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

[Ricky Wong (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

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[mo-lucy-gordon]

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

Done. Ricky Wong (@mo-rickywong)

[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.

[Andrew Coughtrie (andrewcoughtrie)]

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

[Thomas Bendall (tommbendall)]

Should this be removed instead of being commented out?

[Thomas Bendall (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.

[Ricky Wong (mo-rickywong)]

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.

Sorry about the lack of opportunity, from the API point of view. Other than from a code owner perspective, I wasn't sure what a SciTech reviewer would add over Code Review + Code Owners Review. Though I accept that's not my call to make, sorry again.

[Ricky Wong (mo-rickywong)]

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.

I think Thomas Bendall (@tommbendall) is right, left over comments, good spot. Left overs happen on this changes on lots of files

[Thomas Bendall (tommbendall)]

Thanks for making those changes!