From 428b59285ff46d82e8ba2f7917a6b58c57f9ebd0 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 17 Jun 2025 14:46:02 -0400 Subject: [PATCH 01/86] GEOS-Chem update: Merge PR #2900 (Optional FINNv25 emissions) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: PR #2900 does the following: 1. Adds entries for FINN v2.5 biomass burning emissions to HEMCO_Config.rc template files for aerosol-only, carbon, and fullchem simulations. 2. Removes entries for the FINN v1.5 biomass burning extension from HEMCO_Config.rc template files, as FINN v1.5 is now superseded by FINN v2.5. 3. Adds clarifying comments in HEMCO_Diagn.rc template files instructing which settings of ExtNr, Cat, and Hier should be used for online vs. offline biomass burning emissions. 4. Replaces comments in HEMCO_Config.rc and HEMCO_Diagn.rc template files that were directing users to the obsolete HEMCO manual on the GC wiki with comments directing users to the current hemco.readthedocs.io documentation. 5. Restores TMB emission diagnostic entries to the HEMCO_Config.rc.fullchem files for GEOS-Chem Classic and GCHP. 6. Renames OCS biomass burning emissions to EmisOCS_BiomassBurn in GCHP HEMCO_Diagn.rc and HISTORY.rc files, for consistency with the corresponding diagnostic name in GEOS-Chem Classic. 7. Moves EmisOCS_Total to the top of the GCHP HISTORY.rc.carbon template file, which is expected by the script that edits the configuration files for single species carbon 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 f4c75742e..66e3ea565 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit f4c75742e13da440b34c4968797aa150ce114113 +Subproject commit 66e3ea56512527cbb3d303d956334391a43c0401 From 82f896f8ce0ee5ac9eb70068d3170cccc8926416 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 23 Jun 2025 13:14:49 -0400 Subject: [PATCH 02/86] GEOS-Chem update: Merge PR #2889 (Luo 2023 wetdep updates) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 78aa048e2 Merge PR #2889 (Updates for Luo2023) PR #2889 updates the Luo wet deposition scheme accordintg to Luo, G., & Yu, F. (2023). GRL, 50, e2023GL104258. https://doi.org/10.1029/2023GL104258. 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 66e3ea565..78aa048e2 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 66e3ea56512527cbb3d303d956334391a43c0401 +Subproject commit 78aa048e2652fb277239f43363f23835be5aae20 From c5705fb3a4a5290e25201bdbe6c2dfe02af44e9d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 26 Jun 2025 09:44:33 -0400 Subject: [PATCH 03/86] GEOS-Chem update: Merge PR #2916 (ESMF 8.6.1 on Harvard Cannon) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 1a97c01e5 Update ESMF to 8.6.1 in GCHP env file for Harvard Cannon PR #2916 updates the ESMF version from 8.4.2 to 8.6.1 in the sample GCHP environment file "gchp.gcc12_openmpi4_cannon_rocky.env", which is used on the Harvard Cannon cluster. 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 78aa048e2..2a8f81dfd 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 78aa048e2652fb277239f43363f23835be5aae20 +Subproject commit 2a8f81dfda2404d1502272c85122b07de968f58f From 1c1f4526fd37ef471d523083bdf52d395df6215d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 12:30:57 -0400 Subject: [PATCH 04/86] GEOS-Chem update: Merge PR #2974 (Fix Hg ocean flux diags) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 481b4fece Merge PR #2974 (Fix ocean flux diagnostics in Hg simulation) PR #2974 removes the zeroing of the directional Hg ocean flux diagnostics, in order to make the them equal the net flux. 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 3671d504c..481b4fece 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 3671d504cab09196ee960447a361b36ec41fe926 +Subproject commit 481b4fecec1d86fd08f0f0c59a0e7fe16ac82a0b From 1482eafb78e7c88943e1b27937c775a3e2baca17 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 14:46:16 -0400 Subject: [PATCH 05/86] Fix security issues in GitHub actions .github/workflows/cloud-benchmarking-workflow.yml - Use bash-safe string slicing instead of using the "cut" command - Updated comments - Trimmed trailing whitespace .github/workflows/lint-ci-workflows.yml - Define the GITHUB_TOKEN env var to pass the secret token to zizmor - Updated comments - Trimmed trailing whitespace CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- .../workflows/cloud-benchmarking-workflow.yml | 33 +++++++++++-------- .github/workflows/lint-ci-workflows.yml | 9 +++-- CHANGELOG.md | 4 +++ 3 files changed, 31 insertions(+), 15 deletions(-) diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml index 5c4f9fcdd..c7ab9db24 100644 --- a/.github/workflows/cloud-benchmarking-workflow.yml +++ b/.github/workflows/cloud-benchmarking-workflow.yml @@ -1,7 +1,7 @@ # Release pipeline: -# +# # This pipeline triggers the cloud-based benchmarking workflow -# upon pushes to the dev environment. The benchmarking workflow +# upon pushes to the dev environment. The benchmarking workflow # infrastructure code can be found in the following repository: # https://github.com/geoschem/gc-cloud-infrastructure # @@ -9,9 +9,9 @@ # # Notes: # - This workflow requires aws credentials necessary to -# trigger the benchmarking step function via the aws cli. -# The credentials need step function permissions and can -# be added to the repo as an action secret called +# trigger the benchmarking step function via the aws cli. +# The credentials need step function permissions and can +# be added to the repo as an action secret called # AWS_SECRET_ACCESS_KEY and AWS_ACCESS_KEY_ID. name: cloud_benchmarking @@ -29,30 +29,36 @@ jobs: trigger_step_function: runs-on: ubuntu-latest # aws cli comes pre-installed steps: + # for now both use Spot instances -- may need to update to use on demand - uses: actions/checkout@v3 with: fetch-depth: 0 persist-credentials: false + + # By default we use 1Hr benchmarks - name: Set Initial Variables - # By default we use 1Hr benchmarks run: | echo "TIME_PERIOD=1Hr" >> $GITHUB_ENV echo "RESOLUTION=4x5" >> $GITHUB_ENV - echo "GITHUB_SHA_SHORT=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV - echo "COMMIT_NAME=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV - # conditionally overwrite variables if a tag was the triggering event + echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV + + # 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`" >> $GITHUB_ENV + GITHUB_SHA_SHORT="${{ github.event.pull_request.head.sha }}" + echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV if: github.event_name == 'pull_request' + + # We do a 1Month benchmark for tags - name: Reset Variables For Tags - # We do a 1Month benchmark for tags run: | echo "TIME_PERIOD=1Mon" >> $GITHUB_ENV echo "COMMIT_NAME=${GITHUB_REF##*/}" >> $GITHUB_ENV if: startsWith(github.ref, 'refs/tags/') + - name: Generate Primary Key env: AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} @@ -63,6 +69,7 @@ jobs: cd ${{ github.workspace }} echo "DEV_PRIMARY_KEY=gcc-${RESOLUTION}-${TIME_PERIOD}-`git describe --tags`" >> $GITHUB_ENV echo "REF_PRIMARY_KEY=`./.github/workflows/findRefKey.sh ${RESOLUTION} ${TIME_PERIOD} ${GITHUB_SHA}`" >> $GITHUB_ENV + - name: Trigger Step Function env: # Set config options for aws cli @@ -88,7 +95,7 @@ jobs: `"\"timePeriod\": \"${TIME_PERIOD}\","` `"\"tag\": \"${COMMIT_NAME}\","` `"\"numCores\": \"${NUM_CORES}\","` - `"\"memory\": \"40000\","` + `"\"memory\": \"40000\","` `"\"resolution\": \"${RESOLUTION}\","` `"\"sendEmailNotification\": \"true\""` `"},"` diff --git a/.github/workflows/lint-ci-workflows.yml b/.github/workflows/lint-ci-workflows.yml index 80d2d43a7..a91100185 100644 --- a/.github/workflows/lint-ci-workflows.yml +++ b/.github/workflows/lint-ci-workflows.yml @@ -26,12 +26,17 @@ jobs: lint: # The type of runner that the job will run on runs-on: ubuntu-latest + # Make sure jobs can access the secret token + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} strategy: fail-fast: false - # Steps represent a sequence of tasks that will be executed as part of the job + # 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 + # Checks-out your repository under $GITHUB_WORKSPACE, + # so your job can access it - name: Checkout code with: persist-credentials: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 43838d3de..147898ec8 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 +### Fixed +- Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail + ## [14.6.3] - 2025-07-28 ### Added - Added `-DDEBUG` flag to `GEOSChem_Fortran_FLAGS_DEBUG_Intel` and `GEOSChem_Fortran_FLAGS_DEBUG_GNU` to toggle debug-only code From ff86b0fa2869ab57f679e599a1b6112c5f2fd0f8 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 14:56:47 -0400 Subject: [PATCH 06/86] Reorder commands in cloud-benchmarking-workflow.yml for Lint .github/workflows/cloud-benchmarking-workflow.yml - In the "Reset Initial Variables for pull request" task: - Move the "if: github.event_name == 'pull_request' to the top so that the task will immediately exit if not a pull request - Define the PR_SHA and GITHUB_SHA_SHORT environment variables in a bash-safe way - In the "Reset Variables For Tags" task: - Move the "if: startswith" block to the top - In the "Set Initial Variables" task: - Define the GITHUB_SHA_SHORT environment variable in a bash-safe way Signed-off-by: Bob Yantosca --- .../workflows/cloud-benchmarking-workflow.yml | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml index c7ab9db24..ef2c549ce 100644 --- a/.github/workflows/cloud-benchmarking-workflow.yml +++ b/.github/workflows/cloud-benchmarking-workflow.yml @@ -31,33 +31,37 @@ jobs: steps: # for now both use Spot instances -- may need to update to use on demand - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 persist-credentials: false # By default we use 1Hr benchmarks - name: Set Initial Variables + env: + GITHUB_SHA_SHORT: ${GITHUB_SHA:0:7} run: | echo "TIME_PERIOD=1Hr" >> $GITHUB_ENV echo "RESOLUTION=4x5" >> $GITHUB_ENV - echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV - echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV + echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV # Conditionally overwrite variables if a tag was the triggering event - name: Reset Initial Variables for pull request - run: | - GITHUB_SHA_SHORT="${{ github.event.pull_request.head.sha }}" - echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV - echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV if: github.event_name == 'pull_request' + env: + PR_SHA: ${{ github.event.pull_request.head.sha }} + GITHUB_SHA_SHORT: ${PR_SHA:0:7} + run: | + echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_HA_SHORT}" >> $GITHUB_ENV # We do a 1Month benchmark for tags - name: Reset Variables For Tags + if: startsWith(github.ref, 'refs/tags/') run: | echo "TIME_PERIOD=1Mon" >> $GITHUB_ENV echo "COMMIT_NAME=${GITHUB_REF##*/}" >> $GITHUB_ENV - if: startsWith(github.ref, 'refs/tags/') - name: Generate Primary Key env: From c3ab395e550e5c5b3d182973ccba35ab7cb92e1d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 15:18:38 -0400 Subject: [PATCH 07/86] Now run Lint action on main and dev/* branches .github/workflows/lint-ci-workflows.yml - Add "dev/*" to the branches list, this will trigger the Lint workflow when pushing to dev/* branches - Add the GITHUB_TOKEN environment variable to the zizmor task - Trimmed trailing whitespace - Added "permissions: contents:read" to allow Zizmor to read the secret GitHub token CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- .github/workflows/lint-ci-workflows.yml | 24 +++++++++++++++++++----- CHANGELOG.md | 3 +++ 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/.github/workflows/lint-ci-workflows.yml b/.github/workflows/lint-ci-workflows.yml index a91100185..2f09ab478 100644 --- a/.github/workflows/lint-ci-workflows.yml +++ b/.github/workflows/lint-ci-workflows.yml @@ -3,9 +3,10 @@ name: Lint # Controls when the workflow will run on: - # Triggers the workflow on pushes to the "main" branch, i.e., PR merges + # Triggers the workflow on pushes to the "main" or "dev/"* branches, + # i.e., PR merges push: - branches: [ "main" ] + branches: [ "main", "dev/*" ] # Triggers the workflow on pushes to open pull requests with code changes pull_request: @@ -13,8 +14,13 @@ on: - '.github/workflows/*.yml' # Allows you to run this workflow manually from the Actions tab + # (usually leave it blank) workflow_dispatch: +# Allow the jobs to read the secret GitHub token +permissions: + contents: read + # Cancel jobs running if new commits are pushed concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} @@ -22,19 +28,25 @@ concurrency: # 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 - # Make sure jobs can access the secret token - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + # Don't quit the Action at the first strategy: fail-fast: false + # GitHub secret token + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + # 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 @@ -42,11 +54,13 @@ jobs: persist-credentials: false uses: actions/checkout@v4 + # Installs Python 3.x - name: Install Python uses: actions/setup-python@v5 with: python-version: '3.x' + # Installs Python packages - name: Install dependencies run: | python -m pip install --upgrade pip diff --git a/CHANGELOG.md b/CHANGELOG.md index 147898ec8..0df14f6e3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,9 @@ 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 `lint-ci-workflows` to run on `main` and `dev/*` branches + ### Fixed - Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail From fed86bae38bb97b482848e1e1f23fb578ad4ce1b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 16:05:09 -0400 Subject: [PATCH 08/86] Remove the Azure Dev Pipelines workflows .ci-pipelines/*.yml - Removed CHANGELOG.md - Updated accordingly --- .ci-pipelines/build-matrix.yml | 63 -------------------------------- .ci-pipelines/quick-build.yml | 48 ------------------------ .ci-pipelines/release.dockerfile | 43 ---------------------- .ci-pipelines/release.yml | 57 ----------------------------- CHANGELOG.md | 3 ++ 5 files changed, 3 insertions(+), 211 deletions(-) delete mode 100644 .ci-pipelines/build-matrix.yml delete mode 100644 .ci-pipelines/quick-build.yml delete mode 100644 .ci-pipelines/release.dockerfile delete mode 100644 .ci-pipelines/release.yml diff --git a/.ci-pipelines/build-matrix.yml b/.ci-pipelines/build-matrix.yml deleted file mode 100644 index 9015c5e96..000000000 --- a/.ci-pipelines/build-matrix.yml +++ /dev/null @@ -1,63 +0,0 @@ -#============================================================================= -# Build matrix pipeline: -# -# This pipeline checks that pre-releases and the main branch -# compile in a wide variety of build environments. This pipeline -# is intended to be a rigorous check of GEOS-Chem's build. -# -# This pipeline triggers on tagged pre-releases (alpha and beta -# versions, as well as release candidates). Commits to the main -# branch also trigger this pipeline. -#============================================================================= -trigger: - branches: - include: - - main - exclude: - - bugfix* - - dev* - - feature* - tags: - include: # Semantic versioning 2.0.0 examples: - - '*-alpha*' # 12.7.1-alpha.3 - - '*-beta*' # 12.7.0-beta.1 - - '*-rc*' # 12.7.0-rc.1 -pr: none - -# Basic agent set up -pool: - vmImage: 'ubuntu-latest' - - -# Define the "matrix" of build images to try building GEOS-Chem in -strategy: - matrix: - ubuntu_basic: - containerImage: geoschem/buildmatrix:netcdf-ubuntu - gcc8: - containerImage: geoschem/buildmatrix:netcdf-gcc8 - gcc9: - containerImage: geoschem/buildmatrix:netcdf-gcc9 - gcc10: - containerImage: geoschem/buildmatrix:netcdf-gcc10 -container: $[ variables['containerImage'] ] - - -# Try building GEOS-Chem (this is run for each "matrix" entry above) -steps: -- checkout: self - submodules: recursive -- script: | - . /opt/spack/share/spack/setup-env.sh - export CC=gcc - export CXX=g++ - export FC=gfortran - set -x - spack load cmake - spack load netcdf-c - spack load netcdf-fortran - mkdir build - cd build - cmake -DCMAKE_COLOR_MAKEFILE=FALSE $(Build.Repository.LocalPath) - make -j - displayName: 'Building GEOS-Chem' diff --git a/.ci-pipelines/quick-build.yml b/.ci-pipelines/quick-build.yml deleted file mode 100644 index cb62f6613..000000000 --- a/.ci-pipelines/quick-build.yml +++ /dev/null @@ -1,48 +0,0 @@ -#============================================================================= -# Quick build pipeline: -# -# This pipeline checks that commits and open pull requests don't -# introduce compiler errors. This is meant to be a quick and simple -# check that runs frequently. -# -# This pipeline triggers on commits to development and bug-fix -# branches. Commits to the main branch do not trigger this pipeline -# because those are tested against the build matrix. Commits to -# feature branches do not trigger this pipeline, but open pull requests -# and commits to pull requests do. -#============================================================================= -trigger: - branches: - include: - - dev* - - patch* - - bugfix* -pr: - branches: - include: - - '*' - -# Basic agent and container set up -pool: - vmImage: 'ubuntu-latest' -container: geoschem/buildmatrix:netcdf-ubuntu - - -# Try building GEOS-Chem -steps: -- checkout: self - submodules: recursive -- script: | - . /opt/spack/share/spack/setup-env.sh - export CC=gcc - export CXX=g++ - export FC=gfortran - set -x - spack load cmake - spack load netcdf-c - spack load netcdf-fortran - mkdir build - cd build - cmake -DCMAKE_COLOR_MAKEFILE=FALSE $(Build.Repository.LocalPath) - make -j - displayName: 'Building GEOS-Chem' diff --git a/.ci-pipelines/release.dockerfile b/.ci-pipelines/release.dockerfile deleted file mode 100644 index 2a0da0d88..000000000 --- a/.ci-pipelines/release.dockerfile +++ /dev/null @@ -1,43 +0,0 @@ -FROM geoschem/buildmatrix:netcdf-ubuntu - -# Make a directory to install GEOS-Chem to -RUN mkdir /opt/geos-chem && mkdir /opt/geos-chem/bin - -# Copy the GEOS-Chem repository (".") to /gc-src -# This means this docker build command's context must be -# GEOS-Chem's root source code directory -COPY . /gc-src -RUN cd /gc-src \ -&& mkdir build - -RUN echo ". /opt/spack/share/spack/setup-env.sh" >> /init.rc \ -&& echo "export CC=gcc" >> /init.rc \ -&& echo "export CXX=g++" >> /init.rc \ -&& echo "export FC=gfortran" >> /init.rc \ -&& echo "spack load cmake" >> /init.rc \ -&& echo "spack load netcdf-c" >> /init.rc \ -&& echo "spack load netcdf-fortran" >> /init.rc \ -&& echo 'export PATH=$PATH:/opt/geos-chem/bin' >> /init.rc - -# Make bash the default shell -SHELL ["/bin/bash", "-c"] - -# Build fullchem and copy the executable to /opt/geos-chem/bin -RUN source /init.rc \ -&& cd /gc-src/build \ -&& cmake -DCMAKE_COLOR_MAKEFILE=FALSE .. \ -&& make \ -&& cp bin/gcclassic /opt/geos-chem/bin/ \ -&& rm -rf /gc-src/build/* - -# Create fake createRunDir.sh that calls the actual one -RUN echo "#!/usr/bin/env bash" > /opt/geos-chem/bin/createRunDir.sh \ -&& echo "cd /gc-src/run" >> /opt/geos-chem/bin/createRunDir.sh \ -&& echo "bash createRunDir.sh" >> /opt/geos-chem/bin/createRunDir.sh \ -&& chmod +x /opt/geos-chem/bin/createRunDir.sh - -RUN echo "#!/usr/bin/env bash" > /usr/bin/start-container.sh \ -&& echo ". /init.rc" >> /usr/bin/start-container.sh \ -&& echo 'if [ $# -gt 0 ]; then exec "$@"; else /bin/bash ; fi' >> /usr/bin/start-container.sh \ -&& chmod +x /usr/bin/start-container.sh -ENTRYPOINT ["start-container.sh"] diff --git a/.ci-pipelines/release.yml b/.ci-pipelines/release.yml deleted file mode 100644 index 906aebb8e..000000000 --- a/.ci-pipelines/release.yml +++ /dev/null @@ -1,57 +0,0 @@ -#============================================================================= -# Release pipeline: -# -# This pipeline performs deployment actions upon a GEOS-Chem release. -# Currently, the only deployment action is to build and push a docker -# container with GCClassic for the newly release version. This only includes -# the executable for fullchem. -# -# This pipeline is triggered by tagged versions excluding -# pre-releases. -#============================================================================= -trigger: - branches: - exclude: - - '*' - tags: - include: - - '*' - exclude: - - '*-alpha*' - - '*-beta*' - - '*-rc*' - - 'GEOS_*' -pr: none - - -# Basic agent set up -pool: - vmImage: 'ubuntu-latest' - -# Login to Docker Hub, build the image, and push the built image -# to Docker Hub -steps: - - checkout: self - submodules: recursive - - script: VERSION_TAG=`git describe --tags` && echo "##vso[task.setvariable variable=VERSION_TAG]$VERSION_TAG" - displayName: Get the repo's tag - - task: Docker@2 - displayName: Login to Docker Hub - inputs: - command: login - containerRegistry: DockerHub # The name of the service connection in the Azure project - - task: Docker@2 - displayName: Build image - inputs: - command: build - buildContext: $(Build.Repository.LocalPath) # The path to the source code repo - Dockerfile: .ci-pipelines/release.dockerfile - repository: geoschem/gcclassic # Docker Hub repository - tags: $(VERSION_TAG) # Source code repo's tag - - task: Docker@2 - displayName: Push image - inputs: - containerRegistry: DockerHub - repository: geoschem/gcclassic # Docker Hub repository - command: push - tags: $(VERSION_TAG) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0df14f6e3..ab7654418 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,9 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ### Fixed - Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail +### Removed +- Removed the Azure Dev Pipelines workflows; these are now superseded by the `gcclassic-compile-tests` GitHub action + ## [14.6.3] - 2025-07-28 ### Added - Added `-DDEBUG` flag to `GEOSChem_Fortran_FLAGS_DEBUG_Intel` and `GEOSChem_Fortran_FLAGS_DEBUG_GNU` to toggle debug-only code From f15e9ba7e0bce322c8e761ba6da471c289b89986 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 16:07:12 -0400 Subject: [PATCH 09/86] Updated GitHub badges on README.md and index.rst README.md docs/source/index.rst - Removed "Latest pre-release" badge - Added "gcclassic-compile-tests" badge - Changed the order of badges on the page CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 1 + README.md | 15 ++++++--------- docs/source/index.rst | 12 ++++++------ 3 files changed, 13 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab7654418..2adae4bd1 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 - Updated `lint-ci-workflows` to run on `main` and `dev/*` branches +- Updated badges on `README.md` and `docs/source/index.rst` ### Fixed - Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail diff --git a/README.md b/README.md index 075a1e416..e65829f42 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,14 @@ GEOS-Chem Logo

- - - -
- DOI - - - + Latest release + Release date + DOI
+ License + gcclassic-compile-tests + ReadTheDocs

- ## Description This is the offical repository for **GEOS-Chem Classic**. diff --git a/docs/source/index.rst b/docs/source/index.rst index e2a5e353d..bc53f7458 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -6,12 +6,12 @@ GEOS-Chem Classic .. raw:: html

- - -
- DOI - - + Latest release + Release date + DOI
+ License + gcclassic-compile-tests + ReadTheDocs

This site provides instructions for :program:`GEOS-Chem Classic`, From b35ee06322e9dae448aba9684dfa355b93eac024 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 16:34:02 -0400 Subject: [PATCH 10/86] Fix typo in cloud-benchmarking-workflow.yml .github/workflows/cloud-benchmarking-workflow.yml - Fixed typo: "GITHUB_HA_SHORT" -> "GITHUB_SHA_SHORT" - Now use "dev/*" instead of "dev**" as the branch pattern Signed-off-by: Bob Yantosca --- .github/workflows/cloud-benchmarking-workflow.yml | 6 +++--- .github/workflows/gcclassic-compile-tests.yml | 6 ++++++ 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml index ef2c549ce..320bc3362 100644 --- a/.github/workflows/cloud-benchmarking-workflow.yml +++ b/.github/workflows/cloud-benchmarking-workflow.yml @@ -18,12 +18,12 @@ name: cloud_benchmarking on: push: branches: - - dev** + - dev/* tags: - '*' pull_request: branches: - - dev** + - dev/* jobs: trigger_step_function: @@ -54,7 +54,7 @@ jobs: GITHUB_SHA_SHORT: ${PR_SHA:0:7} run: | echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV - echo "COMMIT_NAME=${GITHUB_HA_SHORT}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV # We do a 1Month benchmark for tags - name: Reset Variables For Tags diff --git a/.github/workflows/gcclassic-compile-tests.yml b/.github/workflows/gcclassic-compile-tests.yml index 77940a3b1..037002e08 100644 --- a/.github/workflows/gcclassic-compile-tests.yml +++ b/.github/workflows/gcclassic-compile-tests.yml @@ -1,7 +1,13 @@ +# +# GitHub Actions configuration file to perform "compile-only" +# integration tests for GEOS-Chem Classic that are triggered by +# push or pull requests. +# name: gcclassic-compile-tests on: [pull_request, push] +# Cancel running jobs if new commits are pushed concurrency: group: ${{ github.workflow }}-${{ github.ref || github.run_id }} cancel-in-progress: true From 21668f122316122c0ccd258f67c0388c06620802 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 29 Jul 2025 16:41:09 -0400 Subject: [PATCH 11/86] Fix error w/ commit name in cloud-benchmarking-workflow.yml .github/workflows/cloud-benchmarking-workflow.yml - In the "Set Initial Variables" task: - Remove the "env" section - Now use ${GITHUB_SHA:0:7} to define GITHUB_SHA_SHORT and COMMIT_NAME in the run section - In the "Reset Initial Variables for pull request" task: - Remove PR_SHA from the env section - Set GITHUB_SHA_SHORT to the head sha of the pull request - Now use ${GITHUB_SHA_SHORT:0:7} to define GITHUB_SHA_SHORT and COMMIT_NAME in the run section Signed-off-by: Bob Yantosca --- .github/workflows/cloud-benchmarking-workflow.yml | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/.github/workflows/cloud-benchmarking-workflow.yml b/.github/workflows/cloud-benchmarking-workflow.yml index 320bc3362..bf60a14e1 100644 --- a/.github/workflows/cloud-benchmarking-workflow.yml +++ b/.github/workflows/cloud-benchmarking-workflow.yml @@ -38,23 +38,20 @@ jobs: # By default we use 1Hr benchmarks - name: Set Initial Variables - env: - GITHUB_SHA_SHORT: ${GITHUB_SHA:0:7} run: | echo "TIME_PERIOD=1Hr" >> $GITHUB_ENV echo "RESOLUTION=4x5" >> $GITHUB_ENV - echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV - echo "COMMIT_NAME=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV + echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV # Conditionally overwrite variables if a tag was the triggering event - name: Reset Initial Variables for pull request if: github.event_name == 'pull_request' env: - PR_SHA: ${{ github.event.pull_request.head.sha }} - GITHUB_SHA_SHORT: ${PR_SHA:0:7} + GITHUB_SHA_SHORT: ${{ github.event.pull_request.head.sha }} run: | - echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV - echo "COMMIT_NAME=${GITHUB_SHA_SHORT}" >> $GITHUB_ENV + echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT:0:7}" >> $GITHUB_ENV + echo "COMMIT_NAME=${GITHUB_SHA_SHORT:0:7}" >> $GITHUB_ENV # We do a 1Month benchmark for tags - name: Reset Variables For Tags From 016a27ba3d9b14574973a5c908961c5cd1584824 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 30 Jul 2025 10:51:09 -0400 Subject: [PATCH 12/86] HEMCO update: Merge PR #339 (Add "Lint" GitHub action) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/HEMCO repository: 8dbae83 Merge PR #339 (Add "Lint" GitHub action) PR #339 does the following: 1. The lint-ci-workflows action now runs when updates are made to the main and dev/* branches. 2. We have removed the .ci-pipelines folder, which contained the configuration files for the Microsoft Azure Dev Pipelines C-I tests. Many of these were broken anyway. 3. The windows, mac, and ubuntu GitHub actions have been updated to fix security issues. These actions now also run when pushes or pull requests are made to dev or release branches. Signed-off-by: Bob Yantosca --- src/HEMCO | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/HEMCO b/src/HEMCO index 28e6d8e27..8dbae833a 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 28e6d8e27dfd059f5c6e3ceee0c0844523a0689f +Subproject commit 8dbae833a397da191288c799aa45aaaa3d619324 From deba0f5bff664d9c173745b4d8e325d49a47b69c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 7 Aug 2025 11:50:29 -0400 Subject: [PATCH 13/86] GEOS-Chem update: Merge PR #2984 (Fix GCHP rst for Jacobian tracers) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e4dc17b14 Merge PR #2984 (Fix GCHP restart for Jacobian tracers) PR #2984 adds a logical flag of Is_JacobianTracer in species_database.yml. This allows GCHP perturbation runs to define species "CH4_nnnn", which will be initialized to the initial conditions from the "SPC_CH4" species in GCHP restart 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 481b4fece..e4dc17b14 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 481b4fecec1d86fd08f0f0c59a0e7fe16ac82a0b +Subproject commit e4dc17b1464705eb4eedc3d70f77dad0d91b061b From c6e6f774d77840cc907425d9585008d1a76ce7eb Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 11 Aug 2025 16:42:34 -0400 Subject: [PATCH 14/86] GEOS-Chem update: Merge PR #2988 (Update Compute1 run script) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: bcb78036e Merge PR #2988 (Update Compute1 operation run script) PR #2988 Update operational run script sample for the WashU Compute1 cluster with necessary changes following a system update. 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 e4dc17b14..bcb78036e 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e4dc17b1464705eb4eedc3d70f77dad0d91b061b +Subproject commit bcb78036e3f1f794288922eb0a4107e2def65723 From 6653e9479aaab1624f45c862bd71f466f80ca3c5 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 12 Aug 2025 10:14:21 -0400 Subject: [PATCH 15/86] GEOS-Chem update: Merge PR #2989 (GCHP run scripts for Compute2) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: bcbfb3dd7 Merge PR #2989 (Add operational run scripts for WashU Compute2) PR #2989 adds operational GCHP run scripts for the WashU Compute2 cluster. 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 bcb78036e..bcbfb3dd7 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit bcb78036e3f1f794288922eb0a4107e2def65723 +Subproject commit bcbfb3dd7268a2b3fb70ef0694b492e712c07d80 From b539b3ec99262ac6df251ce28669576f2c3f0efb Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 12 Aug 2025 10:31:32 -0400 Subject: [PATCH 16/86] GEOS-Chem update: Merge PR #2990 (Update GCHP AWS EFA run scripts) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 8bb85739d Merge PR #2990 (Update GCHP AWS EFA run scripts to avoid crashes) PR #2990 Update GCHP AWS EFA operational run script examples to avoid crashes at large core counts. 