From 868ce8b93ad08a7582c1bb593c15b307c9b882ee Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Tue, 16 Apr 2024 14:42:30 -0400 Subject: [PATCH 1/7] 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 2/7] 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 3/7] 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 4/7] 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 be194bb0d0fb7202e4a0337bd2248cde04c90499 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 25 Apr 2024 13:17:25 -0400 Subject: [PATCH 5/7] 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 6/7] 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 b8a28c3ee07b96a8f6b3611862cec457ac2c3905 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Fri, 26 Apr 2024 15:03:28 -0400 Subject: [PATCH 7/7] 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