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HEMCO 3.12.0 release#351

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yantosca merged 70 commits intomainfrom
release/3.12.0
Feb 6, 2026
Merged

HEMCO 3.12.0 release#351
yantosca merged 70 commits intomainfrom
release/3.12.0

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@yantosca yantosca commented Feb 5, 2026 •
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Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

This PR seeks to merge the release/3.12.0 branch into main in anticipation of the HEMCO 3.12.0 release.

The release/3.11.1 branch contains

  • Commits from the dev/no-diff-to-benchmark branch
  • Commits from the docs/dev branch
  • Updated version numbers to 3.11.0 in the usual places.

Expected changes

  • Added DustL23M extension
  • Removed DustDEAD, DustGinoux esxtensions

Related GitHub issue

Integration tests are running

yantosca and others added 30 commits July 29, 2025 17:42
@yantosca
Add "Lint" GitHub action to check for errors in other actions
ad310da 
.github/workflows/lint-ci-workflows.yml
- Configuration file for a GitHub action that will run Zizmor
  on all GitHub action YAML files in .github/workflows to check
  for various errors

README.md
docs/source/index.rst
- Updated GitHub badges: Removed Pre-release, added alt tags

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Removed folder with Azure Dev Pipelines configuration files
ed95301 
.ci-pipelines/*.yml
- Removed configuration files for tests on Azure Dev Pipelines,
  many of these were broken anyway

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Add "persist-credentials: false" to GitHub actions
8d100f9 
.github/workflows/mac.yml
.github/workflows/ubuntu.yml
.github/workflows/windows.yml
- Add "persist-credentials: false" to the "actions/checkout@v4"
  task, so that the GitHub credentials will be not be made
  available to other tasks.  This was a security issue identified
  by the "Lint" action.
- Also run the action for if the branch matches "dev", "dev/**",
  "release", or "release/**"

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge PR #339 (Add "Lint" GitHub action)
8dbae83 
This merge brings PR #339 (Add "Lint" GitHub action to check for
errors in other actions #339, by @yantosca) into the HEMCO
"no-diff-to-benchmark development stream.

PR #339 does the following:

1. The lint-ci-workflows action now runs when updates are
   made to the main and dev/* branches.

2. We have removed the .ci-pipelines folder, which contained the
   configuration files for the Microsoft Azure Dev Pipelines C-I tests.
   Many of these were broken anyway.

3. The windows, mac, and ubuntu GitHub actions have been updated to
   fix security issues. These actions now also run when pushes or
   pull requests are made to dev or release branches.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Update geos-chem-shared-docs to 331f989
2c87185 
This commit informs the HEMCO superproject about the following
commits that were pushed to the geos-chem-shared-docs submodule:

331f989 Update ESMF version in spack/packages.yaml to 8.6.1
4679349 Mention that the aerosol-only sim cannot simulate NH4-NO3-SO4 aerosols

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs submod update to cdc2304 (TransportTracers doc)
7922be6 
This commit informs the HEMCO superproject about the following
commits that were pushed to the geos-chem-shared-docs submodule:

cdc2304 Update TransportTracers simulation page

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs submod update to 804cc68
c1ae75a 
docs/source/geos-chem-shared-docs:
- Updated to 804cc68 (Update nested grid info...)

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs submod update to c9dcd33 (Remove Is_Advected)
10f7119 
This commit informs the GCHP superproject about the following
commits that were made to the geos-chem-shared-docs submodule:

c9dcd33 Remove Is_Advected from species-guide.rst
8f21a5c Fix typos in pm25-pm10-guide.rst
79a1e38 Added PM2.5 and PM10 supplemental guide

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs submod update to 3a38902
58cb064 
This commit informs the HEMCO superproject about the following
commits that were pushed to the geos-chem-shared-docs submodule:

3a38902 Make clear that nested grid & GCAP2 data are on different portals

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@lizziel
Modify for GCHP IMI perturbation runs
e92d516
@1Dandan @lizziel
Update to use REAL type for srcGMaskID
860db55
@1Dandan @lizziel
Update CHANGELOG
ef68faf
@yantosca
Change options to heading 2 in extensions.rst
89a5061 
docs/source/hco-ref-guide/extensions.rst
- In the list of environmental fields used by HEMCO, change
  options to Heading 2, for accessibility purposes.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge PR #330 (Select gridded scale facs based on mask ID)
a7df90f 
This merge brings PR # 330 (Add capability of selecting gridded scaling
factors based on mask ID (needed for IMI with GCHP), by @1Dandan into
the HEMCO 3.12.0 development stream.