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 bcbfb3dd7..8bb85739d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit bcbfb3dd7268a2b3fb70ef0694b492e712c07d80 +Subproject commit 8bb85739dc0863335be224a698ccfa59b3aecdec From 836a9c9fe7d919d5d0697098b1603b3e6a1d3adb Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 13 Aug 2025 11:44:21 -0400 Subject: [PATCH 17/86] GEOS-Chem update: Merge PR #2885 (Updates for MAPL 2.59 compatibility) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: b7e60f96f Merge PR #2885 (Update for MAPL 2.59 compatibility) PR #2885 contains assorted changes related to updating GCHP from MAPL 2.26 to MAPL 2.59. 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 d027524ef..b7e60f96f 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit d027524ef74811633e49a5c9235a05b2d9384215 +Subproject commit b7e60f96fe3e391af9fe2f78bdd3b0e1372000fd From 0a172ddf6901ef84f2ddbc163d9e6ba4bdf28692 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 25 Aug 2025 15:19:52 -0400 Subject: [PATCH 18/86] GEOS-Chem update: Merge PR #2996 (Update GFEIv3 files) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 90799084d Merge PR #2996 (Update GFEIv3 files, from peer review) PR #2996 fixes an issue in the original GFEIv3 files. The files were corrected in July 2025 and redownloaded and processed for use in GEOS-Chem. The corrected files can now be found in ExtData/HEMCO/CH4/v2025-08/GFEIv3/. 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 8bb85739d..90799084d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 8bb85739dc0863335be224a698ccfa59b3aecdec +Subproject commit 90799084ded7e241919217a14f6147eff7a0d8f0 From bfa3424e8de14afa2c8648403be235cb41e90d91 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 25 Aug 2025 16:42:13 -0400 Subject: [PATCH 19/86] GEOS-Chem update: Merge PR #2997 (Pass seconds to Accept_External_Date_Time) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 8db991a59 Merge PR #2997 (Pass seconds to Accept_External_Date_Time) PR #2997 fixes a bug in WRF-GC by making sure that seconds are passed into the routine Accept_External_Date_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 b7e60f96f..8db991a59 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit b7e60f96fe3e391af9fe2f78bdd3b0e1372000fd +Subproject commit 8db991a590899e408cefc75bd1c8546feca827ec From eda84ecbb53ef07b0ea34ee49a1b8cc9d4a22062 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 26 Aug 2025 11:02:17 -0400 Subject: [PATCH 20/86] GEOS-Chem update: Merge PR #3000 (FIx OM/OC ratio for OCPO) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: bfa3424 GEOS-Chem update: Merge PR #2997 (Pass seconds to Accept_External_Date_Time) PR #3000 changes the OM/OC ratio for OCPO in SimpleSOA to 1.4 (instead of 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 8db991a59..aa5e27260 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 8db991a590899e408cefc75bd1c8546feca827ec +Subproject commit aa5e272605e112ad3fae1c9c454829e3b56eee08 From e59b411d0e1249d8e7c23c4d885f766a74e6463d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 26 Aug 2025 16:05:35 -0400 Subject: [PATCH 21/86] Update geos-chem-shared-docs to 331f989 This commit informs the GCClassic superproject about the following commits that were pushed to the geos-chem-shared-docs submodule: 331f989 Update ESMF version in spack/packages.yaml to 8.6.1 4679349 Mention that the aerosol-only sim cannot simulate NH4-NO3-SO4 aerosols Signed-off-by: Bob Yantosca --- 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 3887938a1..331f98934 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 3887938a14f933607b597e04436e1741f102d017 +Subproject commit 331f989340c047ad67d41830cea810790ee246e1 From b86b6ae71960cc1d3f1766fb44622b3e152f2344 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 2 Sep 2025 09:58:46 -0400 Subject: [PATCH 22/86] GEOS-Chem update: Merge PR #3001 (Update conv washout) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 2311ed93a Merge PR #3001 (Update conv washout for G-F and Luo wetdep) PR #3001 does the following: 1. In GF, remove convective washout for default scheme but keep it for LUO_WETDEP based on suggestion from @viral211 2. Adapt Luo2023 WetDep for GF convection. 3. Fix precipitation formation rate unit in Luo2023 convective washout. 4. Update timestep scaling for convective precipitation areal fraction. 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 aa5e27260..2311ed93a 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit aa5e272605e112ad3fae1c9c454829e3b56eee08 +Subproject commit 2311ed93a0bcfc6a13cc7813023cc560f3df2365 From 0e43a0ffefad6fae6550b1b5252dac307ad4a746 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 2 Sep 2025 10:31:17 -0400 Subject: [PATCH 23/86] geos-chem-shared-docs submod update to cdc2304 (TransportTracers doc) This commit informs the GCClassic superproject about the following commits that were pushed to the geos-chem-shared-docs submodule: cdc2304 Update TransportTracers simulation page Signed-off-by: Bob Yantosca --- 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 331f98934..cdc23040b 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 331f989340c047ad67d41830cea810790ee246e1 +Subproject commit cdc23040b0c18fc81841e758a655c7f9627030c3 From 9a639855115f87af5ea08dc5185dddaca9150630 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 4 Sep 2025 15:53:25 -0400 Subject: [PATCH 24/86] Added "GEOS-Chem Classic vertical grids" guide to ReadTheDocs docs/source/supplemental-guides/vertical-grids.rst - Added documentation about GEOS-Chem Classic vertical grids, ported from the GEOS-Chem wiki docs/source/index.rst - Added vertical-grids.rst to the Supplemental Guides toctree CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 4 + docs/source/index.rst | 2 +- .../supplemental-guides/vertical-grids.rst | 1652 +++++++++++++++++ 3 files changed, 1657 insertions(+), 1 deletion(-) create mode 100644 docs/source/supplemental-guides/vertical-grids.rst diff --git a/CHANGELOG.md b/CHANGELOG.md index 43838d3de..a0db4ca2c 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 +### Added +- Added "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs (migrated from the GEOS-Chem wiki). + ## [14.6.3] - 2025-07-28 ### Added - Added `-DDEBUG` flag to `GEOSChem_Fortran_FLAGS_DEBUG_Intel` and `GEOSChem_Fortran_FLAGS_DEBUG_GNU` to toggle debug-only code diff --git a/docs/source/index.rst b/docs/source/index.rst index e2a5e353d..725bb3614 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -82,6 +82,7 @@ modifications to GEOS-Chem Classic source code. :maxdepth: 4 supplemental-guides/directory-structure.rst + supplemental-guides/vertical-grids.rst supplemental-guides/run-script-examples.rst geos-chem-shared-docs/supplemental-guides/load-libraries-guide.rst geos-chem-shared-docs/supplemental-guides/spack-guide.rst @@ -108,4 +109,3 @@ modifications to GEOS-Chem Classic source code. help-and-reference/CONTRIBUTING.md help-and-reference/SUPPORT.md geos-chem-shared-docs/editing_these_docs.rst - diff --git a/docs/source/supplemental-guides/vertical-grids.rst b/docs/source/supplemental-guides/vertical-grids.rst new file mode 100644 index 000000000..dd1c5c2b8 --- /dev/null +++ b/docs/source/supplemental-guides/vertical-grids.rst @@ -0,0 +1,1652 @@ +.. _gcc-vgrids: + +################################ +GEOS-Chem Classic vertical grids +################################ + +On this page we provide information about the various vertical grids +used in GEOS-Chem Classic. + +.. _gcc-grids-hybrid: + +====================== +Hybrid grid definition +====================== + +A hybrid sigma-pressure grid (aka :math:`\eta` grid) uses a +terrain-following coordinate near the surface, which then transitions +to a purely fixed-pressure coordinate. + +The pressure at the bottom edge of grid box :math:`(I,J,L)` of a +hybrid grid may be defined as: + +.. math:: + + P_{edge}(I,J,L) = A_p(L) + B_p(L) \times P_{surface}(I,J) + +where + +- :math:`(I,J,L)` are the lon, lat, and level indices of the grid box; +- :math:`P_{surface}(I,J)` is the "true" surface pressure at lon,lat + location :math:`(I,J)`; +- :math:`A_p(L)` are constants in surface pressure units (Pa or hPa), defined at level edges; +- :math:`B_p(L)` are unitless constants, defined at level edges. + +The values of :math:`A_p(L)` and :math:`B_p(L)` specify the vertical +properties of the grid. In GEOS-Chem, you may find these values in +source code file :file:`GeosUtil/pressure_mod.F90`. + +The pressure at the vertical midpoint of grid box :math:`(I,J,L)` is +computed as the average of the pressures at successive vertical edges: + +.. math:: + + P_{midpoint}(I,J,L) = \frac{P_{edge}(I,J,L) + P_{edge}(I,J,L+1)}{2} + +For the GMAO meteorological products, the :math:`P_{edge}(I,J,L)` and +:math:`P_{midpoint}(I,J,L)` meteorological products vary with the +topography up to 170 hPa. Skyward of 170 hPa, :math:`P_{edge}(I,J,L)` +and :math:`P_{midpoint}(I,J,L)` remain constant for all longitudes +and latitudes :math:`(I,J)`. + +An :math:`\eta` coordinate can be constructed from +:math:`P_{edge}(I,J,L)` and :math:`P_{midpoint}(I,J,L)` as follows: + +.. math:: + + \eta_{edge}(I,J,L) = \frac{P_{edge}(I,J,L) - P_{top}}{P_{surface}(I,J) - P_{top}} + +.. math:: + + \eta_{midpoint}(I,J,L) = \frac{P_{midpoint}(I,J,L) - P_{top}}{P_{surface}(I,J) - P_{top}} + +where :math:`P_{top}` is pressure at the top level of the vertical +grid. GMAO meteorological products use a model top of 0.01 hPa. + +.. _gcc-vgrids_gmao: + +=================================== +Vertical grids for GMAO meteorology +=================================== + +.. _gcc-vgrids-gmao-72: + +72-level vertical grid +---------------------- + +This grid is used by the `GEOS-FP +`_, +`GEOS-IT +`_, +and `MERRA-2 +`_ +meteorological field products from NASA GMAO. It has 72 vertical +levels and 73 edges. + +.. _gcc-vgrids-gmao-72-ind: + +Indexing +~~~~~~~~ + +.. list-table:: + :header-rows: 1 + + * - Instance + - Surface level + - Top-of-atm level + - Direction + * - GEOS-Chem Classic using GMAO met + - 1 + - 72 + - :literal:`positive:up` + * - Emissions data for GEOS-Chem + - 1 + - 72 + - :literal:`positive:up` + * - Processed met fields for GEOS-Chem + - 1 + - 72 + - :literal:`positive:up` + * - Raw met fields for GEOS-Chem + - 72 + - 1 + - :literal:`positive:down` + +.. _gcc-vgrids-gmao-72-ab: + +:math:`A_p` and :math:`B_p` +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists the :math:`A_p` and :math:`B_p` parameters that +define the 72-level vertical grid. The level edge indices run from 1 +(surface) to 73 (top-of atmosphere). + +.. list-table:: + :header-rows: 1 + + * - Level edge index + - :math:`A_p` (hPa) + - :math:`B_p` (unitless) + * - 1 + - 0.0 + - 1.0 + * - 2 + - 0.04804826 + - 0.984952 + * - 3 + - 6.593752 + - 0.963406 + * - 4 + - 13.1348 + - 0.941865 + * - 5 + - 19.61311 + - 0.920387 + * - 6 + - 26.09201 + - 0.898908 + * - 7 + - 32.57081 + - 0.877429 + * - 8 + - 38.98201 + - 0.856018 + * - 9 + - 45.33901 + - 0.8346609 + * - 10 + - 51.69611 + - 0.8133039 + * - 11 + - 58.05321 + - 0.7919469 + * - 12 + - 64.36264 + - 0.7706375 + * - 13 + - 70.62198 + - 0.7493782 + * - 14 + - 78.83422 + - 0.721166 + * - 15 + - 89.09992 + - 0.6858999 + * - 16 + - 99.36521 + - 0.6506349 + * - 17 + - 109.1817 + - 0.6158184 + * - 18 + - 118.9586 + - 0.5810415 + * - 19 + - 128.6959 + - 0.5463042 + * - 20 + - 142.91 + - 0.4945902 + * - 21 + - 156.26 + - 0.4437402 + * - 22 + - 169.609 + - 0.3928911 + * - 23 + - 181.619 + - 0.3433811 + * - 24 + - 193.097 + - 0.2944031 + * - 25 + - 203.259 + - 0.2467411 + * - 26 + - 212.15 + - 0.2003501 + * - 27 + - 218.776 + - 0.1562241 + * - 28 + - 223.898 + - 0.1136021 + * - 29 + - 224.363 + - 0.06372006 + * - 30 + - 216.865 + - 0.02801004 + * - 31 + - 201.192 + - 0.006960025 + * - 32 + - 176.93 + - 8.175413e-09 + * - 33 + - 150.393 + - 0.0 + * - 34 + - 127.837 + - 0.0 + * - 35 + - 108.663 + - 0.0 + * - 36 + - 92.36572 + - 0.0 + * - 37 + - 78.51231 + - 0.0 + * - 38 + - 66.60341 + - 0.0 + * - 39 + - 56.38791 + - 0.0 + * - 40 + - 47.64391 + - 0.0 + * - 41 + - 40.17541 + - 0.0 + * - 42 + - 33.81001 + - 0.0 + * - 43 + - 28.36781 + - 0.0 + * - 44 + - 23.73041 + - 0.0 + * - 45 + - 19.7916 + - 0.0 + * - 46 + - 16.4571 + - 0.0 + * - 47 + - 13.6434 + - 0.0 + * - 48 + - 11.2769 + - 0.0 + * - 49 + - 9.292942 + - 0.0 + * - 50 + - 7.619842 + - 0.0 + * - 51 + - 6.216801 + - 0.0 + * - 52 + - 5.046801 + - 0.0 + * - 53 + - 4.076571 + - 0.0 + * - 54 + - 3.276431 + - 0.0 + * - 55 + - 2.620211 + - 0.0 + * - 56 + - 2.08497 + - 0.0 + * - 57 + - 1.65079 + - 0.0 + * - 58 + - 1.30051 + - 0.0 + * - 59 + - 1.01944 + - 0.0 + * - 60 + - 0.7951341 + - 0.0 + * - 61 + - 0.6167791 + - 0.0 + * - 62 + - 0.4758061 + - 0.0 + * - 63 + - 0.3650411 + - 0.0 + * - 64 + - 0.2785261 + - 0.0 + * - 65 + - 0.211349 + - 0.0 + * - 66 + - 0.159495 + - 0.0 + * - 67 + - 0.119703 + - 0.0 + * - 68 + - 0.08934502 + - 0.0 + * - 69 + - 0.06600001 + - 0.0 + * - 70 + - 0.04758501 + - 0.0 + * - 71 + - 0.0327 + - 0.0 + * - 72 + - 0.02 + - 0.0 + * - 73 + - 0.01 + - 0.0 + +.. _gcc-vgrids-gmao-72-prs-alt: + +Pressures and altitudes +~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists pressures and altitudes of the 72 layer grid for +a column at atmospheric sea level. + +.. code-block:: text + + L Eta Edge Eta Mid Altitude Pressure + (unitless) (unitless) (km) (hPa) + ======================================================== + 0.000000 80.581 0.010 + 72 0.000005 78.146 0.015 + 0.000010 76.357 0.020 + 71 0.000016 74.594 0.026 + 0.000022 73.180 0.033 + 70 0.000030 71.812 0.040 + 0.000037 70.657 0.048 + 69 0.000046 69.440 0.057 + 0.000055 68.392 0.066 + 68 0.000067 67.243 0.078 + 0.000078 66.245 0.089 + 67 0.000093 65.115 0.105 + 0.000108 64.130 0.120 + 66 0.000128 63.004 0.140 + 0.000148 62.021 0.159 + 65 0.000173 60.902 0.185 + 0.000199 59.924 0.211 + 64 0.000232 58.816 0.245 + 0.000265 57.846 0.279 + 63 0.000308 56.752 0.322 + 0.000350 55.794 0.365 + 62 0.000405 54.717 0.420 + 0.000460 53.773 0.476 + 61 0.000529 52.716 0.546 + 0.000599 51.788 0.617 + 60 0.000687 50.754 0.706 + 0.000775 49.844 0.795 + 59 0.000886 48.835 0.907 + 0.000996 47.946 1.019 + 58 0.001135 46.962 1.160 + 0.001274 46.092 1.301 + 57 0.001446 45.134 1.476 + 0.001619 44.286 1.651 + 56 0.001834 43.355 1.868 + 0.002048 42.529 2.085 + 55 0.002312 41.627 2.353 + 0.002576 40.825 2.620 + 54 0.002900 39.951 2.948 + 0.003224 39.173 3.276 + 53 0.003619 38.328 3.677 + 0.004013 37.574 4.077 + 52 0.004492 36.759 4.562 + 0.004971 36.030 5.047 + 51 0.005548 35.244 5.632 + 0.006126 34.539 6.217 + 50 0.006818 33.782 6.918 + 0.007510 33.101 7.620 + 49 0.008336 32.372 8.456 + 0.009162 31.716 9.293 + 48 0.010141 31.015 10.285 + 0.011120 30.382 11.277 + 47 0.012287 29.701 12.460 + 0.013455 29.085 13.643 + 46 0.014844 28.423 15.050 + 0.016232 27.824 16.457 + 45 0.017878 27.180 18.124 + 0.019523 26.596 19.792 + 44 0.021467 25.971 21.761 + 0.023410 25.402 23.730 + 43 0.025699 24.794 26.049 + 0.027987 24.240 28.368 + 42 0.030673 23.648 31.089 + 0.033358 23.108 33.810 + 41 0.036499 22.531 36.993 + 0.039641 22.004 40.175 + 40 0.043326 21.438 43.910 + 0.047011 20.920 47.644 + 39 0.051326 20.364 52.016 + 0.055641 19.855 56.388 + 38 0.060682 19.309 61.496 + 0.065723 18.807 66.603 + 37 0.071600 18.269 72.558 + 0.077477 17.773 78.512 + 36 0.084313 17.243 85.439 + 0.091149 16.753 92.366 + 35 0.099191 16.222 100.514 + 0.107233 15.731 108.663 + 34 0.116695 15.198 118.250 + 0.126157 14.706 127.837 + 33 0.137287 14.170 139.115 + 0.148418 13.674 150.393 + 32 0.161513 13.134 163.661 + 0.174608 12.633 176.930 + 31 0.190061 12.086 192.587 + 0.205513 11.578 208.244 + 30 0.223772 11.021 226.745 + 0.242032 10.504 245.246 + 29 0.263587 9.936 267.087 + 0.285142 9.409 288.927 + 28 0.309854 8.846 313.966 + 0.334566 8.320 339.005 + 27 0.353349 7.943 358.038 + 0.372133 7.582 377.070 + 26 0.390927 7.237 396.112 + 0.409720 6.905 415.155 + 25 0.428528 6.585 434.212 + 0.447337 6.277 453.269 + 24 0.466153 5.980 472.335 + 0.484970 5.692 491.401 + 23 0.503795 5.413 510.475 + 0.522620 5.142 529.550 + 22 0.541449 4.879 548.628 + 0.560278 4.623 567.706 + 21 0.579115 4.375 586.793 + 0.597953 4.132 605.880 + 20 0.616790 3.896 624.967 + 0.635628 3.665 644.054 + 19 0.654471 3.439 663.146 + 0.673314 3.219 682.239 + 18 0.685878 3.074 694.969 + 0.698442 2.932 707.699 + 17 0.711006 2.792 720.429 + 0.723570 2.654 733.160 + 16 0.736134 2.517 745.890 + 0.748698 2.382 758.621 + 15 0.761265 2.249 771.354 + 0.773832 2.118 784.088 + 14 0.786400 1.988 796.822 + 0.798967 1.860 809.556 + 13 0.809021 1.759 819.743 + 0.819075 1.659 829.929 + 12 0.826616 1.584 837.570 + 0.834157 1.510 845.211 + 11 0.841698 1.436 852.852 + 0.849239 1.363 860.493 + 10 0.856781 1.290 868.135 + 0.864323 1.218 875.776 + 9 0.871864 1.146 883.418 + 0.879406 1.075 891.059 + 8 0.886948 1.004 898.701 + 0.894489 0.934 906.342 + 7 0.902031 0.864 913.984 + 0.909573 0.795 921.626 + 6 0.917116 0.726 929.268 + 0.924658 0.657 936.911 + 5 0.932200 0.589 944.553 + 0.939743 0.521 952.195 + 4 0.947285 0.454 959.837 + 0.954828 0.387 967.480 + 3 0.962370 0.320 975.122 + 0.969913 0.254 982.765 + 2 0.977456 0.189 990.408 + 0.984999 0.123 998.051 + 1 0.992500 0.058 1005.650 + 1.000000 -0.006 1013.250 + +.. _gcc-vgrids-gmao-47: + +47-layer reduced vertical grid +------------------------------ + +In order to save computational resources, GEOS-Chem Classic can collapse +the :ref:`gcc-vgrids-gmao-72` down to a 47-level grid (with 48 edges) +"on-the-fly". Groups of 2 and 4 levels are lumped together starting at +~70 hPa. See the table below for more information. + +.. _gcc-vgrids-gmao-47-ind: + +Indexing +~~~~~~~~ + +.. list-table:: + :header-rows: 1 + + * - Instance + - Surface level + - Top-of-atm level + - Direction + * - GEOS-Chem Classic using GMAO met + - 1 + - 47 + - :literal:`positive:up` + +.. _gcc-vgrids-gmao-47-lump: + +Lumping of vertical levels +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 47-level reduced vertical grid + + Bottom Bottom # levels + edge of edge prs lumped + level (hPa) together + + PTOP 0.010 + 47 0.066 4 + 46 0.211 4 + 45 0.617 4 + 44 1.651 4 + 43 4.077 4 + 42 9.293 4 + 41 19.792 4 + 40 28.368 2 + 39 40.175 2 + 38 56.388 2 + 37 78.512 2 + %%%% START LUMPING LEVELS ABOVE HERE %%%%% + 1-36 Levels are the same as in the 72-layer grid + +.. _gcc-vgrids-gmao-47-ab: + +:math:`A_p` and :math:`B_p` +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists the :math:`A_p` and :math:`B_p` parameters that +define the 47 level reduced vertical grid. The level edge indices run +from 1 (surface) to 48 (top-of atmosphere). + +.. list-table:: + :header-rows: 1 + + * - Level edge index + - :math:`A_p` (hPa) + - :math:`B_p` (unitless) + * - 1 + - 0.0 + - 1.0 + * - 2 + - 0.04804826 + - 0.984952 + * - 3 + - 6.593752 + - 0.963406 + * - 4 + - 13.1348 + - 0.941865 + * - 5 + - 19.61311 + - 0.920387 + * - 6 + - 26.09201 + - 0.898908 + * - 7 + - 32.57081 + - 0.877429 + * - 8 + - 38.98201 + - 0.856018 + * - 9 + - 45.33901 + - 0.8346609 + * - 10 + - 51.69611 + - 0.8133039 + * - 11 + - 58.05321 + - 0.7919469 + * - 12 + - 64.36264 + - 0.7706375 + * - 13 + - 70.62198 + - 0.7493782 + * - 14 + - 78.83422 + - 0.721166 + * - 15 + - 89.09992 + - 0.6858999 + * - 16 + - 99.36521 + - 0.6506349 + * - 17 + - 109.1817 + - 0.6158184 + * - 18 + - 118.9586 + - 0.5810415 + * - 19 + - 128.6959 + - 0.5463042 + * - 20 + - 142.91 + - 0.4945902 + * - 21 + - 156.26 + - 0.4437402 + * - 22 + - 169.609 + - 0.3928911 + * - 23 + - 181.619 + - 0.3433811 + * - 24 + - 193.097 + - 0.2944031 + * - 25 + - 203.259 + - 0.2467411 + * - 26 + - 212.15 + - 0.2003501 + * - 27 + - 218.776 + - 0.1562241 + * - 28 + - 223.898 + - 0.1136021 + * - 29 + - 224.363 + - 0.06372006 + * - 30 + - 216.865 + - 0.02801004 + * - 31 + - 201.192 + - 0.006960025 + * - 32 + - 176.93 + - 8.175413e-09 + * - 33 + - 150.393 + - 0.0 + * - 34 + - 127.837 + - 0.0 + * - 35 + - 108.663 + - 0.0 + * - 36 + - 92.36572 + - 0.0 + * - 37 + - 78.51231 + - 0.0 + * - 38 + - 56.38791 + - 0.0 + * - 39 + - 40.17541 + - 0.0 + * - 40 + - 28.36781 + - 0.0 + * - 41 + - 19.7916 + - 0.0 + * - 42 + - 9.292942 + - 0.0 + * - 43 + - 4.076571 + - 0.0 + * - 44 + - 1.65079 + - 0.0 + * - 45 + - 0.6167791 + - 0.0 + * - 46 + - 0.211349 + - 0.0 + * - 47 + - 0.06600001 + - 0.0 + * - 48 + - 0.01 + - 0.0 + +.. _gcc-vgrids-gmao-47-prs-alt: + +Pressures and altitudes +~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists pressures and altitudes of the 47 layer grid for +a column at atmospheric sea level. + +.. code-block:: text + + L Eta Edge Eta Mid Altitude Pressure + (unitless) (unitless) (km) (hPa) + ======================================================== + 0.000000 80.581 0.010 + 47 0.000028 72.180 0.038 + 0.000055 68.392 0.066 + 46 0.000127 63.053 0.139 + 0.000199 59.924 0.211 + 45 0.000399 54.834 0.414 + 0.000599 51.788 0.617 + 44 0.001109 47.135 1.134 + 0.001619 44.286 1.651 + 43 0.002816 40.166 2.864 + 0.004013 37.574 4.077 + 42 0.006588 34.024 6.685 + 0.009162 31.716 9.293 + 41 0.014342 28.654 14.542 + 0.019523 26.596 19.792 + 40 0.023755 25.307 24.080 + 0.027987 24.240 28.368 + 39 0.033814 23.020 34.272 + 0.039641 22.004 40.175 + 38 0.047641 20.836 48.282 + 0.055641 19.855 56.388 + 37 0.066559 18.727 67.450 + 0.077477 17.773 78.512 + 36 0.084313 17.243 85.439 + 0.091149 16.753 92.366 + 35 0.099191 16.222 100.514 + 0.107233 15.731 108.663 + 34 0.116695 15.198 118.250 + 0.126157 14.706 127.837 + 33 0.137287 14.170 139.115 + 0.148418 13.674 150.393 + 32 0.161513 13.134 163.661 + 0.174608 12.633 176.930 + 31 0.190061 12.086 192.587 + 0.205513 11.578 208.244 + 30 0.223772 11.021 226.745 + 0.242032 10.504 245.246 + 29 0.263587 9.936 267.087 + 0.285142 9.409 288.927 + 28 0.309854 8.846 313.966 + 0.334566 8.320 339.005 + 27 0.353349 7.943 358.038 + 0.372133 7.582 377.070 + 26 0.390927 7.237 396.112 + 0.409720 6.905 415.155 + 25 0.428528 6.585 434.212 + 0.447337 6.277 453.269 + 24 0.466153 5.980 472.335 + 0.484970 5.692 491.401 + 23 0.503795 5.413 510.475 + 0.522620 5.142 529.550 + 22 0.541449 4.879 548.628 + 0.560278 4.623 567.706 + 21 0.579115 4.375 586.793 + 0.597953 4.132 605.880 + 20 0.616790 3.896 624.967 + 0.635628 3.665 644.054 + 19 0.654471 3.439 663.146 + 0.673314 3.219 682.239 + 18 0.685878 3.074 694.969 + 0.698442 2.932 707.699 + 17 0.711006 2.792 720.429 + 0.723570 2.654 733.160 + 16 0.736134 2.517 745.890 + 0.748698 2.382 758.621 + 15 0.761265 2.249 771.354 + 0.773832 2.118 784.088 + 14 0.786400 1.988 796.822 + 0.798967 1.860 809.556 + 13 0.809021 1.759 819.743 + 0.819075 1.659 829.929 + 12 0.826616 1.584 837.570 + 0.834157 1.510 845.211 + 11 0.841698 1.436 852.852 + 0.849239 1.363 860.493 + 10 0.856781 1.290 868.135 + 0.864323 1.218 875.776 + 9 0.871864 1.146 883.418 + 0.879406 1.075 891.059 + 8 0.886948 1.004 898.701 + 0.894489 0.934 906.342 + 7 0.902031 0.864 913.984 + 0.909573 0.795 921.626 + 6 0.917116 0.726 929.268 + 0.924658 0.657 936.911 + 5 0.932200 0.589 944.553 + 0.939743 0.521 952.195 + 4 0.947285 0.454 959.837 + 0.954828 0.387 967.480 + 3 0.962370 0.320 975.122 + 0.969913 0.254 982.765 + 2 0.977456 0.189 990.408 + 0.984999 0.123 998.051 + 1 0.992500 0.058 1005.650 + 1.000000 -0.006 1013.250 + +========================================= +Vertical grids for GCAP2/GISS meteorology +========================================= + +.. _gcc-vgrids-gcap-102: + +102-level vertical grid +----------------------- + +GCAP2/GISS meteorology is produced on a grid with 102 vertical +levels. To reduce the amount of computational overhead, GEOS-Chem +Classic can regrid this "on-the-fly" to ether a +:ref:`gcc-vgrids-gcap-74` or a :ref:`gcc-vgrids-gcap-40`. + +.. _gcc-vgrids-gcap-102-ind: + +Indexing +~~~~~~~~ + +.. list-table:: + :header-rows: 1 + + * - Instance + - Surface level + - Top-of-atm level + - Direction + * - GEOS-Chem Classic using GCAP2 met + - 1 + - 102 + - :literal:`positive:up` + +.. _gcc-vgrids-gcap-102-ab: + +:math:`A_p` and :math:`B_p` +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists the :math:`A_p` and :math:`B_p` parameters that +define the 102 level vertical grid. The level edge indices run from 1 +(surface) to 103 (top-of atmosphere). + +.. list-table:: + :header-rows: 1 + + * - Level edge index + - :math:`A_p` (hPa) + - :math:`B_p` (unitless) + + * - 1 + - 0.0 + - 1.0 + * - 2 + - 2.7871507 + - 0.98192363 + * - 3 + - 5.5743014 + - 0.96384725 + * - 4 + - 8.3614521 + - 0.94577088 + * - 5 + - 11.1486028 + - 0.92769451 + * - 6 + - 13.9357536 + - 0.90961814 + * - 7 + - 16.7229043 + - 0.89154176 + * - 8 + - 19.510055 + - 0.87346539 + * - 9 + - 22.2972057 + - 0.85538902 + * - 10 + - 25.0843564 + - 0.83731265 + * - 11 + - 27.8715071 + - 0.81923627 + * - 12 + - 30.6586578 + - 0.8011599 + * - 13 + - 33.4458085 + - 0.78308353 + * - 14 + - 36.2329593 + - 0.76500716 + * - 15 + - 39.02011 + - 0.74693078 + * - 16 + - 41.8087123 + - 0.728845 + * - 17 + - 44.6089278 + - 0.71068389 + * - 18 + - 47.4534183 + - 0.69223563 + * - 19 + - 50.4082336 + - 0.67307185 + * - 20 + - 53.5662786 + - 0.65259001 + * - 21 + - 57.009571 + - 0.63025815 + * - 22 + - 60.7533531 + - 0.60597744 + * - 23 + - 64.7323011 + - 0.58017154 + * - 24 + - 68.8549615 + - 0.55343357 + * - 25 + - 73.0567364 + - 0.5261825 + * - 26 + - 77.2969797 + - 0.49868193 + * - 27 + - 81.5364973 + - 0.47118607 + * - 28 + - 85.734643 + - 0.44395854 + * - 29 + - 89.8565776 + - 0.41722528 + * - 30 + - 93.8754457 + - 0.39116047 + * - 31 + - 97.7709243 + - 0.36589591 + * - 32 + - 101.5277712 + - 0.34153047 + * - 33 + - 105.1350991 + - 0.31813474 + * - 34 + - 108.5878272 + - 0.2957417 + * - 35 + - 111.8859556 + - 0.27435132 + * - 36 + - 115.03021 + - 0.25395891 + * - 37 + - 118.0249453 + - 0.23453623 + * - 38 + - 120.8854039 + - 0.21598441 + * - 39 + - 123.6326345 + - 0.19816694 + * - 40 + - 126.2811535 + - 0.18098968 + * - 41 + - 128.8360417 + - 0.16441967 + * - 42 + - 131.2987506 + - 0.1484475 + * - 43 + - 133.6736353 + - 0.13304493 + * - 44 + - 135.9708571 + - 0.11814604 + * - 45 + - 138.2013035 + - 0.10368024 + * - 46 + - 140.3700552 + - 0.08961456 + * - 47 + - 142.481467 + - 0.07592077 + * - 48 + - 144.5457005 + - 0.06253295 + * - 49 + - 146.5692881 + - 0.04940875 + * - 50 + - 148.5464231 + - 0.03658583 + * - 51 + - 150.4712991 + - 0.02410183 + * - 52 + - 152.3497225 + - 0.01191911 + * - 53 + - 154.1875 + - 0.0 + * - 54 + - 144.546875 + - 0.0 + * - 55 + - 135.1875 + - 0.0 + * - 56 + - 126.078125 + - 0.0 + * - 57 + - 117.1914062 + - 0.0 + * - 58 + - 108.5859375 + - 0.0 + * - 59 + - 100.3671875 + - 0.0 + * - 60 + - 92.5898438 + - 0.0 + * - 61 + - 85.2265625 + - 0.0 + * - 62 + - 78.2226562 + - 0.0 + * - 63 + - 71.5546875 + - 0.0 + * - 64 + - 65.2226562 + - 0.0 + * - 65 + - 59.2226562 + - 0.0 + * - 66 + - 53.5546875 + - 0.0 + * - 67 + - 48.2226562 + - 0.0 + * - 68 + - 43.2226562 + - 0.0 + * - 69 + - 38.5546875 + - 0.0 + * - 70 + - 34.2226562 + - 0.0 + * - 71 + - 30.2226562 + - 0.0 + * - 72 + - 26.5507812 + - 0.0 + * - 73 + - 23.1875 + - 0.0 + * - 74 + - 20.078125 + - 0.0 + * - 75 + - 17.1896562 + - 0.0 + * - 76 + - 14.5684375 + - 0.0 + * - 77 + - 12.2865742 + - 0.0 + * - 78 + - 10.3573086 + - 0.0 + * - 79 + - 8.735375 + - 0.0 + * - 80 + - 7.3664922 + - 0.0 + * - 81 + - 6.2100156 + - 0.0 + * - 82 + - 5.2343633 + - 0.0 + * - 83 + - 4.4119297 + - 0.0 + * - 84 + - 3.7186797 + - 0.0 + * - 85 + - 3.1341479 + - 0.0 + * - 86 + - 2.6404328 + - 0.0 + * - 87 + - 2.2207877 + - 0.0 + * - 88 + - 1.8587369 + - 0.0 + * - 89 + - 1.5477125 + - 0.0 + * - 90 + - 1.2782115 + - 0.0 + * - 91 + - 1.0427319 + - 0.0 + * - 92 + - 0.8367716 + - 0.0 + * - 93 + - 0.6514691 + - 0.0 + * - 94 + - 0.4772511 + - 0.0 + * - 95 + - 0.3168814 + - 0.0 + * - 96 + - 0.1785988 + - 0.0 + * - 97 + - 0.1 + - 0.0 + * - 98 + - 0.056 + - 0.0 + * - 99 + - 0.032 + - 0.0 + * - 100 + - 0.018 + - 0.0 + * - 101 + - 0.01 + - 0.0 + * - 102 + - 0.005 + - 0.0 + * - 103 + - 0.002 + - 0.0 + +.. _gcc-vgrids-gcap-74: + +74-level reduced vertical grid +------------------------------ + +In order to save computational resources, GEOS-Chem Classic can collapse +the :ref:`gcc-vgrids-gcap-102` down to a 74-level grid (with 75 edges) +"on-the-fly". Groups of 2 and 4 levels are lumped together starting at +~85 hPa. See the table below for more information. + +.. _gcc-vgrids-gcap-74-ind: + +Indexing +~~~~~~~~ + +.. list-table:: + :header-rows: 1 + + * - Instance + - Surface level + - Top-of-atm level + - Direction + * - GEOS-Chem Classic using GCAP2 met + - 1 + - 74 + - :literal:`positive:up` + +.. _gcc-vgrids-gcap-74-lump: + +Lumping of vertical levels +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 74-level GISS grid (condensed from 102-layer grid) + + Bottom Bottom # levels + edge of edge prs lumped + level (hPa) together + + PTOP 0.0020000 + 74 0.0320000 4 + 73 0.3168814 4 + 72 1.0427319 4 + 71 2.2207877 4 + 70 4.4119297 4 + 69 8.7353750 4 + 68 17.1896562 4 + 67 23.1875000 2 + 66 30.2226562 2 + 65 38.5546875 2 + 64 48.2226562 2 + 63 59.2226562 2 + 62 71.5546875 2 + 61 85.2265625 2 + %%%% START LUMPING LEVELS ABOVE HERE %%%%% + 1-60 Levels are the same as for the 102 level vertical grid + +.. _gcc-vgrids-gcap-74-ab: + +:math:`A_p` and :math:`B_p` +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists the :math:`A_p` and :math:`B_p` parameters that +define the 74-level vertical grid. The level edge indices run from 1 +(surface) to 75 (top-of atmosphere). + +.. list-table:: + :header-rows: 1 + + * - Level edge index + - :math:`A_p` (hPa) + - :math:`B_p` (unitless) + * - 1 + - 0.0 + - 1.0 + * - 2 + - 2.7871507 + - 0.98192363 + * - 3 + - 5.5743014 + - 0.96384725 + * - 4 + - 8.3614521 + - 0.94577088 + * - 5 + - 11.1486028 + - 0.92769451 + * - 6 + - 13.9357536 + - 0.90961814 + * - 7 + - 16.7229043 + - 0.89154176 + * - 8 + - 19.510055 + - 0.87346539 + * - 9 + - 22.2972057 + - 0.85538902 + * - 10 + - 25.0843564 + - 0.83731265 + * - 11 + - 27.8715071 + - 0.81923627 + * - 12 + - 30.6586578 + - 0.8011599 + * - 13 + - 33.4458085 + - 0.78308353 + * - 14 + - 36.2329593 + - 0.76500716 + * - 15 + - 39.02011 + - 0.74693078 + * - 16 + - 41.8087123 + - 0.728845 + * - 17 + - 44.6089278 + - 0.71068389 + * - 18 + - 47.4534183 + - 0.69223563 + * - 19 + - 50.4082336 + - 0.67307185 + * - 20 + - 53.5662786 + - 0.65259001 + * - 21 + - 57.009571 + - 0.63025815 + * - 22 + - 60.7533531 + - 0.60597744 + * - 23 + - 64.7323011 + - 0.58017154 + * - 24 + - 68.8549615 + - 0.55343357 + * - 25 + - 73.0567364 + - 0.5261825 + * - 26 + - 77.2969797 + - 0.49868193 + * - 27 + - 81.5364973 + - 0.47118607 + * - 28 + - 85.734643 + - 0.44395854 + * - 29 + - 89.8565776 + - 0.41722528 + * - 30 + - 93.8754457 + - 0.39116047 + * - 31 + - 97.7709243 + - 0.36589591 + * - 32 + - 101.5277712 + - 0.34153047 + * - 33 + - 105.1350991 + - 0.31813474 + * - 34 + - 108.5878272 + - 0.2957417 + * - 35 + - 111.8859556 + - 0.27435132 + * - 36 + - 115.03021 + - 0.25395891 + * - 37 + - 118.0249453 + - 0.23453623 + * - 38 + - 120.8854039 + - 0.21598441 + * - 39 + - 123.6326345 + - 0.19816694 + * - 40 + - 126.2811535 + - 0.18098968 + * - 41 + - 128.8360417 + - 0.16441967 + * - 42 + - 131.2987506 + - 0.1484475 + * - 43 + - 133.6736353 + - 0.13304493 + * - 44 + - 135.9708571 + - 0.11814604 + * - 45 + - 138.2013035 + - 0.10368024 + * - 46 + - 140.3700552 + - 0.08961456 + * - 47 + - 142.481467 + - 0.07592077 + * - 48 + - 144.5457005 + - 0.06253295 + * - 49 + - 146.5692881 + - 0.04940875 + * - 50 + - 148.5464231 + - 0.03658583 + * - 51 + - 150.4712991 + - 0.02410183 + * - 52 + - 152.3497225 + - 0.01191911 + * - 53 + - 154.1875 + - 0.0 + * - 54 + - 144.546875 + - 0.0 + * - 55 + - 135.1875 + - 0.0 + * - 56 + - 126.078125 + - 0.0 + * - 57 + - 117.1914062 + - 0.0 + * - 58 + - 108.5859375 + - 0.0 + * - 59 + - 100.3671875 + - 0.0 + * - 60 + - 92.5898438 + - 0.0 + * - 61 + - 85.2265625 + - 0.0 + * - 62 + - 71.5546875 + - 0.0 + * - 63 + - 59.2226562 + - 0.0 + * - 64 + - 48.2226562 + - 0.0 + * - 65 + - 38.5546875 + - 0.0 + * - 66 + - 30.2226562 + - 0.0 + * - 67 + - 23.1875 + - 0.0 + * - 68 + - 17.1896562 + - 0.0 + * - 69 + - 8.735375 + - 0.0 + * - 70 + - 4.4119297 + - 0.0 + * - 71 + - 2.2207877 + - 0.0 + * - 72 + - 1.0427319 + - 0.0 + * - 73 + - 0.3168814 + - 0.0 + * - 74 + - 0.032 + - 0.0 + * - 75 + - 0.002 + - 0.0 + +.. _gcc-vgrids-gcap-40: + +40-level reduced vertical grid +------------------------------- + +In order to save computational resources, GEOS-Chem Classic can collapse +the :ref:`gcc-vgrids-gcap-102` down to a 40-level grid (with 41 edges) +"on-the-fly". + +.. _gcc-vgrids-gcap-40-ind: + +Indexing +~~~~~~~~ + +.. list-table:: + :header-rows: 1 + + * - Instance + - Surface level + - Top-of-atm level + - Direction + * - GEOS-Chem Classic using GCAP2 met + - 1 + - 40 + - :literal:`positive:up` + +.. _gcc-vgrids-gcap-40-ab: + +:math:`A_p` and :math:`B_p` +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The table below lists the :math:`A_p` and :math:`B_p` parameters that +define the 40-level vertical grid. The level edge indices run from 1 +(surface) to 41 (top-of atmosphere). + +.. list-table:: + :header-rows: 1 + + * - Level edge index + - :math:`A_p` (hPa) + - :math:`B_p` (unitless) + * - 1 + - 0.0 + - 1.0 + * - 2 + - 3.597122 + - 0.97601918 + * - 3 + - 7.553957 + - 0.94964029 + * - 4 + - 12.05036 + - 0.91966427 + * - 5 + - 16.906475 + - 0.88729017 + * - 6 + - 22.302158 + - 0.85131894 + * - 7 + - 28.597122 + - 0.80935252 + * - 8 + - 35.791367 + - 0.76139089 + * - 9 + - 43.884892 + - 0.70743405 + * - 10 + - 52.517986 + - 0.6498801 + * - 11 + - 61.510791 + - 0.58992806 + * - 12 + - 70.683453 + - 0.52877698 + * - 13 + - 80.035971 + - 0.46642686 + * - 14 + - 89.028777 + - 0.40647482 + * - 15 + - 97.661871 + - 0.34892086 + * - 16 + - 105.755396 + - 0.29496403 + * - 17 + - 113.309353 + - 0.24460432 + * - 18 + - 120.143885 + - 0.19904077 + * - 19 + - 126.258993 + - 0.15827338 + * - 20 + - 131.834532 + - 0.12110312 + * - 21 + - 136.870504 + - 0.08752998 + * - 22 + - 141.546763 + - 0.05635492 + * - 23 + - 145.863309 + - 0.02757794 + * - 24 + - 150.0 + - 0.0 + * - 25 + - 128.0 + - 0.0 + * - 26 + - 108.0 + - 0.0 + * - 27 + - 90.0 + - 0.0 + * - 28 + - 73.0 + - 0.0 + * - 29 + - 57.0 + - 0.0 + * - 30 + - 43.0 + - 0.0 + * - 31 + - 31.0 + - 0.0 + * - 32 + - 20.0 + - 0.0 + * - 33 + - 10.0 + - 0.0 + * - 34 + - 5.62 + - 0.0 + * - 35 + - 3.16 + - 0.0 + * - 36 + - 1.78 + - 0.0 + * - 37 + - 1.0 + - 0.0 + * - 38 + - 0.562 + - 0.0 + * - 39 + - 0.316 + - 0.0 + * - 40 + - 0.178 + - 0.0 + * - 41 + - 0.1 + - 0.0 From 4adebdfd43f1b6b5efe4b4be0955a58c0fe3fe14 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 4 Sep 2025 17:33:34 -0400 Subject: [PATCH 25/86] Add GEOS-Chem Classic horizontal grids (initial update docs/source/supplemental-guides/horizontal-grids.rst - Added documentation about GEOS-Chem Classic horizontal grids, migrated from the wiki docs/source/index.rst - Add horizontal-grids.rst to the Supplemental Guides toctree CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 3 +- docs/source/index.rst | 1 + .../supplemental-guides/horizontal-grids.rst | 645 ++++++++++++++++++ 3 files changed, 648 insertions(+), 1 deletion(-) create mode 100644 docs/source/supplemental-guides/horizontal-grids.rst diff --git a/CHANGELOG.md b/CHANGELOG.md index a0db4ca2c..6063788a8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,8 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] - TBD ### Added -- Added "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs (migrated from the GEOS-Chem wiki). +- Added "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs +- Added "GEOS-Chem Classic horiziontal grids" supplemental guide in ReadTheDocs ## [14.6.3] - 2025-07-28 ### Added diff --git a/docs/source/index.rst b/docs/source/index.rst index 725bb3614..54990910e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -82,6 +82,7 @@ modifications to GEOS-Chem Classic source code. :maxdepth: 4 supplemental-guides/directory-structure.rst + supplemental-guides/horizontal-grids.rst supplemental-guides/vertical-grids.rst supplemental-guides/run-script-examples.rst geos-chem-shared-docs/supplemental-guides/load-libraries-guide.rst diff --git a/docs/source/supplemental-guides/horizontal-grids.rst b/docs/source/supplemental-guides/horizontal-grids.rst new file mode 100644 index 000000000..6a82be7d0 --- /dev/null +++ b/docs/source/supplemental-guides/horizontal-grids.rst @@ -0,0 +1,645 @@ +.. _gcc-hgrids: + +################################## +GEOS-Chem Classic horizontal grids +################################## + +On this page we provide information about the horizontal grids used by +GEOS-Chem "Classic" simulations. For information about the vertical +coordinates used by GEOS-Chem, please see our Supplemental Guide +entitled :ref:`gcc-vgrids`. + +The FlexGrid feature of GEOS-Chem Classic allows you to specify the +global GEOS-Chem grid definitions (listed below), as well as +custom grids, at runtime. + +.. _gcc-hgrids-global-4x5: + +============ +Global grids +============ + +.. _gcc-hgrids-global-4x5: + +4° x 5° global grid +------------------- + +You can select this grid by specifying these settings in :ref:`cfg-gc-yml`: + +.. code-block:: yaml + + grid: + resolution: 4.0x5.0 + number_of_levels: 72 # You may also set this to 47 + 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: false + buffer_zone_NSEW: [0, 0, 0, 0] + +4° x 5° longitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -180.000 -175.000 -170.000 -165.000 -160.000 -155.000 -150.000 -145.000 + -140.000 -135.000 -130.000 -125.000 -120.000 -115.000 -110.000 -105.000 + -100.000 -95.000 -90.000 -85.000 -80.000 -75.000 -70.000 -65.000 + -60.000 -55.000 -50.000 -45.000 -40.000 -35.000 -30.000 -25.000 + -20.000 -15.000 -10.000 -5.000 0.000 5.000 10.000 15.000 + 20.000 25.000 30.000 35.000 40.000 45.000 50.000 55.000 + 60.000 65.000 70.000 75.000 80.000 85.000 90.000 95.000 + 100.000 105.000 110.000 115.000 120.000 125.000 130.000 135.000 + 140.000 145.000 150.000 155.000 160.000 165.000 170.000 175.000 + +4° x 5° latitude centers +~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -89.000 -86.000 -82.000 -78.000 -74.000 -70.000 -66.000 -62.000 + -58.000 -54.000 -50.000 -46.000 -42.000 -38.000 -34.000 -30.000 + -26.000 -22.000 -18.000 -14.000 -10.000 -6.000 -2.000 2.000 + 6.000 10.000 14.000 18.000 22.000 26.000 30.000 34.000 + 38.000 42.000 46.000 50.000 54.000 58.000 62.000 66.000 + 70.000 74.000 78.000 82.000 86.000 89.000 + +.. _gcc-hgrids-global-2x25: + +2° x 2.5° global grid +~~~~~~~~~~~~~~~~~~~~~ + +You can select this grid by specifying these settings in :ref:`cfg-gc-yml`: + +.. code-block:: yaml + + grid: + resolution: 2.0x2.5 + number_of_levels: 72 # You may also set this to 47 + 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: false + buffer_zone_NSEW: [0, 0, 0, 0] + +2° x 2.5° longitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -180.000 -177.500 -175.000 -172.500 -170.000 -167.500 -165.000 -162.500 + -160.000 -157.500 -155.000 -152.500 -150.000 -147.500 -145.000 -142.500 + -140.000 -137.500 -135.000 -132.500 -130.000 -127.500 -125.000 -122.500 + -120.000 -117.500 -115.000 -112.500 -110.000 -107.500 -105.000 -102.500 + -100.000 -97.500 -95.000 -92.500 -90.000 -87.500 -85.000 -82.500 + -80.000 -77.500 -75.000 -72.500 -70.000 -67.500 -65.000 -62.500 + -60.000 -57.500 -55.000 -52.500 -50.000 -47.500 -45.000 -42.500 + -40.000 -37.500 -35.000 -32.500 -30.000 -27.500 -25.000 -22.500 + -20.000 -17.500 -15.000 -12.500 -10.000 -7.500 -5.000 -2.500 + 0.000 2.500 5.000 7.500 10.000 12.500 15.000 17.500 + 20.000 22.500 25.000 27.500 30.000 32.500 35.000 37.500 + 40.000 42.500 45.000 47.500 50.000 52.500 55.000 57.500 + 60.000 62.500 65.000 67.500 70.000 72.500 75.000 77.500 + 80.000 82.500 85.000 87.500 90.000 92.500 95.000 97.500 + 100.000 102.500 105.000 107.500 110.000 112.500 115.000 117.500 + 120.000 122.500 125.000 127.500 130.000 132.500 135.000 137.500 + 140.000 142.500 145.000 147.500 150.000 152.500 155.000 157.500 + 160.000 162.500 165.000 167.500 170.000 172.500 175.000 177.500 + +2° x 2.5° latitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -89.500 -88.000 -86.000 -84.000 -82.000 -80.000 -78.000 -76.000 + -74.000 -72.000 -70.000 -68.000 -66.000 -64.000 -62.000 -60.000 + -58.000 -56.000 -54.000 -52.000 -50.000 -48.000 -46.000 -44.000 + -42.000 -40.000 -38.000 -36.000 -34.000 -32.000 -30.000 -28.000 + -26.000 -24.000 -22.000 -20.000 -18.000 -16.000 -14.000 -12.000 + -10.000 -8.000 -6.000 -4.000 -2.000 0.000 2.000 4.000 + 6.000 8.000 10.000 12.000 14.000 16.000 18.000 20.000 + 22.000 24.000 26.000 28.000 30.000 32.000 34.000 36.000 + 38.000 40.000 42.000 44.000 46.000 48.000 50.000 52.000 + 54.000 56.000 58.000 60.000 62.000 64.000 66.000 68.000 + 70.000 72.000 74.000 76.000 78.000 80.000 82.000 84.000 + 86.000 88.000 89.500 + +.. _gcc-hgrids-global-05: + +0.5° x 0.625° global grid +~~~~~~~~~~~~~~~~~~~~~~~~~ + +This is the native resolution of the `MERRA-2 `__ reanalysis +product from GMAO. + +The grid coordinates are constructed as follows: + +.. math:: + + Lon_{center}(I) = -180° + 0.625° \times ( I - 1 ),~~~~I = 1..576 + +.. math:: + + Lat_{center}(J) = -90° + 0.5° \times ( J - 1 ),~~~~J = 1..361 + +.. _gcc-hgrids-global-025: + +0.25° x 0.3125° global grid +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This is the native resolution of the `GEOS-5 "forward processing" (which +we call GEOS-FP) `__ operational data product from GMAO. + +The grid coordinates are computed as follows: + +.. math:: + + Lon_{center}(I) = -180° + 0.3125° \times ( I - 1 ),~~~~I = 1..1152 + +.. math:: + + Lat_{center}(I) = -90° + 0.25° \times ( J - 1 ),~~~~J = 1..721 + +============ +Nested grids +============ + +You may choose any nested grid region of interest to use with +GEOS-Chem Classic. You may also use one of the "traditional" nested +grids listed below. + +.. _gcc-hgrids-nested-05-as: + +0.5° x 0.625° AS nested grid +---------------------------- + +You can select this grid by specifying these settings in :ref:`cfg-gc-yml`: + +.. code-block:: yaml + + simulation: + ... + met_field: MERRA2 # or GEOSIT + ... + grid: + resolution: 0.5x0.625 + number_of_levels: 72 # You may also set this to 47 + longitude: + range: [60.0, 150.0] + center_at_180: true + latitude: + range: [-11.0, 55.0] + half_size_polar_boxes: true + nested_grid_simulation: + activate: false + buffer_zone_NSEW: [3, 3, 3, 3] # You may also use [6, 6, 6, 6] if you encounter non-convergence errors in chemistry + +0.5° x 0.625° AS longitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 60.000 60.625 61.250 61.875 62.500 63.125 63.750 64.375 + 65.000 65.625 66.250 66.875 67.500 68.125 68.750 69.375 + 70.000 70.625 71.250 71.875 72.500 73.125 73.750 74.375 + 75.000 75.625 76.250 76.875 77.500 78.125 78.750 79.375 + 80.000 80.625 81.250 81.875 82.500 83.125 83.750 84.375 + 85.000 85.625 86.250 86.875 87.500 88.125 88.750 89.375 + 90.000 90.625 91.250 91.875 92.500 93.125 93.750 94.375 + 95.000 95.625 96.250 96.875 97.500 98.125 98.750 99.375 + 100.000 100.625 101.250 101.875 102.500 103.125 103.750 104.375 + 105.000 105.625 106.250 106.875 107.500 108.125 108.750 109.375 + 110.000 110.625 111.250 111.875 112.500 113.125 113.750 114.375 + 115.000 115.625 116.250 116.875 117.500 118.125 118.750 119.375 + 120.000 120.625 121.250 121.875 122.500 123.125 123.750 124.375 + 125.000 125.625 126.250 126.875 127.500 128.125 128.750 129.375 + 130.000 130.625 131.250 131.875 132.500 133.125 133.750 134.375 + 135.000 135.625 136.250 136.875 137.500 138.125 138.750 139.375 + 140.000 140.625 141.250 141.875 142.500 143.125 143.750 144.375 + 145.000 145.625 146.250 146.875 147.500 148.125 148.750 149.375 + 150.000 + +0.5° x 0.625° AS latitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -11.000 -10.500 -10.000 -9.500 -9.000 -8.500 -8.000 -7.500 + -7.000 -6.500 -6.000 -5.500 -5.000 -4.500 -4.000 -3.500 + -3.000 -2.500 -2.000 -1.500 -1.000 -0.500 0.000 0.500 + 1.000 1.500 2.000 2.500 3.000 3.500 4.000 4.500 + 5.000 5.500 6.000 6.500 7.000 7.500 8.000 8.500 + 9.000 9.500 10.000 10.500 11.000 11.500 12.000 12.500 + 13.000 13.500 14.000 14.500 15.000 15.500 16.000 16.500 + 17.000 17.500 18.000 18.500 19.000 19.500 20.000 20.500 + 21.000 21.500 22.000 22.500 23.000 23.500 24.000 24.500 + 25.000 25.500 26.000 26.500 27.000 27.500 28.000 28.500 + 29.000 29.500 30.000 30.500 31.000 31.500 32.000 32.500 + 33.000 33.500 34.000 34.500 35.000 35.500 36.000 36.500 + 37.000 37.500 38.000 38.500 39.000 39.500 40.000 40.500 + 41.000 41.500 42.000 42.500 43.000 43.500 44.000 44.500 + 45.000 45.500 46.000 46.500 47.000 47.500 48.000 48.500 + 49.000 49.500 50.000 50.500 51.000 51.500 52.000 52.500 + 53.000 53.500 54.000 54.500 55.000 + +.. _gcc-hgrids-nested-05-eu: + +0.5 x 0.625 EU nested grid +-------------------------- + +You can select this grid by specifying these settings in +:ref:`cfg-gc-yml`: + +.. code-block:: yaml + + simulation: + ... + met_field: MERRA2 # or GEOSIT + ... + grid: + resolution: 0.5x0.625 + number_of_levels: 72 # You may also set this to 47 + longitude: + range: [ -30.0, 50.0] + center_at_180: true + latitude: + range: [30.0, 70.0] + half_size_polar_boxes: true + nested_grid_simulation: + activate: false + buffer_zone_NSEW: [3, 3, 3, 3] # You may also use [6, 6, 6, 6] if you encounter non-convergence errors in chemistry + + +0.5° x 0.625° EU longitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -30.000 -29.375 -28.750 -28.125 -27.500 -26.875 -26.250 -25.625 + -25.000 -24.375 -23.750 -23.125 -22.500 -21.875 -21.250 -20.625 + -20.000 -19.375 -18.750 -18.125 -17.500 -16.875 -16.250 -15.625 + -15.000 -14.375 -13.750 -13.125 -12.500 -11.875 -11.250 -10.625 + -10.000 -9.375 -8.750 -8.125 -7.500 -6.875 -6.250 -5.625 + -5.000 -4.375 -3.750 -3.125 -2.500 -1.875 -1.250 -0.625 + 0.000 0.625 1.250 1.875 2.500 3.125 3.750 4.375 + 5.000 5.625 6.250 6.875 7.500 8.125 8.750 9.375 + 10.000 10.625 11.250 11.875 12.500 13.125 13.750 14.375 + 15.000 15.625 16.250 16.875 17.500 18.125 18.750 19.375 + 20.000 20.625 21.250 21.875 22.500 23.125 23.750 24.375 + 25.000 25.625 26.250 26.875 27.500 28.125 28.750 29.375 + 30.000 30.625 31.250 31.875 32.500 33.125 33.750 34.375 + 35.000 35.625 36.250 36.875 37.500 38.125 38.750 39.375 + 40.000 40.625 41.250 41.875 42.500 43.125 43.750 44.375 + 45.000 45.625 46.250 46.875 47.500 48.125 48.750 49.375 + 50.000 + +0.5° x 0.625° EU latitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 30.000 30.500 31.000 31.500 32.000 32.500 33.000 33.500 + 34.000 34.500 35.000 35.500 36.000 36.500 37.000 37.500 + 38.000 38.500 39.000 39.500 40.000 40.500 41.000 41.500 + 42.000 42.500 43.000 43.500 44.000 44.500 45.000 45.500 + 46.000 46.500 47.000 47.500 48.000 48.500 49.000 49.500 + 50.000 50.500 51.000 51.500 52.000 52.500 53.000 53.500 + 54.000 54.500 55.000 55.500 56.000 56.500 57.000 57.500 + 58.000 58.500 59.000 59.500 60.000 60.500 61.000 61.500 + 62.000 62.500 63.000 63.500 64.000 64.500 65.000 65.500 + 66.000 66.500 67.000 67.500 68.000 68.500 69.000 69.500 + 70.000 + +.. _gcc-hgrids-nested-05-na: + +0.5 x 0.625 NA nested grid +-------------------------- + +You can select this grid by specifying these settings in +:ref:`cfg-gc-yml`: + +.. code-block:: yaml + + simulation: + ... + met_field: MERRA2 # or GEOSIT + ... + grid: + resolution: 0.5x0.625 + number_of_levels: 72 # You may also set this to 47 + longitude: + range: [-140.0, -40.0] + center_at_180: true + latitude: + range: [10.0, 70.0] + half_size_polar_boxes: true + nested_grid_simulation: + activate: false + buffer_zone_NSEW: [3, 3, 3, 3] # You may also use [6, 6, 6, 6] if you encounter non-convergence errors in chemistry + +0.5° x 0.625° NA longitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -140.000 -139.375 -138.750 -138.125 -137.500 -136.875 -136.250 -135.625 + -135.000 -134.375 -133.750 -133.125 -132.500 -131.875 -131.250 -130.625 + -130.000 -129.375 -128.750 -128.125 -127.500 -126.875 -126.250 -125.625 + -125.000 -124.375 -123.750 -123.125 -122.500 -121.875 -121.250 -120.625 + -120.000 -119.375 -118.750 -118.125 -117.500 -116.875 -116.250 -115.625 + -115.000 -114.375 -113.750 -113.125 -112.500 -111.875 -111.250 -110.625 + -110.000 -109.375 -108.750 -108.125 -107.500 -106.875 -106.250 -105.625 + -105.000 -104.375 -103.750 -103.125 -102.500 -101.875 -101.250 -100.625 + -100.000 -99.375 -98.750 -98.125 -97.500 -96.875 -96.250 -95.625 + -95.000 -94.375 -93.750 -93.125 -92.500 -91.875 -91.250 -90.625 + -90.000 -89.375 -88.750 -88.125 -87.500 -86.875 -86.250 -85.625 + -85.000 -84.375 -83.750 -83.125 -82.500 -81.875 -81.250 -80.625 + -80.000 -79.375 -78.750 -78.125 -77.500 -76.875 -76.250 -75.625 + -75.000 -74.375 -73.750 -73.125 -72.500 -71.875 -71.250 -70.625 + -70.000 -69.375 -68.750 -68.125 -67.500 -66.875 -66.250 -65.625 + -65.000 -64.375 -63.750 -63.125 -62.500 -61.875 -61.250 -60.625 + -60.000 -59.375 -58.750 -58.125 -57.500 -56.875 -56.250 -55.625 + -55.000 -54.375 -53.750 -53.125 -52.500 -51.875 -51.250 -50.625 + -50.000 -49.375 -48.750 -48.125 -47.500 -46.875 -46.250 -45.625 + -45.000 -44.375 -43.750 -43.125 -42.500 -41.875 -41.250 -40.625 + -40.000 + +0.5° x 0.625° NA latitude centers +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 10.000 10.500 11.000 11.500 12.000 12.500 13.000 13.500 + 14.000 14.500 15.000 15.500 16.000 16.500 17.000 17.500 + 18.000 18.500 19.000 19.500 20.000 20.500 21.000 21.500 + 22.000 22.500 23.000 23.500 24.000 24.500 25.000 25.500 + 26.000 26.500 27.000 27.500 28.000 28.500 29.000 29.500 + 30.000 30.500 31.000 31.500 32.000 32.500 33.000 33.500 + 34.000 34.500 35.000 35.500 36.000 36.500 37.000 37.500 + 38.000 38.500 39.000 39.500 40.000 40.500 41.000 41.500 + 42.000 42.500 43.000 43.500 44.000 44.500 45.000 45.500 + 46.000 46.500 47.000 47.500 48.000 48.500 49.000 49.500 + 50.000 50.500 51.000 51.500 52.000 52.500 53.000 53.500 + 54.000 54.500 55.000 55.500 56.000 56.500 57.000 57.500 + 58.000 58.500 59.000 59.500 60.000 60.500 61.000 61.500 + 62.000 62.500 63.000 63.500 64.000 64.500 65.000 65.500 + 66.000 66.500 67.000 67.500 68.000 68.500 69.000 69.500 + 70.000 + + +0.25 x 0.3125 CH nested grid +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. figure:: GEOSFP_025x03125_CH.png + :alt: GEOSFP_025x03125_CH.png + + GEOSFP_025x03125_CH.png + +This is the `GEOS-FP `__ native-resolution nested-grid over +China. + +`This grid may be specified via FlexGrid with these settings in +input.geos `__ (in +GEOS-Chem 12.4.0 and later). + +0.25° x 0.3125° CH longitude centers: + + 70.0000 70.3125 70.6250 70.9375 71.2500 71.5625 71.8750 72.1875 + 72.5000 72.8125 73.1250 73.4375 73.7500 74.0625 74.3750 74.6875 + 75.0000 75.3125 75.6250 75.9375 76.2500 76.5625 76.8750 77.1875 + 77.5000 77.8125 78.1250 78.4375 78.7500 79.0625 79.3750 79.6875 + 80.0000 80.3125 80.6250 80.9375 81.2500 81.5625 81.8750 82.1875 + 82.5000 82.8125 83.1250 83.4375 83.7500 84.0625 84.3750 84.6875 + 85.0000 85.3125 85.6250 85.9375 86.2500 86.5625 86.8750 87.1875 + 87.5000 87.8125 88.1250 88.4375 88.7500 89.0625 89.3750 89.6875 + 90.0000 90.3125 90.6250 90.9375 91.2500 91.5625 91.8750 92.1875 + 92.5000 92.8125 93.1250 93.4375 93.7500 94.0625 94.3750 94.6875 + 95.0000 95.3125 95.6250 95.9375 96.2500 96.5625 96.8750 97.1875 + 97.5000 97.8125 98.1250 98.4375 98.7500 99.0625 99.3750 99.6875 + 100.0000 100.3125 100.6250 100.9375 101.2500 101.5625 101.8750 102.1875 + 102.5000 102.8125 103.1250 103.4375 103.7500 104.0625 104.3750 104.6875 + 105.0000 105.3125 105.6250 105.9375 106.2500 106.5625 106.8750 107.1875 + 107.5000 107.8125 108.1250 108.4375 108.7500 109.0625 109.3750 109.6875 + 110.0000 110.3125 110.6250 110.9375 111.2500 111.5625 111.8750 112.1875 + 112.5000 112.8125 113.1250 113.4375 113.7500 114.0625 114.3750 114.6875 + 115.0000 115.3125 115.6250 115.9375 116.2500 116.5625 116.8750 117.1875 + 117.5000 117.8125 118.1250 118.4375 118.7500 119.0625 119.3750 119.6875 + 120.0000 120.3125 120.6250 120.9375 121.2500 121.5625 121.8750 122.1875 + 122.5000 122.8125 123.1250 123.4375 123.7500 124.0625 124.3750 124.6875 + 125.0000 125.3125 125.6250 125.9375 126.2500 126.5625 126.8750 127.1875 + 127.5000 127.8125 128.1250 128.4375 128.7500 129.0625 129.3750 129.6875 + 130.0000 130.3125 130.6250 130.9375 131.2500 131.5625 131.8750 132.1875 + 132.5000 132.8125 133.1250 133.4375 133.7500 134.0625 134.3750 134.6875 + 135.0000 135.3125 135.6250 135.9375 136.2500 136.5625 136.8750 137.1875 + 137.5000 137.8125 138.1250 138.4375 138.7500 139.0625 139.3750 139.6875 + 140.0000 + +0.25° x 0.3125° CH latitude centers: + + 15.0000 15.2500 15.5000 15.7500 16.0000 16.2500 16.5000 16.7500 + 17.0000 17.2500 17.5000 17.7500 18.0000 18.2500 18.5000 18.7500 + 19.0000 19.2500 19.5000 19.7500 20.0000 20.2500 20.5000 20.7500 + 21.0000 21.2500 21.5000 21.7500 22.0000 22.2500 22.5000 22.7500 + 23.0000 23.2500 23.5000 23.7500 24.0000 24.2500 24.5000 24.7500 + 25.0000 25.2500 25.5000 25.7500 26.0000 26.2500 26.5000 26.7500 + 27.0000 27.2500 27.5000 27.7500 28.0000 28.2500 28.5000 28.7500 + 29.0000 29.2500 29.5000 29.7500 30.0000 30.2500 30.5000 30.7500 + 31.0000 31.2500 31.5000 31.7500 32.0000 32.2500 32.5000 32.7500 + 33.0000 33.2500 33.5000 33.7500 34.0000 34.2500 34.5000 34.7500 + 35.0000 35.2500 35.5000 35.7500 36.0000 36.2500 36.5000 36.7500 + 37.0000 37.2500 37.5000 37.7500 38.0000 38.2500 38.5000 38.7500 + 39.0000 39.2500 39.5000 39.7500 40.0000 40.2500 40.5000 40.7500 + 41.0000 41.2500 41.5000 41.7500 42.0000 42.2500 42.5000 42.7500 + 43.0000 43.2500 43.5000 43.7500 44.0000 44.2500 44.5000 44.7500 + 45.0000 45.2500 45.5000 45.7500 46.0000 46.2500 46.5000 46.7500 + 47.0000 47.2500 47.5000 47.7500 48.0000 48.2500 48.5000 48.7500 + 49.0000 49.2500 49.5000 49.7500 50.0000 50.2500 50.5000 50.7500 + 51.0000 51.2500 51.5000 51.7500 52.0000 52.2500 52.5000 52.7500 + 53.0000 53.2500 53.5000 53.7500 54.0000 54.2500 54.5000 54.7500 + 55.0000 + +.. _x_0.3125_eu_nested_grid: + +0.25 x 0.3125 EU nested grid +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This is the `GEOS-FP `__ native-resolution nested-grid over +Europe. + +`This grid may be specified via FlexGrid with these settings in +input.geos `__ (in +GEOS-Chem 12.4.0 and later). + +.. figure:: GEOSFP_025x03125_EU.png + :alt: GEOSFP_025x03125_EU.png + + GEOSFP_025x03125_EU.png + +0.25° x 0.3125° EU longitude centers: + + -15.0000 -14.6875 -14.3750 -14.0625 -13.7500 -13.4375 -13.1250 -12.8125 + -12.5000 -12.1875 -11.8750 -11.5625 -11.2500 -10.9375 -10.6250 -10.3125 + -10.0000 -9.6875 -9.3750 -9.0625 -8.7500 -8.4375 -8.1250 -7.8125 + -7.5000 -7.1875 -6.8750 -6.5625 -6.2500 -5.9375 -5.6250 -5.3125 + -5.0000 -4.6875 -4.3750 -4.0625 -3.7500 -3.4375 -3.1250 -2.8125 + -2.5000 -2.1875 -1.8750 -1.5625 -1.2500 -0.9375 -0.6250 -0.3125 + 0.0000 0.3125 0.6250 0.9375 1.2500 1.5625 1.8750 2.1875 + 2.5000 2.8125 3.1250 3.4375 3.7500 4.0625 4.3750 4.6875 + 5.0000 5.3125 5.6250 5.9375 6.2500 6.5625 6.8750 7.1875 + 7.5000 7.8125 8.1250 8.4375 8.7500 9.0625 9.3750 9.6875 + 10.0000 10.3125 10.6250 10.9375 11.2500 11.5625 11.8750 12.1875 + 12.5000 12.8125 13.1250 13.4375 13.7500 14.0625 14.3750 14.6875 + 15.0000 15.3125 15.6250 15.9375 16.2500 16.5625 16.8750 17.1875 + 17.5000 17.8125 18.1250 18.4375 18.7500 19.0625 19.3750 19.6875 + 20.0000 20.3125 20.6250 20.9375 21.2500 21.5625 21.8750 22.1875 + 22.5000 22.8125 23.1250 23.4375 23.7500 24.0625 24.3750 24.6875 + 25.0000 25.3125 25.6250 25.9375 26.2500 26.5625 26.8750 27.1875 + 27.5000 27.8125 28.1250 28.4375 28.7500 29.0625 29.3750 29.6875 + 30.0000 30.3125 30.6250 30.9375 31.2500 31.5625 31.8750 32.1875 + 32.5000 32.8125 33.1250 33.4375 33.7500 34.0625 34.3750 34.6875 + 35.0000 35.3125 35.6250 35.9375 36.2500 36.5625 36.8750 37.1875 + 37.5000 37.8125 38.1250 38.4375 38.7500 39.0625 39.3750 39.6875 + 40.0000 + +0.25° x 0.3125° EU latitude centers: + + 32.7500 33.0000 33.2500 33.5000 33.7500 34.0000 34.2500 34.5000 + 34.7500 35.0000 35.2500 35.5000 35.7500 36.0000 36.2500 36.5000 + 36.7500 37.0000 37.2500 37.5000 37.7500 38.0000 38.2500 38.5000 + 38.7500 39.0000 39.2500 39.5000 39.7500 40.0000 40.2500 40.5000 + 40.7500 41.0000 41.2500 41.5000 41.7500 42.0000 42.2500 42.5000 + 42.7500 43.0000 43.2500 43.5000 43.7500 44.0000 44.2500 44.5000 + 44.7500 45.0000 45.2500 45.5000 45.7500 46.0000 46.2500 46.5000 + 46.7500 47.0000 47.2500 47.5000 47.7500 48.0000 48.2500 48.5000 + 48.7500 49.0000 49.2500 49.5000 49.7500 50.0000 50.2500 50.5000 + 50.7500 51.0000 51.2500 51.5000 51.7500 52.0000 52.2500 52.5000 + 52.7500 53.0000 53.2500 53.5000 53.7500 54.0000 54.2500 54.5000 + 54.7500 55.0000 55.2500 55.5000 55.7500 56.0000 56.2500 56.5000 + 56.7500 57.0000 57.2500 57.5000 57.7500 58.0000 58.2500 58.5000 + 58.7500 59.0000 59.2500 59.5000 59.7500 60.0000 60.2500 60.5000 + 60.7500 61.0000 61.2500 + +.. _x_0.3125_na_nested_grid: + +0.25 x 0.3125 NA nested grid +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This is the `GEOS-FP `__ native-resolution nested-grid over +North America + +`This grid may be specified via FlexGrid with these settings in +input.geos `__ +(in GEOS-Chem 12.4.0 and later). + +.. figure:: GEOSFP_025x03125_NA.png + :alt: GEOSFP_025x03125_NA.png + + GEOSFP_025x03125_NA.png + +0.25° x 0.3125° NA longitude centers: + + -130.0000 -129.6875 -129.3750 -129.0625 -128.7500 -128.4375 -128.1250 -127.8125 + -127.5000 -127.1875 -126.8750 -126.5625 -126.2500 -125.9375 -125.6250 -125.3125 + -125.0000 -124.6875 -124.3750 -124.0625 -123.7500 -123.4375 -123.1250 -122.8125 + -122.5000 -122.1875 -121.8750 -121.5625 -121.2500 -120.9375 -120.6250 -120.3125 + -120.0000 -119.6875 -119.3750 -119.0625 -118.7500 -118.4375 -118.1250 -117.8125 + -117.5000 -117.1875 -116.8750 -116.5625 -116.2500 -115.9375 -115.6250 -115.3125 + -115.0000 -114.6875 -114.3750 -114.0625 -113.7500 -113.4375 -113.1250 -112.8125 + -112.5000 -112.1875 -111.8750 -111.5625 -111.2500 -110.9375 -110.6250 -110.3125 + -110.0000 -109.6875 -109.3750 -109.0625 -108.7500 -108.4375 -108.1250 -107.8125 + -107.5000 -107.1875 -106.8750 -106.5625 -106.2500 -105.9375 -105.6250 -105.3125 + -105.0000 -104.6875 -104.3750 -104.0625 -103.7500 -103.4375 -103.1250 -102.8125 + -102.5000 -102.1875 -101.8750 -101.5625 -101.2500 -100.9375 -100.6250 -100.3125 + -100.0000 -99.6875 -99.3750 -99.0625 -98.7500 -98.4375 -98.1250 -97.8125 + -97.5000 -97.1875 -96.8750 -96.5625 -96.2500 -95.9375 -95.6250 -95.3125 + -95.0000 -94.6875 -94.3750 -94.0625 -93.7500 -93.4375 -93.1250 -92.8125 + -92.5000 -92.1875 -91.8750 -91.5625 -91.2500 -90.9375 -90.6250 -90.3125 + -90.0000 -89.6875 -89.3750 -89.0625 -88.7500 -88.4375 -88.1250 -87.8125 + -87.5000 -87.1875 -86.8750 -86.5625 -86.2500 -85.9375 -85.6250 -85.3125 + -85.0000 -84.6875 -84.3750 -84.0625 -83.7500 -83.4375 -83.1250 -82.8125 + -82.5000 -82.1875 -81.8750 -81.5625 -81.2500 -80.9375 -80.6250 -80.3125 + -80.0000 -79.6875 -79.3750 -79.0625 -78.7500 -78.4375 -78.1250 -77.8125 + -77.5000 -77.1875 -76.8750 -76.5625 -76.2500 -75.9375 -75.6250 -75.3125 + -75.0000 -74.6875 -74.3750 -74.0625 -73.7500 -73.4375 -73.1250 -72.8125 + -72.5000 -72.1875 -71.8750 -71.5625 -71.2500 -70.9375 -70.6250 -70.3125 + -70.0000 -69.6875 -69.3750 -69.0625 -68.7500 -68.4375 -68.1250 -67.8125 + -67.5000 -67.1875 -66.8750 -66.5625 -66.2500 -65.9375 -65.6250 -65.3125 + -65.0000 -64.6875 -64.3750 -64.0625 -63.7500 -63.4375 -63.1250 -62.8125 + -62.5000 -62.1875 -61.8750 -61.5625 -61.2500 -60.9375 -60.6250 -60.3125 + -60.0000 + +0.25° x 0.3125° NA latitude centers: + + 9.7500 10.0000 10.2500 10.5000 10.7500 11.0000 11.2500 11.5000 + 11.7500 12.0000 12.2500 12.5000 12.7500 13.0000 13.2500 13.5000 + 13.7500 14.0000 14.2500 14.5000 14.7500 15.0000 15.2500 15.5000 + 15.7500 16.0000 16.2500 16.5000 16.7500 17.0000 17.2500 17.5000 + 17.7500 18.0000 18.2500 18.5000 18.7500 19.0000 19.2500 19.5000 + 19.7500 20.0000 20.2500 20.5000 20.7500 21.0000 21.2500 21.5000 + 21.7500 22.0000 22.2500 22.5000 22.7500 23.0000 23.2500 23.5000 + 23.7500 24.0000 24.2500 24.5000 24.7500 25.0000 25.2500 25.5000 + 25.7500 26.0000 26.2500 26.5000 26.7500 27.0000 27.2500 27.5000 + 27.7500 28.0000 28.2500 28.5000 28.7500 29.0000 29.2500 29.5000 + 29.7500 30.0000 30.2500 30.5000 30.7500 31.0000 31.2500 31.5000 + 31.7500 32.0000 32.2500 32.5000 32.7500 33.0000 33.2500 33.5000 + 33.7500 34.0000 34.2500 34.5000 34.7500 35.0000 35.2500 35.5000 + 35.7500 36.0000 36.2500 36.5000 36.7500 37.0000 37.2500 37.5000 + 37.7500 38.0000 38.2500 38.5000 38.7500 39.0000 39.2500 39.5000 + 39.7500 40.0000 40.2500 40.5000 40.7500 41.0000 41.2500 41.5000 + 41.7500 42.0000 42.2500 42.5000 42.7500 43.0000 43.2500 43.5000 + 43.7500 44.0000 44.2500 44.5000 44.7500 45.0000 45.2500 45.5000 + 45.7500 46.0000 46.2500 46.5000 46.7500 47.0000 47.2500 47.5000 + 47.7500 48.0000 48.2500 48.5000 48.7500 49.0000 49.2500 49.5000 + 49.7500 50.0000 50.2500 50.5000 50.7500 51.0000 51.2500 51.5000 + 51.7500 52.0000 52.2500 52.5000 52.7500 53.0000 53.2500 53.5000 + 53.7500 54.0000 54.2500 54.5000 54.7500 55.0000 55.2500 55.5000 + 55.7500 56.0000 56.2500 56.5000 56.7500 57.0000 57.2500 57.5000 + 57.7500 58.0000 58.2500 58.5000 58.7500 59.0000 59.2500 59.5000 + 59.7500 60.0000 + +.. _cubed_sphere_grids_used_by_gchp: + +Cubed-sphere grids used by GCHP +------------------------------- + +`GCHP `__ uses cubed-sphere horizontal +grids instead of the traditional cartesian grids. For a good general +description of cubed sphere grids, `please follow this +link `__. + +Cubed-sphere grid resolutions are denoted using the number of grid +points on each face. The table below shows some common cubed-sphere +configurations used by GCHP. At present GCHP uses grids with 72 vertical +layers, but this may increase to 132 layers in the near future. + ++------+------------+--------------+-------------+--------------+---------------------+ +| Grid | | # points | | # of cells | # of layers | | # of cells | Equiv. lat-lon grid | +| | | per face | | at surface | | | (total) | | ++======+============+==============+=============+==============+=====================+ +| C24 | 24 | 3456 | 72 | 248,832 | 4° x 5° | ++------+------------+--------------+-------------+--------------+---------------------+ +| C48 | 48 | 13,824 | 72 | 995,328 | 2° x 2.5° | ++------+------------+--------------+-------------+--------------+---------------------+ +| C90 | 90 | 48,600 | 72 | 3,499,200 | 1° x 1.25° | ++------+------------+--------------+-------------+--------------+---------------------+ +| C180 | 180 | 194,400 | 72 | 13,996,800 | 0.5° x 0.625° | ++------+------------+--------------+-------------+--------------+---------------------+ +| C360 | 360 | 777,600 | 72 | 55,987,200 | 0.25° x 0.3125° | ++------+------------+--------------+-------------+--------------+---------------------+ + +**Reference:** Eastham, S.D., M.S. Long, C.A. Keller, E. Lundgren, R.M. +Yantosca, J. Zhuang, C. Li, C.J. Lee, M. Yannetti, B.M. Auer, T.L. +Clune, J. Kouatchou, W.M. Putman, M.A. Thompson, A.L. Trayanov, A.M. +Molod, R.V. Martin, and D.J. Jacob, *GEOS-Chem High Performance (GCHP): +A next-generation implementation of the GEOS-Chem chemical transport +model for massively parallel applications*, Geosci. Mod. Dev., **11**, +2941-2953, 2018. +`PDF `__ From ef2e529d8ecc339d2b1302cd2a111f9d6d5d8953 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 5 Sep 2025 15:13:29 -0400 Subject: [PATCH 26/86] Updated horizontal grids doc w/ all grids in createRunDir.sh docs/source/supplemental-guides/horizontal-grids.rst - Added grid definitions for all of the global and nested grids that can be created in createRunDir.sh. Tables of lons/lats were generated with a test program using GCPy routine make_grid_LL. Signed-off-by: Bob Yantosca --- .../supplemental-guides/horizontal-grids.rst | 2293 +++++++++++++---- 1 file changed, 1797 insertions(+), 496 deletions(-) diff --git a/docs/source/supplemental-guides/horizontal-grids.rst b/docs/source/supplemental-guides/horizontal-grids.rst index 6a82be7d0..aa25f357d 100644 --- a/docs/source/supplemental-guides/horizontal-grids.rst +++ b/docs/source/supplemental-guides/horizontal-grids.rst @@ -24,141 +24,145 @@ Global grids 4° x 5° global grid ------------------- -You can select this grid by specifying these settings in :ref:`cfg-gc-yml`: +Select this grid by specifying these settings in :ref:`cfg-gc-yml`: .. code-block:: yaml + simulation: + ... + met_field: MERRA2 # or GEOSFP or GEOSIT + ... grid: resolution: 4.0x5.0 - number_of_levels: 72 # You may also set this to 47 + number_of_levels: 72 # or 47 for reduced vertical grid longitude: range: [-180.0, 180.0] - center_at_180: true + center_at_180: true latitude: range: [-90.0, 90.0] - half_size_polar_boxes: true + half_size_polar_boxes: true nested_grid_simulation: activate: false - buffer_zone_NSEW: [0, 0, 0, 0] + buffer_zone_NSEW: [0, 0, 0, 0] -4° x 5° longitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~ +4° x 5° longitudes +~~~~~~~~~~~~~~~~~~ .. code-block:: text - -180.000 -175.000 -170.000 -165.000 -160.000 -155.000 -150.000 -145.000 - -140.000 -135.000 -130.000 -125.000 -120.000 -115.000 -110.000 -105.000 - -100.000 -95.000 -90.000 -85.000 -80.000 -75.000 -70.000 -65.000 - -60.000 -55.000 -50.000 -45.000 -40.000 -35.000 -30.000 -25.000 - -20.000 -15.000 -10.000 -5.000 0.000 5.000 10.000 15.000 - 20.000 25.000 30.000 35.000 40.000 45.000 50.000 55.000 - 60.000 65.000 70.000 75.000 80.000 85.000 90.000 95.000 - 100.000 105.000 110.000 115.000 120.000 125.000 130.000 135.000 - 140.000 145.000 150.000 155.000 160.000 165.000 170.000 175.000 + -180.0000 -175.0000 -170.0000 -165.0000 -160.0000 -155.0000 -150.0000 -145.0000 + -140.0000 -135.0000 -130.0000 -125.0000 -120.0000 -115.0000 -110.0000 -105.0000 + -100.0000 -95.0000 -90.0000 -85.0000 -80.0000 -75.0000 -70.0000 -65.0000 + -60.0000 -55.0000 -50.0000 -45.0000 -40.0000 -35.0000 -30.0000 -25.0000 + -20.0000 -15.0000 -10.0000 -5.0000 0.0000 5.0000 10.0000 15.0000 + 20.0000 25.0000 30.0000 35.0000 40.0000 45.0000 50.0000 55.0000 + 60.0000 65.0000 70.0000 75.0000 80.0000 85.0000 90.0000 95.0000 + 100.0000 105.0000 110.0000 115.0000 120.0000 125.0000 130.0000 135.0000 + 140.0000 145.0000 150.0000 155.0000 160.0000 165.0000 + 170.0000 175.0000 -4° x 5° latitude centers -~~~~~~~~~~~~~~~~~~~~~~~~ +4° x 5° latitudes +~~~~~~~~~~~~~~~~~ .. code-block:: text - -89.000 -86.000 -82.000 -78.000 -74.000 -70.000 -66.000 -62.000 - -58.000 -54.000 -50.000 -46.000 -42.000 -38.000 -34.000 -30.000 - -26.000 -22.000 -18.000 -14.000 -10.000 -6.000 -2.000 2.000 - 6.000 10.000 14.000 18.000 22.000 26.000 30.000 34.000 - 38.000 42.000 46.000 50.000 54.000 58.000 62.000 66.000 - 70.000 74.000 78.000 82.000 86.000 89.000 + -89.0000 -86.0000 -82.0000 -78.0000 -74.0000 -70.0000 -66.0000 -62.0000 + -58.0000 -54.0000 -50.0000 -46.0000 -42.0000 -38.0000 -34.0000 -30.0000 + -26.0000 -22.0000 -18.0000 -14.0000 -10.0000 -6.0000 -2.0000 2.0000 + 6.0000 10.0000 14.0000 18.0000 22.0000 26.0000 30.0000 34.0000 + 38.0000 42.0000 46.0000 50.0000 54.0000 58.0000 62.0000 66.0000 + 70.0000 74.0000 78.0000 82.0000 86.0000 89.0000 .. _gcc-hgrids-global-2x25: 2° x 2.5° global grid -~~~~~~~~~~~~~~~~~~~~~ +--------------------- -You can select this grid by specifying these settings in :ref:`cfg-gc-yml`: +Select this grid by specifying these in :ref:`cfg-gc-yml`: .. code-block:: yaml + simulation: + ... + met_field: MERRA2 # or GEOSFP or GEOSIT + ... grid: resolution: 2.0x2.5 - number_of_levels: 72 # You may also set this to 47 + number_of_levels: 72 # or 47 for reduced vertical grid longitude: range: [-180.0, 180.0] - center_at_180: true + center_at_180: true latitude: range: [-90.0, 90.0] - half_size_polar_boxes: true + half_size_polar_boxes: true nested_grid_simulation: activate: false buffer_zone_NSEW: [0, 0, 0, 0] -2° x 2.5° longitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~ +2° x 2.5° longitudes +~~~~~~~~~~~~~~~~~~~~ .. code-block:: text - -180.000 -177.500 -175.000 -172.500 -170.000 -167.500 -165.000 -162.500 - -160.000 -157.500 -155.000 -152.500 -150.000 -147.500 -145.000 -142.500 - -140.000 -137.500 -135.000 -132.500 -130.000 -127.500 -125.000 -122.500 - -120.000 -117.500 -115.000 -112.500 -110.000 -107.500 -105.000 -102.500 - -100.000 -97.500 -95.000 -92.500 -90.000 -87.500 -85.000 -82.500 - -80.000 -77.500 -75.000 -72.500 -70.000 -67.500 -65.000 -62.500 - -60.000 -57.500 -55.000 -52.500 -50.000 -47.500 -45.000 -42.500 - -40.000 -37.500 -35.000 -32.500 -30.000 -27.500 -25.000 -22.500 - -20.000 -17.500 -15.000 -12.500 -10.000 -7.500 -5.000 -2.500 - 0.000 2.500 5.000 7.500 10.000 12.500 15.000 17.500 - 20.000 22.500 25.000 27.500 30.000 32.500 35.000 37.500 - 40.000 42.500 45.000 47.500 50.000 52.500 55.000 57.500 - 60.000 62.500 65.000 67.500 70.000 72.500 75.000 77.500 - 80.000 82.500 85.000 87.500 90.000 92.500 95.000 97.500 - 100.000 102.500 105.000 107.500 110.000 112.500 115.000 117.500 - 120.000 122.500 125.000 127.500 130.000 132.500 135.000 137.500 - 140.000 142.500 145.000 147.500 150.000 152.500 155.000 157.500 - 160.000 162.500 165.000 167.500 170.000 172.500 175.000 177.500 - -2° x 2.5° latitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~ + -180.0000 -177.5000 -175.0000 -172.5000 -170.0000 -167.5000 -165.0000 -162.5000 + -160.0000 -157.5000 -155.0000 -152.5000 -150.0000 -147.5000 -145.0000 -142.5000 + -140.0000 -137.5000 -135.0000 -132.5000 -130.0000 -127.5000 -125.0000 -122.5000 + -120.0000 -117.5000 -115.0000 -112.5000 -110.0000 -107.5000 -105.0000 -102.5000 + -100.0000 -97.5000 -95.0000 -92.5000 -90.0000 -87.5000 -85.0000 -82.5000 + -80.0000 -77.5000 -75.0000 -72.5000 -70.0000 -67.5000 -65.0000 -62.5000 + -60.0000 -57.5000 -55.0000 -52.5000 -50.0000 -47.5000 -45.0000 -42.5000 + -40.0000 -37.5000 -35.0000 -32.5000 -30.0000 -27.5000 -25.0000 -22.5000 + -20.0000 -17.5000 -15.0000 -12.5000 -10.0000 -7.5000 -5.0000 -2.5000 + 0.0000 2.5000 5.0000 7.5000 10.0000 12.5000 15.0000 17.5000 + 20.0000 22.5000 25.0000 27.5000 30.0000 32.5000 35.0000 37.5000 + 40.0000 42.5000 45.0000 47.5000 50.0000 52.5000 55.0000 57.5000 + 60.0000 62.5000 65.0000 67.5000 70.0000 72.5000 75.0000 77.5000 + 80.0000 82.5000 85.0000 87.5000 90.0000 92.5000 95.0000 97.5000 + 100.0000 102.5000 105.0000 107.5000 110.0000 112.5000 115.0000 117.5000 + 120.0000 122.5000 125.0000 127.5000 130.0000 132.5000 135.0000 137.5000 + 140.0000 142.5000 145.0000 147.5000 150.0000 152.5000 155.0000 157.5000 + 160.0000 162.5000 165.0000 167.5000 170.0000 172.5000 175.0000 177.5000 + +2° x 2.5° latitudes +~~~~~~~~~~~~~~~~~~~ .. code-block:: text - -89.500 -88.000 -86.000 -84.000 -82.000 -80.000 -78.000 -76.000 - -74.000 -72.000 -70.000 -68.000 -66.000 -64.000 -62.000 -60.000 - -58.000 -56.000 -54.000 -52.000 -50.000 -48.000 -46.000 -44.000 - -42.000 -40.000 -38.000 -36.000 -34.000 -32.000 -30.000 -28.000 - -26.000 -24.000 -22.000 -20.000 -18.000 -16.000 -14.000 -12.000 - -10.000 -8.000 -6.000 -4.000 -2.000 0.000 2.000 4.000 - 6.000 8.000 10.000 12.000 14.000 16.000 18.000 20.000 - 22.000 24.000 26.000 28.000 30.000 32.000 34.000 36.000 - 38.000 40.000 42.000 44.000 46.000 48.000 50.000 52.000 - 54.000 56.000 58.000 60.000 62.000 64.000 66.000 68.000 - 70.000 72.000 74.000 76.000 78.000 80.000 82.000 84.000 - 86.000 88.000 89.500 - + -89.5000 -88.0000 -86.0000 -84.0000 -82.0000 -80.0000 -78.0000 -76.0000 + -74.0000 -72.0000 -70.0000 -68.0000 -66.0000 -64.0000 -62.0000 -60.0000 + -58.0000 -56.0000 -54.0000 -52.0000 -50.0000 -48.0000 -46.0000 -44.0000 + -42.0000 -40.0000 -38.0000 -36.0000 -34.0000 -32.0000 -30.0000 -28.0000 + -26.0000 -24.0000 -22.0000 -20.0000 -18.0000 -16.0000 -14.0000 -12.0000 + -10.0000 -8.0000 -6.0000 -4.0000 -2.0000 0.0000 2.0000 4.0000 + 6.0000 8.0000 10.0000 12.0000 14.0000 16.0000 18.0000 20.0000 + 22.0000 24.0000 26.0000 28.0000 30.0000 32.0000 34.0000 36.0000 + 38.0000 40.0000 42.0000 44.0000 46.0000 48.0000 50.0000 52.0000 + 54.0000 56.0000 58.0000 60.0000 62.0000 64.0000 66.0000 68.0000 + 70.0000 72.0000 74.0000 76.0000 78.0000 80.0000 82.0000 84.0000 + 86.0000 88.0000 89.5000 .. _gcc-hgrids-global-05: 0.5° x 0.625° global grid -~~~~~~~~~~~~~~~~~~~~~~~~~ - -This is the native resolution of the `MERRA-2 `__ reanalysis -product from GMAO. +------------------------- -The grid coordinates are constructed as follows: +This is the native resolution of the MERRA-2 and GEOS-IT reanalysis +products from GMAO. The grid coordinates are constructed as follows: .. math:: Lon_{center}(I) = -180° + 0.625° \times ( I - 1 ),~~~~I = 1..576 .. math:: - + Lat_{center}(J) = -90° + 0.5° \times ( J - 1 ),~~~~J = 1..361 .. _gcc-hgrids-global-025: 0.25° x 0.3125° global grid -~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -This is the native resolution of the `GEOS-5 "forward processing" (which -we call GEOS-FP) `__ operational data product from GMAO. +--------------------------- -The grid coordinates are computed as follows: +This is the native resolution of the GEOS-FP operational data product +from GMAO. The grid coordinates are computed as follows: .. math:: @@ -167,7 +171,7 @@ The grid coordinates are computed as follows: .. math:: Lat_{center}(I) = -90° + 0.25° \times ( J - 1 ),~~~~J = 1..721 - + ============ Nested grids ============ @@ -181,465 +185,1762 @@ grids listed below. 0.5° x 0.625° AS nested grid ---------------------------- -You can select this grid by specifying these settings in :ref:`cfg-gc-yml`: +Domain: Asia + +Select this grid by specifying these settings in :ref:`cfg-gc-yml`: .. code-block:: yaml simulation: - ... - met_field: MERRA2 # or GEOSIT + ... + met_field: MERRA2 # or GEOSIT ... grid: resolution: 0.5x0.625 - number_of_levels: 72 # You may also set this to 47 + number_of_levels: 72 # or 47 for reduced vertical grid longitude: range: [60.0, 150.0] - center_at_180: true + center_at_180: true latitude: range: [-11.0, 55.0] - half_size_polar_boxes: true + half_size_polar_boxes: true nested_grid_simulation: - activate: false - buffer_zone_NSEW: [3, 3, 3, 3] # You may also use [6, 6, 6, 6] if you encounter non-convergence errors in chemistry - -0.5° x 0.625° AS longitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. code-block:: text - - 60.000 60.625 61.250 61.875 62.500 63.125 63.750 64.375 - 65.000 65.625 66.250 66.875 67.500 68.125 68.750 69.375 - 70.000 70.625 71.250 71.875 72.500 73.125 73.750 74.375 - 75.000 75.625 76.250 76.875 77.500 78.125 78.750 79.375 - 80.000 80.625 81.250 81.875 82.500 83.125 83.750 84.375 - 85.000 85.625 86.250 86.875 87.500 88.125 88.750 89.375 - 90.000 90.625 91.250 91.875 92.500 93.125 93.750 94.375 - 95.000 95.625 96.250 96.875 97.500 98.125 98.750 99.375 - 100.000 100.625 101.250 101.875 102.500 103.125 103.750 104.375 - 105.000 105.625 106.250 106.875 107.500 108.125 108.750 109.375 - 110.000 110.625 111.250 111.875 112.500 113.125 113.750 114.375 - 115.000 115.625 116.250 116.875 117.500 118.125 118.750 119.375 - 120.000 120.625 121.250 121.875 122.500 123.125 123.750 124.375 - 125.000 125.625 126.250 126.875 127.500 128.125 128.750 129.375 - 130.000 130.625 131.250 131.875 132.500 133.125 133.750 134.375 - 135.000 135.625 136.250 136.875 137.500 138.125 138.750 139.375 - 140.000 140.625 141.250 141.875 142.500 143.125 143.750 144.375 - 145.000 145.625 146.250 146.875 147.500 148.125 148.750 149.375 - 150.000 - -0.5° x 0.625° AS latitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. code-block:: text - - -11.000 -10.500 -10.000 -9.500 -9.000 -8.500 -8.000 -7.500 - -7.000 -6.500 -6.000 -5.500 -5.000 -4.500 -4.000 -3.500 - -3.000 -2.500 -2.000 -1.500 -1.000 -0.500 0.000 0.500 - 1.000 1.500 2.000 2.500 3.000 3.500 4.000 4.500 - 5.000 5.500 6.000 6.500 7.000 7.500 8.000 8.500 - 9.000 9.500 10.000 10.500 11.000 11.500 12.000 12.500 - 13.000 13.500 14.000 14.500 15.000 15.500 16.000 16.500 - 17.000 17.500 18.000 18.500 19.000 19.500 20.000 20.500 - 21.000 21.500 22.000 22.500 23.000 23.500 24.000 24.500 - 25.000 25.500 26.000 26.500 27.000 27.500 28.000 28.500 - 29.000 29.500 30.000 30.500 31.000 31.500 32.000 32.500 - 33.000 33.500 34.000 34.500 35.000 35.500 36.000 36.500 - 37.000 37.500 38.000 38.500 39.000 39.500 40.000 40.500 - 41.000 41.500 42.000 42.500 43.000 43.500 44.000 44.500 - 45.000 45.500 46.000 46.500 47.000 47.500 48.000 48.500 - 49.000 49.500 50.000 50.500 51.000 51.500 52.000 52.500 - 53.000 53.500 54.000 54.500 55.000 + activate: true + buffer_zone_NSEW: [3, 3, 3, 3] # or [6, 6, 6, 6] if you encounter + # non-convergence errors in chemistry + +0.5° x 0.625° AS longitudes +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 60.0000 60.6250 61.2500 61.8750 62.5000 63.1250 63.7500 64.3750 + 65.0000 65.6250 66.2500 66.8750 67.5000 68.1250 68.7500 69.3750 + 70.0000 70.6250 71.2500 71.8750 72.5000 73.1250 73.7500 74.3750 + 75.0000 75.6250 76.2500 76.8750 77.5000 78.1250 78.7500 79.3750 + 80.0000 80.6250 81.2500 81.8750 82.5000 83.1250 83.7500 84.3750 + 85.0000 85.6250 86.2500 86.8750 87.5000 88.1250 88.7500 89.3750 + 90.0000 90.6250 91.2500 91.8750 92.5000 93.1250 93.7500 94.3750 + 95.0000 95.6250 96.2500 96.8750 97.5000 98.1250 98.7500 99.3750 + 100.0000 100.6250 101.2500 101.8750 102.5000 103.1250 103.7500 104.3750 + 105.0000 105.6250 106.2500 106.8750 107.5000 108.1250 108.7500 109.3750 + 110.0000 110.6250 111.2500 111.8750 112.5000 113.1250 113.7500 114.3750 + 115.0000 115.6250 116.2500 116.8750 117.5000 118.1250 118.7500 119.3750 + 120.0000 120.6250 121.2500 121.8750 122.5000 123.1250 123.7500 124.3750 + 125.0000 125.6250 126.2500 126.8750 127.5000 128.1250 128.7500 129.3750 + 130.0000 130.6250 131.2500 131.8750 132.5000 133.1250 133.7500 134.3750 + 135.0000 135.6250 136.2500 136.8750 137.5000 138.1250 138.7500 139.3750 + 140.0000 140.6250 141.2500 141.8750 142.5000 143.1250 143.7500 144.3750 + 145.0000 145.6250 146.2500 146.8750 147.5000 148.1250 148.7500 149.3750 + 150.0000 + +0.5° x 0.625° AS latitudes +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -11.0000 -10.5000 -10.0000 -9.5000 -9.0000 -8.5000 -8.0000 -7.5000 + -7.0000 -6.5000 -6.0000 -5.5000 -5.0000 -4.5000 -4.0000 -3.5000 + -3.0000 -2.5000 -2.0000 -1.5000 -1.0000 -0.5000 0.0000 0.5000 + 1.0000 1.5000 2.0000 2.5000 3.0000 3.5000 4.0000 4.5000 + 5.0000 5.5000 6.0000 6.5000 7.0000 7.5000 8.0000 8.5000 + 9.0000 9.5000 10.0000 10.5000 11.0000 11.5000 12.0000 12.5000 + 13.0000 13.5000 14.0000 14.5000 15.0000 15.5000 16.0000 16.5000 + 17.0000 17.5000 18.0000 18.5000 19.0000 19.5000 20.0000 20.5000 + 21.0000 21.5000 22.0000 22.5000 23.0000 23.5000 24.0000 24.5000 + 25.0000 25.5000 26.0000 26.5000 27.0000 27.5000 28.0000 28.5000 + 29.0000 29.5000 30.0000 30.5000 31.0000 31.5000 32.0000 32.5000 + 33.0000 33.5000 34.0000 34.5000 35.0000 35.5000 36.0000 36.5000 + 37.0000 37.5000 38.0000 38.5000 39.0000 39.5000 40.0000 40.5000 + 41.0000 41.5000 42.0000 42.5000 43.0000 43.5000 44.0000 44.5000 + 45.0000 45.5000 46.0000 46.5000 47.0000 47.5000 48.0000 48.5000 + 49.0000 49.5000 50.0000 50.5000 51.0000 51.5000 52.0000 52.5000 + 53.0000 53.5000 54.0000 54.5000 55.0000 .. _gcc-hgrids-nested-05-eu: -0.5 x 0.625 EU nested grid --------------------------- +0.5° x 0.625° EU nested grid +---------------------------- + +Domain: Europe -You can select this grid by specifying these settings in -:ref:`cfg-gc-yml`: +Select this grid by specifying these settings in :ref:`cfg-gc-yml`: .. code-block:: yaml - + simulation: - ... + ... met_field: MERRA2 # or GEOSIT ... grid: resolution: 0.5x0.625 - number_of_levels: 72 # You may also set this to 47 + number_of_levels: 72 # or 47 for reduced vertical grid longitude: range: [ -30.0, 50.0] - center_at_180: true + center_at_180: true latitude: range: [30.0, 70.0] - half_size_polar_boxes: true + half_size_polar_boxes: true nested_grid_simulation: - activate: false - buffer_zone_NSEW: [3, 3, 3, 3] # You may also use [6, 6, 6, 6] if you encounter non-convergence errors in chemistry - - -0.5° x 0.625° EU longitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. code-block:: text - - -30.000 -29.375 -28.750 -28.125 -27.500 -26.875 -26.250 -25.625 - -25.000 -24.375 -23.750 -23.125 -22.500 -21.875 -21.250 -20.625 - -20.000 -19.375 -18.750 -18.125 -17.500 -16.875 -16.250 -15.625 - -15.000 -14.375 -13.750 -13.125 -12.500 -11.875 -11.250 -10.625 - -10.000 -9.375 -8.750 -8.125 -7.500 -6.875 -6.250 -5.625 - -5.000 -4.375 -3.750 -3.125 -2.500 -1.875 -1.250 -0.625 - 0.000 0.625 1.250 1.875 2.500 3.125 3.750 4.375 - 5.000 5.625 6.250 6.875 7.500 8.125 8.750 9.375 - 10.000 10.625 11.250 11.875 12.500 13.125 13.750 14.375 - 15.000 15.625 16.250 16.875 17.500 18.125 18.750 19.375 - 20.000 20.625 21.250 21.875 22.500 23.125 23.750 24.375 - 25.000 25.625 26.250 26.875 27.500 28.125 28.750 29.375 - 30.000 30.625 31.250 31.875 32.500 33.125 33.750 34.375 - 35.000 35.625 36.250 36.875 37.500 38.125 38.750 39.375 - 40.000 40.625 41.250 41.875 42.500 43.125 43.750 44.375 - 45.000 45.625 46.250 46.875 47.500 48.125 48.750 49.375 - 50.000 - -0.5° x 0.625° EU latitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. code-block:: text - - 30.000 30.500 31.000 31.500 32.000 32.500 33.000 33.500 - 34.000 34.500 35.000 35.500 36.000 36.500 37.000 37.500 - 38.000 38.500 39.000 39.500 40.000 40.500 41.000 41.500 - 42.000 42.500 43.000 43.500 44.000 44.500 45.000 45.500 - 46.000 46.500 47.000 47.500 48.000 48.500 49.000 49.500 - 50.000 50.500 51.000 51.500 52.000 52.500 53.000 53.500 - 54.000 54.500 55.000 55.500 56.000 56.500 57.000 57.500 - 58.000 58.500 59.000 59.500 60.000 60.500 61.000 61.500 - 62.000 62.500 63.000 63.500 64.000 64.500 65.000 65.500 - 66.000 66.500 67.000 67.500 68.000 68.500 69.000 69.500 - 70.000 + activate: true + buffer_zone_NSEW: [3, 3, 3, 3] # or [6, 6, 6, 6] if you encounter + # non-convergence errors in chemistry + +0.5° x 0.625° EU longitudes +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -30.0000 -29.3750 -28.7500 -28.1250 -27.5000 -26.8750 -26.2500 -25.6250 + -25.0000 -24.3750 -23.7500 -23.1250 -22.5000 -21.8750 -21.2500 -20.6250 + -20.0000 -19.3750 -18.7500 -18.1250 -17.5000 -16.8750 -16.2500 -15.6250 + -15.0000 -14.3750 -13.7500 -13.1250 -12.5000 -11.8750 -11.2500 -10.6250 + -10.0000 -9.3750 -8.7500 -8.1250 -7.5000 -6.8750 -6.2500 -5.6250 + -5.0000 -4.3750 -3.7500 -3.1250 -2.5000 -1.8750 -1.2500 -0.6250 + 0.0000 0.6250 1.2500 1.8750 2.5000 3.1250 3.7500 4.3750 + 5.0000 5.6250 6.2500 6.8750 7.5000 8.1250 8.7500 9.3750 + 10.0000 10.6250 11.2500 11.8750 12.5000 13.1250 13.7500 14.3750 + 15.0000 15.6250 16.2500 16.8750 17.5000 18.1250 18.7500 19.3750 + 20.0000 20.6250 21.2500 21.8750 22.5000 23.1250 23.7500 24.3750 + 25.0000 25.6250 26.2500 26.8750 27.5000 28.1250 28.7500 29.3750 + 30.0000 30.6250 31.2500 31.8750 32.5000 33.1250 33.7500 34.3750 + 35.0000 35.6250 36.2500 36.8750 37.5000 38.1250 38.7500 39.3750 + 40.0000 40.6250 41.2500 41.8750 42.5000 43.1250 43.7500 44.3750 + 45.0000 45.6250 46.2500 46.8750 47.5000 48.1250 48.7500 49.3750 + 50.0000 + +0.5° x 0.625° EU latitudes +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + 30.0000 30.5000 31.0000 31.5000 32.0000 32.5000 33.0000 33.5000 + 34.0000 34.5000 35.0000 35.5000 36.0000 36.5000 37.0000 37.5000 + 38.0000 38.5000 39.0000 39.5000 40.0000 40.5000 41.0000 41.5000 + 42.0000 42.5000 43.0000 43.5000 44.0000 44.5000 45.0000 45.5000 + 46.0000 46.5000 47.0000 47.5000 48.0000 48.5000 49.0000 49.5000 + 50.0000 50.5000 51.0000 51.5000 52.0000 52.5000 53.0000 53.5000 + 54.0000 54.5000 55.0000 55.5000 56.0000 56.5000 57.0000 57.5000 + 58.0000 58.5000 59.0000 59.5000 60.0000 60.5000 61.0000 61.5000 + 62.0000 62.5000 63.0000 63.5000 64.0000 64.5000 65.0000 65.5000 + 66.0000 66.5000 67.0000 67.5000 68.0000 68.5000 69.0000 69.5000 + 70.0000 .. _gcc-hgrids-nested-05-na: -0.5 x 0.625 NA nested grid --------------------------- +0.5° x 0.625° NA nested grid +---------------------------- -You can select this grid by specifying these settings in -:ref:`cfg-gc-yml`: +Domain: North America + +Select this grid by specifying these settings in :ref:`cfg-gc-yml`: .. code-block:: yaml - + simulation: - ... - met_field: MERRA2 # or GEOSIT + ... + met_field: MERRA2 # or GEOSIT ... grid: resolution: 0.5x0.625 - number_of_levels: 72 # You may also set this to 47 + number_of_levels: 72 # or 47 for reduced vertical grid longitude: range: [-140.0, -40.0] - center_at_180: true + center_at_180: true latitude: range: [10.0, 70.0] - half_size_polar_boxes: true + half_size_polar_boxes: true nested_grid_simulation: - activate: false - buffer_zone_NSEW: [3, 3, 3, 3] # You may also use [6, 6, 6, 6] if you encounter non-convergence errors in chemistry - -0.5° x 0.625° NA longitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. code-block:: text - - -140.000 -139.375 -138.750 -138.125 -137.500 -136.875 -136.250 -135.625 - -135.000 -134.375 -133.750 -133.125 -132.500 -131.875 -131.250 -130.625 - -130.000 -129.375 -128.750 -128.125 -127.500 -126.875 -126.250 -125.625 - -125.000 -124.375 -123.750 -123.125 -122.500 -121.875 -121.250 -120.625 - -120.000 -119.375 -118.750 -118.125 -117.500 -116.875 -116.250 -115.625 - 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-40.000 - -0.5° x 0.625° NA latitude centers -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. code-block:: text - - 10.000 10.500 11.000 11.500 12.000 12.500 13.000 13.500 - 14.000 14.500 15.000 15.500 16.000 16.500 17.000 17.500 - 18.000 18.500 19.000 19.500 20.000 20.500 21.000 21.500 - 22.000 22.500 23.000 23.500 24.000 24.500 25.000 25.500 - 26.000 26.500 27.000 27.500 28.000 28.500 29.000 29.500 - 30.000 30.500 31.000 31.500 32.000 32.500 33.000 33.500 - 34.000 34.500 35.000 35.500 36.000 36.500 37.000 37.500 - 38.000 38.500 39.000 39.500 40.000 40.500 41.000 41.500 - 42.000 42.500 43.000 43.500 44.000 44.500 45.000 45.500 - 46.000 46.500 47.000 47.500 48.000 48.500 49.000 49.500 - 50.000 50.500 51.000 51.500 52.000 52.500 53.000 53.500 - 54.000 54.500 55.000 55.500 56.000 56.500 57.000 57.500 - 58.000 58.500 59.000 59.500 60.000 60.500 61.000 61.500 - 62.000 62.500 63.000 63.500 64.000 64.500 65.000 65.500 - 66.000 66.500 67.000 67.500 68.000 68.500 69.000 69.500 - 70.000 - - -0.25 x 0.3125 CH nested grid -^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. figure:: GEOSFP_025x03125_CH.png - :alt: GEOSFP_025x03125_CH.png - - GEOSFP_025x03125_CH.png - -This is the `GEOS-FP `__ native-resolution nested-grid over -China. - -`This grid may be specified via FlexGrid with these settings in -input.geos `__ (in -GEOS-Chem 12.4.0 and later). - -0.25° x 0.3125° CH longitude centers: - - 70.0000 70.3125 70.6250 70.9375 71.2500 71.5625 71.8750 72.1875 - 72.5000 72.8125 73.1250 73.4375 73.7500 74.0625 74.3750 74.6875 - 75.0000 75.3125 75.6250 75.9375 76.2500 76.5625 76.8750 77.1875 - 77.5000 77.8125 78.1250 78.4375 78.7500 79.0625 79.3750 79.6875 - 80.0000 80.3125 80.6250 80.9375 81.2500 81.5625 81.8750 82.1875 - 82.5000 82.8125 83.1250 83.4375 83.7500 84.0625 84.3750 84.6875 - 85.0000 85.3125 85.6250 85.9375 86.2500 86.5625 86.8750 87.1875 - 87.5000 87.8125 88.1250 88.4375 88.7500 89.0625 89.3750 89.6875 - 90.0000 90.3125 90.6250 90.9375 91.2500 91.5625 91.8750 92.1875 - 92.5000 92.8125 93.1250 93.4375 93.7500 94.0625 94.3750 94.6875 - 95.0000 95.3125 95.6250 95.9375 96.2500 96.5625 96.8750 97.1875 - 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50.7500 51.0000 51.2500 51.5000 51.7500 52.0000 52.2500 52.5000 - 52.7500 53.0000 53.2500 53.5000 53.7500 54.0000 54.2500 54.5000 - 54.7500 55.0000 55.2500 55.5000 55.7500 56.0000 56.2500 56.5000 - 56.7500 57.0000 57.2500 57.5000 57.7500 58.0000 58.2500 58.5000 - 58.7500 59.0000 59.2500 59.5000 59.7500 60.0000 60.2500 60.5000 - 60.7500 61.0000 61.2500 - -.. _x_0.3125_na_nested_grid: - -0.25 x 0.3125 NA nested grid -^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -This is the `GEOS-FP `__ native-resolution nested-grid over -North America - -`This grid may be specified via FlexGrid with these settings in -input.geos `__ -(in GEOS-Chem 12.4.0 and later). - -.. figure:: GEOSFP_025x03125_NA.png - :alt: GEOSFP_025x03125_NA.png - - GEOSFP_025x03125_NA.png - -0.25° x 0.3125° NA longitude centers: - - -130.0000 -129.6875 -129.3750 -129.0625 -128.7500 -128.4375 -128.1250 -127.8125 - -127.5000 -127.1875 -126.8750 -126.5625 -126.2500 -125.9375 -125.6250 -125.3125 - -125.0000 -124.6875 -124.3750 -124.0625 -123.7500 -123.4375 -123.1250 -122.8125 - 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11.7500 12.0000 12.2500 12.5000 12.7500 13.0000 13.2500 13.5000 - 13.7500 14.0000 14.2500 14.5000 14.7500 15.0000 15.2500 15.5000 - 15.7500 16.0000 16.2500 16.5000 16.7500 17.0000 17.2500 17.5000 - 17.7500 18.0000 18.2500 18.5000 18.7500 19.0000 19.2500 19.5000 - 19.7500 20.0000 20.2500 20.5000 20.7500 21.0000 21.2500 21.5000 - 21.7500 22.0000 22.2500 22.5000 22.7500 23.0000 23.2500 23.5000 - 23.7500 24.0000 24.2500 24.5000 24.7500 25.0000 25.2500 25.5000 - 25.7500 26.0000 26.2500 26.5000 26.7500 27.0000 27.2500 27.5000 - 27.7500 28.0000 28.2500 28.5000 28.7500 29.0000 29.2500 29.5000 - 29.7500 30.0000 30.2500 30.5000 30.7500 31.0000 31.2500 31.5000 - 31.7500 32.0000 32.2500 32.5000 32.7500 33.0000 33.2500 33.5000 - 33.7500 34.0000 34.2500 34.5000 34.7500 35.0000 35.2500 35.5000 - 35.7500 36.0000 36.2500 36.5000 36.7500 37.0000 37.2500 37.5000 - 37.7500 38.0000 38.2500 38.5000 38.7500 39.0000 39.2500 39.5000 - 39.7500 40.0000 40.2500 40.5000 40.7500 41.0000 41.2500 41.5000 - 41.7500 42.0000 42.2500 42.5000 42.7500 43.0000 43.2500 43.5000 - 43.7500 44.0000 44.2500 44.5000 44.7500 45.0000 45.2500 45.5000 - 45.7500 46.0000 46.2500 46.5000 46.7500 47.0000 47.2500 47.5000 - 47.7500 48.0000 48.2500 48.5000 48.7500 49.0000 49.2500 49.5000 - 49.7500 50.0000 50.2500 50.5000 50.7500 51.0000 51.2500 51.5000 - 51.7500 52.0000 52.2500 52.5000 52.7500 53.0000 53.2500 53.5000 - 53.7500 54.0000 54.2500 54.5000 54.7500 55.0000 55.2500 55.5000 - 55.7500 56.0000 56.2500 56.5000 56.7500 57.0000 57.2500 57.5000 - 57.7500 58.0000 58.2500 58.5000 58.7500 59.0000 59.2500 59.5000 - 59.7500 60.0000 - -.. _cubed_sphere_grids_used_by_gchp: - -Cubed-sphere grids used by GCHP -------------------------------- - -`GCHP `__ uses cubed-sphere horizontal -grids instead of the traditional cartesian grids. For a good general -description of cubed sphere grids, `please follow this -link `__. - -Cubed-sphere grid resolutions are denoted using the number of grid -points on each face. The table below shows some common cubed-sphere -configurations used by GCHP. At present GCHP uses grids with 72 vertical -layers, but this may increase to 132 layers in the near future. - -+------+------------+--------------+-------------+--------------+---------------------+ -| Grid | | # points | | # of cells | # of layers | | # of cells | Equiv. lat-lon grid | -| | | per face | | at surface | | | (total) | | -+======+============+==============+=============+==============+=====================+ -| C24 | 24 | 3456 | 72 | 248,832 | 4° x 5° | -+------+------------+--------------+-------------+--------------+---------------------+ -| C48 | 48 | 13,824 | 72 | 995,328 | 2° x 2.5° | -+------+------------+--------------+-------------+--------------+---------------------+ -| C90 | 90 | 48,600 | 72 | 3,499,200 | 1° x 1.25° | -+------+------------+--------------+-------------+--------------+---------------------+ -| C180 | 180 | 194,400 | 72 | 13,996,800 | 0.5° x 0.625° | -+------+------------+--------------+-------------+--------------+---------------------+ -| C360 | 360 | 777,600 | 72 | 55,987,200 | 0.25° x 0.3125° | -+------+------------+--------------+-------------+--------------+---------------------+ - -**Reference:** Eastham, S.D., M.S. Long, C.A. Keller, E. Lundgren, R.M. -Yantosca, J. Zhuang, C. Li, C.J. Lee, M. Yannetti, B.M. Auer, T.L. -Clune, J. Kouatchou, W.M. Putman, M.A. Thompson, A.L. Trayanov, A.M. -Molod, R.V. Martin, and D.J. Jacob, *GEOS-Chem High Performance (GCHP): -A next-generation implementation of the GEOS-Chem chemical transport -model for massively parallel applications*, Geosci. Mod. Dev., **11**, -2941-2953, 2018. -`PDF `__ + activate: true + buffer_zone_NSEW: [3, 3, 3, 3] # or [6, 6, 6, 6] if you encounter + # non-convergence errors in chemistry + +0.5° x 0.625° NA longitudes +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: text + + -140.0000 -139.3750 -138.7500 -138.1250 -137.5000 -136.8750 -136.2500 -135.6250 + -135.0000 -134.3750 -133.7500 -133.1250 -132.5000 -131.8750 -131.2500 -130.6250 + -130.0000 -129.3750 -128.7500 -128.1250 -127.5000 -126.8750 -126.2500 -125.6250 + -125.0000 -124.3750 -123.7500 -123.1250 -122.5000 -121.8750 -121.2500 -120.6250 + -120.0000 -119.3750 -118.7500 -118.1250 -117.5000 -116.8750 -116.2500 -115.6250 + -115.0000 -114.3750 -113.7500 -113.1250 -112.5000 -111.8750 -111.2500 -110.6250 + -110.0000 -109.3750 -108.7500 -108.1250 -107.5000 -106.8750 -106.2500 -105.6250 + -105.0000 -104.3750 -103.7500 -103.1250 -102.5000 -101.8750 -101.2500 -100.6250 + -100.0000 -99.3750 -98.7500 -98.1250 -97.5000 -96.8750 -96.2500 -95.6250 + -95.0000 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8.62500 8.75000 8.87500 + 9.00000 9.12500 9.25000 9.37500 9.50000 9.62500 9.75000 9.87500 + 10.00000 10.12500 10.25000 10.37500 10.50000 10.62500 10.75000 10.87500 + 11.00000 11.12500 11.25000 11.37500 11.50000 11.62500 11.75000 11.87500 + 12.00000 12.12500 12.25000 12.37500 12.50000 12.62500 12.75000 12.87500 + 13.00000 13.12500 13.25000 13.37500 13.50000 13.62500 13.75000 13.87500 + 14.00000 14.12500 14.25000 14.37500 14.50000 14.62500 14.75000 14.87500 + 15.00000 15.12500 15.25000 15.37500 15.50000 15.62500 15.75000 15.87500 + 16.00000 From bfeaa55dd3e09ad7792c2c6cf791be1456e627d6 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 8 Sep 2025 14:26:17 -0400 Subject: [PATCH 27/86] Update overview of vertical grids document docs/source/supplemental-guides/vertical-grids.rst - Added a paragraph "Specifics for GMAO vertical grids" docs/source/geos-chem/geos-chem-shared-docs - Submodule update to 280e8e4 (list-tables in history-guide.rst) Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- .../supplemental-guides/vertical-grids.rst | 19 ++++++++++++------- 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index cdc23040b..280e8e486 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit cdc23040b0c18fc81841e758a655c7f9627030c3 +Subproject commit 280e8e486520a3a11dc21a3dedf0c8053c68988c diff --git a/docs/source/supplemental-guides/vertical-grids.rst b/docs/source/supplemental-guides/vertical-grids.rst index dd1c5c2b8..fa45ff8d3 100644 --- a/docs/source/supplemental-guides/vertical-grids.rst +++ b/docs/source/supplemental-guides/vertical-grids.rst @@ -43,12 +43,6 @@ computed as the average of the pressures at successive vertical edges: P_{midpoint}(I,J,L) = \frac{P_{edge}(I,J,L) + P_{edge}(I,J,L+1)}{2} -For the GMAO meteorological products, the :math:`P_{edge}(I,J,L)` and -:math:`P_{midpoint}(I,J,L)` meteorological products vary with the -topography up to 170 hPa. Skyward of 170 hPa, :math:`P_{edge}(I,J,L)` -and :math:`P_{midpoint}(I,J,L)` remain constant for all longitudes -and latitudes :math:`(I,J)`. - An :math:`\eta` coordinate can be constructed from :math:`P_{edge}(I,J,L)` and :math:`P_{midpoint}(I,J,L)` as follows: @@ -61,7 +55,18 @@ An :math:`\eta` coordinate can be constructed from \eta_{midpoint}(I,J,L) = \frac{P_{midpoint}(I,J,L) - P_{top}}{P_{surface}(I,J) - P_{top}} where :math:`P_{top}` is pressure at the top level of the vertical -grid. GMAO meteorological products use a model top of 0.01 hPa. +grid. + + +Specifics for GMAO vertical grids +--------------------------------- + +The the :math:`P_{edge}(I,J,L)` and :math:`P_{midpoint}(I,J,L)` values +in GMAO meteorological products vary with the topography up to 170 +hPa. Skyward of 170 hPa, :math:`P_{edge}(I,J,L)` and +:math:`P_{midpoint}(I,J,L)` remain constant for all longitudes and +latitudes :math:`(I,J)`. GMAO meteorological products use a model top +of 0.01 hPa. .. _gcc-vgrids_gmao: From 414ad7dad640518e409b6b3701d4ce7692eea393 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 8 Sep 2025 16:31:15 -0400 Subject: [PATCH 28/86] GEOS-Chem update: Merge PR #3014 (Conserve init rst file mass in GCC) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 2dbd206ad Merge PR #3014 (Conserve initial restart file mass in GC-Classic) PR #3014 changes where GC-Classic restart file species concentrations are scaled by pressure for mass conservation, and fixes a problem where mass was not conserved if restart file meteorology did not match run-time meteorology in first timestep. 