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Add CO2, CO, and OCS single-tracer carbon simulations to the integration tests #2236

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merged 7 commits into from Apr 11, 2024

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Name: Melissa Sulprizio
Institution: Harvard

Describe the update

The carbon simulation will soon replace the existing CO2, CH4, and tagCO specialty simulations. We now add single-tracer carbon simulations for CO2, CO, and OCS (CH4 was added previously) to the GCClassic and GCHP integration tests.

Expected changes

This is a zero difference update with respect to the full-chemistry benchmark simulation.

…ation tests

The carbon simulation will soon replace the existing CO2, CH4, and tagCO
specialty simulations. We now add single-tracer carbon simulations for CO2,
CO, and OCS (CH4 was added previously) to the GCClassic and GCHP integration
tests.

Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
@msulprizio msulprizio added topic: Benchmarking and Testing Related to CI, integration tests, or scientific benchmarking Attn: Carbon gases WG Attention: Carbon Gases Working Group labels Apr 5, 2024
@msulprizio msulprizio self-assigned this Apr 5, 2024
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The additional CO, CO2, and OCS integration tests all pass for GCClassic.

Execution tests:
------------------------------------------------------------------------------
gc_4x5_merra2_aerosol...............................Execute Simulation....PASS
gc_4x5_merra2_carbon................................Execute Simulation....PASS
gc_4x5_merra2_carbon_CH4............................Execute Simulation....PASS
gc_4x5_merra2_carbon_CO.............................Execute Simulation....PASS
gc_4x5_merra2_carbon_CO2............................Execute Simulation....PASS
gc_4x5_merra2_carbon_OCS............................Execute Simulation....PASS
gc_4x5_merra2_CH4...................................Execute Simulation....PASS
gc_4x5_merra2_CO2...................................Execute Simulation....PASS
gc_4x5_merra2_fullchem..............................Execute Simulation....PASS

They are failing for GCHP as discussed in #2237.

yantosca and others added 6 commits April 5, 2024 11:52
run/shared/singleCarbonSpecies.sh
- Now also remove lines from HISTORY.rc with a space after the
  species name (such as '_CO ')
- Disable the Emissions collection for OCS-only simulations (as we
  do not yet have OCS emissions).  This is only relevant for GCHP.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/singleCarbonSpecies.sh
- Now use the regexp "[ \t]*" to remove an arbitrary number of
  tabs and spaces when removing lines from the HISTORY.rc file.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/singleCarbonSpecies.sh
- Bug fix: Remove lines beginning with EDGAR8 from ExtData.rc
  for carbon simulations that do not include CH4.  This is now
  necessary since EDGARv8 replaces EDGARv7 in carbon simulations.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCHP/HISTORY.rc.carbon
- Add ", 'GCHPchem"," column to each of the fields in the Metrics
  collection.  This causes an issue in parsing the file.
- Removed "#" separators in the Budget collection

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/singleCarbonSpecies.sh
- Add sed commands to remove CH4_SEEPS, CH4_RES_DAM, CH4_RES_SFC,
  CH4_TERMITES, and CH4_SOILABSORB individually.  The previous
  command to remove anything starting with "CH4_" was removing the
  CH4_LOSS entry of ExtData.rc, which is needed as an input to the
  chemistry mechanism.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
The following fixes were added to address carbon simulations with CO, CO2,
or OCS from crashing as discussed in #2237.

1. Add trailing whitespace after species names in HISTORY.rc.carbon to allow
   for differentiating between CO and CO2.

2. Modify function updateHistory.rc in run/shared/singleCarbonSpecies.sh
   to restore Collection.fields lines that are removed when CH4 is not
   included in the carbon simulation.

Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>

# Conflicts:
#	run/shared/singleCarbonSpecies.sh
@yantosca yantosca added the category: Feature Request New feature or request label Apr 10, 2024
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GCHP integration tests now all pass:

==============================================================================
GCHP: Execution Test Results

GCHP      #6db5506 GEOS-Chem submodule update: Merge PR #1992 (carbon simulation fixes)
GEOS-Chem #0139486ac Add fixes for GCHP carbon simulations with single species (CO, CO2, OCS)
HEMCO     #fddcae5 Update version to 3.8.1 for release

Number of execution tests: 11

Submitted as SLURM job: 27703529
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gchp_merra2_carbon..................................Execute Simulation....PASS
gchp_merra2_carbon_CH4..............................Execute Simulation....PASS
gchp_merra2_carbon_CO...............................Execute Simulation....PASS
gchp_merra2_carbon_CO2..............................Execute Simulation....PASS
gchp_merra2_carbon_OCS..............................Execute Simulation....PASS
gchp_merra2_fullchem................................Execute Simulation....PASS
gchp_merra2_fullchem_benchmark......................Execute Simulation....PASS
gchp_merra2_fullchem_RRTMG..........................Execute Simulation....PASS
gchp_merra2_fullchem_TOMAS15........................Execute Simulation....PASS
gchp_merra2_tagO3...................................Execute Simulation....PASS
gchp_merra2_TransportTracers........................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 11
Execution tests failed: 0
Execution tests not yet completed: 0

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@msulprizio msulprizio added this to the 14.4.0 milestone Apr 10, 2024
@msulprizio msulprizio marked this pull request as ready for review April 10, 2024 20:40
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Thanks @msulprizio! Good to merge!

@msulprizio msulprizio merged commit afb4995 into dev/14.4.0 Apr 11, 2024
@msulprizio msulprizio deleted the feature/carbon-single-spc-tests branch April 11, 2024 13:22
yantosca added a commit that referenced this pull request May 1, 2024
This merge grings PR #2236 (Parameterized Effective Radius for SNA and OM,
by @Haihui-Zhu) atop the PR #2272 (CH4/carbon simulation fixes).

PR #2236 implements a parameterized effective radius for SNA and OM and
updates AOD calculation to account for the spatial and temporal variation in
dry effective radius.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca added a commit that referenced this pull request May 1, 2024
GeosCore/aerosol_mod.F90
- Added the "g" index variable to !$OMP PRIVATE clause

run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.aerosol
run/GCClassic/geoschem_config.yml.templates/geoschem.config.yml.fullchem
run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem
- Now set fastj_input_dir from FAST_JX/v2021-10 to FAST_JX/v2024-05,
  as this folder now has updated org.dat and so4.dat files that
  correspond with the updates in PR #2236.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca added a commit that referenced this pull request May 2, 2024
This merge brings PR #2236 (Parameterized Effective Radius for SNA and OM,
by @Haihui-Zhu) into the GEOS-Chem 14.4.0 development stream.

This PR (1) Implements a parameterized effective radius for SNA and OMU,
and (2) Updates AOD calculation to account for the spatial and temporal
variation in dry effective radius.  New org.dat and so4.dat files with
updated aerosol parameters are now in ExtData/CHEM_INPUTS/FAST_JX/v2024-05.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca added a commit that referenced this pull request May 2, 2024
run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg
- Change fastjx_input_dir to CHEM_INPUTS/FAST_JX/v2024-05-Hg/
- Change cloudj_input_dir to CHEM_INPUTS/FAST_JX/v2024-05/

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Single-species carbon simulations still not working for CO, CO2, and OCS in GCHP
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