[WIP] Change units of Loss_Ox diagnostic from molec/cm3/s to unitless (to fix an issue in tagO3 simulations)
#2096
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…dgr/geos-chem_14.2.0
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
GEOS-Chem 14.2.0
With this commit the GEOS model builds and runs using GEOS-Chem transport tracer simulation with new config files stored in geos-chem/run/GEOS/TransportTracers. The following is currently required to run successfully: 1. CEDSv2 must be turned off in HEMCO_Config.rc 2. ExtData2G must be turned off in CAP.rc Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This commit addresses issue #2055, by using a newer Hg restart file run/shared/download_data.yml - Change the remote restart directory from v2012-12 to v2023-12 CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit addresses issue #2029 by @jessicahaskins: KPP/fullchem/commonIncludeVars.H - Update units (in comment) for SR_MW in comment line - Add units (in comment) for PRESS, RELHUM, SUNCOS, PHOTOL, H2O, K_STRAT, K_TROP, TROP Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #2061 (Add missing units in comments of KPP/fullchem/commonIncludeVars.sh, by @yantosca) into the "no-diff-to-benchmark" development stream. This is a zero-diff update which updates comments in the fullchem mechanism include file commonIncludeVars.sh. The KPP mechanisms were not rebuilt, as this file is #include-d into the mechanism. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
The timers used in benchmarking to track model performance and generate this chart https://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_1-month_benchmark_timing_results include: - GEOS-Chem, - HEMCO - All chemistry - Gas-phase chem - Photolysis - Aerosol chem - Linearized chem - Transport - Convection - Boundary layer mixing - Dry deposition - Wet deposition - Diagnostics - Unit conversion The remaining timers are superfluous. They are removed here to clean up output and reduce unnecessary time spent computing those timers. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
This merge brings PR #2059 (Now read the Hg restart file from GEOSCHEM_RESTARTS/v2023-12, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR now copies updated Hg simulation restart files (that with well-spun-up initial conditions) to GCClassic and GCHP run directories, as was requested by @angothelene in #2055. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Specific humidity will be available in transport tracer sim checkpoints for purposes of post-processing unit conversions. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This avoids an out-of-bound issue when vertically flipping diagnostics with 73 levels in GEOS. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This merge brings PR #2069 (Reduce timers to essential list only, by @msulprizio) into the "no-diff-to-benchmark" development stream. This removes GEOS-Chem timers that are no longer needed. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #2058 (GEOS-Chem Transport Tracers simulation GEOS, by @lizziel) into the GEOS-Chem "no-diff-to-benchmark" development stream. This adds several updates to get the GEOS-Chem Transport Tracers simulation working in the NASA GEOS ESM. It will not affect the GEOS-Chem Classic or GCHP implementations of GEOS-Chem. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit fixes the issue raised in PR #2083 by @lizziel. Integration and parallel test execute scripts now use the run directory name and not the absolute path to determine the executable file name. test/integration/GCClassic/integrationTestExecute.sh test/integration/GCHP/integrationTestExecute.sh test/parallel/GCClassic/parallelTestExecute.sh - Pass ${runDir} instead of ${runAbsPath} to the exe_name function. This will prevent integration test root paths with e.g. "rrtmg" from returning an incorrect executable name. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
CHANGELOG.md - Added note that we now use the run directory and not the absolute path to determine the executable file to use in integration and parallel tests. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #2084 (Use rundir (not absolute path) to select the executable file for integration and parallel tests, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR fixes the issue reported in #2083 by @lizziel. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca
added
topic: Diagnostics
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@yantosca Were there any commits added to this branch ( |
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@msulprizio, yes... this was a branch I used to open a draft PR. I can close this out. |
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Name and Institution (Required)
Name: Bob Yantosca
Institution: Harvard + GCST
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Describe the update
This is a a placeholder PR and should not be merged yet.
As described in #2094 (by @ncolombi and @xpye98), the units of the
Loss_Oxdiagnostic need to be changed frommolec/cm3/stounitlessin order to prevent a problem in the tagO3 simulation. Please see the discussion in #2094 for the time being.What needs to be changed:
Loss_Oxas archived fromGeosCore/fullchem_mod.F90. Specifically, we need to divide theC(ind_LO3)by the mass of all species in the LOx family.Chem_Tagged_O3inGeosCore/tagged_o3_mod.F90, to ingestLoss_Oxin the new units and apply the loss rates.Caveat: We will also need to make sure that this does not affect other specialty simulations that may use archived
Loss_Oxdata.Tagging @msulprizio @lizziel @ncolombi @xpe98 for your reference.
Expected changes
This should be a zero-diff update, as we are only changing the diagnostic output. However, because we are touching the full chemistry module as well, we should benchmark this just to be sure. I recommend that this update be added to the next Y version.
Reference(s)
N/A
Related Github Issue(s)