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 2311ed93a..2dbd206ad 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 2311ed93a0bcfc6a13cc7813023cc560f3df2365 +Subproject commit 2dbd206ad2eedc92fcc60467d7a37302a499ec9a From 97e4e4659fa966f9ba9736b58b347a11b76ffbe9 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Sep 2025 11:58:54 -0400 Subject: [PATCH 29/86] GEOS-Chem update: Merge PR #3019 (Fix parallel error from PR #3014) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: f0e5424cc Merge PR #3019 (Fixed parallelization error in PR #3014) PR #3019 fixes a parallelization error that was inadvertently introduced in PR #3014. 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 2dbd206ad..f0e5424cc 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 2dbd206ad2eedc92fcc60467d7a37302a499ec9a +Subproject commit f0e5424ccb8593f1ff576e9ba46ff5b823bad6c5 From 5e678d38c21285c8b125cb3b44b407e3c133f942 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Sep 2025 12:04:26 -0400 Subject: [PATCH 30/86] GEOS-Chem update: Merge PR #3016 (Update MF & CN scalings for MAPL 2.59) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: dcb1314de Merge PR #3016 (Update mass flux & CN scalings for MAPL 2.59) PR #3016 updates the GCHP mass flux and Courant number import scaling calculation done in setCommonRunSettings.sh for use in ExtData.rc with MAPL 2.59. It only impacts GCHP runs that import mass flux rather than use winds in advection. 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 f0e5424cc..dcb1314de 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit f0e5424ccb8593f1ff576e9ba46ff5b823bad6c5 +Subproject commit dcb1314dee998fd4ed7647c1e9ba7353182a73f1 From f43de86dff81de249afef00b96508fca1834739c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Sep 2025 15:26:21 -0400 Subject: [PATCH 31/86] GEOS-Chem update: Merge PR #3010 (Add LPJ_MERRA2 CH4 inventory ) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a0d32f663 Merge PR #3010 (Add optional LPJ_MERRA2 wetland CH4 emissions) PR #3010 introduces the LPJ_MERRA2 inventory as an option (off by default) so that IMI/CH4 users can more easily utilize the dataset. 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 90799084d..a0d32f663 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 90799084ded7e241919217a14f6147eff7a0d8f0 +Subproject commit a0d32f66329415d6619e3e5f513e16bff43c5f78 From ba74679816ab3689b3d8183f45fc860b17b5ecc9 Mon Sep 17 00:00:00 2001 From: Lizzie Lundgren Date: Tue, 9 Sep 2025 17:02:09 -0400 Subject: [PATCH 32/86] Update docs for option to read restart file via GEOS-Chem not HEMCO Signed-off-by: Lizzie Lundgren --- .../gcclassic-user-guide/restart-files-gc.rst | 60 ++++++++++++++++--- 1 file changed, 53 insertions(+), 7 deletions(-) diff --git a/docs/source/gcclassic-user-guide/restart-files-gc.rst b/docs/source/gcclassic-user-guide/restart-files-gc.rst index 03454208a..22d301215 100644 --- a/docs/source/gcclassic-user-guide/restart-files-gc.rst +++ b/docs/source/gcclassic-user-guide/restart-files-gc.rst @@ -10,10 +10,42 @@ GEOS-Chem restart files How are restart files read into GEOS-Chem? ========================================== -GEOS-Chem restart files are read via `HEMCO -`_. The entries listed below have been -added to :file:`HEMCO_Config.rc` (and may vary slightly for different -simulation types). These fields are obtained from HEMCO and copied to +GEOS-Chem restart files may be read via `HEMCO`_ or via GEOS-Chem. +If using HEMCO then all fields are read as single precision floating point (REAL4). +If using GEOS-Chem then all fields are read with the native precision stored in the file, +e.g. double precision floating point (REAL8) for species concentrations. Using HEMCO is +on by default, but you may choose to use GEOS-Chem instead by updating the +:file:`geoschem_config.yml` configuration file entry :literal:`read_restart_as_real8` +to :literal:`true`. + +There are pros and cons to both methods of reading the GEOS-Chem restart file. +Using HEMCO allows forcing the timestamp of the restart file to match run start date +and time as well as doing custom alterations such as changing the names of the expected +variables in the file. It also allows online regridding and cropping of restart files +at run-time, a requirement for nested grid simulations if using a global restart file. +However, using HEMCO to read the restart file prevents bit-for-bit +reproducibility when restarting a run and also prevents restart file mass conservation. +This is because of the precision loss associated with reading restart fields as REAL4 +when they are stored internally in the model as REAL8. + +Using GEOS-Chem to read restart files enables bit-for-bit reproducibility upon +restart as well as file mass conservation. However, it prevents using HEMCO read +features. In particular it is not appropriate to use if the restart file horizontal +grid does not match the run horizontal grid or if the restart file needs to be cropped. +In both cases the model will fail. The model will also exit with an error message if +using the mercury simulation since this feature has not yet been validated for that +simulation. + +================================ +Using HEMCO to read restart file +================================ + +This section pertains only to using HEMCO to read the GEOS-Chem restart file. +All fields are read in as REAL4. See the section above if you instead wish to read +fields at their native precision. + +The entries for restart files are stored in :file:`HEMCO_Config.rc`. They may vary slightly for different +simulation types. These fields are obtained from HEMCO and copied to the appropriate :code:`State_Chm` and :code:`State_Met` fields in routine :code:`Get_GC_Restart` (located in :file:`GeosCore/hcoi_gc_main_mod.F90`). @@ -115,7 +147,8 @@ When reading **other restart file fields** (time cycle flag: How can I determine the date of a restart file? =============================================== -To determine the date of a netCDF restart file, you may use :command:`ncdump`. +The date of the restart file is in the filename. It is also stored in the +file metadata. You may check the metadata using :command:`ncdump`. For example: .. code-block:: console @@ -126,6 +159,13 @@ The :command:`-t` option will return the time value in human-readable date-time strings rather than numerical values in unit such as :code:`"hours since 1985-1-1 00:00:0.0.` +If using HEMCO to read the restart file then the timestamp in the +filename and within the file must match the simulation start date and time. +You can change this by modifying :file:`HEMCO_Config.rc` (see earlier section +on using HEMCO to read restart files). If using GEOS-Chem +to read the restart file then only the date and time in the filename must +match the simulation start. + .. _restart-files-gc-where: ================================================= @@ -193,8 +233,14 @@ How do I check my initial conditions? ===================================== To ensure you are using the expected initial conditions for your -simulation, please check the GEOS-Chem log file. You should see -something like: +simulation please check the GEOS-Chem log file. You should see +min, max, and sum of all fields stored in the GEOS-Chem restart file +printed to log. If you enable the :literal:`verbose` option in configuration +file :file:`geoschem_config.yml` and your restart file contains meteorology +field :literal:`Met_DELPDRY` then you will also see the global mass per +species computed entirely from restart file values printed to log. This +mass can be compared to global mass printed at the start of each timestep +when in :literal:`verbose` mode to check mass conservation. .. code-block:: console From ac9f50d53e3a6f32792e7677477961f2f4ac9550 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Sep 2025 17:48:32 -0400 Subject: [PATCH 33/86] Link to "GEOS-Chem Classic horizontal grids" from other pages docs/source/geos-chem-shared-docs - Submod update to 804cc68 (Update nested grid info...) docs/source/gcclassic-user-guide/restart-files-what.rst - Change ":option:Restarts/" to ":file:/Restarts" docs/source/getting-started/disk-space.rst - Update tables with recent info of disk space required for the various global & nested meteorology products docs/source/supplemental-guides/horizontal-grids.rst - Fixed duplicate link Signed-off-by: Bob Yantosca --- .../restart-files-what.rst | 4 +- docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/disk-space.rst | 139 +++++++++++++----- .../supplemental-guides/horizontal-grids.rst | 2 +- 4 files changed, 103 insertions(+), 44 deletions(-) diff --git a/docs/source/gcclassic-user-guide/restart-files-what.rst b/docs/source/gcclassic-user-guide/restart-files-what.rst index 1569345b9..e810bc64f 100644 --- a/docs/source/gcclassic-user-guide/restart-files-what.rst +++ b/docs/source/gcclassic-user-guide/restart-files-what.rst @@ -23,7 +23,7 @@ GEOS-Chem simulations use two separate restart files. :file:`GEOSChem.Restart.20190801_0000z.nc4`. The :file:`z` character indicates "Zulu" time (aka UTC). - GEOS-Chem restart files are created in the :option:`Restarts/` + GEOS-Chem restart files are created in the :file:`Restarts/` folder of your :ref:`GEOS-Chem run directory ` directory. .. option:: HEMCO_restart.YYYYMMDDhhmm.nc @@ -35,7 +35,7 @@ GEOS-Chem simulations use two separate restart files. and biogenic emissions in order to facilitate long GEOS-Chem simulations with several run stages. - HEMCO restart files are created in the :option:`Restarts/` + HEMCO restart files are created in the :file:`Restarts/` folder of your :ref:`GEOS-Chem run directory ` directory. When you run a GEOS-Chem simulation, it will write new GEOS-Chem restart diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 280e8e486..804cc68eb 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 280e8e486520a3a11dc21a3dedf0c8053c68988c +Subproject commit 804cc68eb868d0c58c8bdf49686ad0aae93fd117 diff --git a/docs/source/getting-started/disk-space.rst b/docs/source/getting-started/disk-space.rst index faa9f5ac7..c3a463fa8 100644 --- a/docs/source/getting-started/disk-space.rst +++ b/docs/source/getting-started/disk-space.rst @@ -39,49 +39,108 @@ The amount of disk space that you will need depends on two things: .. _merra2-size-table: -.. table:: Disk space needed for 1-year of MERRA-2 data - - +--------------------------------------------+------------------+--------+ - | Resolution | Type | Size | - | | | GB/yr | - +============================================+==================+========+ - | :math:`1^{\circ}{\times}1.25^{\circ}` | Global | ~30 | - +--------------------------------------------+------------------+--------+ - | :math:`2^{\circ}{\times}2.5^{\circ}` | Global | ~110 | - +--------------------------------------------+------------------+--------+ - | :math:`0.5^{\circ}{\times}0.625^{\circ}` | Nested Asia | ~115 | - | | (aka AS) | | - +--------------------------------------------+------------------+--------+ - | :math:`0.5^{\circ}{\times}0.625^{\circ}` | Nested Europe | ~58 | - | | (aka EU) | | - +--------------------------------------------+------------------+--------+ - | :math:`0.5^{\circ}{\times}0.625^{\circ}` | Nested North | ~110 | - | | America (aka NA) | | - +--------------------------------------------+------------------+--------+ +MERRA-2 +~~~~~~~ + +.. list-table:: Disk space needed for 1-year of MERRA-2 data + :header-rows: 1 + :widths: 60 40 + + * - Grid + - Approzimate Size (GB/yr) + * - :ref:`gcc-hgrids-global-4x5` + - 30 + * - :ref:`gcc-hgrids-global-2x25` + - 110 + * - :ref:`gcc-hgrids-nested-05-as` + - 115 + * - :ref:`gcc-hgrids-nested-05-eu` + - 60 + * - :ref:`gcc-hgrids-nested-05-na` + - 110 .. _geosfp-size-table: -.. table:: Disk space needed for 1-year of GEOS-FP data - - +--------------------------------------------+------------------+--------+ - | Resolution | Type | Size | - | | | GB/yr | - +============================================+==================+========+ - | :math:`1^{\circ}{\times}1.25^{\circ}` | Global | ~30 | - +--------------------------------------------+------------------+--------+ - | :math:`2^{\circ}{\times}2.5^{\circ}` | Global | ~120 | - +--------------------------------------------+------------------+--------+ - | :math:`0.25^{\circ}{\times}0.3125^{\circ}` | Nested Asia | ~175 | - | | (aka AS) | | - +--------------------------------------------+------------------+--------+ - | :math:`0.25^{\circ}{\times}0.3125^{\circ}` | Nested Europe | ~175 | - | | (aka EU) | | - +--------------------------------------------+------------------+--------+ - | :math:`0.25^{\circ}{\times}0.3125^{\circ}` | Nested North | ~175 | - | | America (aka NA) | | - +--------------------------------------------+------------------+--------+ - -GCAP 2.0: to be added +GEOS-FP +~~~~~~~ + +.. list-table:: Disk space needed for 1-year of GEOS-FP data + :header-rows: 1 + :widths: 60 40 + + * - Grid + - Approximate Size (GB/yr) + * - :ref:`gcc-hgrids-global-4x5` + - 30 + * - :ref:`gcc-hgrids-global-2x25` + - 120 + * - :ref:`gcc-hgrids-nested-025-af` + - 434 + * - :ref:`gcc-hgrids-nested-025-as` + - 380 + * - :ref:`gcc-hgrids-nested-025-eu` + - 125 + * - :ref:`gcc-hgrids-nested-025-me` + - 175 + * - :ref:`gcc-hgrids-nested-025-na` + - 200 + * - :ref:`gcc-hgrids-nested-025-oc` + - 240 + * - :ref:`gcc-hgrids-nested-025-sa` + - 250 + * - :ref:`gcc-hgrids-nested-025-ru` + - 375 + * - :ref:`gcc-hgrids-nested-0125-af` + - 2,100 [#A]_ + * - :ref:`gcc-hgrids-nested-0125-as` + - 2,200 [#B]_ + * - :ref:`gcc-hgrids-nested-0125-na` + - 1,250 [#C]_ + * - :ref:`gcc-hgrids-nested-025-sa` + - 1,900 [#D]_ + +.. rubric:: Notes + +.. [#A] Winds, pressures, and specific humidity are read at 0.125° x + 0.15625° over the nested Africa domain. Other met fields are + taken from the GEOS-FP :ref:`gcc-hgrids-nested-025-af` archive. + +.. [#B] Winds, pressures, and specific humidity are read at 0.125° x + 0.15625° over the nested Asia domain. Other met fields are + taken from the GEOS-FP :ref:`gcc-hgrids-nested-025-as` archive. + +.. [#C] Winds, pressures, and specific humidity are read at 0.125° x + 0.15625° over the nested North America domain. Other met + fields are taken from the GEOS-FP + :ref:`gcc-hgrids-nested-025-na` archive. + +.. [#D] Winds, pressures, and specific humidity are read at 0.125° x + 0.15625° over the nested South America domain. Other met + fields are taken from the GEOS-FP + :ref:`gcc-hgrids-nested-025-sa` archive. + +.. _geosit-size-table: + +GEOS-IT +~~~~~~~ + +.. list-table:: Disk space needed for 1-year of GEOS-IT data + :header-rows: 1 + :widths: 60 40 + + * - Grid + - Approximate Size (GB/yr) + * - :ref:`gcc-hgrids-global-4x5` + - 26 + * - :ref:`gcc-hgrids-global-2x25` + - 78 + +.. _gcap2-size-table: + +GCAP 2.0 +~~~~~~~~ + +See the U. Rochester data portal: http://atmos.earth.rochester.edu/input/gc/ExtData/ .. _obtaining-emissions-data-and-met-fields: diff --git a/docs/source/supplemental-guides/horizontal-grids.rst b/docs/source/supplemental-guides/horizontal-grids.rst index aa25f357d..f0ebc3173 100644 --- a/docs/source/supplemental-guides/horizontal-grids.rst +++ b/docs/source/supplemental-guides/horizontal-grids.rst @@ -13,7 +13,7 @@ The FlexGrid feature of GEOS-Chem Classic allows you to specify the global GEOS-Chem grid definitions (listed below), as well as custom grids, at runtime. -.. _gcc-hgrids-global-4x5: +.. _gcc-hgrids-global: ============ Global grids From 0842a74ce2b641414869055940743d98cc9d6560 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 10 Sep 2025 16:07:11 -0400 Subject: [PATCH 34/86] Minor documentation updates for 14.7.0 docs/source/gcclassic-user-guide/diag-outputs-hist.rst - Change table to list-table - Rename "LevEdgeDiags" to "StateMetLevEdge" docs/source/gcclassic-user-guide/get-code-steps.rst - Update links to point to the most recent YouTube tutorials Signed-off-by: Bob Yantosca --- .../diag-outputs-hist.rst | 212 +++++++++++------- .../gcclassic-user-guide/get-code-steps.rst | 6 +- 2 files changed, 129 insertions(+), 89 deletions(-) diff --git a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst index e5c26fbd9..f1e8fc658 100644 --- a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst +++ b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst @@ -24,89 +24,129 @@ collections in the :ref:`HISTORY.rc configuration file .. table:: GEOS-Chem History diagnostics output files :align: center - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | History output file | Diagnostic collection | Used in simulations | - +==========================================================+=====================================+=============================+ - | :file:`GEOSChem.AdvFluxVert.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-advfluxvert` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.AerosolMass.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-aerosolmass` | :option:`fullchem` | - | | | :option:`aerosol` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.Aerosols.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-aerosols` | :option:`fullchem` | - | | | :option:`aerosol` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.BoundaryConditions.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-boundaryconditions` | Nested-grid simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.Carbon.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-carbon` | :option:`carbon` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.CH4.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-ch4` | :option:`CH4` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.CloudConvFlux.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-cloudconvflux` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.CO.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-co` | :option:`CH4` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.CO2.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-co2` | :option:`CH4` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.ConcAboveSfc.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-concabovesfc` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.ConcAfterChem.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-concafterchem` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.DryDep.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-drydep` | All simulations with dry- | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.JValues.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-jvalues` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.KppARDiags.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-kppardiags` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.KppDiags.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-kppdiags` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.LevelEdgeDiags.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-leveledgediags` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.MercuryChem.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-mercurychem` | :option:`Hg` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.MercuryEmis.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-mercuryemis` | :option:`Hg` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.MercuryOcean.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-mercuryocean` | :option:`Hg` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.Metrics.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-metrics` | :option:`fullchem` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.ProdLoss.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-prodloss` | :option:`fullchem` | - | | | :option:`aerosol` | - | | | :option:`tagCO` | - | | | :option:`tagO3` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.RadioNuclide.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-radionuclide` | :option:`TransportTracers` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.Restart.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-restart` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.RRTMG.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-rrtmg` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.RxnConst.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-rxnconst` | :option:`fullchem` | - | | | :option:`CH4` | - | | | :option:`Hg` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.RxnRates.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-rxnrates` | :option:`fullchem` | - | | | :option:`CH4` | - | | | :option:`Hg` | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.SatDiagn.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-satdiagn` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.SatDiagnEdge.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-satdiagnedge` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.SpeciesConc.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-speciesconc` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.StateChm.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-statechm` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.StateMet.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-statemet` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.StratBM.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-stratbm` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.Tomas.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-tomas` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.UVFlux.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-uvflux` | All simulations | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.WetLossConv.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-wetlossconv` | All simulations with | - | | | wet-deposited species | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ - | :file:`GEOSChem.WetLossLS.YYYYMMDD_hhhmmz.nc4` | :ref:`histguide-wetlossls` | All simulations with | - | | | wet-deposited species | - +----------------------------------------------------------+-------------------------------------+-----------------------------+ +.. list-table:: GEOS-Chem History diagnostics output files + :header-rows: 1 + :widths: 40 30 30 + + * - History output file + - Diagnostic collection + - Used in simulations + * - :file:`GEOSChem.AdvFluxVert.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-advfluxvert` + - :option:`fullchem` + * - :file:`GEOSChem.AerosolMass.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-aerosolmass` + - :option:`fullchem` + :option:`aerosol` + * - :file:`GEOSChem.Aerosols.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-aerosols` + - :option:`fullchem` + :option:`aerosol` + * - :file:`GEOSChem.BoundaryConditions.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-boundaryconditions` + - Nested-grid simulations + * - :file:`GEOSChem.Carbon.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-carbon` + - :option:`carbon` + * - :file:`GEOSChem.CH4.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-ch4` + - :option:`CH4` + * - :file:`GEOSChem.CloudConvFlux.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-cloudconvflux` + - All simulations + * - :file:`GEOSChem.CO.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-co` + - :option:`CH4` + * - :file:`GEOSChem.CO2.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-co2` + - :option:`CH4` + * - :file:`GEOSChem.ConcAboveSfc.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-concabovesfc` + - :option:`fullchem` + * - :file:`GEOSChem.ConcAfterChem.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-concafterchem` + - :option:`fullchem` + * - :file:`GEOSChem.DryDep.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-drydep` + - All simulations with dry- + * - :file:`GEOSChem.JValues.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-jvalues` + - :option:`fullchem` + * - :file:`GEOSChem.KppARDiags.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-kppardiags` + - :option:`fullchem` + * - :file:`GEOSChem.KppDiags.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-kppdiags` + - :option:`fullchem` + * - :file:`GEOSChem.MercuryChem.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-mercurychem` + - :option:`Hg` + * - :file:`GEOSChem.MercuryEmis.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-mercuryemis` + - :option:`Hg` + * - :file:`GEOSChem.MercuryOcean.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-mercuryocean` + - :option:`Hg` + * - :file:`GEOSChem.Metrics.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-metrics` + - :option:`fullchem` + * - :file:`GEOSChem.ProdLoss.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-prodloss` + - :option:`fullchem` + :option:`aerosol` + :option:`tagCO` + :option:`tagO3` + * - :file:`GEOSChem.RadioNuclide.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-radionuclide` + - :option:`TransportTracers` + * - :file:`GEOSChem.Restart.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-restart` + - All simulations + * - :file:`GEOSChem.RRTMG.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-rrtmg` + - All simulations + * - :file:`GEOSChem.RxnConst.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-rxnconst` + - :option:`fullchem` + :option:`CH4` + :option:`Hg` + * - :file:`GEOSChem.RxnRates.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-rxnrates` + - :option:`fullchem` + :option:`CH4` + :option:`Hg` + * - :file:`GEOSChem.SatDiagn.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-satdiagn` + - All simulations + * - :file:`GEOSChem.SatDiagnEdge.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-satdiagnedge` + - All simulations + * - :file:`GEOSChem.SpeciesConc.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-speciesconc` + - All simulations + * - :file:`GEOSChem.StateChm.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-statechm` + - All simulations + * - :file:`GEOSChem.StateMet.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-statemet` + - All simulations + * - :file:`GEOSChem.StateMetLevEdge.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-statemetlevedge` + - All simulations + * - :file:`GEOSChem.StratBM.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-stratbm` + - All simulations + * - :file:`GEOSChem.Tomas.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-tomas` + - All simulations + * - :file:`GEOSChem.UVFlux.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-uvflux` + - All simulations + * - :file:`GEOSChem.WetLossConv.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-wetlossconv` + - All simulations with + wet-deposited species + * - :file:`GEOSChem.WetLossLS.YYYYMMDD_hhhmmz.nc4` + - :ref:`histguide-wetlossls` + - All simulations with + wet-deposited species diff --git a/docs/source/gcclassic-user-guide/get-code-steps.rst b/docs/source/gcclassic-user-guide/get-code-steps.rst index d9e7ad74b..39db861ee 100644 --- a/docs/source/gcclassic-user-guide/get-code-steps.rst +++ b/docs/source/gcclassic-user-guide/get-code-steps.rst @@ -257,10 +257,10 @@ For more information about downloading the GEOS-Chem source code, please see the following Youtube video tutorials: - `Getting Started with GEOS-Chem - `_ + `_ - - `GEOS-Chem Classic Quickstart Guide (with dry-run) - `_ + - `GEOS-Chem Classic Quickstart Guide (with dry-run simulation) + `_ - `Managing branches between superproject and submodules `_ From e54c055e50686e88881a75e01d49b32a9738a0d0 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 12 Sep 2025 14:31:45 -0400 Subject: [PATCH 35/86] GEOS-Chem update: Merge PR #3029 (Fix parallel error in convection) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 4be45c88d Merge PR #3029 (Fix parallel error in convection_mod.F90) PR #3029 initializes the AER and KIN logicals to TRUE before calling routine WASHOUT in GeosCore/convection_mod.F90. This ensures that these variables are defined even when WASHOUT is not called, avoiding potential parallelization errors. 