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Update dimension to 2D from 3D for OCEAN_CONC for Hg simulations #1925

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merged 3 commits into from
Aug 30, 2023
Merged

Update dimension to 2D from 3D for OCEAN_CONC for Hg simulations #1925

merged 3 commits into from
Aug 30, 2023

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nicholasbalasus
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Name: Nick Balasus
Institution: Harvard University

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Describe the update

Previously, the OCEAN_CONC variable was being read in as a 3D variable and being pushed through vertically regridding needlessly. Now, it is treated as a 2D variable.

Expected changes

No changes to model output (as long as changing from xyz to xy tells HEMCO to ignore the vertical dimensions, which I believe it does @jimmielin). I tested for a 1 day simulation and found no changes, but the integration test should catch anything.

Reference(s)

n/a

Related Github Issue(s)

In support of geoschem/HEMCO#235

@yantosca yantosca self-requested a review August 30, 2023 15:03
@yantosca yantosca self-assigned this Aug 30, 2023
@yantosca yantosca added topic: Configuration Files Related to GEOS-Chem configuration files specialty simulations category: Bug Fix Fixes a previously-reported bug labels Aug 30, 2023
yantosca
yantosca approved these changes Aug 30, 2023
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Thanks @nicholasbalasus! Good to merge. I'll merge locally and test with a new set of integration tests.

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Integration tests are now running.

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GCHP integration tests passed:

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

GCClassic #71e671c GEOS-Chem submod update: Merge PR #1923 (Update carbon_gases_mod)
GEOS-Chem #08838351c Merge PR #1925 (Update OCEAN_CONC in Hg simulations from 2D to 3D)
HEMCO     #daf54d0 Merge PR #235 (Bug fix for vertical regridding)

Number of execution tests: 5

Submitted as SLURM job: 894155
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gchp_merra2_fullchem................................Execute Simulation....PASS
gchp_merra2_fullchem_benchmark......................Execute Simulation....PASS
gchp_merra2_fullchem_RRTMG..........................Execute Simulation....PASS
gchp_merra2_tagO3...................................Execute Simulation....PASS
gchp_merra2_TransportTracers........................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 5
Execution tests failed: 0
Execution tests not yet completed: 0

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

Furthermore, all integration tests were identical to the prior integration test (for #1903 plus geoschem/HEMCO#234):

Checking gchp_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_fullchem_benchmark
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_fullchem_RRTMG
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_tagO3
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_TransportTracers
   -> No differences in OutputDir
   -> No differences in Restarts

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All GEOS-Chem Classic integration tests passed, except for TOMAS (which will be fixed in 14.3.0):

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

GCClassic #c2fc90a GEOS-Chem submod update: Merge PR #1923 (Update carbon_gases_mod)
GEOS-Chem #08838351c Merge PR #1925 (Update OCEAN_CONC in Hg simulations from 2D to 3D)
HEMCO     #daf54d0 Merge PR #235 (Bug fix for vertical regridding)

Using 24 OpenMP threads
Number of execution tests: 26

Submitted as SLURM job: 893931
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gc_05x0625_NA_47L_merra2_CH4........................Execute Simulation....PASS
gc_05x0625_NA_47L_merra2_fullchem...................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem..........................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem_TOMAS15..................Execute Simulation....FAIL
gc_4x5_47L_merra2_fullchem_TOMAS40..................Execute Simulation....FAIL
gc_4x5_merra2_aerosol...............................Execute Simulation....PASS
gc_4x5_merra2_carbon................................Execute Simulation....PASS
gc_4x5_merra2_CH4...................................Execute Simulation....PASS
gc_4x5_merra2_CO2...................................Execute Simulation....PASS
gc_4x5_merra2_fullchem..............................Execute Simulation....PASS
gc_4x5_merra2_fullchem_aciduptake...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_APM..........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_benchmark....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA_SVPOA.............Execute Simulation....PASS
gc_4x5_merra2_fullchem_LuoWd........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_marinePOA....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_RRTMG........................Execute Simulation....PASS
gc_4x5_merra2_Hg....................................Execute Simulation....PASS
gc_4x5_merra2_metals................................Execute Simulation....PASS
gc_4x5_merra2_POPs_BaP..............................Execute Simulation....PASS
gc_4x5_merra2_tagCH4................................Execute Simulation....PASS
gc_4x5_merra2_tagCO.................................Execute Simulation....PASS
gc_4x5_merra2_tagO3.................................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers......................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers_LuoWd................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 24
Execution tests failed: 2
Execution tests not yet completed: 0

While several simulations show differences w/r/t the prior integration test (for #1903 plus geoschem/HEMCO#234), the fullchem benchmark simulation is not affected.

