From aec1a2ef602650e6af1a41aa07f7a3725d950680 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 12 Feb 2024 16:08:09 -0500 Subject: [PATCH 01/36] GEOS-Chem submod update: Merge PR #1717 (Use GCARR_ac when B=0) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: aebdaade0 Merge PR #1717 (Use GCARR_ac rate-law function where B=0) This PR updates several rate law functions where the Arrhenius B parameter is zero to use GCARR_ac instead of GCARR_abc. This should result in better efficiency by not having to compute terms that would evaluate to 1. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index b288af156..aebdaade0 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit b288af1563a9a49a154a93bdd0f88be1f58f3f2f +Subproject commit aebdaade06fbfd6b6186883c39862753c34d682e From 9f4965e59a400edafcc2678543f7122e4f1fc956 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 14 Feb 2024 10:59:40 -0500 Subject: [PATCH 02/36] GEOS-Chem submod update: Merge PR #1828 (Diel + DOW scale factors) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geos-chem/geos-chem repository: 9db97fef2 Merge PR #1828 (Diel+DOW scale factors for CEDS) This PR adds updated diurnal and day-of-week scale factors for the CEDSv2 emissions to the HEMCO_Config.rc template files. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index aebdaade0..9db97fef2 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit aebdaade06fbfd6b6186883c39862753c34d682e +Subproject commit 9db97fef2c3b866d574d6fd3df094628958a1640 From cf181828603701aabeeb672216856abd2d5a68f9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 21 Feb 2024 17:11:13 -0500 Subject: [PATCH 03/36] GEOS-Chem submod update: Merge PR #2145 (Updated timezones for HEMCO) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geos-chem/geos-chem repository: 2d9e6c0ed Merge PR #2145 (Implement updated timezones file for HEMCO) This PR switches from using the Voronoi timezones file to the monthly timezone climatology prepared by @karnvoh and @eamarais. This should account for daylight-savings time more accurately when computing emissions. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 9db97fef2..2d9e6c0ed 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 9db97fef2c3b866d574d6fd3df094628958a1640 +Subproject commit 2d9e6c0ed8b0a1506c50cec0654ee7754d2022b2 From 2e516f8383d72176b79351ad8d37a52f77387ad6 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 23 Feb 2024 16:08:14 -0500 Subject: [PATCH 04/36] GEOS-Chem submodule update: Merge PR #1979 (Updated NOAA GMD surface BCs) Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 2d9e6c0ed..6bc16cd99 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 2d9e6c0ed8b0a1506c50cec0654ee7754d2022b2 +Subproject commit 6bc16cd99b2498c0f436ead69abcf6c46a597c00 From 3dbf81edcb08debea923faf15e92b73b0c7f7b56 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 28 Feb 2024 11:17:05 -0500 Subject: [PATCH 05/36] GEOS-Chem submod update: Merge PR #1998 (Rename YAML tags) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geos-chem/geos-chem repository: 66fb61ab1 Merge PR #1998 (Rename YAML tags for aerosol nitrate photolysis ) This PR renames the YAML tags controlling nitrate aerosol photolysis in the geoschem_config.yml.fullchem to more accurately describe what is being requested. This is a zero-diff update but needs to go into 14.4.0 as it touches run-directory configg files. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 6bc16cd99..66fb61ab1 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 6bc16cd99b2498c0f436ead69abcf6c46a597c00 +Subproject commit 66fb61ab1febc2503fcc149ea570a255e2ebf94c From 04bde0c21bfde7167e583d06106aed050842e739 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 29 Feb 2024 10:03:37 -0500 Subject: [PATCH 06/36] GEOS-Chem submod update: Merge PR #2166 (Remove bpch diags ) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geos-chem/geos-chem repository: b0bc778d7 PR #2166 post-merge fix: Remove #ifdef block in read_input_file 7ab17802a Merge PR #2166 (Remove remaining binary punch diagnostics code) This PR removes all remaining legacy binary punch diagnostics code and documentation. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 66fb61ab1..b0bc778d7 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 66fb61ab1febc2503fcc149ea570a255e2ebf94c +Subproject commit b0bc778d70439c7677230e61148249ecf946b6ab From 8383082b8dff1be3fcc46d0c8aadb157d57407c7 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 5 Mar 2024 16:43:41 -0500 Subject: [PATCH 07/36] GEOS-Chem submod update: Merge PR #2176 (UCX bug fixes ) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geos-chem/geos-chem repository: 5f81b6555 Merge PR #2176 (UCX bug fixes) Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index b0bc778d7..5f81b6555 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit b0bc778d70439c7677230e61148249ecf946b6ab +Subproject commit 5f81b6555eeac80df5cb4116f9697b891a4153d7 From 53363f1c4ec31e18475f7f2a1f21f3a8582b0f5c Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Mon, 18 Mar 2024 10:48:36 -0400 Subject: [PATCH 08/36] GEOS-Chem submodule update: Merge PR #2198 (updated volcano emissions) Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 5f81b6555..bf9239d70 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 5f81b6555eeac80df5cb4116f9697b891a4153d7 +Subproject commit bf9239d70615e62ba6aa92a8a7b602f21a67cd0d From d60a8e9141d21809736cfb9dce23e87ceace31b5 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 20 Mar 2024 11:38:20 -0400 Subject: [PATCH 09/36] GEOS-Chem submod update: Merge PR #2205 (Fix uptake on strat aer) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: ced31f725 PR #2205 post-merge fix: Fixed typo in fullchem_RateLawFuncs.F90 3ce4dfbae Updated the changelog for PR #2205 679d534e3 Merge PR #2205 (Fix uptake coeffs on strat aerosol) This PR corrects an issue where the wrong formula was used to compute uptake of CO, NO2, VOC on strat aerosol in heterogeneous chemistry. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index bf9239d70..ced31f725 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit bf9239d70615e62ba6aa92a8a7b602f21a67cd0d +Subproject commit ced31f7252191225d8dd77ed816ff67b8367ccb8 From c02d35a7f423fa185cc9e35c12fa230f0b4f52a9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 21 Mar 2024 12:58:14 -0400 Subject: [PATCH 10/36] GEOS-Chem submod update: Merge PR #2078 (Fix PBL level calculations) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a1359ddc1 Merge PR #2078 (Fix PBL level calculations) This PR now uses local scale height and level thickness to compute the PBL model top level. This should be more accurate than the previous algorithm, which used a globally-fixed scale height. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index ced31f725..a1359ddc1 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit ced31f7252191225d8dd77ed816ff67b8367ccb8 +Subproject commit a1359ddc1b8574c05174dc9e5420d940fa13122d From 24d40b766c3f50779fc1b258b5cf6d55f917520c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 22 Mar 2024 12:01:25 -0400 Subject: [PATCH 11/36] GEOS-Chem submod update: Merge PR #2211 (Initialize PBL variables) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 4279f837e Further updates in Compute_Pbl_Height for clarity & performance a3c1e5f54 Merge PR #2211 (Initialize PBL variables) This fixes the "bad sum" error encountered in PR #2078, by making sure that variables are zeroed each time that PBL quantities are computed. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index a1359ddc1..4279f837e 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit a1359ddc1b8574c05174dc9e5420d940fa13122d +Subproject commit 4279f837e3e3a9d777108d15b13b056a923b0c72 From 6db5506099b616b0880371eb32042032d97f62af Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 4 Apr 2024 14:36:00 -0400 Subject: [PATCH 12/36] GEOS-Chem submodule update: Merge PR #1992 (carbon simulation fixes) Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 4ebe89937..64796d8f3 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 4ebe8993702934d281a4b297f25803c70966d246 +Subproject commit 64796d8f399a3e539694e47baccce00ff01fc735 From 7df5bae51a576339944e325c0eed308574a4a69e Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 8 Apr 2024 16:42:16 -0400 Subject: [PATCH 13/36] GEOS-Chem submod update: Merge PR #1983 (Updated drydep params) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a4562180c Merge PR #1983 (Updated drydep params for aerosol species) This PR updates several drydep parameters for aerosol species. Signed-off-by: Bob Yantosca 5 --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 64796d8f3..a4562180c 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 64796d8f399a3e539694e47baccce00ff01fc735 +Subproject commit a4562180c42fb1cf4ef54ca2d23094fbb2bc2e58 From 693646b0c8fa1e78de8e5b6ddf0ed5c76cf157bd Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Wed, 10 Apr 2024 18:14:51 -0400 Subject: [PATCH 14/36] GEOS-Chem submodule update: Merge PR #2236 (GCHP single carbon sim fixes) Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index a4562180c..afb49952b 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit a4562180c42fb1cf4ef54ca2d23094fbb2bc2e58 +Subproject commit afb49952bb8058745b073619f3e2e3a1361c1336 From c6b7ab765ea9942ce8ac939c08658c216ad4e15d Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 11 Apr 2024 17:49:41 -0400 Subject: [PATCH 15/36] GEOS-Chem submodule update: Merge pull request #2246 (update volcano emissions through 2023) Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index afb49952b..02f97104b 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit afb49952bb8058745b073619f3e2e3a1361c1336 +Subproject commit 02f97104bbd613e5ec3b54724c1b6acad0141c96 From 85f9efcfbefe5fba9acbfc9cad3a99c2843295f5 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 12 Apr 2024 13:23:17 -0400 Subject: [PATCH 16/36] GEOS-Chem submodule update: Add hotfix to correct typo in volcano emission file name Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 02f97104b..3a052785a 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 02f97104bbd613e5ec3b54724c1b6acad0141c96 +Subproject commit 3a052785a60fc32471241daeae40b14ca4cd7abb From 868ce8b93ad08a7582c1bb593c15b307c9b882ee Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Tue, 16 Apr 2024 14:42:30 -0400 Subject: [PATCH 17/36] Rename subdirectory HEMCO_GridComp to HEMCO Signed-off-by: Lizzie Lundgren --- .gitmodules | 2 +- CHANGELOG.md | 1 + src/GCHP_GridComp/CMakeLists.txt | 2 +- src/GCHP_GridComp/{HEMCO_GridComp => HEMCO}/CMakeLists.txt | 2 +- src/GCHP_GridComp/{HEMCO_GridComp => HEMCO}/HEMCO | 0 5 files changed, 4 insertions(+), 3 deletions(-) rename src/GCHP_GridComp/{HEMCO_GridComp => HEMCO}/CMakeLists.txt (90%) rename src/GCHP_GridComp/{HEMCO_GridComp => HEMCO}/HEMCO (100%) diff --git a/.gitmodules b/.gitmodules index 035f2dc87..fb3a6d46d 100644 --- a/.gitmodules +++ b/.gitmodules @@ -20,7 +20,7 @@ path = src/GCHP_GridComp/GEOSChem_GridComp/geos-chem url = https://github.com/geoschem/geos-chem.git [submodule "HEMCO"] - path = src/GCHP_GridComp/HEMCO_GridComp/HEMCO + path = src/GCHP_GridComp/HEMCO/HEMCO url = https://github.com/geoschem/HEMCO.git [submodule "yaFyaml"] path = src/yaFyaml diff --git a/CHANGELOG.md b/CHANGELOG.md index 3319dca13..bd12dc4c2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Changed - Updated GEOS-Chem submodule to 14.4.0 - Updated HEMCO submodule to 3.9.0 +- Changed subdirectory name HEMCO_GridComp to HEMCO since not its own gridded component ## [14.3.1] - 2024-04-02 ### Added diff --git a/src/GCHP_GridComp/CMakeLists.txt b/src/GCHP_GridComp/CMakeLists.txt index e0a8b7e71..72fd32347 100755 --- a/src/GCHP_GridComp/CMakeLists.txt +++ b/src/GCHP_GridComp/CMakeLists.txt @@ -24,7 +24,7 @@ add_subdirectory(Cloud-J EXCLUDE_FROM_ALL) #--------------- # Add HEMCO #--------------- -add_subdirectory(HEMCO_GridComp EXCLUDE_FROM_ALL) +add_subdirectory(HEMCO EXCLUDE_FROM_ALL) #--------------- # Add GEOS-Chem diff --git a/src/GCHP_GridComp/HEMCO_GridComp/CMakeLists.txt b/src/GCHP_GridComp/HEMCO/CMakeLists.txt similarity index 90% rename from src/GCHP_GridComp/HEMCO_GridComp/CMakeLists.txt rename to src/GCHP_GridComp/HEMCO/CMakeLists.txt index 4c74567a7..6421c3513 100644 --- a/src/GCHP_GridComp/HEMCO_GridComp/CMakeLists.txt +++ b/src/GCHP_GridComp/HEMCO/CMakeLists.txt @@ -1,4 +1,4 @@ -# HEMCO_GridComp/CMakeLists.txt +# HEMCO/CMakeLists.txt add_subdirectory(HEMCO EXCLUDE_FROM_ALL) diff --git a/src/GCHP_GridComp/HEMCO_GridComp/HEMCO b/src/GCHP_GridComp/HEMCO/HEMCO similarity index 100% rename from src/GCHP_GridComp/HEMCO_GridComp/HEMCO rename to src/GCHP_GridComp/HEMCO/HEMCO From 06b00f8846af1984ccfce120b1048ab48bdc2e72 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 18 Apr 2024 09:49:09 -0400 Subject: [PATCH 18/36] Add HETP as git submodule Signed-off-by: Lizzie Lundgren --- .gitmodules | 3 +++ CHANGELOG.md | 1 + src/GCHP_GridComp/HETP | 1 + 3 files changed, 5 insertions(+) create mode 160000 src/GCHP_GridComp/HETP diff --git a/.gitmodules b/.gitmodules index fb3a6d46d..900f1ec22 100644 --- a/.gitmodules +++ b/.gitmodules @@ -34,3 +34,6 @@ [submodule "Cloud-J"] path = src/GCHP_GridComp/Cloud-J url = https://github.com/geoschem/Cloud-J +[submodule "HETP"] + path = src/GCHP_GridComp/HETP + url = https://github.com/geoschem/HETerogeneous-vectorized-or-Parallel.git diff --git a/CHANGELOG.md b/CHANGELOG.md index bd12dc4c2..a064eb68b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Now print container name being read by ExtData when `CAP.EXTDATA` is set to `DEBUG` in `logging.yml` - Added new pre-processer setting GCHP_WRAPPER for use in submodules - Added PLEadv export to FV3 submodule for inclusion in GCHP HISTORY.rc files +- Added git submodule for HETP aerosol thermodynamics ### Changed - Updated GEOS-Chem submodule to 14.3.1 diff --git a/src/GCHP_GridComp/HETP b/src/GCHP_GridComp/HETP new file mode 160000 index 000000000..21ce5d04c --- /dev/null +++ b/src/GCHP_GridComp/HETP @@ -0,0 +1 @@ +Subproject commit 21ce5d04ca0201edc7e9fa94d863d38fe0717c3b From ca1807823bd5f362bb73055a8308ea2643dc8d14 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 18 Apr 2024 09:50:23 -0400 Subject: [PATCH 19/36] Updates for compatibility of HETP with GCHP Signed-off-by: Lizzie Lundgren --- src/GCHP_GridComp/CMakeLists.txt | 6 ++++++ src/GCHP_GridComp/HETP | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/CMakeLists.txt b/src/GCHP_GridComp/CMakeLists.txt index 72fd32347..ac7fe87f9 100755 --- a/src/GCHP_GridComp/CMakeLists.txt +++ b/src/GCHP_GridComp/CMakeLists.txt @@ -6,6 +6,7 @@ set(FV_PRECISION R8 ) # FV3 precision is R8 set(GCHP_WRAPPER TRUE ) # GCHP model configuration set(CLOUDJ_EXTERNAL_CONFIG TRUE ) # Not Cloud-J standalone +set(HETP_EXTERNAL_CONFIG TRUE ) # Not HETP standalone test set(HEMCO_EXTERNAL_CONFIG TRUE ) # Not HEMCO standalone set(GC_EXTERNAL_CONFIG TRUE ) # Not GEOS-Chem Classic set(MAPL_ESMF TRUE ) # HEMCO and GEOS-Chem will use MAPL/ESMF @@ -21,6 +22,11 @@ add_subdirectory(FVdycoreCubed_GridComp EXCLUDE_FROM_ALL) #--------------- add_subdirectory(Cloud-J EXCLUDE_FROM_ALL) +#--------------- +# Add HETP +#--------------- +add_subdirectory(HETP EXCLUDE_FROM_ALL) + #--------------- # Add HEMCO #--------------- diff --git a/src/GCHP_GridComp/HETP b/src/GCHP_GridComp/HETP index 21ce5d04c..ec12b5816 160000 --- a/src/GCHP_GridComp/HETP +++ b/src/GCHP_GridComp/HETP @@ -1 +1 @@ -Subproject commit 21ce5d04ca0201edc7e9fa94d863d38fe0717c3b +Subproject commit ec12b5816f32db01c703ba03ee5a64cc7d5e169d From 5383f0384950742cc29c24b22fad6d3d883e966a Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 18 Apr 2024 13:29:03 -0400 Subject: [PATCH 20/36] Update changelog Signed-off-by: Lizzie Lundgren --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a064eb68b..ac2e20656 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,9 @@ This file documents all notable changes to the GCHP wrapper repository starting The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] - TBD +### Added +- Added git submodule HETP for aerosol thermodynamics in GEOS-Chem + ### Changed - Updated GEOS-Chem submodule to 14.4.0 - Updated HEMCO submodule to 3.9.0 From 3d50d8f12a0c2a9fe395bf996d862a62e5df2a49 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 22 Apr 2024 13:36:19 -0400 Subject: [PATCH 21/36] Now use the "stale" GitHub action instead of StaleBot .github/no-response.yml .github/stale.yml - Removed .github/workflows/stale.yml - Configuration file for GitHub "stale" action, which replaces StaleBot. Use the most recent list of issue/PR labels to never be marked stale. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- .github/no-response.yml | 13 ------------- .github/stale.yml | 19 ------------------- .github/workflows/stale.yml | 38 +++++++++++++++++++++++++++++++++++++ CHANGELOG.md | 6 ++++++ 4 files changed, 44 insertions(+), 32 deletions(-) delete mode 100644 .github/no-response.yml delete mode 100644 .github/stale.yml create mode 100644 .github/workflows/stale.yml diff --git a/.github/no-response.yml b/.github/no-response.yml deleted file mode 100644 index dd2b8cfed..000000000 --- a/.github/no-response.yml +++ /dev/null @@ -1,13 +0,0 @@ -# Configuration for probot-no-response - https://github.com/probot/no-response - -# Number of days of inactivity before an Issue is closed for lack of response -daysUntilClose: 14 -# Label requiring a response -responseRequiredLabel: more information needed -# Comment to post when closing an Issue for lack of response. Set to `false` to disable -closeComment: > - This issue has been automatically closed because there has been no response - to our request for more information from the original author. With only the - information that is currently in the issue, we don't have enough information - to take action. Please reach out if you have or find the answers we need so - that we can investigate further. diff --git a/.github/stale.yml b/.github/stale.yml deleted file mode 100644 index 7011576b3..000000000 --- a/.github/stale.yml +++ /dev/null @@ -1,19 +0,0 @@ -# Number of days of inactivity before an issue becomes stale -daysUntilStale: 30 -# Number of days of inactivity before a stale issue is closed -daysUntilClose: 7 -# Issues with these labels will never be considered stale -exemptLabels: - - never stale - - feature - - discussion -# Label to use when marking an issue as stale -staleLabel: stale -# Comment to post when marking an issue as stale. Set to `false` to disable -markComment: > - This issue has been automatically marked as stale because it has not had - recent activity. If there are no updates within 7 days it will be closed. - You can add the "never stale" tag to prevent the Stale bot from closing - this issue. -# Comment to post when closing a stale issue. Set to `false` to disable -closeComment: Closing due to inactivity diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml new file mode 100644 index 000000000..b14b1f621 --- /dev/null +++ b/.github/workflows/stale.yml @@ -0,0 +1,38 @@ +# This workflow warns and then closes issues that have had no activity for a specified amount of time. +# +# You can adjust the behavior by modifying this file. +# For more information, see: +# https://github.com/actions/stale +name: Mark stale issues + +on: + schedule: + - cron: '0 0 * * *' # Run every night at midnight + +jobs: + stale: + + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + + steps: + - uses: actions/stale@v5 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + stale-issue-label: 'stale' + exempt-issue-labels: + - 'category: Discussion' + - 'category: Feature Request' + - 'deferred' + - 'help needed: Open Research Problem' + - 'help needed: Request Input from Community' + - 'never stale' + - 'TODO: Documentation' + days-before-issue-stale: 30 + days-before-issue-close: 7 + stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.' + close-issue-message: 'Closing due to inactivity' + days-before-pr-stale: -1 + days-before-pr-close: -1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 3319dca13..ea674e3c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,10 +8,16 @@ This file documents all notable changes to the GCHP wrapper repository starting The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] - TBD +### Added +- GitHub Action config file `.github/workflows/stale.yml`, which replaces StaleBot + ### Changed - Updated GEOS-Chem submodule to 14.4.0 - Updated HEMCO submodule to 3.9.0 +### Removed +- GitHub config files `.github/stale.yml` and `.github/no-response.yml` + ## [14.3.1] - 2024-04-02 ### Added - Now print container name being read by ExtData when `CAP.EXTDATA` is set to `DEBUG` in `logging.yml` From ad4667a844eb8d869be74cca3e4984ade2e40cc4 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 22 Apr 2024 14:52:26 -0400 Subject: [PATCH 22/36] GEOS-Chem submod update: Merge PR #2260 (Use "stale" GitHub action) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: b0ed94d (Merge PR #2260 (Replace stalebot with "stale" GitHub action) This PR replaces the obsolete GitHub stalebot with the newer "stale" GitHub action. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 3a052785a..685d2e7cd 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 3a052785a60fc32471241daeae40b14ca4cd7abb +Subproject commit 685d2e7cd6899e0ea6b8352c557e7d6fcfd2c20e From 79397adf4c3e66ee737c52442a848fa9d7510331 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 23 Apr 2024 12:05:01 -0400 Subject: [PATCH 23/36] GEOS-Chem submod update: Merge PR #2072 (Optimized unit conversions) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 2f7c05bba Merge PR #2072 (Only convert units for species that require it) This PR improves the performance of unit conversions by only converting e.g. advected species units before advection, etc. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 685d2e7cd..2f7c05bba 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 685d2e7cd6899e0ea6b8352c557e7d6fcfd2c20e +Subproject commit 2f7c05bbaa8a4ecda80ecc7df446293cba0c1e9f From 8b1f7ca64daf1eae57afcad729b2f2db01d21003 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 24 Apr 2024 16:17:56 -0400 Subject: [PATCH 24/36] GEOS-Chem submod update: Merge PR #2263 (Removed fixed date ranges) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: b54ad6df8 Merge PR #2263 (Remove hardcoded year range for met, restarts, BC) This PR replaces hardcoded year/month/day ranges in HEMCO_Config.rc template files with $YYYY, $MM, $DD, $HH tokens. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 2f7c05bba..b54ad6df8 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 2f7c05bbaa8a4ecda80ecc7df446293cba0c1e9f +Subproject commit b54ad6df874c162e349f3e56028687ca49824569 From 8e7f07962686f39a1c4ec32b76e9eee044f40b86 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 25 Apr 2024 10:53:10 -0400 Subject: [PATCH 25/36] GEOS-Chem submod update: Merge PR #2261 (Add GHGI postmeter emissions) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 6ac253857 Merge PR #2261 (Add missing CH4 postmeter emissions for GHGI) This PR adds an entry for CH4 post-meter emissions for the GHGI Express Extension to the relevant HEMCO_Config.rc template files. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index b54ad6df8..6ac253857 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit b54ad6df874c162e349f3e56028687ca49824569 +Subproject commit 6ac2538576a79190d4984312fadac1a12a3ad3e9 From abc24bbd59a7c62ac959d99a7b871ced8ee0f02a Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 25 Apr 2024 10:56:44 -0400 Subject: [PATCH 26/36] MAPL update: Merge PR #34 (Bug fix for stretched-grid restart attr check) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 850f20a Merge PR #34 (Bug fix for stretched grid restart attribute check) This PR fixes a mismatch between stretched grid coordinates as computed from attributes in the restart file and in the configure files. Signed-off-by: Bob Yantosca --- src/MAPL | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MAPL b/src/MAPL index d61f89a7a..850f20a9b 160000 --- a/src/MAPL +++ b/src/MAPL @@ -1 +1 @@ -Subproject commit d61f89a7ab2a2691bc2b0dd1a42b2871c6420740 +Subproject commit 850f20a9b7b78f8cf58fe4516e49ea2b0d50e31f From be194bb0d0fb7202e4a0337bd2248cde04c90499 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 25 Apr 2024 13:17:25 -0400 Subject: [PATCH 27/36] Move Cloud-J, HEMCO, and HETP directories This commit move the submodules used within GEOS-Chem to within the GEOSChem_GridComp directory so they are alongside GEOS-Chem. Signed-off-by: Lizzie Lundgren --- .gitmodules | 6 ++-- src/GCHP_GridComp/CMakeLists.txt | 36 +++++-------------- .../GEOSChem_GridComp/CMakeLists.txt | 6 ++++ .../{ => GEOSChem_GridComp}/Cloud-J | 0 .../HEMCO/CMakeLists.txt | 0 .../{ => GEOSChem_GridComp}/HEMCO/HEMCO | 0 .../{ => GEOSChem_GridComp}/HETP | 0 7 files changed, 18 insertions(+), 30 deletions(-) rename src/GCHP_GridComp/{ => GEOSChem_GridComp}/Cloud-J (100%) rename src/GCHP_GridComp/{ => GEOSChem_GridComp}/HEMCO/CMakeLists.txt (100%) rename src/GCHP_GridComp/{ => GEOSChem_GridComp}/HEMCO/HEMCO (100%) rename src/GCHP_GridComp/{ => GEOSChem_GridComp}/HETP (100%) diff --git a/.gitmodules b/.gitmodules index 900f1ec22..daea64969 100644 --- a/.gitmodules +++ b/.gitmodules @@ -20,7 +20,7 @@ path = src/GCHP_GridComp/GEOSChem_GridComp/geos-chem url = https://github.com/geoschem/geos-chem.git [submodule "HEMCO"] - path = src/GCHP_GridComp/HEMCO/HEMCO + path = src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO url = https://github.com/geoschem/HEMCO.git [submodule "yaFyaml"] path = src/yaFyaml @@ -32,8 +32,8 @@ path = docs/source/geos-chem-shared-docs url = https://github.com/geoschem/geos-chem-shared-docs.git [submodule "Cloud-J"] - path = src/GCHP_GridComp/Cloud-J + path = src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J url = https://github.com/geoschem/Cloud-J [submodule "HETP"] - path = src/GCHP_GridComp/HETP + path = src/GCHP_GridComp/GEOSChem_GridComp/HETP url = https://github.com/geoschem/HETerogeneous-vectorized-or-Parallel.git diff --git a/src/GCHP_GridComp/CMakeLists.txt b/src/GCHP_GridComp/CMakeLists.txt index ac7fe87f9..747a36058 100755 --- a/src/GCHP_GridComp/CMakeLists.txt +++ b/src/GCHP_GridComp/CMakeLists.txt @@ -5,41 +5,23 @@ #--------------- set(FV_PRECISION R8 ) # FV3 precision is R8 set(GCHP_WRAPPER TRUE ) # GCHP model configuration -set(CLOUDJ_EXTERNAL_CONFIG TRUE ) # Not Cloud-J standalone -set(HETP_EXTERNAL_CONFIG TRUE ) # Not HETP standalone test -set(HEMCO_EXTERNAL_CONFIG TRUE ) # Not HEMCO standalone set(GC_EXTERNAL_CONFIG TRUE ) # Not GEOS-Chem Classic set(MAPL_ESMF TRUE ) # HEMCO and GEOS-Chem will use MAPL/ESMF set(MAPL_ACG ${CMAKE_CURRENT_SOURCE_DIR}/../MAPL/Apps/mapl_acg.pl) -#--------------- -# Add FV3 -#--------------- +#------------------------------------------- +# Add DYNAMICS gridded component (advection) +#------------------------------------------- add_subdirectory(FVdycoreCubed_GridComp EXCLUDE_FROM_ALL) -#--------------- -# Add Cloud-J -#--------------- -add_subdirectory(Cloud-J EXCLUDE_FROM_ALL) - -#--------------- -# Add HETP -#--------------- -add_subdirectory(HETP EXCLUDE_FROM_ALL) - -#--------------- -# Add HEMCO -#--------------- -add_subdirectory(HEMCO EXCLUDE_FROM_ALL) - -#--------------- -# Add GEOS-Chem -#--------------- +#------------------------------------------- +# Add GCHPchem gridded component (GEOS-Chem) +#------------------------------------------- add_subdirectory(GEOSChem_GridComp