EMC flake #471

YihuaWu-NOAA · 2020-07-10T20:22:48Z

Description: see below.

Associated PRs:

#471
NOAA-EMC/fv3atm#141
ufs-community/ufs-weather-model#164

YihuaWu-NOAA · 2020-07-10T21:54:11Z

Description:

Modify files in ufs-weather-model-flake/FV3/gfsphysics/GFS_layer/
GFS_typedefs.F90
GFS_typedefs.meta
Note: Added two variables: lakedepth and LKM (logical)

Modify file in ufs-weather-model-flake/FV3/io/
FV3GFS_io.F90
Note: read in lake depth, and reset lakefraction and lakedepth to 0 when LKM is not one

Modify files in ufs-weather-model-flake/FV3/ccpp/physics/physics/
Added three files:
flake_driver.F90
flake_driver.meta
flake.F90*

  Modified:
      GFS_time_vary_pre.fv3.F90
      Note: Flake need julian day

  Modified:
      GFS_surface_composites.F90
     GFS_surface_composites.meta
    Note: add lake depth, and define the logical variable lake based on lakefraction and lakedepth
    Then, the logical variable lake is passed to flake driver and sfc_ocean.
    When lake is true, flake will be called; when lake is false, ocean model will be called

  Modified
     sfc_ocean.F
     sfc_ocean.meta
    Note: add logical variable, lake, if not lake, calculation will be conducted.

Modify files in ufs-weather-model-flake/FV3/ccpp/suites/
suite_FV3_GFS_v16beta_flake.xml

Modify files in ufs-weather-model-flake/FV3/ccpp/config/
ccpp_prebuild_config.py

Add file in ufs-weather-model-flake/tests/tests
fv3_ccpp_gfs_v16beta_flake

Modify file in ufs-weather-model-flake/tests/fv3_conf/
ccpp_gfs_v16_flake_run.IN

Modify files in ufs-weather-model-flake/parm/
ccpp_v16beta_c96.nml.IN

Modify files in mylakedir/sorc/orog.fd
lakefrac.F90 to create lake fraction and depth and add them to oro_data_tilex.nc

Replace oro_data_tilex.nc files on hera: /scratch2/NCEPDEV/fv3-cam/Yihua.Wu/noscrub/trunk-20200701 which provide model inputs.

Merge remote-tracking branch 'upstream/master' into flake

climbfuji

This is a nice and clean PR. A few minor changes are required wrt commenting out or otherwise hiding debug prints in the flake_driver.F90 file. I also noted a few items to address later in the actual flake.F90 code.

climbfuji · 2020-07-16T12:54:30Z

physics/flake_driver.F90

+      do i = 1, im
+        if (flag(i)) then
+          if( lake(i) ) then
+           print*,'lake depth=',lakedepth


Please comment out or remove this print statement or wrap it in an if (debug) block with debug being a local parameter set to .false. by default.

climbfuji · 2020-07-16T12:57:27Z

physics/flake_driver.F90

+
+!     write(65,1002) julian,xlat(i),w_albedo(I),w_extinc(i),lakedepth(i),elev(i),tb,tt,tsurf(i),T_sfc(i)
+!     print 1002 julian,xlat(i),w_albedo(I),w_extinc(i),lakedepth(i),elev(i),tb,tt,tsurf(i),T_sfc(i)
+     print*,'inside flake driver'


Same as above (and for any other print statements in this file - comment out, remove, or wrap in if (debug) blocks.

climbfuji · 2020-07-16T12:59:03Z

physics/GFS_surface_composites.F90

@@ -182,6 +182,19 @@ subroutine GFS_surface_composites_pre_run (im, frac_grid, flag_cice, cplflx, cpl
        endif
      enddo

+! to prepare to separate lake from ocean in later


This comment is a bit confusing - can you remove the in later part, please?

climbfuji · 2020-07-16T13:02:25Z

physics/flake.F90

+ELSE 
+  T_sfc_n = T_wML_n_flk                    ! No ice-snow cover, use the mixed-layer temperature
+END IF
+if(T_sfc_n.lt.200.0 .or. T_sfc_n.gt.350.0) then


This should be cleaned up in the future - write to an error message and set an error flag, hand back to flake driver and let CCPP abort the model run. Not for this PR, though.

climbfuji · 2020-07-16T13:04:03Z

physics/flake.F90

+
+!  Dimensionless constants in the Monin-Obukhov surface-layer 
+!  similarity relations and in the expressions for the roughness lengths.
+REAL (KIND = kind_phys), PARAMETER ::   &


There is a lot of room for consolidation. Ideally, constants would be defined in/by the host model and then passed from there. I understand that the purpose of this PR is to bring in the flake model with as little changes as possible, so that's fine. Let us keep in mind that we should revisit using constants from the host model later.

