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[PULL REQUEST] Allow negative pKa but skip missing values in routine CALC_HEFF (Closes #1001) #1042
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Implemented init_rd.sh which enables automated run directory creation. The run directory is initialized based on RDI values loaded from the input files. See #459.
Resolved conflicts in: run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem run/GCHP/createRunDir.sh run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
The files containing environment variables for various run directory settings will ideally be used for both GCHP and GCClassic. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…r.sh Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Only the GCHP run directory creation was updated for the RDI variables and automated run directory creation. Here we begin adding RDI variables for and an init_rd.sh script for GCClassic. The *_settings.txt files containing RDI variables for specific simulations, met fields, and resolutions have now been moved to the run/shared/settings/ directory with "_settings" removed from the file names. This was done so that both GCHP and GCClassic can access the same files. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Resolved conflicts in: run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem run/GCClassic/createRunDir.sh run/GCClassic/input.geos.templates/input.geos.fullchem run/GCHP/ExtData.rc.templates/ExtData.rc.TransportTracers run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/createRunDir.sh run/GCHP/input.geos.templates/input.geos.TransportTracers run/GCHP/input.geos.templates/input.geos.fullchem run/GCHP/runConfig.sh.template Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Made the following changes: - Replaced tokens in configuration files with RDI variables - Removed settings files for several simulation types because they contained RDI variables that are set in createRunDir.sh already - Added settings file for GCAP2 (run/shared/settings/modele2.1.txt) - Updated GCHP adjoint configuration file and files for GCHP CO2 simulation so they are consistent with recent updates Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…se RDI variables instead Recent modifications for GCAP 2.0 support added several more uses of "sed" in createRunDir.sh. These have been removed where possible and replaced with RDI variables that will be automatically replaced. For HEMCO settings specific to simulations using GMAO or GCAP2 meteorology, the RDI settings have been set in gmao_hemco.txt and gcap2_hemco.txt which are accessed in createRunDir.sh. Similar updates were also made to setupConfigFiles.sh to remove uses of sed from function set_common_settings. That function is still used to manually add species and modify diagnostic output for specific simulation types. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Run directory variables were previously prefixed with RDI (Run Directory Initialization). It was not immediately obvious what RDI stood for, so we have replaced RDI with the more descriptive RUNDIR. This is a simple swap where all uses of RDI, rdi, or RDI_ have been replaced with RUNDIR, rundir, or RUNDIR_. The run directory variables are now saved to a file named rundir_vars.txt. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
To remove differences in run directory files made with the automated run directory creation updates, the following fixes have been made: 1. Make sure all tokens in HEMCO_Config.rc files are replaced with $RUNDIR_ variables. 2. Remove unused HEMCO settings specific to GCAP 2.0 simulations from the top of HEMCO_Config.rc for several specialty simulations. 3. Make sure to use $GCAP2SCENARIO instead of $SCENARIO for CMIP6 fields consistently throughout HEMCO_Config.rc files. 4. Add dummy HEMCO_Diagn.rc file for tagO3 simulation. 5. In createRunDir.sh set default DustDead tuning factor to -999.0 for resolutions without a recommended scaling. Also make sure to set TOMAS extensions to off when not using that simulation. 6. Fixed a typo for the complexSOA_SVPOA simulation in createRunDir.sh. 7. Make sure to use ${RUNDIR_POP_SPC} instead of {POPs_SPC} in POPs template files. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…rectory creation updates 1. Fix typo in createRunDir.sh for determining DustDead tuning factor used in 4x5 GEOS-FP benchmark and TOMAS simulations (both of which use online dust emissions). 2. Update commonFunctionsForTests.sh used in Integration Tests to add "NA" to the entries for met fields in the new HEMCO_Config.rc.gmao_metfields file as well as the original HEMCO_Config.rc file. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…un directory creation updates 1. Fix typos in createRunDir.sh for GCHP. 2. Add RUNDIR_MET_DIR_NATIVE for native-resolution meteorology fields used by GCHP. GCClassic typically uses meteorology fields at the same resolution as the simulation. 