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 dcb1314de..4be45c88d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit dcb1314dee998fd4ed7647c1e9ba7353182a73f1 +Subproject commit 4be45c88d8fb797cfe9bb2e50c9720513af512a0 From 06bd577e0f4893bca2e1f67670bdfe5997cf56c0 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 12 Sep 2025 15:01:40 -0400 Subject: [PATCH 36/86] Added "Particulate matter in GEOS-Chem" supplemental guide docs/source/geos-chem-shared-docs - Submod update to 79a1e38 (Added PM2.5 and PM10 supplemental guide) docs/source/index.rst - Added pm25-pm10-guide.rst to the supplemental guides toctree CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 1 + docs/source/geos-chem-shared-docs | 2 +- docs/source/index.rst | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6063788a8..ec876b89e 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 "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs - Added "GEOS-Chem Classic horiziontal grids" supplemental guide in ReadTheDocs +- Added "Particulate matter in GEOS-Chem" supplemental guide in ReadTheDocs ## [14.6.3] - 2025-07-28 ### Added diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 804cc68eb..79a1e38d0 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 804cc68eb868d0c58c8bdf49686ad0aae93fd117 +Subproject commit 79a1e38d0aa6f095278907bd8e7d92478f51592d diff --git a/docs/source/index.rst b/docs/source/index.rst index 54990910e..2ecef3d88 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -99,6 +99,7 @@ modifications to GEOS-Chem Classic source code. 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/pm25-pm10-guide.rst geos-chem-shared-docs/supplemental-guides/related-docs.rst .. toctree:: From 5a1d07a75c9421c19c9563a1af03c6cb502bd6ce Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 12 Sep 2025 15:14:09 -0400 Subject: [PATCH 37/86] geos-chem submod submod update: Fix typos in PM2.5 and PM10 docs docs/source/geos-chem-shared-docs - Submod update to 8f21a5c 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 79a1e38d0..8f21a5c96 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 79a1e38d0aa6f095278907bd8e7d92478f51592d +Subproject commit 8f21a5c9643a624d79388297b05ceeb5e1370ce5 From d9885693fc2609bdb30c491c8d9f8f52ccb99f74 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 30 Sep 2025 14:20:51 -0400 Subject: [PATCH 38/86] GEOS-Chem update: Merge PR #3027 (Remove Is_Advected tags) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 7219410db Merge PR #3027 (Remove Is_Advected tags from species database) As described in issue #3024, the Is_Advected species database tag is redundant. PR #3027 removes all Is_Advected:true tags from: run/shared/species_database.yml run/shared/species_database_apm.yml run/shared/species_database_hg.yml run/shared/species_database_tomas.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 f82e547b0..7219410db 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit f82e547b079724f0706a986a372fe1cf6bbd6414 +Subproject commit 7219410db8645ed585d3e9278bea50febdd667bd From 93d49c5f66da5fbced1b80a7fe90df65e1cf83d0 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 30 Sep 2025 15:10:52 -0400 Subject: [PATCH 39/86] Make OMP_NUM_THREADS and OMP_STACKSIZE header 3 in doc (+ other fixes) docs/source/getting-started/login-env-parallel - Promote the OMP_NUM_THREADS and OMP_STACKSIZE sections from option to heading 3. Adjust indentation accordingly docs/source/gcclassic-user-guide/compile-cmake.rst docs/source/gcclassic-user-guide/run-cmd-line.rst docs/source/gcclassic-user-guide/run-script.rst docs/source/gcclassic-user-guide/run-script-examples.rst - Now use ref instead of option to link to OMP_NUM_THREADS docs/source/gcclassic-user-guide/diag-outputs-hist.rst - Remove leftover table declaration (now is list-table) docs/source/geos-chem-shared-docs - Submod update to c9cd33 (Remove Is_Advected from species-guide.rst) Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/compile-cmake.rst | 2 +- .../diag-outputs-hist.rst | 3 - .../gcclassic-user-guide/run-cmd-line.rst | 3 +- .../gcclassic-user-guide/run-script.rst | 3 +- docs/source/geos-chem-shared-docs | 2 +- .../getting-started/login-env-parallel.rst | 98 +++++++++++-------- .../run-script-examples.rst | 10 +- 7 files changed, 66 insertions(+), 55 deletions(-) diff --git a/docs/source/gcclassic-user-guide/compile-cmake.rst b/docs/source/gcclassic-user-guide/compile-cmake.rst index 1fc6398c5..160366db1 100644 --- a/docs/source/gcclassic-user-guide/compile-cmake.rst +++ b/docs/source/gcclassic-user-guide/compile-cmake.rst @@ -290,7 +290,7 @@ values are: Activates OpenMP parallelization. **(Default option)** GEOS-Chem Classic will execute on as many computational cores as - is specified with :option:`OMP_NUM_THREADS`. + is specified with :ref:`env-files-envvars-parallel-threads`. .. option:: n diff --git a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst index f1e8fc658..f3de7572d 100644 --- a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst +++ b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst @@ -21,9 +21,6 @@ The filenames listed below correspond to the default diagnostic collections in the :ref:`HISTORY.rc configuration file `. -.. table:: GEOS-Chem History diagnostics output files - :align: center - .. list-table:: GEOS-Chem History diagnostics output files :header-rows: 1 :widths: 40 30 30 diff --git a/docs/source/gcclassic-user-guide/run-cmd-line.rst b/docs/source/gcclassic-user-guide/run-cmd-line.rst index 54ae3bc45..7f34ee30c 100644 --- a/docs/source/gcclassic-user-guide/run-cmd-line.rst +++ b/docs/source/gcclassic-user-guide/run-cmd-line.rst @@ -56,7 +56,8 @@ The modifications entail: export OMP_NUM_THREADS=`ncpus` to the run script. This will automatically set - :option:`OMP_NUM_THREADS` to the available number of cores. + :ref:`env-files-envvars-parallel-threads` to the available + number of cores. To run GEOS-Chem interactively, type: diff --git a/docs/source/gcclassic-user-guide/run-script.rst b/docs/source/gcclassic-user-guide/run-script.rst index f7925ee7e..df381f39e 100644 --- a/docs/source/gcclassic-user-guide/run-script.rst +++ b/docs/source/gcclassic-user-guide/run-script.rst @@ -161,4 +161,5 @@ the :file:`gcclassic` executable. .. option:: srun -c $OMP_NUM_THREADS Tells SLURM to run the GEOS-Chem Classic executable using the - number of cores specified in :option:`OMP_NUM_THREADS`. + number of cores specified in + :ref:`env-files-envvars-parallel-threads`. diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 8f21a5c96..c9dcd3332 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 8f21a5c9643a624d79388297b05ceeb5e1370ce5 +Subproject commit c9dcd3332e4c3b8fa69703686d1b6f72830c6278 diff --git a/docs/source/getting-started/login-env-parallel.rst b/docs/source/getting-started/login-env-parallel.rst index 17701ba25..7523a3e16 100644 --- a/docs/source/getting-started/login-env-parallel.rst +++ b/docs/source/getting-started/login-env-parallel.rst @@ -28,49 +28,61 @@ 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 +.. _env-files-envvars-parallel-envvars: - The :envvar:`OMP_NUM_THREADS` environment variable sets the number of - computational cores (aka threads) that you would like GEOS-Chem - Classic to use. +================================================= +Environment variables controlling parallelization +================================================= - For example, the command below will tell :program:`GEOS-Chem Classic` - to use 8 cores within parallel sections of code: +.. _env-files-envvars-parallel-threads: - .. code:: console +OMP_NUM_THREADS +--------------- - $ export OMP_NUM_THREADS=8 +The :envvar:`OMP_NUM_THREADS` environment variable sets the number of +computational cores (aka threads) that you would like GEOS-Chem +Classic to use. - We recommend that you define :envvar:`OMP_NUM_THREADS` not only in your - environment file, but also in your :ref:`GEOS-Chem run script - `. +For example, the command below will tell :program:`GEOS-Chem Classic` +to use 8 cores within parallel sections of code: -.. option:: OMP_STACKSIZE +.. code:: console - In order to use :program:`GEOS-Chem Classic` with - `OpenMP parallelization `_, you must - request the maximum amount of stack memory in your Unix environment. - (The stack memory is where local automatic variables and temporary - :envvar:`!$OMP PRIVATE` variables will be created.) + $ export OMP_NUM_THREADS=8 - Add the following lines to your system startup file - (e.g. :file:`.bashrc`) and to your :ref:`GEOS-Chem run scripts - `: +We recommend that you define :envvar:`OMP_NUM_THREADS` +not only in your environment file, but also in your :ref:`GEOS-Chem +run script `. - .. code-block:: bash +.. _env-files-envvars-parallel-stack: - ulimit -s unlimited - export OMP_STACKSIZE=500m +OMP_STACKSIZE +------------- - The :command:`ulimit -s unlimited` will tell the bash shell to use the - maximum amount of stack memory that is available. +In order to use :program:`GEOS-Chem Classic` with +`OpenMP parallelization `_, you must +request the maximum amount of stack memory in your Unix environment. +(The stack memory is where local automatic variables and temporary +:envvar:`!$OMP PRIVATE` variables will be created.) - The environment variable :envvar:`OMP_STACKSIZE` must also be set to a very - large number. In this example, we are nominally requesting 500 MB of - memory. But in practice, this will tell the GNU Fortran compiler to use - the maximum amount of stack memory available on your system. The value - **500m** is a good round number that is larger than the amount of stack - memory on most computer clusters, but you can increase this if you wish. +Add the following lines to your system startup file +(e.g. :file:`.bashrc`) and to your :ref:`GEOS-Chem run scripts +`: + +.. code-block:: bash + + ulimit -s unlimited + export OMP_STACKSIZE=500m + +The :command:`ulimit -s unlimited` will tell the bash shell to use the +maximum amount of stack memory that is available. + +The environment variable :envvar:`OMP_STACKSIZE` must also be set to a very +large number. In this example, we are nominally requesting 500 MB of +memory. But in practice, this will tell the GNU Fortran compiler to use +the maximum amount of stack memory available on your system. The value +**500m** is a good round number that is larger than the amount of stack +memory on most computer clusters, but you can increase this if you wish. .. _env-files-envvars-errors: @@ -80,15 +92,15 @@ Errors caused by incorrect environment variable settings Be on the lookout for these errors: - #. If :option:`OMP_NUM_THREADS` is set to 1, then your - simulation will execute using only one computational core. - This will make your simulation take much longer than - necessary. |br| - |br| - - #. 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 :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. + #. If :ref:`env-files-envvars-parallel-threads` is set to 1, then + your simulation will execute using only one computational + core. This will make your simulation take much longer than + necessary. |br| + |br| + + #. If the :ref:`env-files-envvars-parallel-stack` environment + variable is not included in your environment file (or if it is + set to a very low value), 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. diff --git a/docs/source/supplemental-guides/run-script-examples.rst b/docs/source/supplemental-guides/run-script-examples.rst index d7bc9283b..695a35dba 100644 --- a/docs/source/supplemental-guides/run-script-examples.rst +++ b/docs/source/supplemental-guides/run-script-examples.rst @@ -55,15 +55,15 @@ Save this code to a file named :file:`geoschem.run.slurm`: .. important:: - If you forget to define :envvar:`OMP_NUM_THREADS` in your run - script, then :program:`GEOS-Chem Classic` will execute using one - core. This can cause your simulations to take much longer than is - necessary! + If you forget to define :ref:`env-files-envvars-parallel-threads` + in your run script, then :program:`GEOS-Chem Classic` will execute + using one core. This can cause your simulations to take much + longer than is necessary! Then make :file:`geoschem.run.slurm` executable: .. code-block:: console - + $ chmod 755 geoschem.run.slurm For more information about how Slurm is set up on your particular From 90548c3c79890ed5ef4cb9c8078afceec973926d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 30 Sep 2025 15:47:09 -0400 Subject: [PATCH 40/86] GEOS-Chem update: Merge PR #3020 (Unhide direct GC-Classic rst read) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e256ad747 Merge PR #3020 (Unhide feature to read GC-Classic rst file w/o HEMCO) PR #3020 update adds the option to use GEOS-Chem to read the GC-Classic restart file and therefore preserve native precision stored in the file. This option has been present since 14.6.3 but it was not visible in the geoschem_config.yml files as an option. The default is currently false. 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 7219410db..e256ad747 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 7219410db8645ed585d3e9278bea50febdd667bd +Subproject commit e256ad747216736a4864e8ae22be9b8e1a10642d From 5f47f83321ed88e75b61971b0bd8a7b18f394edb Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 1 Oct 2025 14:49:02 -0400 Subject: [PATCH 41/86] GEOS-Chem update: Merge PR #3055 (Fixed download_data.py) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 5b1ac965f Merge PR #3055 (Fixed issues in download_data.py) PR #3055 does the following: 1. Replaces // in all file paths to /. 2. Now checks for the 0.125 x 0.15625 grid. 3. Now will properly determine the nested-grid suffix for all pre-defined nested grids. 4. Condensed several instances of repeated code by creating internal subroutine write_linked_gmi_files_to_script. 5. Updated Pydoc headers and comments for brevity 6. Trimmed trailing whitespace. 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 e256ad747..5b1ac965f 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e256ad747216736a4864e8ae22be9b8e1a10642d +Subproject commit 5b1ac965f08e48f086d8fce2647540d59f9e1687 From 5e4ed6c4c96a54ea1cd02ce66c00f730af390223 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 6 Oct 2025 12:56:46 -0400 Subject: [PATCH 42/86] RTD update: Stress that nested-grid & GCAP met are in separate portals docs/source/getting-started/quick-start.rst - Add a list table for the configuration files - Add specific instructions for downloading data from the nested-grid and GCAP portals docs/source/supplemental-guides/horizontal-grids.rst - Add ref anchor "_gcc-hgrids-nested:" to Nested Grids section docs/source/geos-chem-shared-docs: - Submod update to 3a38902 Signed-off-by: Bob Yantosca --- docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/quick-start.rst | 67 ++++++++++++++----- .../supplemental-guides/horizontal-grids.rst | 4 ++ 3 files changed, 55 insertions(+), 18 deletions(-) diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index c9dcd3332..3a3890277 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit c9dcd3332e4c3b8fa69703686d1b6f72830c6278 +Subproject commit 3a38902771fbbfe9f8aff0facf52c2d3da81b109 diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst index 9da9e9c7a..0c14a85ab 100644 --- a/docs/source/getting-started/quick-start.rst +++ b/docs/source/getting-started/quick-start.rst @@ -293,20 +293,23 @@ Now, navigate to your run directory: You should review these files before starting a simulation: -- :ref:`geoschem_config.yml ` - - Controls several frequently-updated simulation settings - (e.g. start and end time, which operations to turn on/off, etc.) - -- :ref:`HISTORY.rc ` - - Controls GEOS-Chem diagnostic settings. - -- :ref:`HEMCO_Diagn.rc ` - - Controls emissions diagnostic settings via `HEMCO `_. - -- :ref:`HEMCO_Config.rc ` - - Controls which emissions inventories and other non-emissions data - will be read from disk (via `HEMCO - `_). +.. list-table:: + :header-rows: 1 + :widths: 25 75 + + * - Configuration file + - Description + * - :ref:`geoschem_config.yml ` + - Controls several frequently-updated simulation settings + (e.g. start and end time, which operations to turn on/off, etc.) + * - :ref:`HISTORY.rc ` + - Controls GEOS-Chem diagnostic settings. + * - :ref:`HEMCO_Diagn.rc ` + - Controls emissions diagnostic settings via `HEMCO `_. + * - :ref:`HEMCO_Config.rc ` + - Controls which emissions inventories and other non-emissions data + will be read from disk (via `HEMCO + `_). .. attention:: @@ -387,7 +390,7 @@ Once the dry-run simulation has finished, use the .. note:: Depending on your system, you might have to activate a Conda or - Mamba environment containing a version of Python before running the + environment containing a version of Python before running the :file:`download.data.py` script. Ask your sysadmin. To start the data download, type: @@ -414,8 +417,38 @@ portal using the HTTP data transfer protocol. 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. +At this point the required data files for your simulation should have +been successfully downloaded from the :ref:`GEOS-Chem Input Data +portal ` to your computer system or EC2 instance. +But you may still need to perform a subsequent dry-run simulation to +download additional data that are stored separately from the GEOS-Chem +Input Data portal: + +#. If you plan to run a :ref:`GEOS-Chem Classic nested-grid simulation + ` with meteorology fields that have been cropped to a + :ref:`specific nested grid domain `, then follow + these steps: + + .. code-block:: console + + $ ./gcclassic --dryrun | tee log.dryrun.nested + $ ./download_data.py log.dryrun.nested nested+http # or nested+aws if you have AWSCLI + + This will download the cropped meteorology fields from our + :ref:`GEOS-Chem Nested Input Data portal + ` to your computer system or EC2 instance. + +#. If you plan to perform a GEOS-Chem Classic simulation drven by GCAP + 2.0 meteorology, follow these steps: + + .. code-block:: console + + $ ./gcclassic --dryrun | tee log.dryrun.gcap2 + $ ./download_data.py log.dryrun.gcap2 rochester + + This will download the GCAP 2.0 meteorology data from the + :ref:`GCAP 2.0 data portal hosted at U. Rochester + ` to your computer system or EC2 instance. For more information about dry-run simulations, please see our :ref:`dry-run` chapter. diff --git a/docs/source/supplemental-guides/horizontal-grids.rst b/docs/source/supplemental-guides/horizontal-grids.rst index f0ebc3173..8e78316a8 100644 --- a/docs/source/supplemental-guides/horizontal-grids.rst +++ b/docs/source/supplemental-guides/horizontal-grids.rst @@ -140,6 +140,7 @@ Select this grid by specifying these in :ref:`cfg-gc-yml`: 54.0000 56.0000 58.0000 60.0000 62.0000 64.0000 66.0000 68.0000 70.0000 72.0000 74.0000 76.0000 78.0000 80.0000 82.0000 84.0000 86.0000 88.0000 89.5000 + .. _gcc-hgrids-global-05: 0.5° x 0.625° global grid @@ -172,6 +173,9 @@ from GMAO. The grid coordinates are computed as follows: Lat_{center}(I) = -90° + 0.25° \times ( J - 1 ),~~~~J = 1..721 + +.. _gcc-hgrids-nested: + ============ Nested grids ============ From 62ba1484a9da103a895bcf12c77c9f24743b7cf7 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 6 Oct 2025 14:48:27 -0400 Subject: [PATCH 43/86] GEOS-Chem update: Merge PR #3050 (Fix precision of area from FV3) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 3d8a03ceb (HEAD -> dev/14.7.0) Merge PR #3050 (Fix precision of GCHP import of area from FV3) PR #3050 fixes a bug in GCHP where area was stored in the State_Grid object as REAL*8 but was imported from FV3 advection as REAL*4. The area computed in FV3 is REAL*8 so there is no reason to truncate to REAL*4 for the import. (Requires companion PR geoschem/FVdycoreCubed_GridComp#10.) 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 5b1ac965f..3d8a03ceb 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 5b1ac965f08e48f086d8fce2647540d59f9e1687 +Subproject commit 3d8a03ceb659603830689cb9e12f26f581ac8d11 From 2723f1e7f9acb0a5d9cda97517e51a9d799bfbee Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 7 Oct 2025 14:08:13 -0400 Subject: [PATCH 44/86] GEOS-Chem update: Merge PR #3062 (Updates for GCHP mass cons.) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e4a4cf370 Merge PR #3062 (Updates for GCHP conservation of rst file species mass) PR #3062 adds a new export to the GCHPchem gridded component of GCHP. The new export DELPDRY is set equal to the internal state value of DELP_DRY during initialize, for use in restart species mass conservation in dynamics prior to running offline advection in the first timestep. In addition, an existing print option in advection, to print proxy mass for air and species, is now a run-time option in config file GCHP.rc. There are two companion PRs required with this update: 1. geoschem/FVdycoreCubed_Grid 2. geoschem/GCHP#515 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 3d8a03ceb..e4a4cf370 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 3d8a03ceb659603830689cb9e12f26f581ac8d11 +Subproject commit e4a4cf370998b9e727eaa9d9badfca25c54b4391 From 8118cec1b16dca0fbdec810c9ab8b99bc7f39da2 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 8 Oct 2025 10:43:28 -0400 Subject: [PATCH 45/86] GEOS-Chem update: Merge PR #3066 (Read rst as REAL*8 for bmk sims) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: d4f100a61 Merge PR #3066 (Toggle "read_restart_as_real8" to true for benchmark sims) PR #3066 adds a call to bash function replace_colon_sep_val to change YAML tag "read_restart_as_real8" from false to true in the geoschem_config.yml file that is placed into fullchem benchmark run directories. PR #3066 also sets "read_restart_as_real8: true" by default in the template file geoschem_config.yml.TransportTracers. This is required for mass conservation in 1-yr or 10-yr TransportTracers benchmarks. Signed-off-by: Bob Yantosca GEOS-Chem update: Merge PR #3066 (Read rst as REAL*8 for bmk sims) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: d4f100a61 Merge PR #3066 (Toggle "read_restart_as_real8" to true for benchmark sims) PR #3066 adds a call to bash function replace_colon_sep_val to change YAML tag "read_restart_as_real8" from false to true in the geoschem_config.yml file that is placed into fullchem benchmark run directories. PR #3066 also sets "read_restart_as_real8: true" by default in the template file geoschem_config.yml.TransportTracers. This is required for mass conservation in 1-yr or 10-yr TransportTracers benchmarks. 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 e4a4cf370..d4f100a61 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e4a4cf370998b9e727eaa9d9badfca25c54b4391 +Subproject commit d4f100a613de4356a25c5f0446c8979ba1b3bc22 From e09f99f14736ce28a2cdb29e50dcf7108f62dfef Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 8 Oct 2025 11:32:48 -0400 Subject: [PATCH 46/86] GEOS-Chem update: Merge PR #3011 (Disable PARANOx at 0.25 or finer) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 6b104bc2f Merge PR #3011 (Disable PARANOx at 0.25 deg resolution or finer) PR #3011 disables the PARANOx extension when running GC-Classic fullchem nested-grid simulatiions at 0.25 x 0.3125 and 0.125 x 0.15625 degree resolution, based on the findings of @eamarais. 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 d4f100a61..6b104bc2f 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit d4f100a613de4356a25c5f0446c8979ba1b3bc22 +Subproject commit 6b104bc2ff782952b37e83fc45dc87d3d1901afb From e69030d30a85274bc294476119a244c2be3f5642 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 8 Oct 2025 15:20:06 -0400 Subject: [PATCH 47/86] GEOS-Chem and HEMCO updates: Merge PR #2893 and HEMCO PR #330 This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 5c9935bdd Merge PR #2893 (Fix for emission config for carbon sims) and to the GitHub geoschem/HEMCO repository: a7df90f Merge PR #330 (Select gridded scale facs based on mask ID) These PRs add functionality for the Integrated Methane Inversion (IMI) with GCHP. 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 6b104bc2f..5c9935bdd 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 6b104bc2ff782952b37e83fc45dc87d3d1901afb +Subproject commit 5c9935bdd2111d4869ac98ab7954ed866b0f75c2 diff --git a/src/HEMCO b/src/HEMCO index 8dbae833a..a7df90f01 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 8dbae833a397da191288c799aa45aaaa3d619324 +Subproject commit a7df90f01c93f02cc6c97e859ec22511d366646e From 5956b705fd41b4ff62ae7902e01b15eff0f6fd97 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 9 Oct 2025 17:01:28 -0400 Subject: [PATCH 48/86] Update geoschem-config-yml doc and related pages docs/source/gcclassic-user-guide/diag-outputs-hist.rst - Add missing text to table docs/source/gcclassic-user-guide/dry-run-run.rst - Replace options with references to geoschem-config.rst headers - Promote options to header 3 - Trimmed trailing whitespace docs/source/restart-file-gc - Convert EFYO section from options to a list-table - Reorganized text to fit within 80 chars - Trimmed trailing whitespace - Use :code:`REAL*4` and :code:`REAL*8` docs/source/geos-chem-shared-docs - Submod update to 59850be Signed-off-by: Bob Yantosca --- .../diag-outputs-hist.rst | 26 ++-- .../gcclassic-user-guide/dry-run-run.rst | 122 ++++++++++-------- .../gcclassic-user-guide/restart-files-gc.rst | 110 +++++++++------- docs/source/geos-chem-shared-docs | 2 +- 4 files changed, 142 insertions(+), 118 deletions(-) diff --git a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst index f3de7572d..93912d3a0 100644 --- a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst +++ b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst @@ -33,11 +33,11 @@ collections in the :ref:`HISTORY.rc configuration file - :option:`fullchem` * - :file:`GEOSChem.AerosolMass.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-aerosolmass` - - :option:`fullchem` + - :option:`fullchem` :option:`aerosol` * - :file:`GEOSChem.Aerosols.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-aerosols` - - :option:`fullchem` + - :option:`fullchem` :option:`aerosol` * - :file:`GEOSChem.BoundaryConditions.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-boundaryconditions` @@ -65,7 +65,7 @@ collections in the :ref:`HISTORY.rc configuration file - :option:`fullchem` * - :file:`GEOSChem.DryDep.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-drydep` - - All simulations with dry- + - All simulations with dry-depositing species * - :file:`GEOSChem.JValues.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-jvalues` - :option:`fullchem` @@ -89,9 +89,9 @@ collections in the :ref:`HISTORY.rc configuration file - :option:`fullchem` * - :file:`GEOSChem.ProdLoss.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-prodloss` - - :option:`fullchem` - :option:`aerosol` - :option:`tagCO` + - :option:`fullchem` + :option:`aerosol` + :option:`tagCO` :option:`tagO3` * - :file:`GEOSChem.RadioNuclide.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-radionuclide` @@ -104,13 +104,13 @@ collections in the :ref:`HISTORY.rc configuration file - All simulations * - :file:`GEOSChem.RxnConst.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-rxnconst` - - :option:`fullchem` - :option:`CH4` + - :option:`fullchem` + :option:`CH4` :option:`Hg` * - :file:`GEOSChem.RxnRates.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-rxnrates` - - :option:`fullchem` - :option:`CH4` + - :option:`fullchem` + :option:`CH4` :option:`Hg` * - :file:`GEOSChem.SatDiagn.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-satdiagn` @@ -141,9 +141,7 @@ collections in the :ref:`HISTORY.rc configuration file - All simulations * - :file:`GEOSChem.WetLossConv.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-wetlossconv` - - All simulations with - wet-deposited species + - All simulations with wet-depositing species * - :file:`GEOSChem.WetLossLS.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-wetlossls` - - All simulations with - wet-deposited species + - All simulations with wet-depositing species diff --git a/docs/source/gcclassic-user-guide/dry-run-run.rst b/docs/source/gcclassic-user-guide/dry-run-run.rst index ce9f11209..916da0c37 100644 --- a/docs/source/gcclassic-user-guide/dry-run-run.rst +++ b/docs/source/gcclassic-user-guide/dry-run-run.rst @@ -1,3 +1,7 @@ +.. |br| raw:: html + +
