More fixes to substepping of tracers

[Thomas Bendall (tommbendall)]

PR Summary

Sci/Tech Reviewer: James Kent (@jameskent-metoffice)
Code Reviewer: mo-lucy-gordon

This PR adds three further fixes to the stability of the transport scheme when substepping the transport of tracers separately from the main prognostics.

1. The Watkins algorithm takes into account the substepping, by limiting the threshold of intermediate Lipschitz numbers based on the 3D Lipschitz number that will accumulate over the substepping. This avoids the Watkins algorithm "succeeding" only for a negative reference density to be calculated in later.
2. The timestep used for the "wind flux" when initialising the ffsl_precomputations object is incorrect. This caused the wrong stencil extent to be calculated for substepped transport.
3. Ensuring that the total_ref_flux owned by the flux_precomputations object is deallocated, so does not persist between separately initialised instances.

The situations that this occurs in are very rare, and cannot happen in the GC6 science configuration. However they can be seen with the TR-BDF2 timestepper when running at operational resolutions (e.g. 10 km using a 10 minute time step). There is no test in the test suite that generates this situation so no KGOs change.

• Blocked By: Factor timestep out of solver operators #659
• Diff for changes in this PR: https://github.com/tommbendall/lfric_apps/pull/20/changes

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 Apps rose-stem suite
• 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)

trac.log

Test Suite Results - lfric_apps - tracer_substep_more/run2

Suite Information

Item	Value
Suite Name	tracer_substep_more/run2
Suite User	thomas.bendall
Workflow Start	2026-09-29T08:54:33
Groups Run	all

Dependency	Reference	Main Like
casim	MetOffice/casim@2026.07.1	True
jules	MetOffice/jules@2026.07.1	True
lfric_apps	tommbendall/lfric_apps@tracer_substep_more	False
lfric_core	MetOffice/lfric_core@2026.07.1	True
moci	MetOffice/moci@2026.07.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2026.07.1	True
socrates	MetOffice/socrates@2026.07.1	True
socrates-spectral	MetOffice/socrates-spectral@2026.07.1	True
ukca	MetOffice/ukca@2026.07.1	True

Task Information

✅ succeeded tasks - 1594

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Performance Impact

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Sci/Tech Review

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

Code Review

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[github-actions]

⚠️ Hello Thomas Bendall (@tommbendall)!

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.

[James Kent (jameskent-metoffice)]

This PR improves the Watkins algorithm when there is substepping of tracers. The 3D Lipschitz number is now included in the threshold, and the correct dt is used to multiply the transporting_wind in the transport_controller. The code is clear and well commented.

This PR does not change KGOs as these stability issues are very rare and only become apparent in some of the longer GC tests. I am happy to approve.

[Thomas Bendall (tommbendall)]

Closing as these changes will now be included in #733