cam6_3_071: Updates to deposition module in share code externals #602

fvitt · 2022-06-01T02:12:56Z

These are updates needed to read deposition data from file. Changes to drydep_mod share code replaced hard-wired data in drydep_mod with a netcdf input file. Changes here are needed for the updates to the relevant external share code bases.

closes #601
closes #625

modified: bld/build-namelist modified: bld/namelist_files/namelist_defaults_cam.xml modified: bld/namelist_files/namelist_definition.xml modified: src/chemistry/mozart/mo_neu_wetdep.F90

modified: src/cpl/mct/cam_cpl_indices.F90

modified: Externals.cfg modified: src/chemistry/mozart/mo_chemini.F90 modified: src/chemistry/mozart/mo_drydep.F90 modified: src/chemistry/mozart/mo_neu_wetdep.F90 modified: src/control/camsrfexch.F90 modified: src/cpl/mct/atm_import_export.F90

modified: src/cpl/nuopc/atm_comp_nuopc.F90 modified: src/cpl/nuopc/atm_import_export.F90

Externals.cfg

bld/namelist_files/namelist_defaults_cam.xml

cacraigucar

Hit approve button by accident - it should be request changes

gold2718

I second @cacraigucar's requests and added a few more minor requests.

gold2718 · 2022-06-27T20:32:36Z

src/chemistry/mozart/mo_neu_wetdep.F90

@@ -330,7 +329,7 @@ subroutine neu_wetdep_tend(lchnk,ncol,mmr,pmid,pdel,zint,tfld,delt, &
  end do
 !
 ! compute effective Henry's law coefficients
-! code taken from models/drv/shr/seq_drydep_mod.F90
+! code taken from models/drv/shr/shr_drydep_mod.F90


This file does not exist. Did you mean

Suggested change

! code taken from models/drv/shr/shr_drydep_mod.F90

! code taken from components/cmeps/cesm/nuopc_cap_share/shr_drydep_mod.F90

or

Suggested change

! code taken from models/drv/shr/shr_drydep_mod.F90

! code taken from components/cpl7/driver/shr/shr_drydep_mod.F90

?? Something else??

Removed the comment

gold2718 · 2022-06-27T21:06:32Z

src/cpl/nuopc/atm_import_export.F90

@@ -27,6 +27,7 @@ module atm_import_export
  implicit none
  private ! except

+  public  :: set_options


This is not a good name for the cap level. Please change it to

Suggested change

public :: set_options

public :: read_surface_namelists

or come up with some other appropriate (i.e., more specific) name.

Would you be okay with read_fields_namelists?

Would read_surface_field_namelists be more specific while still being accurate?

Updated as suggested

gold2718 · 2022-06-27T21:06:53Z

src/cpl/nuopc/atm_import_export.F90

@@ -66,14 +67,25 @@ module atm_import_export
 contains
 !===============================================================================

-  subroutine advertise_fields(gcomp, flds_scalar_name, rc)
+  subroutine set_options()


Change name (see above).

gold2718 · 2022-06-27T21:07:41Z

src/cpl/nuopc/atm_comp_nuopc.F90

@@ -29,7 +29,7 @@ module atm_comp_nuopc
  use cam_logfile         , only : iulog
  use spmd_utils          , only : spmdinit, masterproc, iam, mpicom
  use time_manager        , only : get_curr_calday, advance_timestep, get_curr_date, get_nstep, get_step_size
-  use atm_import_export   , only : advertise_fields, realize_fields
+  use atm_import_export   , only : set_options, advertise_fields, realize_fields


Change name (see comment in atm_import_export.F90).

gold2718 · 2022-06-27T21:08:45Z

src/cpl/nuopc/atm_comp_nuopc.F90

+    ! read drv flds options
+    call set_options()


Change name (see comment in atm_import_export.F90).

gold2718 · 2022-06-27T21:09:53Z

src/cpl/nuopc/atm_comp_nuopc.F90

@@ -278,6 +278,9 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
       call shr_sys_abort(subname//'Need to set attribute ScalarFieldIdxNextSwCday')
    endif

+    ! read drv flds options


Please change the comment as this has nothing to do with the driver:

Suggested change

! read drv flds options

! read mediator fields options

updated the comment

modified: src/chemistry/mozart/mo_neu_wetdep.F90 modified: src/cpl/nuopc/atm_comp_nuopc.F90 modified: src/cpl/nuopc/atm_import_export.F90

… comments modified: src/cpl/nuopc/atm_comp_nuopc.F90 modified: src/cpl/nuopc/atm_import_export.F90

modified: src/ionosphere/waccmx/edyn_init.F90

… set ROF_NCPL for weimer test modified: cime_config/config_pes.xml modified: cime_config/testdefs/testlist_cam.xml modified: cime_config/testdefs/testmods_dirs/cam/waccmx_weimer/shell_commands