YihuaWu-NOAA · 2020-07-16T15:06:55Z

Hi, Dom, Thank you very much for the review and comments. The print statements have been removed or commended out. I agree with you, there are rooms for code consolidation. I will do it later in another PR. Best regards. *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Thu, Jul 16, 2020 at 9:07 AM Dom Heinzeller ***@***.***> wrote: ***@***.**** requested changes on this pull request. This is a nice and clean PR. A few minor changes are required wrt commenting out or otherwise hiding debug prints in the flake_driver.F90 file. I also noted a few items to address later in the actual flake.F90 code. ------------------------------ In physics/flake_driver.F90 <#471 (comment)>: > + lake_depth_max = 60.0 + ipr = min(im,10) + +! --- ... set flag for lake points + + do i = 1, im + flag(i) = (wet(i) .and. flag_iter(i)) + enddo + + Kbar=3.5 + DelK=3.0 + + do i = 1, im + if (flag(i)) then + if( lake(i) ) then + print*,'lake depth=',lakedepth Please comment out or remove this print statement or wrap it in an if (debug) block with debug being a local parameter set to .false. by default. ------------------------------ In physics/flake_driver.F90 <#471 (comment)>: > + temp = 0.006918-0.399912*cos(temp)+0.070257*sin(temp)- & + 0.006758*cos(2.0*temp)+0.000907*sin(2.0*temp) - & + 0.002697*cos(3.0*temp)+0.00148*sin(3.0*temp) + w_albedo(I) = 0.06/cos((xlat(i)-temp)/1.2) +! w_albedo(I) = 0.06 +! compute water extinction coefficient as a function of julian day + if(julian.lt.90 .or. julian .gt. 333) then + w_extinc(i) = Kbar-Kbar/DelK + else + w_extinc(i) = Kbar+Kbar/DelK*sin(2*3.14159265*(julian-151)/244) + endif +! w_extinc(i) = 3.0 + +! write(65,1002) julian,xlat(i),w_albedo(I),w_extinc(i),lakedepth(i),elev(i),tb,tt,tsurf(i),T_sfc(i) +! print 1002 julian,xlat(i),w_albedo(I),w_extinc(i),lakedepth(i),elev(i),tb,tt,tsurf(i),T_sfc(i) + print*,'inside flake driver' Same as above (and for any other print statements in this file - comment out, remove, or wrap in if (debug) blocks. ------------------------------ In physics/GFS_surface_composites.F90 <#471 (comment)>: > @@ -182,6 +182,19 @@ subroutine GFS_surface_composites_pre_run (im, frac_grid, flag_cice, cplflx, cpl endif enddo +! to prepare to separate lake from ocean in later This comment is a bit confusing - can you remove the in later part, please? ------------------------------ In physics/flake.F90 <#471 (comment)>: > + +END IF + + +!------------------------------------------------------------------------------ +! Update the surface temperature. +!------------------------------------------------------------------------------ + +IF(h_snow_n_flk.GE.h_Snow_min_flk) THEN + T_sfc_n = T_snow_n_flk ! Snow exists, use the snow temperature +ELSE IF(h_ice_n_flk.GE.h_Ice_min_flk) THEN + T_sfc_n = T_ice_n_flk ! Ice exists but there is no snow, use the ice temperature +ELSE + T_sfc_n = T_wML_n_flk ! No ice-snow cover, use the mixed-layer temperature +END IF +if(T_sfc_n.lt.200.0 .or. T_sfc_n.gt.350.0) then This should be cleaned up in the future - write to an error message and set an error flag, hand back to flake driver and let CCPP abort the model run. Not for this PR, though. ------------------------------ In physics/flake.F90 <#471 (comment)>: > + tpl_L_f , & ! Latent heat of fusion [J kg^{-1}] + h_Ice_min_flk ! Minimum ice thickness [m] + +use machine, only: kind_phys + +!============================================================================== + +IMPLICIT NONE + +!============================================================================== +! +! Declarations + +! Dimensionless constants in the Monin-Obukhov surface-layer +! similarity relations and in the expressions for the roughness lengths. +REAL (KIND = kind_phys), PARAMETER :: & There is a lot of room for consolidation. Ideally, constants would be defined in/by the host model and then passed from there. I understand that the purpose of this PR is to bring in the flake model with as little changes as possible, so that's fine. Let us keep in mind that we should revisit using constants from the host model later. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#471 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQA53TIZE5PQUBY2JBTR333QVANCNFSM4OW456VQ> .

SMoorthi-emc · 2020-07-16T17:05:11Z

physics/GFS_surface_composites.F90

+              lake(i) = .false.
+           endif
+        else
+           lake(i) = .false.


Why not use "flake" instead of "lake"? Even without flake model, lakes exist.
Also, I concur with Dom that instead of "lkm" why not use logical, say "flake_model" (true or flase)?

@YihuaWu-NOAA said that there will be additional options later (lkm=0,1,2,...), so in this case it is ok to keep it as an integer as far as I am concerned.

