Fix writing and reading coupled checkpoints

[Tim Graham (timgraham-Met)]

PR Summary

Sci/Tech Reviewer: Mike Hobson (@mike-hobson)
Code Reviewer: mo-marqh

Checkpointing in the coupled model was broken at apps3.0 when the functionality was implemented to output checkpoints at any time step. This branch fixes that functionality and ensures that in coupled mode checkpoints can only be output at coupling timesteps when it won't affect the results of the model.

• linked Fix coupled checkpointing lfric_core#376

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)

This development has been tested in the GC6 climate workflow (it won't run without it). There are plans in place to improve testing of the coupled model including testing restartability but we would like to fix the broken behaviour more quickly.

trac.log

Test Suite Results - lfric_apps - apps_fix_cpl_chkpt/run1

Suite Information

Item	Value
Suite Name	apps_fix_cpl_chkpt/run1
Suite User	tim.graham
Workflow Start	2026-05-20T10:19:36
Groups Run	all

Dependency	Reference	Main Like
casim	MetOffice/casim@2026.03.1	True
jules	MetOffice/jules@2026.03.1	True
lfric_apps	timgraham-Met/lfric_apps@fix_cpl_chkpt	False
lfric_core	timgraham-Met/lfric_core@fix_cpl_chkpt	True
moci	MetOffice/moci@2026.03.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2026.03.1	True
socrates	MetOffice/socrates@2026.03.1	True
socrates-spectral	MetOffice/socrates-spectral@2026.03.1	True
ukca	MetOffice/ukca@2026.03.1	True

Task Information

✅ succeeded tasks - 1511

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Performance Impact

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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

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PSyclone Approval

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Sci/Tech Review

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

[Mike Hobson (mike-hobson)]

This change (along with its core companion) fixes the checkpointing within coupled runs, so is important to get on main. It is clear and easy to understand code. There are some bits that we might want to think about improving in the future, but nothing important enough to delay getting this into the next LFRic release.

I am happy to approve this.

[Mike Hobson (mike-hobson)]

(Note: Tim Graham (@timgraham-Met) - I did a test merge onto main and ran the test suite and didn't see the failure you mentioned to me, so hopefully it will just go away when the change is brought up to head)

[iboutle]

Just one comment from me - this list is essentially a mix of things which are coming from coupler to atmosphere, and things going from atmosphere to coupler (the latter being the list of fields we need to checkpoint in gungho_model_mod). I wonder if it would make it easier to understand if the list were ordered as such, ie. group the fields coming in together (with a heading comment), and group the fields going out together (again with a heading comment)