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101 calculate no photolysis rate constants #183

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101 calculate no photolysis rate constants #183

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K20shores
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@K20shores K20shores commented Dec 18, 2024 •
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Closes #101

Also needed are these two PRs with the configuration files

There are a number of TODOs I still need to figure out, and I'm not really sure how to test this properly. The paper detailing the implemented algorithm doesn't seem to list individual values for Js, and I'm not sure what values they used for their extra terrestrial flux, but that could be a potential testing avenue if we thinks its worth me tracking down values from references.

cacraigucar and others added 30 commits August 15, 2024 12:48
@cacraigucar
Merge pull request #110 from ESCOMP/development
d9d0e5d 
Pull ZM 0.5 timestep removal into main
@nusbaume
Change Liceense to Apache 2.0
fd27d14 
Replace original, locally-developed license with Apache 2.0 license.
@nusbaume
Remove old license file.
592fe83
@jimmielin
Merge pull request #121 from ESCOMP/development
93a1dbf 
Bring in development #108 (TUV-x) #112 (tropopause_find) to main
@nusbaume
Merge pull request #130 from ESCOMP/development
f8ce60b 
Bring in new directory structure from development
@mwaxmonsky
Merge pull request #146 from ESCOMP/development
67927f1 
Upgrading to atmos_phys0_06_000
@K20shores
stubbing out no calculation module and including reference to the ori…
3c575bf 
…ginal paper
@jimmielin
Upgrading to atmos_phys0_07_000 (#158)
e10f811 
Tag name (The PR title should also include the tag name):
`atmos_phys0_07_000`
Originator(s): @jimmielin

List all `development` PR URLs included in this PR and a short
description of each:
* #141 by @mattldawson @boulderdaze 
* #147 by @peverwhee 
* #144 by @mwaxmonsky 
* #151 by @mattldawson 
* #145 by @jimmielin 

List all test failures: N/A
@K20shores
merging main
0b0467c
@K20shores
merging development
5364878
@K20shores
defining arguments
b3941b9
@K20shores
getting index of constituents, I think
dbd5bab
@K20shores
adding comments to explain what's going on
6d6444a
@K20shores
adding sphers
89d5e3f
@K20shores
trying to set densities
57e2942
@K20shores
more densities
c14d9a0
@K20shores
might have finished the setup to actually calculate the rate
6904d58
@K20shores
adding some of the necessary data
4857eb9
@K20shores
adding many functions
2e769a7
@K20shores
maybe most of it is implemented
286f8e5
@K20shores
some compile error fixes
47af226
@K20shores
more things
289b2e9
@K20shores
grrrr this isn't cam
6726a1b
@K20shores
more errors fixed
1ff9ec7
@K20shores
it compiles
ffdc4e3
@K20shores
more comments
9d4f2a6
@K20shores
trying to get things correct
e1fccfa
@K20shores
correcting some dimensions
29bf3bb
@K20shores
correctly setting some values
f2d520a
@K20shores
trying to correct memory leak?
c156c0a
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Hi @K20shores could you change the base branch of this PR to development? It seems like a lot of the diffs unrelated to this PR are showing in the changed files.

I'm happy to review once the PR is out of draft. Thanks!

@K20shores K20shores changed the base branch from main to development December 19, 2024 15:03
@K20shores K20shores marked this pull request as ready for review December 19, 2024 16:49
@cacraigucar cacraigucar removed their request for review January 27, 2025 23:18
@K20shores K20shores requested a review from boulderdaze February 6, 2025 20:20
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Right now there's a memory leak, but I found out that you can pair valgrind with gdb to identify leaks as the process is running.

  1. Build the docker file
    • From the top level docker build -t atmo -f test/docker/Dockerfile.musica.no_install --build-arg CAM_SIMA_CHEMISTRY_DATA_TAG=add_molecular_weight .
  2. Run the container and setup valgrind to wait for gdb
    • docker run --rm -it atmo
    • valgrind --vgdb=yes --vgdb-error=0 ./test_musica_api
  3. Grab the container id and execute a new shell in that container
    • docker ps, copy the ContainerID for the atmo image
    • Start a new shell in that container, docker exec -it 677e9af20b5f /bin/bash, replacing the ID with the one you copied
  4. Start gdb and make it target the valgrind process
    • gdb ./test_musica_api
    • Then, in the prompt, bring up the text user interface
      • tui enable
    • Then, target the valgrind process
      • target remote | vgdb
    • gdb is now connected to a running valgrind process. You can set breakpoints as you wish, or just type continue and gdb will pause whenever valgrind encounters and issue
    • I find it useful to place the two terminals side by side so that you can easily read the valgrind error message beside the source code displayed in gdb
    • Type kill within gdb to stop the valgrind process
    • You can inspect other options gdb now has from valgrind by typing monitor help
      • monitor leak_check will show what leaks exist where you are in the code right now if you're paused on a breakpoint

mattldawson and others added 6 commits February 11, 2025 08:22
@mattldawson
set NO photo rate inside loop over layers
e9605d8
@mattldawson
update chem mechanism commit
99d4e19
@cacraigucar @nusbaume
@jimmielin @mwaxmonsky @mattldawson
Complete Zhang McFarlane conversion to CCPP (#186)
d6336f1 
Originator(s): Cheryl Craig 

Tag: atmos_phys0_08_000

Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue
number):
Add ccpp'ized ZM - closes #66 

Describe any changes made to the namelist:
A       schemes/zhang_mcfarlane/zm_convr_namelist.xml
            - namelist template for ZM

List all files eliminated and why:  N/A


List all files added and what they do:
A       schemes/cloud_fraction/cloud_fraction_fice.F90
A       schemes/cloud_fraction/cloud_fraction_fice.meta
- Bring in the cloud_fraction_fice portion of the cloud_fraction CAM
code and CCPP'ize it

A       schemes/sima_diagnostics/zm_diagnostics.F90
A       schemes/sima_diagnostics/zm_diagnostics.meta
             - Add the main ZM diagnostics
             
A       schemes/sima_diagnostics/zm_convr_tendency_diagnostics.F90
A       schemes/sima_diagnostics/zm_convr_tendency_diagnostics.meta
A       schemes/sima_diagnostics/zm_evap_tendency_diagnostics.F90
A       schemes/sima_diagnostics/zm_evap_tendency_diagnostics.meta
A       schemes/sima_diagnostics/zm_momtran_tendency_diagnostics.F90
A       schemes/sima_diagnostics/zm_momtran_tendency_diagnostics.meta
A       schemes/sima_diagnostics/zm_tendency_diagnostics.F90
A       schemes/sima_diagnostics/zm_tendency_diagnostics.meta
             - Add ZM tendency diagnostics for each ZM component

A       schemes/utilities/to_be_ccppized_temporary.F90
A       schemes/utilities/to_be_ccppized_temporary.meta
- Add a temporary routine to house init methods which aren't being run
with to_be_ccppized code.
             - Add a call to wv_sat_init
             
A       schemes/zhang_mcfarlane/set_deep_conv_fluxes_to_general.F90
A       schemes/zhang_mcfarlane/set_deep_conv_fluxes_to_general.meta
A       schemes/zhang_mcfarlane/set_general_conv_fluxes_to_deep.F90
A       schemes/zhang_mcfarlane/set_general_conv_fluxes_to_deep.meta
- Add interstitials to move variables back and forth from the ZM deep
variables to general variables for the ZM routine which is used in
shallow convection as well
           
A       test/test_suites/suite_zhang_mcfarlane.xml
             - Suite to test ZM
             
A       to_be_ccppized/error_messages.F90
A       to_be_ccppized/namelist_utils.F90
A       to_be_ccppized/wv_sat_methods.F90
A       to_be_ccppized/wv_saturation.F90
- Add methods which ZM requires, but are not being CCPP-ized at this
point in time

List all existing files that have been modified, and describe the
changes:
(Helpful git command: git diff --name-status
development...<your_branch_name>)
M       doc/ChangeLog
M       doc/NamesNotInDictionary.txt
              - updated with ZM names

M       schemes/zhang_mcfarlane/zm_conv_convtran.F90
M       schemes/zhang_mcfarlane/zm_conv_convtran.meta
M       schemes/zhang_mcfarlane/zm_conv_evap.F90
M       schemes/zhang_mcfarlane/zm_conv_evap.meta
M       schemes/zhang_mcfarlane/zm_conv_momtran.F90
M       schemes/zhang_mcfarlane/zm_conv_momtran.meta
M       schemes/zhang_mcfarlane/zm_convr.F90
M       schemes/zhang_mcfarlane/zm_convr.meta
             - Further refinements needed to CCPP'ize ZM
             
M       suites/suite_cam7.xml
             - Add ZM routines to CAM7

List any test failures:

Is this a science-changing update? New physics package, algorithm
change, tuning changes, etc?
- CCPP'ized ZM which was a package which already existed in CAM

---------

Co-authored-by: Jesse Nusbaumer <[email protected]>
Co-authored-by: Haipeng Lin <[email protected]>
Co-authored-by: mwaxmonsky <[email protected]>
@peverwhee @mattldawson
Add diagnostic output for ALL constituents (#199)
b4e2fb7 
Originator(s): peverwhee

Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue
number):
The sima_state_diagnostics scheme only output the "known" constituents.
This PR adds history add and out field calls for ALL other constituents.
I'm open to discussion about the diagnostic names for these!

Describe any changes made to the namelist: n/a

List all files eliminated and why: n/a

List all files added and what they do: n/a

List all existing files that have been modified, and describe the
changes:
(Helpful git command: `git diff --name-status
development...<your_branch_name>`)
M   schemes/sima_diagnostics/sima_state_diagnostics.F90
- add "history_add_field" and "history_out_field" calls for constituents
outside of the core expected ones.

List any test failures: all CAM-SIMA tests pass

Is this a science-changing update? New physics package, algorithm
change, tuning changes, etc? no - diagnostics update
@boulderdaze @mattldawson
Build MUSICA in CAM-SIMA (#198)
9fcf672 
Originator(s): @boulderdaze

Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue
number):
- Closes #196
- Fixed bugs for the CAM-SIMA build

Describe any changes made to the namelist: 
```
M       schemes/musica/musica_ccpp_namelist.xml -> Specified the path to directory for the configuration
```

List all files eliminated and why: N/A

List all files added and what they do: N/A

List all existing files that have been modified, and describe the
changes:
```
M       schemes/musica/musica_ccpp.F90
M       schemes/musica/musica_ccpp.meta
M       schemes/musica/musica_ccpp_namelist.xml
M       schemes/musica/tuvx/musica_ccpp_tuvx.F90
M       schemes/musica/tuvx/musica_ccpp_tuvx_surface_albedo.F90
M       test/musica/test_musica_api.F90
```
List any test failures: N/A

Is this a science-changing update? New physics package, algorithm
change, tuning changes, etc? No
@mattldawson
update test
a605710
@mattldawson mattldawson marked this pull request as draft February 12, 2025 20:42
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@nusbaume nusbaume Awaiting requested review from nusbaume

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@mwaxmonsky mwaxmonsky Awaiting requested review from mwaxmonsky

@peverwhee peverwhee Awaiting requested review from peverwhee

@boulderdaze boulderdaze Awaiting requested review from boulderdaze

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Calculate NO photolysis rate constants
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@K20shores @jimmielin @boulderdaze @cacraigucar @nusbaume @mwaxmonsky @mattldawson @peverwhee