SMoorthi-emc

I don't see any update to sfc_nst..f file. Did I miss it?

YihuaWu-NOAA · 2020-07-16T19:14:24Z

Hi, Moorthi, Thanks for your review and comments. First of all, I agree with you. And as Dom pointed out that there are rooms for code consolidation. I am wondering if these can be done together in the next PR. Best regards! *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Thu, Jul 16, 2020 at 1:18 PM SMoorthi-emc ***@***.***> wrote: ***@***.**** commented on this pull request. I don't see any update to sfc_nst..f file. Did I miss it? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#471 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQCCKWU57KKIMUNYZU3R34Y6FANCNFSM4OW456VQ> .

climbfuji

The changes look good to me know. @SMoorthi-emc had one comment on using flake instead of lake, see https://github.com/NCAR/ccpp-physics/pull/471/files#r455938014 - can you please answer to this comment?

YihuaWu-NOAA · 2020-07-17T13:38:33Z

Thank you very much! In the next PR, I will work with you all for the comments which have not been addressed in this PR. *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Fri, Jul 17, 2020 at 9:30 AM SMoorthi-emc ***@***.***> wrote: ***@***.**** approved this pull request. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#471 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQCDZOLHSCVWOMHTRN3R4BHAXANCNFSM4OW456VQ> .

YihuaWu-NOAA · 2020-07-17T13:57:21Z

The changes look good to me know. @SMoorthi-emc had one comment on using flake instead of lake, see https://github.com/NCAR/ccpp-physics/pull/471/files#r455938014 - can you please answer to this comment?

Yes, flake can be used instead of lake. I replied Moorthi before, I'd like to do this in the next PR with some code consolidations suggested by you. However, Using flake instead of lake, there will be one more array of variable.