The differences are from:

  • CH4 emissions options (carbon, CH4, tagCH4 simulations)
  • Vertical regridding updates for files that use 72 -> 47L regridding (as expected).
  • Also note, the APM and RRTMG differences are a known issue.
Checking gc_05x0625_NA_47L_merra2_CH4
   -> 5 differences found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
Only in GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir: GEOSChem.StateMet.20190101_0000z.nc4
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0020z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0020z.nc4 

Checking gc_05x0625_NA_47L_merra2_fullchem
   -> 3 differences found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_fullchem/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_fullchem/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_fullchem/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_fullchem/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_fullchem/OutputDir/HEMCO_diagnostics.201907010000.nc 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_fullchem/OutputDir/HEMCO_diagnostics.201907010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_05x0625_NA_47L_merra2_fullchem/Restarts/GEOSChem.Restart.20190701_0020z.nc4 
        GCC_14.2.1_r19/rundirs/gc_05x0625_NA_47L_merra2_fullchem/Restarts/GEOSChem.Restart.20190701_0020z.nc4 

Checking gc_4x5_47L_merra2_fullchem
   -> 3 differences found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_4x5_47L_merra2_fullchem/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_47L_merra2_fullchem/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_4x5_47L_merra2_fullchem/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_47L_merra2_fullchem/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_4x5_47L_merra2_fullchem/OutputDir/HEMCO_diagnostics.201907010000.nc 
        GCC_14.2.1_r19/rundirs/gc_4x5_47L_merra2_fullchem/OutputDir/HEMCO_diagnostics.201907010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_4x5_47L_merra2_fullchem/Restarts/GEOSChem.Restart.20190701_0100z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_47L_merra2_fullchem/Restarts/GEOSChem.Restart.20190701_0100z.nc4 

Checking gc_4x5_47L_merra2_fullchem_TOMAS15
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem_TOMAS40
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_aerosol
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_carbon
   -> 3 differences found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_carbon/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_carbon/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
Only in GCC_14.2.1_r19/rundirs/gc_4x5_merra2_carbon/OutputDir: GEOSChem.StateMet.20190101_0000z.nc4
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_carbon/OutputDir/HEMCO_diagnostics.201901010000.nc 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_carbon/OutputDir/HEMCO_diagnostics.201901010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_carbon/Restarts/GEOSChem.Restart.20190101_0100z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_carbon/Restarts/GEOSChem.Restart.20190101_0100z.nc4 

Checking gc_4x5_merra2_CH4
   -> 6 differences found in OutputDir
      Only in GCC_14.2.1_r18/rundirs/gc_4x5_merra2_CH4/OutputDir: compare_diags.yml
* GCC_14.2.1_r18/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
Only in GCC_14.2.1_r19/rundirs/gc_4x5_merra2_CH4/OutputDir: GEOSChem.StateMet.20190101_0000z.nc4
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0100z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0100z.nc4 

Checking gc_4x5_merra2_CO2
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_aciduptake
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_APM
   -> 2 differences found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_fullchem_APM/Restarts/GEOSChem.Restart.20190701_0100z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_fullchem_APM/Restarts/GEOSChem.Restart.20190701_0100z.nc4 

Checking gc_4x5_merra2_fullchem_benchmark
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_complexSOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_complexSOA_SVPOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_LuoWd
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_marinePOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_RRTMG
   -> 1 difference found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4 
   -> No differences in Restarts

Checking gc_4x5_merra2_Hg
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_metals
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_POPs_BaP
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagCH4
   -> 2 differences found in OutputDir
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_tagCH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_tagCH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_tagCH4/OutputDir/HEMCO_diagnostics.201901010000.nc 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_tagCH4/OutputDir/HEMCO_diagnostics.201901010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r18/rundirs/gc_4x5_merra2_tagCH4/Restarts/GEOSChem.Restart.20190101_0100z.nc4 
        GCC_14.2.1_r19/rundirs/gc_4x5_merra2_tagCH4/Restarts/GEOSChem.Restart.20190101_0100z.nc4 

Checking gc_4x5_merra2_tagCO
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagO3
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_TransportTracers
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_TransportTracers_LuoWd
   -> No differences in OutputDir
   -> No differences in Restarts

Checking Results
   -> No differences in OutputDir
   -> No differences in Restarts

Checking test.yml
   -> No differences in OutputDir
   -> No differences in Restarts

@yantosca yantosca merged commit 0883835 into geoschem:dev/14.2.1 Aug 30, 2023
@yantosca yantosca mentioned this pull request Aug 31, 2023
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@nicholasbalasus nicholasbalasus mentioned this pull request Mar 21, 2024
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