Remove module scope access of namelist variables by coordinate/native jacobian.

[mo-rickywong]

PR Summary

Sci/Tech Reviewer:
Code Reviewer: @mo-lucy-gordon

As part of work to remove configuration namelist access from module scope, configuration variables will need to be passed
by argument. Configuration variables passed by argument to kernels is more involved, so this PR moves the use _config_mod from the Jacobian routines up to the to the kernel level in preparation of further changes.

The main changes is that namelist configuration variables:

• coord_system
• geometry
• topology
• scaled_radius

Are to be passed by argument jacobian routines, i.e.

call coordinate_jacobian(coord_system, geometry, topology, scaled_radius, &
                         ndf_chi, nqp_h, nqp_v, chi1_e, chi2_e, chi3_e,   &
                         ipanel, basis_chi, diff_basis_chi, jac, dj)

The knock-on of this is a large number of kernels/unit-tests need to be updated in lfric_core and lfric_apps. Aswell as a change to the arguments of init_chi_tranforms called in the unit_tests.

Similar changes, but to a large number of files.

Linked PRs

• Modify LFRic Apps files that call native/coordinate Jacobian files lfric_apps#184

Code Quality Checklist

• I have performed a self-review of my own code
• My code follows the project's style guidelines
• Comments have been included that aid understanding and enhance the readability of the code
• My changes generate no new warnings
• All automated checks in the CI pipeline have completed successfully

Testing

• I have tested this change locally, using the LFRic Core rose-stem suite
• If required (e.g. API changes) I have also run the LFRic Apps test suite using this branch
• If any tests fail (rose-stem or CI) the reason is understood and acceptable (e.g. kgo changes)
• I have added tests to cover new functionality as appropriate (e.g. system tests, unit tests, etc.)
• Any new tests have been assigned an appropriate amount of compute resource and have been allocated to an appropriate testing group (i.e. the developer tests are for jobs which use a small amount of compute resource and complete in a matter of minutes)

Rose test-suite Runs Green

Security Considerations

• I have reviewed my changes for potential security issues
• Sensitive data is properly handled (if applicable)
• Authentication and authorisation are properly implemented (if applicable)

Performance Impact

• Performance of the code has been considered and, if applicable, suitable performance measurements have been conducted

AI Assistance and Attribution

• Some of the content of this change has been produced with the assistance of Generative AI tool name (e.g., Met Office Github Copilot Enterprise, Github Copilot Personal, ChatGPT GPT-4, etc) and I have followed the Simulation Systems AI policy (including attribution labels)

Documentation

• Where appropriate I have updated documentation related to this change and confirmed that it builds correctly

PSyclone Approval

• If you have edited any PSyclone-related code (e.g. PSyKAl-lite, Kernel interface, optimisation scripts, LFRic data structure code) then please contact the TCD Team

Sci/Tech Review

• I understand this area of code and the changes being added
• The proposed changes correspond to the pull request description
• Documentation is sufficient (do documentation papers need updating)
• Sufficient testing has been completed

(Please alert the code reviewer via a tag when you have approved the SR)

Code Review

• All dependencies have been resolved
• Related Issues have been properly linked and addressed
• CLA compliance has been confirmed
• Code quality standards have been met
• Tests are adequate and have passed
• Documentation is complete and accurate
• Security considerations have been addressed
• Performance impact is acceptable