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Updates for GEOS-Chem #2

Merged

lizziel merged 37 commits into main from geos-chem

Mar 18, 2024

Contributor

lizziel commented Apr 28, 2023 •

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Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

This PR brings into the main branch all remaining changes made during development of Cloud-J for use in GEOS-Chem. This includes changes for using GEOS-Chem with Cloud-J photolysis in multiple configurations: GEOS-Chem Classic, GCHP, GEOS, and CESM. It also includes several bug fixes for compatibility with GNU and Intel compilers, and one Cloud-J standalone bug fix for computing ice water path input to Cloud_JX. This PR also includes a change in expected spacing of entries in input file FJX_scat-aer.dat which will affect Cloud-J standalone users who have custom LUTs outside of the ones stored in this repository.

Expected changes

See the Changelog (new file added in this PR) for details of all changes in Cloud-J.

Reference(s)

None

Tagging @pratherUCI for review

lizziel added 17 commits

October 28, 2021 14:53


          Set different values for certain parameters if using GEOS-Chem Classic

c5d4a8a

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


          Change GEOS-Chem compiler definition from GCCLASSIC to GEOSCHEM

80aa9de

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


          Add module variables BRANCH and RNAMES for more photolysis species info

cd90d6b

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


          Pass tables data directory path when initializing Cloud-J

e3d03b0

This update enables storing the tables anywhere on the user's system
rather than in Cloud-J.

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


          Update prints to reduce whitespace printed to log to improve readability

75df703

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


          Compute new global variables RNAMES and BRANCH for species info

d290e28

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


          Explicitly declare subroutines in fjx_sub_mod as public or private

9a3fd51

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


          List Cloud_JX declared args; remove CLDFLAG, LNRG, NRANDO since global

02f5d9d

All Cloud_JX arguments are now listed in an easy to read format. Arguments
CLDFLAG, LNRG, and NRANDO are removed as arguments since they are set
during initialization as global, and remain constant during the run,
and so do not need to be passed for use.

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


          Rename Cloud-J global variable FP to FPAR to avoid conflict in GEOS-Chem

b32c4be

FP is reserved for flexible precision in GEOS-Chem.

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


          Bug fix: initialize REFFLX and REFFLIX for case of CLDFLAG = 1

fe312d9

This fix avoids a run error when using gfortran

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


          Change FJX_scat-aer.dat char width of RAAJ and DAAJ from 6 to 7

b930d81

This update is needed to accomodate values used in GEOS-Chem

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


          Change FJX_scat-aer.dat char width of QAA from 7 to 9, and PAA from 6…

6ca5fa9

… to 7

This update is needed to accomodate values used in GEOS-Chem

This update also includes reformatting this section for more consistent
indenting.

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


          First pass of reformatting files for readability

766472c

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


          Minor updates, including fixing write statement format to fit # GC jv…

13b4b78

…alues

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


          Fix bug in Cloud-J standalone for computing ice water path input to C…

d052d2d

…loud-J

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


          Remove unused inputs to ICA_* subroutines called in Cloud_JX

1929de9

This commit also adds print logical as input argument to some of these
subroutines to be available for debugging.

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


          Update comments in cld_sub_mod for clarity

4d612ea

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

lizziel force-pushed the geos-chem branch from bdf192d to 4d612ea Compare

June 2, 2023 18:44

lizziel and others added 12 commits

October 17, 2023 10:23


          Add clear sky option (compilte-time) for testing

b1b7aec

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


          Add debug logicals for turning on/off ice and liquid water cloud

8e68fee

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


          Remove debugging on/off logicals from fjx_sub_mod.F90

0d83efa

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


          Include compile definition for MODEL_GEOSCHEM when building in GCHP

b27c34b

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


          Updates for using MAPL in Cloud-J

96aa415

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


          Fix ANU declaration after use for ifort compatibility

9f0a5a6


          Merge pull request #4 from jimmielin/hplin/fix_decl_ifort

867a70c

Fix ANU declaration after use for ifort compatibility


          Make number of CTM levels set by the calling program during initializ…

cba1bcd

…ation

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


          Remove unused common variables JXL_, JXL1_, and JXL2_

a546892

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


          Pass root thread logical to init subroutines to limit prints to 1 core

365b488

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


          Merge pull request #5 for branch 'feature/pass_am_I_root' into geos-chem

e683f37


          Updates core files to all use cldj_ prefix and .F90 suffix

aced055

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


          Add GitHub config and PR/issue templates

9adf45d

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

Contributor Author

lizziel commented Mar 1, 2024

Merging this in is on the back-burner because it will break compatibility with the Cloud-J standalone tables files.