@SMoorthi-emc

* Feature/ccpp codeowners (NCAR#442) * Per-file CODEOWNERS in ccpp/physics to set up automatic review requests * Code cleanup. Remove used code/variables. Fix minor inconsistencies. (NCAR#440) * Remove ESMF Alarm and TimeInterval variables from module_fv3_config. * Variables nfhmax, nfhmax_hf are unused outside InitializeAdvertise. Declared them as local variables. * There is no need to keep duplicates of all time related variables in atm_int_state when we can easily access them from atm_int_state%Atm. * Remove redundant call to fms_init * Add few missing ESMF_LogFoundError checks in module_fcst_grid_comp.F90 * Delete time_utils.F90. Unused. * print only actual errors to stderr, everything else to stdout * Move realizeConnectedCplFields to module_cplfields from module_cap_cpl * Declare Atmos as module variable, and remove atmos_internalstate_wrapper * Move code from clock_cplIntval to InitializeAdvertise * Removed INTERNAL_FILE_NML from atmos_model.F90 * CCPP cloud cover change for Thompson MP associated with Xu Randall (NCAR#443) * Remove old comments from GFS_typedefs.F90. * Update logic that sets Model%cnvcld = .false. * Wrapper for ccpp-physics NCAR#806, NCAR#807, NCAR#813 (NCAR#447) * CCPP physics updates from PR NCAR#806(only diagnostic changes for RRTMGP - small diag-only RT impact for tests involving RRTMGP),NCAR#807 (only aborting model if sfc emis file not present when needed) ,NCAR#813(only SCM-specific physics changes) * Wrapper for ccpp-physics NCAR#808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (NCAR#452) This PR contains the ccpp physics PR NCAR#808 and NCAR#816. 808 addresses an error in the momentum roughness length over tiles with ice. 816 fixes an occasional segfault bug related to the tsurf variable in NoahMP and updates to "improve snow simulation in NoahMP for P8". * Use 'model set run clock' routine in FV3 NUOPC cap. (NCAR#450) * Add 'SetRunClock' specialization routine to FV3 NUOPC cap, which sets fv3 model clock. FV3 cap does not keep local copy of clock (clock_fv3) as saved module variable anymore. * Minor code cleanup. * Clean up iovr=4 (exponential cloud overlapping method) in RRTMG (NCAR#445) Clean up the exponential cloud overlapping method in RRTMG, which reflects the practice of the pre-2018 operational HWRF model. * Bug fix for dimensions of eta level variables and WAM variables in Fortran code and CCPP metadata (NCAR#431) * Add additional diagnostic arrays for radiation-microphysics development * Bug fixes for WAM model runs with levr < levs * Update inline post with latest UPP release upp_v10.0.11 (NCAR#449) * Update UPP revision * Add foundation temperaure in GFS read interface for inline post. * Wrapper for ccpp-physics NCAR#812 (NCAR#453) * update submodule pointer for regression testing of ccpp-physics#812 * MYNN sfclay (RAP suite) restart reproducibility, P8 suite definition files (NCAR#455) * Fix uninitialized variable zmtnblck in ccpp/data/GFS_typedefs.F90 * Fix typo in CCPP standard name for ncnvwind in ccpp/data/GFS_typedefs.meta * Add ten 2d variables required for MYNNSFC restart reproducibility to ccpp/driver/GFS_restart.F90 * create initial p8 suites, P8 initial SDFs as copies of FV3_GFS_v16_coupled_nsstNoahmpUGWPv1 and FV3_GFS_v16_nsstNoahmpUGWPv1 Co-authored-by: Denise Worthen <[email protected]> * Fixes on initializing snow depth over ice and changes z0ice (NCAR#461) * modify FV3GFS_io.F90 by fixing errors associated with initializing snow depth over ice in the case where both land and water coexist (i.e. fractional grid case) * z0ice is changed to 1.0 cm from 1.1cm in atmos_model.F90 * Radar-derived microphysics temperature tendencies similar to operational HRRR (NCAR#457) - implements a feature of the operational HRRR, radar-derived microphysics temperature tendencies applied in the first N minutes of the forecast to improve clouds in the first few hours. * HRRR-like radar-derived temperature tendencies * Give a warning when convection is enabled with radar tten * Fix uninitialized variable zmtnblck in ccpp/data/GFS_typedefs.F90 * Add ten 2d variables required for MYNNSFC restart reproducibility to ccpp/driver/GFS_restart.F90 * fixing snod bug in atmos_model.F90 (NCAR#465) * Thompson MP cloud tuning (NCAR#463) * Improve cloud fraction when using Thompson MP. See NCAR#809 for more details. * Feature/hwrf legacy (NCAR#459) * Added a new suite definition file: suite_FV3_HAFS_v0_thompson_tedmf_gfdlsf.xml. This SDF is a legacy hwrf SDF but only the GFDL surface layer scheme and the Thompson scheme are kept. * CCPP: Update consistency checks and effective radii calculation for Thompson MP (NCAR#462) * This PR updates the submodule pointer for ccpp-physics for the changes described in NCAR#786 (Update consistency checks and effective radii calculation for Thompson MP) * Unified write_netcdf, add single file 'cubed_sphere_grid' output (NCAR#466) * Unify write_netcdf and write_netcdf_parallel modules. * Add support for writing 'cubed_sphere_grid' history files in a single netcdf file * Code refactoring and cleanup. * Change standard name and unit of CCPP error flag variable in CCPP framework and physics (NCAR#467) *Change standard name and unit of CCPP error flag variable in CCPP framework and physics. * Add code to enable ESMF managed threading (NCAR#469) * Implement ESMF-managed-threading for fcstComp and wrtComp's. * Revisions to repair iovr=5 cloud overlap option (NCAR#471) *This PR addresses part 2 of CCPP issue NCAR#748 to activate the exponential-random cloud overlap method (iovr=5) in RRTMG. * Add 2d decomposition on the write grid comp (NCAR#470) * update write grid comp to have 2D decomposition on output grid. * combine PR#468: Bug fix in FV3GFS_io.F90 for allocation of temp2d Co-authored-by: Ted Mansell <[email protected]> * 4DIAU bug when iau_filter_increments=T (NCAR#458) * Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (NCAR#475) * add lsm_cold_start variable in GFS_typedefs.F90/meta and update ccpp/physics for testing * includes @SMoorthi-emc 's bugfix for gwdps.f. * add lon info in the write group (NCAR#476) * Multiple output grids (NCAR#480) Update fv3 cap and write grid component to enable outputting multiple domains. This is done be creating an array of fcstGrids, and array of rout handles where each element of these arrays correspond to one atm domain. In the write grid component updates were made to allow grid spec parameters for each output grid to be specified separately. Co-authored-by: Gerhard Theurich <[email protected]> * GPU-enabled version of Grell-Freitas convection in ccpp-physics (NCAR#479) * Enable Thompson MP when coupling with UFS-Aerosols (NCAR#484) * Add support for Stochastically Perturbed Parameterizations (SPP) in FV3 and add the FV3_RRFS_v1alpha SDF. (NCAR#454) Adds the necessary code in fv3atm to allow for Stochastically Perturbed Parameterizations (SPP) in a set of RAP/HRRR-based physics parameterizations. Specific to the fv3atm repository, code in this PR defines the necessary variables associated with various SPP-related fields (e.g., logical to activate SPP, parameterization-specific SPP variables, etc.) that are then passed to ccpp-physics. * lateral boundary fix for regional runs (NCAR#482) * Updating pointer to ccpp/physics. * Point to Christina's branches. * Point to NOAA-GSL gsl/develop for ccpp/physics Co-authored-by: Samuel Trahan (NOAA contractor) <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Grant Firl <[email protected]> Co-authored-by: mzhangw <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]> Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: SMoorthi-emc <[email protected]> Co-authored-by: ChunxiZhang-NOAA <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Jeff Whitaker <[email protected]> Co-authored-by: Gerhard Theurich <[email protected]> Co-authored-by: DomHeinzeller <[email protected]> Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: MatthewPyle-NOAA <[email protected]> Co-authored-by: samuel.trahan <[email protected]>

