Fix rare issue with transport of tracers when substepping

[Thomas Bendall (tommbendall)]

PR Summary

Sci/Tech Reviewer: James Kent (@jameskent-metoffice)
Code Reviewer: Yaswant Pradhan (@yaswant)

This PR fixes a rare issue in the transport of tracers, in the situation that tracers are transported consistently (using the dry density flux) but using a new transport controller, because the dry flux used to transport the tracers has been summed over different transport steps. This happens when transporting tracers (a) using the cheap update, (b) on a coarse mesh, or (c) using the TR-BDF2 timestepper introduced in #379.

If the 3D Lipschitz number for the tracer transport is greater than 1, this can trigger the logic to substep the transport. However, this appeared to not be working correctly: the flux_precomputations object should store a ref_field and ref_flux for each stage of the substepped transport (e.g. there would be 6 stages for 2 substeps with VHV splitting), but the model was returning the error:

flux_precomputations%get_ref_mass: step index exceeds number of ref masses stored in this object. If substepping you should pass this an appropriate step into this function

To fix this:

1. In the case that the Watkins algorithm is not used:

• when the total_dry_flux is split into smaller fluxes for different steps, the number of substeps is included to ensure that the factor is appropriate
• the total_dry_flux is set for the flux_precomputations object in case it needs calling in future

2. When the Watkins algorithm is used:

• the Watkins algorithm acts upon the total_dry_flux scaled for a single substep, and the resulting fluxes are then set for all future substeps

This situation does not occur in the test suite, so this PR does not change KGOs.

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 - substep_tracer_fix/run1

Suite Information

Item	Value
Suite Name	substep_tracer_fix/run1
Suite User	thomas.bendall
Workflow Start	2026-03-17T21:28:45
Groups Run	all

Dependency	Reference	Main Like
casim	MetOffice/casim@2026.03.2	True
jules	MetOffice/jules@2026.03.2	True
lfric_apps	tommbendall/lfric_apps@TBendall/substep_tracer_fix	False
lfric_core	MetOffice/lfric_core@2026.03.2	True
moci	MetOffice/moci@2026.03.2	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2026.03.2	True
socrates	MetOffice/socrates@2026.03.2	True
socrates-spectral	MetOffice/socrates-spectral@2026.03.2	True
ukca	MetOffice/ukca@2026.03.2	True

Task Information

✅ succeeded tasks - 1511

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Performance Impact

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• 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)

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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

• All dependencies have been resolved
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• Tests are adequate and have passed
• Documentation is complete and accurate
• Security considerations have been addressed
• Performance impact is acceptable

[James Kent (jameskent-metoffice)]

I have followed through the code and I can see that it now divides the total_flux by the number of substeps, to give an average flux at each substep if the number of substeps is different for tracers and for density.

This bit of code is not tested in the test-suite as it is a rare issue, but as the developer has run the all suite this should have run the C224/C896 lfric_atm tests (if not, I suggest running these just to check everything runs smoothly). I approve this PR.