GCAFS prep emissions update - fire emissions

[bbakernoaa]

Description

Resolves #3712
Resolves #3827
Resolves #4248

This pull request introduces significant updates to the aerosol configuration and emission handling in the UFS-Aerosols system, streamlining file management, improving modularity, and consolidating configuration files. Key changes include restructuring aerosol configuration files, enhancing biomass burning emissions handling, and updating the chemical input file linking process.

Aerosol Configuration Updates:

• Refactored config.aero.j2 to organize settings into distinct sections for aerosol and emission configurations, including the addition of new variables like AERO_EMIS_FIRE_VERSION and AERO_EMIS_FIRE_HIST. [1] [2]

Emission Data Management:

• Consolidated multiple emission configuration files (ExtData.gbbepx, ExtData.qfed, and ExtData.none) into a single file, AERO_ExtData.rc, for better modularity and maintainability. Removed redundant and unused emission entries. [1] [2] [3] [4]

Chemical Input File Handling:

• Added linking of chemical input files (CHEM_INPUT) in forecast_predet.sh to ensure proper file availability during runtime.

Removal of Legacy Code:

• Removed the automated generation of AERO_ExtData.rc in parsing_namelists_GOCART.sh, as the new consolidated configuration file eliminates the need for dynamic generation.

Additional Updates:

• Updated config.com to include new template paths for chemical restart and input files, improving file organization.

Type of change

• Bug fix (fixes something broken)
• New feature (adds functionality)
• Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

• Is this a breaking change (a change in existing functionality)? NO
• Does this change require a documentation update? NO
• Does this change require an update to any of the following submodules? NO
  • EMC verif-global
  • GDAS
  • GFS-utils
  • GSI
  • GSI-monitor
  • GSI-utils
  • UFS-utils
  • UFS-weather-model
  • wxflow

How has this been tested?

• GCAFS noDA cycled on URSA

Checklist

• Any dependent changes have been merged and published
• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have documented my code, including function, input, and output descriptions
• My changes generate no new warnings
• New and existing tests pass with my changes
• This change is covered by an existing CI test or a new one has been added
• Any new scripts have been added to the .github/CODEOWNERS file with owners
• I have made corresponding changes to the system documentation if necessary

[Copilot]

Pull Request Overview

This pull request updates aerosol configuration and emissions handling for the UFS-Aerosols system by consolidating file management and enhancing modularity. Key changes include:

• Removing legacy logic for generating the AERO_ExtData.rc file and consolidating emission configuration files.
• Adding a link to chemical input files in forecast_predet.sh and updating configuration templates in both aerosol and chemical configuration files.
• Refactoring configuration files to improve clarity and maintainability.

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
ush/parsing_namelists_GOCART.sh	Removed legacy dynamic generation of AERO_ExtData.rc.
ush/forecast_predet.sh	Added linking for CHEM_INPUT to ensure chemical input file availability.
parm/ufs/gocart/ExtData.*	Removed obsolete emission configuration files, consolidating them into AERO_ExtData.rc.
parm/ufs/gocart/AERO_ExtData.rc	Updated emission entries to use chemical input paths and adjusted emission factors.
parm/chem/chem_emission.yaml.j2	Updated templating loops for QFED variables and file copying operations.
dev/parm/config/gfs/config.com	Added new chemical template paths.
dev/parm/config/gcafs/config.aero.j2	Reorganized aerosol sections and introduced new aerosol emission settings.

[DavidHuber-NOAA]

@bbakernoaa I have updated the description of this PR to close #4248 once testing is complete.

[bbakernoaa]

@bbakernoaa I have updated the description of this PR to close #4248 once testing is complete.

Thanks now I need to update this workflow branch to point to this new fix directory right?

[DavidHuber-NOAA]

@bbakernoaa Yes, that's correct.

[bbakernoaa]

@DavidHuber-NOAA this should be ready for the ci tests now.

[DavidHuber-NOAA]

Launching on C6 and WCOSS2.

[DavidHuber-NOAA]

It looks like C6 is not triggering automatically, so I will run it manually.

@DavidHuber-NOAA It looks like you entered the PR number incorrectly:

  echo "Selected machines: ${MACHINES}"
  echo "MACHINES=${MACHINES}" >> "${GITHUB_ENV}"
  shell: /usr/bin/bash -e {0}
  env:
    GH_TOKEN: ***
PR 37133 not found
Error: Process completed with exit code 1.

But will still fail on build on C6 until we update GitHub CLI for checkout PRs

[DavidHuber-NOAA]

@bbakernoaa Can you resolve the conflict in gcafs_tasks.py? The tests have finished building but have not started running on C6 and Cactus, so I can still incorporate this update.

[DavidHuber-NOAA]

The tests are now running on Cactus and C6.

[DavidHuber-NOAA]

@bbakernoaa Tests are failing on WCOSS2 and C6 with the following or similar errors:

^[[38;21m2025-11-25 18:12:11,253 - INFO     - chem_fire_emission: Processing historical emissions for 2021-03-22 12:00:00 to 2021-03-30 00:00:00^[[0m
Traceback (most recent call last):
  File "/lfs/h2/emc/ptmp/david.huber/gw_3713/scripts/exglobal_prep_emissions.py", line 23, in <module>
    fireemis.initialize()
  File "/lfs/h2/emc/ptmp/david.huber/gw_3713/sorc/wxflow/src/wxflow/logger.py", line 252, in wrapper
    retval = func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
  File "/lfs/h2/emc/ptmp/david.huber/gw_3713/ush/python/pygfs/task/chem_fire_emission.py", line 119, in initialize
    aero_emis_fire_version = str(self.task_config.AERO_EMIS_FIRE_VERSION)
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lfs/h2/emc/ptmp/david.huber/gw_3713/sorc/wxflow/src/wxflow/attrdict.py", line 79, in __getattr__
    return self.__getitem__(item)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/lfs/h2/emc/ptmp/david.huber/gw_3713/sorc/wxflow/src/wxflow/attrdict.py", line 84, in __missing__
    raise KeyError(name)
KeyError: 'AERO_EMIS_FIRE_VERSION'

It looks like there is a key missing from a dictionary. Can you check this out and test it locally, please?

[bbakernoaa]

@DavidHuber-NOAA yes I'll test it out asap

[bbakernoaa]

@DavidHuber-NOAA There was two small errors that have been corrected. I did a run on gaeac6 using the ci

./generate_workflows.sh -A bil-fire3 -C -c /gpfs/f6/bil-fire3/world-shared/Barry.Baker/EXPTS/

All jobs passed except the arch since i don't have permission to the default archive directory.