Turn off the MEGAN extension for fullchem "non-benchmark" simulations #2372

yantosca · 2024-07-11T15:29:30Z

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

This is the companion PR to #2319. We have updated the run directory creation scripts and HEMCO_Config.rc template files so that the MEGAN emissions are enabled for the full-chemistry "benchmark" simulation and disabled for all other full-chemistry simulations.

Expected changes

This should be a zero-diff update

Related Github Issue

Closes MEGAN extension is turned on by default in GCHP run directory #2319

This commit addresses the issue raised in geos-chem #2319. We have now updated the following files so that only the "benchmark" fullchem simulation uses the MEGAN extension, while other "standard" simulations use the offline emissions. run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol - Replace "on" with ${RUNDIR_MEGAN_EXT} to toggle the MEGAN extension on or off based on the options given to createRunDir.sh. run/GCClassic/createRunDir.sh run/GCHP/createRunDir.sh - Set RUNDIR_MEGAN_EXT='off' for the aerosol-only simulation - Set RUNDIR_MEGAN_EXT='off' for the fullchem non-benchmark simulations - Set RUNDIR_MEGAN_EXT='on' for the fullchem benchmark simulation CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

yantosca · 2024-07-11T15:41:58Z

I created run directories for the GEOS-Chem Classic aerosol-only and fullchem simulations. The MEGAN emissions are only turned on in the benchmark simulation.

$ g "108     MEGAN" */HEMCO_Config.rc
aer_only/HEMCO_Config.rc:174:           108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_apm/HEMCO_Config.rc:197:       108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_benchmark/HEMCO_Config.rc:197: 108     MEGAN                  : on     ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_csoa/HEMCO_Config.rc:197:      108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_csoasvpoa/HEMCO_Config.rc:197: 108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_mpoa/HEMCO_Config.rc:197:      108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_rrtmg/HEMCO_Config.rc:197:     108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_std/HEMCO_Config.rc:197:       108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
fullchem_tomas/HEMCO_Config.rc:197:     108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS

yantosca · 2024-07-11T15:53:41Z

This also works for GCHP:

gchp_fullchem_bmk/HEMCO_Config.rc:196:108     MEGAN                  : on     ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS
gchp_fullchem_std/HEMCO_Config.rc:196:108     MEGAN                  : off    ISOP/ACET/PRPE/C2H4/ALD2/MOH/EOH/MTPA/MTPO/LIMO/SESQ/SOAP/SOAS

yantosca · 2024-07-11T20:28:13Z

All GEOS-Chem Classic integration tests passed:

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

GCClassic #30aeed4 GEOS-Chem submod update: Merge PR #2369 (Fixes for satellite diags)
GEOS-Chem #5971dcb0c Turn off MEGAN extension for standard fullchem simulations
HEMCO     #2192e0e HEMCO 3.9.1 release

Using 24 OpenMP threads
Number of execution tests: 28

Submitted as SLURM job: 39495288
==============================================================================

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

All simulations were identical to PR #2369, except for differences in the HEMCO_diagnostics and HEMCO_restart files in these simulations:

fullchem
fullchem_aciduptake
fullchem_APM
fullchem_complexSOA
fullchem_complexSOA_SVPOA
fullchem_LuoWd
fullchem_marinePOA
fullchem_RRTMG
fullchem_TOMAS15
fullchem (47 levels)
fullchem (nested 0.5 x 0.625 NA)

The differences are that with the MEGAN extension being shut off, certain diagnostics are no longer written to the HEMCO_diagnostics file:

$ ncd gc2369/GCC_it/rundirs/gc_4x5_merra2_fullchem/OutputDir/HEMCO_diagnostics.201907010000.nc > log.ref
$ ncd gc2372/GCC_it/rundirs/gc_4x5_merra2_fullchem/OutputDir/HEMCO_diagnostics.201907010000.nc > log.dev
$ diff log.ref log.dev | g float
2:<     float InvMEGAN_AAXX(time, lat, lon) ;
13:<    float InvMEGAN_FAXX(time, lat, lon) ;
24:<    float InvMEGAN_MBOX(time, lat, lon) ;
35:<    float InvMEGAN_OSQT(time, lat, lon) ;
46:<    float InvMEGAN_BCAR(time, lat, lon) ;
57:<    float InvMEGAN_FARN(time, lat, lon) ;
68:<    float InvMEGAN_OMON(time, lat, lon) ;
79:<    float InvMEGAN_OCIM(time, lat, lon) ;
90:<    float InvMEGAN_CARE(time, lat, lon) ;
101:<   float InvMEGAN_MYRC(time, lat, lon) ;
112:<   float InvMEGAN_SABI(time, lat, lon) ;
123:<   float InvMEGAN_BPIN(time, lat, lon) ;
134:<   float InvMEGAN_APIN(time, lat, lon) ;
145:<   float InvMEGAN_ACET_DIRECT(time, lat, lon) ;
156:<   float InvMEGAN_ACET_MBOX(time, lat, lon) ;

as well as certain fields no longer being writtten to the restart file:

