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commits that were pushed to the GitHub geoschem/geos-chem repository:

e61a51064 Merge GCHP hotfix from PR #2363 on top of PR #2359

This PR implements a hotfix for an issue that had caused GCHP
cloud benchmarks to fail.

Signed-off-by: Bob Yantosca <[email protected]>

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ef2ea60e7 Merge PR #2315 (Fix bugs in PDER, OCPISOA, and TotalOC)

This PR fixes several minor bugs in the complex SOA scheme.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings the GCHP 14.4.2 release into the GCHP
14.5.0 development stream.  14.4.2 is a zero-diff update.  The
CHANGELOG.md has been updated accordingly.

Signed-off-by: Bob Yantosca <[email protected]>

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e29a4c928 Merge PR #2398 (Pass non-zero Ca2, Mg, and K cations to HETP)

PR #2398 uncomments setting Ca2+, K+, and Mg+ cation values passed
to HETP. Previously these values were zero due to an issue in ISORROPIA.
With the update to HETP we can enable these cations.

Signed-off-by: Bob Yantosca <[email protected]>

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0a392d465 Merge PR #2352 (Fixes for ALK4 and R4N2 chemistry from J. Brewer)

R4N2 was a common product of alkane, isoprene, and monoterpene oxidation
and produced organonitrate SOA but we don’t want ALK4 to produce
organonitrate SOA as discusses in #1625. A fix from Jared Brewer is
included in this PR.

Signed-off-by: Bob Yantosca <[email protected]>

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acd335486 PR #2352 post-merge fix: Rebuild fullchem solver files

This PR restores the updated KPP solver files for PR #2352 (ALK4 and
R4N2 chemistry updates, by @JFBrewer).

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings all of the updates from the GEOS-Chem 14.4.3
"no-diff-to-benchmark" release back into the dev/14.5.0 branch.
We will test this merge with its own alpha benchmark.

Signed-off-by: Bob Yantosca <[email protected]>

This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

8f0a16767 PR #2425 post-merge fix: Move 14.4.3 entry to top of CHANGELOG.md

This PR moves a CHANGELOG.md entry for 14.4.3 to its proper place.

Signed-off-by: Bob Yantosca <[email protected]>

This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

586260f10 PR #2318 post-merge fix: Use less drydep fields for the alldiags test
f240c993f PR #2318 post-merge fix: Remove duplicate EmisHCOOH_Total entry
53f9b2e82 PR #2318 post-merge fix: Add missing species to geoschem_config.yml
dd7ba9a9c Merge PR #2318 (Chemistry for RCOOH, ANs, PNs)

and the geoschem/HEMCO repository:

d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
1c6356d Merge PR #285 (Add em. factors for ALK6, C4H6, EBZ, STYR, TMB)
253b0fc Merge HEMCO 3.9.3 back into the 3.10.0 development stream
f2b6ae4 Merge PR #284 (Fix inconsistent pressure units in HEMCO standalone)

These PRs implement new chemistry (from @ktravis213), emissions (from
@kelvinhb), and a bug fix for the HEMCO standalone.

Signed-off-by: Bob Yantosca <[email protected]>

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commits that were pushed to the GitHub geoschem/geos-chem repository:

3073aff2e Merge PR #2428 (Fix mass non-conservation in VDIFF)
c7332ed7a Merge PR #2144 (Restore drydep output in fullchem benchmarks)

This PR does the following:

1. Adds the DryDep collection to all fullchem_benchmark runs
2. Implements a mass conservation fix in VDIFF PBL mixing by
   @nicholasbalasus.  See issue #2409 for details/

Signed-off-by: Bob Yantosca <[email protected]>

docs/source/geos-chem-shared-docs
- Changed compiler from [email protected] to [email protected] in guides

docs/source/user-configuration-files.rst
docs/source/user-guide/rundir-init.rst
docs/source/user-guide/running.rst
- Updated formatting and fixed issues flagged by Sphinx

Signed-off-by: Bob Yantosca <[email protected]>

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commits that were pushed to the GitHub geoschem/geos-chem repository:

602b660c1 PR #2436 post-merge update: Fix typo in ExtData.rc.fullchem
d34c567a4 Merge PR #2436 (Update GFED4 climatology for 2010-2023)
d4c47babf Merge PR #2439 (Update run scripts and env files for Discover)
43d0e9083 Merge PR #2371 (Adding PPN photolysis)

This implements photolysis for the PPN species.  Also, two other
no-diff-to-benchmark updates have been added, namely updating run scripts
for NASA discover and updating the GFED4 climatology file.