EXCLUDE_FROM_ALL) -#--------------- -# Add GCHPctmEnv -#--------------- +#---------------------------------------------------- +# Add GCHPctmEnv gridded component (pre-advection) +#---------------------------------------------------- add_subdirectory(GCHPctmEnv_GridComp EXCLUDE_FROM_ALL) #-------------------------------- diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt b/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt index 595975119..1036e4ec4 100755 --- a/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt +++ b/src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt @@ -19,6 +19,9 @@ set(FASTJX OFF CACHE BOOL # Local variables set(GC_EXTERNAL_CONFIG TRUE) +set(CLOUDJ_EXTERNAL_CONFIG TRUE) # Not Cloud-J standalone +set(HETP_EXTERNAL_CONFIG TRUE) # Not HETP standalone test +set(HEMCO_EXTERNAL_CONFIG TRUE) # Not HEMCO standalone set(GTMM FALSE) set(MECH "fullchem" CACHE STRING "Name of the chemistry mechanism to use") set(GCHP TRUE) @@ -26,6 +29,9 @@ set(MODEL_GCHP TRUE) set(MODEL_GCHPCTM TRUE) # Add directories to build +add_subdirectory(Cloud-J EXCLUDE_FROM_ALL) +add_subdirectory(HETP EXCLUDE_FROM_ALL) +add_subdirectory(HEMCO EXCLUDE_FROM_ALL) add_subdirectory(geos-chem EXCLUDE_FROM_ALL) # Configure build properties for GEOS-Chem diff --git a/src/GCHP_GridComp/Cloud-J b/src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J similarity index 100% rename from src/GCHP_GridComp/Cloud-J rename to src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J diff --git a/src/GCHP_GridComp/HEMCO/CMakeLists.txt b/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/CMakeLists.txt similarity index 100% rename from src/GCHP_GridComp/HEMCO/CMakeLists.txt rename to src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/CMakeLists.txt diff --git a/src/GCHP_GridComp/HEMCO/HEMCO b/src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO similarity index 100% rename from src/GCHP_GridComp/HEMCO/HEMCO rename to src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO diff --git a/src/GCHP_GridComp/HETP b/src/GCHP_GridComp/GEOSChem_GridComp/HETP similarity index 100% rename from src/GCHP_GridComp/HETP rename to src/GCHP_GridComp/GEOSChem_GridComp/HETP From af6448ea7c9272e9d1fc9aa729b70feac97fe33e Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 25 Apr 2024 13:18:23 -0400 Subject: [PATCH 28/36] Update HETP submodule to fix run-time error due to uninitialized variables Signed-off-by: Lizzie Lundgren --- src/GCHP_GridComp/GEOSChem_GridComp/HETP | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/HETP b/src/GCHP_GridComp/GEOSChem_GridComp/HETP index ec12b5816..2a99b2462 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/HETP +++ b/src/GCHP_GridComp/GEOSChem_GridComp/HETP @@ -1 +1 @@ -Subproject commit ec12b5816f32db01c703ba03ee5a64cc7d5e169d +Subproject commit 2a99b24625ed26cf87ae88697ddd6cf8bbdec812 From b62c4bbc9c910240bcb8828986e6fa3d0f884600 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 25 Apr 2024 13:39:12 -0400 Subject: [PATCH 29/36] GEOS-Chem submod update: Merge PR #2249 (Updates from NASA GMAO) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: c87160743 Merge PR #2249 (Updates from NASA GMAO) This PR adds updates from @christophkeller and @viral211 for running GEOS-Chem in the NASA GEOS ESM. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 6ac253857..c87160743 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 6ac2538576a79190d4984312fadac1a12a3ad3e9 +Subproject commit c8716074327e61a1d61a5e65c83daa0b82ed130a From e86ba153852802f8194f6ca77375f61bfbc2304f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 25 Apr 2024 15:01:47 -0400 Subject: [PATCH 30/36] GEOS-Chem submod update: Merge PR #2266 (Remove unused carbon sim options) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: c2b5130ed Merge PR #2266 (Removing unused carbon simulation options) This PR removes several unused entries from the geoschem_config.yml file for the CO2 simulation and carbon simulation w/ CO2-only. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index c87160743..c2b5130ed 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit c8716074327e61a1d61a5e65c83daa0b82ed130a +Subproject commit c2b5130ed95700fcb8c45eeca2843569da6f806e From 07809242bdff2148252191acf1463c8889d3cfc8 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 26 Apr 2024 09:43:14 -0400 Subject: [PATCH 31/36] GEOS-Chem submod update: Merge PR #2254 (Fixes for FRSNO) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 203a480b6 Merge PR #2254 (Fix bug in usage of FRSNO met field) This PR corrects inconsistencies in how the FRSNO met field is used. It is now the fraction of snow in grid box, not fraction of snow on land. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index c2b5130ed..203a480b6 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit c2b5130ed95700fcb8c45eeca2843569da6f806e +Subproject commit 203a480b666012a800e68cf943d816d2ab6506ba From b8a28c3ee07b96a8f6b3611862cec457ac2c3905 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Fri, 26 Apr 2024 15:03:28 -0400 Subject: [PATCH 32/36] Updated changelog Signed-off-by: Lizzie Lundgren --- CHANGELOG.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ac2e20656..0603a28aa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,9 @@ This file documents all notable changes to the GCHP wrapper repository starting in version 14.0.0. See also CHANGELOG files for individual submodules, such as: - src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/CHANGELOG.md -- src/GCHP_GridComp/HEMCO_GridComp/HEMCO/CHANGELOG.md +- src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/CHANGELOG.md +- src/GCHP_GridComp/GEOSChem_GridComp/Cloud-J/CHANGELOG.md +- src/GCHP_GridComp/GEOSChem_GridComp/HETP/CHANGELOG.md - src/MAPL/CHANGELOG.md The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). @@ -15,6 +17,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Updated GEOS-Chem submodule to 14.4.0 - Updated HEMCO submodule to 3.9.0 - Changed subdirectory name HEMCO_GridComp to HEMCO since not its own gridded component +- Moved HEMCO and Cloud-J submodules from GCHP_GridComp to GCHP_GridComp/GEOSChem_GridComp where they are used ## [14.3.1] - 2024-04-02 ### Added From dfe6a3e095850e339acf273b5dad4274f5294713 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 29 Apr 2024 16:16:53 -0400 Subject: [PATCH 33/36] GEOS-Chem submod update: Merge PR #2281 (Change input file paths for GEOS) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 7cb6454d1 (HEAD -> dev/14.4.0) Merge PR #2271 (Change input file paths of config files used w/ GEOS) This PR is necessary due to a data move on the NASA Discover cluster. The paths to configuration files are updated accordingly. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 90da22bed..7cb6454d1 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 90da22bedc673888e0ee0d0b80283a8179ebc2bb +Subproject commit 7cb6454d154d2512167567b236d5568b827d7d99 From 24170f3c71552d1aed4cd55de7a82d202f2b5fe7 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 1 May 2024 10:28:13 -0400 Subject: [PATCH 34/36] GEOS-Chem submod update: Merge PR #2272 (CH4/carbon sim updates) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 7102094f5 Merge PR #2272 (CH4/carbon simulation updates) This PR adds updates/fixes to CH4/carbon simulation configuration files, as well as using smaller mask files for Canada, Mexico, and CONUS. This should avoid computational bottlenecks. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 7cb6454d1..7102094f5 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 7cb6454d154d2512167567b236d5568b827d7d99 +Subproject commit 7102094f5269beaf226f16be3afe33667135d342 From e5ebd88dc5ddac4afcfc74d262f89e2904b919af Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 2 May 2024 12:10:12 -0400 Subject: [PATCH 35/36] GEOS-Chem submod update: Merge PR #2238 (Reff param for SNA/OM aerosols) This commit informs the GCHP superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 546fda291 PR #2236 post-merge fix: Read updated org.dat, so4.dat for Hg simulation c5d1f155d Merge PR #2236 (Param for Reff for SNA/OM aerosols) This PR implements a new parameterization for the effective radius of sulfate/nitrate/ammonium and organic matter aerosols, as described in https://github.com/geoschem/geos-chem/pull/2238. Signed-off-by: Bob Yantosca --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 7102094f5..546fda291 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 7102094f5269beaf226f16be3afe33667135d342 +Subproject commit 546fda29180c491bf4c6fb08fb13b0749cb5d70b From a3dc55d7add050cb0332caafd13ae7ee9668b532 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 3 May 2024 21:43:32 -0400 Subject: [PATCH 36/36] GEOS-Chem submod update: Merge PR #2275 (Cl emissions) Signed-off-by: Melissa Sulprizio --- src/GCHP_GridComp/GEOSChem_GridComp/geos-chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem index 546fda291..c4c4c146e 160000 --- a/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem +++ b/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem @@ -1 +1 @@ -Subproject commit 546fda29180c491bf4c6fb08fb13b0749cb5d70b +Subproject commit c4c4c146ed9cd6bb8af42f080b766a0a0119b4a5