GEOS-Chem (science codebase) 14.5.1 release #2678
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… CO2 - Add missing ship logical to HEMCO_Config.rc.carbon, otherwise ship emissions for CO2 are not included - Update HEMCO_Config.rc.CO2 to: 1. Include DiagnFile to properly save out emissions diagnostics 2. Use same Aviation_SurfCorr_SclFac.1x1.nc file as carbon simulation Signed-off-by: Melissa Sulprizio <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
run/shared/kpp_standalone_interface.yml - Fixed typo: "output_dir" -> "output_directory" Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/fullchem_mod.f90 - Use keyword arguments, for clarity GeosCore/kpp_standalone_interface.F90 - Remove Active_Cell and Active_Cell_Name from KPP_Standalone_YAML - Add new derived type KPP_Standalone_ActiveCell_Type, which is now declared with !$OMP THREADPRIVATE. This contains the Active_Cell and Active_Cell_Name fields. - Added new variable KPP_Standalone_ActiveCell, based on new KPP_Standalone_ActiveCell_Type NOTE: The KPP_Standalone_YAML is initialized outside of a parallel loop, so it does not need to be declared !$OMP THREADPRIVATE. But the choice of whether an (I,J,L) location corresponds to one of the "active_cells" (listed in the kpp_standalone_interface.yml file) happens within a parallelized loop. Thus we need to move the Active_Cell and Active_Cell_Name fields out of KPP_Standalone_YAML and into KPP_Standalone_ActiveCell. Signed-off-by: Bob Yantosca <[email protected]>
# Conflicts: # CHANGELOG.md
run/shared/kpp_standalone_interface.yml - Reorganize file so that "settings:" comes first, then "active_cells:", and then "locations:" - Add "settings:activate" YAML tag to toggle the KPP standalone interface on or off GeosCore/kpp_standalone_interface.F90 - Add call to QFYAML_Add_Get to parse the "settings:activate" YAML tag - Set KPP_Standalone_YAML%SkipIt to .TRUE. if "settings:activate" is false. This will cause the code to ignore saving out the state of the model for the KPP standalone even if kpp_standalone_interface.yml is present in the run directory. Signed-off-by: Bob Yantosca <[email protected]>
run/GCClassic/createRunDir.sh
- Copy run/shared/kpp_standalone_interface.yml to fullchem rundirs
run/shared/cleanRunDir.sh
- Skip removing bpch files (and {diag,tracer}info.dat files), we no
longer generate bpch output
- Add comments and usage examples
- Remove all fort.* files
- Remove OututDir/*.txt files as well (these are KPP standalone
interface files)
CHANGELOG.md
- Updated accordingly
Signed-off-by: Bob Yantosca <[email protected]>
.gitignore - Also ignore *.exe files GeosCore/fullchem_mod.F90 - Remove State_Grid from call to Check_ActiveCell GeosCore/kpp_standalone_interface.F90 - Updated subroutine header comments - Added cosmetic changes for clarity (mostly making code fit within 80 characters, for better readability) - Removed Active_Cell and Active_Cell_name from the KPP_Standalone_Interface_Type (should have been done previously) - Remove State_Grid argument from Check_ActiveCell, this was only used for debugging. Also removed commented out debug prints. - Use Format statements with write statments where expedient - Echo a message when the KPP standalone interface is manually disabled (i.e. when settings:activate = false) - Added display of location names and lon/lats at end of the routine Config_KPP_Standalone - In routine Write_Samples, wrap file I/O in an !$OMP CRITICAL block, in order to prevent more than one thread from writing to each file. - Removed RETURN statement from within !$OMP CRITICAL block, this is not allowed. - Bug fix: Write Kpp_Standalone_ActiveCell%Active_Cell_Name to file, and not Kpp_Standalone_YAML%Active_Cell_Name (which has been removed). Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/kpp_standalone_interface.F90 - Moved to kppsa_interface_mod.F90 GeosCore/kppsa_interface_mod.F90 - Moved from kpp_standalone_interface - Renamed types, variables and routines using "KppSa" prefix: - KPP_Standalone_Interface_Type -> KppSa_Interface_Type - KPP_Standalone_ActiveCell_Type -> KppSa_ActiveCell_Type - KPP_Standalone_YAML -> KppSa_State - KPP_Standalone_ActiveCell -> KppSa_ActiveCell - Check_Domain -> KppSa_Check_Domain - Check_ActiveCell -> KppSa_Check_ActiveCell - Config_KPP_Standalone -> KppSa_Config - Write_Samples -> KppSa_Write_Samples - Cleanup_KPP_Standalone -> KppSa_Cleanup - Added KppSa_Check_Time function to determine if it is time to write KPP standalone