PR #330 is a companion fix to select gridded scaling factor based on
state vector ID from a gridded state vector file.  This was based on
the unused feature of using mask for a scaling factor, and thus would
not interfere with current HEMCO practices.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Promote options to Heading 2 or Heading 3
a5e8510 
docs/source/hco-sa-guide/config-sim.rst
- Add "Run directory configuration files" as Heading 2
- Change option list to a list of Heading 3 entries

docs/source/hco-sa-guide/login-env.rst
- Change OMP_NUM_THREADS from an option to a Heading 3
- Change OMP_STACKSIZE from an option to a Heading 3
- Update links to OMP_NUM_THREADS and OMP_STACKSIZE sections accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-doc submod update to 59850be
08a9b66 
The docs/source/geos-chem-shared-docs repo now points to commit
59850be ("Updated doc/geoschem-config.rst" and "doc/spec-db.rst")

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-doc submod update to 1714833
3a6e866 
The docs/source/geos-chem-shared-docs repo now points to commit
1714833 (Update "Build required software with spack" guide")

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-submod update to 8cc346e (Add doc about restart file)
ca5d6f9 
docs/source/geos-chem-shared-docs
- Submod has been updated to 8cc346e.  Documentation has been added
  to doc/hemco-config.rst to make it more clear that users need to
  change the time cycle flag if the run dies due to restart.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Add word wrapping functionality to hco_chartools_mod
fa98584 
src/Core/hco_chartools_mod.F90
- Added routines HCO_CountMatches and HCO_WordWrapPrint

src/Core/hco_error_mod.F90
- Subroutines HCO_Error and HCO_Warning now call HCO_WordWrapPrint
  so that messages will be wrapped at 78 characters
- In HCO_Error, we now print the location string (if THISLOC is passed)
  after the main message (instead of all together)

CHANGELOG.md
- Updated accordingly
@yantosca
Rewrite "cannot find field for simulation time" error message
2349e69 
src/Core/hcoio_read_std_mod.F90
- Added subroutine IO_ErrMsg to replace the current confusing
  "Cannot find field for simulation time" error message with a
  more explicit message.  If the error occurs for a GEOS-Chem
  restart file, the user is directed to take further action by
  editing the time cycle flags in HEMCO_Config.rc.
- Replaced vague error messages (e.g. "ERROR 4") with descriptive ones.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Move word wrap code to break a circular dependency
b67e0a1 
src/Core/hco_chartools_mod.F90
- Removed the routines HCO_CountMatches and HCO_WordWrapPrint, as this
  was causing a circular dependency

src/Core/hco_error_mod.F90
- Added HCO_CountMatches and HCO_WordWrapPrint as PRIVATE routines

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Fixed typo in comments of hco_error_mod.F90
fb8d0f5 
src/Core/hco_error_mod.F90
- "s" -> "as"

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge PR #345 (Rewrite the "cannot find field for current time" error…
12da969 
… msg)

This merge brings PR #345 (Rewrite the "cannot find field for current
simulation time" error with specific instructions for the user to take,
by @yantosca) into the HEMCO 3.12.0 development stream.

PR #345 This PR seeks to reduce the confusion among GEOS-Chem Classic
by rewriting the "Cannot find file for current simulation time" error
with specific steps that the user can take to get past the error.  It
also adds  word-wrap functionality into src/Core/hco_chartools_mod.F90
so that error messages can be wrapped at 78 characters for better
readability.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Squashed commit of the following:Merge PR #312 (Adding a new dust emi…
7ca8dea 
…ssion scheme into HEMCO)

This merge brings PR #312 (Adding a new dust emission scheme
into HEMCO, by @1Dandan) into the feature/7-dust-bins branch.
This will allow us to test further and add any necessary fixes
before merging into the HEMCO 3.12.0 development stream.

