61 extracting inferno hardwired flammability params

[Eleanor Burke (eleanorgb)]

PR Summary

[#61 ]

Sci/Tech Reviewer:
Code Reviewer:

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.)

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

[Copilot]

Pull request overview

This PR restructures JULES fire-related configuration by introducing a dedicated jules_inferno namelist (and module) for INFERNO/TRIFFID fire parameters, while also refactoring several standalone/ancillary routines into proper Fortran modules and tightening some CI/workflow configuration.

Changes:

• Added jules_inferno_mod and migrated INFERNO/TRIFFID fire switches and parameters (e.g., l_inferno, l_trif_fire, z_burn_max, combustion completeness bounds, and new flammability tunables) out of other modules/namelists.
• Added a new PFT parameter fireveg_c_to_atmos(_io) and updated TRIFFID to use it for fire carbon-to-atmosphere partitioning.
• Refactored fire weather index and multiple standalone/imogen routines into module form; updated metadata/docs and hardened GitHub Actions workflows.

Reviewed changes

Copilot reviewed 81 out of 89 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/util/logging_mod.F90	Uses intrinsic ISO_FORTRAN_ENV import form for output/error units.
src/science/vegetation/veg-veg2a_jls_mod.F90	Switches l_inferno/l_trif_fire imports to jules_inferno_mod.
src/science/vegetation/triffid_jls.F90	Replaces hard-coded fire emission fraction with per-PFT fireveg_c_to_atmos.
src/science/vegetation/sow_mod.F90	Wraps sow subroutine in a Fortran module.
src/science/vegetation/soilcarb_layers_jls_mod.F90	Moves fire burn/completeness params to jules_inferno_mod.
src/science/vegetation/soilcarb_jls.F90	Moves fire burn/completeness params to jules_inferno_mod.
src/science/vegetation/partition_mod.F90	Wraps partition subroutine in a Fortran module.
src/science/vegetation/emerge_mod.F90	Wraps emerge subroutine in a Fortran module.
src/science/vegetation/develop_mod.F90	Wraps develop subroutine in a Fortran module.
src/science/vegetation/crop_mod.F90	Updates crop code to USE newly modularised sow/emerge/develop/partition routines.
src/science/params/pftparm_mod.F90	Adds fireveg_c_to_atmos parameter allocation/IO/validation/printing.
src/science/params/pftparm_io_mod.F90	Adds fireveg_c_to_atmos_io namelist plumbing into PFT parameter IO.
src/science/fire/inferno/inferno_mod.F90	Adds new flammability arguments (RH/SM/rain function) and uses jules_inferno_mod ignition inputs.
src/science/fire/inferno/inferno_io_mod.F90	Plumbs jules_inferno_mod flammability params into INFERNO IO call path.
src/science/fire/fire_weather_index/nesterov_mod.F90	Adds new Nesterov index module implementation.
src/science/fire/fire_weather_index/mcarthur_mod.F90	Adds new McArthur FFDI module implementation.
src/science/fire/fire_weather_index/fire_timestep_mod.F90	Adds timestep manager module for daily fire weather index updates.
src/science/fire/fire_weather_index/fire_mod.F90	Renames switch to l_fire_weather_index.
src/science/fire/fire_weather_index/fire_init.F90	Updates init logic to use l_fire_weather_index.
src/science/fire/fire_weather_index/fire_calc_daily.F90	Adds daily calculation module orchestrating McArthur/Canadian/Nesterov models.
src/science/fire/fire_weather_index/fire_allocate.F90	Adds allocation/init module for fire weather index structures.
src/science/fire/fire_weather_index/canadian_mod.F90	Adds Canadian FWI model module implementation.
src/io/dump/required_vars_for_configuration_mod.F90	Updates required-vars logic to l_fire_weather_index.
src/initialisation/um/read_jules_namelists_mod.F90	Adds UM-side reader for jules_inferno namelist.
src/initialisation/standalone/init_vegetation.F90	Removes INFERNO option logging from vegetation init (moved to inferno init).
src/initialisation/standalone/init_vars_tmp_mod.F90	Wraps temporary init routine in a module (standalone build).
src/initialisation/standalone/init_urban_mod.F90	Wraps init_urban in a module (standalone build).
src/initialisation/standalone/init_prescribed_data_mod.F90	Wraps prescribed data init in a module (standalone build).
src/initialisation/standalone/init_mod.F90	Calls new init_inferno and renames fire init call to fire weather index init.
src/initialisation/standalone/init_jules_sf_diags_mod.F90	Imports l_inferno from jules_inferno_mod.
src/initialisation/standalone/init_irrigation_mod.F90	Wraps irrigation init in a module (standalone build).
src/initialisation/standalone/init_inferno_mod.F90	Adds standalone inferno initialisation and logging.
src/initialisation/standalone/init_imogen_mod.F90	Wraps imogen init in a module and adds imogen_check import.
src/initialisation/standalone/init_fire_weather_index_mod.F90	Renames/rewrites standalone fire init into init_fire_weather_index_mod.
src/initialisation/shared/check_compatible_options_mod.F90	Moves z_burn_max/inferno switches to jules_inferno_mod.
src/control/um/diagnostics_hyd.F90	Imports l_inferno from jules_inferno_mod.
src/control/standalone/standalone_control_mod.F90	Wraps standalone control routine in a module and renames entrypoint.
src/control/standalone/jules.F90	Uses standalone_control module procedure; adds imogen update module imports.