$ ncd gc2369/GCC_it/rundirs/gc_4x5_merra2_fullchem/Restarts/HEMCO_diagnostics.201907010100.nc > rst.ref
$ ncd gc2372/GCC_it/rundirs/gc_4x5_merra2_fullchem/Restarts/HEMCO_diagnostics.201907010100.nc > rst.dev
$ diff rst.ref rst.dev | g float
2:<     float PARDF_DAVG(time, lat, lon) ;
13:<    float PARDR_DAVG(time, lat, lon) ;
24:<    float T_DAVG(time, lat, lon) ;
35:<    float T_PREVDAY(time, lat, lon) ;
46:<    float LAI_PREVDAY(time, lat, lon) ;

yantosca · 2024-07-11T21:04:43Z

All GCHP integration tests passed

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

GCHP      #95a745c GEOS-Chem submod update: Merge PR #2369 (Fixes for satellite diags)
GEOS-Chem #5971dcb0c Turn off MEGAN extension for standard fullchem simulations
HEMCO     #

Number of execution tests: 11

Submitted as SLURM job: 39495563
==============================================================================

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

All tests were zero-diff to PR #2369 except for:

fullchem
fullchem_RRTMG
fullchem_TOMAS15

Due to similar reasons as listed in the previous comment.

run/GCClassic/createRunDir.sh

run/GCClassic/createRunDir.sh - Add a line to set RUNDIR_MEGAN_EXT env var to "on" for GCAP2 met - Reorder the RUNDIR_*_EXT variables alphabetically Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

lizziel

Looks good to merge.

yantosca added this to the 14.4.2 milestone Jul 11, 2024

yantosca self-assigned this Jul 11, 2024

yantosca changed the base branch from main to dev/no-diff-to-benchmark July 11, 2024 15:29

yantosca changed the title ~~Turn off the MEGAN extension for fullchem "non-benchmark" simulations.~~ Turn off the MEGAN extension for fullchem "non-benchmark" simulations Jul 11, 2024

yantosca changed the base branch from dev/no-diff-to-benchmark to dev/14.5.0 July 11, 2024 20:28

yantosca changed the base branch from dev/14.5.0 to dev/no-diff-to-benchmark July 11, 2024 20:29

yantosca requested a review from msulprizio July 11, 2024 21:11

yantosca marked this pull request as ready for review July 11, 2024 21:11

yantosca requested review from lizziel and removed request for msulprizio July 12, 2024 15:17

yantosca mentioned this pull request Jul 12, 2024

Comment out manual InvMEGAN diagnostic creation code geoschem/HEMCO#281

Closed

lizziel reviewed Jul 12, 2024

View reviewed changes

run/GCClassic/createRunDir.sh Outdated Show resolved Hide resolved

Bug fix: Make sure MEGAN is turned on for GCAP2 simulations

207c9c6

run/GCClassic/createRunDir.sh - Add a line to set RUNDIR_MEGAN_EXT env var to "on" for GCAP2 met - Reorder the RUNDIR_*_EXT variables alphabetically Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

yantosca requested a review from lizziel July 12, 2024 17:31

lizziel approved these changes Jul 12, 2024

View reviewed changes

yantosca merged commit 03287a6 into dev/no-diff-to-benchmark Jul 12, 2024

yantosca deleted the bugfix/turn-off-megan-in-std-sims branch July 12, 2024 19:12

This was referenced Jul 12, 2024

Throw a CMake error if FAST-JX is used for any KPP mechanism except Hg geoschem/GCHP#426

Closed

Disable support for FAST-JX except for the Hg simulation #2379

Closed

msulprizio mentioned this pull request Jul 29, 2024

MEGAN extension is turned on by default in GCHP run directory #2319

Closed

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Turn off the MEGAN extension for fullchem "non-benchmark" simulations #2372

Turn off the MEGAN extension for fullchem "non-benchmark" simulations #2372

yantosca commented Jul 11, 2024

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Turn off the MEGAN extension for fullchem "non-benchmark" simulations #2372

Turn off the MEGAN extension for fullchem "non-benchmark" simulations #2372

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yantosca commented Jul 11, 2024

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Describe the update

Expected changes

Related Github Issue

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