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GEOS-Chem 14.3.1, HEMCO 3.8.1, and Cloud-J photolysis (new external) #996

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GEOS-Chem 14.3.1, HEMCO 3.8.1, and Cloud-J photolysis (new external) #996

wants to merge 46 commits into from

Commits on Nov 7, 2023

  1. Initial merge of changes for science updates.

    @jimmielin
    jimmielin committed Nov 7, 2023
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  2. Changes to debug output for clarity

    @jimmielin
    jimmielin committed Nov 7, 2023
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  3. Add SO4 to dry/wet "gas" deposition list. 

    This will not affect existing simulations because SO4 would be overwritten with MAM4 aerosols anyway.
But if MAM4 aerosols will not overwrite GEOS-Chem SO4 in proposed changes, then SO4 must be scavenged (similarly to gas) as a bulk tracer by Neu.
    @jimmielin
    jimmielin committed Nov 7, 2023
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  4. Update Neu wetdep to recognize GEOS-Chem bulk sulfate

    @jimmielin
    jimmielin committed Nov 7, 2023
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Commits on Mar 18, 2024

  1. Merge up to latest CESM-GC code

    @jimmielin
    jimmielin committed Mar 18, 2024
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  2. Revert whitespace artifacts from merge

    @jimmielin
    jimmielin committed Mar 18, 2024
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Commits on Apr 1, 2024

  1. Add Cloud-J external and configure build 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  2. Use GEOS-Chem branch dev/14.3.0 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  3. Chemistry driver updates for building with GEOS-Chem 14.3 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  4. Use GEOS-Chem branch off of 14.3 which contains build fixes for CESM 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  5. Set git to ignore Cloud-J external

    @lizziel
    lizziel committed Apr 1, 2024
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  6. Add two new advected species for GEOS-Chem 14.3: FURA, BUTDI 

    FURA is a gas that is both dry and wet deposited. It is thus added to the
master GEOS-Chem gas wetdep and drydep lists.

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  7. Updates GEOS-Chem photolysis data paths to local dir temporarily 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  8. Update externals 

    - Cloud-J is latest dev branch
- Use GEOS-Chem dev branch
- Use CIME tag compatible with GEOS-Chem

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  9. GEOS-Chem species unit conversion updates for compatibility with 14.3 

    GEOS-Chem unit variable is now integer and not string

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  10. Restrict photolysis initialization prints to single thread 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  11. Update Cloud-J external branch; limit henry's law error msg to one proc 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  12. Initial changelog updates 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  13. Update paths to photolysis and aerosol properties data directories 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  14. Removed GEOS-Chem from atm options with CAM40 and CAM50 

    GEOS-Chem compsets only use CAM60

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  15. Update Cloud-J branch and HEMCO_CESM tag in Externals_CAM.cfg 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  16. Update dep_data_file default used for GEOS-Chem 14.3 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  17. Set geoschem_chem_inputs and geoschem_photo_inputs defaults for GEOS-… 

    …Chemn

These paths go to general chemistry inputs (directory CHEM_INPUTS) and
Cloud-J look-up table inputs directory. GEOS-Chem RRTMG LUTs used for
aerosol optical depths are now used from the Cloud-J directory (previously
they were used from a separate FAST_JX directory). The directories
are no longer hard-coded in chemistry.F90 or the use case files.

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  18. Fix bug in buildnml introduced in cam6_3_148 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  19. Fix bug in chemistry.F90 that came in within previous few commits

    @lizziel
    lizziel committed Apr 1, 2024
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  20. Update Externals files to use tagged versions of Cloud-J and GEOS-Chem 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  21. Use slash at end of GEOS-Chem photol dir; add GEOS-Chem dir defaults 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  22. Use most recent CIME version that works with GEOS-Chem 

    Versions after cime6.0.216 do not work due to incorrect directory
string in case setup script.

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  23. Update changelog 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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  24. Merge pull request #28 from jimmielin/hplin/updates_cgc_part2 

    Batch 2 science updates: aerosol distribution fixes
    @lizziel
    lizziel committed Apr 1, 2024
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  25. Update changelog after bringing in latest cam_development and hplin PR 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 1, 2024
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Commits on Apr 23, 2024

  1. Merge remote-tracking branch 'upstream/cam_development' into feature/… 

    …geoschem_14.3

# Conflicts:
#	Externals.cfg
#	bld/configure
#	doc/ChangeLog
    @lizziel
    lizziel committed Apr 23, 2024
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  2. Update changelog post-merge 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 23, 2024
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Commits on Apr 29, 2024

  1. Update HEMCO-CESM to 1.3.0 which contains HEMCO 3.8.1 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. Add fine-grained timers; minor comment fixes

    @jimmielin
    jimmielin committed Apr 30, 2024
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  2. Fix wrong function call

    @jimmielin
    jimmielin committed Apr 30, 2024
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Commits on May 1, 2024

  1. Change GC_ to GEOSChem_ to avoid prefix misunderstandings

    @jimmielin
    jimmielin committed May 1, 2024
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  2. Increase time requested for GEOS-Chem climo tests 

    Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed May 1, 2024
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  3. Update default lower boundary condition file for FCHIST_GC/FCnudged_GC/ 

    New file will enable runs past 2015-01-16.

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed May 1, 2024
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Commits on May 9, 2024

  1. Add MWs for new species FURA and BUTDI to adv_mass in GEOS-Chem mo_si… 

    …m_dat

Signed-off-by: Lizzie Lundgren <[email protected]>
    @lizziel
    lizziel committed May 9, 2024
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Commits on Jun 24, 2024

  1. Fix to emissions unit conversion to kg/m2

    @jimmielin
    jimmielin committed Jun 24, 2024
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  2. Programmatically generate the species list

    @jimmielin
    jimmielin committed Jun 24, 2024
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  3. Merge pull request #33 from jimmielin/feature/timers 

    Detailed process timers for GEOS-Chem chemistry.F90
    @lizziel
    lizziel committed Jun 24, 2024
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  4. Update comments for clarity on the sources of the species lists

    @jimmielin
    jimmielin committed Jun 24, 2024
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  5. Remove comment as separator

    @jimmielin
    jimmielin committed Jun 24, 2024
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  6. Merge pull request #34 from jimmielin/hplin/geoschem_14.3_fixes 

    Fixes for GEOS-Chem v14.3
    @lizziel
    lizziel committed Jun 24, 2024
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