Add GCHP ctmEnv simulation run directory option by lizziel · Pull Request #2742 · geoschem/geos-chem

lizziel · 2025-02-21T21:49:05Z

Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

This update introduces a new GCHP simulation option called ctmEnv that does not run GEOS-Chem or advection. The GCHPctmEnv gridded component, which is at the same hierarchical ESMF level as GEOS-Chem and FV3, is the only child gridded component of GCHP_GridComp that is run. The purpose of this is to experiment with producing 12 km lat-lon wind exports from c720 mass flux imports using MAPL but it can also be used for other purposes, such as debugging or investigating GCHP's version of MAPL and imports such as meteorology. This simulation does not require a restart file and can be run at very high resolution in a very short amount of time and with fewer resources than required if GEOS-Chem is on.

The ctmEnv simulation option is enabled by building with -DMODEL_CTMENV=y. There is an accompanying update in the GEOS-Chem repository for the option to create a a run directory for the ctmEnv simulation.

Important notes:

All of GCHP is compiled with the exception of code within #ifndef MODEL_CTMENV blocks.
Dynamics is both compiled and initialized. This avoids code dependency issues.
The simulation could be extended in the future to optionally include dynamics with a simple tracer.
The simulation does not use restart files. This enables it to be extremely lightweight and fast when run at high resolutions.

This update will require concurrent merge of geoschem/GCHP#477.

Expected changes

This is a no diff update, but does include some minor tweaks to the run directory of all GCHP simulations. The README is no longer markdown and it now includes simulation-specific build instructions, e.g. to compile with -DMODEL_CTMENV for the ctmEnv simulation.

Reference(s)

None

Related Github Issue

Add GCHP ctmEnv-only simulation option GCHP#477

Updates for Luo2023

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.* run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.* - Replaced header comments directing users to the GC wiki with comments directing users to hemco.readthedocs.io - For aerosol, carbon, fullchem: - Added FINNv25 entries - Removed FINN extension entries (this is now obsolete) run/GCClassic/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.* run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.* - Replaced header comments directing users to the GC wiki with comments directing users to hemco.readthedocs.io - Added header comments instructing users on the proper categories to use for offline biomass burning vs. GFED biomass burning Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

CHANGELOG.md - Added a note under "Fixed" that the TMB emissions entries have been restored in the HEMCO_Config.rc.fullchem template files for GCClassic and GCHP. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

replace SQRT(2.D0/3.D0) into ROOT_TWO_THIRDS

changed 0.006 to 0.006d0 and 0.013 to 0.013d0

numeric constants are followed by d0

Changed 2.749064E-4 to 2.749064D-4

Added comments describing KINC, WUP, TKICE, NUMCD, ICESF, and RADCD

Replaced log(State_Met%RADCD(I,J,L)*2d0) by log2R

run/GCHP/HISTORY.rc.templates/HISTORY.rc.carbon - Changed "EmisOCS_BioBurn" -> "EmisOCS_BiomassBurn" for consistency with the corresponding diagnostic in GCClassic, and to match the HEMCO_Diagn.rc.carbon template. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

run/GCHP/HISTORY.rc.templates/HISTORY.rc.carbon - Moved EmisOCS_Total to the top of the list of EmisOCS diagnostic entries. This is necessary in order to make the single-species OCS simulation diagnostics be created. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@yantosca