Description of changes This moves the hard-wired data from seq_drydep_mod to an input file that can be easily replaced to provide flexibility. Specific notes This PR needs to be coordinated with ESCOMP/CAM#602 See relevant discussion in: ESCOMP/CESM_share#8 Contributors other than yourself, if any: CMEPS Issues Fixed (include github issue #): ESCOMP/CESM_share#8 Are changes expected to change answers? (specify if bfb, different at roundoff, more substantial) bfb Any User Interface Changes (namelist or namelist defaults changes)? Added dep_data_file (in drv_flds_in) for the path of the input data file containing Henrys Law coefficients Testing performed Testing performed if application target is CESM: (recommended) CIME_DRIVER=nuopc scripts_regression_tests.py machines: cheyenne, izumi details (e.g. failed tests): (recommended) CESM testlist_drv.xml machines and compilers: details (e.g. failed tests): (optional) CESM prealpha test machines and compilers details (e.g. failed tests): aux_cam tests machines and compilers: cheyenne-intel, izumi-gnu, izumi-nag details (e.g. failed tests): Testing performed if application target is UFS-coupled: (recommended) UFS-coupled testing description: details (e.g. failed tests): Testing performed if application target is UFS-HAFS: (recommended) UFS-HAFS testing description: details (e.g. failed tests): Hashes used for testing: CESM: repository to check out: ESCOMP/CESM.git branch/hash: UFS-coupled, then umbrella repostiory to check out and associated hash: repository to check out: branch/hash: UFS-HAFS, then umbrella repostiory to check out and associated hash: repository to check out: branch/hash:

Read Henrys Law coefficients from file This moves the hard-wired data from seq_drydep_mod to an input file that can be easily replaced to provide flexibility. This PR needs to be coordinated with ESCOMP/CAM#602 See relevant discussion in: ESCOMP/CESM_share#8

modified: Externals.cfg

modified: cime_config/testdefs/testlist_cam.xml

lizziel · 2022-07-27T15:51:12Z

I am using the updates in this PR (and the related ones) for development of GEOS-Chem in CESM. One of the things that has confused me is that wet deposition requires parameters from dry deposition modules, previously for seq_drydep_mod, and now for shr_drydep_mod. I see the netcdf file that replaces the hard-coded values in seq_drydep_mod.F90 is more generically named to indicate deposition rather than dry deposition (dep_data_file.nc rather than drydep_data_file.nc). Would you consider updating the module names to be generic as well? I can add this comment to the conversations of the relevant PRs if you agree.

fvitt · 2022-07-27T16:17:22Z

@lizziel Your request is a little late for this PR. The PRs for the externals have been merged into the main repos and have been closed. This PR is close to being merged into cam_development as it is. I suggest you open a new issue in https://github.com/ESCOMP/CMEPS for your request.

lizziel · 2022-07-27T17:42:55Z

@fvitt, thanks for the response. I'll open a new issue for this.

nusbaume

Looks good! Just a couple optional cosmetic changes (and a question for the other CAM SEs).

nusbaume · 2022-07-29T20:08:57Z

src/chemistry/mozart/mo_drydep.F90

@@ -18,7 +18,7 @@ module mo_drydep
  use dyn_grid,         only : get_dyn_grid_parm, get_horiz_grid_d
  use scamMod,          only : single_column

-  use seq_drydep_mod,   only : nddvels =>  n_drydep, drydep_list, mapping
+  use shr_drydep_mod,   only : nddvels =>  n_drydep, drydep_list, mapping


I might remove the spaces between only and : here in order to better match the CAM style guide.

nusbaume · 2022-07-29T20:10:57Z

src/chemistry/mozart/mo_neu_wetdep.F90

@@ -12,7 +12,7 @@ module mo_neu_wetdep
  use constituents,     only : pcnst
  use spmd_utils,       only : masterproc
  use cam_abortutils,   only : endrun
-  use seq_drydep_mod,   only : n_species_table, species_name_table, dheff
+  use shr_drydep_mod,   only : n_species_table, species_name_table, dheff


I might remove the spaces between only and : here in order to better match the CAM style guide.

nusbaume · 2022-07-29T20:18:20Z

src/chemistry/mozart/mo_neu_wetdep.F90

  real(r8) :: lats(pcols)
+
+  real(r8), parameter :: rad2deg = 180._r8/pi


@gold2718 @cacraigucar @peverwhee I feel like I have seen this particular calculation in multiple places throughout CAM. Would it make sense to add this (and an inverse deg2rad) into physconst so that this parameter doesn't have to be repeated so much?

I should note that we don't have to necessarily do it for this PR, I just think that if we all agree then it would be good to make an issue for it so one of us can tackle it later.

