Store aerosol-specific optics files in new Aerosol_Optics data directory #2426

lizziel · 2024-08-15T15:52:31Z

Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

This PR moves the aerosol-specific optics data files (so4.dat, dust.dat, etc) into a new data directory with path specified in the Aerosols menu in geoschem_config.yml. Previously these files were stored in the same data directory as photolysis input files. However, since we now have both FAST-JX (for Hg simulation) and Cloud-J (for fullchem and aerosol sims) we would need to store identical files in two different places. This is not ideal. In addition it may cause confusion since these files are no longer used for photolysis in Cloud-J. Aerosol optical properties used in Cloud-J come from input file FJX_scat-aer.dat.

There are a few additional changes in this PR related to this data:

Move the calls to RD_AOD and CALC_AOD from Init_Photolysis to both Init_Aerosol and Init_FastJX. The former is for use in full chemistry and aerosol-only simulations. The latter is for use in the Hg simulation since it still uses Fast-JX and Fast-JX uses arrays computed by CALC_AOD.
Change the criteria to call Init_Aerosol to be based on simulation type rather than Input_Opt logicals for different aerosols. Init_Aerosol is now always called if using the full chemistry or aerosol-only simulation.

Expected changes

This is a no diff update for all simulations.

Reference(s)

None

Related Github Issue

Closes #2403

lizziel · 2024-08-15T15:52:55Z

This update is ready for review but please do not merge yet. Integration tests are in progress.

yantosca

Thanks @lizziel. This is good to merge. I'll start bringing this in.

yantosca · 2024-08-20T20:24:53Z

I fixed a couple of issues, namely:

ALK4P was missing from the advected species list, now added. This was also done in PR Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) #2318.
Added the aerosol_optics input directory to geoschem_config.yml.Hg in ef88bd7

GCHP integration tests all passed:

==============================================================================
GCHP: Execution Test Results

CodeDir       : 8588f5e GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_
MAPL          : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : 20566e803 Bug fix: Add ALK4P to geoschem_config.yml templates
HEMCO         : 41605bd HEMCO 3.9.3 release
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : d20050f Update version to 7.7.3
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 44256832
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The GEOS-Chem Classic Hg integration test failed because it did not have the path to the new aerosol optics folder specified in geoschem_config.yml. We are re-running the GCClassic integration tests to confirm that the fix in ef88bd7 works.

yantosca · 2024-08-20T21:58:15Z

The GEOS-Chem Classic Hg test now passes due to the fix in commit ef88bd7. The "alldiags" test fails but this will be corrected once merged the 14.5.0 development stream.

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : 8da455b GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_
GEOS-Chem : ef88bd76d Add aerosol optics input dir to geoschem_config.yml.Hg template
HEMCO     : 41605bd HEMCO 3.9.3 release
Cloud-J   : d20050f Update version to 7.7.3
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 44365826
==============================================================================

gc_4x5_merra2_Hg....................................Execute Simulation....PASS
gc_4x5_merra2_fullchem_alldiags.....................Execute Simulation....FAIL

Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 1
Execution tests not yet completed: 0

yantosca · 2024-08-20T22:04:10Z

The updates in this PR were used to create the 1-month benchmark outputs listed on PR #2318. See #2318 (comment).

lizziel · 2024-08-26T16:12:57Z

@yantosca, sorry about that. I fixed the Hg simulation issue locally but forgot to push.

lizziel · 2024-08-26T16:17:53Z

I see there are a bunch of commits due to recent merges in dev/14.5.0. I will update the branch to resolve conflicts.

yantosca · 2024-08-26T17:59:18Z

After merging locally atop PR #2144, all GCClassic integration tests passed, except ModelE2.1:

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : edaa239 GEOS-Chem & HEMCO updates: Merge PR #2318, PR #284, PR #285
GEOS-Chem : 3073aff2e Merge PR #2428 (Fix mass non-conservation in VDIFF)
HEMCO     : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
Cloud-J   : d20050f Update version to 7.7.3
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 44765607
==============================================================================

gc_2x25_ModelE2.1_fullchem..........................Execute Simulation....FAIL

Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 1
Execution tests not yet completed: 0

The failure of the ModelE2.1 is described in #2427.

yantosca · 2024-08-26T18:00:25Z

After merging atop PR #2144 (locally), all GCHP integration tests passed.

