From 09c8fad179e6557fa3c2592440e3119315b661eb Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 3 Jul 2024 15:37:02 -0400 Subject: [PATCH 01/99] GEOS-Chem submod update: Merge PR #2359 (Per-species KPP error tol.) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 4288f0d1d Merge PR #2359 (Set KPP dummy species to large ATOL value) This PR adds structural updates to allow per-species setting of the KPP absolute & relative tolerances. This now allows us to assign a large absolute tolerance (1e25) to KPP dummy species, which excludes them from the error norm computations. This results in a faster simulation at the cost of numerical noise. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index dd859ee..4288f0d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit dd859ee45494af71d29f0877f359ff571f697b67 +Subproject commit 4288f0d1d89d6d4c42f71bc0c90280812aa4cfd8 From 600ce53615fc98616c6e203de03169e563138938 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 8 Jul 2024 13:46:07 -0400 Subject: [PATCH 02/99] GEOS-Chem submod update: Merge hotfix from PR #2363 atop PR #2359 This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e61a51064 Merge GCHP hotfix from PR #2363 on top of PR #2359 This PR implements a hotfix for an issue that had caused GCHP cloud benchmarks to fail. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 4288f0d..e61a510 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 4288f0d1d89d6d4c42f71bc0c90280812aa4cfd8 +Subproject commit e61a51064a94246698d7a844239617b1b802ec8f From 6c039818406006936420614900595d948b51f9d7 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 16 Jul 2024 12:30:47 -0400 Subject: [PATCH 03/99] GEOS-Chem submod update: Merge PR #2315 (complexSOA bug fixes) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: ef2ea60e7 Merge PR #2315 (Fix bugs in PDER, OCPISOA, and TotalOC) This PR fixes several minor bugs in the complex SOA scheme. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index e61a510..ef2ea60 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e61a51064a94246698d7a844239617b1b802ec8f +Subproject commit ef2ea60e7caab0784ba139f8e5083f2f77982a6c From 96e3b6b288c28f8a741c2531141ad11158e59867 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 24 Jul 2024 16:17:58 -0400 Subject: [PATCH 04/99] Hotfix: Point to dev/14.5.0 + 14.4.2 in src/GEOS-Chem This hotfix now updates the submodule hash so that it points to commit 0a172283 in src/GEOS-Chem. This is where the 14.4.2 release has been merged into the the dev/14.5.0 branch. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index ef2ea60..0a17228 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit ef2ea60e7caab0784ba139f8e5083f2f77982a6c +Subproject commit 0a172283d089111e17fc45c0dd0a57da563b7bdc From 6f2224053cd83819c55b2f644f2abe1c5eae527c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 26 Jul 2024 09:47:54 -0400 Subject: [PATCH 05/99] GEOS-Chem submod update: Merge PR #2398 (Uncomment cations for HETP) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e29a4c928 Merge PR #2398 (Pass non-zero Ca2, Mg, and K cations to HETP) PR #2398 uncomments setting Ca2+, K+, and Mg+ cation values passed to HETP. Previously these values were zero due to an issue in ISORROPIA. With the update to HETP we can enable these cations. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 0a17228..e29a4c9 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 0a172283d089111e17fc45c0dd0a57da563b7bdc +Subproject commit e29a4c9289b01482f9d1c22528eac76b73023c43 From a6ad1c5b685c0aa3632a6dbb5b002e6927793bf8 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 1 Aug 2024 14:26:21 -0400 Subject: [PATCH 06/99] GEOS-Chem submod update: Merge PR #2352 (ALK4/R4N2 fixes from J. Brewer) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 0a392d465 Merge PR #2352 (Fixes for ALK4 and R4N2 chemistry from J. Brewer) R4N2 was a common product of alkane, isoprene, and monoterpene oxidation and produced organonitrate SOA but we don’t want ALK4 to produce organonitrate SOA as discusses in #1625. A fix from Jared Brewer is included in this PR. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index e29a4c9..0a392d4 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e29a4c9289b01482f9d1c22528eac76b73023c43 +Subproject commit 0a392d465fd194135806f1a120c05697d60cf382 From 0c22a3a5ce10645cc302c36fd3e7315bc8dec9e9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 5 Aug 2024 15:46:35 -0400 Subject: [PATCH 07/99] GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: acd335486 PR #2352 post-merge fix: Rebuild fullchem solver files This PR restores the updated KPP solver files for PR #2352 (ALK4 and R4N2 chemistry updates, by @JFBrewer). Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 0a392d4..acd3354 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 0a392d465fd194135806f1a120c05697d60cf382 +Subproject commit acd3354861ce7c7b1c2d34833361e57dc39f8ff9 From 8da455b7713a536a7ab1e518bff9ef927a8b6641 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 15 Aug 2024 11:58:33 -0400 Subject: [PATCH 08/99] GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_ This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 8f0a16767 PR #2425 post-merge fix: Move 14.4.3 entry to top of CHANGELOG.md This PR moves a CHANGELOG.md entry for 14.4.3 to its proper place. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 000205c..8f0a167 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 000205c86ade5f906f17a628856d8620736111b9 +Subproject commit 8f0a1676789f001d8a1d888905a734cf88f0eb13 From edaa239ad070022c7fb887b753bd71669c21f5f4 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 20 Aug 2024 11:54:58 -0400 Subject: [PATCH 09/99] GEOS-Chem & HEMCO updates: Merge PR #2318, PR #284, PR #285 This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 586260f10 PR #2318 post-merge fix: Use less drydep fields for the alldiags test f240c993f PR #2318 post-merge fix: Remove duplicate EmisHCOOH_Total entry 53f9b2e82 PR #2318 post-merge fix: Add missing species to geoschem_config.yml dd7ba9a9c Merge PR #2318 (Chemistry for RCOOH, ANs, PNs) and the geoschem/HEMCO repository: d0d5fca PR #285 post-merge fix: Update CHANGELOG.md 1c6356d Merge PR #285 (Add em. factors for ALK6, C4H6, EBZ, STYR, TMB) 253b0fc Merge HEMCO 3.9.3 back into the 3.10.0 development stream f2b6ae4 Merge PR #284 (Fix inconsistent pressure units in HEMCO standalone) These PRs implement new chemistry (from @ktravis213), emissions (from @kelvinhb), and a bug fix for the HEMCO standalone. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 8f0a167..586260f 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 8f0a1676789f001d8a1d888905a734cf88f0eb13 +Subproject commit 586260f101557396c49590931a5838a2374b4528 diff --git a/src/HEMCO b/src/HEMCO index 41605bd..d0d5fca 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 41605bda8a89d96f441cb8eb90f3d3c8b21f2b71 +Subproject commit d0d5fca8ceab6f59aa98d6e65952dcfc9f3aef6e From 153a355ee604a1325ed4845ad0b58081c4a24c0a Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 28 Aug 2024 11:06:39 -0400 Subject: [PATCH 10/99] GEOS-Chem submod update: Merge PR #2428 (vdiff) and PR #2144 (drydep) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 3073aff2e Merge PR #2428 (Fix mass non-conservation in VDIFF) c7332ed7a Merge PR #2144 (Restore drydep output in fullchem benchmarks) This PR does the following: 1. Adds the DryDep collection to all fullchem_benchmark runs 2. Implements a mass conservation fix in VDIFF PBL mixing by @nicholasbalasus. See issue #2409 for details/ Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 586260f..3073aff 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 586260f101557396c49590931a5838a2374b4528 +Subproject commit 3073aff2e63d1073f7e63acaa9dba293dbc0553a From 750151fa98667a33de9027c995c38eb4d763e6af Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 28 Aug 2024 17:40:28 -0400 Subject: [PATCH 11/99] geos-chem-shared-docs update: Update packages.yaml to GCC 12.2.0 Signed-off-by: Bob Yantosca --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 07725d7..2f6603f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit 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 +### Changed +- Updated `docs/source/geos-chem-shared-docs/spack/packages.yaml` to use GCC 12.2.0 compilers + ## [14.4.3] - 2024-08-13 ### Changed - Updated GEOS-Chem (science codebase) to 14.4.3 From e7efd491d99811c557256e0ff6ca19ce1f9204cd Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 29 Aug 2024 12:46:38 -0400 Subject: [PATCH 12/99] Update env files from GNU 10.2.0 to 12.2.0 + related updates docs/source/geos-chem-shared-docs - Fixed broken links in supplemental-guides/spack-guide.rst docs/source/getting-started/login-env-files-gnu.rst - Changed label from env-files-gnu10 to env-files-gnu - Added tip box to build software with Spack if necessary docs/source/getting-started/login-env-files-intel.rst - Changed label from _env-files-intel19 to _env-files-intel - Added tip box to build software with Spack if necessary docs/source/getting-started/login-env-compilers.rst docs/source/getting-started/login-env-parallel.rst - Updated references accordingly docs/source/getting-started/login-env.rst - Updated references accordingly - Added tip box to build software with Spack if necessary Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- .../getting-started/login-env-compilers.rst | 4 +- .../getting-started/login-env-files-gnu.rst | 84 +++++++++++++------ .../getting-started/login-env-files-intel.rst | 41 ++++++--- .../getting-started/login-env-files.rst | 2 +- .../getting-started/login-env-parallel.rst | 4 +- docs/source/getting-started/login-env.rst | 7 ++ 7 files changed, 102 insertions(+), 42 deletions(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index ce3c86a..47cb22b 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit ce3c86accdcd73d3c3a46e41be1fcc09775200dd +Subproject commit 47cb22bf9a93dd5c54a597062b41ef4ab1db4ce9 diff --git a/docs/source/getting-started/login-env-compilers.rst b/docs/source/getting-started/login-env-compilers.rst index 6885a8e..e4f6c58 100644 --- a/docs/source/getting-started/login-env-compilers.rst +++ b/docs/source/getting-started/login-env-compilers.rst @@ -4,8 +4,8 @@ Set environment variables for compilers ####################################### -The sample :ref:`GNU ` and :ref:`Intel -` environment files set the **environment +The sample :ref:`GNU ` and :ref:`Intel +` environment files set the **environment variables** listed below in order to select the desired C, C++, and Fortran compilers: diff --git a/docs/source/getting-started/login-env-files-gnu.rst b/docs/source/getting-started/login-env-files-gnu.rst index e8c37bb..05e4e24 100644 --- a/docs/source/getting-started/login-env-files-gnu.rst +++ b/docs/source/getting-started/login-env-files-gnu.rst @@ -1,36 +1,64 @@ -.. _env-files-gnu10: +.. _env-files-gnu: ################################################ -Sample environment file for GNU 10.2.0 compilers +Sample environment file for GNU 12.2.0 compilers ################################################ Below is a sample environment file (based on an enviroment file for the Harvard Cannon computer cluster). This file will load software -libraries built with the GNU 10.2.0 compilers. +libraries built with the `GNU 12.2.0 compilers +`_. + +.. note:: + + This environment file shown below assumes that required software + packages for :program:`GEOS-Chem Classic` are available as + pre-built modules. If your computer system does not have these + packages pre-installed, you can build them with Spack. Please see + our :ref:`spackguide` supplemental guide for detailed instructions. Save the code below (with any appropriate modifications for your own -computer system) to a file named :file:`~/gcclassic.gnu10.env`. +computer system) to a file named :file:`~/gcclassic.gnu12.env`. .. code-block:: bash + ############################################################################### + # + # Environment file for GCClassic + GNU Compiler Collection 12.2.0 + # + ############################################################################### + + # Display message (if we are in a terminal window) + if [[ $- = *i* ]] ; then + echo "Loading modules for GEOS-Chem Classic, please wait ..." + fi + #============================================================================== - # Load software packages (EDIT AS NEEDED) + # Unload all previously-unloaded software #============================================================================== - # Unload all modules first + # Unload packages loaded with "module load" module purge - # Load modules - module load gcc/10.2.0-fasrc01 # gcc / g++ / gfortran - module load openmpi/4.1.0-fasrc01 # MPI - module load netcdf-c/4.8.0-fasrc01 # netcdf-c - module load netcdf-fortran/4.5.3-fasrc01 # netcdf-fortran + #============================================================================== + # Load software packages for GNU 12.2.0 + #============================================================================== + if [[ $- = *i* ]] ; then + echo "... Loading FASRC-built software, please wait ..." + fi + + # Pre-built modules needed for GEOS-Chem + # (NOTE: These may be named differently on your system) + module load gcc/12.2.0-fasrc01 # gcc / g++ / gfortran + module load openmpi/4.1.4-fasrc01 # MPI + module load netcdf-c/4.9.2-fasrc01 # netcdf-c + module load netcdf-fortran/4.6.0-fasrc02 # netcdf-fortran module load flex/2.6.4-fasrc01 # Flex lexer (needed for KPP) module load cmake/3.25.2-fasrc01 # CMake (needed to compile) #============================================================================== # Environment variables and related settings - # (NOTE: Lmod will define _HOME variables for each loaded module + # (NOTE: Lmod will define _HOME variables for each loaded module) #============================================================================== # Make all files world-readable by default @@ -55,13 +83,13 @@ computer system) to a file named :file:`~/gcclassic.gnu10.env`. # netCDF if [[ "x${NETCDF_HOME}" == "x" ]]; then - export NETCDF_HOME="${NETCDF_C_HOME}" + export NETCDF_HOME="${NETCDF_C_HOME}" fi export NETCDF_C_ROOT="${NETCDF_HOME}" - export NETCDF_FORTRAN_ROOT="${NETCDF_FORTRAN_HOME}" + export NETCDF_FORTRAN_ROOT=${NETCDF_FORTRAN_HOME} # KPP 3.0.0+ - export KPP_FLEX_LIB_DIR="${FLEX_HOME}/lib64" + export KPP_FLEX_LIB_DIR=${FLEX_HOME}/lib64 #============================================================================== # Set limits @@ -75,20 +103,28 @@ computer system) to a file named :file:`~/gcclassic.gnu10.env`. #============================================================================== # Print information #============================================================================== - module list - -.. tip:: - Ask your sysadmin how to load software libraries. If you are using - your institution's computer cluster, then chances are there will - be a software module system installed, with commands similar to - those listed above. + module list -Then you can activate these seetings from the command line by typing: + echo "" + echo "Environment:" + echo "" + echo "CC : ${CC}" + echo "CXX : ${CXX}" + echo "FC : ${FC}" + echo "KPP_FLEX_LIB_DIR : ${KPP_FLEX_LIB_DIR}" + echo "MPI_HOME : ${MPI_HOME}" + echo "NETCDF_HOME : ${NETCDF_HOME}" + echo "NETCDF_FORTRAN_HOME : ${NETCDF_FORTRAN_HOME}" + echo "OMP_NUM_THREADS : ${OMP_NUM_THREADS}" + echo "" + echo "Done sourcing ${BASH_SOURCE[0]}" + +To activate the settings contained in the environment file, type: .. code-block:: console - $ . ~/gcclassic.gnu10.env + $ . ~/gcclassic.gnu12.env You may also place the above command within your :ref:`GEOS-Chem run script `, which will be discussed in a subsequent chapter. diff --git a/docs/source/getting-started/login-env-files-intel.rst b/docs/source/getting-started/login-env-files-intel.rst index 4b0494f..d2f3c49 100644 --- a/docs/source/getting-started/login-env-files-intel.rst +++ b/docs/source/getting-started/login-env-files-intel.rst @@ -1,4 +1,4 @@ -.. _env-files-intel19: +.. _env-files-intel: ################################################ Sample environment file for Intel 2023 compilers @@ -8,14 +8,24 @@ Below is a sample environment file (based on an enviroment file for the Harvard Cannon computer cluster). This file will load software libraries built with the Intel 2023 compilers. +.. note:: + + This environment file shown below assumes that required software + packages for :program:`GEOS-Chem Classic` are available as + pre-built modules. If your computer system does not have these + packages pre-installed, you can build them with Spack. Please see + our :ref:`spackguide` supplemental guide for detailed instructions. + Add the code below (with the appropriate modifications for your system) into a file named :file:`~/gcclassic.intel23.env`. .. code-block:: bash - #============================================================================== - # Load software packages (EDIT AS NEEDED) - #============================================================================== + ############################################################################### + # + # Environment file for GCClassic + Intel 2023 compilers + # + ############################################################################### # Unload all modules first module purge @@ -77,14 +87,21 @@ system) into a file named :file:`~/gcclassic.intel23.env`. module list -.. tip:: - - Ask your sysadmin how to load software libraries. If you - are using your institution's computer cluster, then chances - are there will be a software module system installed, with - commands similar to those listed above. - -Then you can activate these settings from the command line by typing: + echo "" + echo "Environment:" + echo "" + echo "CC : ${CC}" + echo "CXX : ${CXX}" + echo "FC : ${FC}" + echo "KPP_FLEX_LIB_DIR : ${KPP_FLEX_LIB_DIR}" + echo "MPI_HOME : ${MPI_HOME}" + echo "NETCDF_HOME : ${NETCDF_HOME}" + echo "NETCDF_FORTRAN_HOME : ${NETCDF_FORTRAN_HOME}" + echo "OMP_NUM_THREADS : ${OMP_NUM_THREADS}" + echo "" + echo "Done sourcing ${BASH_SOURCE[0]}" + +To activate the settings contained in the environment file, type: .. code-block:: console diff --git a/docs/source/getting-started/login-env-files.rst b/docs/source/getting-started/login-env-files.rst index 3e76c85..3ef2e27 100644 --- a/docs/source/getting-started/login-env-files.rst +++ b/docs/source/getting-started/login-env-files.rst @@ -30,7 +30,7 @@ command such as: Keep a separate environment file for each combination of modules that you will use. Example environment files - for :ref:`GNU ` and :ref:`Intel ` + for :ref:`GNU ` and :ref:`Intel ` compilers and related software are provided in the following sections. For general information about how libraries are loaded, see diff --git a/docs/source/getting-started/login-env-parallel.rst b/docs/source/getting-started/login-env-parallel.rst index bd7bfaf..b2a9fba 100644 --- a/docs/source/getting-started/login-env-parallel.rst +++ b/docs/source/getting-started/login-env-parallel.rst @@ -24,8 +24,8 @@ shared-memory (aka serial) parallelization. `_ for more computationally-intensive simulations. -In the the sample environment files for :ref:`GNU ` and -:ref:`Intel `, we define the following **environment +In the the sample environment files for :ref:`GNU ` and +:ref:`Intel `, we define the following **environment varaiables** for OpenMP parallelization: .. option:: OMP_NUM_THREADS diff --git a/docs/source/getting-started/login-env.rst b/docs/source/getting-started/login-env.rst index 156345c..c463c78 100644 --- a/docs/source/getting-started/login-env.rst +++ b/docs/source/getting-started/login-env.rst @@ -12,6 +12,13 @@ Customize your login environment Machine Images (AMIs) all of the required software libraries will be automatically loaded. +.. tip:: + + If your computer system lacks the required software packages for + :program:`GEOS-Chem Classic`, you can build them with the Spack + package manager. For detailed instructions, please see our + :ref:`spackguide` supplemental guide. + Each time you log in to your computer system, you'll need to load the :ref:`software libraries ` needed by GEOS-Chem into your environment. You can do this with a script known From 03ae9d847054163eb3635c630c67c4079a1fc713 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 29 Aug 2024 13:59:53 -0400 Subject: [PATCH 13/99] geos-chem-shared-docs update: Use gcc@12.2.0 in load-libraries-guide.rst This commit informs the GCClassic superproject about the following commits pushed to the geos-chem-shared-docs submodule: a68981b Update gcc@10.2.0 -> gcc@12.2.0 in load-libraries-guide.rst This updates the GCC compiler version from 10.2.0 to 12.2.0 in the various documentation pages. Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 47cb22b..a68981b 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 47cb22bf9a93dd5c54a597062b41ef4ab1db4ce9 +Subproject commit a68981bec91028c8165f220fef683650cb79afe4 From 930deb9fc19e56e8ff9aee12f3f6bb2949437ffe Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 29 Aug 2024 14:25:23 -0400 Subject: [PATCH 14/99] GEOS-Chem submod update: Merge PR #2436, #2439, #2371 (PPN Phot etc.) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 602b660c1 PR #2436 post-merge update: Fix typo in ExtData.rc.fullchem d34c567a4 Merge PR #2436 (Update GFED4 climatology for 2010-2023) d4c47babf Merge PR #2439 (Update run scripts and env files for Discover) 43d0e9083 Merge PR #2371 (Adding PPN photolysis) This implements photolysis for the PPN species. Also, two other no-diff-to-benchmark updates have been added, namely updating run scripts for NASA discover and updating the GFED4 climatology file. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 3073aff..602b660 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 3073aff2e63d1073f7e63acaa9dba293dbc0553a +Subproject commit 602b660c13182a43b5620fad0eaf402d7a18696a From 49908a8ada48a6ef23ca0f56bf4e7859a83a0bff Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 3 Sep 2024 13:19:02 -0400 Subject: [PATCH 15/99] GEOS-Chem submod update: Merge PR #2424, PR #2426, Cloud-J PR #24 This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 1951ea96e Declare PPN as photolyzing in the species database 40a078514 Merge PR #2424 (Support for Cloud-J_v8.0.0) 647c9f579 Merge PR #2426 (Store aerosol-specific optics files in new directory) and to the geoschem/Cloud-J repository: 291a161 Update Cloud-J standalone settings to use UV absorption by H2O by default 6a027b1 Merge pull request #24 from geoschem/feature/cloudj_v8 These PRs move aerosol optics configuration files to a separate folder (out of the CHEM_INPUTS/FAST-JX folder structure) and update Cloud-J to version 8.0.0. Signed-off-by: Bob Yantosca --- src/Cloud-J | 2 +- src/GEOS-Chem | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Cloud-J b/src/Cloud-J index d20050f..291a161 160000 --- a/src/Cloud-J +++ b/src/Cloud-J @@ -1 +1 @@ -Subproject commit d20050f1ef9e3895d58f3041efd2da59ce1ed421 +Subproject commit 291a1612cb30f09fd56e761bdd27a095ab1d9815 diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 602b660..1951ea9 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 602b660c13182a43b5620fad0eaf402d7a18696a +Subproject commit 1951ea96ef14e01c08a1df7da254109050e78c79 From 25bb8331349054b55747e49d03f6cc5fe9496c57 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 4 Sep 2024 10:09:12 -0400 Subject: [PATCH 16/99] Update jinja2 to 3.1.4 in docs/requirements.txt docs/requirements.txt - Use jinja 3.1.4 as there is a dependabot security warning for the previous version 3.1.3. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 3 +++ docs/requirements.txt | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f6603f..de3ddff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Changed - Updated `docs/source/geos-chem-shared-docs/spack/packages.yaml` to use GCC 12.2.0 compilers +### Fixed +- Now use `jinja2==3.1.4` in `docs/requirements.txt` (fixes a security issue) + ## [14.4.3] - 2024-08-13 ### Changed - Updated GEOS-Chem (science codebase) to 14.4.3 diff --git a/docs/requirements.txt b/docs/requirements.txt index 60b3987..71e269d 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -12,4 +12,4 @@ sphinxcontrib-bibtex==2.6.2 sphinx-autobuild==2021.3.14 recommonmark==0.7.1 docutils==0.20.1 -jinja2==3.1.3 +jinja2==3.1.4 From 615cf45885ca6881791cc6d4f286c4d10d721da0 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 5 Sep 2024 13:48:32 -0400 Subject: [PATCH 17/99] Cloud-J submod update: Merge PR #26 (Define max J-values rather than exact) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 6bf4a36 Merge pull request #26 from geoschem/feature/define_max_rather_than_exact_num_jvalues This PR fixes an issue where Cloud-J will stop reading entries from FJX_j2j.dat before the "9999" end-of-file marker. Signed-off-by: Bob Yantosca --- src/Cloud-J | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Cloud-J b/src/Cloud-J index 291a161..6bf4a36 160000 --- a/src/Cloud-J +++ b/src/Cloud-J @@ -1 +1 @@ -Subproject commit 291a1612cb30f09fd56e761bdd27a095ab1d9815 +Subproject commit 6bf4a36d11039783c0b29befc48e93cdff7f6ecb From b577abe96cda9fe5652d4ad21c72b4ea09c7771e Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 6 Sep 2024 09:56:16 -0400 Subject: [PATCH 18/99] GEOS-Chem submod update: Merge PR #2452 (Reorder photo rxns for PNs, ANs) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a5fba9c88 Merge PR #2452 (Reorder photo rxns for PNs and ANs) This PR reorders the photo rxns of the PN and AN species added by @ktravis213 in PR #2318, so that they now follow PPN in the FJX_j2j.dat configuration file for Cloud-J. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 1951ea9..a5fba9c 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 1951ea96ef14e01c08a1df7da254109050e78c79 +Subproject commit a5fba9c88ad279095026be17c31a40bb84802eda From 5e00d7e08a3cb88cf88b1e43e7de6d08094262b9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 13 Sep 2024 10:04:44 -0400 Subject: [PATCH 19/99] GEOS-Chem update: Merge PR #2457 (Update Is_Photolysis tags) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: cd0366015 Merge PR #2457 (Update Is_Photolysis tags in species_database.yml) This PR ensures that photolyzing species (as listed in the KPP fullchem.eqn and FJX_j2j.dat files) have "Is_Photolysis.true" tags in the species_database.yml file. Non-photolyzing species have had these tags removed. Also the JValues collection in the GCHP HISTORY.rc.fullchem file has been updated. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index a5fba9c..cd03660 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit a5fba9c88ad279095026be17c31a40bb84802eda +Subproject commit cd03660155e86b8cea3681c7a9554e5e783511d6 From 0e075b75204ca49009225950c3fc69e6b5ff681f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 16 Sep 2024 16:19:55 -0400 Subject: [PATCH 20/99] GEOS-Chem & HEMCO updates: Merge PR #2462, PR #2430, PR #287 This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: c0aeff427 Merge PR #2462 (Bug fix: ALK6 in HEMCO_Config.rc should be ALK7) 5c31c3470 Merge PR #2430 (Updated Y. Wang soil NOx scheme as an option) and the geos-chem/HEMCO repository c6a9d46 Merge PR #287 (Updated Y. Wang soil NOx scheme as an option) This PR does the following: 1. Implements the U. Iowa soil NOx scheme as an option. This is currently switched off by default. 2. Adds a bug fix in HEMCO configuration files: ALK6 should be called ALK7. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index cd03660..c0aeff4 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit cd03660155e86b8cea3681c7a9554e5e783511d6 +Subproject commit c0aeff427c45a25bc85fe18b5baf2a489dfac863 diff --git a/src/HEMCO b/src/HEMCO index d0d5fca..c6a9d46 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit d0d5fca8ceab6f59aa98d6e65952dcfc9f3aef6e +Subproject commit c6a9d4668ee54af64f785f6c1113a2bc659efc70 From af1ced6d43d0d48a81dd4b19829af47ef3da30c1 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 19 Sep 2024 16:59:48 -0400 Subject: [PATCH 21/99] GEOS-Chem submodupdate: Merge PR #2464 (remove zero J-value diagnostics) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index c0aeff4..dd8cce6 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit c0aeff427c45a25bc85fe18b5baf2a489dfac863 +Subproject commit dd8cce62da7fbb77fd535e9df7207fe5bf883114 From 61606327cd5974f0a51353ea3c7d22620c6a00c7 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 20 Sep 2024 17:00:52 -0400 Subject: [PATCH 22/99] GEOS-Chem submod update: Merge PR #1467 (Fix dry mass fraction of seasalt in aerosol thermodynamics) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index dd8cce6..875a159 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit dd8cce62da7fbb77fd535e9df7207fe5bf883114 +Subproject commit 875a1593f065a345d05b2243ed2c1150ff68d1d2 From 5e45d73f6918d049f369a5f05bbca7d4482a9969 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Tue, 24 Sep 2024 12:37:54 -0400 Subject: [PATCH 23/99] Bugfix: Restore stale workflow functionality The stale workflows are currently failing with the error: Invalid workflow file: .github/workflows/stale.yml#L26 The workflow is not valid. .github/workflows/stale.yml (Line: 26, Col: 11): A sequence was not expected To fix this, the list of exempt-issues-labels in .github/workflows/stale.yml must be a comma separated list. A single quote is placed around the list to allow for use of colons in label names. Signed-off-by: Melissa Sulprizio --- .github/workflows/stale.yml | 2 +- CHANGELOG.