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Update GEPA CH4 emissions to Gridded GHGI v2 #1917
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Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This print is a line of repeated '=' to end a table otherwise printed to root thread only.
This update moves the renaming of mid-run restart files to after the renaming of the end-of-run restart file. This prevents mid-run checkpoint files from having non-standard names if the run crashes at some point. Previously the renaming of mid-run checkpoint files did not happen if the run crashed because the run script would exit prior to reaching execution of that code. This update also include deletion of the end-of-run restart file Restarts/gcchem_internal_checkpoint if the run fails. Depending on where in the run the failure occurs this file may exist. Its presence will prevent a future run and so it must be deleted. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
AUTHORS.txt - Added new code contributors for GEOS-Chem 14.2.0 and 14.2.1 LICENSE.txt - Updated for better readability - Add text of GPLv3 license (used by QFYAML, FAST-JX, KPP) - Add text of Apache license (used by MAPL etc) - Add text of NASA Open Source Agreement (used by MAPL etc) - Trimmed trailing whitespace Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu> Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Some of the prior edits in the AUTHORS.txt file have been clobbered. We have restored these edits. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
…k') into dev/14.2.0
…print_to_root') into dev/14.2.0
…_run_fails') into dev/14.2.0
A second comment character has been added to the entry in HISTORY.rc.fullchem for SpeciesConcMND_?ALL? to avoid saving out both SpeciesConcVV and SpeciesConcMND output for benchmark simulations. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Transport tracer species aoa*, nh*, St80_25, and StOX did not have molecular weights defined because they're not traditional chemical species. This causes issues with unit conversions in the code and results in negative and/or zero SpeciesConc output. To avoid this, we define MW_g: 1.0 for those species. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
1. Move initialization of mask arrays into loop over species. 2. Make sure to do calculations for maintaining the mixing ratio only in the defined region (where Mask is 1) 3. Fix typo in the logic for determining masks of latitude zones. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
The stOX tracer is defined in GMAO's TR_GridComp but is not commonly utilized and isn't needed in GEOS-Chem. It is removed here to avoid confusion. The fields needed for stOX (GLOBAL_O3 and O3_LOSS) are also removed from tracer_mod.F90 and TransportTracer configuration files. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Instead of multiplying the source or sink application by the Mask array, the code now checks if Mask > 0 before applying the source or sink. Multiplying by the Mask array may have inadvertently set species concentrations to zero instead of not implying the source or sink. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
The Budget diagnostics collection is now needed for TransportTracer benchmarking. It is now disabled by default to avoid saving out unnecessary data. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
As suggested by Daniel Jacob, we now skip the SALAAL + SO2 and SALCAL + SO2 reactions if O3 < 1e10 molec/cm3. This concentration is equivalent to 0.5 ppbv, which should be lower than ozone should ever get in the atmosphere. This may help stabilize the full-chemistry mechanism by preventing reaction rates from blowing up. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
In geoschem/geos-chem #1880, @viral211 suggested that we are double-counting the loss of IONO2 by alkaline SALA and SALC in hetchem routines: - IuptkByAlkSALA1stOrd - IuptkByAlkSALC1stOrd and then again in routine - IONO2uptkByH2O To remove the double-counting, we have removed the code that handles the removal of IONO2 by alkaline sea salt aerosol. A more permanent solution by @beckyalexander may be forthcoming in the near future. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
In PR #1893 the lines for IONO2 uptake on tropospheric sulfate were inadvertently commented out in function IONO2uptkByH2O in fullchem_RateLawFuncs.F90. They are now restored. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…rogenerous acid-catalyzed reactions of halogens on sea salt aerosols Pull request #1702 fixed bugs in heterogeneous chemistry by restoring sea salt alkalinity to certain reactions in the halogen chemistry. That update introduced many KPP integrate error messages into the log file. The errors were overlooked because the integration succeeded on the second attempt. In the 1-year full-chemistry benchmark for 14.2.0-rc.0, a sharp decrease in O3 was observed at several locations in the model vs observation plots. It turns out that decrease could be attributed to the changes in #1702. As a result, we now revert those updates to restore model performance. Implementing these fixes at a later date is a science issue and should be fully validated. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
…simulations The GEPA inventory option has been removed from HEMCO configuration files for the CH4 and carbon simulations. It is now superceded by the newer version -- Gridded GHGI v2. The Gridded GHGI dataset now includes two datasets: 1. Gridded GHGI data (main dataset) containing annual methane emissions for 2012-2018 generated from the US GHGI published in 2020. Monthly scale factors are also provided for this dataset. 2. Gridded GHGI Express Extension containing annual methane emissions for 2012-2020 generated from the US GHGI published in 2022. This dataset uses annual source-specific spatial patterns from 2012-2018 from the main dataset to quickly incorporate more recent national methane emission estimates. Emissions for years after 2018 follow the 2018 spatial patterns. Both datasets are implemented as options in HEMCO_Config.rc -- the default is to use the Gridded GHGI Express Extension files. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
NOTE: This branch is off of |
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Thanks @msulprizio. This looks good to merge.