This merge squashes the following commits:

commit 7fa1662
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Sun Apr 6 20:27:57 2025 -0400

    update

commit ad9c7cf
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 17 17:00:57 2025 -0500

    update config

commit 52025d8
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 17 16:28:39 2025 -0500

    Config for GEOSIT

commit 07e6afa
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 17 14:19:48 2025 -0500

    MERRA2 config

commit 9b48a1e
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 17 11:57:17 2025 -0500

    Add annotation for using SNOMAS instead of SNODP

commit d6e34d0
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 17 11:43:39 2025 -0500

    MERRA2 config for DustL23M

commit 3a01a69
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 17 11:29:48 2025 -0500

    MERRA2 config for DustL23M

commit 394ab32
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 14 14:32:06 2025 -0500

    update

commit 2058a8f
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 14 14:25:22 2025 -0500

    update

commit b8a1545
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 14 13:25:41 2025 -0500

    update

commit 4605003
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 14 13:20:17 2025 -0500

    test

commit 097be96
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 14 13:00:02 2025 -0500

    test

commit 4a605a3
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 14 12:55:28 2025 -0500

    test

commit da484ab
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 18:06:45 2025 -0500

    test

commit ab447f0
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 17:52:30 2025 -0500

    test

commit 77efa34
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 17:45:30 2025 -0500

    test

commit 2e71061
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 17:41:08 2025 -0500

    test

commit 6eeae48
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 17:24:29 2025 -0500

    test

commit c7d623e
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 17:05:55 2025 -0500

    test

commit 8c6e299
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 16:48:24 2025 -0500

    update

commit eb7c69d
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 16:41:24 2025 -0500

    update

commit 8b3a8e0
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:37:04 2025 -0500

    update

commit f80a9e3
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:34:19 2025 -0500

    update

commit 8326c2a
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:27:24 2025 -0500

    update

commit 0b4bf2c
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:19:18 2025 -0500

    update

commit 87e875a
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:17:50 2025 -0500

    update

commit 1d3554f
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:03:13 2025 -0500

    update

commit 2bcc764
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 12:01:20 2025 -0500

    update

commit 8e1349d
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 11:50:54 2025 -0500

    update

commit f87a17e
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 11:48:15 2025 -0500

    update

commit 8caafbd
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 11:46:22 2025 -0500

    update

commit 1ea0062
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 13 11:43:10 2025 -0500

    update

commit afda648
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 17:28:04 2025 -0500

    update

commit 98bd123
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 17:25:52 2025 -0500

    update

commit d597e4f
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 16:59:14 2025 -0500

    update

commit 0f62388
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 16:24:11 2025 -0500

    update

commit e5a0465
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 15:27:33 2025 -0500

    update

commit 7ecc0e8
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 15:08:02 2025 -0500

    update

commit 3cc82f8
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 15:07:20 2025 -0500

    update

commit a800558
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:52:44 2025 -0500

    update

commit fb03ab1
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:43:33 2025 -0500

    update

commit 99ed6d5
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:39:30 2025 -0500

    update

commit 57d85ef
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:25:58 2025 -0500

    update

commit 45d4895
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:20:07 2025 -0500

    update

commit cc23785
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:10:38 2025 -0500

    update

commit c5351c6
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 14:09:08 2025 -0500

    update

commit 073221b
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 13:59:18 2025 -0500

    update

commit 64e4b75
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 13:53:04 2025 -0500

    update

commit 965f17f
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Wed Mar 12 13:04:18 2025 -0500

    update

commit 05d768f
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 20:58:00 2025 -0500

    update

commit 65be75b
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 20:52:02 2025 -0500

    update

commit 368767f
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 20:38:04 2025 -0500

    update

commit 1b4be74
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 20:32:38 2025 -0500

    update

commit ae133c5
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 20:28:33 2025 -0500

    update

commit 45bbbc7
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 19:53:15 2025 -0500

    update

commit 88a972d
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 14:47:27 2025 -0500

    update

commit 5ad484d
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 14:25:36 2025 -0500

    update

commit 229f637
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Tue Mar 11 14:17:19 2025 -0500