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index c5b8f3e..4635a44 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -22,7 +22,7 @@ jobs: 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'] + 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.' diff --git a/CHANGELOG.md b/CHANGELOG.md index 07725d7..5575ae0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit 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 +### Fixed +- Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run + ## [14.4.3] - 2024-08-13 ### Changed - Updated GEOS-Chem (science codebase) to 14.4.3 From bb056b30d1f7ef3e28d680f7470b9e288b6cfedf Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 27 Sep 2024 08:44:23 -0400 Subject: [PATCH 24/99] GEOS-Chem submod update: Merge PR #2477 (Fix for double counting CH4 ag burning emissions) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 875a159..580c4e0 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 875a1593f065a345d05b2243ed2c1150ff68d1d2 +Subproject commit 580c4e095b4fe3001e4224f431fa3525a668f520 From dfd1f6f6d5e22fe0ccd493ce6f9d95dc4539037a Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 27 Sep 2024 13:42:32 -0400 Subject: [PATCH 25/99] GEOS-Chem submodule update: Merge PR #2473 (seasonality of CH4 reservoir emissions) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 580c4e0..4f11ef0 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 580c4e095b4fe3001e4224f431fa3525a668f520 +Subproject commit 4f11ef074c0cafae977ff17637985502e3620354 From 347686f48dd72b5f80feede3ab8e29b11e0a6620 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Fri, 27 Sep 2024 14:08:06 -0400 Subject: [PATCH 26/99] GEOS-Chem and HEMCO submodule updates: Add fixes for stale issue Github workflow Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 4f11ef0..7ffdb5b 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 4f11ef074c0cafae977ff17637985502e3620354 +Subproject commit 7ffdb5b64f2ab2a2cdb6030addbeb0fae6b61104 diff --git a/src/HEMCO b/src/HEMCO index c6a9d46..a3d0c9a 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit c6a9d4668ee54af64f785f6c1113a2bc659efc70 +Subproject commit a3d0c9a280672ac1c40e3f322651f23b8196fa4c From 3daf9fceadd58818867f4a8753ac41488d1a250c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 30 Sep 2024 12:15:04 -0400 Subject: [PATCH 27/99] Moved config file doc to geos-chem-shared-docs docs/source/gcclassic-user-guide/geoschem-config.rst docs/source/gcclassic-user-guide/hemco-config.rst docs/source/gcclassic-user-guide/hemco-diagn.rst docs/source/gcclassic-user-guide/phot-chem.rst docs/source/gcclassic-user-guide/spec-db.rst - Moved to geos-chem-shared-docs/doc docs/source/gcclassic-user-guide/config-overview.rst - Now points to relocated files docs/source/geos-chem-shared-docs - Submodule update to CHANGELOG.md - Updated accordingly --- CHANGELOG.md | 2 + .../gcclassic-user-guide/config-overview.rst | 10 +- .../gcclassic-user-guide/geoschem-config.rst | 1797 ----------------- .../gcclassic-user-guide/hemco-config.rst | 225 --- .../gcclassic-user-guide/hemco-diagn.rst | 45 - .../source/gcclassic-user-guide/phot-chem.rst | 100 - docs/source/gcclassic-user-guide/spec-db.rst | 85 - docs/source/geos-chem-shared-docs | 2 +- 8 files changed, 8 insertions(+), 2258 deletions(-) delete mode 100644 docs/source/gcclassic-user-guide/geoschem-config.rst delete mode 100644 docs/source/gcclassic-user-guide/hemco-config.rst delete mode 100644 docs/source/gcclassic-user-guide/hemco-diagn.rst delete mode 100644 docs/source/gcclassic-user-guide/phot-chem.rst delete mode 100644 docs/source/gcclassic-user-guide/spec-db.rst diff --git a/CHANGELOG.md b/CHANGELOG.md index de3ddff..476753b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ## [Unreleased] - TBD ### Changed - Updated `docs/source/geos-chem-shared-docs/spack/packages.yaml` to use GCC 12.2.0 compilers +- Updated documentation for version 14.5.0 +- Moved several doc files (not supplemental guides) that are used in both GCClassic and GCHP the to `geos-chem-shared-docs/doc` folder ### Fixed - Now use `jinja2==3.1.4` in `docs/requirements.txt` (fixes a security issue) diff --git a/docs/source/gcclassic-user-guide/config-overview.rst b/docs/source/gcclassic-user-guide/config-overview.rst index 1f4d7e7..320b29c 100644 --- a/docs/source/gcclassic-user-guide/config-overview.rst +++ b/docs/source/gcclassic-user-guide/config-overview.rst @@ -27,9 +27,9 @@ edit most (if not all) of these configuration files: .. toctree:: :maxdepth: 1 - geoschem-config.rst - hemco-config.rst - hemco-diagn.rst + ../geos-chem-shared-docs/doc/geoschem-config.rst + ../geos-chem-shared-docs/doc/hemco-config.rst + ../geos-chem-shared-docs/doc/hemco-diagn.rst history.rst All of the above-mentioned files are included in your :ref:`GEOS-Chem @@ -52,5 +52,5 @@ you'll need to edit these configuration files: .. toctree:: :maxdepth: 1 - spec-db.rst - phot-chem.rst + ../geos-chem-shared-docs/doc/spec-db.rst + ../geos-chem-shared-docs/doc/phot-chem.rst diff --git a/docs/source/gcclassic-user-guide/geoschem-config.rst b/docs/source/gcclassic-user-guide/geoschem-config.rst deleted file mode 100644 index 2e3d585..0000000 --- a/docs/source/gcclassic-user-guide/geoschem-config.rst +++ /dev/null @@ -1,1797 +0,0 @@ -.. _cfg-gc-yml: - -################### -geoschem_config.yml -################### - -Starting with GEOS-Chem 14.0.0, the :file:`input.geos` configuration -file (plain text) has been replaced with by the -:file:`geoschem_config.yml` file. This file is in `YAML -`_ format, which is a text-based markup syntax used -for representing dictionary-like data structures. - -.. note:: - - The :file:`geoschem_config.yml` file contains several sections. Only - the sections relevant to a given type of simulation are present. - For example, :option:`fullchem` simulation options (such as aerosol - settings and photolysis settings) are omitted from the - :file:`geoschem_config.yml` file for the :option:`CH4` simulation. - -.. _gc-yml-simulation: - -=================== -Simulation settings -=================== - -.. code-block:: yaml - - #============================================================================ - # Simulation settings - #============================================================================ - simulation: - name: fullchem - start_date: [20190701, 000000] - end_date: [20190801, 000000] - root_data_dir: /path/to/ExtData - met_field: MERRA2 - species_database_file: ./species_database.yml - species_metadata_output_file: OutputDir/geoschem_species_metadata.yml - verbose: - activate: false - on_cores: root # Allowed values: root all - use_gcclassic_timers: false - -The :literal:`simulation` section contains general simulation options: - -.. option:: name - - Specifies the type of GEOS-Chem simulation. Accepted - values are - - .. option:: fullchem - - Full-chemistry simulation. - - .. option:: aerosol - - `Aerosol-only simulation - `_. - - .. option:: carbon - - Coupled carbon gases simulation (CH4-CO-CO2-OCS), implemented as - a KPP mechanism (cf :cite:t:`Bukosa_et_al._2023`). - - You must :ref:`configure your build ` with - :literal:`-DMECH=carbon` in order to use this simulation. - - .. option:: CH4 - - `Methane simulation `_. - - This simulation will eventually be superseded by the - :option:`carbon` simulation. - - .. option:: CO2 - - `Carbon dioxide simulation `_. - - This simulation will eventually be superseded by the - :option:`carbon` simulation. - - .. option:: Hg - - `Mercury simulation `_. - - You must :ref:`configure your build ` with - :literal:`-DMECH=Hg` in order to use this simulation. - - .. option:: POPs - - `Persistent organic pollutants (aka POPs) simulation - `_. - - .. attention:: - - The POPs simulation is currently stale. We look to members - of the GEOS-Chem user community take the lead on updating - this simulation. - - .. option:: tagCH4 - - `Methane simulation - `_ with species - tagged by geographic region or other criteria. - - This simulation will eventually be superseded by the - :option:`carbon` simulation. - - .. option:: tagCO - - Carbon dioxide simulation, with species - tagged by geographic region and other criteria. - - This simulation will eventually be superseded by the - :option:`carbon` simulation. - - .. option:: tagO3 - - `Ozone simulation - `_ (using - specified production and loss rates), - with species tagged by geographical region. - - .. option:: TransportTracers - - `Transport Tracers simulation - `_, with - both radionuclide and passive_species. Useful for evaluating - model transport. - - .. option:: metals - - Trace metals simulation - -.. option:: start_date - - Specifies the starting date and time of the simulation in list - notation :literal:`[YYYYMMDD, hhmmss]`. - -.. option:: end_date - - Specifies the ending date and time of the simulation in list - notation :literal:`[YYYYMMDD, hhmmss]`. - -.. option:: root_data_dir - - Path to the root data directory. All of the data that GEOS-Chem - Classic reads must be located in subfolders of this directory. - -.. option:: met_field - - Name of the meteorology product that will be used to drive - GEOS-Chem Classic. Accepted values are: - - .. option:: MERRA2 - - The `MERRA-2 `_ meteorology - product from NASA/GMAO. MERRA-2 is a stable reanalysis product, - and extends from approximately 1980 to present. - **(Recommended option)** - - .. option:: GEOS-FP - - The `GEOS-FP `_ meteorology - product from NASA/GMAO. GEOS-FP is an operational data product - and, unlike MERRA-2, periodically receives science updates. - - .. option:: GCAP2 - - The GCAP-2 meteorology product, archived from the GISS-2 GCM. - GCAP-2 has hundreds of years of data available, making it useful - for simulations of historical climate. - -.. option:: species_database_file - - Path to the :ref:`GEOS-Chem Species Database ` file. This - is stored in the run directory file :file:`./species_database.yml`. - You should not have to edit this setting. - -.. option:: species_metadata_output_file - - Path to the :file:`geoschem-species-metadata.yml` file. This file - contains echoback of information from :ref:`species_database.yml - `, but only for species that are defined in this - simulation (instead of all possible species). This facilitates - interfacing GEOS-Chem with external models such as CESM. - -.. option:: verbose: - - Menu controlling verbose printout. Starting with GEOS-Chem 14.2.0 - and HEMCO 3.7.0, most informational printouts are now deactivated - by default. You may choose to activate them (e.g. for debugging - and/or testing) with the options below: - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - printing extra informational printout to the screen and/or log - file. - - .. option:: on_cores: - - Specify on which computational cores informational printout - should be done. - - .. option:: root - - Print extra informational output only on the root core. Use this - setting for GEOS-Chem Classic. - - .. option:: all - - Print extra informational output on all cores. Consider - using this when using GEOS-Chem as GCHP, or in MPI-based - external models (NASA GEOS, CESM, etc.). - -.. option:: use_gcclassic_timers - - Activates (:literal:`true`) or deactivates (:literal:`false`) - the GEOS-Chem Classic timers. If activated, information about how - long each component of GEOS-Chem took to execute will be printed to - the screen and/or :ref:`GEOS-Chem log file - `. The same information will also be written - in JSON format to a file named :ref:`gcclassic_timers.json - `. - - You can set this option to :literal:`false` unless you are running - benchmark or timing simulations. - -.. _cfg-gc-yml-grid: - -============= -Grid settings -============= - -.. code-block:: YAML - - #============================================================================ - # Grid settings - #============================================================================ - grid: - resolution: 4.0x5.0 - number_of_levels: 72 - longitude: - range: [-180.0, 180.0] - center_at_180: true - latitude: - range: [-90.0, 90.0] - half_size_polar_boxes: true - nested_grid_simulation: - activate: true - buffer_zone_NSEW: [0, 0, 0, 0] - -The :literal:`grid` section contains settings that define the grid used -by GEOS-Chem Classic: - -.. option:: resolution - - Specifies the horizontal resolution of the grid. Accepted values are: - - .. option:: 4.0x5.0 - - The global :math:`4^{\circ}{\times}5^{\circ}` GEOS-Chem Classic - grid. - - .. option:: 2.0x2.5 - - The global :math:`2.0^{\circ}{\times}2.5^{\circ}` GEOS-Chem Classic - grid. - - .. option:: 0.5x0.625 - - The global :math:`0.5^{\circ}{\times}0.625^{\circ}` GEOS-Chem Classic - grid (:option:`MERRA2` only). Can be used for global or nested - simulations. - - .. option:: 0.5x0.625 - - The global :math:`0.25^{\circ}{\times}0.3125^{\circ}` GEOS-Chem - Classic grid (:option:`GEOS-FP` and :option:`MERRA2`). Can be - used for global or nested simulations. - -.. option:: number_of_levels - - Number of vertical levels to use in the simulation. Accepted - values are: - - .. option:: 72 - - Use 72 vertical levels. This is the native vertical resolution - of :option:`MERRA2` and :option:`GEOS-FP`. - - .. option:: 47 - - Use 47 vertical levels (for :option:`MERRA2` and :option:`GEOS-FP`). - - .. option:: 40 - - Use 40 vertical levels (for :option:`GCAP2`). - -.. option:: longitude - - Settings that define the longitude dimension of the grid. There are - two sub-options: - - .. option:: range - - The minimum and maximum longitude values (grid box edges), - specified in list format. - - .. option:: center_at_180 - - If :literal:`true`, then westernmost grid boxes are centered - at :math:`-180^{\circ}` longitude (the International Date Line). - This is true for both :option:`MERRA2` and :option:`GEOS-FP`. - - If :literal:`false`, then the westernmost grid boxes have their - westernmost edges at :math:`-180^{\circ}` longitude. This is - true for the :option:`GCAP2` grid. - -.. option:: latitude - - Settings to define the latitude dimension of the grid. There are - two sub-options: - - .. option:: range - - The minimum and maximum latitude values (grid box edges), - specified in list format. - - .. option:: use_halfpolar_boxes - - If :literal:`true`, then the northernmost and southernmost grid - boxes will be :math:`\frac{1}{2}` the extent of other grid boxes. - This is true for both :option:`MERRA2` and :option:`GEOS-FP`. - - If :literal:`false`, then all grid boxes will have the same extent - in latitude. This is true for the :option:`GCAP2` grid. - -.. option:: nested_grid_simulation - - Settings for nested-grid simulations. There are two sub-options: - - .. option:: activate - - If :literal:`true`, this indicates that the simulation will use a - sub-window of the horizontal grid. - - If :literal:`false`, this indicates that the simulation will use - the entire global grid extent. - - .. option:: buffer_zone_NSEW - - Specifies the nested grid latitude offsets (# of grid boxes) in list - format :literal:`[N-offset, S-offset, E-offset, W-offset]`. These - offsets are used to define an inner window region in which - transport is actually done (aka the "transport window"). This - "transport window" is always smaller than the actual size of the - nested grid region in order to properly account for the boundary - conditions. - - - For global simulations, use: :literal:`[0, 0, 0, 0]`. - - For nested-grid simulations, we recommend using: :literal:`[3, 3, 3, 3]`. - -.. _cfg-gc-yml-timesteps: - -================== -Timesteps settings -================== - -.. code-block:: YAML - - #============================================================================ - # Timesteps settings - #============================================================================ - timesteps: - transport_timestep_in_s: 600 - chemistry_timestep_in_s: 1200 - radiation_timestep_in_s: 10800 - -The :literal:`timesteps` section specifies the frequency at which -various GEOS-Chem operations occur: - -.. option:: transport_timestep_in_s - - Specifies the "heartbeat" timestep of GEOS-Chem.. This is - the frequency at which transport, cloud convection, PBL mixing, and - wet deposition will be done. - - - Recommended value for global simulations: :literal:`600` - - Recommended value for nested simluations: :literal:`300` or smaller - -.. option:: chemistry_timestep_in_s - - Specifies the frequency at which chemistry and emissions will be - done. - - - Recommended value for global simulations :literal:`1200` - - Recommended value for nested simulations :literal:`600` or smaller - -.. option:: radiation_timestep_in_s - - Specifies the frequency at which the `RRTMG - `_ radiative - transfer model will be called (valid for :option:`fullchem` - simulations only). - -.. _cfg-gc-yml-operations: - -=================== -Operations settings -=================== - -This section of :file:`geoschem_config.yml` is included for all -simulations. However, some of the options listed below will be omitted for -simulations that do not require them. - -There are several sub-sections under :literal:`operations`: - -.. _cfg-gc-yml-operations-chemistry: - -Chemistry ----------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - chemistry: - activate: true - linear_chemistry_aloft: - activate: true - use_linoz_for_O3: true - active_strat_H2O: - activate: true - use_static_bnd_cond: true - gamma_HO2: 0.2 - autoreduce_solver: - activate: false - use_target_threshold: - activate: true - oh_tuning_factor: 0.00005 - no2_tuning_factor: 0.0001 - use_absolute_threshold: - scale_by_pressure: true - absolute_threshold: 100.0 - keep_halogens_active: false - append_in_internal_timestep: false - - # ... following sub-sections omitted ... - -The :literal:`operations:chemistry` section contains settings for chemistry: - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - chemistry in GEOS-Chem. - -.. option:: linear_chemistry_aloft - - Determines how linearized chemistry will be applied in the - stratosphere and/or mesosphere. (Only valid for :option:`fullchem` - simulations). - - There are two sub-options: - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - linearized stratospheric chemistry in the stratosphere and/or - mesosphere. - - .. option:: use_linoz_for_O3 - - If :literal:`true`, `Linoz stratospheric ozone chemistry - `_ - will be used. - - If :literal:`false`, Synoz (i.e. a synthetic flux of ozone across - the tropopause) will be used instead of Linoz. - -.. option:: active_strat_H2O - - Determines if water vapor as modeled by GEOS-Chem will be - allowed to influence humidity fields. (Only valid for - :option:`fullchem` simulations) - - There are two sub-options: - - .. option:: activate - - Allows (:literal:`true`) or disallows (:literal:`false` the H2O - species in GEOS-Chem to influence specific humidity and - relative humidity. - - .. option:: use_static_bnd_cond - - Allows (:literal:`true`) or diasallows (:literal:`false`) a - static boundary condition. - - **TODO** Clarify this - -.. option:: gamma_HO2 - - Specifies :math:`\gamma`, the uptake coefficient for :math:`HO_2` - heterogeneous chemistry. - - Recommended value: :literal:`0.2`. - -.. option:: autoreduce_solver - - Menu for controlling the adaptive mechanism auto-reduction feature, - which is available in `KPP - 3.0.0. `_ and later - versions. See :cite:t:`Lin_et_al._2023` for details. - - .. option:: activate - - If :literal:`true`, the mechanism will be integrated using the - Rosenbrock method with the adaptive auto-reduction feature. - - If :literal:`false`, the mechanism will be integrated using the - traditional Rosenbrock method. - - Default value: :literal:`false`. - - .. option:: use_target_threshold - - Contains options for defining :math:`\partial` (the partitioning - threshold between "fast" and "slow" species") by considering the - production and loss of key species (OH for daytime, NO2 for - nighttime). - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - using OH and NO2 to determine :math:`\partial`. - - Default value: :literal:`true`. - - .. option:: oh_tuning_factor - - Specifies :math:`{\alpha}_{OH}`, which is used to compute - :math:`\partial`. - - .. option:: no2 tuning factor - - Specifies :math:`{\alpha}_{NO2}`, which is used to compute - :math:`\partial`. - - .. option:: use_pressure_threshold - - Contains options for setting an absolute threshold - :math:`\partial` that may be weighted by pressure. - - .. option:: scale_by_pressure - - Activates (:literal:`true`) or deactivates (:literal:`false`) - using a pressure-dependent method to determine :math:`\partial`. - - .. option:: absolute_threshold - - The absolute partitioning threshold :math:`\partial`. - - If :option:`scale_by_pressure` is :literal:`true,` and - :option:`use_target_threshold:activate` is :literal:`false` , - the value for :math:`\partial` specified here will be scaled - by the ratio :math:`P / P_{sfc}`. where :math:`P` is the grid box - pressure and :math:`P_{sfc}` is the surface pressure for the - column. - - .. option:: keep_halogens_active - - If :literal:`true`, then all halogen species will be considered - "fast". This may be necessary in order to obtain realistic - results for ozone and other important species. - - If :literal:`false`, then halogen species will be determined as - "slow" or "fast" depending on the partitioning threshold - :math:`\partial`. - - Default value: :literal:`true` - - .. option:: append_in_internal_timestep - - If :literal:`true`, any "slow" species that later become "fast" - will be appended to the list of "fast" species. - - If :literal:`false`, any "slow" species that later become - "fast" will NOT be appended to the list of "fast" species. - - Default value: :literal:`false` - -.. _cfg-gc-yml-operations-convection: - -Convection ----------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - convection: - activate: true - - # ... following sub-sections omitted ... - -The :command:`operations:convection` section contains settings for -`cloud convection `_: - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - cloud convection in GEOS-Chem. - -.. _cfg-gc-yml-operations-drydep: - -Dry deposition --------------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - dry_deposition: - activate: true - CO2_effect: - activate: false - CO2_level: 600.0 - reference_CO2_level: 380.0 - diag_alt_above_sfc_in_m: 10 - - # ... following sub-sections omitted ... - -The :literal:`operations:dry_deposition` section contains settings that -for `dry deposition `_: - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - dry deposition. - -.. option:: CO2_effect - - This sub-section contains options for applying the - `simple parameterization for the CO2 effect on stomatal resistance - `_. - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) the CO2 - effect on stomatal resistance in dry deposition. - - Default value: :literal:`false`. - - .. option:: CO2_level - - Specifies the CO2 level (in ppb). - - .. option:: reference_CO2_level - - Specifies the reference CO2 level (in ppb). - -.. option:: diag_alt_above_sfc_in_m: - - Specifies the altitude above the surface (in m) to used with the - `ConcAboveSfc diagnostic collection `_. - -.. _cfg-gc-yml-operations-pblmix: - -PBL mixing ----------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - pbl_mixing: - activate: true - use_non_local_pbl: true - - # ... following sub-sections omitted ... - -The :literal:`operations:pbl_mixing` section contains settings that -for `planetary boundary layer (PBL) mixing -`_: - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - planetary boundary layer mixing in GEOS-Chem Classic. - -.. option:: use_non_local_pbl - - If :literal:`true`, then the `non-local PBL mixing scheme (VDIFF) - `_ will - be used. (Default option) - - If :literal:`false`, then the `full PBL mixing scheme (TURBDAY) - `_ will - be used. - -.. _cfg-gc-yml-operations-photolysis: - -Photolysis ----------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - photolysis: - activate: true - num_levs_with_cloud: 34 - input_directories: - fastjx_input_dir: /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2024-05/ - cloudj_input_dir: /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2023-05/ - overhead_O3: - use_online_O3_from_model: true - use_column_O3_from_met: true - use_TOMS_SBUV_O3: false - photolyze_nitrate_aerosol: - activate: true - NITs_Jscale: 100.0 - NIT_Jscale: 100.0 - percent_channel_A_HONO: 66.667 - percent_channel_B_NO2: 33.333 - - # ... following sub-sections omitted ... - -The :literal:`operation:photolysis` section contains settings for photolysis. -This section only applies to fullchem, Hg, and aerosol-only simulations. - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - photolysis. - - .. attention:: - - You should always keep photolysis turned on in your - simulations. Disabling photolysis should only be done when - debugging. - -.. option:: num_levs_with_cloud - - Specifies the number of levels that can contain clouds, which is a - required input for the Cloud-J photolysis module. This value is - saved to the :code:`Input_Opt%NLevs_Phot_Cloud` field. - - .. attention:: - - The value of :option:`num_levs_with_cloud` will be set to the - proper value when you create a run directory. Its value depends - on the meteorology that is used to drive your GEOS-Chem - simulation. You should not change this value! - -.. option:: input_directories - - Specifies the location of directories containing photolysis - configuration files. - - .. option:: fastjx_input_dir - - Specifies the path to the legacy FAST_JX configuration files containing - information about species cross sections and quantum yields. - These are used to define several aerosol optical properties - even when FAST-JX is not used. - - Note that FAST-JX is off by default and Cloud-J is used - instead. You can use legacy FAST-JX instead of Cloud-J by - configuring with :literal:`-DFASTJX=y` during build. - - .. option:: cloudj_input_dir - - Specifies the path to the Cloud-J configuration files containing - information about species cross sections and quantum yields. - -.. option:: overhead_O3 - - This section contains settings that control which overhead ozone - sources are used for photolysis - - .. option:: use_online_O3_from_model - - Activates (:literal:`true`) or deactivates (:literal:`false`) using - online O3 from GEOS-Chem in the extinction calculations for photolysis. - - Recommended value: :literal:`true` - - .. option:: use_column_O3_from_met - - Activates (:literal:`true`) or deactivates (:literal:`false`) using - ozone columns (e.g. TO3) from the meteorology fields. - - Recommended value: :literal:`true`. - - .. option:: use_TOMS_SBUV_O3 - - Activates (:literal:`true`) or deactivates (:literal:`false`) using - ozone columns from the TOMS-SBUV archive will be used. - - Recommended value: :literal:`false`. - -.. option:: photolyze_nitrate_aerosol: - - This section contains settings that control options for nitrate - aerosol photolysis. - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - nitrate aerosol photolysis. - - Recommended value: :literal:`true`. - - .. option:: NITs_Jscale - - Scale factor (percent) for JNO3 that photolyzes NITs aerosol. - - .. option:: NIT_Jscale - - Scale factor (percent) for JHNO2 that photolyzes NIT aerosol. - - .. option:: percent_channel_A_HONO - - Fraction of JNITs/JNIT in channel A (HNO2) for NITs photolysis. - - .. option:: percent_channel_B_HO2 - - Fraction of JNITs/JNIT in channel B (NO2) for NITs photolysis. - -.. _cfg-gc-yml-rrtmg: - -RRTMG radiative transfer model ------------------------------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - rrtmg_rad_transfer_model: - activate: false - aod_wavelengths_in_nm: - - 550 - longwave_fluxes: false - shortwave_fluxes: false - clear_sky_flux: false - all_sky_flux: false - fixed_dyn_heating: false - seasonal_fdh: false - read_dyn_heating: false - co2_ppmv: 390.0 - - # .. following sub-sections omitted ... - -The :literal:`operations:rrtmg_rad_transfer_model` section contains -settings for the `RRTMG radiative transfer model -`_: - -This section only applies to :option:`fullchem` simultions. - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) the RRTMG - radiative transfer model. - - Default value: :literal:`false`. - -.. option:: aod_wavelengths_in_nm - - Specify wavelength(s) for the aerosol optical properties in nm - (in `YAML sequence format - `_) - Up to three wavelengths can be selected. The specified wavelengths - are used for the photolysis mechanism (either legacy FAST-JX or - Cloud-J) regardless of whether the RRTMG radiative transfer model is used. - -.. option:: longwave_fluxes - - Activates (:literal:`true`) or deactivates (:literal:`false`) - RRTMG longwave flux calculations. - - Default value: :literal:`false`. - -.. option:: shortwave_fluxes - - Activates (:literal:`true`) or deactivates (:literal:`false`) - RRTMG shortwave calculations. - - Default value: :literal:`false`. - -.. option:: clear_sky_flux - - Activates (:literal:`true`) or deactivates (:literal:`false`) - RRTMG clear-sky flux calculations. - - Default value: :literal:`false`. - -.. option:: all_sky_flux - - Activates (:literal:`true`) or deactivates (:literal:`false`) - RRTMG all-sky flux calculations. - - Default value: :literal:`false`. - -.. option:: fixed_dyn_heating - - Activates (:literal:`true`) or deactivates (:literal:`false`) - fixed dynamic heating (FDH) approximation as described by Forster *et al.* - [`1997 - `_]. - - Default value: :literal:`false`. - -.. option:: seasonal_fdh - - Activates (:literal:`true`) or deactivates (:literal:`false`) - seasonally-evolving fixed dynamic heating (SEFDH) approzimation as - described by Kiehl *et al.* [`1999 - `_]. - - .. attention:: - - This option has not been extensively tested, and is considered - experimental. - - Default value: :literal:`false`. - -.. option:: read_dyn_heating - - Activates (:literal:`true`) or deactivates (:literal:`false`) - reading previously-archived dynamical heating outputs from disk. - - Default value: :literal:`false`. - -.. option:: co2_ppmv - - Specify the value of CO2 [in parts per million by volume] to be - used in radiative forcing calculations. - - Default value: :literal:`390.0`. - - -.. _cfg-gc-yml-transport: - -Transport ---------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - transport: - gcclassic_tpcore: # GEOS-Chem Classic only - activate: true # GEOS-Chem Classic only - fill_negative_values: true # GEOS-Chem Classic only - iord_jord_kord: [3, 3, 7] # GEOS-Chem Classic only - transported_species: - - ACET - - ACTA - - AERI - # ... etc more transported species ... - - # .. following sub-sections omitted ... - -The :literal:`operations:transport` section contains -settings for `species transport -`_: - -.. option:: gcclassic_tpcore - - Contains options that control species transport in GEOS-Chem - Classic with the `TPCORE advection scheme - `_: - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) species - transport in GEOS-Chem Classic. - - Default value: :literal:`true`. - - .. option:: fill_negative_values - - If :literal:`true`, negative species concentrations will be - replaced with zeros. - - If :literal:`false`, no change will be made to species - concentrations. - - Default value: :literal:`true`. - - .. option:: iord_jord_kord - - Specifies advection options (in list format) for TPCORE in the - longitude, latitude, and vertical dimensions. The options are - listed below: - - #. 1st order upstream scheme (use for debugging only) - #. 2nd order van Leer (full monotonicity constraint) - #. Monotonic PPM - #. Semi-monotonic PPM (same as 3, but overshoots are allowed) - #. Positive-definite PPM - #. Un-constrained PPM (use when fields & winds are very smooth) - this option only when the fields and winds are very smooth. - #. Huynh/Van Leer/Lin full monotonicity constraint (KORD only) - - Default (and recommended) value: :literal:`[3, 3, 7]` - -.. option:: transported_species - - A list of species names (in `YAML sequence format - `_) - that will be transported by the TPCORE advection scheme. - -.. _cfg-gc-yml-wetdep: - -Wet deposition --------------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem operations - #============================================================================ - operations: - - # .. preceding sub-sections omitted ... - - wet_deposition: - activate: true - -The :literal:`operations:wet_deposition` section contains settings -for `wet deposition `_. - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - wet deposition in GEOS-Chem Classic. - -.. _gc-yml-aerosols: - -================= -Aerosols settings -================= - -This section of :file:`geoschem_config.yml` is included for -:option:`fullchem` and :option:`aerosol` simulations. - -There are several sub-sections under :literal:`aerosols`: - -.. _cfg-gc-yml-aerosol-carbon: - -Carbon aerosols ---------------- - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem aerosols - #============================================================================ - aerosols: - - carbon: - activate: true - brown_carbon: false - enhance_black_carbon_absorption: - activate: true - hydrophilic: 1.5 - hydrophobic: 1.0 - - # .. following sub-sections omitted ... - -The :literal:`aerosols:carbon` section contains settings for -`carbon aerosols -`_: - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) carbon - aerosols in GEOS-Chem. - - Default value: :literal:`true`. - -.. option:: brown_carbon - - Activates (:literal:`true`) or deactivates (:literal:`false`) brown - carbon aerosols in GEOS-Chem. - - Default value: :literal:`false`. - -.. option:: enhance_black_carbon_absorption - - Options for enhancing the absorption of black carbon aerosols - due to external coating. - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) black - carbon absorption enhancement. - - Default value: :literal:`true`. - - .. option:: hydrophilic - - Absorption enhancement factor for hydrophilic black carbon - aerosol (species name **BCPI**). - - Default value: :literal:`1.5` - - .. option:: hydrophobic - - Absorption enhancement factor for hydrophilic black carbon - aerosol (species name **BCPO**). - - Default value: :literal:`1.0` - -.. _cfg-gc-yml-aerosols-soa: - -Complex SOA ------------ -The :code:`aerosols:complex_SOA` section contains settings for -`the complex SOA scheme used in GEOS-Chem -`_. - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem aerosols - #============================================================================ - aerosols: - - # ... preceding sub-sections omitted ... - - complex_SOA: - activate: true - semivolatile_POA: false - - # ... following sub-sections omitted ... - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - complex SOA scheme. - - Default value: - - - :literal:`true` for the :option:`fullchem` benchmark simulation - - :literal:`false` for all other :option:`fullchem` simulations - -.. option:: semivolatile_POA - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - semi-volatile primary organic aerosol (POA) option. - - Default value: :literal:`false` - -.. _gc-yml-aerosols-dust: - -Mineral dust aerosols ---------------------- -The :literal:`aerosols:dust` section contains settings for -`mineral dust aerosols -`_. - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem aerosols - #============================================================================ - aerosols: - - # ... preceding sub-sections omitted ... - - dust: - activate: true - acid_uptake_on_dust: false - - # ... following sub-sections omitted ... - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) mineral - dust aerosols in GEOS-Chem. - - Default value: :literal:`true` - -.. option:: acid_uptake_on_dust - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - `acid uptake on dust option - `_, - which includes 12 additional species. - - Default value: :literal:`false` - -.. _cfg-gc-yml-aerosols-seasalt: - -Sea salt aerosols ------------------ -The :literal:`aerosols:sea_salt` section contains settings for `sea salt -aerosols -`_: - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem aerosols - #============================================================================ - aerosols: - - # ... preceding sub-sections omitted ... - - sea_salt: - activate: true - SALA_radius_bin_in_um: [0.01, 0.5] - SALC_radius_bin_in_um: [0.5, 8.0] - marine_organic_aerosols: false - - # ... following sub-sections omitted ... - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) sea salt - aerosols. - - Default value: :literal:`true` - -.. option:: SALA_radius_bin_in_um - - Specifies the upper and lower boundaries (in nm) for - accumulation-mode sea salt aerosol (aka **SALA**). - - Default value: :literal:`0.01 nm - 0.5 nm` - -.. option:: SALC_radius_bin_in_um - - Specifies the upper and lower boundaries (in nm) for - coarse-mode sea salt aerosol (aka **SALC**). - - Default value: :literal:`0.5 nm - 8.0 nm` - -.. option:: marine_organic_aerosols - - Activates (:literal:`true`) or deactivates (:literal:`false`) - `emission of marine primary organic aerosols - `_. - This option includes two extra species (**MOPO** and **MOPI**). - - Default value: :literal:`false` - -.. _cfg-gc-yml-aerosols-strat: - -Stratospheric aerosols ----------------------- -The :literal:`aerosols:sulfate` section contains settings for -stratopsheric aerosols. - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem aerosols - #============================================================================ - aerosols: - - # ... preceding sub-sections omitted ... - - stratosphere: - settle_strat_aerosol: true - polar_strat_clouds: - activate: true - het_chem: true - allow_homogeneous_NAT: false - NAT_supercooling_req_in_K: 3.0 - supersat_factor_req_for_ice_nucl: 1.2 - calc_strat_aod: true - - # ... following sub-sections omitted ... - - -.. option:: settle_strat_aerosol - - Activates (:literal:`true`) or deactivates (:literal:`false`) - gravitational settling of stratospheric solid particulate aerosols - (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, - corrected Stokes' Law). - - Default value: :literal:`true` - -.. option:: polar_strat_clouds - - Contains settings for how aerosols are handled in polar - stratospheric clouds (PSC): - - .. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) - formation of polar stratospheric clouds. - - Default value: :literal:`true` - - .. option:: het_chem - - Activates (:literal:`true`) or deactivates (:literal:`false`) - heterogeneous chemistry within polar stratospheric clouds. - - Default value: :literal:`true` - -.. option:: allow_homogeneous_NAT - - Activates (:literal:`true`) or deactivates (:literal:`false`) - heterogeneous formation of NAT from freezing of HNO3. - - Default value: :literal:`false` - -.. option:: NAT_supercooling_req_in_K - - Specifies the cooling (in K) required for homogeneous NAT nucleation. - - Default value: :literal:`3.0` - -.. option:: supersat_factor_req_for_ice_nucl - - Specifies the supersaturation factor required for ice nucleation. - - Recommended values: :literal:`1.2` for coarse grids; :literal:`1.5` for - fine grids. - -.. option:: calc_strat_aod - - Includes (:literal:`true`) or excludes (:literal:`false`) online - stratospheric aerosols in extinction calculations for photolysis. - - Default value: :literal:`true` - -.. _cfg-gc-yml-aerosols-sulfate: - -Sulfate aerosols ----------------- -The :literal:`aerosols:sulfate` section contains settings for `sulfate -aerosols `_: - -.. code-block:: YAML - - #============================================================================ - # Settings for GEOS-Chem aerosols - #============================================================================ - aerosols: - - # ... preceding sub-sections omitted ... - - sulfate: - activate: true - metal_cat_SO2_oxidation: true - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) sulfate aerosols. - - Default value: :literal:`true` - -.. option:: metal_cat_SO2_oxidation - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - `metal catalyzed oxidation of SO2 - `_. - - Default value: :literal:`true` - -.. _cfg-gc-yml-xdiag: - -================= -Extra diagnostics -================= - -The :literal:`extra_diagnostics` section contains settings for GEOS-Chem Classic -diagnostics that are not archived by :ref:`History -` or `HEMCO `_: - -.. _gc-yml-xdiag-obspack: - -Obspack diagnostic ------------------- - -The :literal:`extra_diagnostics:obspack` section contains settings for -the `Obspack diagnostic `_: - -.. code-block:: YAML - - #============================================================================ - # Settings for diagnostics (other than HISTORY and HEMCO) - #============================================================================ - extra_diagnostics: - - obspack: - activate: false - quiet_logfile_output: false - input_file: ./obspack_co2_1_OCO2MIP_2018-11-28.YYYYMMDD.nc - output_file: ./OutputDir/GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4 - output_species: - - CO - - 'NO' - - O3 - - # ... following sub-sections omitted ... - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) ObsPack - diagnostic output. - - Default value: :literal:`true` - -.. option:: quiet_logfile_output - - Deactivates (:literal:`true`) or activates (:literal:`false`) printing - informational output to :literal:`stdout` (i.e. the screen or log file). - - Default value: :literal:`false` - -.. option:: input_file - - Specifies the path to an ObsPack data file (in netCDF format). - -.. option:: output_file - - Specifies the path to the ObsPack diagnostic output file. This - will be a file that contains data at the same locations as - specified in :option:`input_file`. - -.. option:: output_species - - A list of GEOS-Chem species (as a YAML sequence) to archive to the - output file. - -.. _gc-yml-xdiag-plane: - -Planeflight diagnostic ------------------------ -The :literal:`extra_diagnostics:planeflight` section contains settings for -the `GEOS-Chem planeflight diagnostic -`_: - -.. code-block:: YAML - - #============================================================================ - # Settings for diagnostics (other than HISTORY and HEMCO) - #============================================================================ - extra_diagnostics: - - # ... preceding sub-sections omitted ... - - planeflight: - activate: false - flight_track_file: Planeflight.dat.YYYYMMDD - output_file: plane.log.YYYYMMDD - - # ... following sub-sections omitted ... - -.. option:: activate - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - Planeflight diagnostic output. - - Default value: :literal:`false` - -.. option:: flight_track_file - - Specifies the path to a flight track file. This file contains - the coordinates of the plane as a function of time, as well as the - requested quantities to archive. - -.. option:: output_file - - Specifies the path to the Planeflight output file. Requested - quantities will be archived from GEOS-Chem along the flight track - specified in :option:`flight_track_file`. - -.. _cfg-gc-yml-hg: - -===================== -Hg simulation options -===================== - -This section of :file:`geoschem_config.yml` is included for -the `mercury (Hg) simulation `_: - -.. _cfg-gc-yml-hg-src: - -Hg sources ----------- - -The :literal:`Hg_simulation_options:sources` section contains settings -for various mercury sources. - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the Hg simulation - #============================================================================ - Hg_simulation_options: - - sources: - use_dynamic_ocean_Hg: false - use_preindustrial_Hg: false - use_arctic_river_Hg: true - - # ... following sub-sections omitted ... - -.. option:: use_dynamic_ocean_Hg - - Activates (:literal:`true`) or deactivates (:literal:`false`) the online - slab ocean mercury model. - - Default value: :literal:`false` - -.. option:: use_preindustrial_Hg - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - preindustrial mercury simulation. This will turn off all - anthropogenic emissions. - - Default value: :literal:`false` - -.. option:: use_arctic_river_Hg - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - source of mercury from arctic rivers. - - Default value: :literal:`true` - -.. _cfg-gc-yml-hg-chem: - -Hg chemistry ------------- - -The :literal:`Hg_simulation_options:chemistry` section contains settings -for mercury chemistry: - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the Hg simulation - #============================================================================ - Hg_simulation_options: - - # ... preceding sub-sections omitted ... - - chemistry: - tie_HgIIaq_reduction_to_UVB: true - - # ... following sub-sections omitted ... - -.. option:: tie_HgIIaq_reduction_to_UVB - - Activates (:literal:`true`) or deactivates (:literal:`false`) linking the - reduction of aqueous oxidized mercury to UVB radiation. - A lifetime of -1 seconds indicates the species has an infinite lifetime. - - Default value: :literal:`true` - -.. _cfg-gc-yml-carbon: - -========================================= -Options for simulations with carbon gases -========================================= - -These sections of :file:`geoschem_config.yml` are included for -simulations with carbon gases (:option:`carbon`, :option:`CH4`, -:option:`CO2`, :option:`tagCO`, :option:`tagCH4`). - -.. _gc-yml-ch4_obsopt: - -CH4 observational operators ----------------------------- - -The :literal:`CH4_simulation_options:use_observational_operators` section -contains options for using satellite observational operators for CH4: - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the CH4 simulation / Integrated Methane Inversion - #============================================================================ - CH4_simulation_options: - - use_observational_operators: - AIRS: false - GOSAT: false - TCCON: false - - # ... following sub-sections omitted ... - -.. option:: AIRS - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - AIRS observational operator. - - Default value: :literal:`false` - -.. option:: GOSAT - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - GOSAT observational operator. - - Default value: :literal:`false` - -.. option:: TCCON - - Activates (:literal:`true`) or deactivates (:literal:`false`) the - GOSAT observational operator. - - Default value: :literal:`false` - -.. _gc-yml-ch4_anopt: - -CH4 analytical inversion options ---------------------------------- - -The :literal:`ch4_simulation_options:analytical_inversion` section -contains options for analytical inversions with the `Integrated -Methane Inversion workflow (aka IMI) `_. -The IMI will automatically modify several of these options based on -the inversion parameters that you specify. - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the CH4 simulation / Integrated Methane Inversion - #============================================================================ - CH4_simulation_options: - - # ... preceding sub-sections omitted ... - - analytical_inversion: - perturb_OH_boundary_conditions: false - CH4_boundary_condition_ppb_increase_NSEW: [0.0, 0.0, 0.0, 0.0] - -.. option:: perturb_CH4_boundary_conditions - - Activates (:literal:`true`) or deactivatees (:literal:`false`) - perturbation of CH4 nested-grid boundary conditions in analytical - inversions. - - Default value: :literal:`false` - -.. option:: CH4_boundary_condition_ppb_increase_NSEW - - Specifies the perturbation amount (in ppbv) to apply to the north, - south, east and west CH4 nested-grid boundary conditions. Used in - conjunction with the :option:`perturb_CH4_boundary_conditions` - option. - - Default value: :literal:`[0.0, 0.0, 0.0, 0.0]` (no perturbation) - -.. _cfg-gc-yml-co2: - -CO2 Sources ------------ - -The :literal:`CO2_simulation_options:sources` section contains toggles -for activating sources of :math:`CO_2`: - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the CO2 simulation - #============================================================================ - CO2_simulation_options: - - sources: - 3D_chemical_oxidation_source: true - - # ... following sub-sections omitted ... - -.. option:: 3D_chemical_oxidation_source - - Activates (:literal:`true`) or deactivates (:literal:`false`) - :math:`CO_2` production by archived chemical oxidation, as read by - HEMCO. - - Default value: :literal:`true` - -.. _cfg-gc-yml-co2-tagspc: - -CO2 tagged species ------------------- - -The :literal:`CO2_simulation_options:tagged_species` section contains toggles -for activating tagged :math:`CO_2` species: - -.. attention:: - - Tagged :math:`CO_2` tracers should be customized by each user and - the present configuration will not work for resolutions other than - :math:`2.0^{\circ} {\times} 2.5^{\circ}`. - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the CO2 simulation - #============================================================================ - CO2_simulation_options: - - # ... preceding sub-sections omitted ... - - tagged_species: - tag_bio_and_ocean_CO2: false - tag_land_fossil_fuel_CO2: false - - # .. following sub-sections omitted ... - -.. option:: tag_bio_and_ocean_CO2 - - Activates (:literal:`true`) or deactivates (:literal:`false`) tagging of - biosphere regions (28), ocean regions (11), and the rest of the - world (ROW) as specified in :file:`Regions_land.dat` and - :file:`Regions_ocean.dat` files. - -.. option:: tag_land_fossil_fuel_CO2: - - Activates (:literal:`true`) or deactivates (:literal:`false`) tagging of - land and ocean fossil fuel regions. - - -.. _cfg-gc-yml-co: - -CO chemical sources -------------------- - -The :literal:`tagged_CO_simulation_options` section contains settings -for the :option:`carbon` simulation and `tagged CO simulation -`_. - -.. code-block:: YAML - - #============================================================================ - # Settings specific to the tagged CO simulation - #============================================================================ - - tagged_CO_simulation_options: - use_fullchem_PCO_from_CH4: true - use_fullchem_PCO_from_NMVOC: true - -.. option:: use_fullchem_PCO_from_CH4 - - Activates (:literal:`true`) or deactivates (:literal:`false`) applying - the production of :math:`CO` from :math:`CH_4`. This field is - archived from a 1-year or 10-year :option:`fullchem` benchmark - simulation and is read from disk via HEMCO. - - Default value: :literal:`true` - -.. option:: use_fullchem_PCO_from_NMVOC - - Activates (:literal:`true`) or deactivates (:literal:`false`) applying - the production of :math:`CO` from non-methane volatile organic - compounds (VOCs). This field is archived from a 1-year or 10-year - :option:`fullchem` benchmark simulation and is read from disk via - HEMCO. - - Default value: :literal:`true` diff --git a/docs/source/gcclassic-user-guide/hemco-config.rst b/docs/source/gcclassic-user-guide/hemco-config.rst deleted file mode 100644 index f2fea57..0000000 --- a/docs/source/gcclassic-user-guide/hemco-config.rst +++ /dev/null @@ -1,225 +0,0 @@ -.. _cfg-hco-cfg: - -############### -HEMCO_Config.rc -############### - -GEOS-Chem Classic relies on the `Harmonized Emissions Component (aka -HEMCO) `_ for file I/O, regridding, and -computing emissions fluxes. Settings for HEMCO can be updated in the -`HEMCO configuration file -`_, -which is named :file:`HEMCO_Config.rc`. - -The HEMCO online manual at `hemco.readthedocs.io -`_ contains detailed instructions about -the structure and contents of :file:`HEMCO_Config.rc`, so we will not -replicate that content in this Guide. Instead, we will provide a -short summary with links to the relevant documentation. - -.. _cfg-hco-cfg-settings: - -====================== -General HEMCO settings -====================== - -Define general simulation parameters in the `Settings section -`_ -of :file:`HEMCO_Config.rc`. This includes data paths, global -diagnostic options, and verbose output options. - -.. code-block:: kconfig - - ############################################################################### - ### BEGIN SECTION SETTINGS - ############################################################################### - - ROOT: /path/to/hemco/data/dir - METDIR: /path/to/hemco/met/dir - GCAPSCENARIO: not_used - GCAPVERTRES: 47 - Logfile: * - DiagnFile: HEMCO_Diagn.rc - DiagnPrefix: ./OutputDir/HEMCO_diagnostics - DiagnFreq: 00000000 010000 - Wildcard: * - Separator: / - Unit tolerance: 1 - Negative values: 0 - Only unitless scale factors: false - Verbose: false - VerboseOnCores: root # Accepted values: root all - - ### END SECTION SETTINGS ### - -.. _cfg-hco-cfg-extswitches: - -================== -Extension switches -================== - -Turn individual emissions inventories on/off in the `Extension -Switches section -`_ -of :file:`HEMCO_Config.rc`. Emission inventories are -specified as either `Base Emissions -`_ -(i.e. read from files on disk) or `Extensions -`_ -(i.e. computed using meteorological inputs). - -.. code-block:: kconfig - - ############################################################################### - ### BEGIN SECTION EXTENSION SWITCHES - ############################################################################### - # ExtNr ExtName on/off Species Years avail. - 0 Base : on * - # ----- MAIN SWITCHES --------------------------------------------------------- - --> EMISSIONS : true - --> METEOROLOGY : true - --> CHEMISTRY_INPUT : true - # ----- RESTART FIELDS -------------------------------------------------------- - --> GC_RESTART : true - --> HEMCO_RESTART : true - # ----- NESTED GRID FIELDS ---------------------------------------------------- - --> GC_BCs : false - # ----- REGIONAL INVENTORIES -------------------------------------------------- - --> APEI : false # 1989-2014 - --> NEI2016_MONMEAN : false # 2002-2020 - --> DICE_Africa : false # 2013 - # ----- GLOBAL INVENTORIES ---------------------------------------------------- - --> CEDSv2 : true # 1750-2019 - --> CEDS_GBDMAPS : false # 1970-2017 - --> CEDS_GBDMAPS_byFuelType: false # 1970-2017 - - ... etc ... - - # ----------------------------------------------------------------------------- - 100 Custom : off - - 101 SeaFlux : on DMS/ACET/ALD2/MENO3/ETNO3/MOH - 102 ParaNOx : on NO/NO2/O3/HNO3 - --> LUT data format : nc - --> LUT source dir : $ROOT/PARANOX/v2015-02 - 103 LightNOx : on NO - --> CDF table : $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat - 104 SoilNOx : on NO - --> Use fertilizer NOx : true - - ... etc ... - - ### END SECTION EXTENSION SWITCHES ### - -.. _cfg-hco-base: - -============== -Base emissions -============== - -.. note:: - - You do not have to edit this section if you just wish to run - GEOS-Chem Classic with its default emissions configuration. - -Specify how emissions and other data sets will be read from disk in -the `Base Emissions section -`_ -of :file:`HEMCO_Config.rc`. - -.. code-block:: kconfig - - ############################################################################### - ### BEGIN SECTION BASE EMISSIONS - ############################################################################### - - # ExtNrName sourceFile sourceVar sourceTime C/R/E SrcDim SrcUnit Species ScalIDs Cat Hier - - (((EMISSIONS - - #============================================================================== - # --- APEI (Canada) --- - #============================================================================== - (((APEI - 0 APEI_NO $ROOT/APEI/v2016-11/APEI.0.1x0.1.nc NOx 1989-2014/1/1/0 RF xy kg/m2/s NO 25/1002/115 1 30 - 0 APEI_CO $ROOT/APEI/v2016-11/APEI.0.1x0.1.nc CO 1989-2014/1/1/0 RF xy kg/m2/s CO 26/52/1002 1 30 - 0 APEI_SOAP - - - - - - SOAP 26/52/1002/280 1 30 - 0 APEI_SO2 $ROOT/APEI/v2016-11/APEI.0.1x0.1.nc SOx 1989-2014/1/1/0 RF xy kg/m2/s SO2 60/1002 1 30 - 0 APEI_SO4 - - - - - - SO4 60/65/1002 1 30 - 0 APEI_pFe - - - ... etc ... - - ### END SECTION BASE EMISSIONS ### - -.. _cfg-hco-scalefac: - -============= -Scale factors -============= - -Define scale factors for emissions inventories and other data sets in -the `Scale Factors section -`_ -of :file:`HEMCO_Config.rc`. - -.. code-block:: kconfig - - #============================================================================== - # --- Scale factors used for species conversions --- - #============================================================================== - - # Units carbon to species conversions - # Factor = # carbon atoms * MW carbon) / MW species - 40 CtoACET MATH:58.09/(3.0*12.0) - - - xy unitless 1 - 41 CtoALD2 MATH:44.06/(2.0*12.0) - - - xy unitless 1 - 42 CtoALK4 MATH:58.12/(4.3*12.0) - - - xy unitless 1 - - ... etc ... - # VOC speciations - (((RCP_3PD.or.RCP_45.or.RCP_60.or.RCP_85 - 50 KET2MEK 0.25 - - - xy unitless 1 - 51 KET2ACET 0.75 - - - xy unitless 1 - )))RCP_3PD.or.RCP_45.or.RCP_60.or.RCP_85 - - ... etc ... - - ### END SECTION SCALE FACTORS ### - -.. _masks: - -===== -Masks -===== - -Define masks for emissions and other data sets in the `Masks section -`_ -of :file:`HEMCO_Config.rc` - -.. code-block:: kconfig - - ############################################################################### - ### BEGIN SECTION MASKS - ############################################################################### - - # ScalID Name sourceFile sourceVar sourceTime C/R/E SrcDim SrcUnit Oper Lon1/Lat1/Lon2/Lat2 - - (((EMISSIONS - - #============================================================================== - # Country/region masks - #============================================================================== - (((APEI - 1002 CANADA_MASK $ROOT/MASKS/v2018-09/Canada_mask.geos.1x1.nc MASK 2000/1/1/0 C xy 1 1 -141/40/-52/85 - )))APEI - - (((NEI2016_MONMEAN - 1007 CONUS_MASK $ROOT/MASKS/v2018-09/CONUS_Mask.01x01.nc MASK 2000/1/1/0 C xy 1 1 -140/20/-50/60 - )))NEI2016_MONMEAN - - ... etc ... - - )))EMISSIONS - - ### END SECTION MASKS ### - - ### END OF HEMCO INPUT FILE ### diff --git a/docs/source/gcclassic-user-guide/hemco-diagn.rst b/docs/source/gcclassic-user-guide/hemco-diagn.rst deleted file mode 100644 index aff1a92..0000000 --- a/docs/source/gcclassic-user-guide/hemco-diagn.rst +++ /dev/null @@ -1,45 +0,0 @@ -.. _cfg-hco-diagn: - -############## -HEMCO_Diagn.rc -############## - -In your run directory, you will find a copy of the `HEMCO diagnostic configuration file -`_ -(named :file:`HEMCO_Diagn.rc`) corresponding to the -:ref:`HEMCO_Config.rc ` file. You will only need to edit -this file if you wish to change the default diagnostic output configuration. - -A snippet of the :file:`HEMCO_Diagn.rc` for the :option:`fullchem` -simulation is shown below: - -.. code-block:: kconfig - - ############################################################################### - ##### ALD2 emissions ##### - ############################################################################### - EmisALD2_Total ALD2 -1 -1 -1 3 kg/m2/s ALD2_emission_flux_from_all_sectors - EmisALD2_Anthro ALD2 0 1 -1 3 kg/m2/s ALD2_emission_flux_from_anthropogenic - EmisALD2_BioBurn ALD2 111 -1 -1 2 kg/m2/s ALD2_emission_flux_from_biomass_burning - EmisALD2_Biogenic ALD2 0 4 -1 2 kg/m2/s ALD2_emission_flux_from_biogenic_sources - EmisALD2_Ocean ALD2 101 -1 -1 2 kg/m2/s ALD2_emission_flux_from_ocean - EmisALD2_PlantDecay ALD2 0 3 -1 2 kg/m2/s ALD2_emission_flux_from_decaying_plants - EmisALD2_Ship ALD2 0 10 -1 2 kg/m2/s ALD2_emission_flux_from_ships - - -Columns: - -#. netCDF variable name for the requested diagnostic quantity -#. Species name -#. Extension number (:literal:`-1` means sum over all extensions) -#. Category (:literal:`-1` means sum over all categories) -#. Hierarchy (:literal:`-1` means sum over all hierarchies) -#. Dimension of data (:literal:`1`: scalar, :literal:`2`: lon-lat, - :literal:`3`: lon-lat-lev) -#. Units -#. Value for the :literal:`long_name` netCDF variable attribute - -The prefix (e.g. :literal:`OutputDir/HEMCO_diagnostics`) for HEMCO diagnostics -output files are specified in the -`Settings section of the HEMCO_Config.rc file -`_. diff --git a/docs/source/gcclassic-user-guide/phot-chem.rst b/docs/source/gcclassic-user-guide/phot-chem.rst deleted file mode 100644 index 4e76caa..0000000 --- a/docs/source/gcclassic-user-guide/phot-chem.rst +++ /dev/null @@ -1,100 +0,0 @@ -.. _cfg-phot-chem: - -############################################ -Photolysis and chemistry configuration files -############################################ - -.. note:: - - You won't need to edit these configuration files unless you are - changing the photolysis and/or chemistry mechanisms used in your - GEOS-Chem Classic simulation. - -.. _cfg-phot-chm-phot: - -============================== -Photolysis configuration files -============================== - -Configuration files containing photolysis parameters (such as quantum -yields, cross sections, branching ratios, etc.) may be found in -subdirectories of :file:`ExtData/CHEM_INPUTS/CLOUD-J/` and -:file:`ExtData/CHEM_INPUTS/FAST-JX/`. See the :ref:`cfg-gc-yml` -file for the current file path specifications. - -GEOS-Chem versions 14.3.0 and later use the :program:`Cloud-J` -photolysis scheme by default. However, some aerosol properties -(e.g. relative humidity dependence) are still stored in files located -in the :file:`ExtData/CHEM_INPUTS/FAST_JX` directory tree. - -At present, the mercury (Hg) simulation still uses the legacy -:program:`FAST-JX` photolysis scheme. We look to the GEOS-Chem user -community to take the lead on creating configuration files for -:program:`Cloud-J`. - -.. _cfg-phot-chem-chem: - -====================================== -Chemical mechanism configuration files -====================================== - -GEOS-Chem Classic simulations use source code generated by `The -Kinetic PreProcessor `_. -If you need to update the default chemistry mechanism, you will need -to do the following steps: - -#. Modify the relevant KPP configuration files (described below); -#. Run KPP to generate updated source code for GEOS-Chem Classic; -#. :ref:`Compile GEOS-Chem Classic ` to create a new - executable; -#. Start your GEOS-Chem Classic simulation. - -Chemical mechanism configuration files are located in these folders: - -.. option:: KPP/fullchem - - Contains configuration files for the default "full-chemistry" - mechanism (NOx + Ox + aerosols + Br + Cl + I). - - - :file:`fullchem.kpp`: Main configuration file for the - **fullchem** mechanism. - - - :file:`fullchem.eqn`: List of species and reactions - for the **fullchem** mechanism. - -.. option:: KPP/carbon - - Contains configuration files for the carbon gases mechanism - (CH4-CO2-CO-OCS): - - - :file:`carbon.kpp`: Main configuration file for the **carbon** - mechanism. - - - :file:`carbon.eqn`: List of species and reactions for the **carbon** - mechanism. - -.. option:: KPP/custom - - Contains configuration files that you can edit if you need to - create a custom mechanism. We recommend that you create the - custom in this folder and leave :file:`KPP/fullchem` and - :file:`KPP/Hg` untouched. - - - :file:`custom.kpp`: Copy of :file:`fullchem.kpp` - - - :file:`custom.eqn`: Copy of :file:`fullchem.eqn`. - -.. option:: KPP/Hg - - Contains configuration files for the mercury chemistry mechanism: - - - :file:`Hg.kpp`: Main configuration file for the **Hg** - mechanism. - - - :file:`Hg.eqn`: List of species and reactions for the **Hg** - mechanism. - -Please see the following references for more information about KPP: - -#. The KPP user manual (`kpp.readthedocs.io `_) -#. Supplemental Guide: :ref:`kppguide` diff --git a/docs/source/gcclassic-user-guide/spec-db.rst b/docs/source/gcclassic-user-guide/spec-db.rst deleted file mode 100644 index 325f440..0000000 --- a/docs/source/gcclassic-user-guide/spec-db.rst +++ /dev/null @@ -1,85 +0,0 @@ -.. _cfg-spec-db: - -#################### -species_database.yml -#################### - -.. note:: - - You will only need to edit :file:`species_database.yml` if you are - adding new species to a GEOS-Chem simulation. - -The :ref:`GEOS-Chem Species Database ` is a `YAML file -`_ that contains a listing of metadata for each -species used by GEOS-Chem. The Species Database is included in your -run directory as file :file:`species_database.yml`, a snippet of which -is shown below. - -.. code-block:: yaml - - # GEOS-Chem Species Database - # Core species only (neglecting microphysics) - # NOTE: Anchors must be defined before any variables that reference them. - A3O2: - Formula: CH3CH2CH2OO - FullName: Primary peroxy radical from C3H8 - Is_Gas: true - MW_g: 75.10 - ACET: - DD_F0: 1.0 - DD_Hstar: 1.0e+5 - Formula: CH3C(O)CH3 - FullName: Acetone - Henry_CR: 5500.0 - Henry_K0: 2.74e+1 - Is_Advected: true - Is_DryDep: true - Is_Gas: true - Is_Photolysis: true - MW_g: 58.09 - - ... etc ... - - AERI: - DD_DvzAerSnow: 0.03 - DD_DvzMinVal: [0.01, 0.01] - DD_F0: 0.0 - DD_Hstar: 0.0 - Formula: I - FullName: Iodine on aerosol - Is_Advected: true - Is_Aerosol: true - Is_DryDep: true - Is_WetDep: true - MW_g: 126.90 - WD_AerScavEff: 1.0 - WD_KcScaleFac: [1.0, 0.5, 1.0] - WD_RainoutEff: [1.0, 0.0, 1.0] - WD_RainoutEff_Luo: [0.4, 0.0, 1.0] - - ... etc ... - -.. important:: - - Species NO (nitrogen oxide) must be listed in - :file:`species_database.yml` as :code:`'NO':`. This will avoid - YAML readers mis-intepreting this as :literal:`no` (meaning - :literal:`false`). - - -Each species name begins in the first column of the file, followed by -a :literal:`:`. Underneath -the species name follows an indented block of :ref:`species properties -` in :literal:`Property: Value` format. - -Some properties listed above are only applicable to gas-phase species, -and others to aerosol species. But at the very least, each species -should have the following properties defined: - -- :literal:`Formula` -- :literal:`FullName` -- :literal:`MW_g` -- Either :literal:`Is_Gas` or :literal:`Is_Aerosol` - -For more information about species properties, please see -:ref:`spcguide` in the Supplemental Guides section. diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index a68981b..7a3e9db 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit a68981bec91028c8165f220fef683650cb79afe4 +Subproject commit 7a3e9db6ed96e5edf66060734f479389fe40a2f5 From 08cccffc9491a64077b73503a315fc3f6e8036f8 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Mon, 30 Sep 2024 16:08:06 -0400 Subject: [PATCH 28/99] GEOS-Chem submodule update: Merge PR #2489 (fix for coarse-mode seasalt Ca, Mg, K) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 7ffdb5b..ced6447 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 7ffdb5b64f2ab2a2cdb6030addbeb0fae6b61104 +Subproject commit ced6447def626729f69a301dca98bf605f91057f From f13ea9c1f17dd4e40b35244fa37cbaa6733269e3 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 30 Sep 2024 18:27:18 -0400 Subject: [PATCH 29/99] Updated "Speeding up a slow GEOS-Chem simulation" chapter docs/source/gcclassic-user-guide/run-speedup.rst - Changed "Use coarser timesteps" to "Use a coarser chemistry timestep" - Added table of recommended GEOS-Chem Classic timesteps - Cite Philip et al. 2016 - Added section "Use the Rosenbrock solver w/ auto-reduction" - Added section "Reduce the amount of files that need to be read" - Added section "Speeding up GEOS-Chem Classic nested-grid simulations" - Added subsection "Crop nested-grid meteorology inputs" - Added subsection "Increase the size of the transport buffer zone" Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/run-speedup.rst | 153 ++++++++++++++---- docs/source/geos-chem-shared-docs | 2 +- 2 files changed, 123 insertions(+), 32 deletions(-) diff --git a/docs/source/gcclassic-user-guide/run-speedup.rst b/docs/source/gcclassic-user-guide/run-speedup.rst index e56ef67..caaf9d1 100644 --- a/docs/source/gcclassic-user-guide/run-speedup.rst +++ b/docs/source/gcclassic-user-guide/run-speedup.rst @@ -1,7 +1,3 @@ -.. |br| raw:: html - -