output. This allows you to only write output e.g. at the end of a run instead of for each timestep. - Added KppSa_State%SkipWriteAtThisTime field, which is used to determine if we need to exit a routine early. GeosCore/fullchem_mod.F90 - "USE Kpp_Standalone_Interface" -> "USE KppSa_Interface_Mod" - Call renamed routines from kppsa_interface_mod.F90 - Now call KppSa_Check_Domain only if it is the first call to DO_FULLCHEM. This is to avoid repeated computations. - Now call KppSa_Check_Time to determine if we are in the time window when the model state should be archived to disk. - Updated comments and comment headers run/shared/kpp_standalone_interface.yml - Added "start_output_at" to denote starting date time for archiving model state - Added "stop_output_at" to denote ending date time for archiving model state - Updated comments CHANGELOG.md GeosCore/CMakeLists.txt - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/kppsa_interface_mod.F90
- In routine KppSa_Check_Time:
- rRmoved leftover debug print statements
- In routine Kpp_Check_ActiveCell
- Added an IF statement to exit after setting KppSa_State%Active_Cell to .FALSE.
and KppSa_Active_Cell_Name to '' if we are outside of the time
window specified in the kpp_standalone_interface.yml fiel.
- This will ensure that we only archive model state to disk during
the specified time window, which helps with computatonal efficiency.
- In routine KppSa_Config:
- Now write starting & ending date of archival window to log file
Signed-off-by: Bob Yantosca <[email protected]>
run/GCHP/createRunDir.sh - Added an if statement to copy run/shared/kpp_standalone_interface.yml to GCHP fullchem run directories (any option) Signed-off-by: Bob Yantosca <[email protected]>
Changed the CEDS TMB emission fields to actually emit TMB like they're supposed to, instead of emitting HCOOH. I'm not sure if this fix needs to go into any other HEMCO_Config.rc template files, either in run/GCClassic or in other run/ directories, but hopefully we can make any other necessary changes down the line
Fix bug where download_data.py failed if the dryrun log filename contained uppercase characters e.g. 'Log.dryrun'. The solution is to not coerce the dryrun log filename to lowercase.
KPP/standalone - Folder which contains source code from the GitHub repository: https://github.com/geoschem/KPP-Standalone. This is a fork of the https://github.com/KineticPreProcessor/KPP-Standalone repo by Obin Sturm, Mike Long, and Christoph Keller. The branch geoschem-dev is checked out. This is where we can place GEOS-Chem-specific updates without touching the original code in the kpp-standalone branch. branch is set to geoschem-dev, which is the branch to be used for interfacing into the GEOS-Chem model .gitmodules - This was updated by running the command: git submodule add -b geoschem-dev \ https://github.com/geoschem/KPP-Standalone \ KPP/standalone CHANGELOG.md - Updated accordingly KPP/fullchem/Makefile KPP/fullchem/kpp_standalone*.F90 KPP/fullchem/samples_kpp_standalone/* - Removed from the KPP/fullchem folder. KPP/standalone - Folder containing code from https://github.com/geoschem/KPP-Standalone Signed-off-by: Bob Yantosca <[email protected]>
KPP/CMakeLists.txt - Add calls to "add_directory(standalone)" in the fullchem and custom "if" blocks. This will tell CMake to look for the CMakeLists.txt file in the KPP/standalone folder, and to build the standalone files (libKppStandalone.a) after libKPP.a has been built. Signed-off-by: Bob Yantosca <[email protected]>
…sed on species defined In carbon_gases_mod.F90 all chemistry input fields needed for CO2, CH4, and CO chemistry were obtained regardless of the species included in the carbon simulation. Therefore when running the carbon simulation with only one species (e.g. CO2) fields were being obtained that weren't necessary. These fields have been blocked by logical statements checking if the species that needs those fields is advected. Also in this module, the chemistry routine has been updated to only call KPP when CH4 and/or CO are defined as advected species. KPP is not needed for CO2-only simulations. Instead CO2-only simulations utilize the CO2_COPROD field obtained from HEMCO. This field was originally obtained and applied to the species concentration array in subroutine Emiss_Carbon_Gases. The routine name was misleading and has been renamed to CO2_Production. The call to this routine has also been moved from emissions_mod.F90 to Chem_Carbon_Gases in carbon_gases_mod.F90. Notes: When we retire the CO2 simulation, we should be able to also remove the CO2 menu from geoschem_config.yml since it is not needed when using CO2 in the carbon simulation. Signed-off-by: Melissa Sulprizio <[email protected]>
…ns with CO only To make it more clear that the PCO_CH4 fields are read from file, the option in in the CO2 menu of geoschem_config.yml has been renamed from from "use_fullchem_PCO_from_CH4" to "use_archived_PCO_from_CH4 (same for NMVOC source)". The use_archived_PCO_from_CH4 option is now set to false by default for carbon simulations and only set to true in carbon simulations where only CO is advected. Similarly, "3D_chemical_oxidation_source" in the CO2 menu has been renamed to "use_archived_PCO2_from_CO". The carbon mechanism was rebuilt with KPP 3.1.1 here but that is a zero- difference update simply changing the headers of the KPP/carbon/gckpp* files. Signed-off-by: Melissa Sulprizio <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Fixes for running GEOS-Chem 14.5.1 in GEOS
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.Hg - Added MACFARLANE entries for the Australian regional Hg emissions by Macfarlane et al. [2022] - Added scale factor 13 (HgCl2 to Hg) - Added mask 1010 (AUSTRALIA_MASK) CHANGELOG.md - Updated accordingly
run/GCClassic/HISTORY.rc.templates/HISTORY.rc.* - Add a comment to the BoundaryConditions collection header warning users not to change the BoundaryConditions.frequency setting. This must be left at "00000000 030000", as GEOS-Chem Classic nested-grid simulations expect to read boundary conditions every 3 hours. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.Hg - Changed path of AUSTRALIA_MASK file from v2016-04 to v2025-01 Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR #2669 (Implement Australian Hg emissions inventory (2010-2019) from MacFarlane et al. [2022], by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR implements a new emissions inventory for the Hg simulation. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR #2670 (Add comments to GCClassic HISTORY.rc template files advising users not to change BoundaryConditions.frequency, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR adds a warning to the HISTORY.rc template files for users not to change the BoundaryConditions.frequency setting. Signed-off-by: Bob Yantosca <[email protected]>
Signed-off-by: Melissa Sulprizio <[email protected]>
Contains bug fixes for the carbon simulations in GCClassic and GCHP Signed-off-by: Melissa Sulprizio <[email protected]>
test/shared/commonFunctionsForTests.sh - In function get_default_gcc_env_file, now use environment file gcclassic.gcc12_cannon_rocky.env - In function get_default_gchp_env_file, now use environment file gchp.gcc12_openmpi4_cannon_rocky.env CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR #2674 (Change default environment files for integration tests on Harvard Cannon from gnu10 to gnu12 #2674, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR updates the default compiler for integrationt tests that are run on the Harvard Cannon cluster. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR #2675 (Fixed the problem that GCHP cannot read meteorology field from yaml, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. According to @lizziel: I believe this fixes an issue brought in with the updates for GEOS-IT in dev/no-diff-to-benchmark (see PR #2523). It would only show up for GEOS-FP and GEOS-IT runs which we do not test in integration/AWS testing, and is not in any previously released versions. It therefore does not need an update to the changelog. Signed-off-by: Bob Yantosca <[email protected]>
This merge brings the dev/no-diff-to-benchmark branch commits into the GEOS-Chem (science codebase) 14.5.1 release branch, in anticipation of the 14.5.1 release. Signed-off-by: Bob Yantosca <[email protected]>
Updated version numbers in: - CHANGELOG.md Please see CHANGELOG.md for updates added to this version. Signed-off-by: Bob Yantosca <[email protected]>
lizziel
approved these changes
Jan 10, 2025
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Name and Institution (Required)
Name: Bob Yantosca
Institution: Harvard + GCST
Describe the update
This PR seeks to merge the
release/14.5.1branch intomainin anticipation of the GEOS-Chem 14.5.1 release.The
release/14.5.1branch containsdev/no-diff-to-benchmarkExpected changes
This is a no-diff-to-benchmark update
Tagging @msulprizio @lizziel