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
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Rose test-suite Runs Green

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Code Review

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[mo-lucy-gordon]

Overall this looks good but I think there are a few duplicated typos - see the code comments.

[mo-lucy-gordon]

Converted to some suggested typo changes. As these are only simple changes I will pass them to Andy to fix so we can get the tickets committed, as Ricky is away.

[github-actions]

⚠️ Hello @mo-rickywong!

Your CLA signature was found on the base branch, but you appear to have modified the CONTRIBUTORS.md file in this PR.

Please do not edit the CONTRIBUTORS.md file. If you have already signed the CLA, revert changes to the file and your signature will be picked up.

[andrewcoughtrie]

I've applied the small number of spelling corrections suggested by review as @mo-rickywong is away and they are very minor changes.

[tommbendall]

Should this commented out line be left here?

[tommbendall]

Suggested change

	call init_chi_transforms(geometry_spherical,&
	call init_chi_transforms(geometry_spherical, &

[tommbendall]

Suggested change

	topology, &
	topology, &

[tommbendall]

Should this be removed instead of being commented out?

[tommbendall]

Should this be removed instead of being commented out?

[tommbendall]

Should this be removed instead of being commented out?

[tommbendall]

Apologies for sticking my oar in, I just got notified about this PR. I realise it's a technical change rather than a science one, but I'm a bit surprised it didn't need a sci/tech reviewer since it changes the API to an important science routine.

I understand the logic for this change though, so have no objections but have spotted some things that need tidying.

[mo-lucy-gordon]

Apologies for sticking my oar in, I just got notified about this PR. I realise it's a technical change rather than a science one, but I'm a bit surprised it didn't need a sci/tech reviewer since it changes the API to an important science routine.

I understand the logic for this change though, so have no objections but have spotted some things that need tidying.

I presumed the comments were deliberate but Ricky is away right now so we can't ask him.