    update

commit 6060161
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 10 17:57:40 2025 -0500

    update

commit 9bc9104
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 10 17:47:40 2025 -0500

    update

commit d588a47
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 10 13:58:37 2025 -0500

    update

commit 1542c38
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 10 12:58:39 2025 -0500

    update

commit 80333b6
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 10 12:57:38 2025 -0500

    update

commit fda1ee5
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Mon Mar 10 12:23:46 2025 -0500

    update

commit 8398906
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Sat Mar 8 15:16:57 2025 -0600

    update

commit 09e47fd
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 17:01:26 2025 -0600

    update

commit 274cb07
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 16:21:17 2025 -0600

    update

commit 5e53bfb
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 15:50:04 2025 -0600

    update

commit 1ac5cea
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 15:34:17 2025 -0600

    update

commit 6358c26
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 15:12:37 2025 -0600

    update

commit 72c5ac5
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 15:05:37 2025 -0600

    update

commit 5428b03
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 14:48:40 2025 -0600

    update

commit aa2c580
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 14:26:09 2025 -0600

    update

commit 77eebe1
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 14:16:32 2025 -0600

    update

commit af4241a
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 14:14:18 2025 -0600

    update

commit 844209d
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Fri Mar 7 14:10:04 2025 -0600

    HEMCO config for using DustL23M

commit 00b5030
Author: Dandan Zhang <dandan.z@wustl.edu>
Date:   Thu Mar 6 18:07:37 2025 -0600

    Add modified DustL23 dust emission scheme

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Added descriptive error messages in ExtStateInit
89c10de 
src/Extensions/hcox_state_mod.F90
- In routine ExtStateInit, updated the error messages from e.g.
  "ERROR 0 to "Could not allocate ExtState%U10M", etc.
- Cosmetic changes (indentation, whitespace removal)

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Add clarifying comments for ExtState%T2M and ExtState%TS
8b46b75 
src/Extensions/hcox_state_mod.F90
- Keep both ExtState%T2M and ExtState%TS, but add clarifying comments.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Update hcox_dustl23m_mod.F90 for clarity and efficiency
1be2f0e 
src/Extensions/hcox_dustl23m_mod.F90
- Removed assignment statements that set module pointers to NULL,
  as this will declare those pointers as SAVEd
- Updated comments and added subroutine comment headers where needed
- Fixed indentation
- Trimmed trailing whitespace
- Repositioned comments to keep most source code within 80 columns,
  for improved readability
- Declared several local variables that are private to loops as scalars
  rather than arrays, in order to save memory (esp. at high resolution)
- Added more descriptive error messages
- Broke up long equations into multiple terms so that we can test
  if divisions or exponentiations can be done safely
- Use ExtState%TSKIN instead of ExtState%TS
- Added SQ_RT_2 parameter to hold the value of SQRT(2) to avoid
  repeated computation
- Added ONE_THIRD parameter to hold the value of 1/3 to avoid
  repeated computation
- PBLH now points to HcoState%Grid%PBLHEIGHT%Val
- PS now points to HcoState%Grid%PSFC%Val

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Evaluate PBLH in the run phase of HEMCO standalone, plus other fixes
c904e82 
run/HEMCO_sa_Spec.rc
- Updated to be consistent with the new DSTbin* etc. species

src/Interfaces/Standalone/hcoi_standalone_mod.F90
- Now call HCO_SetPBLm in routine HCOI_SA_RUN so that the PBL height
  will evolve with time during a HEMCO standalone run
- Use the name "SNOMAS" instead of "SNOWHGT" when updating the
  ExtDat%SNOWHGT field in the HEMCO extension state object
- Cosmetic changes (indentation, whitespace, comments)

src/Extensions/hcox_dustl23m_mod.F90
- Cosmetic changes (indentation)

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Make sure cleanRunDir.sh is copied to HEMCO standalone rundirs
c7159f7 
run/cleanRunDir.sh
- Updated comment headers (to be consistent with GEOS-Chem)
- Removed GCHP-specific text

run/createRunDir.sh
- Add a statement to copy the cleanRunDir.sh script to the HEMCO
  Standalone run directory that is being created

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Parallelize loops in hcox_dustl23_mod.F90
0a3c780 
src/Extensions/hcox_dustl23m_mod.F90
- Add !$OMP PARALLEL statements to 2-D loops over grid boxes
- Replaced error messages such as "ERROR 3", "ERROR 4" with
  more descriptive messages
- No longer set ExtState%PBLH%DoUse, we get the PBL height now
  from Hcox
- Cosmetic changes (whitespace, indentation, alignment)

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs update: Fixed species list in fullchem.rst
a3e83c7 
This commit informs the HEMCO superproject about the following
commits that were pushed to the geos-chem-shared-docs submodule.

81560a7 Added fixes to species list in simulations/fullchem.rst
5d58359 Updated "editing_these_docs.rst"; now use a Conda env to build RTD

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs update: Fix incorrect info in editing_these_doc…
4214766 
…s.rst

docs/source/geos-chem-shared-docs
- Update workflow in editing_these_docs.rst so that the "make clean"
  commands are issued while sphinx-autobuild is running.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Added DustL23M; removed DustDead and DustGinoux from HEMCO RTD
2e42079 
docs/source/hco-ref-guide/hco.bib
- Removed extraneous comma from Zhang et al 2021 citation
- Added Zhang et al 2025 citation for DustL23M
- Removed Ginoux et al 2001 citation

docs/source/hco-ref-guide/extensions.rst
- Replaced DST{1..4} species names with DSTbin{1..7}
- Replaced DSTAL{1..4} species names with DSTALbin{1..7}
- Removed references to DustGinoux and DustDead
- Added description of DustL2m, plus links

docs/source/geos-chem-shared-docs
- Submodule update to b05026b (Remove obsolete options
  from geoschem-config.rst)

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-submod update to 5b56a42
23aa2ca 
docs/source/geos-chem-shared-docs
- Updated to 5b56a42 (Update supplemental guides for dust species
  etc. in 14.7.0)

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
RTD updates: Replace GCClassic-only refs w/ URL links
d8b94f8 
docs/source/geos-chem-shared-docs
- Submod update to 1ba5a65 (Replace refs to GC-Classic Horizontal
  grids with links)

docs/source/hco-ref-guide/under-the-hood.rst
- Removed ref to DustDead extension

docs/source/index.rst
- Added gcid-special-portals.rst to toctree

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Update HEMCO Standalone dry-run documentation
86a1ad0 
docs/source/hco-sa-guide/config-sim.rst
- Update HEMCO Standalone rundir directory listing
- Add note that you can generate a HEMCO_sa_Spec.rc file
  with GCPy example script make_hemco_sa_spec.py

docs/source/hco-sa-guide/hco-sa-dry-run.rst
- Add explicit instruction to activate and deactivate the GCPy
  Python environment
- Removed references to Mamba
- Make it more explicit that AWS CLI transfer is faster than HTTP
- Cleaned up the skip-download section

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Updated HEMCO standalone dry-run instructions
816aa22 
docs/source/hco-sa-guide/intro.rst
- Changed title to "Introduction to the HEMCO Standalone"

docs/source/hco-sa-guide/hco-sa-dry-run.rst
- Added explicit instructions about activating and
  deactivating the GCPy Python environment
- Move the "Skip download, but create log of unique files" into
  the previous section

docs/source/geos-chem-shared-docs
- Submod update to d857e27

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Further HEMCO ReadTheDocs documentation updates
6c385a3 
docs/source/hco-ref-guide/intro.rst
- Changed the Heading 1 title to "Introduction to HEMCO"

docs/source/hco-sa-guide/compiling.rst
- Convert options to Header 3 subsections
- Added a list table

docs/source/hco-sa-guide/config-sim.rst
- Added named anchors
- Replaced leftover option links with refs
- Now point to GCPy example for creating a HEMCO_sa_Spec.rc file

docs/source/hco-sa-guide/hco-sa-dry-run.rst
- Edited sentences for clarity
- Fixed broken ref link in list table

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge PR #336 (Add 7 dust bins in HEMCO)
f4715d0 
This merge brings PR #336 (Merge PR #312 (7 dust bins in HEMCO)
up to 3.12.0 and add necessary fixes/updates #336, by @yantosca
and @1Dandan) into the GEOS-Chem 14.7.0 development stream.

