Fixes for HEMCO diagnostic config file HEMCO_Diagn.rc

[lizziel]

Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

This PR contains two bug fixes:

1. Update GC-Classic and GCHP HEMCO_Diagn.rc fullchem templates to use offline MOH biogenic emissions rather than online unless using the benchmark simulation. This corrects a problem where EmisMOH_Biogenic was filled with all zeros for non-benchmark fullchem simulations in 14.4.2 since MEGAN is no longer on starting in that version.
2. Auto-set GCHP emissions sources in HEMCO_Diagn.rc based on HEMCO_Config.rc. This update impacts only GCHP emissions for which we have both online and offline sources, namely seasalt, soil NOx, biogenic, and dust emissions. Previously HEMCO_Diagn.rc always specified offline emissions for use in emissions diagnostics unless using the benchmark simulation. This resulted in empty emissions diagnostics if the user changed from offline to online.

Expected changes

This is a no-diff update for benchmark simulations. There are expected changes in the emissions diagnostic collection for non-benchmark full chemistry simulations and they are as follows:

• EmisMOH_Biogenic will no longer be all zeros if using GC-Classic and GCHP
• GCHP emission diagnostics will no longer be zero if offline emissions are changed to online

Reference(s)

None

Related Github Issue

closes #2382
Also related to #2319

[lizziel]

I added these changes on top of dev/14.5.0. I can rebase to be on top of dev/no-diff-to-benchmark instead.

[yantosca]

Thanks @lizziel, this looks OK to merge. Could you revert the integrationTestCreate.sh and commonFunctionsForTests.sh files? The GCAP2 int tests are now in dev/no-diff-to-benchmark... I had to make some updates to that code so this could will cause conflicts.

[lizziel]

Yes, I am going to rebase on dev/no-diff-to-benchmark so don't merge yet!

[yantosca]

No problem Lizzie! I'll approve so you can rebase.

[yantosca]

Thanks @lizziel. I approve these updates, since you will rebase later.

[lizziel]

@yantosca, this is now rebased on dev/no-diff-to-benchmark. I updated the milestone to be 14.4.3.

[yantosca]

Thanks @lizziel! I merged this into dev/no-diff-to-benchmark (locally) and am running integration tests.

[yantosca]

All GEOS-Chem Classic integration tests passed:

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : 60dd1a6 GEOS-Chem submod update: Merge PR #2413 (Fix unit conv in aerosol sim)
GEOS-Chem : 034507531 Merge PR #2402 (Fixes for HEMCO_Diagn.rc)
HEMCO     : e68ebae HEMCO 3.9.2 release
Cloud-J   : 37a4ece Update release version number and date
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 43548446
==============================================================================

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

All tests were zero-diff w/r/t the previous PR #2413, except:

• TOMAS (parallelization error?)
• APM (parallelization error?)

The following fullchem tests were zero-diff w/r/t PR #2413 (as evidenced by identical Restart files), but the EmisMOH_biogenic field in HEMCO_diagnostics is no longer all zeros:

• fullchem
• fullchem_aciduptake
• fullchem_APM
• fullchem_complexSOA
• fullchem_complexSOA_SVPOA
• fullchem_LuoWd
• fullchem_RRTMG

[yantosca]

All GCHP integration tests passed:

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

CodeDir       : 4cadc0d GEOS-Chem submod update: Merge PR #2413 (Fix unit conv in aerosol sim)
MAPL          : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : 034507531 Merge PR #2402 (Fixes for HEMCO_Diagn.rc)
HEMCO         : e68ebae HEMCO 3.9.2 release
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : 37a4ece Update release version number and date
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 43561008
==============================================================================

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

All tests were zero-diff w/r/t the prior PR #2413.

The fullchem_benchmark and fullchem_alldiags tests showed differences in the Emissions collection, that were caused by the updates to setCommonRunSettings.sh added in this PR.