@SMoorthi-emc

* Feature/ccpp codeowners (NCAR#442) * Per-file CODEOWNERS in ccpp/physics to set up automatic review requests * Code cleanup. Remove used code/variables. Fix minor inconsistencies. (NCAR#440) * Remove ESMF Alarm and TimeInterval variables from module_fv3_config. * Variables nfhmax, nfhmax_hf are unused outside InitializeAdvertise. Declared them as local variables. * There is no need to keep duplicates of all time related variables in atm_int_state when we can easily access them from atm_int_state%Atm. * Remove redundant call to fms_init * Add few missing ESMF_LogFoundError checks in module_fcst_grid_comp.F90 * Delete time_utils.F90. Unused. * print only actual errors to stderr, everything else to stdout * Move realizeConnectedCplFields to module_cplfields from module_cap_cpl * Declare Atmos as module variable, and remove atmos_internalstate_wrapper * Move code from clock_cplIntval to InitializeAdvertise * Removed INTERNAL_FILE_NML from atmos_model.F90 * CCPP cloud cover change for Thompson MP associated with Xu Randall (NCAR#443) * Remove old comments from GFS_typedefs.F90. * Update logic that sets Model%cnvcld = .false. * Wrapper for ccpp-physics NCAR#806, NCAR#807, NCAR#813 (NCAR#447) * CCPP physics updates from PR NCAR#806(only diagnostic changes for RRTMGP - small diag-only RT impact for tests involving RRTMGP),NCAR#807 (only aborting model if sfc emis file not present when needed) ,NCAR#813(only SCM-specific physics changes) * Wrapper for ccpp-physics NCAR#808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (NCAR#452) This PR contains the ccpp physics PR NCAR#808 and NCAR#816. 808 addresses an error in the momentum roughness length over tiles with ice. 816 fixes an occasional segfault bug related to the tsurf variable in NoahMP and updates to "improve snow simulation in NoahMP for P8". * Use 'model set run clock' routine in FV3 NUOPC cap. (NCAR#450) * Add 'SetRunClock' specialization routine to FV3 NUOPC cap, which sets fv3 model clock. FV3 cap does not keep local copy of clock (clock_fv3) as saved module variable anymore. * Minor code cleanup. * Clean up iovr=4 (exponential cloud overlapping method) in RRTMG (NCAR#445) Clean up the exponential cloud overlapping method in RRTMG, which reflects the practice of the pre-2018 operational HWRF model. * Bug fix for dimensions of eta level variables and WAM variables in Fortran code and CCPP metadata (NCAR#431) * Add additional diagnostic arrays for radiation-microphysics development * Bug fixes for WAM model runs with levr < levs * Update inline post with latest UPP release upp_v10.0.11 (NCAR#449) * Update UPP revision * Add foundation temperaure in GFS read interface for inline post. * Wrapper for ccpp-physics NCAR#812 (NCAR#453) * update submodule pointer for regression testing of ccpp-physics#812 * MYNN sfclay (RAP suite) restart reproducibility, P8 suite definition files (NCAR#455) * Fix uninitialized variable zmtnblck in ccpp/data/GFS_typedefs.F90 * Fix typo in CCPP standard name for ncnvwind in ccpp/data/GFS_typedefs.meta * Add ten 2d variables required for MYNNSFC restart reproducibility to ccpp/driver/GFS_restart.F90 * create initial p8 suites, P8 initial SDFs as copies of FV3_GFS_v16_coupled_nsstNoahmpUGWPv1 and FV3_GFS_v16_nsstNoahmpUGWPv1 Co-authored-by: Denise Worthen <[email protected]> * Fixes on initializing snow depth over ice and changes z0ice (NCAR#461) * modify FV3GFS_io.F90 by fixing errors associated with initializing snow depth over ice in the case where both land and water coexist (i.e. fractional grid case) * z0ice is changed to 1.0 cm from 1.1cm in atmos_model.F90 * Radar-derived microphysics temperature tendencies similar to operational HRRR (NCAR#457) - implements a feature of the operational HRRR, radar-derived microphysics temperature tendencies applied in the first N minutes of the forecast to improve clouds in the first few hours. * HRRR-like radar-derived temperature tendencies * Give a warning when convection is enabled with radar tten * Fix uninitialized variable zmtnblck in ccpp/data/GFS_typedefs.F90 * Add ten 2d variables required for MYNNSFC restart reproducibility to ccpp/driver/GFS_restart.F90 * fixing snod bug in atmos_model.F90 (NCAR#465) * Thompson MP cloud tuning (NCAR#463) * Improve cloud fraction when using Thompson MP. See NCAR#809 for more details. * Feature/hwrf legacy (NCAR#459) * Added a new suite definition file: suite_FV3_HAFS_v0_thompson_tedmf_gfdlsf.xml. This SDF is a legacy hwrf SDF but only the GFDL surface layer scheme and the Thompson scheme are kept. * CCPP: Update consistency checks and effective radii calculation for Thompson MP (NCAR#462) * This PR updates the submodule pointer for ccpp-physics for the changes described in NCAR#786 (Update consistency checks and effective radii calculation for Thompson MP) * Unified write_netcdf, add single file 'cubed_sphere_grid' output (NCAR#466) * Unify write_netcdf and write_netcdf_parallel modules. * Add support for writing 'cubed_sphere_grid' history files in a single netcdf file * Code refactoring and cleanup. * Change standard name and unit of CCPP error flag variable in CCPP framework and physics (NCAR#467) *Change standard name and unit of CCPP error flag variable in CCPP framework and physics. * Add code to enable ESMF managed threading (NCAR#469) * Implement ESMF-managed-threading for fcstComp and wrtComp's. * Revisions to repair iovr=5 cloud overlap option (NCAR#471) *This PR addresses part 2 of CCPP issue NCAR#748 to activate the exponential-random cloud overlap method (iovr=5) in RRTMG. * Add 2d decomposition on the write grid comp (NCAR#470) * update write grid comp to have 2D decomposition on output grid. * combine PR#468: Bug fix in FV3GFS_io.F90 for allocation of temp2d Co-authored-by: Ted Mansell <[email protected]> * 4DIAU bug when iau_filter_increments=T (NCAR#458) * Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (NCAR#475) * add lsm_cold_start variable in GFS_typedefs.F90/meta and update ccpp/physics for testing * includes @SMoorthi-emc 's bugfix for