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Jules red veg3 couple soil carbon - #166

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Jules red veg3 couple soil carbon#166
Arthur Argles (mo-arthurargles) wants to merge 15 commits into
MetOffice:mainfrom
mo-arthurargles:jules_red_veg3_couple_soil

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@mo-arthurargles Arthur Argles (mo-arthurargles) commented Sep 16, 2026

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PR Summary

Issue #91 - Couples the existing JULES single layer and multilayer 4 pool soil biogeochemistry model to the veg3/RED component.

Sci/Tech Reviewer:
Code Reviewer:

This branch focuses on coupling the vegetation litterfall input from RED/veg3 into the 4 pool soil model in JULES and the layered 4 pool soil model. This development focuses purely on the carbon cylce, we have yet to get the nitrogen scheme fully coupled with RED - which will be done at a later point (issue: #97).

Code Quality Checklist

(Some checks are automatically carried out via the CI pipeline)

  • 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
  • If editing rose-meta/jules-shared then have you supplied a linked UM and LFRic Apps PR?

Testing

  • I have tested this change locally, using the JULES rose-stem suite
  • If shared files have been modified, I have run the UM and LFRic Apps rose stem suites
  • If any tests fail (rose-stem or CI) the reason is understood and acceptable (eg. kgo changes)
  • I have added tests to cover new functionality as appropriate (eg. system tests, unit tests, etc.)

We still need to develop and add a rose-stem test for veg3 scheme. Linked issue here is #100. However, we need a good scientific basis before this.

There is an evaluation rose suite, u-ec255@367491, for a site in Belgium for JULES-RED which also compares against JULES-TRIFFID. A list of the following tests, for both the single and layeredC models:

  1. Do we get similar behaviour to TRIFFID?
  2. Do we conserve carbon across both soil and vegetation?
  3. Do we get a near identical simulated state after dump restart for the final year of run time?

I will attach a presentation here with the results (TODO).

trac.log

Security Considerations

  • I have reviewed my changes for potential security issues
  • Sensitive data is properly handled (if applicable)
  • Authentication and authorisation are properly implemented (if applicable)

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

Approvals

Please request all relevant approvals. See the CodeOwners.txt file for section owners.

Technical

  • JULES Code Owner
  • OpenMP
  • River Routing
  • Rose Stem
  • Rose Metadata
  • Upgrade Macros

Scientific

  • Surface
  • Hydrology
  • Vegetation
  • [] Veg3 RED Demography
  • Biogeochemistry
  • Biogenic fluxes
  • Fire
  • Lakes
  • Evaluation
  • Imogen

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

@mo-arthurargles
Couple veg3 to JULES phenology scheme and add RED diagnostics (MetOff…
c193294 
…ice#90)

- Add veg3_phenol_couple to run phenology on its own timestep and diagnose the mean phenology-driven leaf turnover rate driving litter/RED dynamics, replacing the lai_bal-only estimate
- Thread a_step and new phenology period controls (nstep_phen, dt_phen_360d) through veg3_ctrl/next_gen_biogeochem
- Use veg3 lai/canht/leafC/woodC/lai_bal in sparm, cancap and sf_stom instead of TRIFFID lai_bal estimates when l_red is set
- Add pointer associations for new veg3/RED diagnostic outputs (npp_dr_out, g_leaf_phen, g_leaf_phen_acc, lai_phen, litter fluxes) into trifctl/trif_vars
- Refactor veg3_red_dynamic_mod, splitting growth_onto_mass_class and update_pft_size_structure out of veg3_red_dynamic
- Fix mclass_geom_mult default and mort_base unit conversion in veg3_param_mod

Refs MetOffice#90
@mo-arthurargles
For MetOffice#90, fix bug with the re-initillisation of phenological …
7af5d8c 
…state. Deleted redundant bits of code we don't need to get phenology correctly estimated in veg3_field_mod.F90. Tests now pass umpd3_checker and rose stem tests.
@mo-arthurargles
Adding my name to contributors.
b338a2f
@mo-arthurargles
Fxing typo in GitHub username.
916cd6e
@mo-arthurargles
Merge branch 'main' into jules_red_veg3_couple_phenology
e1b23fb
@mo-arthurargles
Changes address comments from PR GitHub co-pilot for issue MetOffice#90:
58c3039 
1. In phenol_jls.F90 set in variable lai_bal_red to be be REAL(KIND=real_jlslsm) to ensure consistency between other REAL inputs.
2. From veg3_field_mod.F90, remove frac_old from red_veg3_couple_mod.F90 not necessary for this change and not used in the script.
@mo-arthurargles
Uploading changes to hopefully fix the coupling with UM in JULES shar…
a0fcfe5 
…ed routines related to veg3_field_mod.F90.
@mo-arthurargles
Fixing a few issues after Copilot review in MetOffice/pull/160 (MetOf…
52258c0 
…fice#90). Added veg3_field_deallocate during veg3_field_assoc, such that we avoid potential memory issues with pointer when associating with prognostic & diagnositic variables. Fixed typos and inconsistencies with mort_litC description.
@mo-arthurargles
Using umdp3_fixer.py to fix veg3_red_dynamic_mod.F90.
44006fe
@mo-arthurargles
Updating code so we could output more diagnostics related to leaf tur…
b9a659a 
…nover (g_leaf, g_leaf_day, g_leaf_dr_out). Related issue MetOffice#90.
@mo-arthurargles
Merge branch 'MetOffice:main' into jules_red_veg3_couple_soil
5d4959e
@mo-arthurargles
Updating to ensure that "g_leaf_dr_out" is in consistent units for di…
51393ae 
…agnostic purposes, while having a seperate "g_leaf_dr" in turnover per second.
@mo-arthurargles
Merge branch 'MetOffice:main' into jules_red_veg3_couple_phenology
6980dc5
@mo-arthurargles
Merge remote-tracking branch 'origin/jules_red_veg3_couple_phenology'…
ecd59dd 
… into jules_red_veg3_couple_soil
@mo-arthurargles
Merging jules_red_veg3_couple_phenology into jules_red_veg3_couple_so…
5c806bd 
…il (MetOffice#91).
@mo-arthurargles Arthur Argles (mo-arthurargles) added the enhancement New feature or request label Sep 16, 2026
@github-actions github-actions Bot added the cla-signed The CLA has been signed as part of this PR - added by GA label Sep 16, 2026
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Autumn 2026

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Couple Soil Carbon Biogeochemistry into veg3/JULES-RED

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