PR #336 is the is the companion PR to #312 by @1Dandan, which adds
a new HEMCO extension for dust (DustL23M). The original PR was based
off version 3.10.2, which lagged behind the current state of HEMCO.
PR #336 "merges up" PR #312 to a a branch off the main (3.11.2)
branch.  We have also removed the DustDead and DustGinoux HEMCO
extensions.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
geos-chem-shared-docs update to f8fe324 (StateMetLevEdge warning box)
3ec8211 
docs/source/geos-chem-shared-docs
- Submod update to f8fe324
  (Warn that LevelEdgeDiags is renamed to StateMetLevEdge)

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>cd
@yantosca
geos-chem-shared-docs update to 03078d4 (PM2.5, PM10 in older versions)
da94747 
geos-chem-shared-docs
- Submod update to 03078d4, add new documentation for PM2.5 and PM10
  in versions prior to 14.7.0

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Now sum DELPDRY in the vertical instead of averaging it
4def204 
src/Core/hco_interp_mod.F90
- Added logical variable do_sum, which is set to T if "DELPDRY" is
  found in the variable name, or F otherwise
- Pass do_sum as the 8th argument to routine COLLAPSE
- In routine COLLAPSE, set the averaging weights (WGT) to 1 for all
  levels if do_sum = T.  This will sum the variable in the vertical
  rather than average it.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge PR #349 (Now sum DELPDRY when regridding from 72 -> 47 layers)
16b499b 
This merge brings PR #349 (Now sum DELPDRY in the vertical instead of
averaging it when regridding from 72 -> 47 layers, by @yantosca and
@ltmurray) into the GEOS-Chem 14.7.0 development stream.

PR #349 adds a fix so that the Met_DELPDRY restart file variable is
summed in the vertical instead of averaged when regridding from 72
levels to 47 levels.  This fixes an issue first raised by @ltmurray
in geoschem/geos-chem#3170.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge branch 'dev/3.12.0' into release/3.12.0
a905b2c 
This merge brings updates from the dev/3.12.0 branch into the
release/3.12.0 branch, in anticipation of the HEMCO 3.12.0 release.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Merge branch 'docs/dev' into release/3.12.0
034dcb5 
This update brings documentation updates in the "docs/dev"
branch  into the "release/3.12.0", branch, in anticipation
of the HEMCO 3.12.0 release.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Changed version numbers to 3.12.0
52074e2 
Updated version numbers to 3.12.0 in the following files:

- CMakeLists.txt
- docs/source/conf.py
- hco_error_mod.F90
- CHANGELOG.md

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca self-assigned this Feb 5, 2026
@yantosca yantosca added category: Feature Request New feature or request topic: Releases HEMCO releases labels Feb 5, 2026
@yantosca yantosca changed the title Release/3.12.0 HEMCO 3.12.0 release Feb 5, 2026
@yantosca yantosca mentioned this pull request Feb 5, 2026
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yantosca commented Feb 5, 2026 •
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All GEOS-Chem Classic integration tests passed:

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : 02c9c0d Updated version numbers to 14.7.0
GEOS-Chem : e669fbfe3 Hotfix: Use 14.7.0 restart files for fullchem, tagO3, TransporTracers
HEMCO     : 52074e2 Changed version numbers to 3.12.0
Cloud-J   : 1dff6fe Merge pull request #31 from geoschem/release/8.0.2
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 38

Submitted as SLURM job: 59123706
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

All GEOS-Chem Classic tests were zero-diff w/r/t gcc.14.7.0-alpha.18, except

  • Using updated restart files taken from the 1-year carbon simulation
    benchmarks for GEOS-Chem 14.7.0 caused differences in these tests:

    • gc_4x5_merra2_carbon
    • gc_4x5_merra2_carbon_CH4
    • gc_4x5_merra2_carbon_CH4_straddle_00z
    • gc_4x5_merra2_carbon_CO2
    • gc_4x5_merra2_carbon_dryrun
    • gc_4x5_merra2_carbon_OCS

  • Using updated restart files taken from the 1-year TransportTracers
    benchmarks for GEOS-Chem 14.7.0 caused differences in these tests:

