Allow substepping of just tracers

[Thomas Bendall (tommbendall)]

PR Summary

Sci/Tech Reviewer: James Kent (@jameskent-metoffice)
Code Reviewer: Ricky Wong (@mo-rickywong)

Some groups of tracers are transported separately from the standard dynamics prognostics, in the following situations:

• in the BDF stage of TR-BDF2 (added in TR-BDF2 Timestepper #714)
• when transporting tracers on a coarser mesh
• when using the cheap update

The transport of these tracers involves resetting and recalculating various quantities that are shared across a transport step. However the process of resetting this hasn't previously involved all of our standard stability mechanisms, and in particular substepping has been missing.

This PR implements that substepping, which has allowed some failures in high resolution, large timestep TR-BDF2 simulations to be avoided. It also highlighted three subtle science/code issues, which this PR fixes in order to get the tracer transport correct for TR-BDF2:

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.

At present this PR does not change KGOs in the test suite, but it will change KGOs once #714 is merged.

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

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

[James Kent (jameskent-metoffice)]

This change allows the substepping of just tracers by extending the check_reference_field function. This will provide an extra layer of stability for certain optional configs. The code looks correct and I'm happy kgos won't change for this PR. Happy to approve

[Thomas Bendall (tommbendall)]

Ricky Wong (@mo-rickywong) this is ready for code review

[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.

[Thomas Bendall (tommbendall)]

Further investigation of the changes in this PR in operational-type runs highlighted more bugs (in existing transport code) that needed fixing in order to get tracer transport working correctly with TR-BDF2.

These changes have been science reviewed separately as #814, but I have merged them into this branch since they are necessary to get the changes in this PR working correctly, and so that the changes are only code reviewed once.