==============================================================================
GCHP: Execution Test Results

CodeDir       : 548c753 GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files)
MAPL          : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : 3073aff2e Merge PR #2428 (Fix mass non-conservation in VDIFF)
HEMCO         : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : 37a4ece Update release version number and date
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 44765782
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

These files include so4.dat etc which are read by subroutine Rd_AOD. The new data directory is specified in the aerosol menu of geoschem_config.yml. Signed-off-by: Lizzie Lundgren <[email protected]>

These subroutines must be called even if photolysis is off since they are used for aerosol optical depths. Signed-off-by: Lizzie Lundgren <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

…tion Fast-JX, unlike Cloud-J, uses arrays set in CALC_AOD. Since the Hg simulation uses Fast-JX and does not trigger calling Init_Aerosol we need to call RD_AOD and CALC_AOD during Fast-JX initialization. The Hg simulation is the only simulation that uses Fast-JX and it will be deleted in the future once offline aerosol wet concentration files are available for Cloud-J. Signed-off-by: Lizzie Lundgren <[email protected]>

Previously Init_Aerosol was initialized based on various aerosol logicals. A more robust method is to always call Init_Aerosol for the full chemistry and aerosol-only simulations. Signed-off-by: Lizzie Lundgren <[email protected]>

Somehow these subroutines were not previously removed. Signed-off-by: Lizzie Lundgren <[email protected]>

run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg - Add the the aerosols:optics:input_dir YAML tags to specify the location of the aerosol optics folder. This had been omitted, and was causing the Hg simulation to fail with a file-not-found error. Now fixed. Signed-off-by: Bob Yantosca <[email protected]>

lizziel · 2024-08-26T18:48:38Z

I removed the ALK4P update in this branch since it is unnecessary after rebase on latest dev/14.5.0. Conflicts are now resolved and I am running integration tests.

yantosca · 2024-08-26T19:19:30Z

Thanks @lizziel

lizziel · 2024-08-27T13:47:37Z

All integration tests pass except for gc_2x25_ModelE2.1_fullchem due to a known unrelated issue.

yantosca · 2024-08-27T14:10:08Z

All integration tests pass except for gc_2x25_ModelE2.1_fullchem due to a known unrelated issue.

This should now be fixed going forward. I have recreated the missing file described in #2427.

yantosca · 2024-09-03T17:04:26Z

We have added a hotfix to set Is_Photolysis:true to the species_database.yml, and have rerun integration tests. All GEOS-Chem Classic integration tests passed. This set of tests also includes PR #2424 and geoschem/Cloud-J#24.

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : 930deb9 GEOS-Chem submod update: Merge PR #2436, #2439, #2371 (PPN Phot etc.)
GEOS-Chem : 1951ea96e Hotfix: Declare PPN as photolyzing in the species database
HEMCO     : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
Cloud-J   : 291a161 Update Cloud-J standalone settings to use UV absorption by H2O by default
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 45864046
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

yantosca · 2024-09-03T17:06:09Z

We have added a hotfix to set Is_Photolysis:true to the species_database.yml, and have rerun integration tests. All GCHP integration tests passed. This set of tests also includes PR #2424 and geoschem/Cloud-J#24.