- .. _run-speedup: ########################## @@ -11,32 +7,77 @@ Speed up a slow simulation GEOS-Chem Classic performance is continuously monitored by the `GEOS-Chem Support Team `_ by means of -benchmark simulations and ad-hoc timing tests. It has been shown that -running GEOS-Chem with -`recommended timesteps -`_ -from :cite:t:`Philip_et_al._2016`. can increase run times by -approximately a factor of 2. To speed up GEOS-Chem Classic -simulations, users may choose to use any of the following options. - -.. _use-coarser-timesteps: - -===================== -Use coarser timesteps -===================== - -As :ref:`discussed previously `, the default -timesteps for GEOS-Chem Classic are 600 seconds for dynamics, and 1200 -seconds for chemistry and emissions. You can experiment with using -coarser timesteps (such as 1800 seconds for dynamics and 3600 seconds -for emissions & chemistry). - -.. attention:: - - For nested-grid simulations, you might not be able to use coarser - timesteps, or else the Courant limit in transport will be violated. - -.. _turn-off-diagnostics: +benchmark simulations and ad-hoc timing tests. In this chapter, we +provide some practical tips that you can use to speed up your +simulations. + +.. _run-speedup-coarse-timesteps: + +================================ +Use a coarser chemistry timestep +================================ + +The table below contains our recommended GEOS-Chem Classic timestep +settings. + ++----------------------------------------------+-------------+--------------+ +| GEOS-Chem Classic Resolution | Transport | Chemistry | ++==============================================+=============+==============+ +| :math:`4^{\circ}{\times}5^{\circ}` | 600s (10m) | 1200s (20m) | ++----------------------------------------------+-------------+--------------+ +| :math:`2^{\circ}{\times}2.5^{\circ}` | 600s (10m) | 1200s (20m) | ++----------------------------------------------+-------------+--------------+ +| :math:`0.5^{\circ}{\times}0.625^{\circ}` | 300s (5m) | 600s (10m) | ++----------------------------------------------+-------------+--------------+ +| :math:`0.25^{\circ}{\times}0.3125^{\circ}` | 300s (5m) | 600s (10m) | ++----------------------------------------------+-------------+--------------+ +| :math:`0.125^{\circ}{\times}0.15625^{\circ}` | 150s (2.5m) | 300s (5m) | ++----------------------------------------------+-------------+--------------+ + +The `Courant limit +`_ +on the latitude-longitude grid constrains the choice of transport +timestep for a given horizontal resolution. We choose a chemistry +timestep that is double the transport timestep (i.e. +`Strang operator splitting +`_). + +If you wish to speed up your simulation, try increasing the chemistry +timestep. Chemistry is the GEOS-Chem operation that takes the longest +to execute, so increasing the interval between calls to the chemistry +solver will reduce the run time accordingly. But you should also verify +that the increased chemistry timestep allows your simulation to +faithfully capture diurnal variations, etc. + +See :cite:t:`Philip_et_al._2016` for a comprehensive study on +GEOS-Chem timesteps. + +.. _run-speedup-autoreduce: + +============================================= +Use the Rosenbrock solver with auto-reduction +============================================= + +The GEOS-Chem full-chemistry mechanism uses the KPP Rosenbrock solver, +which has an `automatic mechanism reduction option +`_ +as described in :cite:t:`Lin_et_al._2023`. This automatic mechanism +reduction feature separates species into "fast" and "slow" +categories based on their chemical production or loss rates. "Fast" +species are integrated with the full Rosenbrock algorithm, while +"slow" species will have a simple 1st-order loss applied to +them. This approach has been shown to reduce the time spent in +chemistry by 20 to 30 percent. + +The automatic mechanism reduction option is disabled by default, but +can be enabled by toggiing this switch in :ref:`cfg-gc-yml`: + +.. code-block:: yaml + + autoreduce_solver: + activate: false # <=== set to true to activate auto-reduction + +.. _run-speedup-disable-diags: ============================= Turn off unwanted diagnostics @@ -48,7 +89,7 @@ are turned on, the more I/O operations need to be done, resulting in longer simulation execution times. Disabling diagnostics that you do not wish to archive can result in a faster simulation. -.. _disable-debug-options: +.. _run-speedup-disable-debug: ========================= Disable debugging options @@ -67,3 +108,53 @@ Classic simulation, but result in a much slower simulation. If you plan on running a long Classic simulation, make sure that you :ref:`configure and build GEOS-Chem Classic ` so that :option:`CMAKE_BUILD_TYPE` is set to :envvar:`Release`. + +.. _run-speedup-combine-files: + +=============================================== +Reduce the amount of files that need to be read +=============================================== + +If you are developing a new data set (such as an emissions inventory) +for GEOS-Chem, we recommend that you prepare data files with multiple +timestamps rather than one file per timestamp. For example, if your +data set has hourly time resolution, consider creating one file for +each day, with each file containing 24 hours of data, etc. + +The greatest amount of overhead in I/O occurs when new data files (in +netCDF format) are opened. This also usually involves decompression +of the file contents, which is computationally intensive. Reducing +the number of times that GEOS-Chem has to open and close netCDF files +can substantially improve performance. + +.. _run-speedup-nested: + +===================================================== +Speeding up GEOS-Chem Classic nested-grid simulations +===================================================== + +Use these tips to speed up your GEOS-Chem nested-grid simulations: + +.. _run-speedup-nested-crop: + +Crop nested-grid meteorology inputs +----------------------------------- + +Your simulation should not read global high-resolution +(:math:`0.5^{\circ}{\times}0.625^{\circ}` or finer) meteorology +fields. The overhead in reading and regridding these global fields +can significantly impact your simulation. Instead, consider cropping +high-resolution meteorology fields to the extent of your nested domain. +This can easily be done with the netCDF operators or the Climate Data +Operators; see our :ref:`netcdf-guide` supplemental guide for more +information. + +.. _run-speedup-nested-buffer: + +Increase the size of the transport buffer zone +---------------------------------------------- + +By default, nested :option:`buffer_zone_NSEW` option is set to 3 boxes +in each cardinal direction. Increasing this number will reduce the +amount of grid boxes in which transport will be performed, which +should also reduce the overall run time. diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 7a3e9db..679cf4c 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 7a3e9db6ed96e5edf66060734f479389fe40a2f5 +Subproject commit 679cf4c150c0f084ecbb63a1d3b0f9af3df14e8c From 1c6c0adb0d4854983e68b14f3297c003d0271d3a Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Tue, 1 Oct 2024 09:45:37 -0400 Subject: [PATCH 30/99] GEOS-Chem submodule update: Merge PR #2490 (clean up CHANGELOG.md) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index ced6447..c7a6ae6 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit ced6447def626729f69a301dca98bf605f91057f +Subproject commit c7a6ae6277a173aa67b903af3af659ebbd2b36d2 From 2734825426a1e1f512e55df7c114158ecc5df126 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Tue, 1 Oct 2024 13:36:43 -0400 Subject: [PATCH 31/99] Cloud-J submodule update for 8.0.1 release Signed-off-by: Melissa Sulprizio --- CHANGELOG.md | 5 +++++ src/Cloud-J | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5575ae0..7fc2747 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,11 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit 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 +### Changed +- Updated GEOS-Chem to 14.5.0 +- Updated HEMCO to 3.10.0 +- Updated Cloud-J to 8.0.1 + ### Fixed - Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run diff --git a/src/Cloud-J b/src/Cloud-J index 6bf4a36..f8a2b7f 160000 --- a/src/Cloud-J +++ b/src/Cloud-J @@ -1 +1 @@ -Subproject commit 6bf4a36d11039783c0b29befc48e93cdff7f6ecb +Subproject commit f8a2b7f964bde1582fbc38c41d8872bc23a21735 From 440b4d65d3cd4c643b72ded2ca757faf85fc0b6b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 1 Oct 2024 16:24:20 -0400 Subject: [PATCH 32/99] geos-chem-shared-docs update: Add doc about diffs btw GCHP & GCC docs/source/geos-chem-shared-docs: - Added documentation to doc/geoschem-config.rst and doc/hemco-config.rst to make the differences between GCHP and GCClassic more explicit. Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 679cf4c..b5420bb 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 679cf4c150c0f084ecbb63a1d3b0f9af3df14e8c +Subproject commit b5420bbb77f9fea9b26cc36785c441883295b029 From f19794e97b56d720827536f404e57115afc8481f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 2 Oct 2024 11:01:31 -0400 Subject: [PATCH 33/99] geos-chem-shared-doc update: Fixed typo; Added GCHP vs. GCC diffs docs/source/geos-chem-shared-docs - Fixed typo in doc/geoschem-config.rst - Added GCHP vs. GCC usage difference section in the documentation for HEMCO_Diagn.rc Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index b5420bb..8ed145c 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit b5420bbb77f9fea9b26cc36785c441883295b029 +Subproject commit 8ed145c6c813b325c6101392f7ff6e203f851d9b From 9545c59f381e41db15f2f9e163f9ac63ed690613 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 3 Oct 2024 09:29:13 -0400 Subject: [PATCH 34/99] GEOS-Chem submodule update: Merge PR #2493 (rename ALK7 to ALK6) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index c7a6ae6..57cf0df 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit c7a6ae6277a173aa67b903af3af659ebbd2b36d2 +Subproject commit 57cf0dfcdae0d4abbc6094fc119b94f5f5826373 From 347c3a2964194e85d66266d1798fb5128a6359bc Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 3 Oct 2024 10:58:34 -0400 Subject: [PATCH 35/99] GEOS-Chem submodule update: Merge PR #2492 (fixes for GCHP carbon sim) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 57cf0df..51d306d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 57cf0dfcdae0d4abbc6094fc119b94f5f5826373 +Subproject commit 51d306dade21a6c36e5537224b7c533b5489667c From 29b8615096e159253009bc3bcd52da32e5777101 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 15 Oct 2024 14:37:53 -0400 Subject: [PATCH 36/99] geos-chem-shared-docs update: GC input data; GCHP History guide This commit informs the GCClassic superproject about the following commits that were pushed to the geos-chem-shared-docs repository: 65b2a35 Merge "docs/update_guides_for_gchp" into "main" 7f0cfbb Merge PR #3 (Add doc/tutorial for GEOS-Chem input data on AWS) These are documentation updates for the 14.5.0 release. Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 8ed145c..65b2a35 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 8ed145c6c813b325c6101392f7ff6e203f851d9b +Subproject commit 65b2a350db689d858e547228f9b3a261db1bd86e From a6973ae06859a1c703600b63f8c2e42cb6a3d014 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 1 Nov 2024 20:07:32 -0400 Subject: [PATCH 37/99] RTD Updates: Additional updates for GC Input Data repository docs/source/gcclassic-user-guide/download-data.rst - Removed input-overview.rst from toctree - Added gcid-repository-overview.rst to toctree - Added gcid-special-repos.rst to toctree docs/source/gcclassic-user-guide/dry-run-download.rst - Add references to pages in geos-chem-shared-docs/doc folder pertaining to the GEOS-Chem input data - Renamed "Choose a data portal" section to "Choose a data repository", and updated the data repository descriptions docs/source/gcclassic-user-guide/gcid-special-repos.rst - New page describing GEOS-Chem Nested Input Data and GCAP 2.0 @ Rochester repositories docs/source/geos-chem-shared-docs - Updated submodule hash to commit 09a2f03 Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/download-data.rst | 5 +- .../gcclassic-user-guide/dry-run-download.rst | 192 ++++++++++++------ .../gcid-special-repos.rst | 84 ++++++++ docs/source/geos-chem-shared-docs | 2 +- 4 files changed, 219 insertions(+), 64 deletions(-) create mode 100644 docs/source/gcclassic-user-guide/gcid-special-repos.rst diff --git a/docs/source/gcclassic-user-guide/download-data.rst b/docs/source/gcclassic-user-guide/download-data.rst index 99e745b..6bbf6ed 100644 --- a/docs/source/gcclassic-user-guide/download-data.rst +++ b/docs/source/gcclassic-user-guide/download-data.rst @@ -5,7 +5,7 @@ Download input data ################### In the following chapters, you will learn how to download input data -for your GEOS-Chem simulation: +for your GEOS-Chem simulation. .. note:: @@ -18,6 +18,7 @@ for your GEOS-Chem simulation: .. toctree:: :maxdepth: 2 - input-overview.rst + ../geos-chem-shared-docs/doc/gcid-repository-overview.rst + gcid-special-repos.rst restart-files.rst dry-run.rst diff --git a/docs/source/gcclassic-user-guide/dry-run-download.rst b/docs/source/gcclassic-user-guide/dry-run-download.rst index f70fa07..01e2c08 100644 --- a/docs/source/gcclassic-user-guide/dry-run-download.rst +++ b/docs/source/gcclassic-user-guide/dry-run-download.rst @@ -1,3 +1,7 @@ +.. |br| raw:: html + +
+ .. _dry-run-download: ################################# @@ -7,8 +11,8 @@ Download data from dry-run output Once you have successfully executed a GEOS-Chem dry-run, you can use the output from the dry-run (contained in the :file:`log.dryrun` file) to download the data files that GEOS-Chem will need to perform the -corresponding "production" simulation. You may download from one of -several locations, which are described in the following sections. +corresponding "production" simulation. You may download from different +:ref:`data repositories `. .. important:: @@ -34,79 +38,93 @@ several locations, which are described in the following sections. more information, please see `gcpy.readthedocs.io `_. -.. _dry-run-data-download-portal: +.. _dry-run-data-download-repo: -==================== -Choose a data portal -==================== +======================== +Choose a data repository +======================== You can :ref:`download input data ` from one of the following -locations: +repositories: -.. _dry-run-download-washu: +.. _dry-run-download-repo-gc: -The :file:`geoschemdata.wustl.edu` site (aka WashU) ---------------------------------------------------- +GEOS-Chem Input Data +-------------------- -If you are using GEOS-Chem on your institutional computer cluster, we -recommend that you **download data from the WashU (Washington -University in St. Louis) site** (`http://geoschemdata.wustl.edu -`_). This site, which is -maintained by Randall Martin's group at WashU, is the main data site -for GEOS-Chem. +The :ref:`GEOS-Chem Input Data ` repository is the main source +of input data (emissions, meteorology, chemistry inputs, restart +files) for GEOS-Chem. We recommend that you download data from this +repository unless otherwise necessary. + +This repository is curated by the GEOS-Chem Support Team at Washington +University in St. Louis, and is hosted on the AWS S3 bucket +:file:`s3://geos-chem`. .. tip:: - We have also set up a `Globus - `_ endpoint named **GEOS-Chem - data (WashU)** on the WashU site. If you need to - download many years of data, it may be faster to use Globus - (particularly if your home institution supports it). + We have set up a `Globus `_ + endpoint named **GEOS-Chem data (WashU)**, which links to the + GEOS-Chem Input Data repository. If you need to download many + years of data, you may find that using Globus is much faster than + downloading data with a dry-run simulation. Ask your IT support + staff if Globus is supported at your institution. -.. _dry-run-download-aws: +Supported download methods: -The :file:`s3://gcgrid` bucket (aka Amazon) -------------------------------------------- +- AWS CLI (command-line interface) +- HTTP download (e.g via :program:`wget`) +- Globus -If you are running GEOS-Chem Classic on the Amazon Web Services cloud, -you can quickly **download the necessary data for your GEOS-Chem -simulation from the** :file:`s3://gcgrid` **bucket** to the Elastic Block -Storage (EBS) volume attached to your cloud instance. +Repository browser: -Navigate to your GEOS-Chem Classic run directory and type: +- AWS S3 Explorer (https://geos-chem.s3.amazonaws.com/index.html) -.. code-block:: console +.. _dry-run-download-repo-nest: - $ ./download data.py log.dryrun amazon +GEOS-Chem Nested Input Data +--------------------------- -This will start the data download process using the ``aws s3 cp`` -commands, which should execute much more quickly than if you were to -download the data from another location. It will also produce a -**log of unique data files**. +The :ref:`gcid-special-repos-nested` repository contains cropped +GEOS-FP and MERRA-2 meteorological inputs for several nested domains. +These data can be used to perform high-resolution inversions using the +`Integrated Methane Inversion (IMI) `_ +workflow. -.. note:: +This repository is curated by the GEOS-Chem Support Team at +Harvard University and is hosted at the AWS S3 bucket +:file:`s3://gcgrid`. - Downloading from the Amazon Data Portal will NOT incur any - egress charges. This is because the data is covered under the - `AWS Open Data Sponsorship Program - `_. +Supported download methods: -.. _dry-run-download-rochester: +- AWS CLI (command-line interface) +- HTTP download (e.g via :program:`wget`) -The :file:`atmos.earth.rochester.edu` site (aka Rochester) ----------------------------------------------------------- +Repository browser: -The U. Rochester site (which is maintained by Lee Murray's (GitHub: -:literal:`@ltmurray`) research there) contains the GCAP 2.0 met field -data. This met field data is useful if you wish to perform -simulations stretching back into the preindustrial period, or running -into the future. +- AWS S3 Explorer (https://gcgrid.s3.amazonaws.com/index.html) -To download data from the Rochester site, type: +.. _dry-run-download-repo-ur: -.. code-block:: console +GCAP 2.0 meteorology at University of Rochester +----------------------------------------------- + +The `atmos.earth.rochester.edu +`_ repository +contains the GCAP 2.0 meteorology inputs for GEOS-Chem. GCAP 2.0 +meteorology is useful if you wish to perform simulations stretching +back into the preindustrial period, or running into the future. + +This repository is curated by Lee Murray (GitHub: +:literal:`@ltmurray`) at the University of Rochester. - $ ./download data.py log.dryrun rochester +Supported download methods: + +- HTTP download (e.g via :program:`wget`) + +Repository browser: + +- HTTP site (http://atmos.earth.rochester.edu/input/gc/ExtData) .. _dry-run-download-data: @@ -115,19 +133,71 @@ Run the :file:`download_data.py` script on the dryrun log file ============================================================== Navigate to your GEOS-Chem run directory where you executed the dry-run -and type: +and type. + +.. code-block:: console + + $ ./download_data.py log.dryrun REPOSITORY-NAME + +where: + +- :file:`download_data.py` is the dry-run data download program + (written in Python). It is included in each :ref:`GEOS-Chem Classic + run directory ` that you create. |br| + |br| + +- :file:`log.dryrun` is the log file from your GEOS-Chem dry-run + simulation. |br| + |br| + +- :literal:`REPOSITORY-NAME` specifies the data repository that you wish + to download from. Allowed values are: + + .. list-table:: Allowed values for the ``REPOSITORY-NAME`` argument + to ``download_data.py`` + :header-rows: 1 + + * - Value + - Downloads from repository + - Command used + - Method + * - geoschem-s3 + - :ref:`dry-run-download-repo-gc` + - :command:`aws s3 cp` + - AWS CLI + * - geoschem-wget + - :ref:`dry-run-download-repo-gc` + - :command:`wget` + - HTTP + * - nested-s3 + - :ref:`dry-run-download-repo-nest` + - :command:`aws s3 cp` + - AWS CLI + * - nested-wget + - :ref:`dry-run-download-repo-nest` + - :command:`wget` + - HTTP + * - rochester + - :ref:`GCAP 2.0 met data @ Rochester ` + - :command:`wget` + - HTTP + +For example, to download data from the :ref:`dry-run-download-repo-gc` +repository using the AWS CLI download (which is faster than HTTP +download), use this command: .. code-block:: console - $ ./download_data.py log.dryrun washu + $ ./download_data.py log.dryrun geoschem-s3 + +.. note:: -The :file:`download_data.py` Python program is included in the -:ref:`GEOS-Chem run directory ` that you created. This Python -program creates and executes a temporary bash script containing the -appropriate :file:`wget` commands to download the data files. (We have -found that this is the fastest method.) + You must have the `AWS CLI (command-line interface) + `_ software installed on your system + before in order to use the :literal:`geoschem-s3` or + :literal:`nested-s3` options in the table listed above. -The :file:`download_data.py` program will also generate a **log of +The :file:`download_data.py` program will generate a **log of unique data files** (i.e. with all duplicate listings removed), which looks similar to this: @@ -172,13 +242,13 @@ GEOS-Chem run directory: .. code-block:: console - $ ./download_data.py log.dryrun --skip-download + $ ./download_data.py log.dryrun skip-download or for short: .. code-block:: console - $ ./download_data.py log.dryrun --skip + $ ./download_data.py log.dryrun skip This can be useful if you already have the necessary data downloaded to your system but wish to create the log of unique files for documentation diff --git a/docs/source/gcclassic-user-guide/gcid-special-repos.rst b/docs/source/gcclassic-user-guide/gcid-special-repos.rst new file mode 100644 index 0000000..126ef34 --- /dev/null +++ b/docs/source/gcclassic-user-guide/gcid-special-repos.rst @@ -0,0 +1,84 @@ +.. |br| raw:: html + +
+ +.. _gcid-special-repos: + +######################################## +Additional meteorology data repositories +######################################## + +As discussed in the previous chapter, the :ref:`GEOS-Chem Input +Data ` repository is the main source of input data for +:program:`GEOS-Chem Classic`, :program:`GCHP`, and the :program:`HEMCO +standalone model`. This repository contains the entire catalog +of emissions inventories, chemical inputs, initial conditions, and +most years of `GEOS-FP `_, +`MERRA-2 `_, and GEOS-IT meteorology. + +We also maintain two additional data repositories for special data sets. + +.. _gcid-special-repos-nested: + +=========================== +GEOS-Chem Nested Input Data +=========================== + +.. attention:: + + We are still adding data to the GEOS-Chem Nested Input Data + repository. As of this writing (November 2024), not all data may + have been uploaded yet. We thank you for your patience. + +The `GEOS-Chem Nested Input data +`_ +repository stores GEOS-FP and MERRA-2 meteorology fields that have +been cropped to several nested domains. These data can be used to +perform high-resolution inversions with the `Integrated Methane +Inversion (IMI) `_ workflow. + +.. table:: Available nested-grid meteorology (2018 to present day) + :align: center + + +---------+--------------------------+-------------------------------+ + | Product | Horizontal resolution | Nested-grid domains | + +=========+==========================+===============================+ + | GEOS-FP | :math:`0.125^{\circ} | AF (Africa) |br| | + | | {\times}0.15625^{\circ}` | AS (Asia) |br| | + | | | EU (Europe) |br| | + | | | ME (Middle East) |br| | + | | | NA (North America) |br| | + | | | OC (Oceania) |br| | + | | | RU (Russia) |br| | + | | | SA (South America) | + +---------+--------------------------+-------------------------------+ + | MERRA-2 | :math:`0.5^{\circ} | AS (Asia) |br| | + | | {\times}0.625^{\circ}` | EU (Europe) |br| | + | | | NA (North America) |br| | + +---------+--------------------------+-------------------------------+ + +The data can be accessed by: + +- AWS S3 Explorer (https://s3.amazonaws.com/gcgrid/index.html) +- Direct HTTP or wget download +- :ref:`Dry-run simulation ` + +The GEOS-Chem Nested Input Data repository is also part of the `AWS +Open Data Sponsorship Program +`_. + +.. _gcid-special-repos-gcap2: + +======================================== +GCAP2 meteorology hosted at U. Rochester +======================================== + +The `atmos.earth.rochester.edu +`_ repository +(maintained by Lee Murray at the University of Rochester) contains the +GCAP 2.0 meteorological data inputs for use with GEOS-Chem simulations. + +The data can be accessed by: + +- Direct HTTP or wget download (http://atmos.earth.rochester.edu/input/gc/ExtData/) +- :ref:`Dry run simulation ` diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 65b2a35..09a2f03 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 65b2a350db689d858e547228f9b3a261db1bd86e +Subproject commit 09a2f03cd85a36f60b7333a0d744810116ce0820 From a10e19b239e35ae05f9c0eaf96c621a876466252 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 4 Nov 2024 11:22:05 -0500 Subject: [PATCH 38/99] RTD update: GC data portal doc updates + fixes broken links docs/source/gcclassic-user-guide/download-data.rst - Updated toctree docs/source/gcclassic-user-guide/dry-run-download.rst - Terminology change: "repository" -> "portal" - Simplified "Choose a data portal" section with table docs/source/gcclassic-user-guide/dry-run.rst - Removed tip box - Text formatting update docs/source/gcclassic-user-guide/gcid-special-repos.rst -> renamed to docs/source/gcclassic-user-guide/gcid-special-portals.rst docs/source/gcclassic-user-guide/input-overview.rst - Removed (now obsolete) docs/source/gcclassic-user-guide/restart-files-gc.rst docs/source/gcclassic-user-guide/restart-files-what.rst docs/source/gcclassic-user-guide/run-checklist.rst docs/source/getting-started/disk-space.rst - Fixed broken links & references - Text formatting updates docs/source/getting-started/quick-start.rst - Fixed broken links & references - Text formatting updates - Added attention box for resetting the time cycle flag for SPC_ in HEMCO_Config.rc docs/source/geos-chem-shared-docs - Submodule update with further updates for GEOS-Chem data portals Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/download-data.rst | 4 +- .../gcclassic-user-guide/dry-run-download.rst | 170 +++++-------- .../gcclassic-user-guide/dry-run-run.rst | 13 +- docs/source/gcclassic-user-guide/dry-run.rst | 28 +-- ...ial-repos.rst => gcid-special-portals.rst} | 44 ++-- .../gcclassic-user-guide/input-overview.rst | 228 ------------------ .../gcclassic-user-guide/restart-files-gc.rst | 3 +- .../restart-files-what.rst | 7 +- .../gcclassic-user-guide/run-checklist.rst | 9 +- .../gcclassic-user-guide/run-speedup.rst | 2 +- docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/disk-space.rst | 8 +- docs/source/getting-started/quick-start.rst | 95 ++++++-- .../supplemental-guides/nested-grid-guide.rst | 19 +- 14 files changed, 206 insertions(+), 426 deletions(-) rename docs/source/gcclassic-user-guide/{gcid-special-repos.rst => gcid-special-portals.rst} (67%) delete mode 100644 docs/source/gcclassic-user-guide/input-overview.rst diff --git a/docs/source/gcclassic-user-guide/download-data.rst b/docs/source/gcclassic-user-guide/download-data.rst index 6bbf6ed..bac52ca 100644 --- a/docs/source/gcclassic-user-guide/download-data.rst +++ b/docs/source/gcclassic-user-guide/download-data.rst @@ -18,7 +18,7 @@ for your GEOS-Chem simulation. .. toctree:: :maxdepth: 2 - ../geos-chem-shared-docs/doc/gcid-repository-overview.rst - gcid-special-repos.rst + ../geos-chem-shared-docs/doc/gcid-portal-overview.rst + gcid-special-portals.rst restart-files.rst dry-run.rst diff --git a/docs/source/gcclassic-user-guide/dry-run-download.rst b/docs/source/gcclassic-user-guide/dry-run-download.rst index 01e2c08..c818d63 100644 --- a/docs/source/gcclassic-user-guide/dry-run-download.rst +++ b/docs/source/gcclassic-user-guide/dry-run-download.rst @@ -12,7 +12,7 @@ Once you have successfully executed a GEOS-Chem dry-run, you can use the output from the dry-run (contained in the :file:`log.dryrun` file) to download the data files that GEOS-Chem will need to perform the corresponding "production" simulation. You may download from different -:ref:`data repositories `. +:ref:`data repositories `. .. important:: @@ -38,95 +38,42 @@ corresponding "production" simulation. You may download from different more information, please see `gcpy.readthedocs.io `_. -.. _dry-run-data-download-repo: +.. _dry-run-data-download-portal: -======================== -Choose a data repository -======================== +==================== +Choose a data portal +==================== -You can :ref:`download input data ` from one of the following -repositories: +You can :ref:`download input data ` from any of the portals +listed below. -.. _dry-run-download-repo-gc: - -GEOS-Chem Input Data --------------------- - -The :ref:`GEOS-Chem Input Data ` repository is the main source -of input data (emissions, meteorology, chemistry inputs, restart -files) for GEOS-Chem. We recommend that you download data from this -repository unless otherwise necessary. - -This repository is curated by the GEOS-Chem Support Team at Washington -University in St. Louis, and is hosted on the AWS S3 bucket -:file:`s3://geos-chem`. - -.. tip:: - - We have set up a `Globus `_ - endpoint named **GEOS-Chem data (WashU)**, which links to the - GEOS-Chem Input Data repository. If you need to download many - years of data, you may find that using Globus is much faster than - downloading data with a dry-run simulation. Ask your IT support - staff if Globus is supported at your institution. - -Supported download methods: - -- AWS CLI (command-line interface) -- HTTP download (e.g via :program:`wget`) -- Globus - -Repository browser: - -- AWS S3 Explorer (https://geos-chem.s3.amazonaws.com/index.html) - -.. _dry-run-download-repo-nest: - -GEOS-Chem Nested Input Data ---------------------------- - -The :ref:`gcid-special-repos-nested` repository contains cropped -GEOS-FP and MERRA-2 meteorological inputs for several nested domains. -These data can be used to perform high-resolution inversions using the -`Integrated Methane Inversion (IMI) `_ -workflow. - -This repository is curated by the GEOS-Chem Support Team at -Harvard University and is hosted at the AWS S3 bucket -:file:`s3://gcgrid`. - -Supported download methods: - -- AWS CLI (command-line interface) -- HTTP download (e.g via :program:`wget`) - -Repository browser: - -- AWS S3 Explorer (https://gcgrid.s3.amazonaws.com/index.html) - -.. _dry-run-download-repo-ur: - -GCAP 2.0 meteorology at University of Rochester ------------------------------------------------ - -The `atmos.earth.rochester.edu -`_ repository -contains the GCAP 2.0 meteorology inputs for GEOS-Chem. GCAP 2.0 -meteorology is useful if you wish to perform simulations stretching -back into the preindustrial period, or running into the future. - -This repository is curated by Lee Murray (GitHub: -:literal:`@ltmurray`) at the University of Rochester. - -Supported download methods: - -- HTTP download (e.g via :program:`wget`) - -Repository browser: - -- HTTP site (http://atmos.earth.rochester.edu/input/gc/ExtData) + .. list-table:: GEOS-Chem data portals and access methods + :header-rows: 1 + :align: center -.. _dry-run-download-data: + * - Portal + - S3 Explorer + - AWS CLI + - HTTP + - Globus + * - :ref:`GEOS-Chem Input Data ` |br| + (The main source of GEOS-Chem input data) + - Yes + - Yes + - Yes + - Yes + * - :ref:`gcid-special-portals-nested` + - Yes + - Yes + - Yes + - No + * - :ref:`gcid-special-portals-gcap2` + - No + - No + - Yes + - No + +.. _dry-run-download-py: ============================================================== Run the :file:`download_data.py` script on the dryrun log file @@ -137,7 +84,7 @@ and type. .. code-block:: console - $ ./download_data.py log.dryrun REPOSITORY-NAME + $ ./download_data.py log.dryrun PORTAL-NAME where: @@ -150,40 +97,41 @@ where: simulation. |br| |br| -- :literal:`REPOSITORY-NAME` specifies the data repository that you wish +- :literal:`PORTAL-NAME` specifies the data portal that you wish to download from. Allowed values are: - .. list-table:: Allowed values for the ``REPOSITORY-NAME`` argument + .. list-table:: Allowed values for the ``PORTAL-NAME`` argument to ``download_data.py`` :header-rows: 1 + :align: center * - Value - - Downloads from repository - - Command used - - Method - * - geoschem-s3 - - :ref:`dry-run-download-repo-gc` + - Downloads from portal + - With this command + - Via this method + * - geoschem+aws + - :ref:`GEOS-Chem Input Data ` - :command:`aws s3 cp` - AWS CLI - * - geoschem-wget - - :ref:`dry-run-download-repo-gc` + * - geoschem+http + - :ref:`GEOS-Chem Input Data ` - :command:`wget` - HTTP - * - nested-s3 - - :ref:`dry-run-download-repo-nest` + * - nested+aws + - :ref:`gcid-special-portals-nested` - :command:`aws s3 cp` - AWS CLI - * - nested-wget - - :ref:`dry-run-download-repo-nest` + * - nested+http + - :ref:`gcid-special-portals-nested` - :command:`wget` - HTTP * - rochester - - :ref:`GCAP 2.0 met data @ Rochester ` + - :ref:`GCAP 2.0 met data @ Rochester ` - :command:`wget` - HTTP -For example, to download data from the :ref:`dry-run-download-repo-gc` -repository using the AWS CLI download (which is faster than HTTP +For example, to download data from the :ref:`dry-run-download-portal-gc` +portal using the AWS CLI download (which is faster than HTTP download), use this command: .. code-block:: console @@ -194,8 +142,8 @@ download), use this command: You must have the `AWS CLI (command-line interface) `_ software installed on your system - before in order to use the :literal:`geoschem-s3` or - :literal:`nested-s3` options in the table listed above. + before in order to use the :literal:`geoschem+aws` or + :literal:`nested+aws` options in the table listed above. The :file:`download_data.py` program will generate a **log of unique data files** (i.e. with all duplicate listings removed), which @@ -211,17 +159,17 @@ looks similar to this: !!! Meteorology : GEOSFP !!! Grid Resolution : 4.0x5.0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - ./GEOSChem.Restart.20160701_0000z.nc4 --> /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/GEOSCHEM_RESTARTS/v2018-11/initial_GEOSChem_rst.4x5_standard.nc + ./GEOSChem.Restart.20160701_0000z.nc4 --> /path/to/ExtData/GEOSCHEM_RESTARTS/v2018-11/initial_GEOSChem_rst.4x5_standard.nc ./HEMCO_Config.rc ./HEMCO_Diagn.rc ./HEMCO_restart.201607010000.nc ./HISTORY.rc ./input.geos - /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/FJX_j2j.dat - /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/FJX_spec.dat - /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/dust.dat - /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/h2so4.dat - /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/jv_spec_mie.dat + /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/FJX_j2j.dat + /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/FJX_spec.dat + /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/dust.dat + /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/h2so4.dat + /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/jv_spec_mie.dat ... etc ... This name of this "unique" log file will be the same as the log file diff --git a/docs/source/gcclassic-user-guide/dry-run-run.rst b/docs/source/gcclassic-user-guide/dry-run-run.rst index 4a60732..b8ad155 100644 --- a/docs/source/gcclassic-user-guide/dry-run-run.rst +++ b/docs/source/gcclassic-user-guide/dry-run-run.rst @@ -6,15 +6,6 @@ Execute a dry-run simulation Follow the steps below to perform a GEOS-Chem Classic dry-run simulation: -.. tip:: - - Also be sure to watch our video tutorial `Using the updated - dry-run capability in GEOS-Chem 13.2.1 and later versions - `_ - at our `GEOS-Chem Youtube Channel - `_, which will guide you - through these steps. - ========================== Complete preliminary setup ========================== @@ -32,7 +23,7 @@ files `: #. :option:`start_date`: Set the start date and time for your simulation. #. :option:`end_date`: Set the end date and time for your simulation. - #. :option:`met_field`: Check if the meteorology setting + #. :option:`met_field`: Check if the meteorology setting (:option:`GEOS-FP`, :option:`MERRA2`, :option:`GCAP2`) is correct for your simulation. #. :option:`root_data_dir`: Make sure that the path to @@ -57,7 +48,7 @@ files `: sets for your simulation have been switched on. .. tip:: - + You can reduce the amount of data that needs to be downloaded for your simulation by turning off inventories that you don't need. diff --git a/docs/source/gcclassic-user-guide/dry-run.rst b/docs/source/gcclassic-user-guide/dry-run.rst index 07bb573..535aae3 100644 --- a/docs/source/gcclassic-user-guide/dry-run.rst +++ b/docs/source/gcclassic-user-guide/dry-run.rst @@ -7,20 +7,20 @@ Download data with a dry-run simulation .. tip:: If you are located at an institution with many other GEOS-Chem - users, then the :ref:`necessary input data ` might - have already been downloaded and stored in a commmon directory on - your system. Ask your sysadmin or IT support staff. - - Please see our :ref:`input-overview` chapter for other ways in - which you can download the necessary input data for GEOS-Chem. - -A "dry-run" is a is a :program:`GEOS-Chem Classic` simulation that -steps through time, but does not perform computations or read data -files from disk. Instead, a dry-run simulation prints a list of all -data files that a regular GEOS-Chem simulation would have read. The -dry-run output also denotes whether each data file was found on disk, -or if it is missing. This output can be fed to a script which will -download the missing data files to your computer system. + users, then the necessary input data might have already been + downloaded and stored in a commmon directory on your system. Ask + your sysadmin or IT support staff. + + Please see our :ref:`data` chapter for other ways in which you can + download the necessary input data for GEOS-Chem. + +A :program:`dry-run` is a is a :program:`GEOS-Chem Classic` simulation +that steps through time, but does not perform computations or read +data files from disk. Instead, a dry-run simulation prints a list of +all data files that a regular GEOS-Chem simulation would have +read. The dry-run output also denotes whether each data file was found +on disk, or if it is missing. This output can be fed to a script which +will download the missing data files to your computer system. You may generate dry-run output for any of the GEOS-Chem Classic simulation types (:option:`fullchem`, :option:`carbon`, diff --git a/docs/source/gcclassic-user-guide/gcid-special-repos.rst b/docs/source/gcclassic-user-guide/gcid-special-portals.rst similarity index 67% rename from docs/source/gcclassic-user-guide/gcid-special-repos.rst rename to docs/source/gcclassic-user-guide/gcid-special-portals.rst index 126ef34..49e62b9 100644 --- a/docs/source/gcclassic-user-guide/gcid-special-repos.rst +++ b/docs/source/gcclassic-user-guide/gcid-special-portals.rst @@ -2,23 +2,23 @@
-.. _gcid-special-repos: +.. _gcid-special-portals: -######################################## -Additional meteorology data repositories -######################################## +####################################### +Additional portals for meteorology data +####################################### As discussed in the previous chapter, the :ref:`GEOS-Chem Input -Data ` repository is the main source of input data for +Data ` portal is the main source of input data for :program:`GEOS-Chem Classic`, :program:`GCHP`, and the :program:`HEMCO -standalone model`. This repository contains the entire catalog +standalone model`. This portal contains the entire catalog of emissions inventories, chemical inputs, initial conditions, and most years of `GEOS-FP `_, `MERRA-2 `_, and GEOS-IT meteorology. -We also maintain two additional data repositories for special data sets. +We also maintain two additional data portals for special data sets. -.. _gcid-special-repos-nested: +.. _gcid-special-portals-nested: =========================== GEOS-Chem Nested Input Data @@ -27,15 +27,16 @@ GEOS-Chem Nested Input Data .. attention:: We are still adding data to the GEOS-Chem Nested Input Data - repository. As of this writing (November 2024), not all data may + portal. As of this writing (November 2024), not all data may have been uploaded yet. We thank you for your patience. The `GEOS-Chem Nested Input data `_ -repository stores GEOS-FP and MERRA-2 meteorology fields that have -been cropped to several nested domains. These data can be used to -perform high-resolution inversions with the `Integrated Methane -Inversion (IMI) `_ workflow. +portal stores GEOS-FP and MERRA-2 meteorology fields that have +been cropped to specific :ref:`nested-grid ` domains. +These data can be used to perform high-resolution inversions with the +`Integrated Methane Inversion (IMI) `_ +workflow. .. table:: Available nested-grid meteorology (2018 to present day) :align: center @@ -63,20 +64,21 @@ The data can be accessed by: - Direct HTTP or wget download - :ref:`Dry-run simulation ` -The GEOS-Chem Nested Input Data repository is also part of the `AWS +The GEOS-Chem Nested Input Data portal is also part of the `AWS Open Data Sponsorship Program `_. -.. _gcid-special-repos-gcap2: +.. _gcid-special-portals-gcap2: -======================================== -GCAP2 meteorology hosted at U. Rochester -======================================== +=========================================== +GCAP 2.0 meteorology hosted at U. Rochester +=========================================== The `atmos.earth.rochester.edu -`_ repository -(maintained by Lee Murray at the University of Rochester) contains the -GCAP 2.0 meteorological data inputs for use with GEOS-Chem simulations. +`_ portal +(curated by Lee Murray at the University of Rochester) contains the +GCAP 2.0 meteorological data inputs for use with GEOS-Chem +simulations. The data can be accessed by: diff --git a/docs/source/gcclassic-user-guide/input-overview.rst b/docs/source/gcclassic-user-guide/input-overview.rst deleted file mode 100644 index 28352f3..0000000 --- a/docs/source/gcclassic-user-guide/input-overview.rst +++ /dev/null @@ -1,228 +0,0 @@ -.. _input-overview: - -################################ -Input data for GEOS-Chem Classic -################################ - -GEOS-Chem Classic reads (via `HEMCO `_) -several data files from disk during a simulation. These can be -grouped into the following categories: - -#. :ref:`init-cond` (aka :ref:`restart-files`) -#. :ref:`chem-inputs` -#. :ref:`emis-inputs` -#. :ref:`met` - -============ -Data portals -============ - -Input data files for GEOS-Chem can be downloaded from one of the -following portals: - -.. option:: WashU - - The primary data portal for GEOS-Chem, - `geoschemdata.wustl.edu `_ - - The WashU data portal may be unavailable at times due to - regularly-scheduled maintenance periods. Please check the - `WashU IT status page `_ for more - information. - -.. option:: Amazon - - GEOS-Chem data on the Amazon cloud, `s3://gcgrid - `_. You can - browse the contents of the data via the - `AWS S3 Explorer `_. - - .. note:: - - Downloading from the Amazon Data Portal will NOT incur any - egress charges. This is because the data is covered under the - `AWS Open Data Sponsorship Program - `_. - -.. option:: Rochester - - Portal for the GCAP 2.0 meteorological data files, - `atmos.earth.rochester.edu - `_ - -.. _init-cond: - -============================= -Initial conditions input data -============================= - -Initial conditions include: - -- Initial species concentrations (aka :ref:`restart-files`) used to - start a GEOS-Chem simulation. - -.. table:: - :align: center - - +--------------------------------------------------+---------------------+ - | Download method | From portals | - +==================================================+=====================+ - | :ref:`Dry run simulation ` | :option:`WashU` | - | | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Run :ref:`bashdatacatalog ` | :option:`WashU` | - | on the :file:`InitialConditions.csv` file [1]_ | | - +--------------------------------------------------+---------------------+ - | Direct data download (:program:`FTP` or | :option:`WashU` | - | :program:`wget`) | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Direct data download | :option:`Amazon` | - | (:program:`AWS S3 Explorer`) [2]_ | | - +--------------------------------------------------+---------------------+ - | Globus, use endpoint **GEOS-Chem data (WashU)** | :option:`WashU` | - +--------------------------------------------------+---------------------+ - -.. rubric:: Notes - -.. [1] We provide :file:`InitialConditions.csv` files (for each - GEOS-Chem version since 13.0.0) at our `input-data-catalogs - `_ Github repository. -.. [2] Direct link: `s3.amazonaws.com/gcgrid/index.html `_ - -.. _chem-inputs: - -==================== -Chemistry input data -==================== - -Chemistry input data includes: - -- Quantum yields and cross sections for photolysis using either ``Cloud-J`` or legacy ``FAST-JX`` -- Climatology data for :program:`Linoz` -- Boundary conditions for :program:`UCX` stratospheric chemistry routines - -.. table:: - :align: center - - +--------------------------------------------------+---------------------+ - | Download method | From portals | - +==================================================+=====================+ - | :ref:`Dry run simulation ` | :option:`WashU` | - | | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Run :ref:`bashdatacatalog ` | :option:`WashU` | - | on the | | - | :file:`ChemistryInputs.csv` [3]_ | | - +--------------------------------------------------+---------------------+ - | Direct data download (:program:`FTP` or | :option:`WashU` | - | :program:`wget`) | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Direct data download | :option:`Amazon` | - | (:program:`AWS S3 Explorer`) [2]_ | | - +--------------------------------------------------+---------------------+ - | Globus, use endpoint **GEOS-Chem data (WashU)** | :option:`WashU` | - +--------------------------------------------------+---------------------+ - -.. rubric:: Notes - -.. [3] We provide :file:`ChemistryInputs.csv` files (for each - GEOS-Chem version since 13.0.0) at our `input-data-catalogs - `_ Github repository. - -.. _emis-inputs: - -==================== -Emissions input data -==================== - -Emissions input data includes the following data: - -- Emissions inventories -- Input data for HEMCO Extensions -- Input data for GEOS-Chem specialty simulations -- Scale factors -- Mask definitions -- Surface boundary conditions -- Leaf area indices -- Land cover map - -.. table:: - :align: center - - +--------------------------------------------------+---------------------+ - | Download method | From portals | - +==================================================+=====================+ - | :ref:`Dry run simulation ` | :option:`WashU` | - | | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Run :ref:`bashdatacatalog ` | :option:`WashU` | - | on the :file:`EmissionsInputs.csv` file [4]_ | | - +--------------------------------------------------+---------------------+ - | Direct data download (:program:`FTP` or | :option:`WashU` | - | :program:`wget`) | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Direct data download | :option:`Amazon` | - | (:program:`AWS S3 Explorer`) [2]_ | | - +--------------------------------------------------+---------------------+ - | Globus, use endpoint **GEOS-Chem data (WashU)** | :option:`WashU` | - +--------------------------------------------------+---------------------+ - -.. rubric:: Notes - -.. [4] We provide :file:`EmissionsInputs.csv` files (for each - GEOS-Chem version since 13.0.0) at our `input-data-catalogs - `_ Github repository. - -.. _met: - -====================== -Meteorology input data -====================== - -:ref:`As described previously `, GEOS-Chem Classic -be driven by the following meteorology products: - -#. `MERRA-2 `_ -#. `GEOS-FP `_ -#. `GCAP 2.0 `_ - -.. attention:: - - We are still evaluating GEOS-Chem with the new NASA GEOS-IT - meterorology product. For the time being, you should use one of - the other meteorology options. - -.. table:: - :align: center - - +--------------------------------------------------+---------------------+ - | Download method | From portals | - +==================================================+=====================+ - | :ref:`Dry run simulation ` | :option:`WashU` | - | | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Run :ref:`bashdatacatalog ` | :option:`WashU` | - | on the :file:`MeteorologyInputs.csv` file [5]_ | | - +--------------------------------------------------+---------------------+ - | Direct data download (:program:`FTP` or | :option:`WashU` | - | :program:`wget`) | :option:`Amazon` | - | | :option:`Rochester` | - +--------------------------------------------------+---------------------+ - | Direct data download | :option:`Amazon` | - | (:program:`AWS S3 Explorer`) [2]_ | | - +--------------------------------------------------+---------------------+ - | Globus, use endpoint **GEOS-Chem data (WashU)** | :option:`WashU` | - +--------------------------------------------------+---------------------+ - -.. rubric:: Notes - -.. [5] We provide :file:`MeteorologyInputs.csv` files (for each - GEOS-Chem version since 13.0.0) at our `input-data-catalogs - `_ Github repository. diff --git a/docs/source/gcclassic-user-guide/restart-files-gc.rst b/docs/source/gcclassic-user-guide/restart-files-gc.rst index c4e96ee..20a97fe 100644 --- a/docs/source/gcclassic-user-guide/restart-files-gc.rst +++ b/docs/source/gcclassic-user-guide/restart-files-gc.rst @@ -134,8 +134,7 @@ Where can I get a restart file for my simulation? GEOS-Chem Classic :ref:`run directories ` are configured to use sample GEOS-Chem restart files in :program:`netCDF` format. These -files are available for download at the :option:`WashU` and -:option:`Amazon` data portals. +files are available for download at the :ref:`gcid-data` portal. .. tip:: diff --git a/docs/source/gcclassic-user-guide/restart-files-what.rst b/docs/source/gcclassic-user-guide/restart-files-what.rst index 1a845a6..1569345 100644 --- a/docs/source/gcclassic-user-guide/restart-files-what.rst +++ b/docs/source/gcclassic-user-guide/restart-files-what.rst @@ -4,8 +4,9 @@ What is a restart file? ####################### -Restart files contain the initial conditions (cf. :ref:`init-cond`) -for a GEOS-Chem simulation. GEOS-Chem simulations need two restart files. +Restart files contain species concentrations, as well as other +quantities that are needed to initialize GEOS-Chem simulations. +GEOS-Chem simulations use two separate restart files. .. option:: GEOSChem.Restart.YYYYMMDD_hhmmz.nc4 @@ -31,7 +32,7 @@ for a GEOS-Chem simulation. GEOS-Chem simulations need two restart files. **Description:** The :ref:`HEMCO restart file `. HEMCO archives certain quantities (mostly pertaining to soil NOx - and biogenic emissions) in order to facilitate long GEOS-Chem + and biogenic emissions in order to facilitate long GEOS-Chem simulations with several run stages. HEMCO restart files are created in the :option:`Restarts/` diff --git a/docs/source/gcclassic-user-guide/run-checklist.rst b/docs/source/gcclassic-user-guide/run-checklist.rst index 3475d4f..e55712c 100644 --- a/docs/source/gcclassic-user-guide/run-checklist.rst +++ b/docs/source/gcclassic-user-guide/run-checklist.rst @@ -55,14 +55,15 @@ Each-time setup .. attention:: - Prior to running with :option:`GEOS-FP` meteorology, be aware + Prior to running with GEOS-FP meteorology, be aware that it is an operational (i.e. evolving) product that is subject to assimilation system updates. - On the other hand, the :option:`MERRA-2` meterology is a 40+ + On the other hand, the MERRA-2 meterology is a 40+ year reanalysis product performed with a "frozen" version of the - NASA GEOS assimilation system. Thus, :option:`MERRA-2` is - preferable for studies ranging over multiple years or decades. + NASA GEOS assimilation system. Thus, `MERRA-2 + `_ is preferable for studies + ranging over multiple years or decades. #. :ref:`Configure and build ` the source code into an executable file. |br| diff --git a/docs/source/gcclassic-user-guide/run-speedup.rst b/docs/source/gcclassic-user-guide/run-speedup.rst index caaf9d1..9c41e9d 100644 --- a/docs/source/gcclassic-user-guide/run-speedup.rst +++ b/docs/source/gcclassic-user-guide/run-speedup.rst @@ -146,7 +146,7 @@ fields. The overhead in reading and regridding these global fields can significantly impact your simulation. Instead, consider cropping high-resolution meteorology fields to the extent of your nested domain. This can easily be done with the netCDF operators or the Climate Data -Operators; see our :ref:`netcdf-guide` supplemental guide for more +Operators; see our :ref:`ncguide` supplemental guide for more information. .. _run-speedup-nested-buffer: diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 09a2f03..b5229c8 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 09a2f03cd85a36f60b7333a0d744810116ce0820 +Subproject commit b5229c83cac0bfa7e128fdd2315492cafb973d0a diff --git a/docs/source/getting-started/disk-space.rst b/docs/source/getting-started/disk-space.rst index 74bb30c..faa9f5a 100644 --- a/docs/source/getting-started/disk-space.rst +++ b/docs/source/getting-started/disk-space.rst @@ -6,7 +6,7 @@ Disk space requirements The following sections will help you assess how much disk space you will need on your server to store GEOS-Chem Classic :ref:`input data -` and :ref:`output data `. +` and :ref:`output data `. .. _req-hard-disk-limits: @@ -24,8 +24,8 @@ information. Emissions input fields ---------------------- -Please see our :ref:`Emissions input data ` section for -more information. +Please see our :ref:`Emissions input data ` +section for more information. .. _req-hard-disk-met: @@ -101,7 +101,7 @@ sections. `_; #. Direct access from the `Amazon data portal using AWS S3 Explorer `_. -Also see our :ref:`input-overview` for more data download options. +Also see our :ref:`data` chapter for more data download options. .. _data-generated-by-geos-chem: diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst index 6bc10b6..2fd219a 100644 --- a/docs/source/getting-started/quick-start.rst +++ b/docs/source/getting-started/quick-start.rst @@ -1,3 +1,7 @@ +.. |br| raw:: html + +
+ .. _quick: ################ @@ -119,8 +123,8 @@ simulations follow the same pattern as the examples shown below. provide :ref:`registration information `. Please answer all of the questions, as it will help us to keep track of GEOS-Chem usage worldwide. We will also add your - information to the `GEOS-Chem People and Projects web page - `_. + information to the `GEOS-Chem Users web page + `_. .. _quick-load: @@ -209,8 +213,8 @@ where the error happened and why. $ cmake . -DCMAKE_BUILD_TYPE=Debug -See the :ref:`GEOS-Chem documentation ` for more -information on configuration options. +:ref:`Click here ` for more information on +configuration options. .. _quick-cmp-inst: @@ -226,7 +230,7 @@ with the :literal:`-j` flag from the :file:`build/` directory: .. code-block:: console - # cd /path/to/gc_4x5_merra2_fullchem/build # Skip if you are already here + $ cd /path/to/gc_4x5_merra2_fullchem/build # Skip if you are already here $ make -j Upon successful compilation, install the compiled executable to your @@ -278,7 +282,39 @@ You should review these files before starting a simulation: - :ref:`HEMCO_Config.rc ` - Controls which emissions inventories and other non-emissions data - will be read from disk (via `HEMCO `_). + will be read from disk (via `HEMCO + `_). + +.. attention:: + + If you wish to spin up a GEOS-Chem simulation with a restart file + that has (1) missing species or (2) a timestamp that does not + match the start date in :ref:`geoschem_config.yml `, + simply change the time cycle flag for the :literal:`SPC_` entry in + :ref:`HEMCO_Config.rc ` from + + .. code-block:: console + + * SPC_ ... $YYYY/$MM/$DD/$HH EFYO xyz 1 * - 1 1 + + to + + .. code-block:: console + + * SPC_ ... $YYYY/$MM/$DD/$HH CYS xyz 1 * - 1 1 + + This will direct HEMCO to read the closest date + available (:literal:`C`), to use the simulation year + (:literal:`Y`), and to skip any species (:literal:`S`) not found + in the restart file. + + Skipped species will be assigned the initial concentration + (units: :math:`mol\ mol^{-1}` w/r/t dry air) specified by its + :option:`BackgroundVV` entry in :ref:`species_database.yml + `. If the species does not have a + :option:`BackgroundVV` value specified, then its initial + concentration will be set to :math:`1.0{\times}10^{-20}` + instead. Please see our :ref:`customguide` Supplemental Guide to learn how you can customize your simulation by activating alternate science options @@ -293,16 +329,18 @@ in your simulations. Before you can run your GEOS-Chem Classic simulation, you must first :ref:`download the required input data `. These data include: -- Meteorological fields (e.g. GEOS-FP, MERRA-2, GEOS-IT, or GCAP2) -- Emissions inventories -- Inputs for GEOS-Chem modules (e.g. Cloud-J) +- :ref:`Meteorological fields ` (e.g. GEOS-FP, + MERRA-2, GEOS-IT, or GCAP2) +- :ref:`Emissions inventories ` +- :ref:`Inputs for GEOS-Chem modules (e.g. Cloud-J) ` +- :ref:`Initial conditions for starting GEOS-Chem simulations ` .. tip:: If your institution has several GEOS-Chem users, then someone may have already downloaded these data for you. If this is the case, you may :ref:`start running your your GEOS-Chem Classic simulation - `. + ` right away. The easiest way to download data is to perform a :ref:`dry-run simulation `. This is a GEOS-Chem Classic simulation that @@ -321,15 +359,7 @@ list of data files to be downloaded. Once the dry-run simulation has finished, use the :file:`download_data.py` file (included in your run directory) to -:ref:`download the required data `. Type: - -.. code-block:: console - - $ ./download_data.py log.dryrun --washu - -This will download data from the :option:`WashU` data portal. You -may also download from the :option:`Amazon` or :option:`Rochester` -data portals. +:ref:`download the required data `. .. note:: @@ -337,6 +367,33 @@ data portals. Mamba environment containing a version of Python before running the :file:`download.data.py` script. Ask your sysadmin. +To start the data download, type: + +.. code-block:: console + + $ ./download_data.py log.dryrun geoschem+http + +This will download data from the :ref:`GEOS-Chem Input Data ` +portal using the HTTP data transfer protocol. + +.. tip:: + + If you have `AWS CLI (command line interface) + `_ installed on your system, you + can use this command instead: + + .. code-block:: console + + $ ./download_data.py log.dryrun geoschem+aws + + This will use the AWS CLI data download protocol instead, which + should be faster than regular HTTP connections. This is the + command you should use if you are running GEOS-Chem Classic in an + AWS EC2 instance. + +We also maintain :ref:`separate data portals ` +for special nested-grid domains as well as the GCAP 2.0 meteorology. + For more information about dry-run simulations, please see our :ref:`dry-run` chapter. diff --git a/docs/source/supplemental-guides/nested-grid-guide.rst b/docs/source/supplemental-guides/nested-grid-guide.rst index 2cd2fa8..b8524ce 100644 --- a/docs/source/supplemental-guides/nested-grid-guide.rst +++ b/docs/source/supplemental-guides/nested-grid-guide.rst @@ -238,11 +238,20 @@ simulations on different nested domains. How can I find which data are available for nested grid simulations? -------------------------------------------------------------------- -You will download meteorology and emissions data from one of the -:ref:`GEOS-Chem data portals `. You can browse the -WashU data portal (`http://geoschemdata.wustl.edu/ExtData -`_) to see if the data you need -are available. +You can browse the contents of the GEOS-Chem data portals by pointing +your browser to one of the following links: + +- :ref:`GEOS-Chem Input Data ` + + - https://geos-chem.s3.amazonaws.com/index.html + +- :ref:`GEOS-Chem Nested Input Data ` + + - https://gcgrid.s3.amazonaws.com/index.html + +- :ref:`GCAP 2.0 meteorology @ U. Rochester ` + + - http://atmos.earth.rochester.edu/input/gc/ExtData/ .. _nestgrid-faq-errors: From 09a5db3ec202fac6c32fb0ae2760c47594242c40 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 5 Nov 2024 12:11:37 -0500 Subject: [PATCH 39/99] Update dry-run download; Add warnings about GEOS-FP docs/source/gcclassic-user-guide/dry-run-download.rst - Reduce indentation for GEOS-Chem data portals & access methods - Update log.dryrun.unique output to remove obsolete file listings docs/source/gcclassic-user-guide/run-checklist.rst docs/source/help-and-reference/known-bugs.rst - Add "important" box with warning about GEOS-FP convection switch Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/dry-run-download.rst | 97 ++++++++++--------- .../gcclassic-user-guide/run-checklist.rst | 25 ++++- docs/source/help-and-reference/known-bugs.rst | 17 ++++ 3 files changed, 91 insertions(+), 48 deletions(-) diff --git a/docs/source/gcclassic-user-guide/dry-run-download.rst b/docs/source/gcclassic-user-guide/dry-run-download.rst index c818d63..ff93dee 100644 --- a/docs/source/gcclassic-user-guide/dry-run-download.rst +++ b/docs/source/gcclassic-user-guide/dry-run-download.rst @@ -47,31 +47,34 @@ Choose a data portal You can :ref:`download input data ` from any of the portals listed below. - .. list-table:: GEOS-Chem data portals and access methods - :header-rows: 1 - :align: center - - * - Portal - - S3 Explorer - - AWS CLI - - HTTP - - Globus - * - :ref:`GEOS-Chem Input Data ` |br| - (The main source of GEOS-Chem input data) - - Yes - - Yes - - Yes - - Yes - * - :ref:`gcid-special-portals-nested` - - Yes - - Yes - - Yes - - No - * - :ref:`gcid-special-portals-gcap2` - - No - - No - - Yes - - No +.. list-table:: GEOS-Chem data portals and access methods + :header-rows: 1 + + * - Portal + - S3 Explorer + - AWS CLI + - HTTP + - Bashdatacatalog + - Globus + * - :ref:`GEOS-Chem Input Data ` |br| + (The main source of GEOS-Chem input data) + - Yes + - Yes + - Yes + - Yes + - Yes + * - :ref:`gcid-special-portals-nested` + - Yes + - Yes + - Yes + - No + - No + * - :ref:`gcid-special-portals-gcap2` + - No + - No + - Yes + - No + - No .. _dry-run-download-py: @@ -151,25 +154,31 @@ looks similar to this: .. code-block:: text - !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - !!! LIST OF (UNIQUE) FILES REQUIRED FOR THE SIMULATION - !!! Start Date : 20160701 000000 - !!! End Date : 20160701 010000 - !!! Simulation : standard - !!! Meteorology : GEOSFP - !!! Grid Resolution : 4.0x5.0 - !