gwdps.f. * add lon info in the write group (NCAR#476) * Multiple output grids (NCAR#480) Update fv3 cap and write grid component to enable outputting multiple domains. This is done be creating an array of fcstGrids, and array of rout handles where each element of these arrays correspond to one atm domain. In the write grid component updates were made to allow grid spec parameters for each output grid to be specified separately. Co-authored-by: Gerhard Theurich <[email protected]> * GPU-enabled version of Grell-Freitas convection in ccpp-physics (NCAR#479) * Enable Thompson MP when coupling with UFS-Aerosols (NCAR#484) * Add support for Stochastically Perturbed Parameterizations (SPP) in FV3 and add the FV3_RRFS_v1alpha SDF. (NCAR#454) Adds the necessary code in fv3atm to allow for Stochastically Perturbed Parameterizations (SPP) in a set of RAP/HRRR-based physics parameterizations. Specific to the fv3atm repository, code in this PR defines the necessary variables associated with various SPP-related fields (e.g., logical to activate SPP, parameterization-specific SPP variables, etc.) that are then passed to ccpp-physics. * lateral boundary fix for regional runs (NCAR#482) * Feature: NSSL Microphysics support (NCAR#472) Supports CCPP with new NSSL microphysics scheme, which has separate hydrometeor categories for graupel and hail (Mansell et al. 2010, JAS). This PR allows fv3atm to compile correctly with CCPP+NSSL, but a further update to atmos_cubed_sphere is needed to run correctly. The NSSL scheme is used in NSSL's daily FV3 convection-allowing forecasts, and the scheme itself is aimed at this scale (dx <= 4km). Testing is underway also with a preliminary Warn-on-Forecast FV3 ensemble. * Add p8b SDF (NCAR#491) * add p8 suite files * fix 2phases intermediate restart Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: Jun Wang <[email protected]> * Split CCPP finalize into physics_finalize and (framework) finalize; minor CCPP cleanup and documentation updates (NCAR#487) * Minor cleanup and documentation updates for CCPP; split CCPP finalize into physics_finalize and (framework) finalize * Add 'valid time' variable using ISO string format (NCAR#492) Add 'valid time' variable using ISO string format to netcdf history files. Use double precision variable to set value of 'time' attribute in wrt comp import state Update ccpp/physics (setting surface-related interstitial variables for SCM prescribed-surface-flux mode) Update inline_post_stub.F90 subroutine interfaces to match inline_post.F90 Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Grant Firl <[email protected]> * Fix Lambert Conformal Conic mapping in the write component on the southern hemisphere (NCAR#497) Subroutine `lambert` in the write component has been fixed to do the mapping on the southern hemisphere correctly. * Rectify total number of Thompson MP species for PBL mixing (NCAR#509) * update upp revision (NCAR#505) * move some parameters in mynn surface layer to namelist options * land surface upgrades for p8c (NCAR#499) * Added capability for cdmbgwd(1) to scale GSL blocking drag (NCAR#502) * release/p8c: it is related to ccpp-physics PBL and cumulus updates plus a bug fix to the Thompson scheme PR NCAR#882 (NCAR#503) * change ccpp-physics branch to feature/p8c_pbl_cp branch * change ccpp/physics in feature/p8c_pbl_cp branch * revised GFS_typedefs.F90 for the paramters in the saSAS scheme * sync upp * Revert "sync upp" This reverts commit 429d0469c92d200fa058aca6c6bd17adac7f9568. * sync upp to 0185bb9 * Merge remote-tracking branch remote/main for ccpp-physics and update .gitmodules * Bring AQM model into UFS (NCAR#511) * Reset to zero coupling arrays for accumulated snow, large scale rain, and convective rain at the end of each coupling step if coupling with chemistry model. * Properly set kind type of literal constants defining zero and one. * Initialize to zero canopy resistance output variablein noah/osu land-surface model subdriver. * Re-implement radiation diagnostic output involving spectral band layer cloud optical depths (0.55 and 10 mu channels) to prevent floating invalid errors due to uninitialized optical depth arrays. * Temporarily disable filling export fields during the NUOPC Realize phase since it breaks coupling with aerosol component. * Increase maximum number of input aerosol scavenging factors to accommodate AQM/CMAQ 5.2.1 chemical tracers. * Remove inst_pres_height_surface from chemistryFieldNames as its imported already elsewhere Co-authored-by: Raffaele Montuoro <[email protected]> * RRTMGP for prototype 8 (NCAR#498) * Add explict treatment of convective cloud to RRTMGP. * Some cleanup and bug fixes from previous commit. working now with Thompson MP plus radiatively active convective cloud. * Updated physics. New interstitials. * Added explicit MYNN-EDMF cloud coupling to RRTMGP. * Added switches for sgs clouds in GP. * Replaced cld_mynn_ naming convention with cld_pbl_ * Fixed inconsistency between G/GP in Thompson MP. * Some more cleanup of cloud-fraction... * Pulled in Qingfu's changes to ccpp-physics * Synced physics with main * Updated physics. * Revert change from previous commits (sampling of different cloud types). New SDFs for p8c * Changed arguments to implied shape. * Renamed scheme file in SDF. Now common to both RRTMG and RRTMGP SDFs * Syntax error in ccpp-physics * Revert changes to names * Renamed p8_rrtmgp SDFs * Added bounding to temperature at layer-interface used by RRTMGP. * Reorder loop * Combined gp sw and lw aerosol routines. Modest speedup (~4%) * HAFS related moving-nesting, nest coupling, and movable output grid capabilities (NCAR#501) * Add the storm-following or specified moving-nesting capability for both the regional and global configuration. * Expand the UFS/HAFS FV3ATM-HYCOM ocean coupling to support the static and moving nesting configuration. * Expand the write grid component to support outputting the moving nest domain properly. * Five HAFS related moving-nesting regression tests are added to test these newly added features. The regional_hafs RT was removed. Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Daniel Rosen <[email protected]> Co-authored-by: man.zhang <[email protected]> Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: A-Kyle <[email protected]> Co-authored-by: Gerhard Theurich <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> * Split GFS_typedefs.F90, rename CCPP_interstitial, import ccpp_t from ccpp_types (NCAR#508) * Split GFS_typedefs.F90: move GFS_interstitial_type to CCPP_typedefs.F90; Rename CCPP_interstitial to GFDL_interstitial; Import ccpp_t from ccpp_types instead of ccpp_api * Add bugfix in ccpp/data/GFS_typedefs.meta: mark input_nml_file as active only if the number of lines in the file is greater than zero * Fix uninitialized min_rand variable in Thompson MP when using SPP (NCAR#516) * Pass SPP namelist entries outside of stochastic physics routines. * Fixes to SPP metadata * Add active attribute to spp_prt_list * Add active metadata flag to spp_stddev_cutoff * Add active metadata flag for spp_var_list * A bug fix for wet scavenging of aerosols and a minor modification for moisture property calculation (NCAR#520) * Update ccpp_prebuild_config.py for one-to-one CCPP physics schemes/files (NCAR#519) * point to gsl/merge-develop branch * Point to gsl/merge-develop-to-community branch for ccpp/physics * Corrections to merge + joe updates * Point .gitmodules to Sam's fork * Correct issues found by reviewers * Rename mynnpbl to mynnedmf * Remove some empty _init and _finalize routines and update a comment in sgscloud_radpre * Feature/lndp noahmp2 : add land perturbation scheme for Noah-MP fractional veg (NCAR#513) Updates to allow land perturbation scheme to be applied for Noah-MP. Main code changes: -added lsm_noahmp model option to lndp_type==2 land perturbation scheme (fv3-atm, stochastic_physics) -updated comments -cleaned up the namelists to make the different options clearer. Removed misleading lndp_each_step variable from gfs_physics_nml, and replaced it with "lndp_model_type" in the nam_sfcperts namelist for the different forecast types (cycling DA, short forecasts, perturbing only initial conditions) (fv3-atm, stochastic_physics, ufs-weather-model) NOTE: see note below, re: specification of smc perturbation for RAP/HRRR/etc (lndp_model_type==2) -revised code in stochastic_physics_wrapper to only allocate arrays that will be used when passed into lndp_apply_perts (fv3-atm) -deleted unused albedo arrays in stochastic_physics_wrapper and lndp_apply_perts (fv3-atm, stochastic_physics) -fixed bug causing precision errors when calculating the soil moisture ice content (often ~0.0; stochastic_physics) -fixed bug in which lndp_apply_perts wasn't called for nscyc = 0. (fv3-atm) -increased max_nvar_lndp at Jeff Ator's request (fv3-atm) -added a new test for the Noah-MP and lndp==2 combination (ufs-weather-model) * Add \file to smoke files * Add hailcast code in atmos_cubed_sphere (NCAR#528) * Combine PROD and REPRO build options into 'Release' build type (NCAR#524) Combined PROD and REPRO build modes into 'Release' build type. Now only 'Debug' and 'Release' build type are supported. Both build types must produce bit-for-bit reproducible outputs using different number of threads, mpi tasks, different domain decomposition, have reproducible restarts etc. * Unify inline post (NCAR#521) * Unify global and regional inline posts and add bug fix for dx/dy computation. * Update upp revision to dc8bc68 * Set up different configurations of read max/min 2m T for global and regional FV3. * adding bug fix from jili dong and removing U* averaging * adding bug fix from jili dong and removing U* averaging * Remove some commented-out code from cu_gf_driver in ccpp-physics. * Turn rrtmg smoke band 10 into a model namelist variable * Switch ccpp-physics smoke arguments to implied shape * Remove some stops and gotos from ccpp-physics smoke * Remove some hard-coded constants and rename some meta entries * Change RRTMGP to RRTMG in two P8 SDFs (NCAR#527) * Change RRTMGP to RRTMG in suite_FV3_GFS_v17_p8 and suite_FV3_GFS_v17_coupled_p8 * deleted or modified some SDFs related to RRTMGP or Thompson schemes * added a new SDF file for P8 with rrtmgp * Rename some standard_names, change a unit, and remove a "use physcons" * NSSL ccpp-physics bugfixes and new ccpp-framework debugging feature (NCAR#529) * Set num3d correctly when using radar_tten * Only add cnv_3d_ud_mf to the restart files when needed * Pass some chemistry varibles to mynn_bl_driver correctly * Correct argument passing within mynn edmf * point to NCAR main ccpp/physics * merge gsl institutional fork (NCAR#526) Merge in GSL institutional fork * point to sam's repo * ccpp/physics: Change to GSL CODEOWNERS * Returned the comments on soil resistance back. * point to gsl/develop for ccpp/physics Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Grant Firl <[email protected]> Co-authored-by: mzhangw <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]> Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: SMoorthi-emc <[email protected]> Co-authored-by: ChunxiZhang-NOAA <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Jeff Whitaker <[email protected]> Co-authored-by: Gerhard Theurich <[email protected]> Co-authored-by: DomHeinzeller <[email protected]> Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: MatthewPyle-NOAA <[email protected]> Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Jessica Meixner <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: joeolson42 <[email protected]> Co-authored-by: HelinWei-NOAA <[email protected]> Co-authored-by: mdtoyNOAA <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: dustinswales <[email protected]> Co-authored-by: Bin Liu <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Daniel Rosen <[email protected]> Co-authored-by: man.zhang <[email protected]> Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: A-Kyle <[email protected]> Co-authored-by: ClaraDraper-NOAA <[email protected]> Co-authored-by: BinLi-NOAA <[email protected]>