Signed-off-by: Bob Yantosca <[email protected]>

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1951ea96e Declare PPN as photolyzing in the species database
40a078514 Merge PR #2424 (Support for Cloud-J_v8.0.0)
647c9f579 Merge PR #2426 (Store aerosol-specific optics files in new directory)

and to the geoschem/Cloud-J repository:

291a161 Update Cloud-J standalone settings to use UV absorption by H2O by default
6a027b1 Merge pull request #24 from geoschem/feature/cloudj_v8

These PRs move aerosol optics configuration files to a separate folder
(out of the CHEM_INPUTS/FAST-JX folder structure) and update Cloud-J
to version 8.0.0.

Signed-off-by: Bob Yantosca <[email protected]>

docs/requirements.txt
- Use jinja 3.1.4 as there is a dependabot security warning for
  the previous version 3.1.3.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

…exact)

This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

6bf4a36 Merge pull request #26 from geoschem/feature/define_max_rather_than_exact_num_jvalues

This PR fixes an issue where Cloud-J will stop reading entries from
FJX_j2j.dat before the "9999" end-of-file marker.

Signed-off-by: Bob Yantosca <[email protected]>

…ANs)

This commit informs the GCHPsuperproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

a5fba9c88 Merge PR #2452 (Reorder photo rxns for PNs and ANs)

This PR reorders the photo rxns of the PN and AN species added by
@ktravis213 in PR #2318, so that they now follow PPN in the
FJX_j2j.dat configuration file for Cloud-J.

Signed-off-by: Bob Yantosca <[email protected]>

This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

cd0366015 Merge PR #2457 (Update Is_Photolysis tags in species_database.yml)

This PR ensures that photolyzing species (as listed in the KPP
fullchem.eqn and FJX_j2j.dat files) have "Is_Photolysis.true" tags
in the species_database.yml file.  Non-photolyzing species have
had these tags removed.  Also the JValues collection in the GCHP
HISTORY.rc.fullchem file has been updated.

Signed-off-by: Bob Yantosca <[email protected]>

This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

c0aeff427 Merge PR #2462 (Bug fix: ALK6 in HEMCO_Config.rc should be ALK7)
5c31c3470 Merge PR #2430 (Updated Y. Wang soil NOx scheme as an option)

and the geos-chem/HEMCO repository

c6a9d46 Merge PR #287 (Updated Y. Wang soil NOx scheme as an option)

This PR does the following:

  1. Implements the U. Iowa soil NOx scheme as an option.
     This is currently switched off by default.

  2. Adds a bug fix in HEMCO configuration files: ALK6 should
     be called ALK7.

Signed-off-by: Bob Yantosca <[email protected]>

Signed-off-by: Melissa Sulprizio <[email protected]>

…salt in aerosol thermodynamics)

Signed-off-by: Melissa Sulprizio <[email protected]>

The stale workflows are currently failing with the error:

    Invalid workflow file: .github/workflows/stale.yml#L26
    The workflow is not valid. .github/workflows/stale.yml (Line: 26, Col: 11): A sequence was not expected

To fix this, the list of exempt-issues-labels in .github/workflows/stale.yml
must be a  comma separated list. A single quote is placed around the list to
allow for use of colons in label names.

Signed-off-by: Melissa Sulprizio <[email protected]>

…ag burning emissions)

Signed-off-by: Melissa Sulprizio <[email protected]>

…oir emissions)

Signed-off-by: Melissa Sulprizio <[email protected]>

…ub workflow

Signed-off-by: Melissa Sulprizio <[email protected]>

…lt Ca, Mg, K)

Signed-off-by: Melissa Sulprizio <[email protected]>

Signed-off-by: Melissa Sulprizio <[email protected]>

Signed-off-by: Melissa Sulprizio <[email protected]>

- Now point to geoschem_config.yml, HEMCO_Config.rc, and HEMCO_Diagn.rc,
  species_database.yml, and aerosol/chem/photolysis configuration files
  in the documentation in geos-chem-shared-docs/doc folder
- Updated the configuration file overview page accordingly
- Now use ".. option::" tags for easier searching of items
- Reformatted text using ReST best practices
- Trimmed trailing whitespace