NOTE: Although it says there are 34 changed files, this is because this branch was opened prior to several fixes that have since gone into dev/14.2.0 and dev/14.2.1 branches. The only changes of note are the ones to the HEMCO_Config.rc and ExtData.rc.
# | ||
# NOTES: | ||
# - This is the main Gridded GHGI v2 dataset based off the US GHGI published in 2020 |
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@msulprizio: Question: the time cycle flags are now EFY instead of C, which will stop the run unless the simulation is within the 2012-2018 date range. Is this the intended behavior now? Just wanted to confirm.
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ah I see this is not the default option. No problem then.
All GEOS-Chem integration tests passed (except for TOMAS, which is a known issue: ==============================================================================
GEOS-Chem Classic: Execution Test Results
GCClassic #f3509f8 Merge PR #1946 (Fix build issues in GCClassic w/ the custom mech)
GEOS-Chem #e696799c2 Merge PR #1917 (Update GEPA CH4 emissions to Gridded GHGI v2)
HEMCO #daf54d0 Merge PR #235 (Bug fix for vertical regridding)
Using 24 OpenMP threads
Number of execution tests: 26
Submitted as SLURM job: 1747431
==============================================================================
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 Also all integration tests were identical to the prior integration test (PR #1946) except for:
Checking gc_05x0625_NA_47L_merra2_CH4
-> 4 differences found in OutputDir
* GCC_14.2.1_r22_g10/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4
GCC_r23/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4
GCC_r23/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4
GCC_r23/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc
GCC_r23/rundirs/gc_05x0625_NA_47L_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc
-> 1 difference found in Restarts
* GCC_14.2.1_r22_g10/rundirs/gc_05x0625_NA_47L_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0020z.nc4
GCC_r23/rundirs/gc_05x0625_NA_47L_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0020z.nc4
Checking gc_05x0625_NA_47L_merra2_fullchem
-> No differences in OutputDir
-> No differences in Restarts
Checking gc_4x5_47L_merra2_fullchem
-> No differences in OutputDir
-> No differences in Restarts
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
-> 2 differences found in OutputDir
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_carbon/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4
GCC_r23/rundirs/gc_4x5_merra2_carbon/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_carbon/OutputDir/HEMCO_diagnostics.201901010000.nc
GCC_r23/rundirs/gc_4x5_merra2_carbon/OutputDir/HEMCO_diagnostics.201901010000.nc
-> 1 difference found in Restarts
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_carbon/Restarts/GEOSChem.Restart.20190101_0100z.nc4
GCC_r23/rundirs/gc_4x5_merra2_carbon/Restarts/GEOSChem.Restart.20190101_0100z.nc4
Checking gc_4x5_merra2_CH4
-> 4 differences found in OutputDir
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4
GCC_r23/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.CH4.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4
GCC_r23/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.Metrics.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4
GCC_r23/rundirs/gc_4x5_merra2_CH4/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc
GCC_r23/rundirs/gc_4x5_merra2_CH4/OutputDir/HEMCO_diagnostics.201901010000.nc
-> 1 difference found in Restarts
* GCC_14.2.1_r22_g10/rundirs/gc_4x5_merra2_CH4/Restarts/GEOSChem.Restart.20190101_0100z.nc4
GCC_r23/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
-> No differences in OutputDir
-> No differences in Restarts
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_r22_g10/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4
GCC_r23/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
-> No differences in OutputDir
-> No differences in Restarts
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 |
All GCHP integration tests passed: ==============================================================================
GCHP: Execution Test Results
GCClassic #9285236 GEOS-Chem submod update: Merge PR #1946 (Fix custom mech build issues)
GEOS-Chem #e696799c2 Merge PR #1917 (Update GEPA CH4 emissions to Gridded GHGI v2)
HEMCO #daf54d0 Merge PR #235 (Bug fix for vertical regridding)
Number of execution tests: 5
Submitted as SLURM job: 1747529
==============================================================================
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! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% All GCHP integration tests were also zero-diff w/r/t the prior integration test: (PR #1946) 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 |
This merge brings the updates for the GEOS-Chem carbon simulation (with single tracer rundirectory option) up to date with the latest state of the 14.2.1 development stream. This also brings updates from 14.2.0-alpha.19 into the bugfix/carbon-single-tracer branch. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Name and Institution (Required)
Name: Melissa Sulprizio
Institution: Harvard / GCST
Confirm you have reviewed the following documentation
Describe the update
This update removed the gridded EPA (GEPA) option from HEMCO_Config.rc for CH4, tagCH4, and carbon simulations and replaces it with the latest version (Gridded GHGI v2).
Expected changes
This update only impacts CH4, tagCH4, and carbon simulations. It modified emissions over the US.
Reference(s)
Maasakkers, J.D., E.E. McDuffie, M.P. Sulprizio, C. Chen, M. Schultz, L. Brunelle, R. Thrush, J. Steller, C. Sherry, D.J. Jacob, S. Jeong, B. Irving, and M. Weitz, A gridded inventory of annual 2012-2018 U.S. anthropogenic methane emissions, submitted to Environ. Sci. Technol. 2023, https://doi.org/10.31223/X5RQ3M.
Related Github Issue(s)