==============================================================================
GCHP: Execution Test Results

CodeDir       : 6d817f8 GEOS-Chem submod update: Merge PR #2436, #2439, #2371 (PPN Phot etc.)
MAPL          : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : 1951ea96e Hotfix: Declare PPN as photolyzing in the species database
HEMCO         : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : 291a161 Update Cloud-J standalone settings to use UV absorption by H2O by default
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 45866935
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

yantosca changed the base branch from main to dev/14.5.0 August 15, 2024 17:52

yantosca self-requested a review August 15, 2024 20:03

yantosca self-assigned this Aug 15, 2024

yantosca added category: Feature Request New feature or request topic: Structural Modifications Related to GEOS-Chem structural modifications (as opposed to scientific updates) no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations labels Aug 15, 2024

yantosca added this to the 14.5.0 milestone Aug 15, 2024

yantosca approved these changes Aug 19, 2024

View reviewed changes

yantosca mentioned this pull request Aug 20, 2024

Adding PPN photolysis #2371

Closed

lizziel and others added 8 commits August 26, 2024 14:42

Store optical properties *.dat files in new data directory

bb2cc85

These files include so4.dat etc which are read by subroutine Rd_AOD. The new data directory is specified in the aerosol menu of geoschem_config.yml. Signed-off-by: Lizzie Lundgren <[email protected]>

Move RD_AOD and CALC_AOD from photolysis module to aerosols module

388db30

These subroutines must be called even if photolysis is off since they are used for aerosol optical depths. Signed-off-by: Lizzie Lundgren <[email protected]>

Call RD_AOD and CALC_AOD within Init_Aerosol subroutine

a436582

Signed-off-by: Lizzie Lundgren <[email protected]>

Update changelog

c746667

Signed-off-by: Lizzie Lundgren <[email protected]>

Remove RD_AOD and CALC_AOD from photolysis_mod

99bfba4

Somehow these subroutines were not previously removed. Signed-off-by: Lizzie Lundgren <[email protected]>

lizziel force-pushed the feature/move_aerosol_optics_files branch from ef88bd7 to 75d885d Compare August 26, 2024 18:44

This was referenced Sep 3, 2024

Support for Cloud-J version 8.0.0 #2424

Merged

Feature/cloudj v8 geoschem/Cloud-J#24

Merged

yantosca merged commit 647c9f5 into dev/14.5.0 Sep 3, 2024

yantosca deleted the feature/move_aerosol_optics_files branch September 3, 2024 17:11

msulprizio mentioned this pull request Sep 25, 2024

Store aerosol *.dat files in new data directory CHEM_INPUTS/Aerosol_Optics #2403

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Store aerosol-specific optics files in new Aerosol_Optics data directory #2426

Store aerosol-specific optics files in new Aerosol_Optics data directory #2426

lizziel commented Aug 15, 2024 •

edited

Loading

lizziel commented Aug 15, 2024

yantosca left a comment

yantosca commented Aug 20, 2024

yantosca commented Aug 20, 2024

yantosca commented Aug 20, 2024

lizziel commented Aug 26, 2024

lizziel commented Aug 26, 2024 •

edited

Loading

yantosca commented Aug 26, 2024

yantosca commented Aug 26, 2024 •

edited

Loading

lizziel commented Aug 26, 2024

yantosca commented Aug 26, 2024

lizziel commented Aug 27, 2024

yantosca commented Aug 27, 2024

yantosca commented Sep 3, 2024

yantosca commented Sep 3, 2024

Store aerosol-specific optics files in new Aerosol_Optics data directory #2426

Store aerosol-specific optics files in new Aerosol_Optics data directory #2426

Conversation

lizziel commented Aug 15, 2024 • edited Loading

Name and Institution (Required)

Describe the update

Expected changes

Reference(s)

Related Github Issue

lizziel commented Aug 15, 2024

yantosca left a comment

Choose a reason for hiding this comment

yantosca commented Aug 20, 2024

yantosca commented Aug 20, 2024

yantosca commented Aug 20, 2024

lizziel commented Aug 26, 2024

lizziel commented Aug 26, 2024 • edited Loading

yantosca commented Aug 26, 2024

yantosca commented Aug 26, 2024 • edited Loading

lizziel commented Aug 26, 2024

yantosca commented Aug 26, 2024

lizziel commented Aug 27, 2024

yantosca commented Aug 27, 2024

yantosca commented Sep 3, 2024

yantosca commented Sep 3, 2024

lizziel commented Aug 15, 2024 •

edited

Loading

lizziel commented Aug 26, 2024 •

edited

Loading

yantosca commented Aug 26, 2024 •

edited

Loading