src/control/shared/surf_couple_extra_mod.F90	Switches l_inferno and fire weather index flag imports to new modules/flags.
src/control/shared/jules_vegetation_mod.F90	Removes INFERNO-related switches/namelist entries from vegetation module.
src/control/shared/jules_soil_biogeochem_mod.F90	Removes z_burn_max from soil biogeochem namelist; validates via inferno module.
src/control/shared/jules_inferno_mod.F90	New module defining inferno switches/params + namelist read/print/check routines.
src/control/rivers-standalone/rivers_control_mod.F90	Renames rivers standalone control module/subroutine to avoid generic control.
src/control/rivers-standalone/river.F90	Updates driver to call rivers_control.
src/control/imogen/rndm_mod.F90	Wraps rndm in a module for explicit USE.
src/control/imogen/response_mod.F90	Wraps response in a module for explicit USE.
src/control/imogen/radf_non_co2_mod.F90	Wraps non-CO2 radiative forcing routine in a module.
src/control/imogen/radf_co2_mod.F90	Wraps CO2 radiative forcing routine in a module.
src/control/imogen/radf_ch4_mod.F90	Wraps CH4 forcing routines in a module and cleans some locals.
src/control/imogen/pattern_scaling_mod.F90	Wraps pattern scaling in a module.
src/control/imogen/ocean_co2_mod.F90	Wraps ocean CO2 in a module and updates dependency import.
src/control/imogen/invert_mod.F90	Wraps invert in a module for explicit USE.
src/control/imogen/imogen_update_clim_mod.F90	Wraps update clim in a module and adds explicit module dependencies.
src/control/imogen/imogen_update_carb_mod.F90	Wraps update carb in a module and adds explicit module dependencies.
src/control/imogen/imogen_check_mod.F90	Wraps imogen_check in a module for explicit USE.
src/control/imogen/drdat_mod.F90	Wraps drdat in a module for explicit USE.
src/control/imogen/diffcarb_land_co2_mod.F90	Wraps diffcarb land CO2 in a module for explicit USE.
src/control/imogen/diffcarb_land_ch4_mod.F90	Wraps diffcarb land CH4 in a module for explicit USE.
src/control/imogen/diff_atmos_ch4_mod.F90	Wraps diff atmos CH4 in a module and fixes END/subroutine closure.
src/control/imogen/delta_temp_mod.F90	Wraps delta temp in a module and adds explicit dependency import.
src/control/imogen/day_calc_mod.F90	Wraps day calc in a module and adds explicit rndm import.
src/control/imogen/clim_calc_mod.F90	Wraps clim calc in a module and tightens ainfo intent.
rose-stem/app/fab_jules/bin/intel_rivers.json	Updates rivers build list to new fire weather index fire_mod path.
rose-stem/app/fab_jules/bin/gfortran_10_plus_rivers.json	Updates rivers build list to new fire weather index fire_mod path.
rose-meta/jules-um/HEAD/rose-meta.conf	Imports shared inferno metadata; adds trigger for new PFT param.
rose-meta/jules-standalone/versions.py	Adds upgrade macro vn8.2→vn8.2_t61 to migrate settings to new namelists/params.
rose-meta/jules-standalone/HEAD/rose-meta.conf	Imports shared inferno metadata; replaces old fire_switches metadata with jules_fire_weather_index.
rose-meta/jules-shared/jules-vegetation/HEAD/rose-meta.conf	Removes vegetation-level inferno/trif_fire entries (now in inferno metadata).
rose-meta/jules-shared/jules-pftparm/HEAD/rose-meta.conf	Adds metadata for fireveg_c_to_atmos_io.
rose-meta/jules-shared/jules-model-environment/HEAD/rose-meta.conf	Adds trigger for fireveg_c_to_atmos_io.
rose-meta/jules-shared/jules-inferno/HEAD/rose-meta.conf	New shared metadata section defining jules_inferno namelist.
rose-meta/jules-lfric/HEAD/rose-meta.conf	Adds placeholder for fireveg_c_to_atmos_io in LFRic metadata.
etc/fcm-make/make.cfg	Simplifies explicit dependency configuration for standalone jules.F90.
etc/fcm-make/make-river.cfg	Updates prescribed init filename and fire fire_mod path for rivers build.
etc/fcm-make/compiler/cray_12_plus.cfg	Updates compiler override path for renamed prescribed init module file.
doc/source/namelists/pft_params.nml.rst	Documents new fireveg_c_to_atmos namelist member.
doc/source/namelists/jules_vegetation.nml.rst	Removes inferno-related members from vegetation namelist docs.
doc/source/namelists/jules_soil_biogeochem.nml.rst	Removes z_burn_max docs from soil biogeochem namelist docs.
doc/source/namelists/fire.nml.rst	Updates docs to include JULES_FIRE_WEATHER_INDEX and JULES_INFERNO namelists.
doc/pyproject.toml	Adds project URLs metadata for documentation build project.
CONTRIBUTORS.md	Adds contributor entry for eleanorgb.
.github/zizmor.yml	Adds zizmor linter config with targeted rule ignores.
.github/workflows/user-guide.yaml	Hardens workflow (pinned actions, safer env usage, reduced caching/credentials).
.github/workflows/umdp3_fixer.yaml	Pins reusable workflow revision and sets minimal permissions.
.github/workflows/trigger-project-workflow.yaml	Pins reusable workflow revision, tightens permissions, adds repo guard.
.github/workflows/track-review-project.yaml	Pins reusable workflow revision, tightens permissions, adds explicit secret mapping.
.github/workflows/cla-check.yaml	Adds concurrency controls, minimal permissions, pins reusable workflow revision.
.github/workflows/check-cr-approved.yaml	Pins reusable workflow revision and tightens permissions.
.github/pull_request_template.md	Improves template formatting and fixes typos (e.g., “understanding”, “Biogeochemistry”).