    • gc_4x5_merra2_TransportTracers
    • gc_4x5_merra2_TransportTracers_dryrun
    • gc_4x5_merra2_TransportTracers_LuoWd

  • Using updated restart files taken from the 1-year fullchem benchmarks
    for GEOS-Chem 14.7.0 caused differences in these tests:

    • gc_05x0625_NA_47L_merra2_fullchem
    • gc_4x5_47L_merra2_fullchem
    • gc_4x5_merra2_fullchem
    • gc_4x5_merra2_fullchem_aciduptake
    • gc_4x5_merra2_fullchem_alldiags
    • gc_4x5_merra2_fullchem_APM
    • gc_4x5_merra2_fullchem_APM_dryrun
    • gc_4x5_merra2_fullchem_benchmark
    • gc_4x5_merra2_fullchem_benchmark_dryrun
    • gc_4x5_merra2_fullchem_complexSOA
    • gc_4x5_merra2_fullchem_complexSOA_SVPOA
    • gc_4x5_merra2_fullchem_dryrun
    • gc_4x5_merra2_fullchem_LuoWd
    • gc_4x5_merra2_fullchem_marinePOA
    • gc_4x5_merra2_fullchem_RRTMG
    • gc_4x5_merra2_fullchem_RRTMG_dryrun
    • gc_4x5_merra2_tagO3_dryrun
    • gc_4x5_merra2_aerosol
    • gc_4x5_merra2_aerosol_dryrun

All GCHP integration tests passed:

==============================================================================
GCHP: Execution Test Results

CodeDir       : c35c62f Updated version numbers to 14.7.0
MAPL          : d1d528e5 Merge pull request #39 from geoschem/feature/mapl_2.55.0
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : 01bbf2f Merge pull request #9 from geoschem/feature/turn_off_f2py_builds_in_gchp
FMS           : 259759d1 Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : 348620f Merge PR #11 (Scale tracers by pressure ratio in first timestep)
geos-chem     : e669fbfe3 Hotfix: Use 14.7.0 restart files for fullchem, tagO3, TransporTracers
HEMCO         : 52074e2 Changed version numbers to 3.12.0
Cloud-J       : 1dff6fe Merge pull request #31 from geoschem/release/8.0.2
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables
GFE           : bac529f Merge pull request #40 from Goddard-Fortran-Ecosystem/feature/mathomp4/update-gftl-1.15.2

Number of execution tests: 12

Submitted as SLURM job: 59125665
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

All GCHP tests were zero-diff w/r/t gchp.14.7.0-alpha.18 except:

  • Using updated restart files taken from the 1-year carbon simulation
    benchmarks for GEOS-Chem 14.7.0 caused differences in these tests:

    • gc_4x5_merra2_carbon
    • gc_4x5_merra2_carbon_CH4
    • gc_4x5_merra2_carbon_CH4_straddle_00z
    • gc_4x5_merra2_carbon_CO2
    • gc_4x5_merra2_carbon_dryrun
    • gc_4x5_merra2_carbon_OCS

  • Using updated restart files taken from the 1-year TransportTracers
    benchmarks for GEOS-Chem 14.7.0 caused differences in these tests:

    • gchp_merra2_TransportTracers

  • Using updated restart files taken from the 1-year fullchem benchmarks
    for GEOS-Chem 14.7.0 caused differences in these tests:

    • gchp_merra2_fullchem
    • gchp_merra2_fullchem_alldiags
    • gchp_merra2_fullchem_benchmark
    • gchp_merra2_fullchem_RRTMG
    • gchp_merra2_tagO3

This was referenced Feb 5, 2026
Merged
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@yantosca yantosca marked this pull request as ready for review February 6, 2026 18:43
@yantosca yantosca requested a review from msulprizio February 6, 2026 18:56
@yantosca
geos-chem-shared-docs submod update to 03078d4
d111240 
Updated the geos-chem-shared-docs to the latest point
as of the HEMCO 3.12 release.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca merged commit e23c43b into main Feb 6, 2026
25 of 29 checks passed
@yantosca yantosca deleted the release/3.12.0 branch February 6, 2026 19:39
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