Use default value for initial chemical species mixing ratios

[mattldawson]

Tag name (required for release branches):
Originator(s): Matt Dawson

Description (include the issue title, and the keyword ['closes', 'fixes', 'resolves'] followed by the issue number):
This PR updates to use a newer version of atmospheric_physics that includes setting the default_value of constituent instances created for chemical species based on data in the MICM species configuration files. The updates to CAM-SIMA remove the hard-coded initial species mixing ratios for Terminator and Chapman mechanisms and instead set the initial mixing ratios for chemical species based on the default_value of the corresponding constituent, which allows any mechanism to be run. This is needed to demonstrate the run-time configurability of the chemical system.

@nusbaume - I wasn't sure if the logic for setting default values for constituents should be restricted to chemical species or not. If it makes sense to set this value for any constituent, I can modify this PR, but would need some guidance on where in the workflow to set the default value to avoid overwriting conditions explicitly set in other parts of the code.

Describe any changes made to build system:
updated commits for atmospheric_physics and cam-sima-chemistry-data repos.

Describe any changes made to the namelist:
none

List any changes to the defaults for the input datasets (e.g. boundary datasets):
none

List all files eliminated and why:
musica_sima_namelist.F90 - no namelist parameters are needed for musica now that CAM-SIMA is not restricted to Terminator and Chapman

List all files added and what they do:
none

List all existing files that have been modified, and describe the changes:
(Helpful git command: git diff --name-status development...<your_branch_name>)

File	Description
src/physics/utils/musica_sima_namelist.F90	Removed use of deleted musica namelist module
src/physics/utils/musica_ccpp_dependencies.F90	Replaced hard-coded initial mixing ratios for MICM species with constituent default_value
src/control/runtime_opts.F90	Removed call to musica_ccpp_dependencies_readnl
src/control/cam_comp.F90	Updated set_initial_musica_concentrations call to include properties for accessing default_value
cime_config/atm_musica_config.py	Updated CHEMISTRY_DATA_TAG
.gitmodules	Updated atmospheric_physics submodule tag

If there are new failures (compared to the test/existing-test-failures.txt file),
have them OK'd by the gatekeeper, note them here, and add them to the file.
If there are baseline differences, include the test and the reason for the
diff. What is the nature of the change? Roundoff?
will add after tests are run

derecho/intel/aux_sima:

derecho/gnu/aux_sima:

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:
this should only affect chemistry

CAM-SIMA date used for the baseline comparison tests if different than latest:

[Copilot]

Pull Request Overview

This PR replaces hard-coded initial mixing ratios for chemical species with default values from the updated atmospheric_physics MICM configuration, removes the obsolete MUSICA namelist module, and updates submodule references.

• Remove musica_sima_namelist and namelist reading/calls
• Initialize TUV-x species from hard-coded list and MICM species via default_value
• Update CAM-SIMA init and timestep routines to pass constituent_properties
• Bump submodule tags for atmospheric_physics and cam-sima-chemistry-data

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/physics/utils/musica_sima_namelist.F90	Deleted obsolete namelist module
src/physics/utils/musica_ccpp_dependencies.F90	Replaced MUSICA species logic with TUV-x array and MICM default_value
src/control/runtime_opts.F90	Removed call to musica_ccpp_dependencies_readnl
src/control/cam_comp.F90	Updated set_initial_musica_concentrations call to include properties
cime_config/atm_musica_config.py	Updated CHEMISTRY_DATA_TAG
.gitmodules	Updated atmospheric_physics submodule tag

Comments suppressed due to low confidence (3)

src/physics/utils/musica_ccpp_dependencies.F90:157

• This default_value assignment introduces new behavior for setting initial mixing ratios from MICM species configuration. Consider adding unit tests to verify that default_value is correctly retrieved and applied for all species in micm_species_set.

      call constituent_properties(i_constituent)%default_value( &

src/physics/utils/musica_ccpp_dependencies.F90:51

• [nitpick] The name tuvx_species may not clearly convey that this array holds initial mixing ratios. Consider renaming to something like initial_tuvx_species or tuvx_initial_species for better clarity.

  type(species_t), allocatable :: tuvx_species(:)

src/physics/utils/musica_ccpp_dependencies.F90:147

• The use of FILE and LINE macros may not be supported by all Fortran compilers. Consider using a constant subroutine name parameter or the standard mechanisms (e.g., the ISO_FORTRAN_ENV module) to report file and line information.

      call endrun(errmsg, file=__FILE__, line=__LINE__)

[Copilot]

[nitpick] These two use cam_ccpp_cap statements import symbols from the same module. Consider merging them into a single use cam_ccpp_cap listing both cam_constituents_array and cam_model_const_properties to improve clarity.

Suggested change

	use cam_ccpp_cap, only: cam_constituents_array
	use cam_ccpp_cap, only: cam_model_const_properties
	use cam_ccpp_cap, only: cam_constituents_array, cam_model_const_properties

[jimmielin]

Thanks @mattldawson!

[boulderdaze]

Looks good!

[nusbaume]

Thanks @mattldawson! I pushed up one last change to remove the musica_config namelist variable from the definition file (as the namelist reader for it was already removed), but otherwise it looks good to me!

Also I think for now just setting the initial/default values for the chemical species only is fine, as some CAM physics schemes seem to require specialized initialization logic for their relevant constituent variables, and so until that is all sorted out it is probably safest to keep things separate. Thanks for checking though!