Suppressed comments (5)

src/science/fire/inferno/inferno_mod.F90:252

• l_cf_old_inferno is hard-coded to .TRUE., which forces the legacy RH/rain behaviour and makes the newly-plumbed flam_* namelist parameters effectively unused.
  src/science/fire/inferno/inferno_mod.F90:295
• The new rain-suppression branch uses EXP(-flam_rain_const * rain_l). With flam_rain_const constrained to be <= 0.0 in check_jules_inferno, this makes flammability increase with rain (wrong sign).
  src/control/shared/jules_inferno_mod.F90:126
• This ereport call reports the wrong routine name (check_jules_vegetation), which makes errors harder to trace; also errorstatus doesn't need resetting here if it's initialised once.
  src/control/shared/jules_inferno_mod.F90:179
• Allowing flam_fuel_up == flam_fuel_low will later cause a division-by-zero when normalising fuel availability. This check should require a strictly greater upper bound.
  src/science/fire/inferno/inferno_io_mod.F90:320
• Fuel normalisation still uses hard-coded thresholds (0.02/0.2), so the new flam_fuel_low/flam_fuel_up namelist settings are ignored.

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

[Copilot]

Pull request overview

Copilot reviewed 81 out of 89 changed files in this pull request and generated 2 comments.

Suppressed comments (7)

src/control/shared/jules_inferno_mod.F90:118

• errorstatus is not initialised before being passed to ereport in most branches (it is only assigned when ignition_method is invalid). This can cause inconsistent or silent error handling depending on the compiler/runtime state.
  src/control/shared/jules_inferno_mod.F90:129
• flam_sm_func is used as a selector in calc_flam, but the namelist checker does not validate it. If a user sets an unexpected value, calc_flam can use an uninitialised f_sm_l.
  src/science/fire/inferno/inferno_mod.F90:252
• l_cf_old_inferno is hard-coded to .TRUE., which means the new jules_inferno namelist parameters (flam_*) are effectively ignored (relative humidity bounds and flam_rain_const are overridden). This defeats the purpose of extracting these parameters for tuning.
  src/science/fire/inferno/inferno_mod.F90:295
• The new rainfall scaling branch applies EXP(-flam_rain_const * rain_l), but check_jules_inferno requires flam_rain_const <= 0.0. With the leading minus this makes rainfall increase flammability and can overflow. The exponent should be consistent with the sign convention and should use a clearly defined rain unit.
  src/science/fire/inferno/inferno_io_mod.F90:320
• Fuel normalisation is still hard-coded to 0.02/0.2, so the extracted flam_fuel_low/flam_fuel_up tunables are not actually used.
  rose-meta/jules-standalone/versions.py:99
• The upgrade macro sets flam_rhum_low/flam_rhum_up to 0.1/0.9, but the model computes relative humidity in percent (0–100) and check_jules_inferno expects 0–100. This would drastically change behaviour for upgraded apps.

        self.add_setting(config, ["namelist:jules_inferno", "flam_rhum_low"], "0.1")
        self.add_setting(config, ["namelist:jules_inferno", "flam_rhum_up"], "0.9")

doc/source/namelists/fire.nml.rst:169

• The literal word "buggy" in the namelist documentation looks like a placeholder and will ship to users.

buggy