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - ./GEOSChem.Restart.20160701_0000z.nc4 --> /path/to/ExtData/GEOSCHEM_RESTARTS/v2018-11/initial_GEOSChem_rst.4x5_standard.nc - ./HEMCO_Config.rc - ./HEMCO_Diagn.rc - ./HEMCO_restart.201607010000.nc - ./HISTORY.rc - ./input.geos - /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/FJX_j2j.dat - /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/FJX_spec.dat - /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/dust.dat - /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/h2so4.dat - /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2019-10/jv_spec_mie.dat + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + !!! LIST OF (UNIQUE) FILES REQUIRED FOR THE SIMULATION + !!! Start Date : 20190701 000000 + !!! End Date : 20190701 010000 + !!! Simulation : fullchem + !!! Meteorology : MERRA2 + !!! Grid Resolution : 4.0x5.0 + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + ./HEMCO_Config.rc + ./HEMCO_Config.rc.gmao_metfields + ./HEMCO_Diagn.rc + ./HISTORY.rc + ./Restarts/GEOSChem.Restart.20190701_0000z.nc4 --> /home/ubuntu/ExtData/GEOSCHEM_RESTARTS/GC_14.5.0/GEOSChem.Restart.fullchem.20190701_0000z.nc4 + ./Restarts/HEMCO_restart.201907010000.nc + ./geoschem_config.yml + /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/FJX_j2j.dat + /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/FJX_scat-aer.dat + /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/FJX_scat-cld.dat + /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/FJX_scat-ssa.dat + /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/FJX_spec.dat + /path/to/ExtData/CHEM_INPUTS/FastJ_201204/fastj.jv_atms_dat.nc + /path/to/ExtData/CHEM_INPUTS/Linoz_200910/Linoz_March2007.dat + /path/to/ExtData/CHEM_INPUTS/Olson_Land_Map_201203/Olson_2001_Drydep_Inputs.nc + /path/to/ExtData/CHEM_INPUTS/UCX_201403/NoonTime/Grid4x5/InitCFC_JN2O_01.dat + ... etc ... This name of this "unique" log file will be the same as the log file diff --git a/docs/source/gcclassic-user-guide/run-checklist.rst b/docs/source/gcclassic-user-guide/run-checklist.rst index e55712c..8a9c639 100644 --- a/docs/source/gcclassic-user-guide/run-checklist.rst +++ b/docs/source/gcclassic-user-guide/run-checklist.rst @@ -55,16 +55,33 @@ Each-time setup .. attention:: - Prior to running with GEOS-FP meteorology, be aware - that it is an operational (i.e. evolving) product - that is subject to assimilation system updates. + Be aware that GEOS-FP meteorology is an operational + (i.e. evolving) product that is subject to assimilation + system updates. - On the other hand, the MERRA-2 meterology is a 40+ + On the other hand, the MERRA-2 meteorology is a 40+ year reanalysis product performed with a "frozen" version of the NASA GEOS assimilation system. Thus, `MERRA-2 `_ is preferable for studies ranging over multiple years or decades. + .. important:: + + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020, specifically enhanced vertical + transport. In addition, there is a bug in convective + precipitation flux following the switch where all values are + zero. While this bug is automatically fixed by computing fluxes + online for runs starting on or after June 1 2020, the fix + assumes meteorology year corresponds to simulation year. Due to + these issues we recommend splitting up GEOS-FP runs in time such + that a single simulation does not run across June + 1, 2020. Instead. set one run to stop on June 1 2020 and then + restart a new run from there. If you wish to use a GEOS-FP + meteorology year different from your simulation year please + create a GEOS-Chem GitHub issue for assistance. + #. :ref:`Configure and build ` the source code into an executable file. |br| |br| diff --git a/docs/source/help-and-reference/known-bugs.rst b/docs/source/help-and-reference/known-bugs.rst index 59debd7..e60eeeb 100644 --- a/docs/source/help-and-reference/known-bugs.rst +++ b/docs/source/help-and-reference/known-bugs.rst @@ -23,6 +23,23 @@ are currently unresolved. We hope to fix these in future releases. diagnostic collection may not be working as expected. We are currently investigating. +.. important:: + + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020, specifically enhanced vertical + transport. In addition, there is a bug in convective + precipitation flux following the switch where all values are + zero. While this bug is automatically fixed by computing fluxes + online for runs starting on or after June 1 2020, the fix + assumes meteorology year corresponds to simulation year. Due to + these issues we recommend splitting up GEOS-FP runs in time such + that a single simulation does not run across June + 1, 2020. Instead. set one run to stop on June 1 2020 and then + restart a new run from there. If you wish to use a GEOS-FP + meteorology year different from your simulation year please + create a GEOS-Chem GitHub issue for assistance. + ============================ Bugs that have been resolved ============================ From 765987a078c2d3714fdf33e43e9ab51bd00dd406 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 5 Nov 2024 12:30:49 -0500 Subject: [PATCH 40/99] Moved gcid-special-portals.rst to geos-chem-shared-docs/doc docs/source/gcclassic-user-guide/gcid-special-portals.rst - Moved to geos-chem-shared-docs/doc/gcid-special-portals.rst docs/source/gcclassic-user-guide/download-data.rst - Toctree now points to geoschem-shared-docs/doc/gcid-special-portals.rst docs/source/gcclassic/dry-run-run.rst - Add warning box about GEOS-FP convection switch docs/source/geos-chem-shared-docs - Submodule update to 54890ed Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/download-data.rst | 2 +- .../gcclassic-user-guide/dry-run-run.rst | 18 ++++ .../gcid-special-portals.rst | 86 ------------------- docs/source/geos-chem-shared-docs | 2 +- 4 files changed, 20 insertions(+), 88 deletions(-) delete mode 100644 docs/source/gcclassic-user-guide/gcid-special-portals.rst diff --git a/docs/source/gcclassic-user-guide/download-data.rst b/docs/source/gcclassic-user-guide/download-data.rst index bac52ca..df110f7 100644 --- a/docs/source/gcclassic-user-guide/download-data.rst +++ b/docs/source/gcclassic-user-guide/download-data.rst @@ -19,6 +19,6 @@ for your GEOS-Chem simulation. :maxdepth: 2 ../geos-chem-shared-docs/doc/gcid-portal-overview.rst - gcid-special-portals.rst + ../geos-chem-shared-docs/doc/gcid-special-portals.rst restart-files.rst dry-run.rst diff --git a/docs/source/gcclassic-user-guide/dry-run-run.rst b/docs/source/gcclassic-user-guide/dry-run-run.rst index b8ad155..8299112 100644 --- a/docs/source/gcclassic-user-guide/dry-run-run.rst +++ b/docs/source/gcclassic-user-guide/dry-run-run.rst @@ -26,6 +26,24 @@ files `: #. :option:`met_field`: Check if the meteorology setting (:option:`GEOS-FP`, :option:`MERRA2`, :option:`GCAP2`) is correct for your simulation. + + .. important:: + + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020, specifically enhanced vertical + transport. In addition, there is a bug in convective + precipitation flux following the switch where all values are + zero. While this bug is automatically fixed by computing fluxes + online for runs starting on or after June 1 2020, the fix + assumes meteorology year corresponds to simulation year. Due to + these issues we recommend splitting up GEOS-FP runs in time such + that a single simulation does not run across June + 1, 2020. Instead. set one run to stop on June 1 2020 and then + restart a new run from there. If you wish to use a GEOS-FP + meteorology year different from your simulation year please + create a GEOS-Chem GitHub issue for assistance. + #. :option:`root_data_dir`: Make sure that the path to :file:`ExtData` is correct. diff --git a/docs/source/gcclassic-user-guide/gcid-special-portals.rst b/docs/source/gcclassic-user-guide/gcid-special-portals.rst deleted file mode 100644 index 49e62b9..0000000 --- a/docs/source/gcclassic-user-guide/gcid-special-portals.rst +++ /dev/null @@ -1,86 +0,0 @@ -.. |br| raw:: html - -
- -.. _gcid-special-portals: - -####################################### -Additional portals for meteorology data -####################################### - -As discussed in the previous chapter, the :ref:`GEOS-Chem Input -Data ` portal is the main source of input data for -:program:`GEOS-Chem Classic`, :program:`GCHP`, and the :program:`HEMCO -standalone model`. This portal contains the entire catalog -of emissions inventories, chemical inputs, initial conditions, and -most years of `GEOS-FP `_, -`MERRA-2 `_, and GEOS-IT meteorology. - -We also maintain two additional data portals for special data sets. - -.. _gcid-special-portals-nested: - -=========================== -GEOS-Chem Nested Input Data -=========================== - -.. attention:: - - We are still adding data to the GEOS-Chem Nested Input Data - portal. As of this writing (November 2024), not all data may - have been uploaded yet. We thank you for your patience. - -The `GEOS-Chem Nested Input data -`_ -portal stores GEOS-FP and MERRA-2 meteorology fields that have -been cropped to specific :ref:`nested-grid ` domains. -These data can be used to perform high-resolution inversions with the -`Integrated Methane Inversion (IMI) `_ -workflow. - -.. table:: Available nested-grid meteorology (2018 to present day) - :align: center - - +---------+--------------------------+-------------------------------+ - | Product | Horizontal resolution | Nested-grid domains | - +=========+==========================+===============================+ - | GEOS-FP | :math:`0.125^{\circ} | AF (Africa) |br| | - | | {\times}0.15625^{\circ}` | AS (Asia) |br| | - | | | EU (Europe) |br| | - | | | ME (Middle East) |br| | - | | | NA (North America) |br| | - | | | OC (Oceania) |br| | - | | | RU (Russia) |br| | - | | | SA (South America) | - +---------+--------------------------+-------------------------------+ - | MERRA-2 | :math:`0.5^{\circ} | AS (Asia) |br| | - | | {\times}0.625^{\circ}` | EU (Europe) |br| | - | | | NA (North America) |br| | - +---------+--------------------------+-------------------------------+ - -The data can be accessed by: - -- AWS S3 Explorer (https://s3.amazonaws.com/gcgrid/index.html) -- Direct HTTP or wget download -- :ref:`Dry-run simulation ` - -The GEOS-Chem Nested Input Data portal is also part of the `AWS -Open Data Sponsorship Program -`_. - -.. _gcid-special-portals-gcap2: - -=========================================== -GCAP 2.0 meteorology hosted at U. Rochester -=========================================== - -The `atmos.earth.rochester.edu -`_ portal -(curated by Lee Murray at the University of Rochester) contains the -GCAP 2.0 meteorological data inputs for use with GEOS-Chem -simulations. - -The data can be accessed by: - -- Direct HTTP or wget download (http://atmos.earth.rochester.edu/input/gc/ExtData/) -- :ref:`Dry run simulation ` diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index b5229c8..54890ed 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit b5229c83cac0bfa7e128fdd2315492cafb973d0a +Subproject commit 54890ed71c0cab6f82b2ace84516267bc96eb10c From b81423c86cc7165843a8d4c8761d7c21d8ca4f6c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 5 Nov 2024 16:09:43 -0500 Subject: [PATCH 41/99] RTD update: Fixed more links/refs and text formatting issues docs/source/gcclassic-user-guide/compile-cmake.rst - Add proper indentation to a ".. note::" block docs/source/gcclassic-user-guide/rundir-carbon.rst docs/source/gcclassic-user-guide/rundir-fullchem.rst docs/source/getting-started/quick-start.rst - Add "important" box about GEOS-FP convection issue - Trimmed trailing whitespace docs/source/gcclassic-user-guide/dry-run-download.rst - Fixed incorrect portal name "geoschem-s3" -> "geoschem+s3" docs/source/geos-chem-shared-docs - Submodule update to cd0f4ad (fix broken links & refs) docs/source/help-and-reference/known-bugs.rst - Renamed link text to avoid a "duplicate link" warning docs/source/index.rst - Removed geos-chem-input-data-on-aws.rst from toctree, as this is now moved to geos-chem-shared-docs/doc/gcid-portal-overview.rst Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/compile-cmake.rst | 13 ++++++------- .../gcclassic-user-guide/dry-run-download.rst | 8 ++++---- .../gcclassic-user-guide/rundir-carbon.rst | 17 +++++++++++++++++ .../gcclassic-user-guide/rundir-fullchem.rst | 17 +++++++++++++++++ docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/quick-start.rst | 17 +++++++++++++++++ docs/source/help-and-reference/known-bugs.rst | 2 +- docs/source/index.rst | 1 - 8 files changed, 63 insertions(+), 14 deletions(-) diff --git a/docs/source/gcclassic-user-guide/compile-cmake.rst b/docs/source/gcclassic-user-guide/compile-cmake.rst index 16bea85..96a294f 100644 --- a/docs/source/gcclassic-user-guide/compile-cmake.rst +++ b/docs/source/gcclassic-user-guide/compile-cmake.rst @@ -433,17 +433,16 @@ Classic contains code from the various repositories: .. note:: - If you are cloning GEOS-Chem Classic between official releases, you - may the see :code:`Current status` reported like this: + If you are cloning GEOS-Chem Classic between official releases, you + may the see :code:`Current status` reported like this: - .. code-block:: console + .. code-block:: console - X.Y.Z-alpha.n-C-gabcd1234.dirty or + X.Y.Z-alpha.n-C-gabcd1234.dirty or - X.Y.Z.rc.n-C.gabcd1234.dirty + X.Y.Z.rc.n-C.gabcd1234.dirty - We will explain these formats below. |br| - |br| + We will explain these formats below. #. `HEMCO (Harmonized Emissions Component) submodule `_: diff --git a/docs/source/gcclassic-user-guide/dry-run-download.rst b/docs/source/gcclassic-user-guide/dry-run-download.rst index ff93dee..e2f964a 100644 --- a/docs/source/gcclassic-user-guide/dry-run-download.rst +++ b/docs/source/gcclassic-user-guide/dry-run-download.rst @@ -133,13 +133,13 @@ where: - :command:`wget` - HTTP -For example, to download data from the :ref:`dry-run-download-portal-gc` -portal using the AWS CLI download (which is faster than HTTP -download), use this command: +For example, to download data from the :ref:`GEOS-Chem Input Data +` portal using the AWS CLI download (which is faster than +HTTP download), use this command: .. code-block:: console - $ ./download_data.py log.dryrun geoschem-s3 + $ ./download_data.py log.dryrun geoschem+s3 .. note:: diff --git a/docs/source/gcclassic-user-guide/rundir-carbon.rst b/docs/source/gcclassic-user-guide/rundir-carbon.rst index 915e26b..7652873 100644 --- a/docs/source/gcclassic-user-guide/rundir-carbon.rst +++ b/docs/source/gcclassic-user-guide/rundir-carbon.rst @@ -136,6 +136,23 @@ simulation. We'll use the carbon gases simulation as an example. followed by :command:`ENTER`. |br| |br| + .. important:: + + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020, specifically enhanced vertical + transport. In addition, there is a bug in convective + precipitation flux following the switch where all values are + zero. While this bug is automatically fixed by computing fluxes + online for runs starting on or after June 1 2020, the fix + assumes meteorology year corresponds to simulation year. Due to + these issues we recommend splitting up GEOS-FP runs in time such + that a single simulation does not run across June + 1, 2020. Instead. set one run to stop on June 1 2020 and then + restart a new run from there. If you wish to use a GEOS-FP + meteorology year different from your simulation year please + create a GEOS-Chem GitHub issue for assistance. + #. The next menu will prompt you for the horizontal resolution that you wish to use: diff --git a/docs/source/gcclassic-user-guide/rundir-fullchem.rst b/docs/source/gcclassic-user-guide/rundir-fullchem.rst index 8896a84..b5b0ebb 100644 --- a/docs/source/gcclassic-user-guide/rundir-fullchem.rst +++ b/docs/source/gcclassic-user-guide/rundir-fullchem.rst @@ -138,6 +138,23 @@ GEOS-Chem full-chemistry simulation. :command:`1` followed by :command:`ENTER`. |br| |br| + .. important:: + + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020, specifically enhanced vertical + transport. In addition, there is a bug in convective + precipitation flux following the switch where all values are + zero. While this bug is automatically fixed by computing fluxes + online for runs starting on or after June 1 2020, the fix + assumes meteorology year corresponds to simulation year. Due to + these issues we recommend splitting up GEOS-FP runs in time such + that a single simulation does not run across June + 1, 2020. Instead. set one run to stop on June 1 2020 and then + restart a new run from there. If you wish to use a GEOS-FP + meteorology year different from your simulation year please + create a GEOS-Chem GitHub issue for assistance. + #. The next menu will prompt you for the horizontal resolution that you wish to use: diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 54890ed..cd0f4ad 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 54890ed71c0cab6f82b2ace84516267bc96eb10c +Subproject commit cd0f4ad1dd13648c3fe9bf8bb13c7bf5ef517125 diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst index 2fd219a..da46b40 100644 --- a/docs/source/getting-started/quick-start.rst +++ b/docs/source/getting-started/quick-start.rst @@ -126,6 +126,23 @@ simulations follow the same pattern as the examples shown below. information to the `GEOS-Chem Users web page `_. +.. important:: + + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020, specifically enhanced vertical + transport. In addition, there is a bug in convective + precipitation flux following the switch where all values are + zero. While this bug is automatically fixed by computing fluxes + online for runs starting on or after June 1 2020, the fix + assumes meteorology year corresponds to simulation year. Due to + these issues we recommend splitting up GEOS-FP runs in time such + that a single simulation does not run across June + 1, 2020. Instead. set one run to stop on June 1 2020 and then + restart a new run from there. If you wish to use a GEOS-FP + meteorology year different from your simulation year please + create a GEOS-Chem GitHub issue for assistance. + .. _quick-load: ======================== diff --git a/docs/source/help-and-reference/known-bugs.rst b/docs/source/help-and-reference/known-bugs.rst index e60eeeb..2c228f6 100644 --- a/docs/source/help-and-reference/known-bugs.rst +++ b/docs/source/help-and-reference/known-bugs.rst @@ -44,4 +44,4 @@ are currently unresolved. We hope to fix these in future releases. Bugs that have been resolved ============================ -These `bug reports (on GitHub) `_ have been resolved. +These `bugs (reported on GitHub) `_ have been resolved. diff --git a/docs/source/index.rst b/docs/source/index.rst index 7a95fae..e8895ed 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -84,7 +84,6 @@ modifications to GEOS-Chem Classic source code. geos-chem-shared-docs/supplemental-guides/parallel-guide.rst supplemental-guides/nested-grid-guide.rst geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.rst - geos-chem-shared-docs/supplemental-guides/geos-chem-input-data-on-aws.rst geos-chem-shared-docs/supplemental-guides/related-docs.rst .. toctree:: From 694e24ffa1e864fda0a203748f42f7ce96da0606 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 6 Nov 2024 16:44:31 -0500 Subject: [PATCH 42/99] Update warning boxes about GEOS-FP in dry-run & rundir doc docs/source/gcclassic-user-guide/dry-run-run.rst docs/source/gcclassic-user-guide/rundir-carbon.rst docs/source/gcclassic-user-guide/rundir-fullchem.rst - Edit the "important" box with the warning about GEOS-FP convection to make it more clear that the user should choose MERRA-2 to avoid discontinuities across June 1, 2020. docs/source/geos-chem-shared-docs - Submodule update, now link to GCClassic & HEMCO dry-run-instructions from the GEOS-Chem Input Data portal documentation --- .../gcclassic-user-guide/dry-run-run.rst | 22 +++++++------------ .../gcclassic-user-guide/rundir-carbon.rst | 18 +++++---------- .../gcclassic-user-guide/rundir-fullchem.rst | 18 +++++---------- docs/source/geos-chem-shared-docs | 2 +- 4 files changed, 21 insertions(+), 39 deletions(-) diff --git a/docs/source/gcclassic-user-guide/dry-run-run.rst b/docs/source/gcclassic-user-guide/dry-run-run.rst index 8299112..3a39fa9 100644 --- a/docs/source/gcclassic-user-guide/dry-run-run.rst +++ b/docs/source/gcclassic-user-guide/dry-run-run.rst @@ -29,20 +29,14 @@ files `: .. important:: - The convection scheme used for GEOS-FP met generation changed - from RAS to Grell-Freitas with impact on GEOS-FP meteorology - files starting June 1, 2020, specifically enhanced vertical - transport. In addition, there is a bug in convective - precipitation flux following the switch where all values are - zero. While this bug is automatically fixed by computing fluxes - online for runs starting on or after June 1 2020, the fix - assumes meteorology year corresponds to simulation year. Due to - these issues we recommend splitting up GEOS-FP runs in time such - that a single simulation does not run across June - 1, 2020. Instead. set one run to stop on June 1 2020 and then - restart a new run from there. If you wish to use a GEOS-FP - meteorology year different from your simulation year please - create a GEOS-Chem GitHub issue for assistance. + The convection scheme used for GEOS-FP met generation changed + from RAS to Grell-Freitas with impact on GEOS-FP meteorology + files starting June 1, 2020. For this reason we recommend + using MERRA-2 instead of GEOS-FP if running a simulation + across June 1, 2020 to avoid unexpected + discontinuities. Additional information about the impact of + the convection change is at `geoschem/geos-chem#1409 + `_. #. :option:`root_data_dir`: Make sure that the path to :file:`ExtData` is correct. diff --git a/docs/source/gcclassic-user-guide/rundir-carbon.rst b/docs/source/gcclassic-user-guide/rundir-carbon.rst index 7652873..199e73f 100644 --- a/docs/source/gcclassic-user-guide/rundir-carbon.rst +++ b/docs/source/gcclassic-user-guide/rundir-carbon.rst @@ -140,18 +140,12 @@ simulation. We'll use the carbon gases simulation as an example. The convection scheme used for GEOS-FP met generation changed from RAS to Grell-Freitas with impact on GEOS-FP meteorology - files starting June 1, 2020, specifically enhanced vertical - transport. In addition, there is a bug in convective - precipitation flux following the switch where all values are - zero. While this bug is automatically fixed by computing fluxes - online for runs starting on or after June 1 2020, the fix - assumes meteorology year corresponds to simulation year. Due to - these issues we recommend splitting up GEOS-FP runs in time such - that a single simulation does not run across June - 1, 2020. Instead. set one run to stop on June 1 2020 and then - restart a new run from there. If you wish to use a GEOS-FP - meteorology year different from your simulation year please - create a GEOS-Chem GitHub issue for assistance. + files starting June 1, 2020. For this reason we recommend + using MERRA-2 instead of GEOS-FP if running a simulation + across June 1, 2020 to avoid unexpected + discontinuities. Additional information about the impact of + the convection change is at `geoschem/geos-chem#1409 + `_. #. The next menu will prompt you for the horizontal resolution that you wish to use: diff --git a/docs/source/gcclassic-user-guide/rundir-fullchem.rst b/docs/source/gcclassic-user-guide/rundir-fullchem.rst index b5b0ebb..d02bd2e 100644 --- a/docs/source/gcclassic-user-guide/rundir-fullchem.rst +++ b/docs/source/gcclassic-user-guide/rundir-fullchem.rst @@ -142,18 +142,12 @@ GEOS-Chem full-chemistry simulation. The convection scheme used for GEOS-FP met generation changed from RAS to Grell-Freitas with impact on GEOS-FP meteorology - files starting June 1, 2020, specifically enhanced vertical - transport. In addition, there is a bug in convective - precipitation flux following the switch where all values are - zero. While this bug is automatically fixed by computing fluxes - online for runs starting on or after June 1 2020, the fix - assumes meteorology year corresponds to simulation year. Due to - these issues we recommend splitting up GEOS-FP runs in time such - that a single simulation does not run across June - 1, 2020. Instead. set one run to stop on June 1 2020 and then - restart a new run from there. If you wish to use a GEOS-FP - meteorology year different from your simulation year please - create a GEOS-Chem GitHub issue for assistance. + files starting June 1, 2020. For this reason we recommend + using MERRA-2 instead of GEOS-FP if running a simulation + across June 1, 2020 to avoid unexpected + discontinuities. Additional information about the impact of + the convection change is at `geoschem/geos-chem#1409 + `_. #. The next menu will prompt you for the horizontal resolution that you wish to use: diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index cd0f4ad..14adeb4 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit cd0f4ad1dd13648c3fe9bf8bb13c7bf5ef517125 +Subproject commit 14adeb4d8a9cfbdebd688033e4c22dd034ac105b From 2d8b6e06b29a4f6aba2ab42e69f6d27fd53c72da Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 7 Nov 2024 11:25:31 -0500 Subject: [PATCH 43/99] Submod update: Merge GC PR #2555 & HEMCO PR #295 (14.5.0 dry run) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a8bb552d1 Merge PR #2555 (Dry run updates for GEOS-Chem Classic 14.5.0) e9d951f Merge PR #295 (Add HEMCO-standalone dry run scripts) This PR updates the subroutine hashes to GEOS-Chem and HEMCO submodules, which now have updates for the GEOS-Chem 14.5.0 and HEMCO 3.10.0 dry run simulations. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 51d306d..a8bb552 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 51d306dade21a6c36e5537224b7c533b5489667c +Subproject commit a8bb552d138b6d1fa684a2fa187e3a9a754caf2e diff --git a/src/HEMCO b/src/HEMCO index a3d0c9a..e9d951f 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit a3d0c9a280672ac1c40e3f322651f23b8196fa4c +Subproject commit e9d951fd702a82d76ba2a73653b74e7b1eae8e4c From 09b682209bb24da7328b508f77204f67353ced9c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 7 Nov 2024 15:15:55 -0500 Subject: [PATCH 44/99] Update version numbers to 14.5.0 CHANGELOG.md CMakeLists.txt docs/source/conf.py - Updated version number to 14.5.0, in anticipation of the GEOS-Chem Classic 14.5.0 release Signed-off-by: Bob Yantosca --- CHANGELOG.md | 2 +- CMakeLists.txt | 2 +- docs/source/conf.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 476753b..2c59ac8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit 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 +## [14.5.0] - 2024-11-07 ### Changed - Updated `docs/source/geos-chem-shared-docs/spack/packages.yaml` to use GCC 12.2.0 compilers - Updated documentation for version 14.5.0 diff --git a/CMakeLists.txt b/CMakeLists.txt index c193cfd..0446acd 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.13) project (geos-chem-classic - VERSION 14.4.3 + VERSION 14.5.0 LANGUAGES Fortran ) diff --git a/docs/source/conf.py b/docs/source/conf.py index 1c46044..6457dec 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,7 +23,7 @@ author = 'GEOS-Chem Support Team' # The full version, including alpha/beta/rc tags -release = '14.4.3' +release = '14.5.0' # -- General configuration --------------------------------------------------- From f56c7050cd679e40bf4efe82b5953a3ab9d761da Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 8 Nov 2024 13:19:42 -0500 Subject: [PATCH 45/99] Merge 14.5.0 release into dev/no-diff-to-benchmark This merge brings in the updates from the 14.5.0 release back into the dev/no-diff-to-benchmark branch. See the CHANGELOG.md for updates. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 6bbd81f..68e6933 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 6bbd81fae499fc2cb566722be1a38a1567bf6e4c +Subproject commit 68e69335df4fb48f547b88bb21101db6c3f07751 From 131a4074e03bbdb4043eba429f598cad98d83f2d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 19 Nov 2024 17:37:50 -0500 Subject: [PATCH 46/99] GEOS-Chem updates: Merge PR #2560 and PR #2508 This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: af83cf8ca Merge PR # (Allow upcase logfile name in download_data.py) f149b460d Merge PR #2560 (Fix trace metals sim name in config files) These PRs add minor zero-diff fixes. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 68e6933..af83cf8 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 68e69335df4fb48f547b88bb21101db6c3f07751 +Subproject commit af83cf8ca6831c93bf176dfc0584d86d6e25645b From e99538a1920a47db7e82569297154ee5795c7e99 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 20 Nov 2024 13:49:39 -0500 Subject: [PATCH 47/99] GEOS-Chem update: Merge PR #2532 (Add allocate guards) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 67ce84a59 Merge PR #2532 (Add allocate guards in pressure_mod) This PR adds checks to make sure that we do not allocate arrays that are already allocated. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index af83cf8..67ce84a 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit af83cf8ca6831c93bf176dfc0584d86d6e25645b +Subproject commit 67ce84a59446153b9430fab912654fa34639cc4e From 63e90224ffa18e3ececbd2c053fe709f97821300 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 20 Nov 2024 16:36:28 -0500 Subject: [PATCH 48/99] GEOS-Chem update: Merge PR #2544 (SatDiagn counter fixes) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: cad65f085 Merge PR #2544 (Fixes for SatDiagn diagnostic counters) This PR fixes adds fixes to prevent the counters for the SatDiagn and SatDiagnEdge diagnostic collections from being inadvertently reset to zero. This had caused diagnostic fields to be steadily decreasing with time. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 67ce84a..cad65f0 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 67ce84a59446153b9430fab912654fa34639cc4e +Subproject commit cad65f085494216f617496334520da18dd7ef785 From 89816686b4858ef37f198266712f387f57f04af0 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 21 Nov 2024 13:49:27 -0500 Subject: [PATCH 49/99] GEOS-Chem update: Merge PR #2580 (Remove duplicate WD_RetFactor) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 135bdaaf3 Merge PR #2580 (Remove duplicate WD_RetFactor for HgClHO2) This PR removes a duplicated YAML tag in species_database.yml. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index cad65f0..135bdaa 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit cad65f085494216f617496334520da18dd7ef785 +Subproject commit 135bdaaf33d944a418b1765f854972c26e65a287 From 2b7306a3d49d021c5d498914ce7083f4a541532b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 21 Nov 2024 15:29:49 -0500 Subject: [PATCH 50/99] GEOS-Chem update: Merge PR #2486 (Prevent seg fault in qfyaml) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 7507eb590 Merge PR #2486 (Prevent seg fault in qfyaml) This PR fixes a seg fault that occurs in Headers/qfyaml_mod.F90 with certain compilers (such as Intel 2022.2.1) Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 135bdaa..7507eb5 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 135bdaaf33d944a418b1765f854972c26e65a287 +Subproject commit 7507eb590ce78e7c28281c679375d9d438c8c19e From 0560047fdc1e08ca84d10cfb13549de5e5a0d7b3 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 21 Nov 2024 16:52:29 -0500 Subject: [PATCH 51/99] GEOS-Chem update: Merge PR #2542 (CESM fix: exclude HEMCO deps) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e2157dc98 Merge PR #2542 (CESM fix: exclude hard dependencies on HEMCO) This PR fixes build issues when compiling GEOS-Chem in CESM. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 7507eb5..e2157dc 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 7507eb590ce78e7c28281c679375d9d438c8c19e +Subproject commit e2157dc986d4ff02c106b77c7a7b56ccb6d544ce From a8aeb02f32664a1840d0ad6038e6e6ae52161f9b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 21 Nov 2024 17:04:56 -0500 Subject: [PATCH 52/99] GEOS-Chem update: Merge PR #2578 (Fixes for GCHP adjoint ) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 62f3db08b Merge PR #2578 (Fixes to compile GCHP adjoint) This PR fixes several compilation issues when building the GCHP adjoint. It does not affect "forward" GEOS-Chem Classic or GCHP simulations. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index e2157dc..62f3db0 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e2157dc986d4ff02c106b77c7a7b56ccb6d544ce +Subproject commit 62f3db08bca6a4e5a6b16e9a9b647b3bdc29e43f From 1eae7f9324ed9ccfcefc4c85ef7ba93dc5849b71 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 22 Nov 2024 10:56:13 -0500 Subject: [PATCH 53/99] Add CMake commands to build the KPP executable file src/CMakeLists.txt - Add CMake commands to define the KPP executable file, where it should be installed, and what it depends on. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 8 +++++++- src/CMakeLists.txt | 27 +++++++++++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 227f0a8..d771b4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,13 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit - src/HEMCO/CHANGELOG.md - src/Cloud-J/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). +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 code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected ## [14.5.0] - 2024-11-08 ### Changed diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 1dd29e8..b77da8e 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -38,6 +38,33 @@ set_target_properties(${EXE_FILE_NAME} RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin ) +#----------------------------------------------------------------------------- +# Define the KPP standalone executable: +# 1. Specify a cache variable with the default target name +# 2. Specify the location of the main program +# 3. Specify libraries that the main program depends on +# 4. Store the binary exectuable file in the bin folder (pre-install) +# +# At present build KPP standalone only for fullchem or custom mechanisms. +#----------------------------------------------------------------------------- +if("${MECH}" STREQUAL fullchem OR "${MECH}" STREQUAL custom) + set(KPPSA_FILE_NAME kpp_standalone CACHE STRING + "Default name for the KPP standalone executable file") + mark_as_advanced(KPPSA_FILE_NAME) + + add_executable(${KPPSA_FILE_NAME} + GEOS-Chem/KPP/standalone/kpp_standalone.F90 + ) + target_link_libraries(${KPPSA_FILE_NAME} + PUBLIC + KPPStandalone + ) + set_target_properties(${KPPSA_FILE_NAME} + PROPERTIES + RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin + ) +endif() + #----------------------------------------------------------------------------- # When "make install" is run, copy the target to the destination folder # (which is typically one directory higher than the CMake build folder) From 9d6297522a8a5ffc8d99a43a4c3b688be00a3cae Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 22 Nov 2024 11:47:14 -0500 Subject: [PATCH 54/99] Update src/CMakeLists.txt to install KPP standalone executable src/CMakeLists.txt - Added install command to place the kpp_standalone executable file in the run directory Signed-off-by: Bob Yantosca --- src/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index b77da8e..bc07138 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -98,6 +98,7 @@ foreach(INSTALL_PATH ${COMBINED_INSTALL_DIRS}) # Installation path is a GEOS-Chem run directory, # Therefore we will install the executable there. install(TARGETS ${EXE_FILE_NAME} RUNTIME DESTINATION ${INSTALL_PATH}) + install(TARGETS ${KPPSA_FILE_NAME} RUNTIME DESTINATION ${INSTALL_PATH}) endif() endforeach() From 8cc2c4be981791b61d51ca69a3cff69428844fb8 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 26 Nov 2024 16:20:32 -0500 Subject: [PATCH 55/99] GEOS-Chem update: Merge PR #2593 (Prevent duration < frequency) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 4a10fac7e Merge PR #2593 (Prevent duration < frequency in History diags) This PR fixes an issue where empty diagnostic files could be created if the collection duration setting was less than the frequency setting. Now an error will be thrown and the run will halt. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 62f3db0..4a10fac 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 62f3db08bca6a4e5a6b16e9a9b647b3bdc29e43f +Subproject commit 4a10fac7ecf084230c9dd79447f0c9b0debc2fed From 384f5d32b80db7b1f40affb4a1af8e55cf7783b5 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 2 Dec 2024 13:28:09 -0500 Subject: [PATCH 56/99] GEOS-Chem update: Merge PR #2588 (Add KPP Standalone) This merge brings PR #2588 (Add KPP Standalone into GEOS-Chem 14.5.1, by @yantosca and @obin1) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR does the following: 1. Adds an interface to save out the model state for input into the KPP Standalone box model 2. Adds the https://github.com/KineticPreProcessor/KPP-Standalone repo as a Git submodule. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 4a10fac..a4e36e9 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 4a10fac7ecf084230c9dd79447f0c9b0debc2fed +Subproject commit a4e36e912cda9ce1eb9963398d3698bf06cf792b From f69f4152323371a10e9803c4b8bd6957623cb91a Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Tue, 3 Dec 2024 13:08:50 -0500 Subject: [PATCH 57/99] Submodule updates for GEOS-Chem #2608 and HEMCO #296 Submodule src/GEOS-Chem a4e36e9..ed893d0: > Merge pull request #2608 from geoschem/bugfix/tagged_CO_restart Submodule src/HEMCO deaa192..d00af43: > Merge pull request #296 from geoschem/bugfix/reduce_hemco_read_prints_in_mpi Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index a4e36e9..ed893d0 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit a4e36e912cda9ce1eb9963398d3698bf06cf792b +Subproject commit ed893d05489da667e9cc28b28b78e71bede20527 diff --git a/src/HEMCO b/src/HEMCO index deaa192..d00af43 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit deaa1923f3d3e06e264c4ccbe0e3b7dc32edcc20 +Subproject commit d00af432cd94c2da456d5be160a4d5279753f9ab From 3be5820ab9196069b8e46582231825de5eaaee9a Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Wed, 4 Dec 2024 15:37:48 -0500 Subject: [PATCH 58/99] Submodule update: GEOS-Chem #2612 Submodule src/GEOS-Chem ed893d0..990e8e4: > Merge pull request #2612 from geoschem/bugfix/typo_in_tagco_restart_date Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index ed893d0..990e8e4 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit ed893d05489da667e9cc28b28b78e71bede20527 +Subproject commit 990e8e408271b6a8c73f74c694baeabd3f3cfd97 From dc666fc76441d3215e10cefce0c34282166a5bf7 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 5 Dec 2024 11:28:38 -0500 Subject: [PATCH 59/99] Bug fix" Now use "submodules: recursive" in Azure config files .ci-pipelines/build-matrix.yml .ci-pipelines/quick-build.yml - Changed "submodules: true" to "submodules: recursive" so that all levels of submodules will be fetched when cloning GEOS-Chem code in the continuous integration tests. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- .ci-pipelines/build-matrix.yml | 2 +- .ci-pipelines/quick-build.yml | 2 +- CHANGELOG.md | 3 +++ 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.ci-pipelines/build-matrix.yml b/.ci-pipelines/build-matrix.yml index b4e6104..9015c5e 100644 --- a/.ci-pipelines/build-matrix.yml +++ b/.ci-pipelines/build-matrix.yml @@ -46,7 +46,7 @@ container: $[ variables['containerImage'] ] # Try building GEOS-Chem (this is run for each "matrix" entry above) steps: - checkout: self - submodules: true + submodules: recursive - script: | . /opt/spack/share/spack/setup-env.sh export CC=gcc diff --git a/.ci-pipelines/quick-build.yml b/.ci-pipelines/quick-build.yml index 8adc7c3..cb62f66 100644 --- a/.ci-pipelines/quick-build.yml +++ b/.ci-pipelines/quick-build.yml @@ -31,7 +31,7 @@ container: geoschem/buildmatrix:netcdf-ubuntu # Try building GEOS-Chem steps: - checkout: self - submodules: true + submodules: recursive - script: | . /opt/spack/share/spack/setup-env.sh export CC=gcc diff --git a/CHANGELOG.md b/CHANGELOG.md index d771b4a..d2905aa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,9 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ### Added - Added code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected +### Changed +- Changed `submodules: true` to `submodules: recursive` in `.ci-pipelines/*.yml` files, which will fetch all levels of submodules in Azure CI tests. + ## [14.5.0] - 2024-11-08 ### Changed - Updated GEOS-Chem to 14.5.0 From 9ec79fb7c08c853c99f28c5cda8c077ab8795fb0 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 5 Dec 2024 11:15:27 -0500 Subject: [PATCH 60/99] Submodule updates: GEOS-Chem #2553 and #2523 Submodule src/GEOS-Chem be335b7..990e8e4 (rewind): < Merge pull request #2553 from geoschem/bugfix/geos < Merge pull request #2523 from yuanjianz/bugfix/Grell_Friedas_convection Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 990e8e4..be335b7 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 990e8e408271b6a8c73f74c694baeabd3f3cfd97 +Subproject commit be335b7a5083147ac2e7122c38e4a0d6c426d4b0 From 177d95baf4cbbf09ac08d499e640041298f17ebb Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Fri, 6 Dec 2024 11:07:15 -0500 Subject: [PATCH 61/99] Submodule update: GEOS-Chem #2615 Submodule src/GEOS-Chem be335b7..1a09d12: > Merge pull request #2615 from geoschem/bugfix/ gchp_integration_test_issue_from_rundir_creation_message_change Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index be335b7..1a09d12 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit be335b7a5083147ac2e7122c38e4a0d6c426d4b0 +Subproject commit 1a09d129e0285a9a9687392810a7afaf941622ba From 123f6f721a8b24d3e30313e7bd2a5e3ed012b692 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 9 Dec 2024 10:50:25 -0500 Subject: [PATCH 62/99] GEOS-Chem update: Merge PR #2617 (KPP submodule update) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 29f6c72c4 Merge PR #2617 (KPP standalone submodule update) This PR updates the KPP/standalone submodule hash to point to a bug fix (write KPP standalone output with 3-digit exponents, to avoid corrupted output). Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 1a09d12..29f6c72 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 1a09d129e0285a9a9687392810a7afaf941622ba +Subproject commit 29f6c72c4bae70527311357a24c9adda59363979 From 879b900442cd4b496e0df4b34ad778b0816198a1 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 9 Dec 2024 17:39:39 -0500 Subject: [PATCH 63/99] RTD Update: Added KPP-Standalone Supplemental Guide docs/source/geos-chem-shared-docs - Submodule update: Added KPP-Standalone Supplemental Guide (bc4d75c) docs/source/index.rst - Added KPP-Standalone Supplemental Guide to toctree CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 4 ++++ docs/source/geos-chem-shared-docs | 2 +- docs/source/index.rst | 1 + 3 files changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 227f0a8..4a1b31b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ This file documents all notable changes to the GEOS-Chem Classic wrapper reposit 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 ReadTheDocs Supplemental Guide on using the KPP-Standalone Box Model and KPP-Standalone Interface in GEOS-Chem + ## [14.5.0] - 2024-11-08 ### Changed - Updated GEOS-Chem to 14.5.0 diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 14adeb4..bc4d75c 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 14adeb4d8a9cfbdebd688033e4c22dd034ac105b +Subproject commit bc4d75c60ba7967885a56125e20026010c10c3c1 diff --git a/docs/source/index.rst b/docs/source/index.rst index e8895ed..fcaab7e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -84,6 +84,7 @@ modifications to GEOS-Chem Classic source code. geos-chem-shared-docs/supplemental-guides/parallel-guide.rst supplemental-guides/nested-grid-guide.rst geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.rst + geos-chem-shared-docs/supplemental-guides/using-kpp-standalone.rst geos-chem-shared-docs/supplemental-guides/related-docs.rst .. toctree:: From b698203faa40f95e16665dd41c744f54761b47b2 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 12 Dec 2024 10:38:05 -0500 Subject: [PATCH 64/99] GEOS-Chem submodule update: Merge PR #2626 Fix CH4 livestock emissions hotspots and seasonality by reverting to EDGARv7 livestock emissions Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 29f6c72..857cfe3 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 29f6c72c4bae70527311357a24c9adda59363979 +Subproject commit 857cfe3b8e2cda5f23465361a2f5ee1b71c17d81 From f866ce2767090c0662e6c7a3fcc84d65d65720bb Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 12 Dec 2024 15:19:34 -0500 Subject: [PATCH 65/99] GEOS-Chem update: Merge PR #2634 (Update kpp_standalone_interface.yml) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 20a93f331 Merge PR #2634 (Add sonde sites to kpp_standalone_interface.yml ) This PR updates the kpp_standalone_interface.yml file that is placed into rundirs using either fullchem and custom simulations. Extra "active cells" (sites to write output) have been added. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 857cfe3..20a93f3 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 857cfe3b8e2cda5f23465361a2f5ee1b71c17d81 +Subproject commit 20a93f331b7308767757fcb2040beaeeae8deedf From 7f7b6ff99666b9ad2e72f0ec05c2f12011cc5964 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 16 Dec 2024 11:21:49 -0500 Subject: [PATCH 66/99] Fixed CMake error to prevent KPP standalone being built in carbon sim src/CMakeLists.txt - Defined the KPPSA_FILE_NAME variable for all mechanisms - Call "add_executable(KPPSA_FILE_NAME ...) for all mechanisms - Added an else block to disable the KPPSA_FILE_NAME executable from being built except for fullchem & custom mechanisms - Wrapped the installation command for the KPPSA_FILE_NAME executable in an if block to ensure it is only built for fullchem & custom mechanisms. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 3 +++ src/CMakeLists.txt | 29 +++++++++++++++++++++-------- 2 files changed, 24 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d2905aa..3891bc0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,9 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ### Changed - Changed `submodules: true` to `submodules: recursive` in `.ci-pipelines/*.yml` files, which will fetch all levels of submodules in Azure CI tests. +### Fixed +- Fixed logic error in `src/CMakeLists.txt` that attempted to build the KPP standalone for the carbon simulation (see geoschem/GCClassic #78) + ## [14.5.0] - 2024-11-08 ### Changed - Updated GEOS-Chem to 14.5.0 diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index bc07138..90bd4bd 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -44,17 +44,20 @@ set_target_properties(${EXE_FILE_NAME} # 2. Specify the location of the main program # 3. Specify libraries that the main program depends on # 4. Store the binary exectuable file in the bin folder (pre-install) +# 5. If not fullchem or custom mechanism, prevent executable from being built # # At present build KPP standalone only for fullchem or custom mechanisms. +# +# This should now fix the issue reported by @msulprizio in: +# https://github.com/geoschem/GCClassic/issues/78 #----------------------------------------------------------------------------- +set(KPPSA_FILE_NAME kpp_standalone CACHE STRING + "Default name for the KPP standalone executable file") +mark_as_advanced(KPPSA_FILE_NAME) +add_executable(${KPPSA_FILE_NAME} + GEOS-Chem/KPP/standalone/kpp_standalone.F90 +) if("${MECH}" STREQUAL fullchem OR "${MECH}" STREQUAL custom) - set(KPPSA_FILE_NAME kpp_standalone CACHE STRING - "Default name for the KPP standalone executable file") - mark_as_advanced(KPPSA_FILE_NAME) - - add_executable(${KPPSA_FILE_NAME} - GEOS-Chem/KPP/standalone/kpp_standalone.F90 - ) target_link_libraries(${KPPSA_FILE_NAME} PUBLIC KPPStandalone @@ -63,6 +66,11 @@ if("${MECH}" STREQUAL fullchem OR "${MECH}" STREQUAL custom) PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin ) +else() + set_target_properties(${KPPSA_FILE_NAME} + PROPERTIES + EXCLUDE_FROM_ALL TRUE + ) endif() #----------------------------------------------------------------------------- @@ -98,7 +106,12 @@ foreach(INSTALL_PATH ${COMBINED_INSTALL_DIRS}) # Installation path is a GEOS-Chem run directory, # Therefore we will install the executable there. install(TARGETS ${EXE_FILE_NAME} RUNTIME DESTINATION ${INSTALL_PATH}) - install(TARGETS ${KPPSA_FILE_NAME} RUNTIME DESTINATION ${INSTALL_PATH}) + + # Only install KPP standalone for fullchem/custom mechanisms. + # See: htps://github.com/geoschem/GCClassic/issues/78 + if("${MECH}" STREQUAL fullchem OR "${MECH}" STREQUAL custom) + install(TARGETS ${KPPSA_FILE_NAME} RUNTIME DESTINATION ${INSTALL_PATH}) + endif() endif() endforeach() From 6d4a4ece13d57d0371f498a8e614b2cee1dddf65 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 17 Dec 2024 11:24:05 -0500 Subject: [PATCH 67/99] RTD Updates: KPP standalone guide and fixed broken link docs/source/geos-chem-shared-docs - Submodule update to 4fc0461 (kpp_standalone_interface.yml update) docs/source/getting_started/login-env-parallel.rst - Fixed broken link to "Segmentation fault after TPCORE initialization" section in the "Understand error messages and what they mean" supplemental guide. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 3 +++ docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/login-env-parallel.rst | 10 ++++------ 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a1b31b..6fad63c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Added - Added ReadTheDocs Supplemental Guide on using the KPP-Standalone Box Model and KPP-Standalone Interface in GEOS-Chem +### Fixed +- Fixed broken links in ReadTheDocs documentation + ## [14.5.0] - 2024-11-08 ### Changed - Updated GEOS-Chem to 14.5.0 diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index bc4d75c..4fc0461 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit bc4d75c60ba7967885a56125e20026010c10c3c1 +Subproject commit 4fc0461c48a92ab09bd06f5eacb333aee7dbaebb diff --git a/docs/source/getting-started/login-env-parallel.rst b/docs/source/getting-started/login-env-parallel.rst index b2a9fba..17701ba 100644 --- a/docs/source/getting-started/login-env-parallel.rst +++ b/docs/source/getting-started/login-env-parallel.rst @@ -88,9 +88,7 @@ Be on the lookout for these errors: #. If :option:`OMP_STACKSIZE` environment variable is not included in your environment file (or if it is set to a very low value), - you might encounter a `segmentation fault error after the TPCORE - transport module is initialized - `_. - In this case, GEOS-Chem Classic "thinks" that it does - not have enough memory to perform the simulation, even though - sufficient memory may be present. + you might encounter a :ref:`errguide-segfault-tpcore` error. In + this case, GEOS-Chem Classic "thinks" that it does not have + enough memory to perform the simulation, even though sufficient + memory may be present. From 258398cd80ebcc45298bdbd3b3e65c8fd5e4a32e Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 19 Dec 2024 13:55:01 -0500 Subject: [PATCH 68/99] Submodule updates: GEOS-Chem #2642 and #2643, HEMCO #298 Submodule src/GEOS-Chem 20a93f3..9c352ab: > Merge pull request #2642 from geoschem/bugfix/cesm_fixes > Merge pull request #2643 from geoschem/feature/clean_up_hemco_log_and_error_handling Submodule src/HEMCO d00af43..c76adbb: > Merge pull request #298 from geoschem/feature/improve_log_flexibility_in_hemco Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 20a93f3..9c352ab 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 20a93f331b7308767757fcb2040beaeeae8deedf +Subproject commit 9c352abb8807ff252c6370756d554a3c51fc2c72 diff --git a/src/HEMCO b/src/HEMCO index d00af43..c76adbb 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit d00af432cd94c2da456d5be160a4d5279753f9ab +Subproject commit c76adbbe7ce9a09e291f60353783d31134bac4a7 From be31b4c58695cee0c638b4b484f877cdbc3216cf Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Fri, 20 Dec 2024 16:06:34 -0500 Subject: [PATCH 69/99] Submodule updates: GEOS-Chem #2661, HEMCO #300 Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 9c352ab..bc66f2a 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 9c352abb8807ff252c6370756d554a3c51fc2c72 +Subproject commit bc66f2abbb9198136ec1190a9bae146bf547cd83 diff --git a/src/HEMCO b/src/HEMCO index c76adbb..b94f2e0 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit c76adbbe7ce9a09e291f60353783d31134bac4a7 +Subproject commit b94f2e09ec592a956d4b5c36675e433acff12ff5 From 15d17fbe84e39d290bf1394895068ec9cca2a2a9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 3 Jan 2025 12:28:45 -0500 Subject: [PATCH 70/99] geos-chem-shared-docs update: Updated error-guide.rst This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 18712bb Add extra examples to supplemental-guides/error-guide.rst This update adds documentation for additional common errors to the "Understanding what error messages mean" supplemental guide. Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 4fc0461..18712bb 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 4fc0461c48a92ab09bd06f5eacb333aee7dbaebb +Subproject commit 18712bb6a61caa921be73ee993996b35cfc8c0da From 0ba41cacdfba9387efe8831047e9b1aed1fefa81 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 7 Jan 2025 13:58:42 -0500 Subject: [PATCH 71/99] GEOS-Chem update: Merge PR #2669 (Australian Hg emissions) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: f43e771fa Merge PR #2669 (Implement Australian Hg emissions) This PR implements a new emissions inventory for the Hg simulation, based on MacFarlane et al. [2022]. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index bc66f2a..f43e771 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit bc66f2abbb9198136ec1190a9bae146bf547cd83 +Subproject commit f43e771fa0084ad76ee1570790a362f57a1b24d9 From 799dae72a3c6538d9a65a0d79279a14e8f828aaf Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 7 Jan 2025 14:05:55 -0500 Subject: [PATCH 72/99] GEOS-Chem update: Merge PR # (BC freq warnings in HISTORY.rc) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 3de2b85f6 Merge PR #2670 (Warn users not to change BC freq in HISTORY.rc) This PR adds a warning to the HISTORY.rc template files. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index f43e771..3de2b85 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit f43e771fa0084ad76ee1570790a362f57a1b24d9 +Subproject commit 3de2b85f6b129cb4efb6b3e6f3c693fd1da6a70a From 9428533e5dcd751bd95477ee5c3bde22db184c9f Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Wed, 8 Jan 2025 13:56:33 -0500 Subject: [PATCH 73/99] GEOS-Chem update: Merge PR #2554 (bug fixes for carbon simulations) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 3de2b85..ac0b765 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 3de2b85f6b129cb4efb6b3e6f3c693fd1da6a70a +Subproject commit ac0b765c60c723b51a07dd37e2b0a7abe9b43cbd From b0c9eb18f5a3cb432723a986d8a4941a41843d44 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 9 Jan 2025 15:23:41 -0500 Subject: [PATCH 74/99] GEOS-Chem update: Merge PR #2674 (Harvard int tests use GCC12) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: ab77f5279 Merge PR #2674 (Harvard Cannon int test now use GNU12 compilers) This PR changes the default compiler used by integration tests on Harvard Cannon from GCC 10.2.0 to GCC 12.2.0. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index ac0b765..ab77f52 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit ac0b765c60c723b51a07dd37e2b0a7abe9b43cbd +Subproject commit ab77f52792a3bdcb9f9f69556d93105e032da36f From d9885f1e9586f50e29cbf6e5da36d600329a9a97 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 9 Jan 2025 17:11:51 -0500 Subject: [PATCH 75/99] GEOS-Chem update: Merge PR #2675 (Bugfix: GCHP read met from YAML) This commit informs the GCClassicsuperproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 48358bc0a Merge PR #2675 (Bugfix for GCHP to read meteorology from YAML) According to @lizziel: I believe this fixes an issue brought in with the updates for GEOS-IT in dev/no-diff-to-benchmark (see PR #2523). It would only show up for GEOS-FP and GEOS-IT runs which we do not test in integration/AWS testing, and is not in any previously released versions. It therefore does not need an update to the changelog. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index ab77f52..48358bc 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit ab77f52792a3bdcb9f9f69556d93105e032da36f +Subproject commit 48358bc0aadc25e88f8f66b5f36621efcc08830f From 9c964c8428ce48a26d6108565d20153c001ee3e2 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 10 Jan 2025 13:54:31 -0500 Subject: [PATCH 76/99] GCClassic 14.5.1 release This is the official release commit of GEOS-Chem Classic aka GCClassic) 14.5.1. Updated version numbers in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py Updated GEOS-Chem submodule to version 14.5.1 Updated HEMCO submodule to version 3.10.1 Updated geos-chem-shared-docs submodule to commit 18712bb Also updated CHANGELOG.md with the latest information. Signed-off-by: Bob Yantosca --- CHANGELOG.md | 9 ++------- CMakeLists.txt | 2 +- docs/source/conf.py | 2 +- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 5 files changed, 6 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 198fa25..b0e2d90 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,21 +9,16 @@ 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 +## [14.5.1] - 2025-01-10 ### Added - Added code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected +- Added ReadTheDocs Supplemental Guide on using the KPP-Standalone Box Model and KPP-Standalone Interface in GEOS-Chem ### Changed - Changed `submodules: true` to `submodules: recursive` in `.ci-pipelines/*.yml` files, which will fetch all levels of submodules in Azure CI tests. ### Fixed - Fixed logic error in `src/CMakeLists.txt` that attempted to build the KPP standalone for the carbon simulation (see geoschem/GCClassic #78) - -## [Unreleased] - TBD -### Added -- Added ReadTheDocs Supplemental Guide on using the KPP-Standalone Box Model and KPP-Standalone Interface in GEOS-Chem - -### Fixed - Fixed broken links in ReadTheDocs documentation ## [14.5.0] - 2024-11-08 diff --git a/CMakeLists.txt b/CMakeLists.txt index 0446acd..a4f9f66 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.13) project (geos-chem-classic - VERSION 14.5.0 + VERSION 14.5.1 LANGUAGES Fortran ) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6457dec..45fa8ce 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,7 +23,7 @@ author = 'GEOS-Chem Support Team' # The full version, including alpha/beta/rc tags -release = '14.5.0' +release = '14.5.1' # -- General configuration --------------------------------------------------- diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 48358bc..b0e03cc 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 48358bc0aadc25e88f8f66b5f36621efcc08830f +Subproject commit b0e03cc0f7c06b899824a69744b67e9632675cbd diff --git a/src/HEMCO b/src/HEMCO index b94f2e0..0ae25d2 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit b94f2e09ec592a956d4b5c36675e433acff12ff5 +Subproject commit 0ae25d22f61667e8d81e04415e94f133604f415b From ae50776b68278e001b267019f5eef201a240db6a Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 15 Jan 2025 15:41:06 -0500 Subject: [PATCH 77/99] RTD updates: Add clarifying text to ObsPack, Planeflight diag pages docs/source/gcclassic-user-guide/obspack.rst - Add "attention" block advising users to pre-process ObsPack GLOBALVIEWplus CH4 files before reading into GEOS-Chem - Added updated link to NOAA ObsPack data site docs/source/gcclassic-user-guide/planeflight.rst - Add clarifying text (as a footnote) specifying the types of data that can be input with altitude coordinates CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 5 ++ docs/source/gcclassic-user-guide/obspack.rst | 30 ++++++++- .../gcclassic-user-guide/planeflight.rst | 66 +++++++++++-------- 3 files changed, 69 insertions(+), 32 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b0e2d90..5734246 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,11 @@ 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 clarifying text about which types of data can use altitude coordinates for the Planeflight diagnostic in RTD documentation +- Added warning for users to preprocess ObsPack GLOBALVIEWplus CH4 data files before reading into GEOS-Chem in RTD documentation + ## [14.5.1] - 2025-01-10 ### Added - Added code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected diff --git a/docs/source/gcclassic-user-guide/obspack.rst b/docs/source/gcclassic-user-guide/obspack.rst index c8274f1..c46417e 100644 --- a/docs/source/gcclassic-user-guide/obspack.rst +++ b/docs/source/gcclassic-user-guide/obspack.rst @@ -11,6 +11,30 @@ measurements). This feature was written by Andy Jacobson of NOAA and Andrew Schuh of Colorado State University and implemented in GEOS-Chem 12.2.0. +.. attention:: + + The GEOS-Chem ObsPack diagnostic was originally developed for use + with the `ObsPack GLOBALVIEWplus CO2 product + `_. The + data files in this product contain a particular netCDF variable + named :literal:`CT_sampling_strategy` that GEOS-Chem uses to + quickly determine the time-averaging window for aggregating + observations. + + We have recently learned that the `ObsPack GLOBALVIEWplus CH4 data + product `_ + currently lacks the :literal:`CT_sampling_strategy` variable, and + thus is incompatible with GEOS-Chem. + + The best workaround for now is to preprocess ObsPack GLOBALVIEWplus + CH4 data files with one of the following Python tools before + attempting to read them into GEOS-Chem: + + - `process_obspack `_ + by James East + - `gcpy_campaigns `_ + by Jessica Haskins + .. _specifying_obspack_diagnostic_options: ===================================== @@ -47,9 +71,9 @@ YYYY/MM/DD date on which you would like to obtain ObsPack diagnostic output from GEOS-Chem. (The ObsPack diagnostic will skip over days on which it cannot find an input file.) -ObsPack input files can be downloaded from NOAA (see -`https://www.esrl.noaa.gov/gmd/ccgg/obspack/ -`_). +ObsPack input files can be downloaded the NOAA website: +`https://gml.noaa.gov/ccgg/obspack/ +`_. .. attention:: diff --git a/docs/source/gcclassic-user-guide/planeflight.rst b/docs/source/gcclassic-user-guide/planeflight.rst index 5d61999..6286d39 100644 --- a/docs/source/gcclassic-user-guide/planeflight.rst +++ b/docs/source/gcclassic-user-guide/planeflight.rst @@ -10,7 +10,7 @@ along flight tracks or at the position of ground observations. This can be more efficient in terms of storage than saving out 3-D data files via the :ref:`GEOS-Chem History diagnostics `. -.. attention:: +.. important:: Several diagnostic quantities were disabled when the SMVGEAR chemistry solver was replaced with the FlexChem implementation of @@ -214,34 +214,42 @@ you will specify the points that make up the flight track. .. table:: :align: center - +---------------+-----------------------------------------------+ - | Quantity | Description | - +===============+===============================================+ - | ``POINT`` | A sequential index of flight track points. | - +---------------+-----------------------------------------------+ - | ``TYPE`` | Identifier for the plane (or station) | - +---------------+-----------------------------------------------+ - | ``DD`` | Day of the observation | - +---------------+-----------------------------------------------+ - | ``MM`` | Month of the observation | - +---------------+-----------------------------------------------+ - | ``YYYY`` | Year of the observation | - +---------------+-----------------------------------------------+ - | ``HH`` | Hour of the observation (UTC) | - +---------------+-----------------------------------------------+ - | ``MM`` | Minute of the observation (UTC) | - +---------------+-----------------------------------------------+ - | ``LAT`` | Latitude (deg), range -90 to +90 | - +---------------+-----------------------------------------------+ - | ``LON`` | Longitude (deg), range -180 to +180 | - +---------------+-----------------------------------------------+ - | ``ALT/PRE`` | Altitude [m] or Pressure [hPa] of | - | | the observation | - +---------------+-----------------------------------------------+ - | ``OBS`` | Value of the observation (if known), | - | | used to compare to model output | - +---------------+-----------------------------------------------+ - + +--------------+-----------------------------------------------+ + | Quantity | Description | + +==============+===============================================+ + | ``POINT`` | A sequential index of flight track points. | + +--------------+-----------------------------------------------+ + | ``TYPE`` | Identifier for the plane (or station) | + +--------------+-----------------------------------------------+ + | ``DD`` | Day of the observation | + +--------------+-----------------------------------------------+ + | ``MM`` | Month of the observation | + +--------------+-----------------------------------------------+ + | ``YYYY`` | Year of the observation | + +--------------+-----------------------------------------------+ + | ``HH`` | Hour of the observation (UTC) | + +--------------+-----------------------------------------------+ + | ``MM`` | Minute of the observation (UTC) | + +--------------+-----------------------------------------------+ + | ``LAT`` | Latitude (deg), range -90 to +90 | + +--------------+-----------------------------------------------+ + | ``LON`` | Longitude (deg), range -180 to +180 | + +--------------+-----------------------------------------------+ + | ``ALT/PRE`` | Altitude [m] or Pressure [hPa] of | + | | the observation [#A]_ | + +--------------+-----------------------------------------------+ + | ``OBS`` | Value of the observation (if known), | + | | used to compare to model output | + +--------------+-----------------------------------------------+ + +.. rubric:: + +.. [#] Altitude is only supported for CCGG or tower data. All other + observations must specify pressure in hPa. This can be + obtained from the "static pressure" field as measured by the + aircraft. See this `code block in planeflight_mod.F90 + `_ + for details. .. important:: From 8147cd96894fd6162a93c6c1ad8b628c28ef0a58 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 16 Jan 2025 14:20:18 -0500 Subject: [PATCH 78/99] Bump jinja2 to 3.1.5 as suggested by Dependabot docs/requirements.txt - Bumped jinja2 to version 3.1.5, as suggested by GitHub Dependabot. This is a security fix. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 4 ++++ docs/requirements.txt | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b0e2d90..3c7e70e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,10 @@ 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 +### Changed +- Bumped `jinja2` to version 3.1.5 in `docs/requirements.txt` to fix a security issue + ## [14.5.1] - 2025-01-10 ### Added - Added code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected diff --git a/docs/requirements.txt b/docs/requirements.txt index 71e269d..c0752da 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -12,4 +12,4 @@ sphinxcontrib-bibtex==2.6.2 sphinx-autobuild==2021.3.14 recommonmark==0.7.1 docutils==0.20.1 -jinja2==3.1.4 +jinja2==3.1.5 From 5a3c427ac22c0dd1e0a86fd503e48ed69b888b1f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 17 Jan 2025 11:15:26 -0500 Subject: [PATCH 79/99] GEOS-Chem and HEMCO updates: .zenodo.json and jinja2 updates This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 255a13d88 Merge PR #2690 (Add .zenodo.json to auto-populate DOI fields) and to the GitHub geoschem/HEMCO repository: 9cf873a Merge PR #304 (Add .zenodo.json; Update jinja2 to 3.1.5) Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index b0e03cc..255a13d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit b0e03cc0f7c06b899824a69744b67e9632675cbd +Subproject commit 255a13d88d00299aeb4812e7708ff3fb3fbb8b99 diff --git a/src/HEMCO b/src/HEMCO index 0ae25d2..9cf873a 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 0ae25d22f61667e8d81e04415e94f133604f415b +Subproject commit 9cf873a8adeeb666a3ae9346ad7f6ec357c67f4b From 2004c3a457660a6833c8edac8a3bf9114ee9947e Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 17 Jan 2025 16:14:31 -0500 Subject: [PATCH 80/99] GEOS-Chem update: Merge PR #2684 (Fix CO2 weekly SF in GCHP) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a3e623f7e Merge PR #2684 (Fix CO2 weekly scale factors in GCHP) This PR fixes a typo in the ExtData.rc.carbon file so that the CO2 weekly scale factors are read and applied properly. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 255a13d..a3e623f 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 255a13d88d00299aeb4812e7708ff3fb3fbb8b99 +Subproject commit a3e623f7e7929bd92716b68061300627e444e706 From cc6119e499714e67a5e2334f6139b8d65c4d6aca Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 22 Jan 2025 14:02:07 -0500 Subject: [PATCH 81/99] geos-chem-shared-docs update: Explain data download is free This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: acf07e2 Updated GEOS-Chem Input Data doc to say download is free Also updated the CHANGELOG.md accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 1 + docs/source/geos-chem-shared-docs | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5734246..862b1c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ### Added - Added clarifying text about which types of data can use altitude coordinates for the Planeflight diagnostic in RTD documentation - Added warning for users to preprocess ObsPack GLOBALVIEWplus CH4 data files before reading into GEOS-Chem in RTD documentation +- Added text to RTD stating that data download from `s3://geos-chem` is and `s3://gcgrid` is free ## [14.5.1] - 2025-01-10 ### Added diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 18712bb..acf07e2 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 18712bb6a61caa921be73ee993996b35cfc8c0da +Subproject commit acf07e2fdb9f3f292f9415c9e67f2d69ebd36e6b From fbb95ebdd404d777eb3a57a49f73251a314d6842 Mon Sep 17 00:00:00 2001 From: Melissa Sulprizio Date: Thu, 23 Jan 2025 11:58:31 -0500 Subject: [PATCH 82/99] GEOS-Chem update: Merge PR #2673 (Update to GRPI rice emissions) Signed-off-by: Melissa Sulprizio --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index a3e623f..6b056e0 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit a3e623f7e7929bd92716b68061300627e444e706 +Subproject commit 6b056e0dfeaa9e7beb7866189325bcfca6788788 From 855843e0b44b156de2133515e35879a9ab2b5a52 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 23 Jan 2025 15:59:52 -0500 Subject: [PATCH 83/99] RTD Update: Warn about using older compiler versions docs/source/getting-started/compilers.rst - Add warning text stating compilers older than Intel 19 may cause unexpected results - Add text recommending GNU compilers version 10 or later if possible CHANGELOG.md - Updated accordingly --- CHANGELOG.md | 3 +++ docs/source/getting-started/compilers.rst | 20 ++++++++++++-------- 2 files changed, 15 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 862b1c8..793974e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,9 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Added warning for users to preprocess ObsPack GLOBALVIEWplus CH4 data files before reading into GEOS-Chem in RTD documentation - Added text to RTD stating that data download from `s3://geos-chem` is and `s3://gcgrid` is free +### Changed +- Updated RTD documentation to state that older Intel compilers may cause unexpected results; Also updated to recommend GCC 10 and later. + ## [14.5.1] - 2025-01-10 ### Added - Added code to `src/CMakeLists.txt` to build & install the KPP standalone executable when `fullchem` or `custom` mechanisms are selected diff --git a/docs/source/getting-started/compilers.rst b/docs/source/getting-started/compilers.rst index eaf30dd..b9cf31d 100644 --- a/docs/source/getting-started/compilers.rst +++ b/docs/source/getting-started/compilers.rst @@ -27,19 +27,19 @@ The GCST has tested :program:`GEOS-Chem Classic` with these versions - 23.0.0 - 19.0.5.281 - 19.0.4 -- 18.0.5 -- 17.0.4 -- 15.0.0 -- 13.0.079 -- 11.1.069 + +Older compiler versions than these may either be incompatible with +GEOS-Chem, or may cause unexpected results. We hope to be able to +port GEOS-Chem to the latest Intel 2024 compiler suite (:literal:`icx` +for C, C++ and :literal:`ifx` for Fortran) in the near future. **Best way to install:** `Direct from Intel `_ -(may require purchase of a site license or a student license) +(Older versions may require purchase of a site license or a student license) .. tip:: - Intel 2021 may be obtained for free, or installed with a + Intel 2021 and later may be obtained for free, or installed with a package manager such as `Spack `_. .. _req-soft-compilers-gnu: @@ -69,6 +69,10 @@ The GCST has tested :program:`GEOS-Chem Classic` with these versions - 7.1.0 - 6.2.0 +We recommend using GCC 10 or later if possible. We have not +thoroughly tested GEOS-Chem with compiler versions more recent than +GCC 12 as of January 2025. + **Best way to install:** :ref:`With Spack `. @@ -81,7 +85,7 @@ Other compilers We currently have no plans to port GEOS-Chem to compilers other than :ref:`req-soft-compilers-intel` and :ref:`req-soft-compilers-gnu`. But when we interface -GEOS-Chem into external models (such as `CESM +GEOS-Chem into external models (such as `CESM `_); all compilers used by the parent model can successfully parse GEOS-Chem source code. From 2b205bdc5461766df7ef341ed928eba646fa8033 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Thu, 30 Jan 2025 13:26:30 -0500 Subject: [PATCH 84/99] Submodule update: GEOS-Chem #2692 and #2616 Submodule src/GEOS-Chem 6b056e0..8ea94bc: > Merge pull request #2692 from geoschem/feature/updated_cluster_env_and_run_scripts > Merge pull request #2616 from yuanjianz/feature/geosit_preprocessed_cs Signed-off-by: Lizzie Lundgren --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 6b056e0..8ea94bc 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 6b056e0dfeaa9e7beb7866189325bcfca6788788 +Subproject commit 8ea94bc3225053085d9466e466a1a360096c303c From a245e609a3a2cf87e12c3fa8c2f5b3069aa81fab Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 30 Jan 2025 16:10:19 -0500 Subject: [PATCH 85/99] Now only build KPP-Standalone when -DKPPSA=y CMakeScripts/GC-ConfigureClassic.cmake - Added boolean cache variable KPPSA and print its value src/CMakeLists.txt - Only execute the block where KPPSA_FILE_NAME is defined as a target if the KPPSA boolean variable is true. This will only build the KPP-Standalone executable when -DKPPSA=y is passed from the cmd line. CHANGELOG.md - Updated accordingly TODO: Update KPP-Standalone documentation accordingly in ReadTheDocs, which is located in the geos-chem-shared-docs submodule Signed-off-by: Bob Yantosca --- CHANGELOG.md | 1 + CMakeScripts/GC-ConfigureClassic.cmake | 10 +++++- src/CMakeLists.txt | 44 ++++++++++++++------------ 3 files changed, 34 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c7e70e..c3450c6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] - TBD ### Changed - Bumped `jinja2` to version 3.1.5 in `docs/requirements.txt` to fix a security issue +- Changed the build sequence so that the KPP-Standalone is only built when configuring with `-DKPPSA=y` ## [14.5.1] - 2025-01-10 ### Added diff --git a/CMakeScripts/GC-ConfigureClassic.cmake b/CMakeScripts/GC-ConfigureClassic.cmake index eb311c0..efd3d02 100755 --- a/CMakeScripts/GC-ConfigureClassic.cmake +++ b/CMakeScripts/GC-ConfigureClassic.cmake @@ -175,6 +175,14 @@ function(configureGCClassic) ) gc_pretty_print(VARIABLE HCOSA IS_BOOLEAN) + #------------------------------------------------------------------------- + # Build the KPP-Standalone? + #------------------------------------------------------------------------- + set(KPPSA OFF CACHE BOOL + "Switch to build the KPP-Standalone Box Model" + ) + gc_pretty_print(VARIABLE KPP_STANDALONE IS_BOOLEAN) + #------------------------------------------------------------------------- # Build Luo et al wetdep scheme? # (Currently a research option... turn OFF by default) @@ -208,7 +216,7 @@ function(configureGCClassic) INTERFACE FASTJX ) endif() - + #------------------------------------------------------------------------- # Export the following variables to GEOS-Chem directory's scope #------------------------------------------------------------------------- diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 90bd4bd..576eec4 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -39,6 +39,8 @@ set_target_properties(${EXE_FILE_NAME} ) #----------------------------------------------------------------------------- +# If GEOS-Chem Classic has been configured with -DKPPSA=y, then: +# # Define the KPP standalone executable: # 1. Specify a cache variable with the default target name # 2. Specify the location of the main program @@ -51,26 +53,28 @@ set_target_properties(${EXE_FILE_NAME} # This should now fix the issue reported by @msulprizio in: # https://github.com/geoschem/GCClassic/issues/78 #----------------------------------------------------------------------------- -set(KPPSA_FILE_NAME kpp_standalone CACHE STRING - "Default name for the KPP standalone executable file") -mark_as_advanced(KPPSA_FILE_NAME) -add_executable(${KPPSA_FILE_NAME} - GEOS-Chem/KPP/standalone/kpp_standalone.F90 -) -if("${MECH}" STREQUAL fullchem OR "${MECH}" STREQUAL custom) - target_link_libraries(${KPPSA_FILE_NAME} - PUBLIC - KPPStandalone - ) - set_target_properties(${KPPSA_FILE_NAME} - PROPERTIES - RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin - ) -else() - set_target_properties(${KPPSA_FILE_NAME} - PROPERTIES - EXCLUDE_FROM_ALL TRUE - ) +if (${KPPSA}) + set(KPPSA_FILE_NAME kpp_standalone CACHE STRING + "Default name for the KPP standalone executable file") + mark_as_advanced(KPPSA_FILE_NAME) + add_executable(${KPPSA_FILE_NAME} + GEOS-Chem/KPP/standalone/kpp_standalone.F90 + ) + if("${MECH}" STREQUAL fullchem OR "${MECH}" STREQUAL custom) + target_link_libraries(${KPPSA_FILE_NAME} + PUBLIC + KPPStandalone + ) + set_target_properties(${KPPSA_FILE_NAME} + PROPERTIES + RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin + ) + else() + set_target_properties(${KPPSA_FILE_NAME} + PROPERTIES + EXCLUDE_FROM_ALL TRUE + ) + endif() endif() #----------------------------------------------------------------------------- From 11e7d2e93f93c931088b6a7133634fba87062d75 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 30 Jan 2025 16:51:53 -0500 Subject: [PATCH 86/99] Fixed CMake gc_pretty_print statement for KPPSA variable CMakeScripts/GC-ConfigureClassic.cmake - Bug fix: Now print KPPSA instead of KPP_STANDALONE to the screen with function gc_pretty_print Signed-off-by: Bob Yantosca --- CMakeScripts/GC-ConfigureClassic.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeScripts/GC-ConfigureClassic.cmake b/CMakeScripts/GC-ConfigureClassic.cmake index efd3d02..f07e81d 100755 --- a/CMakeScripts/GC-ConfigureClassic.cmake +++ b/CMakeScripts/GC-ConfigureClassic.cmake @@ -181,7 +181,7 @@ function(configureGCClassic) set(KPPSA OFF CACHE BOOL "Switch to build the KPP-Standalone Box Model" ) - gc_pretty_print(VARIABLE KPP_STANDALONE IS_BOOLEAN) + gc_pretty_print(VARIABLE KPPSA IS_BOOLEAN) #------------------------------------------------------------------------- # Build Luo et al wetdep scheme? From ef2e2ffd616e9d35f6e1110bc0f71cd05bc818f1 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 6 Feb 2025 11:03:38 -0500 Subject: [PATCH 87/99] GEOS-Chem update: Merge PR #2712 (Build KPPSA upon request) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 60381876d Merge PR #2712 (Only build KPP-Standalone upon request) This PR now asks the user if they wish to build the KPP-Standalone executable at run directory creation time. A reminder will be printed to configure with -DKPPSA=y, and the kpp_standalone_interface.yml file will be copies to the run directory. Signed-off-by: Bob Yantosca --- src/GEOS-Chem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 8ea94bc..6038187 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 8ea94bc3225053085d9466e466a1a360096c303c +Subproject commit 60381876dabf72562a480e344d0afd54e4252029 From bbe956dea8bf253d3596910ed67a7edf65c4e96c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 6 Feb 2025 11:52:10 -0500 Subject: [PATCH 88/99] geos-chem-shared-docs update: Update KPP-Standalone guide This commit informs the GCClassic superproject about the following commits that were pushed to the geos-chem-shared-docs repository: 02c4c26 Update KPP-Standalone guide for on-request build Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index acf07e2..02c4c26 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit acf07e2fdb9f3f292f9415c9e67f2d69ebd36e6b +Subproject commit 02c4c26ff093e13029a0ab310d4f18558d5543e1 From 541d420ac81fab8ff2ed8ddb182fbe5de2a1eb8c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 7 Feb 2025 11:07:07 -0500 Subject: [PATCH 89/99] Update fullchem rundir creation example for KPP-Standalone build docs/source/gcclassic-user-guide/rundir-fullchem.rst - Add a numbered list item explaining that the user will be prompted if they wish to build the KPP-Standalone Box Model. Also provide a link to the KPP-Standalone supplemental guide. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 1 + .../gcclassic-user-guide/rundir-fullchem.rst | 31 ++++++++++++++++++- 2 files changed, 31 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 793974e..01a6c3b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ### Changed - Updated RTD documentation to state that older Intel compilers may cause unexpected results; Also updated to recommend GCC 10 and later. +- Updated RTD documentation for fullchem rundir creation, which now asks users if they wish to build KPP-Standalone ## [14.5.1] - 2025-01-10 ### Added diff --git a/docs/source/gcclassic-user-guide/rundir-fullchem.rst b/docs/source/gcclassic-user-guide/rundir-fullchem.rst index d02bd2e..0fe33bc 100644 --- a/docs/source/gcclassic-user-guide/rundir-fullchem.rst +++ b/docs/source/gcclassic-user-guide/rundir-fullchem.rst @@ -263,7 +263,7 @@ GEOS-Chem full-chemistry simulation. |br| -#. The last menu will prompt you with: +#. The next menu will prompt you with: .. code-block:: console @@ -282,6 +282,35 @@ GEOS-Chem full-chemistry simulation. Initialized empty Git repository in /path/to/gc_4x5_merra2_fullchem/.git/ + |br| + +#. The next (and final) menu will ask you: + + .. code-block:: console + + ----------------------------------------------------------- + Do you want to build the KPP-Standalone Box Model? (y/n) + ----------------------------------------------------------- + >>> + + + Type :program:`y` and then :command:`ENTER` you wish to build the + :program:`KPP-Standalone Box Model`, or :program:`n` then + :program:`ENTER` to skip this step. If you choose to build + KPP-Standalone, you will be given this reminder: + + .. code-block:: console + + >>>> REMINDER: You must compile with options: -DKPPSA=y <<<< + + Please see the Supplemental Guide entitled :ref:`kppsa-guide` + for further usage instructions. + + Lastly, you will see a message to indicate that run directory + creation has completed successfully. + + .. code-block:: console + Created /path/to/gc_4x5_merra2_fullchem You may now navigate to this directory and start editing the :ref:`GEOS-Chem From b5f2d46db3ddc73c5aa908696ae8105864447788 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 7 Feb 2025 15:59:28 -0500 Subject: [PATCH 90/99] geos-chem-shared-docs update: Point to KPP-Standalone GCPy doc This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: aeeb8e9 Add link to KPP-Standalone documentation on GCPy ReadTheDocs This PR adds a paragraph to the KPP-Standalone documentation stating that plotting scripts are available on GCPy (with link to documentation). Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 02c4c26..aeeb8e9 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 02c4c26ff093e13029a0ab310d4f18558d5543e1 +Subproject commit aeeb8e974ad80dae22e9b2d11d371f1c31efb1b1 From ba5b7be47d2f8930f71e63f537f310197e47a979 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 12 Feb 2025 12:01:34 -0500 Subject: [PATCH 91/99] Change version numbers to 14.5.2 and update geos-chem hash CHANGELOG.md CMakeLists.txt docs/source/conf.py - Updated version numbers to 14.5.2 src/GEOS-Chem - Now points to GEOS-Chem (sci codebase) 14.5.2 release commit Signed-off-by: Bob Yantosca --- CHANGELOG.md | 2 +- CMakeLists.txt | 2 +- docs/source/conf.py | 2 +- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3450c6..e9155e1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ 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 +## [14.5.2] - 2025-02-12 ### Changed - Bumped `jinja2` to version 3.1.5 in `docs/requirements.txt` to fix a security issue - Changed the build sequence so that the KPP-Standalone is only built when configuring with `-DKPPSA=y` diff --git a/CMakeLists.txt b/CMakeLists.txt index a4f9f66..bad9315 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.13) project (geos-chem-classic - VERSION 14.5.1 + VERSION 14.5.2 LANGUAGES Fortran ) diff --git a/docs/source/conf.py b/docs/source/conf.py index 45fa8ce..a7228f8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,7 +23,7 @@ author = 'GEOS-Chem Support Team' # The full version, including alpha/beta/rc tags -release = '14.5.1' +release = '14.5.2' # -- General configuration --------------------------------------------------- diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 6038187..483ceec 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 60381876dabf72562a480e344d0afd54e4252029 +Subproject commit 483ceeca689a58e388ec6ef328270a2f4223708f diff --git a/src/HEMCO b/src/HEMCO index 9cf873a..0ae25d2 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 9cf873a8adeeb666a3ae9346ad7f6ec357c67f4b +Subproject commit 0ae25d22f61667e8d81e04415e94f133604f415b From 32719375a8a51b9c9a78c5dbd9c2b50e008e5ed9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 25 Feb 2025 13:14:10 -0500 Subject: [PATCH 92/99] GEOS-Chem update: Merge PR #2713 (CESM reads AEIC2019 every timestep) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 37da3740b Merge PR #2713 (Read AEIC2019 every timestep in CESM) This PR updates the HEMCO configuration file used with CESM to read AEIC emissions every model timestep. This avoids introducing small differences when the model runs are broken up in time. Signed-off-by: Bob Yantosca Date: Mon, 3 Mar 2025 13:39:36 -0500 Subject: [PATCH 93/99] RTD updates: AWS-CLI + bug fix in planeflight doc docs/source/geos-chem-shared-docs - Submodule update to c769e00 docs/source/gcclassic-user-guide/planeflight.rst - Fixed bugs in the rubric section CHANGELOG.md - Updated accordingly --- CHANGELOG.md | 4 ++++ docs/source/gcclassic-user-guide/planeflight.rst | 16 ++++++++-------- docs/source/geos-chem-shared-docs | 2 +- 3 files changed, 13 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f25a54..b7c1ab5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,10 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Changed the build sequence so that the KPP-Standalone is only built when configuring with `-DKPPSA=y` - Updated RTD documentation to state that older Intel compilers may cause unexpected results; Also updated to recommend GCC 10 and later. - Updated RTD documentation for fullchem rundir creation, which now asks users if they wish to build KPP-Standalone +- Updated RTD docs to state that users wishing not to open AWS account can use AWS CLI commands with `--no-sign-request1` + +### Fixed +- Fixed error with the `rubric` section in the RTD planeflight documentation ## [14.5.1] - 2025-01-10 ### Added diff --git a/docs/source/gcclassic-user-guide/planeflight.rst b/docs/source/gcclassic-user-guide/planeflight.rst index 6286d39..57ac9f4 100644 --- a/docs/source/gcclassic-user-guide/planeflight.rst +++ b/docs/source/gcclassic-user-guide/planeflight.rst @@ -242,14 +242,14 @@ you will specify the points that make up the flight track. | | used to compare to model output | +--------------+-----------------------------------------------+ -.. rubric:: - -.. [#] Altitude is only supported for CCGG or tower data. All other - observations must specify pressure in hPa. This can be - obtained from the "static pressure" field as measured by the - aircraft. See this `code block in planeflight_mod.F90 - `_ - for details. +.. rubric:: Notes + +.. [#A] Altitude is only supported for CCGG or tower data. All other + observations must specify pressure in hPa. This can be + obtained from the "static pressure" field as measured by the + aircraft. See this `code block in planeflight_mod.F90 + `_ + for details. .. important:: diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index aeeb8e9..c769e00 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit aeeb8e974ad80dae22e9b2d11d371f1c31efb1b1 +Subproject commit c769e0007cc02270016e68e738623ac97b1fbcb5 From d8afa2c6f4fcb562837adec6dc39ea074e965259 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Tue, 4 Mar 2025 14:18:30 -0500 Subject: [PATCH 94/99] Update HEMCO submodule with PRs #299, #304, and #306 Submodule src/HEMCO 0ae25d2..d7563e7: > Merge pull request #306 from geoschem/bugfix/remove_cesm_core_dependency > Merge pull request #299 from K20shores/ci > Merge PR #304 (Add .zenodo.json; Update jinja2 to 3.1.5) Signed-off-by: Lizzie Lundgren --- src/HEMCO | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/HEMCO b/src/HEMCO index 0ae25d2..d7563e7 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 0ae25d22f61667e8d81e04415e94f133604f415b +Subproject commit d7563e71b9a0a8b32bd153fa0295d0e1ef443806 From 14b847bbe5478014f20ab5e15bccc50eacc74ed2 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 4 Mar 2025 17:04:05 -0500 Subject: [PATCH 95/99] Update verwion numbers and submodule hashes for 14.5.3 release Updated version numbers to 14.5.3 in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py Updated src/GEOS-Chem submodule to the 14.5.3 release commit Updated src/HEMCO submodule to the 3.10.2 release commit Signed-off-by: Bob Yantosca --- CHANGELOG.md | 15 +++++++++++---- CMakeLists.txt | 2 +- docs/source/conf.py | 2 +- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 5 files changed, 15 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b7c1ab5..1f9a337 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,17 @@ 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). +## [14.5.3] - 2025-03-05 +### Added +- Updated RTD docs to state that users wishing not to open AWS account can use AWS CLI commands with `--no-sign-request1` + +### Changed +- Updated GEOS-Chem submodule to 14.5.3 +- Updated HEMCO submodule to 3.10.2 + +### Fixed +- Fixed error with the `rubric` section in the RTD planeflight documentation + ## [14.5.2] - 2025-02-12 ### Added - Added clarifying text about which types of data can use altitude coordinates for the Planeflight diagnostic in RTD documentation @@ -20,10 +31,6 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Changed the build sequence so that the KPP-Standalone is only built when configuring with `-DKPPSA=y` - Updated RTD documentation to state that older Intel compilers may cause unexpected results; Also updated to recommend GCC 10 and later. - Updated RTD documentation for fullchem rundir creation, which now asks users if they wish to build KPP-Standalone -- Updated RTD docs to state that users wishing not to open AWS account can use AWS CLI commands with `--no-sign-request1` - -### Fixed -- Fixed error with the `rubric` section in the RTD planeflight documentation ## [14.5.1] - 2025-01-10 ### Added diff --git a/CMakeLists.txt b/CMakeLists.txt index bad9315..fde0378 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.13) project (geos-chem-classic - VERSION 14.5.2 + VERSION 14.5.3 LANGUAGES Fortran ) diff --git a/docs/source/conf.py b/docs/source/conf.py index a7228f8..15ec884 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,7 +23,7 @@ author = 'GEOS-Chem Support Team' # The full version, including alpha/beta/rc tags -release = '14.5.2' +release = '14.5.3' # -- General configuration --------------------------------------------------- diff --git a/src/GEOS-Chem b/src/GEOS-Chem index 37da374..86cd586 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 37da3740bdea9a371a41802c9978d8da0fc53dc5 +Subproject commit 86cd586260e4f2a9db7efd06cea19a5fe0bdc9e8 diff --git a/src/HEMCO b/src/HEMCO index d7563e7..baa9ce5 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit d7563e71b9a0a8b32bd153fa0295d0e1ef443806 +Subproject commit baa9ce52be6c959e0561d6567565045e7c286096 From 6228f49884567b031a5c297fb47b2f2cf18ab186 Mon Sep 17 00:00:00 2001 From: Joe Wallwork Date: Mon, 31 Mar 2025 12:02:35 +0100 Subject: [PATCH 96/99] Add linting workflow --- .github/workflows/lint.yml | 61 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 .github/workflows/lint.yml diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..e72f78d --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,61 @@ +# Workflow to run linting checks on source +name: Lint + +# Controls when the workflow will run +on: + # Triggers the workflow on pushes to the "main" branch, i.e., PR merges + push: + branches: [ "main" ] + + # Triggers the workflow on pushes to open pull requests with code changes + pull_request: + paths: + - '.github/workflows/cloud-benchmarking-workflow.yml' + - '.github/workflows/gcclassic-compile-tests.yml' + - '.github/workflows/lint.yml' + - '.github/workflows/stale.yml' + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Cancel jobs running if new commits are pushed +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +# Workflow run - one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "lint" + lint: + # The type of runner that the job will run on + runs-on: ubuntu-latest + strategy: + fail-fast: false + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - name: Checkout code + with: + persist-credentials: false + uses: actions/checkout@v4 + + - name: Install Python + uses: actions/setup-python@v5 + with: + python-version: '3.x' + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m venv ci_venv + . ci_venv/bin/activate + pip install zizmor==0.9.2 + + # Apply GitHub Actions linter, zizmor + - name: zizmor + if: always() + run: | + cd ${{ github.workspace }} + . ci_venv/bin/activate + zizmor .github/workflows/*.yml From 66076f3f2a86ce3d10e625eb5207f2b6b5931319 Mon Sep 17 00:00:00 2001 From: Joe Wallwork Date: Mon, 31 Mar 2025 11:24:45 +0100 Subject: [PATCH 97/99] Persist credentials when checking out --- .github/workflows/cloud-benchmarking-workflow.yml | 1 + .github/workflows/gcclassic-compile-tests.yml | 2 ++ 2 files changed, 3 insertions(+) diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml index f658a61..5c4f9fc 100644 --- a/.github/workflows/cloud-benchmarking-workflow.yml +++ b/.github/workflows/cloud-benchmarking-workflow.yml @@ -33,6 +33,7 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 0 + persist-credentials: false - name: Set Initial Variables # By default we use 1Hr benchmarks run: | diff --git a/.github/workflows/gcclassic-compile-tests.yml b/.github/workflows/gcclassic-compile-tests.yml index 0c0a552..77940a3 100644 --- a/.github/workflows/gcclassic-compile-tests.yml +++ b/.github/workflows/gcclassic-compile-tests.yml @@ -19,6 +19,8 @@ jobs: steps: - name: Checkout code + with: + persist-credentials: false uses: actions/checkout@v4 - name: Install dependencies From 36353ed93349906408be493a647b8ae9bc902a1b Mon Sep 17 00:00:00 2001 From: Joe Wallwork Date: Mon, 31 Mar 2025 11:27:11 +0100 Subject: [PATCH 98/99] Fix vulnerability in cloud benchmarking workflow --- .github/workflows/cloud-benchmarking-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml index 5c4f9fc..932d6b9 100644 --- a/.github/workflows/cloud-benchmarking-workflow.yml +++ b/.github/workflows/cloud-benchmarking-workflow.yml @@ -44,8 +44,8 @@ jobs: # conditionally overwrite variables if a tag was the triggering event - name: Reset Initial Variables for pull request run: | - echo "GITHUB_SHA_SHORT=`echo ${{ github.event.pull_request.head.sha }} | cut -c1-7`" >> $GITHUB_ENV - echo "COMMIT_NAME=`echo ${{ github.event.pull_request.head.sha }} | cut -c1-7`" >> $GITHUB_ENV + echo "GITHUB_SHA_SHORT=${{ github.event.pull_request.head.sha | substr(0, 7) }}" >> $GITHUB_ENV + echo "COMMIT_NAME=${{ github.event.pull_request.head.sha | substr(0, 7) }}" >> $GITHUB_ENV if: github.event_name == 'pull_request' - name: Reset Variables For Tags # We do a 1Month benchmark for tags From 56416f6c70981b130067781f0e1f0a65d9b02c24 Mon Sep 17 00:00:00 2001 From: Joe Wallwork Date: Mon, 31 Mar 2025 11:24:35 +0100 Subject: [PATCH 99/99] Fix formatting of stale workflow --- .github/workflows/lint.yml | 5 +---- .github/workflows/stale.yml | 2 +- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index e72f78d..80d2d43 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -10,10 +10,7 @@ on: # Triggers the workflow on pushes to open pull requests with code changes pull_request: paths: - - '.github/workflows/cloud-benchmarking-workflow.yml' - - '.github/workflows/gcclassic-compile-tests.yml' - - '.github/workflows/lint.yml' - - '.github/workflows/stale.yml' + - '.github/workflows/*.yml' # Allows you to run this workflow manually from the Actions tab workflow_dispatch: diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index 4635a44..eb31154 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -7,7 +7,7 @@ name: Mark stale issues on: schedule: - - cron: '0 0 * * *' # Run every night at midnight + - cron: '0 0 * * *' # Run every night at midnight jobs: stale: