and archive the data to a local disk that we can then use in the next simulation. - -Example Fully Coupled Simulation to Create Data to Force Next Example Simulation - -> cd scripts -> ./create_newcase -case myBCN1850 -res f09_g16 -compset B1850CN -mach bluefire -> cd myBCN1850 -> ./configure -case -# Set histaux_a2x3hr to .true. in cpl.buildnml.csh so output from the atmosphere model -# will be saved 3 hourly -$EDITOR BuildConf/cpl.buildnml.csh -# Now build -> ./myBCN1850.bluefire.build -# The following sets the archival disk space (you could also use an editor) -> ./xmlchange -file env_run.xml -id DOUT_S_ROOT -val '/glade/home/$USER/$CASE' -# Make sure files are archived to disk, but NOT to long term storage -# (you could also use an editor) -> ./xmlchange -file env_run.xml -id DOUT_S -val TRUE -> ./xmlchange -file env_run.xml -id DOUT_L_MS -val FALSE -# Set the run length to run a total of 20 years (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 9 -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -> ./xmlchange -file env_run.xml -id STOP_N -val 2 -# Now run as normal -> ./myBCN1850.bluefire.submit - - - - -Now we run an I compset forced with the data from the previous simulation using -the &CPLHIST; option to DATM_MODE. See - for more information on the -&datm; settings for &CPLHIST; mode. - -Example Simulation Forced with Data from the Previous Simulation - -> cd scripts -> ./create_newcase -case frcwmyBCN1850 -res f09_g16 -compset I1850SPINUPCN -mach bluefire -> cd frcWmyBCN1850 -# The following sets the casename to point to for atm forcing (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_CASE -val "myBCN1850" -# The following sets the align year and years to run over for atm forcing -# (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_ALIGN -val "1" -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_START -val "1" -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_END -val "20" -# Set the datapath in the template to the archival path from the case above -> sed -E 's#set datapath = ".+"#set datapath = "/glade/home/$USER/%c/cpl/hist"#' \ - Tools/Templates/datm.cpl7.template > new.datm.cpl7.template -> mv -f new.datm.cpl7.template Tools/Templates/datm.cpl7.template -> chmod +x Tools/Templates/datm.cpl7.template -> ./configure -case -# Now build and run as normal -> ./frcwmyBCN1850.bluefire.build -> ./frcwmyBCN1850.bluefire.submit - - - - -In order to accomplish this we needed to edit the &datm; template file. See - for more information on doing this. -If your input case was at a resolution besides f09 you would have to edit -the &datm; template file even further to use a domain file at the input resolution. - - - - - - -Doing perturbation error growth tests - -Doing perturbation error growth tests is a way to validate a port of -the model to a new machine or to verify that changes are only roundoff. -The steps are the same in either case, but in the discussion below I will -assume you are doing a port validation to a new machine (but in parentheses -I will put a reminder that it could also be for code-mods). -The basic idea is to run a case on the trusted machine (trusted code) and -another with initial conditions perturbed by roundoff and compare the results of -the two. The difference between these two simulations (the error) will grow over time -and describe a curve that we compare with the error growth on the new machine (code -changes). The error growth on the new machine is the difference between the non-perturbed -state on the trusted machine and the non-perturbed state on the new machine (code -changes). If the new machine (code changes) are well-behaved -the plot of this error growth compared to the error growth curve on the trusted machine -should be similar. If the -changes are NOT well-behaved the changes from the new machine (code changes) will be -larger than the perturbation changes. In summary the simulations and steps that need to be performed are: - - -Run a simulation with the trusted code on the trusted machine. -(optionally you can use a dataset from inputdata repository). - - - -Run a simulation with the trusted code on the trusted machine with initial conditions -perturbed by roundoff (using a namelist item to do so). -(this is optional is you are using inputdata repository datasets) - - - -Run a simulation with the new code on the non-trusted machine (code changes). - - -Do a plot of the RMS difference of history variables between simulation 1 and simulation 2. - - -Do a plot of the RMS difference of history variables between simulation 1 and simulation 3. - - -Compare the two plots in steps 4 and 5. - - -If the plots compare well the new machine (code changes) is running as well as the trusted machine. - - -If the plots do NOTcompare well the new machine is -NOTrunning as well as the trusted machine. Typically the -recommendation here is to lower the optimization level on the new machine and try -again (or in the case of code changes, modify or simplify the code changes to get -something that should be closer). - -The history variables we have used to do this is either 'TSOI', and/or 'TSA'. 'TSOI' are -the 3D snow and soil temperatures for vegetated land-units. If there is a change in -soil physics it should show up in this field (and it should show up even for something -that is at a pretty deep soil depth). However, as 'TSOI' is only for vegetated -land-units, changes in lake or urban land-units -- will NOT show up. 'TSA' by contrast is -the 2m surface temperature across all land-units, so changes in urban or lake land-units -will show up. However, changes in deep soil physics will only show up as it propagates -to the surface. So one field may show something that the other doesn't. In the examples, -we use 'TSOI', but 'TSA' can be used as well. And in most cases you should check both. - - - -Now we will give a detailed description of the procedure with examples and the -exact steps to perform. - - -Using Perturbation Error Growth Analysis to Verify a Port to a New Machine - -Running non-perturbed on trusted machine - -The first step is to run a non-perturbed case on the trusted machine. You need to run -all of the steps with the same compset and same resolution. For these examples we will -use 2-degree resolution with the ICN compset for 2000 conditions. You need to run for -three days with a cold-start. - - - -As we describe below, This is optional if you will be using datasets from the -inputdata repository to take place of this step. - - - - -Example non-perturbed error growth simulation - -> cd scripts -> ./create_newcase -case trustedMachinePergro0 -compset ICN -res f19_g16 \ --mach bluefire -> cd trustedMachinePergro0 -# Set the non-perturbed PERGRO use-case -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val pergro0_pd -# Set coldstart on so arbitrary initial conditions will be used -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -# Set PERGRO on in the configure -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-pergro on" -append -# Now configure and build -> ./configure -case -> ./trustedMachinePergro0.bluefire.build -# Set it to run for three days and turn archiving off -> ./xmlchange -file env_run.xml -id STOP_N -val 3 -> ./xmlchange -file env_run.xml -id DOUT_S -val FALSE -# Run the case and then you will save the history file output for later use -> ./trustedMachinePergro0.bluefire.submit - - - - - -If you aren't able to do this step, as you don't have access to a trusted machine, you -can use datasets that are available from the svn inputdata repository to take place of -running it yourself. The disadvantage is that this is only done for certain model -versions and for exactly the configuration/namelist given here. You won't be able to -test it for your own custom code or configurations. - - - - -Running perturbed on the trusted machine - -The next step is to run a perturbed case on the trusted machine. - -Example perturbed error growth simulation - -> cd scripts -> ./create_newcase -case trustedMachinePergroRnd -compset ICN -res f19_g16 \ --mach bluefire -> cd trustedMachinePergroRnd -# Set the perturbed PERGRO use-case -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val pergro_pd -# Set coldstart on so arbitrary initial conditions will be used -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -# Set PERGRO on in the configure -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-pergro on" -append -# Now configure and build -> ./configure -case -> ./trustedMachinePergroRnd.bluefire.build -# Set it to run for three days and turn archiving off -> ./xmlchange -file env_run.xml -id STOP_N -val 3 -> ./xmlchange -file env_run.xml -id DOUT_S -val FALSE -# Run the case and then you will save the history file output for later use -> ./trustedMachinePergroRnd.bluefire.submit - - - - - -If you aren't able to do this step, as you don't have access to a trusted machine, you -can use datasets that are available from the svn inputdata repository to take place of -running it yourself. The disadvantage is that this is only done for certain model -versions and for exactly the configuration/namelist given here. You won't be able to -test it for your own custom code or configurations. - - - - -Running non-perturbed on the new machine - -The next step is to run a non-perturbed case on the new machine. Here -we will demonstrate using the machine intrepid. For the previous two steps -you have the option of using datasets provided in the subversion inputdata -repository to take their place -- however this step is required. - -> cd scripts -> ./create_newcase -case newMachinePergro0 -compset ICN -res f19_g16 \ --mach intrepid -> cd newMachinePergro0 -# Set the non-perturbed PERGRO use-case -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val pergro0_pd -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -# Set PERGRO on in the configure -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-pergro on" -append -# Now configure and build -> ./configure -case -> ./newMachinePergro0.intrepid.build -# Set it to run for three days and turn archiving off -> ./xmlchange -file env_run.xml -id STOP_N -val 3 -> ./xmlchange -file env_run.xml -id DOUT_S -val FALSE -# Run the case and then you will save the history file output for later use -> ./newMachinePergro0.intrepid.submit - - - - - -Plotting the differences - -You can use the cprnc program to compute root mean square differences -between the relevant history files. See for more information -on it and how to build it. On many platforms you will need to set some environment -variables in order to complete the build (see for -more information on building the tools). - -# Build the cprnc program -> cd models/lnd/clm/tools/cprnc -> gmake -# Now go to your case directory and run cprnc on the trusted-machine with and without -# perturbation -> cd ../../../../../scripts/trustedMachinePergro0 -> ../../models/lnd/clm/tools/cprnc/cprnc trustedMachinePergro0.clm2.h0.001-01-01.00000.nc \ -../trustedMachinePergroRnd/trustedMachinePergroRnd.clm2.h0.001-01-01.00000.nc > trustedPergro.log -# Copy the history file from the new machine to here -# -# And now run cprnc on the trusted-machine and the new machine both without perturbation -> ../../models/lnd/clm/tools/cprnc/cprnc trustedMachinePergro0.clm2.h0.001-01-01.00000.nc \ -../newMachinePergro0/newMachinePergro0.clm2.h0.001-01-01.00000.nc > newPergro.log -# Now extract out the RMS differences of TSOI for both -# You may want to extract out the RMS differences for TSA as well -# Changes in urban or lake land-units won't be detected with TSOI -> grep "RMS TSOI" trustedPergro.log | awk '{print $3}' > RMStrusted.dat -> grep "RMS TSOI" newPergro.log | awk '{print $3}' > RMSnewmachine.dat -# And plot the two curves up to your screen -> env TYPE=x11 RMSDAT=RMSnewmachine.dat RMSDAT2=RMStrusted.dat ncl \ -../../models/lnd/clm/tools/ncl_scripts/pergroPlot.ncl - -Here is a sample plot for several trusted machines: bluefire, intrepid, jaguar, -and edinburgh (with both the lahey and intel compilers). -The green line is the error growth for bluefire, the red is the error growth -for intrepid, the dashed navy is for jaguar, the dashed maroon is for the intel -compiler on edinburgh, and the thick dashed goldenrod line is for edinburgh with the -lahey compiler. Note, the data for this plot is in -models/lnd/clm/tools/ncl_scripts the files are named: -according to the legend. Note, that the lines tend to cluster together and follow -quite closely to the bluefire line which is our main trusted machine. -
    -Sample Good Perturbation Error Growth Curves (within roundoff) - - - -
    -     - - -When you do NOT have access to a trusted machine you can use the trusted file from -bluefire that is available on the inputdata repository. - -# Build the cprnc program -> cd models/lnd/clm/tools/cprnc -> gmake -# Get the unperturbed file from the subversion repository -> cd ../../../../../scripts/newMachinePergro0 -> set dir = "lnd/clm2/pergrodata" -> set file = bluefirePergro0.ICN.0001-01-01_1.9x2.5_gx1v6_simyr2000_clm4-cesm1_0_3.c110617.nc -> echo "trustedfile = DIN_LOC_ROOT/$dir/$file" > clm.input_data_list -> ../ccsm_utils/Tools/check_input_data -datalistdir . -export -inputdata $DIN_LOC_ROOT -# And now run cprnc on the bluefire file and the new machine both without perturbation -> ../../models/lnd/clm/tools/cprnc/cprnc $file \ -../newMachinePergro0/newMachinePergro0.clm2.h0.001-01-01.00000.nc > newPergro.log -# Now extract out the RMS difference -# You may want to extract out the RMS differences for TSA as well -# Changes in urban or lake land-units won't be detected with TSOI -> grep "RMS TSOI" newPergro.log | awk '{print $3}' > RMSnewmachine.dat -# And plot the new curve versus the trusted curve up to your screen -> env TYPE=x11 RMSDAT=RMSnewmachine.dat \ -RMSDAT2=../../models/lnd/clm/tools/ncl_scripts/RMSbluefire.dat \ -../../models/lnd/clm/tools/ncl_scripts/pergroPlot.ncl - - - -In the figure below we now show example of curves for changes that are larger than -roundoff. Once again the green curve is the trusted error growth from bluefire. The -other curves are for changes that may be fairly small, but are larger than roundoff. The -goldenrod curve is for using the 1850, and the navy is for using the 1999 Nitrogen -deposition files rather than for year 2000. The red is for using the 1850 aerosol -dataset rather than 2000, and the maroon is for adding the snow combination bug in. The -differences in changes that are greater than roundoff is that the curves climb very -steeply to the 10-6 value and then level off, while the -curve for bluefire climbs much more slowly and gradually. The curves also don't mimic -each other in any way, like the trusted machine plots do. -
    -Sample Bad Perturbation Error Growth Curves (changes greater than roundoff) - - - -
    - -     -     -     -     - - -Running stand-alone &clm; with transient historical &CO2; -concentration - -In this case you want to run a simulation with stand-alone &clm; responding -to changes in &CO2; for a historical period. -For this example, we will start with the "I_1850-2000_CN" compset that -has transient: land-use, Nitrogen and Aerosol deposition already. You could -also use another compset if you didn't want these other features to be transient. -In order to get &CO2; to be transient we need to edit the -&datm; template so that we add an extra streams file to describe how -&CO2; varies over the historical period. You also need -a &netcdf; datafile that datm can read that gives the variation. You could -supply your own file, but we have a standard file that is used by CAM for this -and our example will make use of this file. - - - -Most everything here has to do with changing datm rather than &clm; -to allow this to happen. As such the user that wishes to do this should -first become more familiar with datm and read the -&cesm; Data -Model User's Guide especially as it pertains to the datm. Note, also -that in this example we show how to edit the datm "buildnml" file for your -case, but you could do something similar by editing the datm template. - - - - -This section documents the process for doing something that is non-standard. -There may be errors with the documentation and process, and you may have to do -some work before all of this works for you. If that is the case, we recommend -that you do further research into understanding the process and the files, as -well as understanding the datm and how it works. You may have to read documentation -found in the code for datm as well as "csm_share". - - - -The datm has "streams" files that have rough XML-like syntax and specify the -location and file to get data from, as well as information on the variable names -and the data locations of the grid points. The datm expects specific variable names -and the datm "maps" the expected variable names from the file to the names expected -by datm. The file we are working with here is a file with a single-point, that covers -the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 -degrees in longitude). Since it's a single point it's a little easier to work with -than datasets that may be at a given horizontal resolution. The datm also expects -that variables will be in certain units, and only expects a limited number of -variables so arbitrary fields can NOT be exchanged this way. However, the process -would be similar for datasets that do contain more than one point. - - -The three things that are needed: a domain file, a data file, and a streams text file. -The domain file is a CF-compliant &netcdf; file that has information -on the grid points (latitudes and longitudes for cell-centers and vertices, mask -, fraction, and areas). The datafile is a CF-compliant &netcdf; file with the data that -will be mapped. The streams text file is the XML-like file that tells datm how to find -the files and how to map the variables datm knows about to the variable names on the -&netcdf; files. Note, that in our case the domain file and the data file are the same -file. In other cases, the domain file may be separate from the data file. - - -First we are going to create a case, and we will edit -the Buildconf/datm.buildnml.csh so that we add a -&CO2; data stream in. There is a streams text file -available in models/lnd/clm/doc/UsersGuide/co2_streams.txt, -that includes file with a &CO2; time-series from 1765 to 2007. - -Example Transient Simulation with Historical &CO2; - -> cd scripts -> ./create_newcase -case DATM_CO2_TSERIES -res f19_g16 -compset I_1850-2000_CN \ --mach bluefire -> cd DATM_CO2_TSERIES -# Set CCSM_BGC to CO2A so that CO2 will be passed from atmosphere to land -> ./xmlchange -file env_conf.xml -id CCSM_BGC -val CO2A -# Set CLM_CO2_TYPE to diagnostic so that the land will use the value sent from the atmosphere -> ./xmlchange -file env_conf.xml -id CLM_CO2_TYPE -val diagnostic -> ./configure -case -> cd Buildconf -# Copy the sample streams file over -> cp ../../../models/lnd/clm/doc/UsersGuide/co2_streams.txt . - - -The first thing we will do is to edit the datm buildnml script to add -a CO2 file stream in. To do this we will apply a patch with the differences -needed. The patch file addco2_datm.buildnml.diff is -in models/lnd/clm/doc/UsersGuide and looks like this... - -&co2streams_diff; - -So to apply the patch you do this... - -> cd scripts/DATM_CO2_TSERIES/Buildconf -> patch < ../../../models/lnd/clm/doc/UsersGuide/addco2_datm.buildnml.diff - -Once, you've done that you can build and run your case normally. - - - -The patch assumes you are using a I_1850-2000_CN compset out of the box, with -DATM_PRESAERO equal to trans_1850-2000. So it assumes standard -Qian atmosphere forcing, and transient prescribed aerosols from streams files. If your case changes -anything here the patch will fail, and you will need to put the changes in by hand. - - - - - -If the patch fails, you will have to add the changes to the -datm.buildnml.csh found in the above -patch file by hand. Basically, it adds an extra streams file for &CO2; to the end of the streams variable, -and other arrays associated with streams (adding mapalgo as a new array with bilinear for everything, but -the &CO2; file which should be "nn" for nearest neighbor). - - - - - -The streams file above is hard-coded for the path of the file on &ncar; computers. To use it on an outside -machine you'll need to edit the filepath in the streams file to point to the location where you have the file. - - - - -After going through these steps, you will have a case where you have datm reading -in an extra streams text file that points to a data file with &CO2; -data on it that will send that data to the &clm;. - - -     - diff --git a/doc/UsersGuide/stylesheethtml2docbook.xsl b/doc/UsersGuide/stylesheethtml2docbook.xsl deleted file mode 100644 index 13c30ff71d..0000000000 --- a/doc/UsersGuide/stylesheethtml2docbook.xsl +++ /dev/null @@ -1,579 +0,0 @@ - - - - - -wb -file:///epicuser/AISolutions/graphics/AIWorkbench/ - - - - - - - - - - <xsl:value-of select=".//html:h1[1] - |.//html:h2[1] - |.//html:h3[1]"/> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inlinemediaobject - - mediaobject - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Matched -
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    -     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Attempting to count columns on a non-table element - - - Row parameter is not a valid row - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -     - diff --git a/doc/UsersGuide/tools.xml b/doc/UsersGuide/tools.xml deleted file mode 100644 index f5fd8beac4..0000000000 --- a/doc/UsersGuide/tools.xml +++ /dev/null @@ -1,1396 +0,0 @@ - - -Using the &clm; tools to create your own input datasets - -There are several tools provided with &clm; that allow you to create your own input -datasets at resolutions you choose, or to interpolate initial conditions to a different -resolution, or used to compare &clm; history files between different cases. The tools are -all available in the models/lnd/clm/tools directory. Most of the tools -are &FORTRAN; stand-alone programs in their own directory, but there is also a suite of -&ncl; -scripts in the ncl_scripts directory. Some of the &ncl; scripts are -very specialized and not meant for general use, and we won't document them here. They -still contain documentation in the script itself and the README file in the tools -directory. But, the list of generally important scripts and programs are: - - - cprnc to compare &netcdf; files with a time axis. - - - interpinic to interpolate initial condition files. - - - mkgriddata to create grid datasets. - - - mkdatadomain to create domain files from grid datasets -used by &datm; or docn. - - - mksurfdata to create surface datasets from grid datasets. - - - ncl_scripts/getregional_datasets.pl script to extract a -region or a single-point from global input datasets. See the single-point chapter -for more information on this. - - - ncl_scripts/npdepregrid.ncl interpolate the Nitrogen -deposition datasets to a new resolution. - - - ncl_scripts/aerdepregrid.ncl interpolate the Aerosol -deposition datasets to a new resolution. - - - - - -In the sections to come we will go into detailed description of how to use each of -these tools in turn. First, however we will discuss the common environment variables -and options that are used by all of the &FORTRAN; tools. Second, we go over the outline -of the entire file creation process for all input files needed by &clm; for a new -resolution, then we turn to each tool. In the last section we will -discuss how to customize files for particular observational sites. - - - -Common environment variables and options used in building the &FORTRAN; -tools - -The &FORTRAN; tools all have similar makefiles, and similar options for building. -All of the Makefiles use GNU Make extensions and thus require that you use GNU make -to use them. They also auto detect the type of platform you are on, using "uname -s" -and set the compiler, compiler flags and such accordingly. There are also environment -variables that can be set to set things that must be customized. All the tools use -&netcdf; and hence require the path to the &netcdf; libraries and include files. -On some platforms (such as Linux) multiple compilers can be used, and hence there -are env variables that can be set to change the &FORTRAN; and/or "C" compilers used. -The tools other than cprnc also allow finer control, by also -allowing the user to add compiler flags they choose, for both &FORTRAN; and "C", as -well as picking the compiler, linker and and add linker options. Finally the tools -other than cprnc allow you to turn -optimization on (which is off by default but on for the mksurfdata and -interpinic -programs) with the OPT flag so that the -tool will run faster. To get even faster performance, the interpinic, -mksurfdata, and -mkgriddata programs allow you to also use the SMP to -turn on multiple shared memory processors. -When SMP=TRUE you set the number of threads used by the program with -the OMP_NUM_THREADS environment variable. - - -Options used by all: cprnc, interpinic, -mkdatadomain, mkgriddata, and -mksurfdata - -LIB_NETCDF -- sets the location of the &netcdf; library. -INC_NETCDF -- sets the location of the &netcdf; include files. -USER_FC -- sets the name of the &FORTRAN; compiler. - -Options used by: interpinic, mkdatadomain, -mkgriddata, and mksurfdata - -MOD_NETCDF -- sets the location of the &netcdf; &FORTRAN; module. -USER_LINKER -- sets the name of the linker to use. -USER_CPPDEFS -- adds any CPP defines to use. -USER_CFLAGS -- add any "C" compiler flags to use. -USER_FFLAGS -- add any &FORTRAN; compiler flags to use. -USER_LDFLAGS -- add any linker flags to use. -USER_CC -- sets the name of the "C" compiler to use. -OPT -- set to TRUE to compile the code optimized (TRUE or FALSE) - -Options used by: interpinic, mkgriddata, and mksurfdata: - -SMP -- set to TRUE to turn on shared memory parallelism (i.e. -&omp;) (TRUE or FALSE) -Filepath -- list of directories to build source code from. -Srcfiles -- list of source code filenames to build executable from. - -Options used only by cprnc: - -EXEDIR -- sets the location where the executable will be built. -VPATH -- colon delimited path list to find the source files. - -More details on each environment variable. - - -LIB_NETCDF - -This variable sets the path to the &netcdf; library file -(libnetcdf.a). If not -set it defaults to /usr/local/lib. In order to use the tools -you need to build the &netcdf; library and be able to link to it. In order to build -the model with a particular compiler you may have to compile the &netcdf; library with -the same compiler (or at least a compatible one). - - - - - -INC_NETCDF - -This variable sets the path to the &netcdf; include directory (in order to find -the include file netcdf.inc). -if not set it defaults to /usr/local/include. - - - - - -MOD_NETCDF - -This variable sets the path to the &netcdf; module directory (in order to find -the &netcdf; &FORTRAN90; module file when &netcdf; is used with a &FORTRAN90; -use statement. When not set it defaults to the -LIB_NETCDF value. - - - - - -USER_FC - -This variable sets the command name to the &FORTRAN90; compiler to use when -compiling the tool. The default compiler to use depends on the platform. And -for example, on the AIX platform this variable is NOT used - - - - - -USER_LINKER - -This variable sets the command name to the linker to use when linking the object -files from the compiler together to build the executable. By default this is set to -the value of the &FORTRAN90; compiler used to compile the source code. - - - - - -USER_CPPDEFS - -This variable adds additional optional values to define for the C preprocessor. -Normally, there is no reason to do this as there are very few CPP tokens in the CLM -tools. However, if you modify the tools there may be a reason to define new CPP -tokens. - - - - - -USER_CC - -This variable sets the command name to the "C" compiler to use when -compiling the tool. The default compiler to use depends on the platform. And -for example, on the AIX platform this variable is NOT used - - - - - -USER_CFLAGS - -This variable adds additional compiler options for the "C" compiler to use -when compiling the tool. By default the compiler options are picked according -to the platform and compiler that will be used. - - - - - -USER_FFLAGS - -This variable adds additional compiler options for the &FORTRAN90; compiler to use -when compiling the tool. By default the compiler options are picked according -to the platform and compiler that will be used. - - - - - -USER_LDFLAGS - -This variable adds additional options to the linker that will be used when linking -the object files into the executable. By default the linker options are picked according -to the platform and compiler that is used. - - - - - -SMP - -This variable flags if shared memory parallelism (using i&omp;) should be used when -compiling the tool. It can be set to either TRUE or -FALSE, by default it is set to FALSE, so -shared memory parallelism is NOT used. When set to TRUE you can -set the number of threads by using the OMP_NUM_THREADS environment -variable. Normally, the most you would set this to would be to the number of on-node -CPU processors. Turning this on should make the tool run much faster. - - - -Note, that depending on the compiler answers may be different when SMP -is activated. - - - - - - -OPT - -This variable flags if compiler optimization should be used when -compiling the tool. It can be set to either TRUE or -FALSE, by default it is set to FALSE for -mkdatadomain and TRUE for -mksurfdata and interpinic. -Turning this on should make the tool run much faster. - - - -Note, you should expect that answers will be different when OPT -is activated. - - - - - - -Filepath - -All of the tools are stand-alone and don't need any outside code to operate. The -Filepath is the list of directories needed to compile -and hence is always simply "." the current directory. Several tools use -copies of code outside their directory that is in the &cesm; -distribution (either csm_share code or &clm; source code). - - - - - -Srcfiles - -The Srcfiles lists the filenames of the source code to use -when building the tool. - - - - - -EXEDIR - -The cprnc tool uses this variable to set the location of where the executable -will be built. The default is the current directory. - - - - - -VPATH - -The cprnc tool uses this variable to set the colon delimited pathnames of where -the source code exists. The default is the current directory. - - - - - - - - - -There are several files that are copies of the original files from either -models/lnd/clm/src/main, -models/csm_share/shr, or copies from other tool -directories. By having copies the tools can all be made stand-alone, but -any changes to the originals will have to be put into the tool directories -as well. - - - -The README.filecopies (which can be found in -models/lnd/clm/tools) is repeated here. - -&filecopies; - - - - - -General information on running the &FORTRAN; tools - -The tools run either one of two ways, with a namelist to provide options, or -with command line arguments (and NOT both). interpinic and -cprnc run with command line arguments, and the other tools -run with namelists. - - -Running &FORTRAN; tools with namelists - -mkgridata, mksurfdata and -mkdatadomain run with namelists that are read from -standard input. Hence, you create a namelist and then run them by -redirecting the namelist file into standard input as follows: - -./program < namelist - -For programs with namelists there is at least one sample namelist with the -name "program".namelist (i.e. mksurfdata.namelist -for the mksurfdata program). There may also be other sample -namelists that end in a different name besides "namelist". Namelists that you create -should be similar to the example namelist. The namelist values are also documented -along with the other namelists in the: - -models/lnd/clm/bld/namelist_files/namelist_definition.xml -file and default values in the: - -models/lnd/clm/bld/namelist_files/namelist_defaults_clm_tools.xml -file. - - - -Running &FORTRAN; tools with command line options - -interpinic and cprnc run with command line -arguments. The detailed sections below will give you more information on the command -line arguments specific to each tool. Also running the tool without any arguments -will give you a general synopsis on how to run the tool. For example to get help -on running interpinic do the following. - -cd models/lnd/clm/tools/interpinic -gmake -./interpinic - - - - -Running &FORTRAN; tools built with SMP=TRUE - -When you enable SMP=TRUE on your build of one of the tools that -make use of it, you are using &omp; for shared memory parallelism (SMP). In -SMP loops are run in parallel with different threads run on different processors -all of which access the same memory (called on-node). Thus you can only usefully -run up to the number of processors that are available on a single-node of the machine -you are running on. For example, on the &ncar; machine bluefire there are 32 processors -per node, but the SMT hardware on the machine allows you to submit twice as many -threads or 64 threads. So to run the mksurfdata on bluefire -optimized, with 64 threads you would do the following: - -cd models/lnd/clm/tools/mksurfdata -gmake OPT=TRUE SMP=TRUE -setenv OMP_NUM_THREADS 64 -./mksurfdata < mksurfdata.namelist - - - - - - -The File Creation Process - - -When just creating a replacement file for an existing one, the relevant tool should -be used directly to create the file. When you are creating a set of files for a new -resolution there are some dependencies between the tools that you need to keep in mind -when creating them. The main dependency is that the mkgriddata MUST -be done first as the grid dataset is then input into the other tools. Also look at -. - - - -Creating a complete set of files for input to &clm; - -Create grid and fraction datasets - -First use mkgriddata to create grid and fraction datasets. -See for more information on this. - - - - -Create domain dataset (if NOT already done) - -Next use mkdatadomain to create a domain file for use by -&datm; from the grid and fraction datasets just created. This is required, unless -a domain file already created was input into mkgriddata on -the previous step. -See for more information on this. - - - - -Create surface datasets - -Next use mksurfdata to create a surface dataset, using the grid -dataset as input. -See for more information on this. - - - - -Interpolate aerosol deposition datasets (optional) - -By default the atmosphere model will interpolate -these datasets on the fly, so you don't normally need to do this step. -A reason you might want to do this is to make the read and interpolation faster, -by reducing the amount of data read in and removing the need for the interpolation. -So, if you do, you can use aerdepregrid.ncl to regrid aerosol -deposition datasets to your new resolution using the grid dataset as input. -See for more information on this. - - - - -Interpolate Nitrogen deposition datasets (optional, but only needed if running &clmcn;) - -By default Nitrogen deposition is read in from stream -files at 2-degree resolution and interpolated to the resolution you are running at, -so you don't need to do this step. As with aerosol deposition datasets a reason -you might want to do this is to make the read and interpolation faster, -by reducing the amount of data read in and removing the need for the interpolation. -So, if you do you can use ndepregrid.ncl -to regrid Nitrogen deposition datasets to your new resolution using the grid dataset -as input. -See for more information on this. - - - - -Create some sort of initial condition dataset - - -You then need to do one of the following three options to have an initial dataset -to start from. - - - - - -Use spinup-procedures to create initial condition datasets - -The first option is to do the spinup procedures from arbitrary initial conditions -to get good initial datasets. This is the most robust method to use. -See , , or - for more information on this. - - - - -Use <command>interpinic</command> to interpolate existing initial -condition datasets - -The next option is to interpolate from spunup datasets at a different resolution, using -interpinic. -See for more information on this. - - - - -Start up from arbitrary initial conditions - -The last alternative is to run from arbitrary initial conditions without using any -spun-up datasets. This is inappropriate when using &clmcn; (bgc=cn or cndv) as it -takes a long time to spinup Carbon pools. - - -This is NOT recommended as many fields in &clm; take a long time to equilibrate. - - - - - - - - - - -Enter the new datasets into the &buildnml; XML database - -The last optional thing to do is to enter the new datasets into the &buildnml; -XML database. See for more information on -doing this. This is optional because the user may enter these files into their -namelists manually. The advantage of entering them into the database is so that -they automatically come up when you create new cases. - - - - - - - - -Using the <command>cprnc</command> tool to compare two history files - -cprnc is a tool shared by both CAM and &clm; to compare two -&netcdf; history files. -It differences every field that has a time-axis that is also shared on both files, -and reports a summary of the difference. The summary includes the three largest -differences, as well as the root mean square (RMS) difference. It also gives some -summary information on the field as well. You have to enter at least one file, and up to -two files. With one file it gives you summary information on the file, and with two it -gives you information on the differences between the two. At the end it will give you a -summary of the fields compared and how many fields were different and how many were -identical. - - -Options: - --m = do NOT align time-stamps before comparing --v = verbose output --ipr --jpr --kpr - -See the cprnc -README file for more details which is -repeated here: - -&cprnc_readme; - - - -To compare files with OUT a time axis you can use the cprnc.ncl -&ncl; script in models/lnd/clm/tools/ncl_scripts. It won't give -you the details on the differences but will report if the files are identical or -different. - - - - - - -Using <command>interpinic</command> to interpolate initial conditions to different -resolutions - -"interpinic" is used to interpolate initial conditions from one resolution to another. -In order to do the interpolation you must first run &clm; to create a restart file to -use as the "template" to interpolate into. Running from arbitrary initial conditions -(i.e. finidat = ' ') for a single time-step is sufficient to do this. Make sure the -model produces a restart file. You also need to make sure that you setup the same -configuration that you want to run the model with, when you create the template file. - - -Command line options to interpinic: - --i = Input filename to interpolate from --o = Output interpolated file, and starting template file - - - -There is a sample template file in the models/lnd/clm/tools/interpinic -directory and can be used to run interpolate to. -However, this file was created with an older version of &clm; and hence -we actually recommend that you would do a short run with &clm; to create a template file -to use. - - - - -Example of running &clm; to create a template file for -<command>interpinic</command> to interpolate to - -> cd scripts -> ./create_newcase -case cr_f10_TmpltI1850CN -res f10_f10 -compset I1850CN \ --mach bluefire -> cd cr_f10_TmpltI1850CN -# Set starting date to end of year -> ./xmlchange -file env_conf.xml -id RUN_STARTDATE -val 1948-12-31 -# Set year align to starting year -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_ALIGN -val 1948 -# Set to run a cold start -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -# Set to run only a single day, so a restart file will be created on Jan/1/1949 -> ./xmlchange -file env_run.xml -id STOP_N -val 1 -# Then configure, build and run as normal -> ./configure -case -> ./cr_f10_TmpltI1850CN.bluefire.build -> ./cr_f10_TmpltI1850CN.bluefire.submit -# And copy the resulting restart file to your interpinic directory -> cd ../models/lnd/clm/tools/interpinic -> cp /ptmp/$LOGIN/cr_f10_TmpltI1850CN/run/cr_f10_TmpltI1850CN.clm2.r.1949-01-01-00000.nc . - - - - -In the next example we build interpinic optimized with shared -memory on for 64 threads so that it runs as fast as possible, to interpolate one of -the standard 1-degree datasets to the above 10x15 template file that we created. - - -Example of building and running <command>interpinic</command> to -interpolate a 1-degree <filename>finidat</filename> dataset to 10x15 - -> cd models/lnd/clm/tools/interpinic -> gmake OPT=TRUE SMP=TRUE -> env OMP_NUM_THREADS=64 ./interpinic -o cr_f10_TmpltI1850CN.clm2.r.1949-01-01-00000.nc / --i /fs/cgd/csm/inputdata/ccsm4_init/b40.1850.track1.1deg.006/0863-01-01/b40.1850.track1.1deg.006.clm2.r.0863-01-01-00000.nc - - - - -Running interpinic at high resolution can take a long time, so we -recommend that you always build it optimized and with shared memory processing on, to -cut down the run time as much as possible. - - - - -interpinic does NOT work for CNDV (bgc=cndv). - - - - - - -In we give a simpler way to run -interpinic for several standard resolutions at once, with a script -to loop over several resolutions. This is useful for &clm; developers who need to -create many finidat files at once. - - - - - -Using <command>mkgriddata</command> to create grid datasets - -mkgriddata is used to create grid, fraction, and topography -datasets to run &clm; at a new resolution. It is typically the first step in creating -datasets needed to run &clm; at a new resolution (followed by -mksurfdata, and -then the interpolation programs, aerdepregrid.ncl, and -ndepregrid.ncl when running with CN). - - - -mkgriddata namelist - -mkgriddata is controlled by a namelist. There are ten different -namelist items, and you need to use enough of them so that files will be output. -The different types of input datasets contain different input data types, that -correspond to the three different types of output files: grid, fraction, and topography. -Output files for each of these will only be output if there is input data that -correspond to these. If you only have input data for grid locations -- you will only -get an output grid file. If you have both grid and fraction data you will get grid and -fraction data files. If you also have topography data you will also get topo files. - - -Namelist options to mkgriddata include: - -mksrf_fnavyoro -- Navy orography file to use for land fraction -and surface heights. -mksrf_frawtopo -- Raw topography file with just surface -heights. -mksrf_fcamfile -- CAM initial conditions file with -land-fractions and topography -mksrf_fclmgrid -- &clm; grid file -mksrf_fccsmdom -- &cesm; domain file -mksrf_fcamtopo -- CAM topography file -mksrf_lsmlon -- number of longitude for regional grid -mksrf_lsmlatnumber of latitudes for regional grid -mksrf_edgen -- Northern edge for regional grid -mksrf_edgee -- Southern edge for regional grid -mksrf_edges -- Eastern edge for regional grid -mksrf_edgew -- Western edge for regional grid - - - -You need to enter one of the following four options: - - mksrf_fnavyoro - high resolution topo dataset (topo data) - mksrf_lsmlon - number of longitudes - mksrf_lsmlat - number of latitudes - mksrf_edgen - northern edge of grid (degrees) - mksrf_edgee - eastern edge of grid (degrees) - mksrf_edges - southern edge of grid (degrees) - mksrf_edgew - western edge of grid (degrees) - -or - - mksrf_fcamfile - CAM topo file (grid and possibly fraction data) - -or - - mksrf_fccsmdom - &cesm; domain file (both grid, and fraction data) - -or - - mksrf_fclmgrid - &clm; grid or surface dataset file (grid data) - -Note, you can provide more than one of the needed datasets, and the output -data will be determined by the datasets according to an order of precedence. -The order of precedence for data is as follows: - -mksrf_fcamfile -mksrf_fclmgrid -mksrf_fnavyoro -mksrf_fccsmdom - -Grid data then will be established by the file with the highest precedence. -&cesm; domain files sometimes have latitudes and longitudes that are "off" from -the standard by a small amount. By establishing an order of precedence you can ensure -that grid locations exactly match a given standard file, even if the values in the domain -file are off from that. - - - -There are three different major modes for using "mkgriddata" to create grid files -for &clm;: - -mksrf_fnavyoro -- Navy orography file to use for land fraction -and surface heights. -mksrf_frawtopo -- Raw topography file with just surface -heights. -mksrf_fcamfile -- CAM initial conditions file with -land-fractions and topography -mksrf_fclmgrid -- &clm; grid file -mksrf_fccsmdom -- &cesm; domain file -mksrf_fcamtopo -- CAM topography file -mksrf_lsmlon -- number of longitude for regional grid -mksrf_lsmlat -- number of latitudes for regional grid -mksrf_edgen -- Northern edge for regional grid -mksrf_edgee -- Southern edge for regional grid -mksrf_edges -- Eastern edge for regional grid -mksrf_edgew -- Western edge for regional grid - - - -You need to enter one of the following four options: - - mksrf_fnavyoro - high resolution topo dataset (topo data) - mksrf_lsmlon - number of longitudes - mksrf_lsmlat - number of latitudes - mksrf_edgen - northern edge of grid (degrees) - mksrf_edgee - eastern edge of grid (degrees) - mksrf_edges - southern edge of grid (degrees) - mksrf_edgew - western edge of grid (degrees) - -or - - mksrf_fcamfile - CAM topo file (grid and possibly fraction data) - -or - - mksrf_fccsmdom - &cesm; domain file (both grid, and fraction data) - -or - - mksrf_fclmgrid - &clm; grid or surface dataset file (grid data) - -Note, you can provide more than one of the needed datasets, and the output -data will be determined by the datasets according to an order of precedence. -The order of precedence for data is as follows: - -mksrf_fcamfile -mksrf_fclmgrid -mksrf_fnavyoro -mksrf_fccsmdom - -Grid data then will be established by the file with the highest precedence. -&cesm; domain files sometimes have latitudes and longitudes that are "off" from -the standard by a small amount. By establishing an order of precedence you can ensure -that grid locations exactly match a given standard file, even if the values in the domain -file are off from that. - - - -There are three different major modes for using mkgriddata to -create grid files for &clm;: - -Convert &cesm; domain files to &clm; grid files -Create single point or regional area grid files -Convert CAM files to &clm; grid files - - - - - -Convert &cesm; domain files to &clm; grid files - -&cesm; domain files such as used for &datm;, include all the information -needed to create &clm; grid and fraction files. - -Example <command>mkgriddata</command> namelist to convert &cesm; 4x5 domain files to &clm; grid files - -&clmexp - mksrf_fccsmdom= -'/fs/cgd/csm/inputdata/lnd/dlnd7/domain.lnd.4x5_gx3v5.060404.nc' - mksrf_fclmgrid= -'/fs/cgd/csm/inputdata/lnd/clm2/griddata/griddata_4x5_060404.nc' -/ - - - - -Notice that in the above example, a &clm; grid file is included as well, even though -it's not required. The reason for this is to ensure that the latitude and longitudes -on the output files exactly match a standard grid file. - - - - - - -Create single point or regional area grid files - -The process to create single-point or regional area &clm; grid files is the same. -You enter the number of latitudes and longitudes you want on your output file and -the extent of the grid: North, East, South and West. You also tell -mkgriddata that -you are entering a "regional" grid and you also enter the standard Navy orography -dataset (or your own orography file if desired). For a single point you simply -enter "1" for the number of latitudes and longitudes, but you still enter the -grid extent (of the single grid cell). Here is a sample regional namelist to create -a 5x5 regional grid over the Amazon: - -Example <command>mkgriddata</command> namelist to create regional grid over Amazon - -&clmexp - mksrf_fnavyoro= -"/fs/cgd/csm/inputdata/lnd/clm2/rawdata/mksrf_navyoro_20min.c010129.nc" - mksrf_lsmlon = 5 - mksrf_lsmlat = 5 - mksrf_edgee = 303.75 - mksrf_edgew = 286.25 - mksrf_edges = -15. - mksrf_edgen = -4. -/ - - - - - -Currently you can NOT have regional grids that straddle both -sides of the Greenwich (longitude = zero) line. - - - - -You should enter longitudes with values from 0 to 360 East. - - - - - -Convert <acronym>CAM</acronym> files to &clm; grid files (deprecated) - -Older CAM initial files included all the information needed to create &clm; -grid files. Newer CAM files no longer include land fraction data. Hence you -can use CAM files to give you the grid coordinates, but you need other data -to give you the land-mask and topography. Since, CAM files no longer -contain the needed information, this option is now deprecated. In most cases you should -use one of the other two options. - - - - - - - -Using <command>mkdatadomain</command> to create domain datasets for &datm; or docn from &clm; grid datasets - -"mkdatadomain" is used to convert &clm; grid and fraction datasets into domain datasets -that can be used by either the "datm" or "docn" models. Most often &clm; users will want -to convert the grid datasets they just created using mkgriddata into -domain datasets to be used by &datm; for an "I" case. mkdatadomain is -controlled by a namelist, and has a very straight forward operation with only four -namelist items all of which are required. You specify which output mode you want "datm" -or "docn", and then set the input &clm; grid and frac datasets, and the output domain file. - - -Example <command>mkdatadomain</command> namelist to create a domain file from -&clm; frac and grid data files - -&domain_nl - dtype = "datm" - f_fracdata = -'/fs/cgd/csm/inputdata/lnd/clm2/griddata/fracdata_4x5_USGS_070110.nc' - f_griddata = -'/fs/cgd/csm/inputdata/lnd/clm2/griddata/griddata_4x5_060404.nc' - f_domain = -'domain.lnd.fv4x5_USGS.090117.nc' -/ - - - - - -Using mksurfdata to create surface datasets from grid datasets - -mksurfdata is used to create surface-datasets from grid datasets and raw datafiles -at half-degree resolution to produce files that describe the surface characteristics -needed by &clm; (fraction of grid cell covered by different land-unit types, and fraction -for different vegetation types, as well as things like soil color, and soil texture, -etc.). To run mksurfdata you can either use the -mksurfdata.pl script which will create namelists for you using the &buildnml; -XML database, or you can run it by hand using a namelist that you provide (possibly -modeled after an example provided in the -models/lnd/clm/tools/mksurfdata directory). The namelist for -mksurfdata is sufficiently complex that we recommend using the -mksurfdata.pl tool to build them. In the next section -we describe how to use the mksurfdata.pl script and the following -section gives more details on running mksurfdata by hand and the -various namelist input variables to it. - - -Running <command>mksurfdata.pl</command> - -The script mksurfdata.pl can be used to run the -mksurfdata program for several configurations, resolutions, -simulation-years and simulation year ranges. It will create the needed namelists for -you and move the files -over to your inputdata directory location (and create a list of the files created, and -for developers this file is also a script to import the files into the svn inputdata -repository). It will also use the &buildnml; XML database -to determine the correct input files to use, and for transient cases it will create -the appropriate mksrf_fdynuse file with the list of files for each -year needed for this case. And in the case of urban single-point -datasets (where surface datasets are actually input into mksurfdata) -it will do the additional processing required so that the output dataset -can be used once again by mksurfdata. Because, it figures out -namelist and input files for you, it is recommended that you use this script for creation -of standard surface datasets. If you need to create surface datasets for customized -cases, you might need to run mksurfdata on it's own. But you -could use mksurfdata.pl with the "-debug" option to give you -a namelist to start from. -For help on mksurfdata.pl you can use the "-help" option as below: - -> cd models/lnd/clm/tools/mksurfdata -> mksurdata.pl -help - -The output of the above command is: - -&mksurfdatapl; - - - -To run the script with optimized mksurfdata for a 4x5 degree grid -for 1850 conditions, on bluefire you would do the following: - -Example of running <command>mksurfdata.pl</command> to create a 4x5 resolution -<filename>fsurdat</filename> for a 1850 simulation year - -> cd models/lnd/clm/tools/mksurfdata -> gmake -> mksurfdata.pl -y 1850 -r 4x5 - - - - - - -Running <command>mksurfdata</command> by Hand - -In the above section we show how to run mksurfdata through -the mksurfdata.pl using input datasets that are in the &buildnml; -XML database. When you are running with input datasets that are NOT available in -the XML database you either need to add them as outlined in -, or you need to run mksurfdata -by hand, as we will outline here. - - - -Preparing your <command>mksurfdata</command> namelist - -When running mksurfdata by hand you will need to prepare your -own input namelist. There are sample namelists that are setup for running on the -&ncar; machine bluefire. You will need to change the filepaths to -run on a different machine. The list of sample namelists include - -mksurfdata.namelist -- standard sample namelist. -mksurfdata.regional -- sample namelist to -build for a regional grid dataset (5x5_amazon) -mksurfdata.singlept -- sample namelist to -build for a single point grid dataset (1x1_brazil) - -Note, that one of the inputs mksrf_fdynuse is a filename that -includes the filepaths to other files. The filepaths in this file will have to -be changed as well. You also need to make sure that the line lengths remain the same -as the read is a formatted read, so the placement of the year in the file, must remain -the same, even with the new filenames. One advantage of the mksurfdata.pl -script is that it will create the mksrf_fdynuse file for you. - - -We list the namelist items below. Most of the namelist items are filepaths to give to -the input half degree resolution datasets that you will use to scale from to the -resolution of your grid dataset. -You must first specify the input grid dataset for the resolution to output for: - -mksrf_fgrid Grid dataset - -Then you must specify settings for input high resolution datafiles - -mksrf_ffrac land fraction and land mask dataset -mksrf_fglacier Glacier dataset -mksrf_fglacierregion Glacier region ID dataset -mksrf_flai Leaf Area Index dataset -mksrf_flanwat Land water dataset -mksrf_forganic Organic soil carbon dataset -mksrf_fmax Max fractional saturated area dataset -mksrf_fsoicol Soil color dataset -mksrf_fsoitex Soil texture dataset -mksrf_ftopo Topography dataset (this is used to limit -the extent of urban regions and is used for glacier multiple elevation classes) - -mksrf_furban Urban dataset -mksrf_fvegtyp PFT vegetation type dataset -mksrf_fvocef Volatile Organic Compound Emission Factor -dataset -mksrf_fgdp GDP dataset -mksrf_fpeat Peatland dataset -mksrf_fabm Agricultural fire peak month dataset -mksrf_ftopostats Topography statistics dataset -mksrf_fvic VIC parameters dataset -mksrf_fch4 Inversion-derived CH4 parameters dataset - -You specify the ASCII text file with the land-use files. - -mksrf_fdynuse "dynamic land use" for transient -land-use/land-cover changes. This is an ASCII text file that lists the filepaths -to files for each year and then the year it represents (note: you MUST change the -filepaths inside the file when running on a machine NOT at &ncar;). -We always use this file, even for creating datasets of a fixed year. Also note -that when using the "pft_" settings this file will be an XML-like file with settings -for PFT's rather than filepaths (see below). - - - -And optionally you can specify settings for: - -all_urban If entire area is urban (typically used for -single-point urban datasets, that you want to be exclusively urban) -no_inlandwet If TRUE, set wetland to 0% over land -(renormalizing other landcover types as needed); wetland will only be used for ocean -points. (Only applies to CLM4.5 version of mksurfdata_map, for which the default is -TRUE.) -mksrf_firrig Irrigation dataset, if you want -activate the irrigation model over generic cropland -(experimental mode, normally NOT used) -mksrf_gridnm Name of output grid resolution (if not -set the files will be named according to the number of longitudes by latitudes) -mksrf_gridtype Type of grid (default is 'global') -nglcec number of glacier multiple elevation classes. -Can be 0, 1, 3, 5, or 10. When using the resulting dataset with &clm; you can then run -with glc_nec of either 0 or this value. - (experimental normally use the default of 0, when running with the land-ice -model in practice only 10 has been used) -numpft number of Plant Function Types (PFT) -in the input vegetation mksrf_fvegtyp dataset. You change -this to 20, if you want to create a dataset with prognostic crop activated. The -vegetation dataset also needs to have prognostic crop types on it as well. - (experimental normally not changed from the default of 16) -outnc_large_files If output should be in &netcdf; large file -format -outnc_double If output should be in double -precision (normally we turn this on) -pft_frc array of fractions to override PFT -data with for all gridpoints (experimental mode, normally NOT used). -pft_idx array of PFT indices to override PFT -data with for all gridpoints (experimental mode, normally NOT used). -soil_clay percent clay soil to override -all gridpoints with (experimental mode, normally NOT used). -soil_color Soil color to override -all gridpoints with (experimental mode, normally NOT used). -soil_fmax Soil maximum fraction to override -all gridpoints with (experimental mode, normally NOT used). -soil_sand percent sandy soil to -override all gridpoints with (experimental mode, normally NOT used). - - - -After creating your namelist, -when running on a non &ncar; machine you will need to get the files -from the inputdata repository. -In order to retrieve the files needed for mksurfdata you can do the following on your -namelist to get the files from the inputdata repository, using the -check_input_data script which also allows you to export data to -your local disk. - -Getting the raw datasets for <command>mksurfdata</command> to your local -machine using the <command>check_input_data</command> script - -> cd models/lnd/clm/tools/mksurfdata -# First remove any quotes and copy into a filename that can be read by the -# check_input_data script -> sed "s/'//g" namelist > clm.input_data_list -# Run the script with -export and give the location of your inputdata with $CSMDATA -> ../../../../../scripts/ccsm_utils/Tools/check_input_data -datalistdir . \ --inputdata $CSMDATA -check -export -# You must then do the same with the flanduse_timeseries file referred to in the namelist -# in this case we add a file = to the beginning of each line -> awk '{print "file = "$1}' landuse_timeseries_hist_simyr2000-2000.txt > clm.input_data_list -# Run the script with -export and give the location of your inputdata with $CSMDATA -> ../../../../../scripts/ccsm_utils/Tools/check_input_data -datalistdir . \ --inputdata $CSMDATA -check -export - - - - -Experimental options to <command>mksurfdata</command> - -The options: pft_frc, pft_idx, soil_clay, soil_color, soil_fmax, and soil_sand are also -new and considered experimental. They provide a way to override the PFT and soil -values for all grid points to the given values that you set. This is useful for -running with single-point tower sites where the soil type and vegetation is known. -Note that when you use pft_frc, all other landunits will be zeroed out, and the -sum of your pft_frc array MUST equal 100.0. Also note that when using the "pft_" -options the mksrf_fdynuse file instead of having filepath's -will be an XML-like file with PFT settings. Unlike the file of file-paths, you will -have to create this file by hand, mksurfdata.pl will NOT be able -to create it for you (other than the first year which will be set to the values -entered on the command line). Note, that when &ptclm; is run, it CAN create these -files for you from a simpler format (see ). -Instead of a filepath you have a list of XML elements that give information on the PFT's -and harvesting for example: - -<pft_f>100</pft_f><pft_i>1</pft_i><harv>0,0,0,0,0</harv><graz>0</graz> - -So the <pft_f> tags give the PFT fractions and the <pft_i> tags give the -index for that fraction. Harvest is an array of five elements, and grazing is a single -value. Like the usual file each list of XML elements goes with a year, and there is -limit on the number of characters that can be used. - - - - - -Standard Practices when using <command>mksurfdata</command> - -In this section we give the recommendations for how to use mksurfdata -to give similar results to the files that we created when using it. - - -If you look at the standard surface datasets that we have created and provided for use, -there are three practices that we have consistently done in each (you also see these in -the sample namelists and in the mksurfdata.pl script). The first is -that we always output data in double precision (hence outnc_double -is set to .true.). The next is that we always use the procedure -for creating transient datasets (using mksrf_fdynuse) even when -creating datasets for a fixed simulation year. This is to ensure that the fixed year -datasets will be consistent with the transient datasets. When this is done a -"landuse_timeseries" dataset will be created -- but will NOT be used in &clm;. If you look -at the sample namelist mksurfdata.namelist you note that it -sets mksrf_fdynuse to the file -landuse_timeseries_hist_simyr2000.txt, where the single file entered is -the same PFT file used in the rest of the namelist (as mksrf_fvegtyp). -The last practice that we always do is to always set mksrf_ftopo, -even if glacier elevation classes are NOT active. This is -important in limiting urban areas based on topographic height, and hence is important -to use all the time. The glacier multiple elevation classes will be used as well if -you are running a compset with the active glacier model. - - -There are two other important practices for creating urban single point datasets. The -first is that you often will want to set all_urban to -.true. so that the dataset will have 100% of the gridcell output -as urban rather than some mix of: urban, vegetation types, and other landunits. The -next practice is that most of our specialized urban datasets have custom values for -the urban parameters, hence we do NOT want to use the global urban dataset to get -urban parameters -- we use a previous version of the surface dataset for the urban -parameters. However, in order to do this, we need to append onto the previous surface -dataset the grid and land mask/land fraction information from the grid and fraction -datasets. This is done in mksurfdata.pl using the NCO -program ncks. An example of doing this for the Mexico City, Mexico -urban surface dataset is as follows: - -> ncks -A $CSMDATA/lnd/clm2/griddata/griddata_1x1pt_mexicocityMEX_c090715.nc \ -$CSMDATA/lnd/clm2/surfdata/surfdata_1x1_mexicocityMEX_simyr2000_c100407.nc -> ncks -A $CSMDATA/lnd/clm2/griddata/fracdata_1x1pt_mexicocityMEX_navy_c090715.nc \ -$CSMDATA/lnd/clm2/surfdata/surfdata_1x1_mexicocityMEX_simyr2000_c100407.nc - -Note, if you look at the current single point urban surface datasets you will note -that the above has already been done. - - -The final issue is how to build mksurfdata. When NOT optimized -mksurfdata is very slow, and can take many hours to days to -even run for medium resolutions such as one or two degree. So usually you will want -to run it optimized. Possibly you also want to use shared memory parallelism using -&omp; with the SMP option. The problem with running optimized is that -answers will be different when running optimized versus non-optimized for most -compilers. So if you want answers to be the same as a previous surface dataset, you -will need to run it on the same platform and optimization level. Likewise, running -with or without &omp; may also change answers (for most compilers it will NOT, however -it does for the IBM compiler). However, answers should be the same regardless of the -number of threads used when &omp; is enabled. Note, that the output surface datasets -will have attributes that describe whether the file was written out optimized or not, -with threading or not and the number of threads used, to enable the user to more -easily try to match datasets created previously. For more information on the different -compiler options for the &clm4; tools see . - - - - - - - -Using &ncl; scripts <command>ndepregrid.ncl</command> and -<command>aerdepregrid.ncl</command> to interpolate aerosol deposition datasets - -Unlike the other tools, these are &ncar; Command Language (&ncl;) scripts -and you will need to get a copy of &ncl; in order to use them. You also won't have to -build an executable in order to use them, hence no Makefile is provided. &ncl; is provided -for free download as either binaries or source code from: -http://www.ncl.ucar.edu/. The &ncl; -web-site also contains documentation on &ncl; and it's use. - - -By default at this point neither of these scripts HAS to be used, -as the model is now constructed to read aerosol and Nitrogen deposition from 2-degree -datasets and interpolate to the model resolution on the fly. The main reason you might -want to do this now, is for better performance for single-point simulations. - - -Both the ndepregrid.ncl and aerdepregrid.ncl -scripts have similar interfaces and you customize the output resolution and -characteristics based on the settings of environment variables that you set (if you -don't set any of the variables, the script has defaults that it will use). -The list of environment variables that can be set are: - -RES -- output resolution name -RCP -- representative concentration pathway for future scenarios -(example 2.6, 4.5, 6, or 8.5) -SIM_YR -- simulation year (example 1850 or 2000) -SIM_YR_RNG -- simulation year range (example 1850-2000 or -1850-2100) -GRDFIL -- full pathname of grid file to use -(in place of getting the default grid file based on the RES value) -CSMDATA -- &cesm; inputdata directory -CLM_ROOT -- root directory for &clm; (models/lnd/clm directory) - - - - -You MUST provide either RES or both -GRDFIL AND RES. If you -just give RES the default namelist database in -models/lnd/clm/bld will be used to find the default grid -file based on the resolution name RES. If you provide -GRDFIL the input pathname of the gridfile provided will be used, -and the output filename will include RES as part of it's name -to designate it as an output file at that resolution. - - - -Both scripts assume that you will be interpolating from a native resolution of 1.9x2.5 -and using the default files found in the namelist database to interpolate from. If you -want to interpolate from another resolution or use other files, you would need to edit -the scripts to do so. Both scripts also use a bilinear interpolation to do the -regridding. The environment variables: RCP, SIM_YR, -and SIM_YR_RNG will be used to query the namelist database to -determine which native dataset to interpolate from. If you don't provide valid -values for these variables, it won't be able to find a dataset to interpolate from. -You can use the build-namelist script to query what the valid values for these can -be. Likewise, when you use RES to determine the grid file to interpolate -to, it needs to be a valid value from the namelist database. - - -The scripts can be used to interpolate from (and create output) constant or -transient datasets. -Constant datasets specify the SIM_YR and set SIM_YR_RNG -to constant (which is also the default). Transient datasets need -to specify both SIM_YR and SIM_YR_RNG, where -SIM_YR is set to the first year in the interval (typically 1850). - - -The default for CSMDATA works for &ncar; computers, but will need to -be set to the top level directory location of your &cesm; input data on other computers. -If you set this as a default for your shell when you login (for example with your -$HOME/.cshrc if you use csh) you won't have to set it each time -you run the script. CLM_ROOT will default to the proper location -when you run it in the models/lnd/clm/tools/ncl_script -directory. It is only useful if you want to run the script out of a different -directory. - - -Using <command>ndepregrid.ncl</command> to interpolate Nitrogen deposition datasets - -ndepregrid.ncl interpolates the Nitrogen deposition datasets from one resolution -to another. - - - -Interpolating Nitrogen deposition files is no longer needed, because the model can -read Nitrogen deposition files at one resolution and interpolate to the resolution the -model is running at on the fly. Interpolating to another -resolution is only useful for very course resolutions, if you want to save some computing -resources in reading larger datasets. For example, this may be useful in obtaining -single-point datasets. - - - -For example, to interpolate to an output resolution of 0.9x1.25, for a constant -simulation-year of 1850, you would do the following: - -> env RES=0.9x1.25 SIM_YR=1850 ncl ndepregrid.ncl - - - - - -Using <command>aerdepregrid.ncl</command> to interpolate Aerosol deposition datasets - -aerdepregrid.ncl interpolates the Aerosol deposition datasets from one resolution. -It can be used to interpolate either constant datasets (for example: -aerosoldep_monthly_2000_0.9x1.25_c090828.nc) or transient datasets (for example: -aerosoldep_monthly_1849-2006_0.9x1.25_c090830.nc). - - - -Interpolating aerosol deposition files is no longer needed, because the &datm; model can -read aerosol deposition files at one resolution and interpolate to the resolution the -model is running at on the fly. Interpolating to another -resolution is only useful for very course resolutions, if you want to save some computing -resources in reading larger datasets. For example, this may be useful in obtaining -single-point datasets. - - - -For example, to interpolate to an output resolution of 4x5, for a transient -simulation-year range of 1850 to 2100 and the rcp of 8.5, you would do the following: - -> env RES=4x5 SIM_YR=1850 SIM_YR_RNG=1850-2100 RCP=8.5 ncl ndepregrid.ncl - - - - - - -How to Customize Datasets for particular Observational Sites - -There are two ways to customize datasets for a particular observational site. The first -is to customize the input to the tools that create the dataset, and the second is to -over-write the default data after you've created a given dataset. Depending on the tool -it might be easier to do it one way or the other. In we list the files that are most likely to be -customized and the way they might be customized. Of those files, the ones you are most -likely to customize are: fatmlndfrc, fsurdat, faerdep (for &datm;), and -stream_fldfilename_ndep. Note mksurfdata as documented previously -has options to overwrite the vegetation and soil types. For more information on this also see - and &ptclm; uses these methods to -customize datasets see . - - -Another aspect of customizing your input datasets is customizing the input atmospheric -forcing datasets. See the for more -information on this. Also the chapter on &ptclm; in -has information on using the AmeriFlux tower site data as atmospheric forcing. - - - - -Conclusion of tools description - -We've given a description of how to use the different tools with &clm; to create -customized datasets. In the next chapter we will talk about how to make these -files available for build-namelist so that you can easily create simulations -that include them. In the chapter on single-point and regional datasets we also -give an alternative way to enter new datasets without having to edit files. - - - - - diff --git a/doc/UsersGuide/trouble_shooting.xml b/doc/UsersGuide/trouble_shooting.xml deleted file mode 100644 index 418cfabaae..0000000000 --- a/doc/UsersGuide/trouble_shooting.xml +++ /dev/null @@ -1,545 +0,0 @@ - - -Trouble Shooting Problems - -In this chapter we give some guidance on what to do when you encounter some of the -most common problems. We can't cover all the problems that a user could potentially -have, but we will try to help you recognize some of the most common situations. -And we'll give you some suggestions on how to approach the problem to come up with -a solution. - - -In general you will run into one of three type of problems: - -configure-time -build-time -run-time - -You may also run into problems with create_newcase itself, or -with the archiving scripts -- for those problems you should consult the -&cesmrel; Scripts User's Guide. - - - -Trouble with Configuration - -The first type of problem happens when you invoke the configure -case -command. This indicates there is something wrong with your template files, or input -datasets, or the details of what you are trying to configure the model to do. -There's also a trouble-shooting chapter in the &cesmrel; -Scripts User's Guide. Many of the problems with configuration can be resolved -with the guidelines given there. Here we will restrict ourselves to problems from the -&clm; or &datm; templates or input files. - -Example of configure problem with missing datasets - -> ./create_newcase -case T31rcp6 -res T31_g37 -compset IRCP60CN \ --mach bluefire -> ./configure -case - -The following is what is displayed to the screen. - -Generating resolved namelist, prestage, and build scripts -configure done. -adding use_case 1850-2100_rcp6_transient defaults for var clm_demand with val flanduse_timeseries -adding use_case 1850-2100_rcp6_transient defaults for var clm_start_type with val startup -adding use_case 1850-2100_rcp6_transient defaults for var model_year_align_ndep with val -1850 -adding use_case 1850-2100_rcp6_transient defaults for var rcp with val 6 -adding use_case 1850-2100_rcp6_transient defaults for var sim_year with val 1850 -adding use_case 1850-2100_rcp6_transient defaults for var sim_year_range with val -1850-2100 -adding use_case 1850-2100_rcp6_transient defaults for var stream_year_first_ndep with val -1850 -adding use_case 1850-2100_rcp6_transient defaults for var stream_year_last_ndep with val -2100 -adding use_case 1850-2100_rcp6_transient defaults for var use_case_desc with val Simulate -transient land-use, aerosol and Nitrogen deposition changes with historical data from -1850 to 2005 and then with the RCP6 scenario from AIM - -build-namelist - No default value found for flanduse_timeseries. - Are defaults provided for this resolution and land mask? -ERROR: generate_resolved.csh error for lnd template -configure error: configure generated error in attempting to created resolved scripts - - -The important thing to note here is the line: - -ERROR: generate_resolved.csh error for lnd template - -which tells us that the problem is in the land template. It may also indicate problems -in one of the other templates (atm, ccsm, cpl, glc, ice, or ocn), in which case you -should consult the appropriate model user's guide, and examine the given template file -in Tools/Templates. For more information on working with template -files see . - - -In the example above, it's obvious that the problem is coming from the &clm; &buildnml;, -in other situations it might not be so obvious where the problem is occurring. In such -cases it might be useful to add a "set echo" command to the top of the template file so -that each command in the template will be echoed to the screen and you can see what -is happening and where the error is occurring. - -set echo - - - -In the example, the error is that the &clm; XML database does NOT have a -flanduse_timeseries for the given resolution, rcp scenario and ocean mask. -That means you will need to create the file and then supply the file into your case. See - for more information on creating files, and see - for more information on adding files to the -XML database. Alternatively, you can provide the file to your case by creating -a user namelist as shown in . - - - -The two most common problems from your &clm; template will be errors from the &clm; -&configure; or &buildnml;. For more information on these scripts see: - and -the section on &CLMBLDNML;. - - - - - -Trouble with Building - -Here's an example of running the build for a case and having it fail in the land model -build. As you can see it lists which model component is being built and the build log -for that component. - - CCSM BUILDEXE SCRIPT STARTING - - Build Libraries: mct pio csm_share -Sat Jun 19 21:21:19 MDT 2010 /ptmp/erik/test_build/mct/mct.bldlog.100619-212107 -Sat Jun 19 21:22:18 MDT 2010 /ptmp/erik/test_build/pio/pio.bldlog.100619-212107 -Sat Jun 19 21:23:18 MDT 2010 -/ptmp/erik/test_build/csm_share/csm_share.bldlog.100619-212107 -Sat Jun 19 21:24:00 MDT 2010 /ptmp/erik/test_build/run/cpl.bldlog.100619-212107 -Sat Jun 19 21:24:00 MDT 2010 /ptmp/erik/test_build/run/atm.bldlog.100619-212107 -Sat Jun 19 21:24:06 MDT 2010 /ptmp/erik/test_build/run/lnd.bldlog.100619-212107 -ERROR: clm.buildexe.csh failed, see /ptmp/erik/test_build/run/lnd.bldlog.100619-212107 -ERROR: cat /ptmp/erik/test_build/run/lnd.bldlog.100619-212107 - -You can then examine the build log that failed and see what went wrong. Most compilers -will give the full filepath and line number for the file that filed to compile. - - - - -Trouble with Running - -Tracking down problems while the model is running is much more difficult to do -than configure or build problems. In this section we will give some suggestions -on how to find run time problems. Below we show the log file results of a job -that aborted while running. - - CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY -Sun Jun 20 18:24:06 MDT 2010 -- CSM EXECUTION BEGINS HERE -Sun Jun 20 18:24:35 MDT 2010 -- CSM EXECUTION HAS FINISHED -Model did not complete - see /ptmp/erik/test_run/run/cpl.log.100620-182358 - -In the next section we will talk about using the different log files to track -down problems, and find out where the problem is coming from. In the section -after that we give some general advice on debugging problems and some suggestions -on ideas that may be helpful to track the problem down. Some of the examples -below are from the &KnownBugs; file. - - -Tracking Problems by Querying Log Files - -The first thing to do when tracking down problems is to query the different log -files to see if you can discover where the problem occurs, and any error messages about -it. It's important to figure out if the problem comes in at initialization or in the -run phase of the model, and in which model component the problem happens. There -are different log files for the different major components, and they all end -with the date and time in YYMMDD-HHMMSS format (2-digit: year, month, day, hour -minute and second). When the model runs to completion the log files will be copied -to the logs directory in the script directory, but when the -model fails they will remain in the run directory. Here's an example list of -log files from an "I" case where the model dies in the land model initialization. -For "I" cases the sea-ice and ocean components are just stubs and don't create -log files (and unless running with the active land-ice model "glc" log files won't -be created either). - -atm.log.100620-182358 -ccsm.log.100620-182358 -cpl.log.100620-182358 -lnd.log.100620-182358 - - - - -The coupler log file - -The first log file to check is the coupler log file so that you can see where -the model dies and which model component it fails in. When the model dies at -initialization the last model component listed is the component that failed. - - -Example of a case that fails in the &clm; land model initialization. - -(seq_timemgr_clockPrint) Prev Time = 00001201 00000 -(seq_timemgr_clockPrint) Next Time = 99991201 00000 -(seq_timemgr_clockPrint) Intervl yms = 9999 0 0 - -(seq_mct_drv) : Initialize each component: atm, lnd, ocn, and ice -(seq_mct_drv) : Initialize atm component -(seq_mct_drv) : Initialize lnd component - - - - - -The ccsm log file - -The ccsm log files are to some extent the "garbage collection" of log output. The -&clm; sends it's output from it's master processor, but sends other output and possibly -errors to the ccsm log file. Because, of this, often error messages are somewhere in the -ccsm log file. However, since there is so much other output it may be difficult to find. -For example, here is some output from an older version of &cesm; (&cesm102;) where the -RTM river routing file (before it was converted to &netcdf;) was not provided and -the error on the open statement for the file was embedded near the end of the ccsm log -file. - -NODE# NAME -( 0) be1105en.ucar.edu -"/gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/lnd/clm/src/riverroute/RtmMod.F90", line -239: 1525-155 The file name provided in the OPEN statement for unit 1 has zero length or -contains all blanks. The program will recover by ignoring the OPEN statement. -"/gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/lnd/clm/src/riverroute/RtmMod.F90", line -241: 1525-001 The READ statement on the file fort.1 cannot be completed because the end -of the file was reached. The program will stop. - -Running: ./ccsm.exe -Please wait... - -Memory usage for ./ccsm.exe (task # 0) is: 51696 KB. Exit status: 1. Signal: 0 - -Although the example is from an earlier version of the model it still serves to -illustrate finding problems from the ccsm log file. - - -When working with the ccsm log file, for a run-time problem, you will need to be able -to separate it's output into three categories: pre-crash, crash, and post-crash. The -pre-crash section is everything that is normal output for good operation of the model. -The crash section is the section where the model dies and reports on the actual problem. -the post-crash section is the cleanup and finalization after the model dies. The most -important part of this of course is the crash section. The tricky part is distinguishing -it from the other sections. Also because the ccsm log file most likely has duplicated -output from multiple processors it is even more difficult to distinguish the different -sections and to some extent the sections may be intertwined, as different processors -reach the different sections at different times. Because, of this reducing the number of -processors for your simulation may help you sort out the output in the file (see -). Also much of the output from the ccsm log file are -system level information having to do with &mpi; multiprocessing. Usually you can ignore -this information, but it makes it more difficult to trudge through. - - -Sometimes the ccsm log file is the ONLY file available, because the model terminates -early in initialization. In this case understanding the output in the ccsm log file -becomes even more important. This also indicates the model did NOT advance far enough -to reach the initialization of the individual model components. This may mean that the -initialization of the multiprocessing for &mpi; and/or &omp; failed, or that the -reading of the driver namelist file "drv_in" failed. - - -Here we show those three sections for a ccsm log file where a two task job failed on -reading the namelist file. For a typical job with many tasks similar sections of this -will be repeated not just twice but for each task and hence make it harder to read. - - -Pre-crash section of the ccsm log file - -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. -ATTENTION: 0031-378 MP_EUIDEVICE setting ignored when LoadLeveler is not being used. -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. - 0:INFO: 0031-724 Executing program: </usr/local/lsf/7.0/aix5-64/bin/lsnrt_run> - 1:INFO: 0031-724 Executing program: </usr/local/lsf/7.0/aix5-64/bin/lsnrt_run> - 0:/contrib/bin/ccsm_launch: process 401894 bound to logical CPU 0 on host be0310en.ucar.edu ... - 1:/contrib/bin/ccsm_launch: process 439264 bound to logical CPU 1 on host be0310en.ucar.edu ... - 0:INFO: 0031-619 64bit(us, Packet striping on) ppe_rmas MPCI_MSG: MPI/MPCI library was compiled on Wed Aug 5 13:36:06 2009 - 0: - 1:LAPI version #14.26 2008/11/23 11:02:30 1.296 src/rsct/lapi/lapi.c, lapi, rsct_rpt53, rpt53s004a 09/04/29 64bit(us) library compiled on Wed Apr 29 15:30:42 2009 - 1:. - 1:LAPI is using lightweight lock. - 0:LAPI version #14.26 2008/11/23 11:02:30 1.296 src/rsct/lapi/lapi.c, lapi, rsct_rpt53, rpt53s004a 09/04/29 64bit(us) library compiled on Wed Apr 29 15:30:42 2009 - 0:. - 0:LAPI is using lightweight lock. - 0:Use health ping for failover/recovery - 1:Use health ping for failover/recovery - 0:Initial communication over instance 2. - 1:Initial communication over instance 0. - 1:IB RDMA initialization completed successfully - 1:The MPI shared memory protocol is used for the job - 0:IB RDMA initialization completed successfully - 0:LAPI job ID for this job is: 1684890719 - 0:The MPI shared memory protocol is used for the job - 0:(seq_comm_setcomm) initialize ID ( 7 GLOBAL ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 2 ATM ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 1 LND ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 4 ICE ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 5 GLC ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 3 OCN ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 6 CPL ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 8 CPLATM ) join IDs = 6 2 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 9 CPLLND ) join IDs = 6 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 10 CPLICE ) join IDs = 6 4 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 11 CPLOCN ) join IDs = 6 3 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 12 CPLGLC ) join IDs = 6 5 ( npes = 2) ( nthreads = 1) - 0: - 0: (seq_comm_printcomms) ID layout : global pes vs local pe for each ID - 0: gpe LND ATM OCN ICE GLC CPL GLOBAL CPLATM CPLLND CPLICE CPLOCN CPLGLC nthrds - 0: --- ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ - 0: 0 : 0 0 0 0 0 0 0 0 0 0 0 0 1 - 1: 1 : 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1: - 0: (t_initf) Read in prof_inparm namelist from: drv_in - 1: (seq_io_init) cpl_io_stride, iotasks or root out of bounds - resetting to defaults 4 0 1 - 0: piolib_mod.f90 1353 1 2 1 2 - 1: piolib_mod.f90 1353 1 2 1 2 - 0: pio_support::pio_die:: myrank= 0 : ERROR: piolib_mod.f90: 1354 : not enough procs for the stride - 1: pio_support::pio_die:: myrank= 1 : ERROR: piolib_mod.f90: 1354 : not enough procs for the stride - - - -Crash section of the ccsm log file - - 0: - 0: Traceback: - 1: - 1: Traceback: - 0: Offset 0x00000c4c in procedure __pio_support_NMOD_piodie, near line 88 in file pio_support.F90.in - 1: Offset 0x00000c4c in procedure __pio_support_NMOD_piodie, near line 88 in file pio_support.F90.in - 0: Offset 0x00000fd0 in procedure __piolib_mod_NMOD_init, near line 1354 in file piolib_mod.F90 - 1: Offset 0x00000fd0 in procedure __piolib_mod_NMOD_init, near line 1354 in file piolib_mod.F90 - 1: Offset 0x00000398 in procedure __seq_io_mod_NMOD_seq_io_init, near line 247 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/shr/seq_io_mod.F90 - 0: Offset 0x00000398 in procedure __seq_io_mod_NMOD_seq_io_init, near line 247 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/shr/seq_io_mod.F90 - 0: Offset 0x0001aa88 in procedure ccsm_driver, near line 465 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/driver/ccsm_driver.F90 - 0: --- End of call chain --- - 1: Offset 0x0001aa88 in procedure ccsm_driver, near line 465 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/driver/ccsm_driver.F90 - 1: --- End of call chain --- - - - -Post-crash section of the ccsm log file - - 1:Communication statistics of task 1 is associated with task key: 1684890719_1 - 0:Communication statistics of task 0 is associated with task key: 1684890719_0 - 0: - 0:Running: ./ccsm.exe - 0:Please wait... - 0: - 0:Memory usage for ./ccsm.exe (task # 0) is: 198892 KB. Exit status: 134. Signal: 0 - 1: - 1:Running: ./ccsm.exe - 1:Please wait... - 1: - 1:Memory usage for ./ccsm.exe (task # 0) is: 198572 KB. Exit status: 134. Signal: 0 -INFO: 0031-656 I/O file STDOUT closed by task 0 -INFO: 0031-656 I/O file STDERR closed by task 0 -ERROR: 0031-250 task 0: IOT/Abort trap -INFO: 0031-656 I/O file STDOUT closed by task 1 -INFO: 0031-656 I/O file STDERR closed by task 1 -ERROR: 0031-250 task 1: IOT/Abort trap -INFO: 0031-639 Exit status from pm_respond = 0 -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. -Job /usr/local/lsf/7.0/aix5-64/bin/poejob /contrib/bin/ccsm_launch /contrib/bin/job_memusage.exe ./ccsm.exe - -TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME -===== ========== ================ ======================= =================== -00000 be0310en /contrib/bin/ccs Exit (134) 08/31/2010 12:32:57 -00001 be0310en /contrib/bin/ccs Exit (134) 08/31/2010 12:32:57 - - - - - -The &clm; log file - -Of course when you are working with and making changes to &clm;, most of your focus -will be on the &clm; log file and the errors it shows. As already pointed out -if you don't see errors in the lnd.log.* file you should look -in the ccsm.log.* to see if any errors showed up there. - - -Here's an example of the lnd.log.* file when running -&PTSMODE; with initial conditions (this is bug 1025 in the &KnownBugs; file). - - Successfully initialized variables for accumulation - - reading restart file I2000CN_f09_g16_c100503.clm2.r.0001-01-01-00000.nc - Reading restart dataset - ERROR - setlatlon.F:Cant get variable dim for lat or lsmlat - ENDRUN: called without a message string - - - - - -The &datm; log file - -When working with "I cases" the second most common problems after &clm; problems are -problems with the data atmosphere model. So examining the atm.log.* -is important. - - -Here's an example of a problem that occurs when the wrong prescribed aerosol file -is given to a pt1_pt1 simulation. - -(datm_comp_init) atm mode = CLMNCEP -(shr_strdata_init) calling shr_dmodel_mapSet for fill -(shr_strdata_init) calling shr_dmodel_mapSet for remap - ('shr_map_getWts') ERROR: yd outside bounds 19.5000000000000000 -(shr_sys_abort) ERROR: ('shr_map_getWts') ERROR yd outside 90 degree bounds -(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping - - - - - -The batch log files - -The names of the batch log files will depend on the batch system of the machine -that is being used. They will normally be in the script directory. Usually, they -don't contain important information, but they are a last resort place to look for -error messages. On the &ncar; IBM system "bluefire" the batch files are called -with names that start with "poe" and then either "stderr" or "stdout", with the -job number at the end. - - - - - - -General Advice on Debugging Run time Problems - -Here are some suggestions on how to track down a problem while running. In general -if the problem still occurs for a simpler case, it will be easier to track down. - -Run in DEBUG mode -Run with a smaller set of processors -Run in serial mode with a single processor -Run at a lower resolution -Run a simpler case -Run with a debugger - - - - -Run in DEBUG mode - -The first thing to try is to run in DEBUG mode so that float point trapping will be -triggered as well as array bounds checking and other things the compiler can turn -on to help you find problems. To do this edit the &envbuild; file and set DEBUG - to TRUE as follows: - -> ./xmlchange -file env_build.xml -id DEBUG -val TRUE - - - - - -Run with a smaller set of processors - -Another way to simplify the system is to run with a smaller set of processors. You -will need to clean the configure and edit the env_mach_pes.xml. -For example, to run with four processors: - -> ./configure -cleanall -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val 4 -> ./configure -case - -Another recommended simplification is to run without threading, so set the -NTHRDS for each component to "1" if it isn't already. Sometimes, -multiprocessing problems require a certain number of processors before they occur -so you may not be able to debug the problem without enough processors. But, it's always -good to reduce it to as low a number as possible to make it simpler. For threading -problems you may have to have threading enabled to find the problem, but you can run -with 1, 2, or 3 threads to see what happens. - - - - -Run in serial mode with a single processor - -Simplifying to one processor removes all multi-processing problems and makes -the case as simple as possible. If you can enable USE_MPI_SERIAL -you will also be able to run interactively rather than having to submit to a job -queue, which sometimes makes it easier to run and debug. If you can use -USE_MPI_SERIAL you can also use threading, but still run interactively -in order to use more processors to make it faster if needed. - -> ./configure -cleanall -# Set tasks and threads for each component to 1 -# You could also set threads to something > 1 for speed, but still -# run interactively if threading isn't an issue. -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_ATM -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_LND -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_ICE -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_OCN -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_CPL -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_GLC -val 1 -# If mpi-serial capability is available on the machine you are using -# set USE_MPI_SERIAL to true so that you can run interactively -> ./xmlchange -file env_conf.xml -id USE_MPI_SERIAL -val TRUE -> ./configure -case -# Then build your case -# And finally run, by running the *.run script interactively -# (If you were able to set USE_MPI_SERIAL to true) - - - - - -Run at a lower resolution - -If you can create a new case running at a lower resolution and replicate the problem -it may be easier to solve. This of course requires creating a whole new case, and trying -out different lower resolutions. - - - - -Run a simpler case - -Along the same lines, you might try running a simpler case, trying another compset -with a simpler setup and see if you can replicate the problem and then debug from that -simpler case. Again, of course you will need to create new cases to do this. - - - - -Run with a debugger - -Another suggestion is to run the model with a debugger such as: dbx, -gdb, or totalview. Often to run with a debugger -you will need to reduce the number of processors as outlined above. Some debuggers such -as dbx will only work with one processor, while more advanced -debuggers such as totalview can work with both &mpi; tasks and OMP -threads. Even simple debuggers though can be used to query core files, to see where -the code was at when it died (for example using the where in -dbx for a core file can be very helpful. For help in running -with a debugger you will need to contact your system administrators for the machine -you are running on. - - - - - - - - diff --git a/doc/design/directory_organization.rst b/doc/design/directory_organization.rst new file mode 100644 index 0000000000..eee5db90ae --- /dev/null +++ b/doc/design/directory_organization.rst @@ -0,0 +1,18 @@ +.. sectnum:: + +.. contents:: + +===================================================== + General notes about file and directory organization +===================================================== + +- Various checklists (useful for developers) are scattered throughout the repository, in + the location that is most closely related to the given process. To aid discovery of + these checklists, these have the naming convention ``README.CHECKLIST.*``. + +- Unit tests are stored in the ``test`` subdirectory of each ``src`` directory. For + example, unit tests of biogeophysics modules reside in + ``src/biogeophysics/test``. Within each test subdirectory, there are further + subdirectories for each set of unit tests. These typically correspond to a single module + (e.g., ``src/biogeophysics/test/Irrigation_test`` contains tests of + ``src/biogeophysics/IrrigationMod.F90``), but that is not a strict requirement. diff --git a/doc/design/oo_design.rst b/doc/design/oo_design.rst index 6d2a355867..30eba818cd 100644 --- a/doc/design/oo_design.rst +++ b/doc/design/oo_design.rst @@ -14,4 +14,18 @@ CESM (possibly because of compiler bugs that prevented the general use of constr this purpose?). As more object orientation was added, we continued to use an ``Init`` method for this purpose to remain consistent with existing code. -At this point, we could probably refactor this to use constructors. +We could probably refactor this to use constructors. However, we still occasionally run +into trouble with some compilers in the assignment that results from writing:: + + foo_inst = foo_type(...) + +Some components seem to get set to garbage occasionally with some compilers when doing +that. (This was encountered 2018-09-11 with intel17.0.1). It's possible that this is user +error rather than a compiler bug, but in any case, it's harder to get that to work +robustly. So for now, we're generally sticking with using:: + + call foo_inst%Init(...) + +rather than:: + + foo_inst = foo_type(...) diff --git a/doc/design/water_tracers.rst b/doc/design/water_tracers.rst new file mode 100644 index 0000000000..b52d653393 --- /dev/null +++ b/doc/design/water_tracers.rst @@ -0,0 +1,172 @@ +.. sectnum:: + +.. contents:: + +================================== + Overview of this design document +================================== + +This documents some of the high-level design decisions in the implementation of water +tracers, which are used for water isotopes and potentially other tracers. + +============================================================= + Distinction between bulk-only vs. bulk-and-tracer variables +============================================================= + +Options considered for how to set up the water data structures +============================================================== + +Some water variables need to have separate instances for each water tracer, whereas some +apply only to bulk water. An example of the latter is snow depth. + +Broadly speaking, we considered three ways to store information for each tracer: + +1. Single instance of ``waterstate_type`` (etc.), with an extra dimension on arrays for + which we need values for each tracer. Bulk water is the first index in these arrays. + +2. Like (1), single instance of ``waterstate_type`` (etc.), with an extra dimension on + arrays for which we need values for each tracer. Bulk water is a separate variable, so + we have things like ``h2osoi_liq_col(c,j)`` for bulk, and + ``h2osoi_liq_col_tracer(c,j,m)`` for tracers). + +3. Multiple instances of ``waterstate_type`` (etc.), with no extra dimension required for + individual variables. + +We decided to go with option (3) for a number of reasons: + +1. This is consistent with what is done for carbon isotopes. It has felt like this design + has worked well for carbon isotopes, and we felt it made sense to keep these two + consistent unless there was a good reason to treat them differently. + +2. With the object-oriented design laid out in `Object-oriented design for water tracer + types`_, it is easy to change a variable from bulk-only to bulk-and-tracer, or vice + versa. + +3. In contrast to (1), science routines that operate on bulk water can be written without + needing to worry about the extra dimension. Similarly, unit tests remain relatively + easier to set up. + +4. In contrast to (2), tracers get their history and restart variables added + automatically, avoiding duplication and the potential of getting out-of-sync with the + bulk. + +5. We can explicitly pass the bulk instance of (e.g.) ``waterstate_type`` to science + routines that expect to be operating on this bulk instance, making the intent of code + more clear. + +6. Compared with (1), it's easier to search the code for where tracers are handled. + +There were some downsides to this option, though, both short-term and long-term: + +1. This required more up-front work to set up the object-oriented infrastructure + +2. As discussed in more depth in `All water-related variables should go in one of the + water* types`_, this required moving all water-related fluxes into one of the main + water types, rather than having water variables distributed amongst science + modules. However, even with one of the other possible designs, we might have wanted to + move these variables, because with any of these designs: Any derived type with water + variables needs to have extra infrastructure for dealing with water tracers. So if we + kept water variables distributed amongst various types, this tracer-handling would also + be distributed in many places. + +Object-oriented design for water tracer types +============================================= + +The object-oriented design for water tracer types was fleshed out in discussions here: +https://github.com/ESCOMP/ctsm/pull/395. + +One item of particular note is that we use inheritance to define the full list of +variables used for bulk water: The set of bulk water variables is the set of +bulk-and-tracer variables plus some additional variables that just apply to bulk water; we +avoid duplication by having bulk types that extend the basic types (e.g., +``waterstatebulk_type`` extends ``waterstate_type``). Some benefits of this +inheritance-based design are: + +1. Having a separate derived type for bulk water allows science routines to declare that + they expect an argument of the bulk water type. + +2. This allows us to easily migrate variables back and forth between being bulk-only or + being bulk-and-tracer: You can simply move the variable (along with its associated + allocations, history addfld calls, etc.) between (for example) ``waterstatebulk_type`` + and ``waterstate_type`` without needing to change all of the science modules that + reference that variable (because they generally reference it through the bulk + instance). + +All water-related variables should go in one of the water* types +================================================================ + +An implication of this design (discussed in greater detail here: +https://github.com/ESCOMP/ctsm/pull/395#issuecomment-392299340) is that all water +variables should be defined in one of the centralized water* types. This is in contrast to +our general desire to have variables live in the modules that compute them. This is needed +to avoid having to split up a bunch of science modules into two types: a type that needs +multiple instances (for each water tracer) and a type that only needs a single instance +(for bulk water, or variables that are not water-related at all). + +We would still like to keep some variables local to the science modules – especially +variables that can be made private to those modules. But the fluxes were never handled in +a completely (textbook) object-oriented fashion anyway, since they were accessed publicly +by other modules, so we're not too sad to move these public flux variables back out to the +generic flux types. And while this has the disadvantage of losing the attachment of a +variable to the module that computes that variable, it has some advantages, too, in terms +of understanding the suite of water flux variables, and reducing the number of instances +that need to get passed all around (e.g., we won't need to pass irrigation_inst to as many +places). + +======================== + Loops over all tracers +======================== + +Initially, I was hoping that we could keep loops over tracers in WaterType, for the +following reasons: + +1. To keep this complexity out of other modules + +2. To make it easier to change the details of how the bulk and tracer instances are + stored, if we ever need to: By keeping as many of the loops as possible in WaterType, + we reduce the number of places that would need to be changed + +However, it was starting to get too awkward to require all loops over tracers to happen in +WaterType (or some other centralized location): I had originally imagined that we wouldn't +need too many loops over tracers, but it turns out that we need loops over tracers in a +lot of places. Requiring all of these loops over tracers to be in WaterType both (a) +bloats that module, and (b) adds extra indirection (which makes it harder to understand +the code, because you're bouncing back and forth between more modules, and has possible +performance implications as we break routines into tiny pieces for this purpose). + +So we allow loops over tracers (or bulk plus tracers) anywhere in the code. See comments +at the top of WaterType.F90 for example code showing how to write these loops. + +Note that the bulk instances (``waterfluxbulk_inst``, etc.) can be obtained in two ways: + +1. Using ``water_inst%water*bulk_inst`` + +2. As one of the indices in ``water_inst%bulk_and_tracers(:)%water*_inst`` + +Method (2) is just meant to be used when you are doing the same operation on bulk water +and all water tracers. Reasons why it is better, or necessary, to use method (1) when you +are really just working with bulk water are: + +- This makes it more explicit and clear that you are working with bulk water + +- When passing an argument to a subroutine whose dummy argument is of type + ``water*bulk_type``, method (2) only works if you surround the call with a ``select + type`` statement, which is awkward, to say the least. (Subroutines that expect bulk + water should generally declare their dummy arguments to be of type ``water*bulk_type``, + as discussed in `Object-oriented design for water tracer types`_.) + +============================================== + Infrastructure for looping through variables +============================================== + +Some operations (for now just the tracer consistency check) need to be run on every water +tracer. In order to facilitate this, and to reduce the likelihood that a variable will +accidentally be left out of the tracer consistency check, we have introduced +infrastructure for holding a list of pointers to all tracer-related variables. + +Variables in all of the types that apply to water tracers as well as bulk should be +allocated via the routines ``AllocateVar1d`` or ``AllocateVar2d``, rather than simple +``allocate`` statements. These routines add a pointer to the given variable in the +appropriate water tracer container structure. This allows us to later loop through all +such variables in order to call the tracer consistency check (and later, possibly other +routines as well) on each variable. diff --git a/doc/release-clm5.0.ChangeLog b/doc/release-clm5.0.ChangeLog deleted file mode 100644 index 4d43ab1115..0000000000 --- a/doc/release-clm5.0.ChangeLog +++ /dev/null @@ -1,3299 +0,0 @@ -=============================================================== -Tag name: release-clm5.0.30 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Tue Jan 21 13:50:48 MST 2020 -One-line Summary: Update FATES to sci.1.30.0_api.8.0.0 - -Purpose of this version: ------------------------- - -Update FATES to sci.1.30.0_api.8.0.0, and point to the NGEET version, rather -than NCAR/fates-release version. - -One change to soil-moisture (also check if gridcell weight is non-zero, before specifying prescribed soil moisture. -Also update mosart with cold start bug fix. Update rtm, cism, and cime to versions on cesm2.1.2 release tag. -Fix some issues with PTCLM. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #847 #871 - Fixes #847 -- issues with prescribed soil moisture - Fixes #871 -- don't check for valid resolution for CESM cases by default - -Science changes since: release-clm5.0.28 - FATES science update from sci-1.27.1 to sci.1.30.0 - -Software changes since: release-clm5.0.28 - FATES API update from api.7.3.0 to api.8.0.0 - -Changes to User Interface since: release-clm5.0.28 - fates paramfile is updated - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (35 tests are different because of fates param file update) - - unit-tests (components/clm/src): - - cheyenne - PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - izumi_nag --------- OK - izumi_pgi --------- OK - izumi_intel ------- OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: Yes, but only when running with FATES - - Summarize any changes to answers, i.e., - - what code configurations: with FATES active - - what platforms/compilers: all - - nature of change: similar climate - -Detailed list of changes: ------------------------- - -Externals being used: all externals updated - - cism: cism-release-cesm2.1.2_01 - rtm: release-cesm2.0.04 - mosart: release-cesm2.0.04 - cime: cim5.6.28 - FATES: sci.1.30.0_api.8.0.0 - PTCLM: PTCLM2_20200121 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #846 -(https://github.com/ESCOMP/ctsm/pull) - #846 -- Update to fates sci.1.30.0_api.8.0.0 - -=============================================================== -=============================================================== -Tag name: release-clm5.0.29 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Tue Nov 19 12:14:02 MST 2019 -One-line Summary: Some answer changes needed for prescribed soil-moisture and clm4_5 defaults (1850-ndep, and urbantv settings) - -Purpose of this version: ------------------------- - -Some answer changes needed for prescribed soil-moisture. And clm4_5 defaults for 1850 Nitrogen deposition and or urbantv -settings were made to be consistent with clm5_0. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #175, #817, #832 #833 - - Fixes #817 -- Have clm4_5 use the same ndep file as clm5_0 for 1850 - Fixes #175 -- Have clm4_5 use the same settings for urbantv years as clm5_0 - Fixes #832 -- don't override with missing value, let the model set it - Fixes #833 -- time interpolation of soilm causes bad values for some missing points - -Science changes since: release-clm5.0.28 - - Defaults for clm4_5, prescribed soil-moisture - - Some defaults were changed for clm4_5 to be consistent with clm5_0 (use of the same 1850-ndep file, - and changes in the urbantv year settings) - - Prescribed soil-moisture was changes so that if time-interpolation produces large values, they - will be marked as missing (spval). Also points where the input prescribed soil moisture is missing - are now ignored (and run normally). - -Software changes since: release-clm5.0.28 - - -Changes to User Interface since: release-clm5.0.28 - - Behavior of soilm_ignore_data_if_missing changes! - - Behavior of soilm_ignore_data_if_missing changes. Now if true will ignore any points - where the prescribed soil moisture dataset is missing. So for these points the model - will run normally (as if prescribed soil moisture was off). Before it would mark them - as missing, but modify h2osoi_ice/liq in an odd fashion. - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (10 tests are different) - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - NOT run - hobart --- NOT run - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - NOT run - hobart --- NOT run - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - izumi_nag --------- OK - izumi_pgi --------- OK - izumi_intel ------- OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: Yes for some! prescribed soil-moisture and clm4_5 (1850-ndep, and urbantv settings) - - Summarize any changes to answers, i.e., - - what code configurations: prescribed soil-moisture, or clm4_5 due to default changes in 1850-ndep and urbantv - - what platforms/compilers: all - - nature of change: similar climate - - Will new REFCASES need to be made for cesm and/or CAM?: No - -Detailed list of changes: ------------------------- - -Externals being used: No changes - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.03 - mosart: release-cesm2.0.03 - cime: cim5.6.25 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #841 -(https://github.com/ESCOMP/ctsm/pull) - - #841 -- Some answer changes for release branch - -=============================================================== -=============================================================== -Tag name: release-clm5.0.28 -Originator(s): erik (Erik Kluzek) -Date: Thu Nov 14 23:03:39 MST 2019 -One-line Summary: Several bit-for-bit fixes especially around soil-moisture streams - -Purpose of this version: ------------------------- - -A list of several bit-for-bit fixes. Some very minor and other's more extensive. - -mksurfdata_map was extended so that when you specify vegetation types, you can let it use the natural and crop coverage -from the input datasets. This allows you to for example run a global simulation with all vegetation types in every grid cell. -This can be useful in seeing what types of vegetation grow in each grid cell. Also simplify some of the logic that allowed -for old format PFT datasets that didn't include crop information. Since, we don't have or need to work with such datasets -this complex logic could be removed. Also added some new unit tests for mksurfdata and the defining PFT values. - -Add time interpolation alogrithm type to most of the stream files, so it can be changed via namelist. Add historical data to the -Nitrogen deposition future scenario datasets. - -Add namelist control variables for soilm_offset, and tint_algo for most of the streams. tint_algo allows you to control the time -interpolation and change it to a simpler one (like upper) in order to show that the streams output agrees with the streams data -input. soilm_offset allows the user to change the time-stamp offset if the time-stamp isn't at the middle of averaging interval. -This is important for the soil moisture streams for a case where you want to use the output of a CTSM simulation for soil-moisture -as normally the time-stamp is the end of the interval (so you could use -1296000 to roughly compensate for the time-stamps to be -at the end of the month rather than mid-month). Add a namelist item to continue when soil moisture is prescribed and a gridpoint -is missing on the input streams file, but required for the simulation running. Also add an optional history field H2OSOI_PRESCRIBED_GRC -that corresponds to the input soil moisture streams, so you can ensure the prescribe soil moisture is working correctly and agrees -with the input dataset. - -Fix the threading bug for soil-moisture and LAI streams. This is done by adding a new "advance" subroutine that does the streams -advance part of the calculation in a non-OpenMP area of the CLM driver, while the "interp" subroutine remains in the Open-MP -loop. - -Include missing prescribed testmods directory. Allow branches with use_init_interp=T with a log message about it. -Move tests from hobart to izumi. - -This is bit-for-bit - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #809, #804, #786, #702, #791, #150 #830, #831, #832, #836 - Fixes #809 -- mkmapdata old version of intel - Fixes #804 -- allow mksurfdata_map to prescribe vegetation cover for globe - Fixes #786 -- allow use_init_interp for a branch - Fixes #702 -- add historical period to start of ndep SSP files - Fixes #791 -- fix threading for prescribed LAI and soil-moisture - Fixes #150 -- remove extra logic in mksurfdata_map for old format and missing crops - Fixes #830 -- time offset is assumed to be zero for soil moisture streams - Fixes #831 -- add namelist tint_algo settings for input streams - partial for #832 -- an option to override if soil moisture stream has missing data where needed - Fixes #836 -- add izumi as a place that can run tools tests - -Science changes since: release-clm6.0.27 - None, answers are the same. Some more flexibility was added with namelist control as follows in the next section. - -Software changes since: release-clm6.0.27 - New namelist items: ndep_tintalgo, soilm_offset, soilm_ignore_data_if_missing, lai_tintalgo, lightng_tintalgo, popdens_tintalgo - urbantv_tintalgo - If maxpatch_pft's is not set to a regular value (with or without crops) will now abort, with an option to override if needed - - Move tests from hobart to izumi. prescribed test-mod directory that wasn't there before is now there. - Add some assert debug checking for lai and soilm streams. - Add some new unit tests for mksurfdata_map - -Changes to User Interface since: release-clm6.0.27 - Note, that streams text files are now legitimate XML files - -Testing: regular --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - izumi ---- Not working (needs a cime update) - - tools-tests (components/clm/test/tools): - - cheyenne - OK - hobart --- OK - izumi ---- OK - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_intel ------ OK - izumi_nag --------- OK - izumi_pgi --------- OK (fail on run needs some cime updates) - izumi_intel ------- OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: No (bit-for-bit) (other than two tests on hobart because of cime issue #3302) - -Detailed list of changes: ------------------------- - -Externals being used: Update cime - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.03 - mosart: release-cesm2.0.03 - cime: cim5.6.25 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #814 -(https://github.com/ESCOMP/ctsm/pull) - #814 -- A few fixes and extend mksurfdata to set PFT/CFT fractions but use veg-cover from dataset - -=============================================================== -=============================================================== -Tag name: release-clm5.0.27 -Originator(s): erik (Erik Kluzek) -Date: Tue Aug 13 14:31:50 MDT 2019 -One-line Summary: Add presoribed soil moisture streams as an option, and a few fixes - -Purpose of this version: ------------------------- - -Add new prescribed moisture streams feature from Sean Swenson. This allows the user -to specify a steams file for soil moisture and use it in place of the model prognostically -determining soil moisture. To turn it on set use_soil_moisture_streams=T. You can also -set the filename to use with stream_fldfilename_soilm, and there are other _soilm namelist -items to control the years to run over. The file MUST be on the same grid as the model resolution. - -Update 0.125x0.125 mapping and surfdata data, and fix hirespft data issues. Update cime -with SSP1-2.6 presaero data. So now can run the SSP1-2.6 CMIP6 future scenario. -Update rtm release branch to rtm1_0_69, which brings in a fix for cold starts. - -Move mksurfdata changes from ctsm1.0.dev053 over, which fixes a rare soil color bug. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #757 #629 #343 #276 - Fixes #757 -- Softlinks in inputdata repo saved as a link rather than a datafile - Fixes #629 -- Remove unused fields on surface datasets (add option for glc fields) - Fixes #343 -- Move config_archive to ctsm - Fixes #276 -- Add some CLM tests for CESM to run - -CIME Issues fixed (include issue #): #3163 #3170 - #3170 -- fixes creation of empty file from inputdata download - #3163 -- JOB_WALLCLOCK error - -Science changes since: release-clm5.0.26 - Add SSP1-2.6 prescribed aerosol - Fix soil color bug in mksurfdata_map - -Software changes since: release-clm5.0.26 - Add ability to run with prescribed soil moisture streams - -Changes to User Interface since: release-clm5.0.26 - New soil_moisture_streams namelist - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - OK - hobart --- OK - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - hobart --- OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: No bit-for-bit - -Detailed list of changes: ------------------------- - -Externals being used: Update cime and rtm - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.03 - mosart: release-cesm2.0.03 - cime: cim5.6.20 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: ctsm1.0.dev053 - -Pull Requests that document the changes (include PR ids): #781 -(https://github.com/ESCOMP/ctsm/pull) - - #781 -- Prescribed soil moisture on release branch and some other updates and fixes - -=============================================================== -=============================================================== -Tag name: release-clm5.0.26 -Originator(s): sacks (Bill Sacks) -Date: Mon Jul 29 18:11:26 MDT 2019 -One-line Summary: Add a CN precision control call to fix problems related to small negative values - -Purpose of this version: ------------------------- - -Small negative values (roughly roundoff-level different from zero) in -frootc (and possibly other quantities) were occasionally creating -problems with carbon isotope fluxes and FPI in the first time step of -the year, at the time of transient landcover change. This tag fixes the -problem by introducing an extra call to SoilBiogeochemPrecisionControl -in between computing the patch-level transient landcover fluxes and -moving these to column-level. In particular, this truncates small -negative values of decomp_cpools_vr_col to zero, which prevents the -previous blow-ups. - -For most of the problematic fields, the explanation seems to be: frootc -can sometimes be negative; this is intentional. Negative frootc causes -negative dwt_frootc_to_litter if the patch in question is shrinking. The -resulting negative fluxes cause problems in the ciso calculation. This -can be worked around by inserting an extra precision control call -between the calculation of the dwt fluxes and the ciso fluxes, so that -small negative dwt fluxes are set to 0. - -This does not necessarily fully explain the issue with FPI, but the -insertion of the extra precision control call fixes that issue, too. - -For more details, see the discussion in -https://github.com/ESCOMP/ctsm/issues/741 - - -CTSM Master Tag This Corresponds To: N/A - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#741 - -Science changes since: release-clm5.0.25 - None - -Software changes since: release-clm5.0.25 - Extra call to SoilBiogeochemPrecisionControl - -Changes to User Interface since: release-clm5.0.25 - None - -Testing: --------- - - build-namelist tests: - - cheyenne - not run - - unit-tests (components/clm/src): - - cheyenne - not run - hobart --- not run - - tools-tests (components/clm/test/tools): - - cheyenne - not run - hobart --- not run - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - not run - hobart --- not run - - regular tests (aux_clm): - - cheyenne_intel ---- ok - cheyenne_gnu ------ ok - hobart_nag -------- ok - hobart_pgi -------- ok - hobart_intel ------ ok - - ok means tests pass (other thana expected failures), answers change - as expected for some tests - - regular tests (prealpha): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - - regular tests (prebeta): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: Transient cases and a few other - configurations as noted below - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff / same climate - - According to Keith Oleson's analysis of the LMWG diagnostics: - Changes are possibly greater than roundoff-level, but are not - climate changing or scientifically meaningful. - - Other than transient cases (including cases with transient glacier - area as well as those with transient natural vegetation / crop - area), the test suite showed differences in the following cases: - - - Two present-day tests that specify changes in soil layer - structure - (ERI_D_Ld9.ne30_g16.I2000Clm50BgcCruGs.cheyenne_intel.clm-vrtlay - and - ERS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_intel.clm-deepsoil_bedrock), - have changes in many fields (for the latter: mostly looks - roundoff-level, but a few greater than roundoff-level diffs) - - - The present-day ciso test, - ERP_D_Ld5.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_gnu.clm-ciso_flexCN_FUN, - has changes in a few c13 and c14 fields - - - There are changes in many fields in SSP tests - - - ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_intel.clm-noFUN_flexCN - (and a similar test on hobart) have roundoff-level changes in - SMINN_vr, SMIN_NH4_vr and SMIN_NO3_vr - - URL for LMWG diagnostics output for new climate: - http://webext.cgd.ucar.edu/I20TR/clm50_cesm20R_2deg_GSWP3V1_issue741_hist/lnd/clm50_cesm20R_2deg_GSWP3V1_issue741_hist.1995_2014-clm50_cesm20R_2deg_GSWP3V1_hist.1995_2014/setsIndex.html - - Will new REFCASES need to be made for cesm and/or CAM?: No - (This will likely be true if the LII tests failed) - -Detailed list of changes: ------------------------- - -Externals being used: No updates - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cim5.6.16 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): None -(https://github.com/ESCOMP/ctsm/pull) - -=============================================================== -=============================================================== -Tag name: release-clm5.0.25 -Originator(s): erik (Erik Kluzek) -Date: Wed May 29 11:16:13 MDT 2019 -One-line Summary: Change two files from NetCDF-4 format to NetCDF-3 (because some machines have trouble with NetCDF-4 in pnetcdf) - -Purpose of this version: ------------------------- - -There are two files in NetCDF-4 format that the model uses. Copy these files to NetCDF-3 classic format and point -to the new version in the CLM XML database (use nccopy -k classic). There are some machines that have trouble with -reading NetCDF-4 files in pnetcdf. - -There are still some NetCDF-4 files for mksurfdata_map, but some of these are required to be in NetCDF-4 format. And we only -support mksurfdata_map and mkmapdata on cheyenne. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #734 - Fixes #734 -- Isotope historical files are in NetCDF-4 format need them in NetCDF-3 or NetCDF-5 - -Science changes since: release-clm5.0.24 - None - -Software changes since: release-clm5.0.24 - None - -Changes to User Interface since: release-clm5.0.24 - None - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (6 tests compare different to baseline) - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (prealpha): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: No! bit-for-bit - -Detailed list of changes: ------------------------- - -Externals being used: No updates - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cim5.6.16 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #737 -(https://github.com/ESCOMP/ctsm/pull) - - #737 -- Convert the file from NetCDF-4 classic format to NetCDF-3 classic format - -=============================================================== -=============================================================== -Tag name: release-clm5.0.24 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Wed May 22 13:33:48 MDT 2019 -One-line Summary: Correct ndep end year for SSPs, 2-degree CMIP6WACCMDECK with C-isotopes off, fixes mksurfdata for high resolution - -Purpose of this version: ------------------------- - -Fix a couple small issues. Correct end year for ndep for SSP's so can run to the end of 2100. Some fixes to mksurfdata_map for high -resolution surface datasets. Have 2-degree WACCM-CMIP6DECK match a user-mod directory without carbon isotopes on. Remove the -ne120np4 and conus_30_x8 surface dataset files, as they can't be used (see #673). - -Remove 8x16, 32x64 resolutions as they are no longer needed and there are problems with them. Add in the mapping files needed for -94x192. Check that special landunit percent area's is not less than 0.0, and don't let PCT_WET be less than zero for areas with -ocean (see #673). - -Change some of the longer single point tests to use Qian forcing (as faster, less memory, less problems). Add compsets for this. -This change was also done on master. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #673, #714, #716, #717, #726 - - Fixes #726 -- Some resolutions fail in mksurfdata_map - Fixes #717 -- Change end year for ndep to 2101 for SSP's - Fixes #716 -- 2 degree CMIP6WACCMDECK needs Carbon isotopes off - Fixes #714 -- Fails on cheyenne for some longer single point simulations - Fixes #673 -- Ice shelf wetland fix in mksurfdata_map can lead to glacier+lake > 100% on surface datasets - -Science changes since: release-clm5.0.23 - Turn Carbon isotopes off for 2-degree CMIP6WACCMDECK - -Software changes since: release-clm5.0.23 - End year for ndep is now 2101, so will run to end of 2100 - Fixes to mksurfdata_map for high resolutions - -Changes to User Interface since: release-clm5.0.23 - Remove ne120np, conus_30_x8 surface datasets - Remove 8x16, and 32x64 resolutions - Add 94x192 mapping files, so can work in mksurfdata_map - -Testinw: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (15 SSP tests are different as expected) - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart ---PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - hobart --- PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: No - -Detailed list of changes: ------------------------- - -Externals being used: (cime goes from branch to full tag) - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cim5.6.16 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #720 -(https://github.com/ESCOMP/ctsm/pull) - - #720 -- Fix a couple small issues, 2-degree no-ciso for WACCMDECK and ndep end year 2101 - -=============================================================== -=============================================================== -Tag name: release-clm5.0.23 -Originator(s): erik (Erik Kluzek) -Date: Wed May 15 15:31:15 MDT 2019 -One-line Summary: Update cime to bring in CO2 transient files for the CMIP6 SSP's as well as presaero for three of them - -Purpose of this version: ------------------------- - -With updated cime with transient CO2 for all CMIP6 SSP scenarios and prescribed aerosol files for three of -the CMIP6 SSP scenarios (SSP3-7.0, SSP2-4.5, SSP5-8.5). Previously all SSP scenaros would run, and use the -closest SSP nitrogen deposition file, now only the ones that are available work (Tier I). Also CLM4.5 used -the old CMIP5 ndep files, and now they use the CMIP6 ones available. - -Fix some small issues with some of the tools - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #707 #708 #711 #712 - Fixes #707 -- Missing mapping files for hirespft - Fixes #708 -- time_bnds not set by tools/ncl_scripts/getco2_historical.ncl - Fixes #711 -- Model assumes the closest SSP scenario for ndep - Fixes #712 -- Missing CO2 files for SSP1-1.9 and SSP4-3.4 - -New issues found: #714 -- Fails with cheyenne_gnu for some longer single point tests - -Science changes since: release-clm5.0.22 - Forcing period is different for present day compsets (I2000, I2003, and I2010) - SSP scenarios now have CMIP6 transient CO2 and presaero (for SP3-7.0, SSP2-4.5, SSP5-8.5) - clm4.5 will use CMIP6 SSP ndep datasets rather than CMIP5 - -Software changes since: release-clm5.0.22 - None - -Changes to User Interface since: release-clm5.0.22 - Now SSP cases that don't have needed datasets will fail - -Testing: regular --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - OK (36 tests are different as expected) - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (fates): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.22 - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: Present day compsets, SSP compsets, and Clm45 compsets - - what platforms/compilers: All - - nature of change: New datasets, new forcing period for present day - - Will new REFCASES need to be made for cesm and/or CAM?: No - (This will likely be true if the LII tests failed) - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: branch_tags/cime5.6.15_a01 (same as cim5.6.16) - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #713 -(https://github.com/ESCOMP/ctsm/pull) - #713 -- Fix a few issues, and update cime to a version with CO2 SSP files as well as three presaero SSP files - -=============================================================== -=============================================================== -Tag name: release-clm5.0.22 -Originator(s): erik (Erik Kluzek) -Date: Wed May 8 13:32:51 MDT 2019 -One-line Summary: Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change - -Purpose of this version: ------------------------- - -We currently have a bug so that for transient land-use change cases answers are different starting in soil -carbon when Carbon isotopes (use_c13, or use_c14) are on versus off. Answers are identical if there is no -land-use change. The bug does cause bulk Carbon (C12) to be slightly different, but qualitatively the same. -There is a significant impact to the Carbon isotope simulation however. The bug was causing changes in isotopic -pools to be directed to the bulk Carbon. Because, isotopes are so much smaller than bulk Carbon, this doesn't -cause a marked difference in the bulk Carbon simulation. But, the lack of the change in the isotopic pool -does have a meaningful impact on the simulation of the Carbon isotopic fields. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #262 #675 - Fixes #675 -- Carbon isotopes under transient land-use change - Fixes #262 -- hirespft option to mksurfdata.pl - -Issues found: #707 - #707 -- missing hirespft mapping files - -Science changes since: release-clm5.0.21 - Fix Carbon isotope issue under transient land-use change - -Software changes since: release-clm5.0.21 - Bring in mapping files for 3x3min MODISv2 grid for most resolutions - -Changes to User Interface since: release-clm5.0.21 - None - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart ---PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.21 - -Changes answers relative to baseline: Yes, but only when Carbon isotopes on under transient land-use change! - - Summarize any changes to answers: - - what code configurations: Bgc with use_c13 or use_c14 T and with a transient land-use change after each year boundary - - what platforms/compilers: All - - nature of change: same climate for bulk Carbon, isotopic Carbon is quite different for regions with land-use change - - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - /oleson/clm50_release-clm5.0.20_1deg_GSWP3V1_isofix2_hist - - URL for LMWG diagnostics output for new climate: -http://webext.cgd.ucar.edu/I20TR/clm50_release-clm5.0.20_1deg_GSWP3V1_isofix2_hist/lnd/clm50_release-clm5.0.20_1deg_GSWP3V1_isofix2_hist.1995_2014-clm50_release-clm5.0.20_1deg_GSWP3V1_isofix_hist.1995_2014/setsIndex.html - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime5.6.14 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: ctsm1.0.dev036 - -Pull Requests that document the changes (include PR ids): #698 -(https://github.com/ESCOMP/ctsm/pull) - - #698 -- Bring the carbon isotope fix to the release branch - -=============================================================== -=============================================================== -Tag name: release-clm5.0.21 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Fri May 3 16:10:35 MDT 2019 -One-line Summary: New ndep files, update fates, fix some issues - -Purpose of this version: ------------------------- - -New nitrogen deposition files for future scenarios: SSP245 and SSP370. And now points -to the closest reasonable new CMIP6 SSP ndep file that we have (for clm50, clm45 points -to the old RCP files). - -Update FATES to s1.21.0.a7.0.0. Which brings in a list of improvements and bug fixes. New -options include fates-hydro and fates-parteh - -Point to all of the available CO2 files, so we can convert them for use by datm. - -Bring in new high resolution PFT land-mask SCRIP grid file (MODISv2), as a start to get the -hirespft -option to work in mksrfdata.pl. Mapping files still need to be created. - -Add a test that turning on Carbon isotopes does NOT change answers (currently triggered because of #667) - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #706, #700, #678, #664, #642, #672, and #262 - Fix #706 -- Add cmip6_nociso_deck user-mods directory and point to it for f19 CMIP6DECK compsets - Fix #700 -- Stream start/align incorrect for SSP's - Fix #678 -- Wrong mask name for clm40 - Fix #664 -- Typo in SSP5-3.4 c13 isotope file - Fix #642 -- Update ESMF libarary for maps to ESMF7.1.0r - Fix #672 -- mksurfdata.pl aborts with error - Fix #262 -- hirespft option to mksurfdata.pl doesn't work (partial now needs maps) - -Science changes since: release-clm5.0.20 - Updated domain files for f19 resolution causes a small change in answers - - FATES updated from version 1.8.1 to 1.21.0. List of improvements include: - Some new options that came in various versions: fates-hydro, variable SLA Profile and Wood CN Ratio, parteh, - optional maintenance respiration throttling, optional trimming logic to roots - Changes to Norman Canopy radiation - A bug to some pointers that spread outside where they should have. - Some bug fixes in allometry - The Plant Allocation Reactive Transport Extensible Hypotheses (PARTEH) v1 software infrastructure has been added. - Key changes that enable simulation of a coastal salt mars - Remove Lasslop wind effects on fire Rate of Spread - Fixes to fire mortality diagnostics, patch disturbance area checks and trimming - -Software changes since: release-clm5.0.20 - - hirespft dataset now uses the MODISv2 mask - -Changes to User Interface since: release-clm5.0.20 - New ndep files for SSP245 and SSP370. For Clm50 point to one of the new ndep files for every SSP - even if the exact one isn't yet available (for Clm45 it points to the CMIP5 RCP scenarios) - - New fates namelist option: fates_parteh_mode (switches nutrient model in FATES) - - Remove fates finidat file - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - OK (67 tests different because of new fates parameter file, and first/align changes for SSP's) - - unit-tests (components/clm/src): - - cheyenne - OK - - tools-tests (components/clm/test/tools): - - cheyenne - OK - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: FATES and f19 resolution - - what platforms/compilers: All - - nature of change: - f19 is a small change due to updated domain files - FATES science changed from version 1.8.1 to 1.21.0 - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime5.6.14 - FATES: fates_s1.21.0_a7.0.0_br_rev2 - PTCLM: PTCLM2_180611 - - -CTSM Tag versions pulled over from master development branch: Pull LCISO test from ctsm1.0.dev036 - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - - #695 -- Add more ndep files, fix some bugs, point to new SSP CO2 files - #687 -- Update fates version on release branch - -=============================================================== -=============================================================== -Tag name: release-clm5.0.20 -Originator(s): erik (Erik Kluzek) -Date: Tue Mar 12 16:08:55 MDT 2019 -One-line Summary: Update all fsurdat files and bring in files for future scenarios, remove CMIP5 rcp options, bring in some bug fixes - -Purpose of this version: ------------------------- - -Update all surface datasets and add datasets needed for future scenarios. Remove CLM40-RCP options. - -Also bring in change for reseeding so that reseeding happens for generic crop and -to increase the threshold from exactly zero to 1 (still very small). Fix QSNOEVAP history field. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many changes missing) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #621, #608, #624 #653 - #621 -- Fully remove CMIP5 rcp's (for clm40,clm45,clm50) and implement CMIP6 ssp_rcp's for clm45/clm50 - #608 -- Odd (blocky) spatial patterns in generic crop leafc for BGC simulation when initialized from BGC-Crop - #624 -- QSNOEVAP history output incorrect - #653 -- To save disk on fsurdat files use zwt0 on finindated file - -Science changes since: release-clm5.0.19 - Surface datasets no longer have wetland over Antarctica - QSNOEVAP output corrected - reseeding changes so that it happens over generic crop and also raise the threshold from identically zero - to 1 (which is still very small) - -Software changes since: release-clm5.0.19 - Remove the option to run CMIP5 rcp scenarios - -Changes to User Interface since: release-clm5.0.19 - "-rcp" option to build-namelist is removed and replaced with "-ssp_rcp" - New use-cases for all eight of the SSP's - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.19 - -Changes answers relative to baseline: Yes! (for clm4_5/clm5_0) - - Summarize any changes to answers, i.e., - - what code configurations: clm4_5/clm5_0 - - what platforms/compilers: All - - nature of change: similar climate, new fsurdat files (Antarctica fix), and QSNOEVAP, and reseed fix - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime5.6.12 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #625 #611 #651 -(https://github.com/ESCOMP/ctsm/pull) - #651 -- New datasets and capability to run CMIP6 future scenarios - #625 -- Correct QSNOEVAP history variable - #611 -- Reseed generic crops and increase totvegc threshold from 0 to 1 for reseeding - -=============================================================== -=============================================================== -Tag name: release-clm5.0.19 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Fri Mar 8 13:58:16 MST 2019 -One-line Summary: Update cime version to one with updates for cheyenne after the Mar/5th/2019 downtime that resulting in mpt2.16 not being able to be used - -Purpose of this version: ------------------------- - -Update cime version with changes needed to run on cheyenne after the Mar/5th/2019 downtime that resulted in the model -NOT being able to run - -CIME important updates: - Update fv1.9x2.5,gx1v7 grids - Initial port to CGD machine izumi - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many changes missing) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #655 #654 - -Science changes since: None - -Software changes since: New f19_g17 grids, works on izumi, works on cheyenne_intel after the downtime - -Changes to User Interface since: None - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - hobart --- PASS - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.18 - -Changes answers relative to baseline: Yes, but only f19_g17 resolutions - - Summarize any changes to answers, i.e., - - what code configurations: any at f19_g17 resolution - - what platforms/compilers: All - - nature of change: larger than roundoff/same climate - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime5.6.12 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #656 -(https://github.com/ESCOMP/ctsm/pull) - #656 -- update cime - -=============================================================== -=============================================================== -Tag name: release-clm5.0.18 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Wed Feb 13 19:01:26 MST 2019 -One-line Summary: Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory - -Purpose of this version: ------------------------- - -New NoAnthro compsets: I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro and tests for it. -More updates to surface dataset generation, to reduce the fields that are output, removing ones -that aren't used. - -New tools/contrib directory with initial add of some useful scripts for users. Currently unsupported -and only expected to run on cheyenne. The following scripts are added: - - run_clm_historical ---- does all the setup and submission required to do a 1850-2010 CLM historical - subset_surfdata ------- create regional domain, surface data, and rtm directional files by - extracting data from global datasets - singlept -------------- create single point domain, surface data, and datm forcing files by - extracting data from global datasets - SpinupStability.ncl --- This script assesses the equilibrium state of a spinup run - run_clmtowers --------- This script will run any number of flux tower sites. - -Add new default f09 Potential Vegetation (PtVg) surface dataset. For mksurfdata new high resolution -PFT datasets (at 3x3min) for 2005. New rawdata PFT files from 0850-1849. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many changes missing) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): Fixes #629 #557 #262 - #629 -- Unused fields from fsurdat files - #557 -- No anthro compset - #262 -- hirespft option doesn't work for mksurfdata.pl - -Science changes since: release-clm5.0.17 - None - -Software changes since: release-clm5.0.17 - PtVg and pre-millenial raw PFT datasets - reduce fields created on fsurdat files - -Changes to User Interface since: release-clm5.0.17 - New NoAnthro compsets: I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro - Add new option "-vic" to mksurfdata.pl to output fields needed for VIC (only have a few resolutions with VIC on by default) - Add 2005 high resolution datasets that can be used for the -hirespft option to mksrfdata.pl - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - OK - hobart --- OK - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (prealpha): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - - regular tests (prebeta): - - cheyenne_intel - OK - cheyenne_gnu --- OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.17 - -Changes answers relative to baseline: No (bit-for-bit) - -Detailed list of changes: ------------------------- - -Externals being used: Change cime to cime5.6.11 (just a name change) - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime5.6.11 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #619 #620 #634 -(https://github.com/ESCOMP/ctsm/pull) - - #619 -- Begin adding "contrib" tools directory - #620 -- Add NoAnthro compset and tests - #634 -- Remove some of the fields added to fsurdat files in mksurfdata_map - - -=============================================================== -=============================================================== -Tag name: release-clm5.0.17 -Originator(s): Keith Oleson, Bill Sacks -Date: Wed Jan 23 11:03:22 MST 2019 -One-line Summary: History fields for vertically-resolved sums of soil C and N, and minor fixes - -Purpose of this version: ------------------------- - -Main change is from Keith Oleson: Add history fields for -vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, -C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and -C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, -including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', -'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output -'SOILC_vr', 'SOILN_vr', and similarly for C isotopes. - -Also minor fixes: -- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61) -- Remove FATES-related commented-out code in OzoneMod (this has been - moved to https://github.com/ESCOMP/ctsm/issues/618) -- Minor tweak to run_sys_tests - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev025 - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#61 - -Science changes since: release-clm5.0.16 - None - -Software changes since: release-clm5.0.16 - See above - -Changes to User Interface since: release-clm5.0.16 - None - -Testing: --------- - - build-namelist tests: - - cheyenne - not run - - unit-tests (components/clm/src): - - cheyenne - pass - hobart --- not run - - tools-tests (components/clm/test/tools): - - cheyenne - not run - hobart --- not run - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - not run - hobart --- not run - - regular tests (aux_clm): - - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass - - regular tests (prealpha): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - - regular tests (prebeta): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.16 - -Changes answers relative to baseline: NO - - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime_cesm2_1_rel_06 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: ctsm1.0.dev025 - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/551 - -=============================================================== -=============================================================== -Tag name: release-clm5.0.16 -Originator(s): erik (Erik Kluzek) -Date: Tue Jan 15 15:13:43 MST 2019 -One-line Summary: PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere - -Purpose of this version: ------------------------- - -no-anthro changes on release branch. Update of mksurfdata for Antarctic. Also start adding in newly created SSP-RCP datasets that are easy to add in. -Also add in new option for dribble_crophrv_xsmrpool_2atm. - -CTSM Master Tag This Corresponds To: N/A - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #553 #533 #589 #547 #545 - #553 -- More robust mksurfdata_map logic for determining where to put wetlands - #533 -- Add -no-anthro option to mksurfdata_map - #589 -- Existence of content in the lai_streams namelist makes it confusing to users - #547 -- Add conus_30_x8 grid as valid option for CTSM and mksurfdata_map - #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers - -Science changes since: release-clm5.0.15 - mksurfdata now properly makes Antarctica teated as glacier rather than wetland - Add in option to create all of the SSP-RCP future scenarios in mksurfdata_map - Add dribble_crophrv_xsmrpool_2atm, to do slow release of crop harvested XSMRPOOL to atmosphere - (only active by default when co2_type="prognostic") - -Software changes since: release-clm5.0.15 - Add no-anthro option for mksurfdata_map - -Changes to User Interface since: release-clm5.0.15 - New namelist option: dribble_crophrv_xsmrpool_2atm - Add SSP-RCP future scenarios can be done in mksurfdata_map - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - hobart --- - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.15 - -Changes answers relative to baseline: No bit-for-bit - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime_cesm2_1_rel_06 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: N/A - -Pull Requests that document the changes (include PR ids): #567 #561 #564 #616 #610 -(https://github.com/ESCOMP/ctsm/pull) - - #616 -- No anthro options to tools, and all future scenarios in place, plus a few small issue fixes - #610 -- Add option to dribble XSMRPOOL at crop harvest to atmosphere over a half year - #567 -- ignore patterns for vim - #564 -- Update mksurfdata_map to include glaciers outside of pft landmask - #561 -- Add list of checks for new surface datasets - -=============================================================== -=============================================================== -Tag name: release-clm5.0.15 -Originator(s): sacks (Bill Sacks) -Date: Thu Dec 6 10:14:30 MST 2018 -One-line Summary: Option for rain-to-snow to immediately run off in some regions - -Purpose of this version: ------------------------- - -Up until now: When repartition_rain_snow is .true. (which is the default -for CLM5), rain that falls when the near-surface temperature is cold is -converted to snow. This repartitioning was put in place for two -reasons: (1) Downscaling to elevation classes: changing the balance -between rain and snow for different elevation classes; (2) Correcting -problems in CAM. However, members of the Land Ice Working Group would -like to change this behavior so that, when CAM produces cold-temperature -rain, this rain immediately runs off rather than being converted to -snow. The purpose of this is to reduce the too-high SMB over portions of -Greenland in CESM2 coupled runs (which results in part from CAM's -generation of liquid precipitation despite very cold temperatures). - -This new behavior is implemented in a glacier region-specific manner, -based on a new namelist flag, glacier_region_rain_to_snow_behavior. It -is not at all ideal to make this aspect of the physics differ by region, -but this has been requested by members of the Land Ice Working Group in -order to address biases over Greenland while having minimal impact on -the climate (so that the climate can stay very similar to that of the -official CMIP6 runs). Note that, unlike other glacier region-specific -behaviors, this one applies to all landunits, not just glaciers. This -also seems a bit non-ideal, but we want the physics to be the same for -all landunit types in a given region, and we also want this behavior to -apply to vegetated columns because they are used for glacial -inception (and we want this alternate behavior to apply to glacial -inception, too, in order to decrease some instances of inception). - -The justification for this new physics is: In the case of (1) above: If -CAM is generating rain at a given elevation / temperature, that doesn't -necessarily imply that an equal water equivalent of snow would be -generated at a higher elevation / lower temperature: indeed, in reality, -there might not be any precipitation falling at that higher elevation / -lower temperature. In the case of (2) above: There seem to be problems -with CAM's microphysics that cause it to produce too much rain when -temperatures are very cold; it seems (at least to some people) equally -justifiable to throw this cold rain away (by sending it to the ocean as -runoff) as it is to convert this cold rain to snow. - -Note: I don't think any changes are needed in -BalanceCheck (unfortunately), since BalanceCheck currently uses the -post-downscaling precipitation fluxes, and the pre-lnd2atm runoff -fluxes (i.e., the new runoff flux isn't included in the terms in -BalanceCheck, and it doesn't need to be because BalanceCheck uses the -post-downscaling precipitation fluxes). (See also -https://github.com/ESCOMP/ctsm/issues/201#issuecomment-444264954 .) - -CTSM Master Tag This Corresponds To: N/A - - At least for now, we are bringing this to the release branch but not to - master. Here is an excerpt from the email explaining this rationale: - - My question is: Should I do this: - - (1) Just on a branch off of the release-clm5.0 branch, with no plan to - bring it back to release-clm5.0 or master - - (2) On the release-clm5.0 branch, but not bring it back to master - - (3) On the release-clm5.0 branch and master - - My inclination right now is towards (2). I don't really like (1) because - this change will be wanted for a number of CMIP6-related experiments, - and it feels like it could be a pain to keep this branch up-to-date with - the evolving release-clm5.0 branch. However, the changes are going to be - a bit messy and having this be region-specific isn't really physically - justifiable (it's just being done that way to keep the climate as close - as possible to the official CMIP6 runs), so I'm not sure we really want - this on master. If we did anything on master, I could imagine having a - globally-applicable switch controlling this behavior, rather than having - it apply to just certain glacier regions. - - Bette: The main reason I could see for bringing this to master is if you - imagine needing to use this new option in isotope-enabled runs, since - the isotope-enabled version of CTSM won't be on the release-clm5.0 - branch. Do you think it's likely that you'd need to do that, or would - the isotope-enabled runs use the standard CMIP6 physics settings in this - respect? - -Summary of changes: -------------------- - -Science changes since: release-clm5.0.14 - None by default: just introduces a new option - -Software changes since: release-clm5.0.14 - Introduces a new option, glacier_region_rain_to_snow_behavior, - controlling whether would-be rain-to-snow conversion ends up as snow - or instead ends up as liquid runoff. - -Changes to User Interface since: release-clm5.0.14 - Introduces a new option, glacier_region_rain_to_snow_behavior, - controlling whether would-be rain-to-snow conversion ends up as snow - or instead ends up as liquid runoff. - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - ok - - Tests pass, namelists differ as expected - - unit-tests (components/clm/src): - - cheyenne - pass - hobart --- not run - - tools-tests (components/clm/test/tools): - - cheyenne - not run - hobart --- not run - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - not run - hobart --- not run - - regular tests (aux_clm): - - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass - - regular tests (prealpha): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - - regular tests (prebeta): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.14 - -Changes answers relative to baseline: NO - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime_cesm2_1_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: none - -Pull Requests that document the changes (include PR ids): - ESCOMP/ctsm#586 - Option for rain-to-snow to immediately run off in - some regions - -=============================================================== -=============================================================== -Tag name: release-clm5.0.14 -Originator(s): erik (Erik Kluzek) -Date: Thu Nov 29 11:46:41 MST 2018 -One-line Summary: Update cime and fix surface dataset for f05 1850 non-crop case - -Purpose of this version: ------------------------- - -Update cime to next version being used in cesm2.1.0 release. And fix the XML for f05 -surface dataset for 1850 and non-crop. Test that all six f05 cases work (1850/2000/Hist,crop/non-crop). - - -CTSM Master Tag This Corresponds To: - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #576 - -Science changes since: release-clm5.0.13 - None - -Software changes since: release-clm5.0.13 - Fix XML for f05 1850 non-crop fsurdat file - -Changes to User Interface since: release-clm5.0.13 - cpl auxilary history files names change - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - - tools-tests (components/clm/test/tools): - - cheyenne - OK - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - hobart --- OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - Also following PASS: - SMS.f05_f05_mg17.I1850Clm50BgcCrop.cheyenne_intel.clm-default - SMS.f05_f05_mg17.I1850Clm50Sp.cheyenne_intel.clm-default - SMS.f05_f05_mg17.I2000Clm50BgcCrop.cheyenne_intel.clm-default - SMS.f05_f05_mg17.I2000Clm50Sp.cheyenne_intel.clm-default - SMS.f05_f05_mg17.IHistClm50BgcCrop.cheyenne_intel.clm-default - SMS.f05_f05_mg17.IHistClm50Sp.cheyenne_intel.clm-default - - regular tests (prealpha): - - cheyenne_intel - PASS - cheyenne_gnu --- PASS - hobart_nag ----- PASS - - regular tests (prebeta): - - cheyenne_intel - PASS - cheyenne_gnu --- PASS - hobart_nag ----- PASS - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.13 - -Changes answers relative to baseline: No (bit-for-bit) - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime_cesm2_1_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: none - -Pull Requests that document the changes (include PR ids): #579 -(https://github.com/ESCOMP/ctsm/pull) - #579 -- Fix bug in XML for surface dataset for f05 1850 non-crop - -=============================================================== -=============================================================== -Tag name: release-clm5.0.13 -Originator(s): erik (Erik Kluzek) -Date: Wed Nov 14 11:28:00 MST 2018 -One-line Summary: Update externals with new CO2/presearo/rtm/mosart, add science_support, change testing - -Purpose of this version: ------------------------- - -Update externals with new CO2 and prescribed aerosols. As well as rtm and mosart that now -properly does history output in double precision. Add science support to three new transient -compsets for clm4_0/clm4_5/clm5_0. Do some changes to testing. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev015 (with changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): Fixes #560 #558 - #560 New science supported compsets - #558 Add IHist test for aux_cime_baselines -CIME Issues fixed (include issue #): #2688 #2687 - #2688 Prescribed aerosols for CMIP6 forcing - #2687 New CO2 streams for CMIP6 - -Science changes since: release-clm5.0.012 - New CMIP6 prescribed aerosol forcing - New CMIP6 CO2 streams - New rtm/mosart history properly output in double-precision - (old "single"-precision mode was incorrect). It was actually - still double in terms of size, but in rare cases could be off - by single precision rounding level. - -Software changes since: release-clm5.0.012 - Added science_support for several compsets (at f09_g17 and f19_g17): - HIST_DATM%CRUv7_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - HIST_DATM%GSWP3v1_CLM45%SP_SICE_SOCN_RTM_SGLC_SWAV - HIST_DATM%GSWP3v1_CLM40%SP_SICE_SOCN_RTM_SGLC_SWAV - Add testing for above - -Changes to User Interface since: release-clm5.0.012 - rtm/mosart history output is double precision - - Added clim_2010 option for DATM_PRESAERO - Added 20tr.latbnd option for DATM_CO2_TSERIES - GSWP3v1 and CRUNCEPv7 forcing sets appropriate years for compsets starting with 2010 - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart ---PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.12 - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: Nearly everything (only 5 test cases were identical) - - what platforms/compilers: All - - nature of change: CO2 for transient cases is different, and presearo is different for everything - Modest change to climate - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.02 - mosart: release-cesm2.0.03 - cime: cime_cesm2_1_rel_04 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #563 -(https://github.com/ESCOMP/ctsm/pull) - - #563 -- Update externals (cime, mosart, rtm) for release branch, add new science support compsets/tests - -=============================================================== -=============================================================== -Tag name: release-clm5.0.12 -Originator(s): erik (Erik Kluzek) -Date: Sat Nov 3 21:19:25 MDT 2018 -One-line Summary: New IC files for clm45/clm50 coupled cases, add 2010 compset - -Purpose of this version: ------------------------- - -Improve logic for picking initial condition files (finidat). Add new finidat files -for when coupled to CAM (LND_TUNING_MODE=clm*_cam6.0) for both 1850 (from CMIP6 B1850 case) -and 2000/2010 (from CMIP6 BHIST case). - -Logic for picking finidat files now will pick a finidat file that it interpolates from -provided the default settings allow use_init_interp to be true. This makes it more likely -to pick a file to startup from if at all possible, rather than dying with an error that -a finidat couldn't be found (which the user could override to get the new behavior by adding -use_init_interp=T to their user_nl_clm). - -In namelist settings for finding finidat files for sim_yr=2000, be explict on which tuning mode -is being matched and duplicate the clm4_5/clm5_0 GSWP3v1/CRUv7 matches. This gets it to match -the correct ones and allows them to be distinquished in the future. - -Added CLM_NML_USE_CASE=2010_control, and settings for sim_yr=2010, which is needed for some new CAM compsets. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev015 (with changes) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #558 #544 $504 - #558 Replace a failing test in aux_cime_baselines - #544 Transient cases coupled to CAM are matching the wrong IC file (2000 instead of 1850) - $504 Add a 2010 use_case - -Science changes since: release-clm5.0.11 - * None - -Software changes since: release-clm5.0.11 - * Improve logic for finding initial conditions, don't abort if can find a file to interpolate from and interpolation is allowed - -Changes to User Interface since: release-clm5.0.11 - * Added 2010_control to CLM_NML_USE_CASE - * Added -sim_yr 2010 to CLM_BLDNML_OPTS - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - OK (106 tests differ from baseline because of new IC files) - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart ---PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.11 - -Changes answers relative to baseline: No not for aux_clm tests! Will change answers when coupled to CAM with new IC files - - Summarize any changes to answers, i.e., - - what code configurations: LND_TUNING_MODE=clm#_#_cam6.0 - - what platforms/compilers: All - - nature of change: Updated initial conditions that use CMIP6 BHIST and B1850 - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime_cesm2_0_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): #555 -(https://github.com/ESCOMP/ctsm/pull) - - #555 -- New initial conditions when coupled to CAM - -=============================================================== -=============================================================== -Tag name: release-clm5.0.11 -Originator(s): erik (Erik Kluzek) -Date: Tue Oct 30 10:50:49 MDT 2018 -One-line Summary: Bring fix for transient Bgc/Sp to release branch (from ctsm1.0.dev013) - -Purpose of this version: ------------------------- - -Fix transient non-crop cases that had constant crop area so that crop area will change in time -(and hence natural veg area will also change corresponding to it). - -Also bring in changes to update mksurfdata_map to handle SSP-RCP future scenarios. Right now -it can handle SSP5-8.5 out of the box. Also add a new test for that. - - -CTSM Master Tag This Corresponds To: ctsm1.0 - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): #538 - #538 -- In transient pft simulations with use_crop=.false., %crop does not advance from 1850 value - -Science changes since: release-clm5.0.10 - Fix so crop areas will change beyond 1850 for transient Bgc or Sp cases for clm45/clm50 - -Software changes since: release-clm5.0.10 - None - -Changes to User Interface since: release-clm5.0.10 - New -ssp_rcp option to mksurfdata.pl - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart ---PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.10 - -Changes answers relative to baseline: Yes, for transient clm45/clm50 Bgc/SP - - Summarize any changes to answers, i.e., - - what code configurations: clm45/clm50 transient Bgc/Sp - - what platforms/compilers: All - - nature of change: crop areas now increawse in time rather than remaining at 1850 levels - Simulation to demonstrate new climate: - - casename: dll/clm50_r267_1deg_GSWP3V1_iso_hist_nocrop_transientfix - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime_cesm2_0_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: ctsm1.0.dev013 - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - #552 -- Move fix for transient non-crop to release-clm5.0 branch - -=============================================================== -=============================================================== -Tag name: release-clm5.0.10 -Originator(s): sacks (Bill Sacks) -Date: Mon Oct 29 06:55:41 MDT 2018 -One-line Summary: Bring in CMIP6 compset modifiers, output usermods and bit-for-bit fixes from dev014 and dev015 - -Purpose of this version: ------------------------- - -Bring in all changes from ctsm1.0.dev014 and ctsm1.0.dev015: - -From ctsm1.0.dev015: - -(1) Support %BGC-CROP-CMIP6DECK and %BGC-CROP-CMIP6WACCMDECK compset - modifiers, so that we can turn on the necessary options - (output-related and others) via new CMIP6-specific compsets. - -(2) Turn on carbon isotopes in CMIP6 runs (from Erik Kluzek) - -(3) Remove setting of CCSM_BGC=CO2A in the cmip6 usermods - -(4) Add usermods directories for getting typical extra output that's - wanted in many cases: output_crop, output_crop_highfreq, output_bgc, - output_bgc_highfreq, output_sp, and output_sp_highfreq. These can be - enabled by adding something like '--user-mods-dir output_crop' on - the create_newcase line (that short-hand works for an I compset; for - F or B compsets, you need to provide the full path to the usermod - directory). - -(4) Allow holes in the number of history tapes. Holes are cases where, - for example, we have h0, h1 and h3 tapes, but no h2 tape (because - there are no fields on the h2 tape). (This is needed for (3).) - -(5) Fix reading and writing of 1-d logical global arrays. This fixes - ESCOMP/ctsm#24 for real (rather than just preventing an attempt to - read/write 1-d logical arrays, as was done in the previous 'fix'). - -(6) Add C13_NBP and C14_NBP diagnostic fields (from Keith Oleson) - -(7) Make a bunch of carbon isotope diagnostic fields inactive by default - -(8) Don't allow interpolation (use_init_interp) from a case without - carbon isotopes to a case with carbon isotopes: Due to - https://github.com/ESCOMP/ctsm/issues/67, interpolation from a case - without carbon isotopes to a case with carbon isotopes yields - incorrect initialization values for the carbon isotopes. Now that - we're turning carbon isotopes on via some semi-out-of-the-box - usermods (for cmip6), it is becoming more important to check to make - sure someone doesn't shoot themselves in the foot this way. - -(9) Add tests of the new output usermods as well as of the CMIP6 compset - modifiers - -From ctsm1.0.dev014: Four miscellaneous minor, bit-for-bit bug fixes: - -(1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim - Edwards: ESCOMP/ctsm#526) - -(2) Change uppercase DEBUG variables to lowercase debug (requested by - Jim Edwards to avoid conflicting with the DEBUG CPP token) - (Fixes ESCOMP/ctsm#534) - -(3) Remove unnecessary line of code in LunaMod.F90 that was causing - problems with some compilers due to an uninitialized variable - (Fixes ESCOMP/ctsm#322) - -(4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim - Edwards: ESCOMP/ctsm#531) - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev015 (but doesn't yet -include ctsm1.0.dev013) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): -- Fixes #322 (ERS_D_Ld5.f19_g16.I2000Clm50BgcCruGs run FAIL (intel)) -- Fixes #534 (Rename DEBUG to debug in a few places) -- Fixes #24 for real (ncd_io_1d_log_glob is broken) -- Fixes #529 (Organize usermods_dirs to facilitate running cases with - the right output) - -Science changes since: release-clm5.0.09 - -None - -Software changes since: release-clm5.0.09 - -See above for full list - -Changes to User Interface since: release-clm5.0.09 - -- New namelist variable, just for testing purposes: - for_testing_allow_interp_non_ciso_to_ciso. This bypasses an error - check, and should only be used in tests. - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - unit-tests (components/clm/src): - - cheyenne - pass - hobart --- not run - - tools-tests (components/clm/test/tools): - - cheyenne - not run - hobart --- not run - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - not run - hobart --- not run - - regular tests (aux_clm): - - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass - - regular tests (prealpha): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - - regular tests (prebeta): - - cheyenne_intel - not run - cheyenne_gnu --- not run - hobart_nag ----- not run - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.09 - -Changes answers relative to baseline: NO - - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime_cesm2_0_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: -- ctsm1.0.dev014 -- ctsm1.0.dev015 - -Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/531 - fix build issue with xlf compiler -- https://github.com/ESCOMP/ctsm/pull/526 - fix cime issue 2822 and pylint chk -- https://github.com/ESCOMP/ctsm/pull/536 - Allow holes in the number of - history tapes and reorganize cmip6 usermods (main PR containing all of - these changes) -- https://github.com/ESCOMP/ctsm/pull/527 - Add carbon_isotope user-mod - directory to turn on c13 and c14 -- https://github.com/ESCOMP/ctsm/pull/539 - Support a %CMIP6DECK compset - modifier - -=============================================================== -=============================================================== -Tag name: release-clm5.0.09 -Originator(s): erik (Erik Kluzek) -Date: Tue Oct 23 00:00:50 MDT 2018 -One-line Summary: Bring in bit-for-bit changes from master up to ctsm1.0.dev012: AnnEt init, snowmip fields - -Purpose of this version: ------------------------- - -Bring in new diagnostic fields added by Justin Perket, Sean Swenson and Mark Flanner -for Snow-MIP. Most of those are fields that represent "Snow Free" data. - -Also bring in fixes for a list of issues. Add handling of the new CO2 which includes -both latitude-band and global average versions. Add some changes to make it easier -for input data processing including NOT doing the slow 1km map file creation. Have -the number of steps that are skipped at startup dependent on the time-step size. Add -a test for some requirements of WACCMX (time-step and use of ESMF). Calculations of -local time are now done in a global subroutine, that can handle negative longitudes. -Fix how FFIX_TO_SMINN is handled for history output. The namelist logical "calc_human_stress_indices" -changed from logical to a character string of three values: FAST, NONE, ALL. FAST -is the default so the less expensive ones are output, NONE turns them all off, and ] -ALL does all of them including the expensive ones. - -InitAccVars was mistakenly setting qflx_evap_tot_col rather than -AnnET. This fix allows us to remove now-redundant cold start and restart -code for AnnET. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev012 - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): - Fix #428 -- Update getco2_historical.ncl to handle latitude varying CO2 - Fix #474 -- Add ability to send GRIDFILE to regridbatch.sh script - Fix #475 -- Have number of steps to skip balance-check based on time - Fix #476 -- Add a test for WACCMX standalone - Fix #450 -- Add option to use global average of terrain standard deviation on surfdata files - (partial fix with simplest option) - Fix #482 -- Add extra field on CO2 streams file for global/time-averaged data - Fix #481 -- FFIX_TO_SMINN needs to be output when FUN is on - Fix #491 -- Calculations of local noon assume that longitude is 0 to 360 rather than -180 to 180 - Fix #480 InitAccVars for AnnET initializing the wrong variable - Fix #285 Remove an un-needed restart variable (partially) - -Science changes since: release-clm5.0.08 - - * None - -Software changes since: release-clm5.0.08 - - New fields and fix a list of issues - -Changes to User Interface since: release-clm5.0.08 - - New namelist: - use_ssre -- Turn on show free fields needed for SnowMIP - - Changed namelist: - calc_human_stress_indices changed from logical to character with options: ALL, FAST, NONE - - New history fields: - Mostly added Snow Free (SF) fields - ALBDSF - ALBISF - FSRSF - FSRSFND - FSRSFNDLN - FSRSFNI - FSRSFVD - FSRSFVDLN - FSRSFVI - SSRE_FSR - SSRE_FSRND - SSRE_FSRNDLN - SSRE_FSRNI - SSRE_FSRVD - SSRE_FSRVDLN - SSRE_FSRVI - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart ---PASS - - tools-tests (components/clm/test/tools): - - cheyenne - OK (PTCLM tests fail) - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.08 - -Changes answers relative to baseline: No bit-for-bit - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime_cesm2_0_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: - ctsm1.0.dev008, ctsm1.0.dev009, ctsm1.0.dev012 - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - #543 -- Update release branch to ctsm1.0.dev012 - -=============================================================== -=============================================================== -Tag name: release-clm5.0.08 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Fri Sep 28 14:17:52 MDT 2018 -One-line Summary: Updated CMIP6 ndep file for historical transient Bgc cases, 1850_control same as before - -Purpose of this version: ------------------------- - -Update the ndep file for transient cases for CLM50 to the CMIP6 version that has identical -data for 1849-1850 to the previous CMIP6 1850_control (with different mid-month times however), and -new 3-member ensemble average/5-year smoothing from the WACCM case: b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.00[123]. -The new data is monthly rather than yearly, which means there will be a seasonal cycle to nitrogen deposition -for transient cases now. The midmonth times/dates are different for the multi-year file from -the previous file, so answers change when using it for 1850_control cases even though the data is exactly the same. -Because, of that we are still pointing to the previous 1850 CMIP6 ndep file. - -CLM4.5 is still using the previous CMIP5 ndep dataset. - -CTSM Master Tag This Corresponds To: ctsm1.0.dev008 (minus ctsm1.0.dev005 and ctsm1.0.dev001) - -Summary of changes: -------------------- - -Science changes since: New cmip6 ndep file for transient cases - -Software changes since: None - -Changes to User Interface since: None - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - - regular tests (aux_clm): PASS (limited testing) - PASS SMS_D.f09_g16.I1850Clm50BgcSpinup.cheyenne_intel.clm-cplhist - PASS SMS_D_Ld3.f10_f10_musgs.I1850Clm50BgcCrop.cheyenne_intel.clm-default - PASS SMS_D_Ly2.1x1_brazil.IHistClm50BgcQianGs.cheyenne_intel.clm-ciso_bombspike1963 - PASS SMS_D_Ly2.1x1_numaIA.IHistClm50BgcCropGs.cheyenne_intel.clm-ciso_bombspike1963 - PASS SMS_Ld5.f10_f10_musgs.I1850Clm45BgcCrop.cheyenne_intel.clm-crop - PASS SMS_Ld5.f19_g17.IHistClm50Bgc.cheyenne_intel.clm-decStart - PASS SMS_Ld5_D.f09_g16.I1850Clm50BgcCrop.cheyenne_intel.clm-cmip6 - PASS SMS_Lm1.f09_g17_gl4.I1850Clm50Bgc.cheyenne_intel.clm-clm50KitchenSink - PASS SMS_Lm1.f19_g17_gl4.I1850Clm50Bgc.cheyenne_intel.clm-clm50dynroots - PASS SMS_Lm1_D.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-snowlayers_3_monthly - PASS ERP_P36x2_D_Ld5.f10_f10_musgs.IHistClm45BgcCruGs.cheyenne_intel.clm-decStart - - Tests that are different from baseline (as expected) - DIFF SMS_D_Ly2.1x1_brazil.IHistClm50BgcQianGs.cheyenne_intel.clm-ciso_bombspike1963 - DIFF SMS_D_Ly2.1x1_numaIA.IHistClm50BgcCropGs.cheyenne_intel.clm-ciso_bombspike1963 - DIFF SMS_Ld5.f19_g17.IHistClm50Bgc.cheyenne_intel.clm-decStart - DIFF SMS_Lm1_D.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-snowlayers_3_monthly - - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.07 - -Changes answers relative to baseline: Yes! for CLM4.5/CLM5.0 CN or Bgc transient cases - - Summarize any changes to answers, i.e., - - what code configurations: IHist Clm45Bgc* and Clm50Bgc (Bgc or Cn) - - what platforms/compilers: All - - nature of change: Changes in climate for Nitrogen - New nitrogen deposition and change from yearly to monthly - -Detailed list of changes: ------------------------- - -Externals being used: Update cime - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime_cesm2_0_rel_05 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: None - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - - #522 -- Point to the new ndep historical file for all cases, also update cime - -=============================================================== -=============================================================== -Tag name: release-clm5.0.07 -Originator(s): erik (Erik Kluzek) -Date: Wed Aug 8 14:02:04 MDT 2018 -One-line Summary: Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007 - -Purpose of this version: ------------------------- - -This is a duplicate of the previous tag, since the previous tag ended up being off of the release-clm5.0 branch. -All the details of the tag are the same as the previous one. - -=============================================================== -=============================================================== -Tag name: release-clm5.0.06 -Originator(s): erik (Erik Kluzek) -Date: Tue Aug 7 14:49:04 MDT 2018 -One-line Summary: Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007 - -Purpose of this version: ------------------------- - -Bring in a list of simple fixes that came to CTSM master. Also change so glacier initialization is *ALWAYS* done -at startup (time step zero) even if it isn't cold or interpolated initial conditions. Also synchronize some of the -files in the doc directory with the files in ctsm/master. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev007 (minus ctsm1.0.dev005 and ctsm1.0.dev001) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): -- Fixes #340 (Avoid generating dynamic landunit adjustment fluxes for - glacier changes in the first timestep) -- Fixes #24 (ncd_io_1d_log_glob is broken) -- Fixes #120 (Incorrect comments in Biogeophysics1Mod.F90 -- Fixes #245 (Put all .gitignore entries in top-level file) -- Fixes #272 (Code should error on missing mxsoil_color when SOIL_COLOR - is used) -- Fixes #283 (Add more helpful message about need to do init_interp with - wrong number of vertical layers) -- Fixes #367 (For cmip6 runs: Turn on cpl hist output needed to drive a - TG compset) -- Fixes #412 (Fix documentation of init_interp_method) -- Fixes #419 (Do not allow SOYFIXN diagnostic field with FUN) -- Fixes #465 (Remove backwards compatibility check for snw_rds) - -Science changes since: release-clm5.0.05 (always do glacier initialization at startup even if NOT cold or interpolated startup) - -Software changes since: release-clm5.0.05 - remove ncd_io_1d_log_glob, remove a backwards compatability check for snw_rds on restart file - -Changes to User Interface since: release-clm5.0.05 - Add another field to cmip6_outputA, Remove SOYFIXN history field when FUN is on - Add error for missing mxsoil_color, better error message for wrong # of vertical soil layers, - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.05 - -Changes answers relative to baseline: possibly at startup - - Summarize any changes to answers, i.e., - - what code configurations: startup with Glacier model and NOT a cold or interpolated start - - what platforms/compilers: All - - nature of change: nearly identical - - Only tests that showed differences in answers were: - - ERI_N2_Ld9.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-default - SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime5.6.10 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: ctsm1.0.dev006, ctsm1.0.dev007 - - ctsm1.0.dev007 sacks 08/05/2018 Avoid glacier dynamic landunit adjustments in first time step - ctsm1.0.dev006 sacks 08/04/2018 Minor bug fixes, cleanup, documentation and enhancements - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - - #473 -- Always do glacier startup even if not cold or interpoalted start (ctsm1.0.dev007) - #468 -- Minor bug fixes (ctsm1.0.dev006) - -=============================================================== -=============================================================== -Tag name: release-clm5.0.05 -Originator(s): erik (Erik Kluzek) -Date: Sun Aug 5 23:31:45 MDT 2018 -One-line Summary: Update 1850 ndep file, and last year for transient streams - -Purpose of this version: ------------------------- - -Update to latest Nitrogen Deposition file from simulations with WACCM for 1850. -Also fix an issue with the last year for historical transient cases. - - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): $461 - #461 -- increase year last for streams - -Science changes since: release-clm5.0.04 - New ndep file, and updated last year for transient streams - -Software changes since: None - -Changes to User Interface since: None - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - hobart --- PASS - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - hobart --- OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (fates): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (clm_short): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-clm5.0.04 - -Changes answers relative to baseline: Yes - - Summarize any changes to answers, i.e., - - what code configurations: for 1850 Bgc cases and after 2005 for transient cases - - what platforms/compilers: All - - nature of change: similar climate - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime5.6.10 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - - #471 -- update ndep and last year of streams - -=============================================================== -=============================================================== -Tag name: release-clm5.0.04 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Wed Jul 18 04:04:57 MDT 2018 -One-line Summary: Fix some NFIX variables, update cime/cism for upgraded hobart new glade, new diagnostic fields, update cmip6 output - -Purpose of this version: ------------------------- - -Add some new diagnostic fields. Some needed for CMIP6. Update the CMIP6 user-mods output. -Fix a couple issues. Get full list of history tapes working correctly. Check for valid range -of CO2. New IC file interpolated from the previous one for f19_g17_gl4 for 2000 Clm50BgcCrop - -Update cime and cism so can work on upgraded hobart. Also fix an issue that the Nag6.2 compiler found -in CTSM. Also get working with glade changes that happened on cheyenne, DIN_LOC_ROOT_CLMFORC was -changed to a new directory. - -Nitrogen Fixation flux arrays were being set to missing value over non-vegetated landunits. This sets them to zero everywhere -and averages in the zero's at the gridcell level for history output. It also reads in restarts with missing values and converts -them to zero's. - -There are also some tools updates, getting the tools working on the new upgraded hobart.cgd.ucar.edu. - -And mksurfdata_map is updated to add some *_MAX files on the landuse.timeseries files that will allow us to conserve memory -for transient cases. - - -CTSM Master Tag This Corresponds To: ctsm1.0.dev004 (minus ctsm1.0.dev001) - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): - - #210 -- increase number of history tapes - $427 -- Check for zero CO2 - #429 -- New IC for present day - #441 -- Changes in glade invalidate previous softlinks and data locations - #438 -- Illegal argument aliasing caught by nag6.2 - #433 -- with hobart upgrade CTSM not working - #435 -- intel build for tools - #426 -- Nitrogen Fixation flux variables - #433 -- hobart broken, got it working for tools - -Science changes since: release-clm5.0.03 - - Changes to Nitrogen fixation flux arrays so that they are zero everywhere and the zeros are averaged in for history output. - Answers change because of interpolated initial conditions for 2000 simulation year at f19_g17_gl4 - -Software changes since: release-clm5.0.03 - - Get working on updated hobart. Add some new fields to mksurfdata_map tool. - -Changes to User Interface since: release-clm5.0.03 - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - - regular tests (clm_short): - - cheyenne_intel ---- PASS - cheyenne_gnu ------ PASS - hobart_nag -------- PASS - hobart_intel ------ PASS - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: clm5.0.dev013 - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: Clm50 2000 and NFIX history variables - - what platforms/compilers: All - - nature of change: similar climate - -Detailed list of changes: ------------------------- - -Externals being used: - - cism: release-cesm2.0.04 - rtm: release-cesm2.0.00 - mosart: release-cesm2.0.00 - cime: cime5.6.10 - FATES: fates_s1.8.1_a3.0.0 - PTCLM: PTCLM2_180611 - -CTSM Tag versions pulled over from master development branch: ctsm1.0.dev002, ctsm1.0dev003, ctsm1.0dev004 - -=============================================================== -=============================================================== -Tag name: release-clm5.0.03 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Tue Jun 12 15:32:53 MDT 2018 -One-line Summary: Second release branch tag for CESM2.0 release, fixing DA and tools and README files, identical to clm5.0.dev013 - -Purpose of this version: ------------------------- - -Update cime and cism to newer versions used in release. These bring in some answer -changes. The cime version updates the orbit for 2000 compsets. The cism version -changes answers for two fields with NO_EVOLVE and more fields for EVOLVE. - -Fixes an important bug needed for use with Data Assimulation. Several changes -to testing. Adding wallclock as needed, changing a few compsets so science -supported compsets are used, added tput_tolerance to some tests known to be -variable. - -Many changes to the clm tools for creating input files. Added the version by -querying "git describe" and adding it as an attribute to NetCDF files. Changes -to get tools working, and tested. Also changed so that tools can be run in either -a CTSM checkout or a CESM checkout. - -Updated README files so they are accurate. - -CTSM Master Tag This Corresponds To: clm5.0.dev013 - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): - #188 -- Global PTCLM tools test fails - #187 -- PTCLM tools tests fail baseline comparisons due to a seg fault - #259 -- Most README files in ctsm are incorrect - #386 -- Shorten some currently very long debug tests - #387 -- Lots of testmods still set orb_iyear and orb_iyear_align - #388 -- Add "git describe" to input files that are created - #389 -- Post data-assimilation processing broken with multi-driver - #393 -- Increase wallclock - #399 -- minor format update needed in namelist_definition_clm4_5.xml - #402 -- Some smaller tests can be slow.. - #411 -- Refactor tools aren't useful anymore - #414 -- PTCLM tests aren't working - #415 -- mkprocdata_map tests aren't working because of bad return statement in script type: bug - other - #418 -- Path needs to be updated for getco2 script type: bug - other - -Science changes since release-clm5.0.01: None - -Software changes since release-clm5.0.01: - Fix an important bug for data assimulation. Work on the CLM tools for creating input files. - Some changes to the CLM testing. - -Changes to User Interface since release-clm5.0.01: None - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - hobart --- PASS - - tools-tests (components/clm/test/tools): - - cheyenne - PASS - hobart --- PASS - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - hobart --- OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (prealpha): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - - regular tests (prebeta): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: release-5.0.01 - -Changes answers relative to baseline: Yes - -Changes answers relative to baseline: Yes! Because of changes in cism and cime - - Summarize any changes to answers: - - what code configurations: All 2000 compsets and some cases with cism - - what platforms/compilers: All - - nature of change: similar climate - -Detailed list of changes: ------------------------- - -Externals being used: - cime cime_cesm2_0_rel_03 - cism release-v2.1.01 - rtm release-cesm2.0.00 - mosart release-cesm2.0.00 - fates fates_s1.8.1_a3.0.0 - PTCLM PTCLM2_180611 - - -CTSM Tag versions pulled over from master development branch: clm5.0.dev013 - -=============================================================== -=============================================================== -Tag name: release-clm5.0.01 -Originator(s): erik (Erik Kluzek) -Date: Tue May 22 10:09:15 MDT 2018 -One-line Summary: First release branch tag for CESM2.0 release, identical to clm5.0.dev012 - -Purpose of this version: ------------------------- - -This is the first release branch tag for the CESM2.0 release for CTSM. There are many changes -to software mostly to fix a list of issues. There are some changes to the science that change -answers to fix some small problems, but don't have a large effect on simulations. Externals are -updated to new versions, fixing issues, and in most cases changing answers. The cime version -was updated and brings in some new features. - - -CTSM Master Tag This Corresponds To: clm5.0.dev012 - -Summary of changes: -------------------- - -Issues fixed (include CTSM Issue #): - #379 -- Problems with Hist decStart restart tests due to variable orbital year - #260 -- max daylength doesn't change over time for varying orbital parameters - #363 -- PE Layout - $374 -- Turn BFBFLAG on for testing (so PE layout changes won't appear to change answers) - #382 -- Write statement for VIC - $383 -- mkmapdata intel version` - #68 --- gnu compiler workaround - #364 -- crop f05 datasets - #362 -- svn checkout - #318 -- quadratic bug - #249 -- bypass balance checks for DART - #341 -- add model_doi_url - #346 -- New mode of operation for init_interp: Copy subgrid areas, too - #347 -- endrun message behavior - #345 -- Add a cmip6_evolving_icesheet usermods directory - #351 -- FATES external to https - #310 -- With FUN on soil nitrification flux is not subtracted out of plant uptake of of soil NH4 or NO3 - #313 -- Issues with initial condition files - #298 -- Don't allocate memory for zero-weight PFTs and urban columns - #317 -- c14 bombspike and c13 timeseries code can use the wrong year, with irreproducible behavior - #320 -- I1850Clm50Sp compset mistakenly uses SGLC - #326 -- init_interp can change answers for absorbed radiation in non-existent snow layers - #325 -- init_interp can change answers over the CISM domain - #213 -- usability issue for CPLHIST that Keith found. - #210 -- Recent request to increase number of tapes to 10. - #169 -- usability issue for running hybrid or branch cases with crop that keeps biting Mike Mills. - #68 --- workaround for gnu compiler bug - #46 --- needed for multi-instance - #66 --– need to relax tolerance for negative C/N values in order for CLM45 Crop to work - #65 --– need to change a check from "> 0" to "> [small val]" - #240 -- from Jim - #255 -- get PTCLM working - #253 -- bad clm40 IC file - #304 -- Energy imbalance over land per coupler diagnostics - #271 -- Add some land ice fields for cmip6 - #255 -- PTCLMmkdata doesn't work in the CLM git checkout - -CIME Issues fixed (include issue #): [If none, remove this line] -- ESMCI/cime#2598 (datm doesn't restart properly with variable year orbit) - -Science changes since: clm5.0.000 - - - Max day length is recalculated every time-step so works with a variable orbit - - CISM updates with answer changes - - Update 1850 Nitrogen deposition file used when coupled to cam - - By default orbit for 1850 is for 1850 conditions and for transient is variable by simulation year - - Soil nitrification flux wasn't taken out of plant uptake of either soil NH3 or NO3, with FUN on, and now it is. - - FATES version updated with science changes - - New initial condition files for most configurations - - Bug fixes for energy imbalance associated with surface water and lakes - -Softare changes since: clm5.0.000 - - - Update PE layouts for f45, f09, and f19 - - Turn BFBFLAG on for most testing - - Some fixes to tools for batch submission - - Update cime version - - Update mosart and RTM - - Add f05 crop datasets - - Add pauseResume test and don't do balance checks for two steps after Data Assimulation is done - - Don't allocate memory for zero-weight natveg patches and urban - - Fix some issues with init_interp for glaciers and snow covered areas - - Add some land ice diagnostic vars needed for CMIP6 - - Fix LND_TUNING_MODE for fully coupled case, update some README files/PTCLM - -Changes to User Interface since: clm5.000 - - New namelist item: init_interp_method - - xmlquery will now accept derived attributes. - - New XML variables, PAUSE_ACTIVE_XXX. - - jobid now added to CaseStatus case_submit entry. - - Splits GLC2OCN_RMAPNAME xml variable into - GLC2OCN_LIQ_RMAPNAME and GLC2OCN_ICE_RMAPNAME, and similarly for - GLC2OCN_RMAPTYPE - - New --retry option to create_test. - - Add --clean-depends to case.build, this argument can take a component list and will - clean all components if one is not provided. - -Testing: --------- - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - unit-tests (components/clm/src): - - cheyenne - PASS - - tools-tests (components/clm/test/tools): - - cheyenne - OK - - PTCLM testing (components/clm/tools/shared/PTCLM/test): - - cheyenne - OK - - regular tests (aux_clm): - - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - regular tests (prealpha): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - - regular tests (prebeta): - - cheyenne_intel - OK - cheyenne_gnu --- OK - hobart_nag ----- OK - -Summary of Answer changes: -------------------------- - -Baseline version for comparison: clm5.0.000 - -Changes answers relative to baseline: Yes - - Summarize any changes to answers, i.e., - - what code configurations: - all Clm45 and Clm50 - all 1850, all IHIST cases, all with CISM, all CLM50-BGC with FUN on - all with FATES, all with use_init_interp=T, - all CLM40, CLM45, and cLM%0 because of new initial conditions - - what platforms/compilers: all - - nature of change: similar climate - - URL for LMWG diagnostics output for new climate: - -Detailed list of changes: ------------------------- - -Externals being used: - - cism updated from cism2_1_46 to release-v2.1.00 (answer changes) - rtm updated from rtm1_0_65 to rtm1_0_66 - mosart updated from mosart1_0_30 to mosart1_0_31 - cime updated from cime5.4.0-alpha.03 to a67dceae95567cc7529c4cfed153017f4b65b210 - (answer changes due to new orbit) - fates updated from fates_s1.4.1_a3.0.0_rev3 to fates_s1.8.1_a3.0.0 (answer changes due to science updates) - PTCLM updated from PTCLM2_171216c to PTCLM2_180214 - -CTSM Tag versions pulled over from master development branch: - - clm5.0.dev012 sacks 05/17/2018 Fixes for variable_year orbital mode - clm5.0.dev011 erik 05/16/2018 1850 ndep update, cism update, PE layouts, - turn BFBFLAG for testing - clm5.0.dev010 erik 05/15/2018 Update cime version to version in cesm2.0.beta10, - changes answers for 1850 compsets because of orbit - clm5.0.dev009 sacks 05/10/2018 New init_interp method - clm5.0.dev008 erik 04/27/2018 With FUN subtract out soil nitrification flux of plant - uptake of soil NH3 and NO3 - clm5.0.dev007 erik 04/24/2018 Bring in a few answer changing things: FATES, - cism updates, IC file fix, - testing 1850 compset use 1850 orbit - clm5.0.dev006 sacks 04/12/2018 Don't allocate memory for zero-weight natveg - patches and urban - clm5.0.dev005 sacks 04/10/2018 Two fixes for init_interp - clm5.0.dev004 erik 04/09/2018 List of important bug fixes - clm5.0.dev003 erik 03/09/2018 Bug fixes for energy imbalance associated - with surface water and lakes - clm5.0.dev002 sacks 02/25/2018 Add some land ice diagnostic vars needed for CMIP6 - clm5.0.dev001 erik 02/14/2018 Fix LND_TUNING_MODE for fully coupled case, - update some README files/PTCLM - -=============================================================== -=============================================================== -Tag name: clm5.0.000 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Feb 05 2018 -One-line Summary: Initial version of CLM5.0 - -This is the initial science version of CLM5.0. - -Developments for CLM5.0 build on the progress made in CLM4.5. Most major components of the model have been updated with particularly -notable changes made to soil and plant hydrology, snow density, river modeling, carbon and nitrogen cycling and coupling, and crop -modeling. -The updates to CLM science are documented here: - -https://escomp.github.io/ctsm-docs/doc/build/html/tech_note/Introduction/CLM50_Tech_Note_Introduction.html#clm5-0 - -This version has production versions of CLM5.0 CMIP6 land-use change files for 1850, historical, and 2000. It has preliminary -versions of CMIP6 forcing files for Nitrogen deposition and population density. Further updates are needed for prescribed aerosols, -and future scenarios. - -Spunup initial conditions are provided for several CLM physics and forcing combinations from simulations run at 1-degree resolution -(fv 0.9x1.25 with g1xv6 ocean mask). - -=============================================================== - diff --git a/doc/source/_static/css/custom.css b/doc/source/_static/css/custom.css new file mode 100644 index 0000000000..10abb45722 --- /dev/null +++ b/doc/source/_static/css/custom.css @@ -0,0 +1,17 @@ +/* Make equation numbers float to the right */ +.eqno { + margin-left: 5px; + float: right; +} +/* Hide the link... */ +.math .headerlink { + display: none; + visibility: hidden; +} +/* ...unless the equation is hovered */ +.math:hover .headerlink { + display: inline-block; + visibility: visible; + /* Place link in margin and keep equation number aligned with boundary */ + margin-right: -0.7em; +} diff --git a/doc/source/_static/pop_ver.js b/doc/source/_static/pop_ver.js new file mode 100644 index 0000000000..b8c58658a8 --- /dev/null +++ b/doc/source/_static/pop_ver.js @@ -0,0 +1,37 @@ +$(document).ready(function() { + /* For a URL that looks like + https://blah.github.io/versions/VERSIONFOO/html/bar/index.html, set cur_version_dir to + 'VERSIONFOO' (i.e., the portion of the path following 'versions'). + */ + var proj_end = document.baseURI.indexOf("versions") + 9; + var end = document.baseURI.indexOf("/", proj_end); + var cur_version_dir = document.baseURI.substring(proj_end, end); + var mylist = $("#version-list"); + mylist.empty(); + $.getJSON(version_json_loc, function(data) { + if (data.hasOwnProperty(cur_version_dir)) { + /* First add the current version so that it appears first in the drop-down + menu and starts as the selected element of the menu. 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