+ .. _dry-run-run: ############################ @@ -19,59 +23,71 @@ Make sure that you have done the following steps; Then doublecheck these settings in the following :ref:`configuration files `: -.. option:: geoschem_config.yml - - #. :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:`GEOS-FP`, :option:`MERRA2`, :option:`GCAP2`) is - correct for your simulation. - - .. attention:: - - The convection scheme used to generate archived GEOS-FP - meteorology files changed from RAS to Grell-Freitas starting - 01 June 2020 with impact on vertical transport. Discussion - and analysis of the impact is available at - https://github.com/geoschem/geos-chem/issues/1409. - - To fix this issue, different GEOS-Chem convection schemes are - called based on simulation start time. This ensures - comparability in GEOS-Chem runs using GEOS-FP fields - generated using the RAS convection scheme and fields - generated using Grell-Freitas, but only if the simulation - does not cross the 01 June 2020 boundary. We therefore - recommend splitting up GEOS-FP runs in time such that a - single simulation does not span this date. For example, - configure one run to end on 01 June 2020 and then use its - output restart to start another run on 01 June - 2020.. Alternatively consider using MERRA2 which was entirely - generated with RAS, or GEOS-IT which was entirely generated - with Grell-Freitas. If you wish to use a GEOS-FP meteorology - year different from your simulation year please create a - GEOS-Chem GitHub issue for assistance to avoid accidentally - using zero convective precipitation flux. - - #. :option:`root_data_dir`: Make sure that the path to - :file:`ExtData` is correct. - -.. option:: HISTORY.rc - - #. Set the frequency and duration for each :ref:`diagnostic - collection ` to be consistent with the - settings in :option:`geoschem_config.yml`. - -.. option:: HEMCO_Config.rc - - #. Check the `Settings section - `_ - to make sure that diagnostic frequency :envvar:`DiagnFreq`: is - set to the interval that you wish (e.g. :envvar:`Monthly`, - :envvar:`Daily`, :envvar:`YYYYMMDD hhmmss`, etc). - #. Check the `Extension Settings section - `_, - to make sure all of the required emissions inventories and data - sets for your simulation have been switched on. + +geoschem_config.yml +------------------- + +#. :ref:`gc-yml-simulation-start`: Set the start date and time for + your simulation. |br| + |br| + +#. :ref:`gc-yml-simulation-end`: Set the end date and time for your + simulation. |br| + |br| + +#. :ref:`gc-yml-simulation-met`: Check if the meteorology setting + (:option:`GEOS-FP`, :option:`GEOS-IT`, :option:`MERRA2`, + :option:`GCAP2`) is correct for your simulation. + + .. attention:: + + The convection scheme used to generate archived GEOS-FP + meteorology files changed from RAS to Grell-Freitas starting + 01 June 2020 with impact on vertical transport. Discussion + and analysis of the impact is available at + https://github.com/geoschem/geos-chem/issues/1409. + + To fix this issue, different GEOS-Chem convection schemes are + called based on simulation start time. This ensures + comparability in GEOS-Chem runs using GEOS-FP fields + generated using the RAS convection scheme and fields + generated using Grell-Freitas, but only if the simulation + does not cross the 01 June 2020 boundary. We therefore + recommend splitting up GEOS-FP runs in time such that a + single simulation does not span this date. For example, + configure one run to end on 01 June 2020 and then use its + output restart to start another run on 01 June + 2020.. Alternatively consider using MERRA2 which was entirely + generated with RAS, or GEOS-IT which was entirely generated + with Grell-Freitas. If you wish to use a GEOS-FP meteorology + year different from your simulation year please create a + GEOS-Chem GitHub issue for assistance to avoid accidentally + using zero convective precipitation flux. + +#. :ref:`gc-yml-simulation-root`: Make sure that the path to + :file:`ExtData` is correct. + +HISTORY.rc +---------- + +#. Set the frequency and duration for each :ref:`diagnostic + collection ` to be consistent with the + settings in :ref:`cfg-gc-yml`. + +HEMCO_Config.rc +--------------- + +#. Check the `Settings section + `_ + to make sure that diagnostic frequency :envvar:`DiagnFreq`: is + set to the interval that you wish (e.g. :envvar:`Monthly`, + :envvar:`Daily`, :envvar:`YYYYMMDD hhmmss`, etc). |br| + |br| + +#. Check the `Extension Settings section + `_, + to make sure all of the required emissions inventories and data + sets for your simulation have been switched on. .. tip:: diff --git a/docs/source/gcclassic-user-guide/restart-files-gc.rst b/docs/source/gcclassic-user-guide/restart-files-gc.rst index 22d301215..771e105a7 100644 --- a/docs/source/gcclassic-user-guide/restart-files-gc.rst +++ b/docs/source/gcclassic-user-guide/restart-files-gc.rst @@ -10,44 +10,52 @@ GEOS-Chem restart files How are restart files read into GEOS-Chem? ========================================== -GEOS-Chem restart files may be read via `HEMCO`_ or via GEOS-Chem. -If using HEMCO then all fields are read as single precision floating point (REAL4). -If using GEOS-Chem then all fields are read with the native precision stored in the file, -e.g. double precision floating point (REAL8) for species concentrations. Using HEMCO is -on by default, but you may choose to use GEOS-Chem instead by updating the -:file:`geoschem_config.yml` configuration file entry :literal:`read_restart_as_real8` -to :literal:`true`. - -There are pros and cons to both methods of reading the GEOS-Chem restart file. -Using HEMCO allows forcing the timestamp of the restart file to match run start date -and time as well as doing custom alterations such as changing the names of the expected -variables in the file. It also allows online regridding and cropping of restart files -at run-time, a requirement for nested grid simulations if using a global restart file. -However, using HEMCO to read the restart file prevents bit-for-bit -reproducibility when restarting a run and also prevents restart file mass conservation. -This is because of the precision loss associated with reading restart fields as REAL4 -when they are stored internally in the model as REAL8. - -Using GEOS-Chem to read restart files enables bit-for-bit reproducibility upon -restart as well as file mass conservation. However, it prevents using HEMCO read -features. In particular it is not appropriate to use if the restart file horizontal -grid does not match the run horizontal grid or if the restart file needs to be cropped. -In both cases the model will fail. The model will also exit with an error message if -using the mercury simulation since this feature has not yet been validated for that -simulation. +GEOS-Chem restart files may be read via `HEMCO +`_ or via GEOS-Chem. If using HEMCO then +all fields are read as single precision floating point +(:code:`REAL*4`). If using GEOS-Chem then all fields are read with +the native precision stored in the file, e.g. double precision +floating point (:code:`REAL*8`) for species concentrations. Using +HEMCO is on by default, but you may choose to use GEOS-Chem instead by +updating the :file:`geoschem_config.yml` configuration file entry +:literal:`read_restart_as_real8` to :literal:`true`. + +There are pros and cons to both methods of reading the GEOS-Chem +restart file. Using HEMCO allows forcing the timestamp of the restart +file to match run start date and time as well as doing custom +alterations such as changing the names of the expected variables in +the file. It also allows online regridding and cropping of restart +files at run-time, a requirement for nested grid simulations if using +a global restart file. However, using HEMCO to read the restart file +prevents bit-for-bit reproducibility when restarting a run and also +prevents restart file mass conservation. This is because of the +precision loss associated with reading restart fields as +:code:`REAL*4` when they are stored internally in the model as +:code:`REAL*8`. + +Using GEOS-Chem to read restart files enables bit-for-bit +reproducibility upon restart as well as file mass +conservation. However, it prevents using HEMCO read features. In +particular it is not appropriate to use if the restart file horizontal +grid does not match the run horizontal grid or if the restart file +needs to be cropped. In both cases the model will fail. The model will +also exit with an error message if using the mercury simulation since +this feature has not yet been validated for that simulation. ================================ Using HEMCO to read restart file ================================ -This section pertains only to using HEMCO to read the GEOS-Chem restart file. -All fields are read in as REAL4. See the section above if you instead wish to read -fields at their native precision. +This section pertains only to using HEMCO to read the GEOS-Chem +restart file. All fields are read in as :code:`REAL*4`. See the +section above if you instead wish to read fields at their native +precision. -The entries for restart files are stored in :file:`HEMCO_Config.rc`. They may vary slightly for different -simulation types. These fields are obtained from HEMCO and copied to -the appropriate :code:`State_Chm` and :code:`State_Met` fields in -routine :code:`Get_GC_Restart` (located in +The entries for restart files are stored in +:file:`HEMCO_Config.rc`. They may vary slightly for different +simulation types. These fields are obtained from HEMCO and +copied to the appropriate :code:`State_Chm` and :code:`State_Met` +fields in routine :code:`Get_GC_Restart` (located in :file:`GeosCore/hcoi_gc_main_mod.F90`). .. code-block:: console @@ -74,24 +82,26 @@ GEOS-Chem species (the :file:`SPC_` entry) use HEMCO time cycle flag :code:`EFYO` by default. Other restart file fields use the time cycle flag :code:`EY`. These are explained below. -.. option:: E - - :command:`Exact`: Stops with an error if the date of the - simulation is different than the file timestamp. - -.. option:: F - - :command:`Forced`: Stops with an error if the file isn't found. - -.. option:: Y - - :command:`Simulation Year`: Only reads the data for the simulation - year but not for other years. - -.. option:: O - - :command:`Once`: Does not keep cycling in time but only reads the - file once. +.. list-table:: HEMCO time cycle flags used with GEOS-Chem restart files + :header-rows: 1 + :widths: 10 20 70 + + * - Flag + - Name + - Description + * - :command:`E` + - :command:`Exact` + - Stops with an error if the date of the simulation is different + than the file timestamp. + * - :command:`F` + - :command:`Forced` + - Stops with an error if the file isn't found. + * - :command:`Y` + - :command:`Simulation Year` + - Only reads the data for the simulation year but not for other years. + * - :command:`O` + - :command:`Once` + - Does not keep cycling in time but only reads the file once. When reading the **species concentrations** (time cycle flag: :code:`EFYO`) from the restart file, HEMCO will cause your simulation diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 3a3890277..59850bef7 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 3a38902771fbbfe9f8aff0facf52c2d3da81b109 +Subproject commit 59850bef7a33911b2ed49652121e27111cb62202 From 744613fd80bb0e0b7b725710758ebedab2893ef4 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 9 Oct 2025 17:27:36 -0400 Subject: [PATCH 49/86] Add info about GEOS-IT to nested-grid-guide.rst docs/source/supplemental-guides/nestgrid-guide.rst - Add GEOS-IT to the list of met fields - Convert the bullet list of data portals to a list-table - Add a note that the cropped met fields are stored at the GEOS-Chem Nested Input Data portal Signed-off-by: Bob Yantosca --- .../supplemental-guides/nested-grid-guide.rst | 37 +++++++++++-------- 1 file changed, 22 insertions(+), 15 deletions(-) diff --git a/docs/source/supplemental-guides/nested-grid-guide.rst b/docs/source/supplemental-guides/nested-grid-guide.rst index b8524ce7f..dc72b8571 100644 --- a/docs/source/supplemental-guides/nested-grid-guide.rst +++ b/docs/source/supplemental-guides/nested-grid-guide.rst @@ -9,10 +9,11 @@ Run nested-grid simulations ########################### A **nested-grid simulation** is a GEOS-Chem Classic simulation running -at the native horizontal resolution of the GEOS-FP (0.25° x 0.3125°) -or MERRA-2 (0.5° x 0.6125°) meteorology fields over a subset of +at the native horizontal resolution of the :option:`GEOS-FP` (0.25° x +0.3125° or 0.125° x 0.15625°), :option:`GEOS-IT` (0.5° x 0.625°), or +:option:`MERRA2` (0.5° x 0.625°) meteorology fields over a subset of the globe. Nested-grid simulations use boundary conditions for -transport that are archived from a global simulatoin. +transport that are archived from a global simulation. Follow these steps to set up a GEOS-Chem Classic nested-grid simulation: @@ -241,18 +242,24 @@ How can I find which data are available for nested grid simulations? 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/ - +.. list-table:: + :header-rows: 1 + + * - Portal + - Link + * - :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/ + +As of October 2025, the GEOS-Chem Nested Input Data portal stores +:option:`GEOS-FP`, :option:`GEOS-IT`, and :option:`MERRA2` meteorology +fields that have been cropped to one of the +:ref:`traditional nested-grid domains `. These +data have since been removed from the main GEOS-Chem Input Data portal. + .. _nestgrid-faq-errors: Where can I find out more info about nested grid errors? From c7fc0478fad4c4cbab2a9fc1a56e0e25997cf565 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 10 Oct 2025 15:54:52 -0400 Subject: [PATCH 50/86] geos-chem-shared-doc submod update to 1714833 The docs/source/geos-chem-shared-docs repo now points to commit 1714833 (Update "Build required software with spack" guide") Signed-off-by: Bob Yantosca --- 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 59850bef7..17148337b 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 59850bef7a33911b2ed49652121e27111cb62202 +Subproject commit 17148337b6083e561bbc69ea27aeff765e9cec5f From ab50ab2b9e3d10dce985aced27f421d30fcac2d4 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 16 Oct 2025 10:24:23 -0400 Subject: [PATCH 51/86] GEOS-Chem update: Merge PR #3074 (Fix error in carbon sim) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 89336ce92 Merge PR #3074 (Fix typos causing carbon simulations to crash) PR #3074 fixes an out-of-bounds error in KPP/carbon/carbon_Funcs.F90 when the Carbon diagnostic collection is enabled. The Carbon collection is now also turned on by default so as to allow our integration tests to catch similar errors. 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 5c9935bdd..89336ce92 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 5c9935bdd2111d4869ac98ab7954ed866b0f75c2 +Subproject commit 89336ce92bbfa47672763aa893b6a63a783726f6 From 56f63e0e70e6dfac5783d4633998dd8ebb2b1a22 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 16 Oct 2025 11:20:46 -0400 Subject: [PATCH 52/86] GEOS-Chem update: Merge PR #3073 (Fix typo in GCHP run script) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 6b8455bb7 Merge PR #3073 (Fix typo in GCHP operational run script) PR #3073 fixes an search error in e Harvard example script gchp.submit_consecutive_jobs.sh. It was searching for "DURATION" but should have searched for "Run_Duration", 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 89336ce92..6b8455bb7 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 89336ce92bbfa47672763aa893b6a63a783726f6 +Subproject commit 6b8455bb77bd95c7a18a52612fd35f50269f65e5 From 8cb2fc03db0e73448c6ea95a69805b7b9e3d919a Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 20 Oct 2025 11:44:10 -0400 Subject: [PATCH 53/86] geos-chem-submod update to 8cc346e (Add doc about restart file) docs/source/geos-chem-shared-docs - Submod has been updated to 8cc346e. Documentation has been added to doc/hemco-config.rst to make it more clear that users need to change the time cycle flag if the run dies due to restart. Signed-off-by: Bob Yantosca --- 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 17148337b..8cc346ebf 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 17148337b6083e561bbc69ea27aeff765e9cec5f +Subproject commit 8cc346ebfe16182d5cd12ade2681da84ee48a5a3 From 52ded6d6c04d6dbb068a8553510bc927b59fd10f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 23 Oct 2025 14:21:34 -0400 Subject: [PATCH 54/86] GEOS-Chem update: Merge PR #3087 (Fix bug in ObsPack sampling) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 65ae1f305 Merge PR #3087 (Fix bug in ObsPack sampling) PR #3087 updates the logic so that ObsPack data points that are instantaneously-sampled (i.e. having CT_sampling_strategy = 4) and that lie within 1/2 model timestep of the end of the day will be included in the sampling. This fixes a bug in #3084 that was reported by @mattloman. 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 6b8455bb7..65ae1f305 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 6b8455bb77bd95c7a18a52612fd35f50269f65e5 +Subproject commit 65ae1f3050f928c1e4dec968b67495d3b2251997 From ecc2328366e24a96e850976a9eb26b88d9b8a05e Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 23 Oct 2025 14:58:50 -0400 Subject: [PATCH 55/86] GEOS-Chem update: Merge PR #3086 (Fix LPJ path in ExtData.rc) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: b4225f205 Merge PR #3086 (Fix LPJ wetland path in ExtData.rc) PR #3086 changes the path for LPJ wetlands emissions in the GCHP carbon-simulation ExtData.rc to use the HEMCO data directory. Previously the path was local on the Harvard Cannon compute cluster. 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 65ae1f305..b4225f205 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 65ae1f3050f928c1e4dec968b67495d3b2251997 +Subproject commit b4225f205a11da6fe01a368c6ad3e1a8e3773562 From 7a4ff7b4bdb63f89cd728399fbf0569972328011 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 28 Oct 2025 10:49:04 -0400 Subject: [PATCH 56/86] HEMCO update: Merge PR #345 (Rewrite error message for clarity) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/HEMCO repository: 12da969 Merge PR #345 (Rewrite the "cannot find field for current time" error msg) PR #345 This PR seeks to reduce the confusion among GEOS-Chem Classic by rewriting the "Cannot find file for current simulation time" error with specific steps that the user can take to get past the error. It also adds word-wrap functionality into src/Core/hco_chartools_mod.F90 so that error messages can be wrapped at 78 characters for better readability. Signed-off-by: Bob Yantosca --- src/HEMCO | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/HEMCO b/src/HEMCO index a7df90f01..12da96925 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit a7df90f01c93f02cc6c97e859ec22511d366646e +Subproject commit 12da96925cbfcb3f22e8b008a798442a15e0dfaf From 17b19c21dda8221cad96a29b350bacdc163fbd85 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 29 Oct 2025 13:34:15 -0400 Subject: [PATCH 57/86] GEOS-Chem update: Merge PR #3095 (Fix carbon sim diagnostic error) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: c39a8f9a3 Merge PR #3095 (Fix diagnostic error for CO2-only or OCS-only sims) PR #3095 fixes an out-of-bounds error that can occur in the CO2-only and OCS-only carbon simulations when the State_Diag%OHconcAfterChem diagnostic is selected to be archived, but when the OHdiurnalFac array is not allocated. To fix the error we enclose the IF block where the diagnostic is updated with in the IF ( id_CH4_adv > 0 .or. id_CO_adv > 0 ) block. 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 b4225f205..c39a8f9a3 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit b4225f205a11da6fe01a368c6ad3e1a8e3773562 +Subproject commit c39a8f9a3889b5b505b03ef357ec4c9c50b264be From 3b4adf385de11a65941687560094c2ab3d1abe98 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 30 Oct 2025 13:21:59 -0400 Subject: [PATCH 58/86] geos-chem-shared-docs update: Update dust species for 14.7.0 docs/source/geos-chem-shared-docs - Submodule update to 1e39c0a (Update list of dust species for 14.7.0) 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 8cc346ebf..1e39c0a49 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 8cc346ebfe16182d5cd12ade2681da84ee48a5a3 +Subproject commit 1e39c0a499fd93d1d631a0270ec1aa63ea98ac4d From 002ac473cd3ca50600a240c77bf7c6880b3c2dbe Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 17 Nov 2025 10:04:39 -0500 Subject: [PATCH 59/86] GEOS-Chem update: Merge PR #2685 (Retire CO2, CH4, tagCO sims) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a52cb2407 Merge PR #2685 (Retire CO2, CH4, and tagged CO simulations) PR #2685 removes source code and configuration files for the individual CH4, CO2, and tagCO simulations, as these are now superseded by the carbon simulation. 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 c39a8f9a3..a52cb2407 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit c39a8f9a3889b5b505b03ef357ec4c9c50b264be +Subproject commit a52cb240771f71f73ba1198afa43fb4f0d427b15 From 8c73df57a2dd8b72a3eedacb466bcea7c5bc2127 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 19 Nov 2025 15:05:29 -0500 Subject: [PATCH 60/86] HEMCO update: Merge PR #346 (Use gcc 15 in "Mac" GitHub action) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/HEMCO repository: HEMCO update: Merge PR #346 (Use gcc 15 in "Mac" GitHub action) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/HEMCO repository: 43ad195 Merge PR #346 (Replace gcc 12 w/ gcc 15 in Mac GitHub Action ) PR #346 removes GNU Compiler Collection 12 and replaces it with version 15 in the "Mac" GitHub Action, which tries to build HEMCO on MacOS. GCC 12 evidently has been "delisted" from the Mac "HomeBrew" package manager, and this causes the compilation test with GCC 12 to fail. Signed-off-by: Bob Yantosca 43ad195 Merge PR #346 (Replace gcc 12 w/ gcc 15 in Mac GitHub Action ) PR #346 removes GNU Compiler Collection 12 and replaces it with version 15 in the "Mac" GitHub Action, which tries to build HEMCO on MacOS. GCC 12 evidently has been "delisted" from the Mac "HomeBrew" package manager, and this causes the compilation test with GCC 12 to fail. Signed-off-by: Bob Yantosca --- src/HEMCO | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/HEMCO b/src/HEMCO index 12da96925..43ad1958b 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 12da96925cbfcb3f22e8b008a798442a15e0dfaf +Subproject commit 43ad1958b490b9e233c7f222891d9966d8227f1f From 6473bd4e891931b86ba65029f5ab2da19089cf78 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 19 Nov 2025 16:54:52 -0500 Subject: [PATCH 61/86] Updated RTD doc for removal of individual carbon simulations docs/source/gcclassic-user-guide/compile-cmake.rst - Replaced hardwired Cloud-J version number with "G.H.I" docs/source/gcclassic-user-guide/rundir-carbon.rst docs/source/gcclassic-user-guide/rundir-fullchem.rst - Removed CH4, CO2, TaggedCO options from the run directory script example output docs/source/geos-chem-shared-docs - Submod update to 325a105 (Update RTD pages...) Signed-off-by: Bob Yantosca --- docs/source/gcclassic-user-guide/compile-cmake.rst | 2 +- docs/source/gcclassic-user-guide/rundir-carbon.rst | 3 --- docs/source/gcclassic-user-guide/rundir-fullchem.rst | 3 --- docs/source/geos-chem-shared-docs | 2 +- 4 files changed, 2 insertions(+), 8 deletions(-) diff --git a/docs/source/gcclassic-user-guide/compile-cmake.rst b/docs/source/gcclassic-user-guide/compile-cmake.rst index 160366db1..0df37abe4 100644 --- a/docs/source/gcclassic-user-guide/compile-cmake.rst +++ b/docs/source/gcclassic-user-guide/compile-cmake.rst @@ -132,7 +132,7 @@ generate output similar to this: ================================================================= ================================================================= Cloud-J G.H.I - Current status: 8.0.2 + Current status: G.H.I ================================================================= ================================================================= GEOS-Chem X.Y.Z (science codebase) diff --git a/docs/source/gcclassic-user-guide/rundir-carbon.rst b/docs/source/gcclassic-user-guide/rundir-carbon.rst index d04c682e2..e7d3e836e 100644 --- a/docs/source/gcclassic-user-guide/rundir-carbon.rst +++ b/docs/source/gcclassic-user-guide/rundir-carbon.rst @@ -74,9 +74,6 @@ simulation. We'll use the carbon gases simulation as an example. 6. Tagged O3 7. Trace metals 8. TransportTracers - 9. CH4 - 10. CO2 - 11. Tagged CO >>> To select the GEOS-Chem carbon gases specialty simulation, type diff --git a/docs/source/gcclassic-user-guide/rundir-fullchem.rst b/docs/source/gcclassic-user-guide/rundir-fullchem.rst index 08ebc6bd7..e90b444e4 100644 --- a/docs/source/gcclassic-user-guide/rundir-fullchem.rst +++ b/docs/source/gcclassic-user-guide/rundir-fullchem.rst @@ -71,9 +71,6 @@ GEOS-Chem full-chemistry simulation. 6. Tagged O3 7. Trace metals 8. TransportTracers - 9. CH4 - 10. CO2 - 11. Tagged CO >>> To create a run directory for the full-chemistry simulation, type diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 1e39c0a49..325a105a7 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 1e39c0a499fd93d1d631a0270ec1aa63ea98ac4d +Subproject commit 325a105a7b03365ab50103e8aa8210100f7648c2 From 0fbfc6421be1c9b40948df53e95446fcea21b8a6 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 20 Nov 2025 17:20:06 -0500 Subject: [PATCH 62/86] geos-chem-shared-docs update: Update lists of species Updated the geos-chem-shared-docs submodule to cb1d355, which includes these commits: cb1d355 Update list of species for carbon and Hg simulations 1d5eed5 Remove TDST from list of species in fullchem.rst 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 325a105a7..cb1d35531 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 325a105a7b03365ab50103e8aa8210100f7648c2 +Subproject commit cb1d35531c5af8ff353b9328e48c53f97720adeb From 30b7c25182682c31e293a24fc222f98bee8642a8 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 21 Nov 2025 10:26:17 -0500 Subject: [PATCH 63/86] GEOS-Chem update: Merge PR #3115 (Fix prod/loss diagnostic mapping) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e1bf9abcb Merge PR #3115 (Fix prod/loss diagnostic species mapping) PR #3115 passes the TaggedDiag_List to Init_State_Chm (and other internal routines) so that we can determine if a prod/loss species or wildcard has been requested for diagnostic archiveal before attempting to populate mapping arrays. This fixes the error raised by @eamarais in #3106. 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 a52cb2407..e1bf9abcb 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit a52cb240771f71f73ba1198afa43fb4f0d427b15 +Subproject commit e1bf9abcb5eff8e829293f1a1384ac51cf4afd1b From 05cf975e92d76108f9ed98a444c211ef8542202c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 21 Nov 2025 12:21:20 -0500 Subject: [PATCH 64/86] GEOS-Chem update: Merge PR #3104 (Remove div by TS_EMIS in aer-only code) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e43a5a01d Merge PR 3104 (Do not divide PH2O2m by TS_EMIS in aer-only code) PR #3104 removes an extraneous division by the emissions timestep in the aerosol-only simulation. 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 e1bf9abcb..e43a5a01d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e1bf9abcb5eff8e829293f1a1384ac51cf4afd1b +Subproject commit e43a5a01deb79f11cf6aea238f4f908ae6ee6f2d From af5481702bfeb859ea84be7c1608dbbd78674e94 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 21 Nov 2025 17:20:17 -0500 Subject: [PATCH 65/86] geos-chem-submod-update to f5f39e7 (Updated "editing-these-docs.rst") docs/source/geos-chem-shared-docs - Submod update to f5f39e7 (Updated the "Editing this User Gude 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 cb1d35531..f5f39e763 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit cb1d35531c5af8ff353b9328e48c53f97720adeb +Subproject commit f5f39e7639b3c8abcdf494d03150703995e958e0 From 59bb77c664ce084c3527e96997b7646fb96817cc Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 24 Nov 2025 11:28:37 -0500 Subject: [PATCH 66/86] Added "read_the_docs_environment.yml" for creating a RTD conda env docs/read_the_docs_environment.yml - Added this environment file with the proper specifications to create the "rtd_env" Conda environment containing Sphinx + dependencies docs/source/geos-chem-shared-docs - Updated "editing_these_docs.rst" with instructions on how to install Sphinx via Conda and build the docs from within the rtd_env Conda environment CHANGELOG.md - Updated accordingly --- CHANGELOG.md | 6 +++++- docs/read_the_docs_environment.yml | 24 ++++++++++++++++++++++++ docs/source/geos-chem-shared-docs | 2 +- 3 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 docs/read_the_docs_environment.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index ec876b89e..72c9d8090 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,10 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Added "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs - Added "GEOS-Chem Classic horiziontal grids" supplemental guide in ReadTheDocs - Added "Particulate matter in GEOS-Chem" supplemental guide in ReadTheDocs +- Added `docs/read_the_docs_environment.yml` Conda environment file + +### Changed +- Updated `geos-chem-shared-docs/editing_these_docs.rst` with instructions for using a Conda environment to build RTD doc ## [14.6.3] - 2025-07-28 ### Added @@ -23,7 +27,7 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Updated `CMakeLists.txt` to set compilation option `mcmodel=small` for ARM-based CPUs, as ARM does not support `mcmodel=medium` - Updated ReadTheDocs documentation to state that we are using Spack v0.23.1 in the Spack installation guide - Updated GEOS-Chem submodule to 14.6.3 -- Updated HEMCO submodule to 3.11.2 +- Updated HEMCO submodule to 3.11. ## [14.6.2] - 2025-06-12 ### Changed diff --git a/docs/read_the_docs_environment.yml b/docs/read_the_docs_environment.yml new file mode 100644 index 000000000..5aefcac13 --- /dev/null +++ b/docs/read_the_docs_environment.yml @@ -0,0 +1,24 @@ +--- +# ====================================================================== +# ReadTheDocs environment file +# +# If you wish to build a Mamba/Conda environment with the dependencies +# needed for building the ReadTheDocs documentation, use: +# +# $ mamba env create -n rtd_env --file=read_the_docs_environment.yml +# ====================================================================== +name: rtd_env +channels: + - conda-forge + - nodefaults +dependencies: + - python==3.12.0 + - sphinx==7.2.6 + - sphinx_rtd_theme==2.0.0 + - sphinxcontrib-bibtex==2.6.2 + - sphinx-autobuild==2021.3.14 + - recommonmark==0.7.1 + - docutils==0.20.1 + - jinja2==3.1.6 + + diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index f5f39e763..5d58359fd 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit f5f39e7639b3c8abcdf494d03150703995e958e0 +Subproject commit 5d58359fdc0d81634ef37c702f3a3c7a39dfdb10 From 7cb309d6ac4a9797e9f6fbe563238bdf3fdf4185 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 24 Nov 2025 16:12:28 -0500 Subject: [PATCH 67/86] geos-chem-shared-docs update: Fixed species list in fullchem.rst This commit informs the GCClassic superproject about the following commits that were pushed to the geos-chem-shared-docs submodule. 81560a7 Added fixes to species list in simulations/fullchem.rst 5d58359 Updated "editing_these_docs.rst"; now use a Conda env to build RTD Signed-off-by: Bob Yantosca --- 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 5d58359fd..81560a7ee 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 5d58359fdc0d81634ef37c702f3a3c7a39dfdb10 +Subproject commit 81560a7ee2115dab8238d5d4bf3caaac18e200d3 From 1ed24a13131628bd898a7b615c5c3141385c972d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 24 Nov 2025 16:37:44 -0500 Subject: [PATCH 68/86] geos-chem-shared-docs update: Fix incorrect info in editing_these_docs.rst docs/source/geos-chem-shared-docs - Update workflow in editing_these_docs.rst so that the "make clean" commands are issued while sphinx-autobuild is running. Signed-off-by: Bob Yantosca --- 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 81560a7ee..5289c7d6c 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 81560a7ee2115dab8238d5d4bf3caaac18e200d3 +Subproject commit 5289c7d6caac428da8f61439a8532fe3899a36b0 From ccac042365f90612fe7ed704930c3ef2c8669fdc Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 25 Nov 2025 18:30:53 -0500 Subject: [PATCH 69/86] RTD updates: Consistency updates for geos-chem-shared-docs docs/source/geos-chem-shared-docs - Submodule update to 5f56a42: - Update supplemental guides for dust species etc. in 14.7.0 - Removed obsolete options from geoschem-config.rst docs/source/gcclassic-user-guide/diag-outputs-hist.rst - Removed references to CO, CH4, CO2 collections docs/source/gcclassic-user-guide/restart-files-gc.rst docs/source/getting-started/quick-start.rst - Fixed broken links docs/source/supplemental-guides/directory-structure.rst - Changed "ReST" to "reST" docs/source/supplemental-guides/run-script-examples.rst - Now use gnu12 environment file Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/diag-outputs-hist.rst | 14 ++------------ .../gcclassic-user-guide/restart-files-gc.rst | 8 ++++---- docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/quick-start.rst | 8 ++++---- .../supplemental-guides/directory-structure.rst | 14 +++++++------- .../supplemental-guides/run-script-examples.rst | 2 +- 6 files changed, 19 insertions(+), 29 deletions(-) diff --git a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst index 93912d3a0..065531824 100644 --- a/docs/source/gcclassic-user-guide/diag-outputs-hist.rst +++ b/docs/source/gcclassic-user-guide/diag-outputs-hist.rst @@ -45,18 +45,9 @@ collections in the :ref:`HISTORY.rc configuration file * - :file:`GEOSChem.Carbon.