3. In commonFunctionsForTests.sh only modify HEMCO_Config.rc.gmao_metfields if the file exists (i.e. only for GCClassic run directories). For GCHP runs, meteorology fields are specified in ExtData.dat and don't need to be modified for nested-grid simulations. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…undir_creation This merge brings puts feature/automated-rundir-creation on top of the 13.4.0-alpha.2 tag. This introduces the updates for automatic run-directory creation, which will simplify the process of creating integration tests. After successful validation, this will be tagged as 13.4.0-alpha.3. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
We have restored the IF block that exits from INIT_UCX unless we are doing either a fullchem or an aerosol simulation. This seems to have been clobbered by a git merge. Now fixed. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
We now test if there are existing links to ChemDir, HcoDir, and MetDir before unlinking. This seems to prevent an issue with these links not being generated. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merges HEMCO 3.2.2 into the automatic rundir creation branch. We have also fixed a conflict in ExtData.rc.fullchem, so that ExtData.rc uses the same offline dust subfolder (v2021-08) as HEMCO_Config.rc Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
We have now restored the correct paths for GEOS-Chem restart files in download_data.yml. This may have been clobbered by a Git merge. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
…osols This fix corrects the issue first reported by Viral Shah in geoschem/geos-chem #1034. We only need to do HCL uptake when SO2 chemistry is called with when FullRun=.TRUE.. The quick fix was to add FullRun to the IF block where the computations occur. NOTE: This issue does not occur in the new KPP sulfur chemistry code: KPP/fullchem/fullchem_SulfurChemFuncs.F90. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit fixes the issue originally raised in geoschem/geos-chem #1001. Because missing values in the species database are -999, the condition IF ( pKa > 0 ) in CALC_HEFF (in module GeosUtil/henry_mod.F0) basically ignores pH in the effective Henry's law constant computations for cloud water in heterogenous chemistry. We have now set the condition to IF ( pKa > -100 ), which allows for negative pKa values, but which will skip missing values. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GCHP integration tests all passed successfully ==============================================================================
GCHP: Execution Test Results
Number of execution tests: 3
==============================================================================
Execution tests:
------------------------------------------------------------------------------
gchp_fullchem_benchmark_merra2_c48...............Execute Simulation.....PASS
gchp_fullchem_standard_merra2_c24................Execute Simulation.....PASS
gchp_TransportTracers_geosfp_c24.................Execute Simulation.....PASS
Summary of execution test results:
------------------------------------------------------------------------------
Execution tests passed: 3
Execution tests failed: 0
Execution tests not completed: 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% All execution tests passed! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% however, all of the GCC fullchem integration tests did not pass Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 42
Execution tests failed: 38
Execution tests not yet completed: 0 I am currently investigating. |
GeosUtil/henry_mod.F90: - Bug fix: Make sure pH > 0 and thisPka > -100 before computing the pH adjustment for effective Henry's law constant. KPP/fullchem/fullchem_HetStateFuncs.F90: - Bug fix: Remove V_tot from argument list in calls to Compute_L2G_Local, and pass pH = H%pHCloud. This corrects an issue where pH of the cloud was not being properly factored into computations. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_HetStateFuncs.F90: - In the prior commit (4e72c59), we did not add the L2G output argument to the calls to Compute_L2G_Local. Now fixed. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
A rerun of the GCHP integration tests had all tests pass. We are waiting for a rerun of GCC integration tests to complete. |
laestrada
approved these changes
Dec 6, 2021
The GCC fullchem integration tests now all pass. See issue #1001 for details. |
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This is the corresponding PR for #1001. It fixes an error that had caused pH to be neglected in the computation of Henry's law in cloud water (for heterogeneous chemistry).