Restore dry deposition output in GCHP & GCClassic fullchem benchmark simulations #2144
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yantosca
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category: Feature Request
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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. |
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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. |
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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. |
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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? |
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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. |
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@yantosca What is the status of this PR? Should it be included in 14.4.0? |
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@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. |
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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. |
run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem - Change ##'DryDep' -> #'DryDep', which will activate this collection in benchmark simulations. run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Change @#'DryDep' -> #'DryDep', which will activate this collection in benchmark simulations. - Also reduce the DryDep collection species to only those species we need for benchmark plots/tables CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
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I have rebased this PR off 14.5.0-alpha.4 and will rerun integration tests. |
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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 |
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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 $ 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 |
CHANGELOG.md - Restored missing line that was inadvertenly deleted - Place `` around "State_Chm%CH4_EMIS" run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Removed extra slash in comments Signed-off-by: Bob Yantosca <[email protected]>
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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. |
run/GCHP/HISTORY.rc.fullchem - Add the DryDepChm_O3 and DryDepMix_O3 fields to the DryDep colletction out-of-bounds error. This is to be consistent w/ GCClassic as well. Signed-off-by: Bob Yantosca <[email protected]>
run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Only keep the fields that are necessary for fullchem benchmarks in the DryDep collection. This is similar to what is being done in PR #2144 (which will be merged later). Signed-off-by: Bob Yantosca <[email protected]>
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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: 0The failure is caused by a missing data file on the GCAP2 40L grid, as described in PR #2427. |
… bmks) This merge brings PR # (Add the DryDep collection to the benchmark summary table, and DryDepVel plots to 1-mon cloud benchmarks, by @yantosca) into the GCPy development stream. The GEOS-Chem `DryDep` collection was restored to all fullchem benchmark simulations in geoschem/geos-chem#2144. This is the corresponding GCPy PR, which includes code to: 1. Add the `DryDep` collection to the benchmark summary table 2. Plot dry deposition velocities in 1-hr cloud benchmarks Signed-off-by: Bob Yantosca <[email protected]>
Name and Institution (Required)
Name: Bob Yantosca
Institution: Harvard + GCST
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Describe the update
This is the companion PR to #2139. We have updated the template
HISTORY.rc.fullchemfiles for both GCHP and GCClassic so as to activate theDryDepcollection 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.
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