          Remove redunction file close; update global var file for clarity

18bc5ba

These are no diff updates

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

Contributor Author

lizziel commented Mar 11, 2024

This PR is almost ready for review. I pushed the latest updates for GEOS-Chem in offline, GEOS, and CESM and now need to address the resulting conflicts in the standalone model.

lizziel mentioned this pull request

Updates for GEOS-Chem 14.3 in CESM geoschem/geos-chem#2154

Merged

lizziel added 4 commits

March 12, 2024 15:35


          Updates for Cloud-J standalone for compatibility with GEOS-Chem changes

417a9ea

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


          Update standalone FJX_scat-aer.dat with format changes

43afee3

Spaces were added in several columns. See github history
or code comments in cldj_init_mod.F90 for details.

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


          Add initialization fix to avoid error detected by gfortran

6fca3e6

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


          Add changelog

8921f2b

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

lizziel force-pushed the geos-chem branch from fbec0e1 to 8921f2b Compare

March 13, 2024 21:03

lizziel marked this pull request as ready for review

March 13, 2024 21:13

lizziel requested review from yantosca and pratherUCI

March 13, 2024 21:14

lizziel added the enhancement label

Contributor Author

lizziel commented Mar 14, 2024

This PR is now ready for review. I confirmed that the changes cause no differences in Cloud-J standalone output when using default settings.

lizziel self-assigned this

yantosca mentioned this pull request

SegFault for test run #8

Closed

yantosca requested changes

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Contributor

yantosca left a comment

Hi @lizziel, thanks for this. I made several minor comments about mostly formatting, precision, and array initialization issues. Let me know if you have any more questions.

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yantosca self-requested a review

March 14, 2024 16:50

Contributor Author

lizziel commented Mar 14, 2024

Thanks @yantosca for your detailed review! I tried to keep the Cloud-J as close to the original as possible to avoid divergence. Your comments will be very helpful when we go through and do general improvements to the code.

@pratherUCI, once we start making general code improvements it will be more difficult to bring in updates you have based on older versions. Would you be able to start working off of this version (once merged) moving forward to avoid problems down the road?

yantosca approved these changes

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Contributor

yantosca left a comment

Thanks @lizziel. I agree, we can make no-diff updates later. No need to hold up this PR. Good to merge!

Collaborator

pratherUCI commented Mar 15, 2024

I went thru all the changes. They make sense and indeed help. I approve.
Michael

There is no reason why the standalone version that I continue to develop could not now begin with the new version.

There are two remaining issues for us:

The next version of Cloud-J standalone is v8.0c, it has been changed (minorly) to include H2O absorption. At the time I also went through all the old commons and removed dead variables (as you did). I will check my list. So how is best to proceed.
BTW, this code enabled me to include NO2 absorption (small effects vs H2O). The major change is in one input table, a few lines of code, and then the clean up. This is not urgent, the only change is the H2O abs.
Prather, Michael (2023). An updated cloud-overlap photolysis module for atmospheric chemistry models, UCI Cloud-J v8.0, with near-UV H2O absorption [Dataset]. Dryad. https://doi.org/10.7280/D1Q398
I have intentionally ignored development for the aerosol code until there was a reason to update. GEOS Chem should have updated aerosol tables that address rel hum, etc. We need someone who is interested in the aerosol simulations and I can work with them.

Michael

Contributor Author

lizziel commented Mar 18, 2024

Hi @pratherUCI, thanks for reviewing the code. I will create a new GitHub issue to discuss putting in the next version of Cloud-J.

lizziel mentioned this pull request

Open

This was referenced Mar 18, 2024

Now use short submodule names in .gitmodules geoschem/GCHP#394

Merged

Now use short submodule names in .gitmodules geoschem/GCClassic#52

Merged

Now use short submodule names in .gitmodules geoschem/HEMCO#266

Merged

lizziel merged commit 3162ea8 into main

2 checks passed

lizziel deleted the geos-chem branch

March 18, 2024 18:53

lizziel mentioned this pull request

Add GCHP_WRAPPER cpp definition geoschem/GCHP#396

Merged

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