Extra fields need to be written to checkpoint dump for lfric_atm glomap_mode dust_and_clim

[stevemullerworth]

PR Summary

Sci/Tech Reviewer: @alanjhewitt
Code Reviewer: @harry-shepherd

On a new run (NRUN), lfric_atm may read ancillary files some of which contain fixed boundary values. Three of these are dust_mrel, soil_clay and soil_sand, which are used with certain glomap settings. However, continuation runs (CRUNs) do not read such ancillaries. Therefore, the fields need to be written to and read from the checkpoint dump.

Currently, several CRUN tests are therefore running with values for these fields set by initialisation in the code rather than input values. An effect of this is that an NRUN+CRUN will not match the results of an NRUN of the same total length. A failure of a nrun-crun test would show up in the test suite except for the fact that the CRUN in the relevant test is only one timestep long, and differences don't appear in the checksum file till the second timestep.

This fix changes the logic in create_physics_prognostics to additionally read/write these checkpoint fields if glomap_mode is set to dust_and_clim, which affects lfric_atm nwp_gal9 configurations. The change involved some slight reorganisation of the order of the fields to reduce the risk of the checkpoint_flag value being incorrectly overwritten for other fields.

Three of the DA jobs are initialised from checkpoint dumps rather than start dumps. Therefore, the existing checkpoint dumps need to be updated with these fields. Current changes point to an updated file in the developer's data directory. This file would need to be incorporated in BIG_DATA. This new file was generated by using ncks an nco tool to add the three fields to the existing checkpoint dump. I checked with Ian Boutle who was happy with this approach.

Before NRUN/CRUN comparability testing can be improved (to prevent future issues that show up after one timestep) PR #193 also needs to be committed. If #193 is committed, then this issue could extend the length of the nwp_gal9 nrun-crun test to validate this change.

CLA was signed in #193, I expect to merge on main with this change, so won't sign CLA just yet.

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 - checkpoint_dust_forpr2/run3

Suite Information

Item	Value
Suite Name	checkpoint_dust_forpr2/run3
Suite User	steve.mullerworth
Workflow Start	2026-01-30T09:36:39
Groups Run	all

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@2025.12.1	True
lfric_apps	stevemullerworth/lfric_apps@checkpoint_dust	False
lfric_core	MetOffice/lfric_core@2025.12.1	True
moci	MetOffice/moci@2025.12.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True
socrates	MetOffice/socrates@2025.12.1	True
socrates-spectral	MetOffice/socrates-spectral@2025.12.1	True
ukca	MetOffice/ukca@2025.12.1	True

Task Information

✅ succeeded tasks - 1454

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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

• Where appropriate I have updated documentation related to this change and confirmed that it builds correctly

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

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• Tests are adequate and have passed
• Documentation is complete and accurate
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• Performance impact is acceptable

[github-actions]

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[alanjhewitt]

I am happy with the code changes here - they are consistent with the ticket description.

I didnt review the new startdump file, I think Steve may need to get approval from Ian Boutle for this replacement file.

Also, at the time this development is merged tey will need to be put in the official directory.

SciTech approved.

Passing to code review.

[harry-shepherd]

I am happy with the code changes here - they are consistent with the ticket description.

I didnt review the new startdump file, I think Steve may need to get approval from Ian Boutle for this replacement file.

Also, at the time this development is merged tey will need to be put in the official directory.

SciTech approved.

Passing to code review.

@stevemullerworth has got approval from @iboutle regarding this file

[harry-shepherd]

Steve has created a new start dump for this configuration. Following discussion with the SSD team this has been installed in:

$BIG_DATA_DIR/start_dumps/basic-gal/yak/PR202/20210324T0000Z_lfric_ice_dust_t+3.nc