Implementation of TOMAS in GCHP #1378
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run/shared/species_database.yml - Following geoschem/geos-chem #1414, we have added the attribute "WD_CoarseAer: true" for SO4s and NITs species. SO4s and NITs should be treated exactly like coarse-mode aerosols in wet scavenging. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit adds the reaction requested in geoschem/geos-chem #1235 KPP/custom/custom.eqn KPP/fullchem/fullchem.eqn - Added MO2 + NO3 = NO2 + CH2O + HO2 with constant rxn rate of 1.0d-12 KPP/fullchem/*.map KPP/fullchem/gckpp*.F90 - Rebuilt with KPP 2.5.0 NOTE: We will bring this update in with KPP 2.5.0 and then rebuild the mechanism with KPP 3.0.0 before releasing GEOS-Chem 14.1.0. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/custom/custom.eqn KPP/fullchem/fullchem.eqn - Apply the bug fix provided by @khbates in geoschem/geos-chem #1274, namely to change the Arrhenius A coefficient of the ETO = HO2 + CH2O rxn from 9.5d-13 to 9.5d+13 KPP/fullchem/gckpp_Rates.F90 - Rebuilt with KPP 2.5.0 NOTES: (1) This commit builds on top of geoschem/geos-chem PR #1444, and thus must be merged on top of PR #1444. (2) For now we have rebuilt the fullchem mechanism with KPP 2.5.0, but we will rebuild all KPP mechanisms prior to the 14.1.0 release. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/custom/custom.eqn
KPP/fullchem/fullchem.eqn
- HOBr + SO2 = SO4s + HBr is now HOBr + SO2 = SO4 + HBr
- HOCl + SO2 = SO4s + HCl is now HOCl + SO2 = SO4 + HCl
- Updated comments
KPP/fullchem/gckpp*.map
KPP/fullchem/gckpp*.F90
- Rebuilt with KPP 2.5.0
NOTES:
(1) We will rebuild all mechanisms with KPP 3.0.0 before the official
release of GEOS-Chem 14.1.0.
(2) This commit is built on top of the commit 234c429 (Bug fix: change
sign in the Arrhenius A coefficient of ETO = HO2 + 2CH2O), and should
be merged afterwards.
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/species_database.yml run/shared/species_database_hg.yml - As suggested by @XueyingYu-1993, we are changing the molecular weight of methane from 16.05 g/mol to 16.04 g/mol in the species_database*yml files. This fixes a roundoff error that was caused by adding the rounded value of 4H (4.04) with C (12.01). The actual value for MW_g of CH4 should be 16.0425 g/mol or 16.04 when rounded to 2 places. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
… feature/Hg0drydep+updateconfig This brings @arifein's updates for Hg0 drydep up to dev/14.1.0, stored in branch feature/Hg0drydep+updateconfig. We will add some configuration file updates (requested by the Hg & POPs working in subsequent commits to this branch. Resolved conflicts in: GeosCore/drydep_mod.F90 Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg - As described in geoschem/geos-chem PR #1367, we now point to the CHEM_INPUTS/FAST_JX/v2022-10-Hg data folder for FAST-JX, as the FJX_j2j.dat file was modified. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCClssic/HEMCO_Config.rc.templates/HEMCO_Config.rc - Removed BrOX_GC entries (Br*_GC and Br*_TOMCAT) - Removed JBrO entries (RUNDIR_JBrO and RUNDIR_JNO2) - Removed AERO_HG2_PARTITION fields - Updated comments Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCClassic/createRunDir.sh - Make sure that we copy README.md instead of README to the run directory. This might have been clobbered by a Git merge. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.Hg - Add GMA_* switches to turn on AMEP/UNEM GMA data by default - Set WHET switch to false - Add entries to read AMEP/UNEP GMA data from the netCDF file $ROOT/MERCURY/v2022-10/GMA_emissions_Hg.0.25x0.25.2015.nc These updates were tested with a 1-day Hg simulation, which ran to completion. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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A fix was pushed to the HEMCO repository to resolve the TOMAS compile issue. All GCClassic simulations now pass compilation tests: TOMAS simulations are still failing the GCClassic execution tests: The issue is an error in hcox_tomas_jeagle_mod.F90. I am working on a fix. |
Also updated GCHP/HEMCO_Config.templates/HEMCO_Config.rc.fullchem to ensure consistency with GCClassic version. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Make sure we only compile for the default and TOMAS options. Also add a fix to link to the correct gchp executable. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
(1) Put two ## in front of 'Tomas' in the collection list to avoid
activating that collecton for benchmark simulations.
(2) Moved the 'Tomas' collection entries further down in HISTORY.rc so
that collections are in alphabetical order.
(3) Remove TOMAS species from SpeciesConc collection or else benchmark
simulations will crash because it can't find those species.
(4) Added code to setupConfigFiles.sh to activate the TOMAS collection
and to add the TOMAS species to the SpeciesConc list for TOMAS simulations
only.
(5) Added Tomas collection to GCClassic HISTORY.rc.fullchem
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
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GCHP integration tests have now been updated to include TOMAS simulations. All GCHP compilation tests are passing: The GCHP execution tests for TOMAS simulations are failing however: Further investigation is needed. |
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The error in the GCHP TOMAS simulations is: |
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Hi @msulprizio and @Jourdan-He; Thanks for all your help with these TOMAS updates! I'm about to start work on the TOMAS side of things to move the TOMAS arrays out of sulfate_mod.F90 and into state_chm_mod.F90. As I'm relatively new to this work flow - could you advise me on the steps to follow to make sure that I am modifying the correct version of the code? |
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@BettyCroft My goal is to try to get the TOMAS simulation running in GCHP so we can at least merge these update into |
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Thanks @msulprizio, I'll also tag @theloniuspunk here so that he has an update on these developments. |
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GCClassic integration tests are all passing except for TOMAS. The TOMAS simulations are failing with the following error in the GEOS-Chem log file: |
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Hi @msulprizio and @Jourdan-He - I have just submitted a pull request for the bug fix for TOMAS sulfate production rates. Not sure that I named it all that well - it is called Feature/tomaswork and #1569 |
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Resolved conflicts in: CHANGELOG.md GeosCore/sulfate_mod.F90 Headers/state_diag_mod.F90 run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem test/GCClassic/intTestCreate.sh# test/GCHP/intTestCompile_slurm.sh test/GCHP/intTestCreate.sh test/shared/commonFunctionsForTests.sh Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
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This has now been merged into dev/14.2.0. |
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Hi @msulprizio, Thank you for all your work with this PR. |
msulprizio
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to geoschem/GCClassic
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Apr 7, 2023
For more details see - geoschem/geos-chem#1378 - geoschem/HEMCO#164 Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
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Thanks, Melissa!
…On Fri, Apr 7, 2023, 8:02 AM BettyCroft ***@***.***> wrote:
Hi @msulprizio <https://github.com/msulprizio>, Thank you for all your
work with this PR.
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This is the PR adding TOMAS simulations in GCHP. It supersedes #1261 originally from @BettyCroft. This PR should be merged along with:
I have test run the merge on a single node simulation, and it's completed successfully.