It's minor in the sense that the parameter is baked into the code (no run-time cost).
A better solution for cases like this will come when all the dycores use the new physics grid infrastructure which has coordinates in both radians and degrees.

gold2718

Looks okay to me

fvitt added 6 commits May 24, 2022 16:42

read Henry's law coeff, etc., from file

2d37401

modified: bld/build-namelist modified: bld/namelist_files/namelist_defaults_cam.xml modified: bld/namelist_files/namelist_definition.xml modified: src/chemistry/mozart/mo_neu_wetdep.F90

use the new shr_drydep_mod module

7e39c73

modified: src/cpl/mct/cam_cpl_indices.F90

more changes to use shr_drydep_mod module

e46c67d

modified: Externals.cfg modified: src/chemistry/mozart/mo_chemini.F90 modified: src/chemistry/mozart/mo_drydep.F90 modified: src/chemistry/mozart/mo_neu_wetdep.F90 modified: src/control/camsrfexch.F90 modified: src/cpl/mct/atm_import_export.F90

use external branches

94b75ae

Separate namelist reads from advertise fields (PORT fix)

41f8b16

modified: src/cpl/nuopc/atm_comp_nuopc.F90 modified: src/cpl/nuopc/atm_import_export.F90

Merge branch 'dep_data_file' of github.com:fvitt/CAM into dep_data_file

3db9350

fvitt added the BFB bit for bit tag label Jun 1, 2022

fvitt requested a review from cacraigucar June 1, 2022 02:12

fvitt self-assigned this Jun 1, 2022

This was referenced Jun 1, 2022

Read Henrys Law coefficients from file ESCOMP/CESM_CPL7andDataComps#15

Merged

Read Henrys Law coefficients from file ESCOMP/CMEPS#303

Merged

cacraigucar approved these changes Jun 27, 2022

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cacraigucar requested changes Jun 27, 2022

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cacraigucar requested review from gold2718, nusbaume and peverwhee June 27, 2022 19:38

gold2718 requested changes Jun 27, 2022

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peverwhee approved these changes Jun 29, 2022

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fvitt added 5 commits June 29, 2022 13:26

rename "set_options" as "read_fields_namelists"

70422a4

modified: src/chemistry/mozart/mo_neu_wetdep.F90 modified: src/cpl/nuopc/atm_comp_nuopc.F90 modified: src/cpl/nuopc/atm_import_export.F90

Use "read_surface_fields_namelists" subroutine name; minor updates to…

eb225e8

… comments modified: src/cpl/nuopc/atm_comp_nuopc.F90 modified: src/cpl/nuopc/atm_import_export.F90

Corrections to coordinate maps for oplus and geomag history grids

c9f48b6

modified: src/ionosphere/waccmx/edyn_init.F90

moved waccmx test back to izumi

cb51740

increase ntasks for f09 waccmx; specify pelayout for f09 wiemer test;…

86621e9

… set ROF_NCPL for weimer test modified: cime_config/config_pes.xml modified: cime_config/testdefs/testlist_cam.xml modified: cime_config/testdefs/testmods_dirs/cam/waccmx_weimer/shell_commands

Use offical tags for externals

d54dd78

modified: Externals.cfg

cacraigucar approved these changes Jul 26, 2022

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fvitt requested a review from gold2718 July 27, 2022 13:13

fvitt added 2 commits July 27, 2022 07:54

move FW4madSD izumi test from nag to gnu

965c39d

modified: cime_config/testdefs/testlist_cam.xml

Merge branch 'waccmx_pio' of github.com:fvitt/CAM into waccmx_pio

5aecdb8

nusbaume approved these changes Jul 29, 2022

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gold2718 approved these changes Jul 29, 2022

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cacraigucar changed the title ~~Updates to deposition module in share code externals~~ part of cam6_3_071: Updates to deposition module in share code externals Aug 1, 2022

fvitt added 2 commits August 1, 2022 14:17

merge to head of ESCOMP/cam_development

d11894f

Merge remote-tracking branch 'origin/waccmx_pio' into dep_data_file

ae66d84

cacraigucar changed the title ~~part of cam6_3_071: Updates to deposition module in share code externals~~ cam6_3_071: Updates to deposition module in share code externals Aug 1, 2022

fvitt added 3 commits August 1, 2022 16:12

initial ChangeLog entries

ec2dec7

ChangeLog updates

d2e4196

ChangeLog updates

c66fb05

fvitt merged commit 7d7b2e6 into ESCOMP:cam_development Aug 3, 2022

billsacks mentioned this pull request Sep 1, 2022

seq_drydep_mod should be replaced by shr_drydep_mod ESCOMP/CTSM#1822

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cam6_3_071: Updates to deposition module in share code externals #602

cam6_3_071: Updates to deposition module in share code externals #602

fvitt commented Jun 1, 2022 •

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	! code taken from models/drv/shr/shr_drydep_mod.F90
	! code taken from components/cmeps/cesm/nuopc_cap_share/shr_drydep_mod.F90

	! code taken from models/drv/shr/shr_drydep_mod.F90
	! code taken from components/cpl7/driver/shr/shr_drydep_mod.F90

		real(r8) :: lats(pcols)

		real(r8), parameter :: rad2deg = 180._r8/pi

cam6_3_071: Updates to deposition module in share code externals #602

cam6_3_071: Updates to deposition module in share code externals #602

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lizziel commented Jul 27, 2022

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fvitt commented Jun 1, 2022 •

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