*This PR addresses part 2 of CCPP issue NCAR#748 to activate the exponential-random cloud overlap method (iovr=5) in RRTMG.

This EMC flake physics

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YihuaWu-NOAA requested review from climbfuji, grantfirl, JulieSchramm and llpcarson as code owners July 10, 2020 20:22

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This is EMC flake model NCAR/ufs-weather-model#60

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climbfuji mentioned this pull request Jul 10, 2020

EMC-Flake #462

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climbfuji changed the title ~~This EMC flake physics~~ EMC flake Jul 10, 2020

climbfuji changed the base branch from dtc/develop to master July 10, 2020 21:42

This was referenced Jul 13, 2020

This is EMC flake model ufs-community/ufs-weather-model#164

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This is EMC flake model NOAA-EMC/fv3atm#141

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YihuaWu-NOAA added 2 commits July 15, 2020 20:15

Updated the four files for S2S

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To resolve conflict if any

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Merge remote-tracking branch 'upstream/master' into flake

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climbfuji requested a review from SMoorthi-emc July 16, 2020 13:07

Removed some print lines

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YihuaWu-NOAA and others added 3 commits July 17, 2020 14:14

Changed radians to radian in flake_driver.meta file

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Delete CCPP_VARIABLES_FV3.html

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climbfuji merged commit 82a73dd into NCAR:master Jul 20, 2020

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EMC flake #471

EMC flake #471

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EMC flake #471

EMC flake #471

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