Restore dry deposition output in GCHP & GCClassic fullchem benchmark simulations

[yantosca]

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Confirm you have reviewed the following documentation

• Contributing guidelines

Describe the update

This is the companion PR to #2139. We have updated the template HISTORY.rc.fullchem files for both GCHP and GCClassic so as to activate the DryDep collection in benchmark simulations. Also, for the GCHP simulation, we have reduced the number of species output to netCDF to only those that are absolutely needed for the benchmarks (as described in #2135).

Expected changes

This PR will activate dry deposition output for full-chemistry benchmark simulations, so that plots of dry deposition velocity can be made. Also the dry-deposition flux of O3 will be archived so as to be able to compute the Ox budget.

Related Github Issue(s)

• See The DryDep collection is not activated for GCHP fullchem benchmarks #2139
• See GCHP 14.3.0-rc.0 runs crashing when some diagnostic collections are turned on #2135
• See Reduce entries in GCHP HISTORY.rc #2142

[yantosca]

I left the base branch as main so that this PR wouldn't auto-close when dev/14.3.0 was removed. This can go into the dev/14.4.0 branch once we start working on it.

[lizziel]

Do we need to turn on dry deposition diagnostics for GCHP and GC-Classic fullchem benchmarks by default? I think the dry dep diagnostics are only needed for 1-year benchmarks.

[msulprizio]

That's correct, I think. The setup script I have for GCClassic 1-year benchmark uncomments the DryDep (and other) diagnostics in HISTORY.rc. We could set up a similar script for GCHP.

[msulprizio]

Alternatively, we could activate the drydep plots (for a subset of species) in 1-month benchmarks. It might be useful to diagnose changes there as well. @yantosca any thoughts?

[yantosca]

Yes, I was thinking we could activate a subset of species for the 1-month as well. That way we can detect any changes caused by LAI updates etc.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the Stale bot from closing this issue.

[msulprizio]

@yantosca What is the status of this PR? Should it be included in 14.4.0?

[yantosca]

@msulprizio: It could go into 14.4.0. We'd need to doublecheck the HISTORY.rc files and maybe also make a corresponding update in the GCPy template YAML files though. I haven't had time to work on this lately but we could try to get it in before the 14.4.0 freeze date.

[lizziel]

It looks like integration tests should be able to test out the HISTORY.rc file changes, and the GCPy updates could go in later, whenever we decide to add drydep plots to the benchmark. I updated the milestone to be 14.4.0.

[yantosca]

I have rebased this PR off 14.5.0-alpha.4 and will rerun integration tests.

[yantosca]

All GEOS-Chem Classic integration tests passed:

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

GCClassic #0c22a3a GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files)
GEOS-Chem #cb86824f5 Archive "Drydep" diags in fullchem bmks; Reduce GCHP "DryDep" output
HEMCO     #e68ebae HEMCO 3.9.2 release

Using 24 OpenMP threads
Number of execution tests: 28

Submitted as SLURM job: 42911370
==============================================================================

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

The DryDep collection files were generated in the fullchem_benchmark run directory:

$ gc_4x5_merra2_fullchem_benchmark/OutputDir
$ ls
GEOSChem.AdvFluxVert.20190701_0000z.nc4  GEOSChem.Metrics.20190701_0000z.nc4
GEOSChem.AerosolMass.20190701_0000z.nc4  GEOSChem.SpeciesConc.20190701_0000z.nc4
GEOSChem.Aerosols.20190701_0000z.nc4     geoschem_species_metadata.yml
GEOSChem.DryDep.20190701_0000z.nc4       GEOSChem.StateMet.20190701_0000z.nc4
GEOSChem.JValues.20190701_0000z.nc4      HEMCO_diagnostics.201907010000.nc

[yantosca]

All GCHP integration tests passed:

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

GCHP      #548c753 GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files)
GEOS-Chem #cb86824f5 Archive "Drydep" diags in fullchem bmks; Reduce GCHP "DryDep" output
HEMCO     #

Number of execution tests: 11

Submitted as SLURM job: 42912361
==============================================================================
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Also, the "DryDep" collection file was created in the gchp_merra2_fullchem_benchmark run directory:

$ cd rundirs/gchp_merra2_fullchem_benchmark/OutputDir/
$ ls
GEOSChem.AerosolMass.20190701_0000z.nc4          GEOSChem.GCHPctmEnvLevEdge.20190701_0000z.nc4
GEOSChem.Aerosols.20190701_0000z.nc4             GEOSChem.JValues.20190701_0000z.nc4
GEOSChem.DryDep.20190701_0000z.nc4               GEOSChem.Metrics.20190701_0000z.nc4
GEOSChem.Emissions.20190701_0000z.nc4            GEOSChem.SpeciesConc.20190701_0000z.nc4
GEOSChem.FV3Dynamics.20190701_0000z.nc4          geoschem_species_metadata.yml
GEOSChem.GCHPctmEnvLevCenter.20190701_0000z.nc4  GEOSChem.StateMet.20190701_0000z.nc4

[msulprizio]

Thanks @yantosca. Please see my comments below.

[msulprizio]

Now approved for merging. Thanks @yantosca!

[yantosca]

Thanks @msulprizio. I am waiting on the results of a 1-month benchmark. I will merge up into 14.5.0 (locally) and rerun integration tests just to make sure there aren't any merge issues.

[yantosca]

After merging (locally) atop PR #2318, all GEOS-Chem Classic integration tests passed, except ModelE2.1.

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

CodeDir   : edaa239 GEOS-Chem & HEMCO updates: Merge PR #2318, PR #284, PR #285
GEOS-Chem : c7332ed7a Merge PR #2144 (Restore drydep output in fullchem benchmarks)
HEMCO     : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
Cloud-J   : d20050f Update version to 7.7.3
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: 44355766
==============================================================================
...
gc_2x25_ModelE2.1_fullchem..........................Execute Simulation....FAIL
... 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 1
Execution tests not yet completed: 0

The failure is caused by a missing data file on the GCAP2 40L grid, as described in PR #2427.