Signed-off-by: Bob Yantosca <[email protected]>

docs/source/user-guide/config-files/cap_restart
- Updated the text so that it flows better and is less awkward

Signed-off-by: Bob Yantosca <[email protected]>

docs/source/geos-chem-shared-docs
- Added GCHP vs. GCC usage differences section in HEMCO_Diagn.rc doc

docs/source/user-guide/configuration-files.rst
- Now use reference links to the setCommonRunSettings.sh doc in the
  NOTE at the top of the page
- Now split the configuration files into "Commonly-updated configuration
  files" and "Less commonly-updated configuration files" to make it
  clear that some config files don't normally need to be updated
  except under certain circumstances.
- Trimmed whitespace

Signed-off-by: Bob Yantosca <[email protected]>

docs/source/geos-chem-shared-docs:
- Fixed typo ":ref:`ExtData.rc`" -> ":file:`ExtData.rc`"

Signed-off-by: Bob Yantosca <[email protected]>

Signed-off-by: Melissa Sulprizio <[email protected]>

…ulation

- geos-chem: Merge PR #2492 fixes for GCHP carbon simulation
- MAPL: Merge PR #37 conatining fix to vertically flip imports with dimensionless pressure proxy lev coordinates

Signed-off-by: Melissa Sulprizio <[email protected]>

This commit informs the GCHP superproject about the following
commits that were pushed to the geos-chem-shared-docs repository:

65b2a35 Merge "docs/update_guides_for_gchp" into "main"
7f0cfbb Merge PR #3 (Add doc/tutorial for GEOS-Chem input data on AWS)

These are documentation updates for the 14.5.0 release.

Signed-off-by: Bob Yantosca <[email protected]>

Current MAPL does not reliably build with GCC 13.

Signed-off-by: Lizzie Lundgren <[email protected]>

docs/source/geos-chem-shared-docs
- Submodule update to cd0f4ad, w/ recent doc updates for 14.5.0

docs/source/getting-started/quick-start.rst
- Add "Important" box for GEOS-FP convection
- Now use consistent $ prompt in examples

docs/source/index.rst
- Update toctree link to the GEOS-Chem Input Data on AWS, which
  was renamed to geos-chem-shared-docs/doc/gcid-portal-overview.rst

docs/HEMCO_Config.rc
docs/HEMCO_Diagn.rc
- Removed; Documentation for these is in geos-chem-shared-docs now

docs/source/user-guide/config-files/HISTORY.rc
- Fixed incorrect option name: "ref_date:" -> "ref_date"

docs/source/user-guide/config-files/setCommonRunSettings.sh
- Fixed incorrect option name: "extdata" -> "extdata-rc"

docs/source/user-guide/debugging.rst
- Added |br| break definition
- Fixed links to the debug-guide and error-guide in geos-chem-shared-docs
- Updated code formatting to fit w/in 80 cols (mostly)
- Trimmed trailing whitespace

docs/source/user-guide/getting-input-data.rst
- Add text and link to new GEOS-Chem Input Data portal doc
- Updated code formatting to fit w/in 80 cols (mostly)
- Trimmed trailing whitespace

docs/source/user-guide/rundir-config.rst
- Removed "-----" breaks
- Updated code formatting to fit w/in 80 cols (mostly)
- Now use proper heading section delimiters
- Trimmed trailing whitespace

docs/source/user-guide/rundir-init.rst
- Add "Important" box for GEOS-FP convection

Signed-off-by: Bob Yantosca <[email protected]>

docs/source/geos-chem-shared-docs
- RTD update: Link to dy-run instructions from GC Input Data doc

Signed-off-by: Bob Yantosca <[email protected]>

This commit informs the GCClassic superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

a8bb552d1 Merge PR #2555 (Dry run updates for GEOS-Chem Classic 14.5.0)
e9d951f Merge PR #295 (Add HEMCO-standalone dry run scripts)

This PR updates the subroutine hashes to GEOS-Chem and HEMCO submodules,
which now have updates for the GEOS-Chem 14.5.0 and HEMCO 3.10.0
dry run simulations.

Signed-off-by: Bob Yantosca <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

Updated version numbers in:
- CHANGELOG.md
- CMakeLists.txt
- docs/source/conf.py

Also updated CHANGELOG.md with the latest information.

Signed-off-by: Bob Yantosca <[email protected]>