This merge brings PR # (Add FINN v2.5 biomass burning as an optional inventory #2900, by @yantosca on behalf of @eamarais) into the GEOS-Chem 14.7.0 development stream. This PR does the following: 1. Adds entries for FINN v2.5 biomass burning emissions to HEMCO_Config.rc template files for aerosol-only, carbon, and fullchem simulations. 2. Removes entries for the FINN v1.5 biomass burning extension from HEMCO_Config.rc template files, as FINN v1.5 is now superseded by FINN v2.5. 3. Adds clarifying comments in HEMCO_Diagn.rc template files instructing which settings of ExtNr, Cat, and Hier should be used for online vs. offline biomass burning emissions. 4. Replaces comments in HEMCO_Config.rc and HEMCO_Diagn.rc template files that were directing users to the obsolete HEMCO manual on the GC wiki with comments directing users to the current hemco.readthedocs.io documentation. 5. Restores TMB emission diagnostic entries to the HEMCO_Config.rc.fullchem files for GEOS-Chem Classic and GCHP. 6. Renames OCS biomass burning emissions to EmisOCS_BiomassBurn in GCHP HEMCO_Diagn.rc and HISTORY.rc files, for consistency with the corresponding diagnostic name in GEOS-Chem Classic. 7. Moves EmisOCS_Total to the top of the GCHP HISTORY.rc.carbon template file, which is expected by the script that edits the configuration files for single species carbon simulations. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Changed grid box width at the center to grid box width at the southern, northern, western, eastern edges

Calculate grid box widths by using longitudes and latitudes at edges

Replaced grid box widths at center with grid box widths at edges

Changed DXS(NX,NY), DXN(NX,NY), DYW(NX,NY), and DYE(NX,NY) to DXSN(NX,NY+1) and DYWE(NX+1,NY).

Calculate DXSN_M and DYWE_M.

Using DXSN and DYWE to calculate KINC

Optimized the calculation of DXSN and DYWE

… in ExtData

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

@yantosca

…sims) This merge brings PR #3066 (Toggle "read_restart_as_real8" from false to true for fullchem benchmark simulations, by @yantosca) into the GEOS-Chem 14.7.0 development stream. PR #3066 adds a call to bash function replace_colon_sep_val to change YAML tag "read_restart_as_real8" from false to true in the geoschem_config.yml file that is placed into fullchem benchmark run directories. PR #3066 also sets "read_restart_as_real8: true" by default in the template file geoschem_config.yml.TransportTracers. This is required for mass conservation in 1-yr or 10-yr TransportTracers benchmarks. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@yantosca

This merge brings PR # (Turn off PARANOx for GEOS-Chem Classic 0.25 x 0.3125 and 0.125 x 0.15625 grids, by @yantosca and @eamarais) into the GEOS-Chem 14.7.0 development stream. PR #3011 disables the PARANOx extension when running GC-Classic fullchem nested-grid simulatiions at 0.25 x 0.3125 and 0.125 x 0.15625 degree resolution, based on the findings of @eamarais. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@1Dandan

This merge brings PR # (Fix for emission configurations for carbon simulations #2893, by @1Dandan) into the GEOS-Chem 14.7.0 development stream. PR #2893 is the companion to HEMCO PR #330, which adds functionality for the Integrated Methane Inversion (IMI) with GCHP. Configuration files have been updated accordingly. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

…y retrieve the run duration string The Harvard example script gchp.submit_consecutive_jobs.sh was grepping setCommonRunSettings.sh for the string "DURATION=" to retrieve the run duration. At some point this string should have been changed to "Run_Duration=" to match what is now in setCommonRunSettings.sh. This fix will once more print to screen the run duration when executing gchp.submit_consecutive_jobs.sh instead of returning a blank string. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>

…ed to crash When enabling the Carbon collection in HISTORY.rc, GEOS-Chem crashes with an out-of-bounds error in KPP/carbon/carbon_Funcs.F90. This can be tracked to the uses of incorrect ind_ variable names -- ind_COfromCH4 should be ind_PCOfromCH4 and ind_COfromNMVOC should be ind_PCOfromNMVOC to reflect the species name change introduced in pull request #2800. We now also turn on the Carbon collection in HISTORY.rc by default to catch potential bugs like this during integration tests. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>

@msulprizio

This merge brings PR #3074 (Fix typos causing carbon simulations with the Carbon collection enabled to crash #3074, by @msulprizio) into the GEOS-Chem 14.7.0 development stream. PR #3074 fixes an out-of-bounds error in KPP/carbon/carbon_Funcs.F90 when the Carbon diagnostic collection is enabled. The Carbon collection is now also turned on by default so as to allow our integration tests to catch similar errors. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@msulprizio

This merge brings PR # (Fix typo in GCHP operational run script for Harvard Cannon to properly retrieve the run duration string, by @msulprizio) into the 14.7.0 development stream. PR #3073 fixes an search error in e Harvard example script gchp.submit_consecutive_jobs.sh. It was searching for "DURATION" but should have searched for "Run_Duration", Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

The previous path worked only on the Harvard Cannon cluster. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

ObsPack/obspack_mod.F90 - In routine ObsPack_Read_Input: - Define local variables tsDyn and halfTsDyn for convenience - In routine ObsPack_Sample - Added endOfDay, tsDyn, halfTsDyn, Interval, Tomorrow variables - Now include instantaneous ObsPack data in the sampling if: (a) We are within 1 model timestamp of the end of the model date (b) The data timestamp is within 1/2 model timestep of the end of the model date CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@yantosca

This merge brings PR # (Bug fix: Include instantaneous ObsPack data lying within 1/2 model timestep of the end of the model date in the sampling, by @yantosca) into the GEOS-Chem 14.7.0 development stream. PR #3087 updates the logic so that ObsPack data points that are instantaneously-sampled (i.e. having CT_sampling_strategy = 4) and that lie within 1/2 model timestep of the end of the day will be included in the sampling. This fixes a bug in #3084 that was reported by @mattloman. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@lizziel

This merge brings PR # (Fix LPJ wetland path in GCHP carbon ExtData.rc to use HEMCO directory, by @lizziel) into the GEOS-Chem 14.7.0 development stream. PR #3086 changes the path for LPJ wetlands emissions in the GCHP carbon-simulation ExtData.rc to use the HEMCO data directory. Previously the path was local on the Harvard Cannon compute cluster. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GeosCore/carbon_gases_mod.F90 - Moved the diagnostic archival of State_Diag%OHconcAfterChem to within the IF ( id_CH4_adv > 0 .or. id_CO_adv > 0 ) block to prevent an out-of-bounds error for CO2 or OCS simulations, in which OH is not used CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

@yantosca

This merge brings PR #3095 (Do not reference OHdiurnalFac in carbon_gases_mod.F90 for carbon simulations where OH is not used, by @yantosca) into the GEOS-Chem 14.7.0 development stream. PR #3095 fixes an out-of-bounds error that can occur in the CO2-only and OCS-only carbon simulations when the State_Diag%OHconcAfterChem diagnostic is selected to be archived, but when the OHdiurnalFac array is not allocated. To fix the error we enclose the IF block where the diagnostic is updated with in the IF ( id_CH4_adv > 0 .or. id_CO_adv > 0 ) block. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

README can be ascii Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

…match The run script is only in the operational run scripts folder for Harvard for primary use by GCST. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

lizziel · 2025-10-29T18:41:44Z

This is now rebased on dev/14.7.0.

…ctmEnv Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

yantosca · 2026-01-30T17:22:03Z

FYI @lizziel: I changed the base to main so that this PR won't get closed once we merge dev/14.7.0.

lizziel added category: Feature Request New feature or request topic: GCHP Only Related to items that only affect GCHP labels Feb 21, 2025

lizziel self-assigned this Feb 21, 2025

lizziel mentioned this pull request Feb 21, 2025

Add GCHP ctmEnv-only simulation option geoschem/GCHP#477

Draft

lizziel changed the title ~~Add GCHP ctmEnv-only simulation option~~ Add GCHP ctmEnv-only simulation run directory option Feb 21, 2025

lizziel changed the title ~~Add GCHP ctmEnv-only simulation run directory option~~ Add GCHP ctmEnv simulation run directory option Feb 21, 2025

yantosca added no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations topic: Run Directories Related to run directory issues and run directory creation labels May 1, 2025

lizziel force-pushed the feature/gchp_ctmenv_only_simulation branch from e831fad to 61aff9a Compare June 10, 2025 20:57

ganluoasrc and others added 21 commits June 11, 2025 00:28

Add files via upload

13ed557

Updates for Luo2023

Add files via upload

695f22a

Updates for Luo2023

Add files via upload

1630605

Updates for Luo2023

Changelog update: TMB emission entries are restored HEMCO_Config.rc

660e063

CHANGELOG.md - Added a note under "Fixed" that the TMB emissions entries have been restored in the HEMCO_Config.rc.fullchem template files for GCClassic and GCHP. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Update vdiff_mod.F90

d80929f

replace SQRT(2.D0/3.D0) into ROOT_TWO_THIRDS

Update vdiff_mod.F90

9642af3

changed 0.006 to 0.006d0 and 0.013 to 0.013d0

Update vdiff_mod.F90

9be09a8

numeric constants are followed by d0

Update vdiff_mod.F90

4e7c2a3

Changed 2.749064E-4 to 2.749064D-4

Update state_met_mod.F90

f0cf8f1

Added comments describing KINC, WUP, TKICE, NUMCD, ICESF, and RADCD

Update vdiff_mod.F90

f112a76

Replaced log(State_Met%RADCD(I,J,L)*2d0) by log2R

Update state_grid_mod.F90

e293141

Changed grid box width at the center to grid box width at the southern, northern, western, eastern edges

Update gc_grid_mod.F90

37f8f41

Calculate grid box widths by using longitudes and latitudes at edges

Update vdiff_mod.F90

fba2b74

Replaced grid box widths at center with grid box widths at edges

Update state_grid_mod.F90

693a4e2

Changed DXS(NX,NY), DXN(NX,NY), DYW(NX,NY), and DYE(NX,NY) to DXSN(NX,NY+1) and DYWE(NX+1,NY).

Update gc_grid_mod.F90

00fd2af

Calculate DXSN_M and DYWE_M.

Update vdiff_mod.F90

8d22e7b

Using DXSN and DYWE to calculate KINC

Update state_grid_mod.F90

1252234

Optimized the calculation of DXSN and DYWE

1Dandan and others added 24 commits October 7, 2025 14:41

Update CHANGELOG

017f64a

Fix typo in CHANGELOG

fbcc3ce

Update time range for ResMe, HISTORY.rc, and remove unnecessary lines…

868b4e9

… in ExtData

Restore necessary entries in ExtData.rc

e1aca10

Revert back to use GFED daily

1109ce8

Update CHANGELOG

cd1cfed

Updated changelog

d09d7a1

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Fix LPJ wetland path in GCHP carbon ExtData.rc to use HEMCO directory

b06c4ba

The previous path worked only on the Harvard Cannon cluster. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Initial commit of GCHP ctmEnv simulation (skips GEOS-Chem and advection)

843245f

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Rename GCHP run directory README to exclude markdown extension

35b8d6c

README can be ascii Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Add GCHP run script for ctmEnv simulation; make setCommonRunSettings …

87f4954

…match The run script is only in the operational run scripts folder for Harvard for primary use by GCST. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update GCHP rundir creation script for ctmEnv simulation

7db8745

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

lizziel force-pushed the feature/gchp_ctmenv_only_simulation branch from c31d020 to 7db8745 Compare October 29, 2025 18:41

lizziel added 2 commits October 30, 2025 16:59

Update GCHP new HISTORY.rc template to use REAL4 diagnostics for GCHP…

d141646

…ctmEnv Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update GCHP ctmEnv-only run script for recent changes to error handling

74d0fdc

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

yantosca changed the base branch from dev/14.7.0 to main January 30, 2026 17:21

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Add GCHP ctmEnv simulation run directory option#2742

Add GCHP ctmEnv simulation run directory option#2742
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