Add KPP Standalone into GEOS-Chem 14.5.1

[yantosca]

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

This PR brings the updates that were formerly in geos-chem PR #2382 and geos-chem PR #2383 into the dev/no-diff-to-benchmark branch. These will ship in 14.5.1.

Expected changes

This is a zero-diff update

Related Github Issue

• Add KPP standalone model to GEOS-Chem 14.5.1 GCClassic#73
• KPP standalone interface from Obin Sturm #2482
• KPP Standalone from Obin Sturm #2483

[lizziel]

We should link to a tag here rather than a branch.

[yantosca]

Thanks @lizziel. I'll do this.

[yantosca]

@lizziel: In commit 0947b8f we now pull from the GC_Interface tag, which is on the geoschem-dev branch.

[submodule "KPP/standalone"]
        path = KPP/standalone
        url = https://github.com/geoschem/KPP-Standalone
        tag = "GC_Interface"

[lizziel]

We should use a version rather than a branch.

[yantosca]

@lizziel: The main branch of the KPP-Standalone repo (which is called kpp-standalone) contains the gckpp_*F90 files that were built by KPP. For the interface to GEOS-Chem, I didn't want to carry these, so I created a new branch geoschem-dev (akin to to the gchp-dev branch in the MAPL fork) so that I wouldn't touch the code in the kpp-standalone branch.

I've merged the kpp-standalone branch into the geoschem-dev branch (but removed the gckpp* etc files). That way the kpp_standalone.F90 and kpp_standalone_init.F90 codes are up to date.

Do you have any other recommendations how we can manage this? I was thinking something like how you manage the MAPL repo but am open to other ideas.

[yantosca]

Changelog updated in commits 0947b8f and f14b9a4

[lizziel]

I don't think these changes are part of this PR.

[yantosca]

Changelog updated in commits 0947b8f and f14b9a4

[lizziel]

Do we need to keep this debug code?

[yantosca]

Removed in 0947b8f

[lizziel]

Rather than use 1 could we use something more descriptive like --force? We should probably also remove restart files to keep only the restart of the current date too, for a true forced rundir clean.

[yantosca]

Thanks @lizzie. The --force argument will work with this script as-is. Basically I test for a non-empty first argument:

#----------------------------------------------------------------------------
# Clean data files in OutputDir.
# These are netCDF files (*.nc) and KPP standalone interface files (*.txt).
#----------------------------------------------------------------------------
if [[ "x${1}" == "x" ]]; then      # User confirmation required
    rm -Iv ./OutputDir/*.nc*
    rm -Iv ./OutputDir/*.txt
else                               # User Confirmation not required
    rm -fv ./OutputDir/*.nc*
    rm -fv ./OutputDir/*.txt*
fi

I've kept the cleanRunDir.sh file as-is but only added the documentation.

I also updated it to remove *.txt files in OutputDir as these would be the KPP interface outputs.

[yantosca]

@lizziel: I would propose to remove the restart files (except for current date) in a future PR. That would involve a little more logic.

[lizziel]

Add this new feature to the changelog

[yantosca]

This was an existing feature but was uncommented. I can add it to the CHANGELOG.

[yantosca]

Now updated in 0947b8f