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-carbon` - :option:`carbon` - * - :file:`GEOSChem.CH4.YYYYMMDD_hhhmmz.nc4` - - :ref:`histguide-ch4` - - :option:`CH4` * - :file:`GEOSChem.CloudConvFlux.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-cloudconvflux` - All simulations - * - :file:`GEOSChem.CO.YYYYMMDD_hhhmmz.nc4` - - :ref:`histguide-co` - - :option:`CH4` - * - :file:`GEOSChem.CO2.YYYYMMDD_hhhmmz.nc4` - - :ref:`histguide-co2` - - :option:`CH4` * - :file:`GEOSChem.ConcAboveSfc.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-concabovesfc` - :option:`fullchem` @@ -91,7 +82,6 @@ collections in the :ref:`HISTORY.rc configuration file - :ref:`histguide-prodloss` - :option:`fullchem` :option:`aerosol` - :option:`tagCO` :option:`tagO3` * - :file:`GEOSChem.RadioNuclide.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-radionuclide` @@ -105,12 +95,12 @@ collections in the :ref:`HISTORY.rc configuration file * - :file:`GEOSChem.RxnConst.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-rxnconst` - :option:`fullchem` - :option:`CH4` + :option:`carbon` :option:`Hg` * - :file:`GEOSChem.RxnRates.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-rxnrates` - :option:`fullchem` - :option:`CH4` + :option:`carbon` :option:`Hg` * - :file:`GEOSChem.SatDiagn.YYYYMMDD_hhhmmz.nc4` - :ref:`histguide-satdiagn` diff --git a/docs/source/gcclassic-user-guide/restart-files-gc.rst b/docs/source/gcclassic-user-guide/restart-files-gc.rst index 771e105a7..8081636fc 100644 --- a/docs/source/gcclassic-user-guide/restart-files-gc.rst +++ b/docs/source/gcclassic-user-guide/restart-files-gc.rst @@ -145,10 +145,10 @@ When reading **other restart file fields** (time cycle flag: 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}` + :ref:`spcguide-defs-other-bkgdvv` entry in + :ref:`species_database.yml `. If the species does not + have a :ref:`spcguide-defs-other-bkgdvv` value specified, then its + initial concentration will be set to :math:`1.0{\times}10^{-20}` instead. .. _restart-files-gc-date: diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 5289c7d6c..5b56a4297 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 5289c7d6caac428da8f61439a8532fe3899a36b0 +Subproject commit 5b56a429783c287247e9d320a0182522b650d015 diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst index 0c14a85ab..0acff7aed 100644 --- a/docs/source/getting-started/quick-start.rst +++ b/docs/source/getting-started/quick-start.rst @@ -336,10 +336,10 @@ You should review these files before starting a simulation: 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}` + :ref:`spcguide-defs-other-bkgdvv` entry in + :ref:`species_database.yml `. If the species does + not have a :ref:`spcguide-defs-other-bkgdvv` 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 diff --git a/docs/source/supplemental-guides/directory-structure.rst b/docs/source/supplemental-guides/directory-structure.rst index e6f93e693..eba105817 100644 --- a/docs/source/supplemental-guides/directory-structure.rst +++ b/docs/source/supplemental-guides/directory-structure.rst @@ -22,13 +22,13 @@ GEOS-Chem Classic reside. | +---geos-chem-shared-docs # Submodule containing shared documentation files | | # (such as common supplemental guides) | | - | +---getting-started # Markup files (ReST format) for ReadTheDocs + | +---getting-started # Markup files (reST format) for ReadTheDocs | | - | +---help-and-reference # Markup files (ReST format) for ReadTheDocs + | +---help-and-reference # Markup files (reST format) for ReadTheDocs | | | +---_static # Static content (e.g. images) for ReadTheDocs | | - | +---supplemental-guides # Markup files (ReST format) for ReadTheDocs + | +---supplemental-guides # Markup files (reST format) for ReadTheDocs | # (Content specific to GEOS-Chem Classic) | +---run # Link to src/GEOS-Chem/run/GCClassic @@ -138,11 +138,11 @@ GEOS-Chem Classic reside. | | | +---geos-chem-shared-docs # Submodule containing shared documentation files | | | | # (such as common supplemental guides) | | | | - | | | +---hco-ref-guide # Markup files (ReST format) for ReadTheDocs + | | | +---hco-ref-guide # Markup files (reST format) for ReadTheDocs | | | | - | | | +---hco-sa-guide # Markup files (ReST format) for ReadTheDocs + | | | +---hco-sa-guide # Markup files (reST format) for ReadTheDocs | | | | - | | | +---reference # Markup files (ReST format) for ReadTheDocs + | | | +---reference # Markup files (reST format) for ReadTheDocs | | | | | | | +---_static # Static content (e.g. images) for ReadTheDocs | | | @@ -185,4 +185,4 @@ GEOS-Chem Classic reside. | +---spack # Link to docs/source/geos-chem-shared-docs/spack | - +---test # Link to src/GEOS-Chem/test \ No newline at end of file + +---test # Link to src/GEOS-Chem/test diff --git a/docs/source/supplemental-guides/run-script-examples.rst b/docs/source/supplemental-guides/run-script-examples.rst index 695a35dba..9c3ab53df 100644 --- a/docs/source/supplemental-guides/run-script-examples.rst +++ b/docs/source/supplemental-guides/run-script-examples.rst @@ -37,7 +37,7 @@ Save this code to a file named :file:`geoschem.run.slurm`: ### particularly if you are running at very fine resolution (e.g. nested-grid) ############################################################################### # Source the environment file that you created - source /path/to/gcclassic.gnu10.env + source /path/to/gcclassic.gnu12.env # Set the proper # of threads for OpenMP # SLURM_CPUS_PER_TASK ensures this matches the number you set with -c above From e2017d777caa65397026a21801bfd48047bece9f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 1 Dec 2025 11:48:38 -0500 Subject: [PATCH 70/86] geos-chem-shared-docs submod update to 1ba5a65 docs/source/geos-chem-shared-docs - Updated to 1ba5a65 (Replace refs to GC-Classic Horizontal Grids with links) 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 5b56a4297..1ba5a650f 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 5b56a429783c287247e9d320a0182522b650d015 +Subproject commit 1ba5a650f3fe0a7a25cbb7c5c44993e185f9a494 From 9cb0a4976a484559c2ea40b0da20ba7adf85d08b Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 1 Dec 2025 13:39:53 -0500 Subject: [PATCH 71/86] GEOS-Chem update: Merge PR #3113 (Consolidate Hg metadata) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: e852c244d Merge PR #3113 (Consolidate Hg metadata into species_database.yml) PR #3113 does the following: 1. Consolidates all metadata for Hg species (currently present in run/shared/species_database_hg.yml) into the run/shared/species_database.yml. 2. Removes metadata for obsolete tagged Hg species. 3. Updates run/GCClassic/createRunDir.sh accordingly so that we just copy run/shared/species_database.yml to the run directory. 4. Adds IUPAC names for Hg species in under the FullName tag of 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 e43a5a01d..e852c244d 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e43a5a01deb79f11cf6aea238f4f908ae6ee6f2d +Subproject commit e852c244d5a9b231dd5452a3153f95e3abd3edb3 From be99f43b41616ce86baedf89f56449a16787d556 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 1 Dec 2025 15:40:48 -0500 Subject: [PATCH 72/86] GEOS-Chem update: Merge PR #3121 (Add int test straddling 00 UTC) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 3236dc5a7 Merge PR #3121 (Add GC-Classic int test straddling 00 UTC) PR #3121 introduces a new GEOS-Chem Classic integration test (based on gc_4x5_merra2_carbon_CH4) that straddles a UTC date boundary. The test starts at 20190101T18:00:00 UTC and ends on 20190102T01:00:00 UTC. This is one of the "wish list" integration tests described in #714. 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 e852c244d..3236dc5a7 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit e852c244d5a9b231dd5452a3153f95e3abd3edb3 +Subproject commit 3236dc5a7e2c22dbf7480af68675c23dd331895b From 0bf92e87019f1709788671f2519c77d194656864 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 2 Dec 2025 12:30:10 -0500 Subject: [PATCH 73/86] Update dry-run documentation to be clearer docs/source/gcclassic-user-guide/dry-run-download.rst docs/source/getting-started/quick-start.rst - Updated dry-run instructions to be more specific about activating the Conda environment. Also split into subsections. docs/source/geos-chem-shared-docs - Submod update to d785e727 (species-guide.rst updates) CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- .../gcclassic-user-guide/dry-run-download.rst | 158 +++++++++++++----- docs/source/geos-chem-shared-docs | 2 +- docs/source/getting-started/quick-start.rst | 84 +++++++--- 3 files changed, 176 insertions(+), 68 deletions(-) diff --git a/docs/source/gcclassic-user-guide/dry-run-download.rst b/docs/source/gcclassic-user-guide/dry-run-download.rst index e2f964a3b..1f215ee62 100644 --- a/docs/source/gcclassic-user-guide/dry-run-download.rst +++ b/docs/source/gcclassic-user-guide/dry-run-download.rst @@ -11,32 +11,7 @@ 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 different -:ref:`data repositories `. - -.. important:: - - Before you use the :file:`download_data.py` script, make sure to - initialize a Mamba or Conda environment with the relevant command - shown below: - - .. code-block:: console - - $ mamba activate ENV-NAME # If using Mamba - - $ conda activate ENV-NAME # If using Conda - - Here :literal:`ENV-NAME` is the name of your environment. - - Also make sure that you have installed the PyYAML module to your - conda environment. PyYAML will allow the :file:`download_data.py` - script to read certain configurable settings from a YAML file in - your run directory. - - The Python environment for GCPy has all of the proper packages - that you need to download data from a dry-run simulation. For - more information, please see `gcpy.readthedocs.io - `_. +corresponding "production" simulation. .. _dry-run-data-download-portal: @@ -76,18 +51,47 @@ listed below. - No - No +Most of the data that you will need is contained in the +:ref:`GEOS-Chem Input Data ` portal. + +.. _dry-run-download-activate: + +==================================== +Activate the GCPy Python environment +==================================== + +You will need to activate a Python environment before you can start +downloading data. We recommend using the Python environment for `GCPy +`_, as it has all of the relevant +packages installed. If you `installed GCPy from PyPI +`_, +then no further action is needed. On the other hand, if you +`installed GCPy from conda-forge +`_, +you will need to activate the GCPy Python environment with this +command: + +.. code-block:: console + + $ conda activate gcpy_env + (gcpy_env) $ + +The prefix :literal:`(gcpy_env)` will be added to the command prompt, +which lets you know that the Python environment is active. (If you +installed GCPy from PyPI, you will not see this prefix.) + .. _dry-run-download-py: ============================================================== 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. +Navigate to your GEOS-Chem run directory. The command that you will +use to download data takes the form: .. code-block:: console - $ ./download_data.py log.dryrun PORTAL-NAME + (gcpy_env) $ ./download_data.py log.dryrun PORTAL-NAME where: @@ -132,21 +136,33 @@ where: - :ref:`GCAP 2.0 met data @ Rochester ` - :command:`wget` - HTTP + * - skip-download + - :ref:`Skips downloading data ` + - N/A + - N/A 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: +` portal, use this command: + +.. code-block:: console + + (gcpy_env) $ ./download_data.py log.dryrun geoschem+http + +But if you have `AWS CLI (command-line interface) +`_ set up on your machine, use +this command instead: .. code-block:: console - $ ./download_data.py log.dryrun geoschem+s3 + (gcpy_env) $ ./download_data.py log.dryrun geoschem+aws -.. note:: +This will result in a much faster data transfer than by HTTP. This is +also the command you will use if you are running GEOS-Chem Classic on +an AWS EC2 cloud instance. - You must have the `AWS CLI (command-line interface) - `_ software installed on your system - before in order to use the :literal:`geoschem+aws` or - :literal:`nested+aws` options in the table listed above. +=============================================== +(Optional) Examine the log of unique data files +=============================================== The :file:`download_data.py` program will generate a **log of unique data files** (i.e. with all duplicate listings removed), which @@ -187,13 +203,7 @@ example, we passed :file:`log.dryrun` to :file:`download_data.py`, so the "unique" log file will be named :file:`log.dryrun.unique`. This "unique" log file can be very useful for documentation purposes. -.. _dry-run-download-skip: - -============================================= -Skip download, but create log of unique files -============================================= - -If you wish to only produce the \*log of unique data files without +If you wish to only produce the **log of unique data files** without downloading any data, then type the following command from within your GEOS-Chem run directory: @@ -210,3 +220,63 @@ or for short: 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 purposes (such as for benchmark simulations, etc.) + +.. _dry-run-download-deactivate: + +====================================== +Deactivate the GCPy Python environment +====================================== + +Once you have downloaded all of the data needed for your GEOS-Chem +Classic simulation, you can deactivate the GCPy Python environment. + +.. code-block:: console + + (gcpy_env) $ conda deactivate + $ + +This will remove the :literal:`(gcpy_env)` prefix from the command prompt. + +=============================================== +(Optional) Download additional meteorology data +=============================================== + +You may need to perform a subsequent dry-run simulation to download +additional data that are stored separately from the :ref:`GEOS-Chem +Input Data portal `: + +#. If you plan to run a :ref:`GEOS-Chem Classic nested-grid simulation + ` with meteorology fields that have been cropped to a + :ref:`specific nested grid domain `, then follow + these steps: + + .. code-block:: console + + $ ./gcclassic --dryrun | tee log.dryrun.nested + + $ conda activate gcpy_env # Skip if using GCPy from PyPI + + (gcpy_env) $ ./download_data.py log.dryrun.nested nested+http # or nested+aws if you have AWSCLI + + (gcpy_env) $ conda deactivate # Skip if using GCPy from PyPI + + This will download the cropped meteorology fields from our + :ref:`GEOS-Chem Nested Input Data portal + ` to your computer system or EC2 instance. + +#. If you plan to perform a GEOS-Chem Classic simulation drven by GCAP + 2.0 meteorology, follow these steps: + + .. code-block:: console + + $ ./gcclassic --dryrun | tee log.dryrun.gcap2 + + $ conda activate gcpy_env # Skip if using GCPy from PyPI + + (gcpy_env) $ ./download_data.py log.dryrun.gcap2 rochester + + (gcpy_env) $ conda deactivate # Skip if using GCPy from PyPI + + This will download the GCAP 2.0 meteorology data from the + :ref:`GCAP 2.0 data portal hosted at U. Rochester + ` to your computer system or EC2 instance. diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs index 1ba5a650f..d857e2747 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit 1ba5a650f3fe0a7a25cbb7c5c44993e185f9a494 +Subproject commit d857e27470c3a48a5f4ae945b037d2da654a798b diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst index 0acff7aed..bd16b54ad 100644 --- a/docs/source/getting-started/quick-start.rst +++ b/docs/source/getting-started/quick-start.rst @@ -368,6 +368,9 @@ Before you can run your GEOS-Chem Classic simulation, you must first you may :ref:`start running your your GEOS-Chem Classic simulation ` right away. +7a. Run GEOS-Chem Classic in "dry-run" mode +-------------------------------------------- + The easiest way to download data is to perform a :ref:`dry-run simulation `. This is a GEOS-Chem Classic simulation that steps through time, but does not perform computations or read data @@ -383,46 +386,71 @@ To start a dry-run simulation, type this command: This will generate the :file:`log.dryrun` log file, which contains the list of data files to be downloaded. +7b. Download the data (requires Python) +--------------------------------------- + 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 `. -.. note:: +You will need to activate a Python environment before you can download +the data. We recommend using the Python environment for `GCPy +`_, as it has all of the relevant +packages installed. If you have `installed GCPy from PyPI +`_, then no further action is needed. On the other hand, if you +`installed GCPy from conda-forge +`_, +you will need to activate the GCPy Python environment with this command: + +.. code-block:: console - Depending on your system, you might have to activate a Conda or - environment containing a version of Python before running the - :file:`download.data.py` script. Ask your sysadmin. + $ conda activate gcpy_env -To start the data download, type: +The prefix :literal:`(gcpy_env)` will be added to the command line prompt, +which lets you know that the Python environment is active. (If you +installed GCPy from PyPI, you will not see this prefix.) + +You may now begin downloading data from the :ref:`GEOS-Chem Input Data +` portal: .. code-block:: console - $ ./download_data.py log.dryrun geoschem+http + (gcpy_env) $ ./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. +The data will be transfered using HTTP protocol. But if you have `AWS +CLI (command line interface) `_ installed +on your system, you can this command instead: -.. tip:: +.. code-block:: console - If you have `AWS CLI (command line interface) - `_ installed on your system, you - can use this command instead: + (gcpy_env) $ ./download_data.py log.dryrun geoschem+aws - .. code-block:: console +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. - $ ./download_data.py log.dryrun geoschem+aws +If you have activated the GCPy Python environment, you may now +deactivate it: - 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. +.. code-block:: console + (gcpy_env) $ conda deactivate + $ + +This will remove the :literal:`(gcpy_env)` prefix from the command +prompt. + At this point the required data files for your simulation should have been successfully downloaded from the :ref:`GEOS-Chem Input Data portal ` to your computer system or EC2 instance. -But you may still need to perform a subsequent dry-run simulation to -download additional data that are stored separately from the GEOS-Chem -Input Data portal: + +7c. (Optional) Download additional meteorology data +--------------------------------------------------- + +You may need to perform a subsequent dry-run simulation to download +additional data that are stored separately from the :ref:`GEOS-Chem +Input Data portal `: #. If you plan to run a :ref:`GEOS-Chem Classic nested-grid simulation ` with meteorology fields that have been cropped to a @@ -432,7 +460,12 @@ Input Data portal: .. code-block:: console $ ./gcclassic --dryrun | tee log.dryrun.nested - $ ./download_data.py log.dryrun.nested nested+http # or nested+aws if you have AWSCLI + + $ conda activate gcpy_env # Skip if using GCPy from PyPI + + (gcpy_env) $ ./download_data.py log.dryrun.nested nested+http # or nested+aws if you have AWSCLI + + $ conda deactivate # Skip if using GCPy from PyPI This will download the cropped meteorology fields from our :ref:`GEOS-Chem Nested Input Data portal @@ -444,7 +477,12 @@ Input Data portal: .. code-block:: console $ ./gcclassic --dryrun | tee log.dryrun.gcap2 - $ ./download_data.py log.dryrun.gcap2 rochester + + $ conda activate gcpy_env # Skip if using GCPy from PyPI + + (gcpy_env) $ ./download_data.py log.dryrun.gcap2 rochester + + $ conda deactivate # Skip if using GCPy from PyPI This will download the GCAP 2.0 meteorology data from the :ref:`GCAP 2.0 data portal hosted at U. Rochester From 670b215ef17bdcd98aae780cc1c675b22b488bd7 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Tue, 9 Dec 2025 15:42:49 -0500 Subject: [PATCH 74/86] GEOS-Chem update: Merge PR #3118 (Fix error in DryDepChm diag) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 34042ced5 Merge PR #3118 (Fix OOB errors in DryDepChm diagnostic) PR #3118 fixes an out-of-bounds error in the dry deposition diagnostics that was responsible for creating striped patterns in diagnostic output as first reported by @yc-chan. 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 3236dc5a7..34042ced5 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 3236dc5a7e2c22dbf7480af68675c23dd331895b +Subproject commit 34042ced58cc407896ee29056346af428f0545b9 From 33d6725b330d9c2f32b00535a0ddba38a94935f3 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Thu, 11 Dec 2025 16:27:13 -0500 Subject: [PATCH 75/86] GEOS-Chem update: Merge PR #3131 (Fix vertical flipping for C720) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: a3a795878 Merge PR #3131 (Fix vertical flipping of GEOS-FP C720 met fields) PR #3131 is the companion PR to geoschem/GCHP#529. These PRs fix a bug by splitting the single category for vertical direction of imports into 4 categories (mass flux, wind, humidity, and everything else), which is needed for GCHP C720. 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 34042ced5..a3a795878 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit 34042ced58cc407896ee29056346af428f0545b9 +Subproject commit a3a7958789be9c66f13365991216c5b052828b8e From 4bddc5b8231a4dd8508f44cc3676e4974bc9b646 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 15 Dec 2025 14:49:39 -0500 Subject: [PATCH 76/86] GEOS-Chem & HEMCO updates: Merge PR #2946 & PR #336 (7 dust bins ) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: d65b73ff5 Merge PR #2946 (Add 7 dust bins in GEOS-Chem) f4715d0 Merge PR #336 (Add 7 dust bins in HEMCO) GEOS-Chem PR #2946 and HEMCO PR #336 add the DustL23M extension from @1Dandan, and replace DST{1..4} species with DSTbin{1..7}. 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 a3a795878..d65b73ff5 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit a3a7958789be9c66f13365991216c5b052828b8e +Subproject commit d65b73ff57871751ec97a764be0a06fdb1fa1587 diff --git a/src/HEMCO b/src/HEMCO index 43ad1958b..f4715d013 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 43ad1958b490b9e233c7f222891d9966d8227f1f +Subproject commit f4715d0138fe1c48cbb914cfe742fc471aed40e4 From a89fa9a5b6e16dcfe662722e263158e5b747877d Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Mon, 15 Dec 2025 16:58:19 -0500 Subject: [PATCH 77/86] geos-chem-shared-docs update to f8fe324 (StateMetLevEdge warning box) docs/source/geos-chem-shared-docs - Submod update to f8fe324 (Warn that LevelEdgeDiags is renamed to StateMetLevEdge) 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 d857e2747..f8fe32426 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit d857e27470c3a48a5f4ae945b037d2da654a798b +Subproject commit f8fe32426c5e2bee7ec93079a813d56f9bc1a728 From ea265a6a43ed75a9dafec7add9b4669e61a87693 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 19 Dec 2025 16:24:48 -0500 Subject: [PATCH 78/86] geos-chem-shared-docs update to 03078d4 (PM2.5, PM10 in older versions) geos-chem-shared-docs - Submod update to 03078d4, add new documentation for PM2.5 and PM10 in versions prior to 14.7.0 Signed-off-by: Bob Yantosca --- 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 f8fe32426..03078d470 160000 --- a/docs/source/geos-chem-shared-docs +++ b/docs/source/geos-chem-shared-docs @@ -1 +1 @@ -Subproject commit f8fe32426c5e2bee7ec93079a813d56f9bc1a728 +Subproject commit 03078d47075177a7c2684664a6afe15024272234 From 342656bcd14a7dbd09127ed07699789224600c7c Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Wed, 21 Jan 2026 14:05:02 -0500 Subject: [PATCH 79/86] HEMCO update: Merge PR #349 (Sum Met_DELPDRY when vertically regridding) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: 16b499b Merge PR #349 (Now sum DELPDRY when regridding from 72 -> 47 layers) PR #349 adds a fix so that the Met_DELPDRY restart file variable is summed in the vertical instead of averaged when regridding from 72 levels to 47 levels. This fixes an issue first raised by @ltmurray in https://github.com/geoschem/geos-chem/issues/3170. Signed-off-by: Bob Yantosca --- src/HEMCO | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/HEMCO b/src/HEMCO index f4715d013..16b499b6f 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit f4715d0138fe1c48cbb914cfe742fc471aed40e4 +Subproject commit 16b499b6fc46a1d6f4b3ab8a80ce876fc848d005 From 43900af22f5f89fbaf034b8f31955ee9bcafb53f Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 30 Jan 2026 12:40:09 -0500 Subject: [PATCH 80/86] GEOS-Chem update: Merge PR #3187 (Fix typo in GCC rundir creation w/ GEOS-FP) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: f3ef58547 Merge PR #3187 (Fix typo in GCClassic rundir creation w/ GEOS-FP) In pull request #3131, the GEOS-FP met settings file geosfp.preprocessed_ll.txt was renamed to geosfp.nonadv_preprocessed_ll.txt. This was not updated in GCClassic/createRunDir.sh so when creating a GEOS-FP run directory for GCClassic the met settings were not properly set. For example, in geoschem_config.rc it still listed met_field: ${RUNDIR_MET}. Fixing the filename corrects this issue. 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 d65b73ff5..f3ef58547 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit d65b73ff57871751ec97a764be0a06fdb1fa1587 +Subproject commit f3ef585474d0b1a8a27e76669ea5054ba8be4d4e From 1267e5f6e6d0435bd6e4217b782cc92e2c878a45 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 30 Jan 2026 17:20:32 -0500 Subject: [PATCH 81/86] GEOS-Chem update: Merge PR #3147 (Update path to carbon sim rst files) This commit informs the GCClassic superproject about the following commits that were pushed to the GitHub geoschem/geos-chem repository: dafdefa50 Merge PR #3147 (Update sample carbon sim restart file) PR #3147 updates "run/GCClassic/download_data.yml" and "run/GCHP/createRunDir.sh" to point to the GEOSCHEM_RESTARTS/GC_14.7.0 folder. This is where updated carbon simulation restart files (generated from a 10-year benchmark) are stored. 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 f3ef58547..dafdefa50 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit f3ef585474d0b1a8a27e76669ea5054ba8be4d4e +Subproject commit dafdefa50adb77f01cab2c5ab3052bb02b218d2d From a122f005e711a69e11108ae2682cb15f48bc34f1 Mon Sep 17 00:00:00 2001 From: yuyao-cyber <64072369+yuyao-cyber@users.noreply.github.com> Date: Fri, 30 Jan 2026 16:50:19 -0600 Subject: [PATCH 82/86] add gcclassic doc --- .DS_Store | Bin 0 -> 6148 bytes docs/.DS_Store | Bin 0 -> 6148 bytes docs/source/.DS_Store | Bin 0 -> 6148 bytes .../run-gcc-on-aws-ec2.rst | 74 ++++++++++++++++++ 4 files changed, 74 insertions(+) create mode 100644 .DS_Store create mode 100644 docs/.DS_Store create mode 100644 docs/source/.DS_Store create mode 100644 docs/source/supplemental-guides/run-gcc-on-aws-ec2.rst diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..ac773817bb620cd5d5b5ab5922998746482869e6 GIT binary patch literal 6148 zcmeHKL5~tK6nT2A00T!~7sB3muJ*Ytjh)$TDAF%v|?Mj zW)CRjH%{q{9NMRtKCO703ZsBgVAB-fwOgPnol}dRP;&joO+W0qe(1u3w}&dy{%>h0 z5nZKYFsk&NPN+do!9Bsszo1@<_dUhi1@9SkXh40iJc_VeM0(FiwJC0=xZLJ~>rj_Q z;18L<+@|=N;_ZQVik`NxKQ*Z)N86M=U(;jpE5){`M0cY-OzNE7@#5Tgbk3K7CwG%$v(XQa5l^5Zrr*1 z_^dtfFM{whx(*ZAwxwOuxPUJx{2lg3XB7Bhz{6$#0;a7AK^qXzL9Vv@)YQpv`IZQm zJfv@+wvGv8&iX(}GBTLnF$Jlq<&a2vZ6kPw2&XO$Ql1|R$@Jvs3Y*j^(-)(FQD7q!;QhfyVytMK zE0kLYGI<36TBw$WGXGg%j;*nxajp<=U_w!WiYoLKLnu1xZS7alI9I6XB=qG&=$3`P zp$OSJzHdu+5*39eHwqX9mKDgT$0DEqjmz)<%Ovw;6fg?>R|*KL?$m1-l0I8k2FGWu ujr0zQjs4~dB?Xy2j%9(5;#)}4@XqD}u%dCU5H&FKM?lJ8GNZshRp1W|iSm^I literal 0 HcmV?d00001 diff --git a/docs/.DS_Store b/docs/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..aa2a52246e96c8b42ff8c9a2538c8c578f564be6 GIT binary patch literal 6148 zcmeHK&u`N(6n@^yk}x6V0D{Y;NL;JY@k^Vygfb2sxDW&fKp|NIiwqs7>{#VvNhA= z0ENo2O(`YRJ}BkEQnc-`3RngHHwAd_x^#?Pdqg>%*}rKiQ;hM!a2I9!n=*JD|Ioz0 zqJm1wdB2~D|FjUlMKy9Klu=AA9m0>{OFEziUQQLAB2SH;3Nzt$ig6hHsLZoqHptv-o<&P;q<;BR0C66_jtSy+Ym`lr}*+?<%apVO1FXxhQxi&$Il zo!f96&)IZdM2B)5wMjc_hDrU5TaTqI)0v;7Pl|jT`xo!Ys!fV2uN9%la)dm8T2z@F z59O%J8pVzDfakeh>|dTtb_Tcl!S3F)A58YH5BkB)8@H!Z&%Jc@+MP%7QF&a+_n1CR z;9ypE!Qc!&z?obAX;fFGtX`vk#+k)hTuBAY-|TL#|KI=p`+uHfTUG(9z)C3~di&A-5KA(5>(b)*t_@IL rqOfsXr%_Q*nd?|Nd=+0oQHHUA9bjm%(}*6J{SZ(x*vcyKPZjtMeb1M| literal 0 HcmV?d00001 diff --git a/docs/source/.DS_Store b/docs/source/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..4f45bda416d62c726e97abba3057af89a782eee1 GIT binary patch literal 6148 zcmeHK&5qMB5FU36ZCD{H*cDumB5`e(E`MUhrIh8sl_EF*DoLB|Mw_*(B&DFLQm()| z@CqDx6W)ard}F&6O+f+<2vweH{7vln$$U}bnutVqGTbL>5K$eW56-+zcIk?ZjJhsQBDDL`TnX9EBslw58eBw1r~b`NRgx? z+M_YOHE;XU`%}q#heq%pP=f3ke#lQPn!t)Eg*Ad5(~zRoJmP98&n`S8)Xfkxpkvsl zurgQy@CaWt8fGco@Ou#j{ur)wHW7a+vAZo>}m`y4P=9p3U~#x10XmgL%`R9o%R){aZKh z%;#Qx_uBP)kNYRdsZ{UK7(`&x(Q@A60^Y;;P0C*PQkf{pk7$u?k!9o2HeBD{_)cAe zjseHOpEAJT2OrAVu~-dutyAG!ZGh# zzmCPipa~~o4;{FI|8r + +**Verify the Environment**. The spack environment named :literal:`gc-env` is configured to load automatically. You can verify the compiler is ready in the spack directory :literal:`/data/spack/opt/spack`: + +.. code-block:: console + + $ which gfortran + +3. Download Code and Data +--------------------------- + +Now you can download the GC Classic source code and data files to your instance's :literal:`/data` directory. You can follow :ref:`quick-start` to run GCClassic with Slurm scheduler. + +.. warning:: + + **Do not use your home directory (~) for simulations**. The root disk is small (30 GB). Always work inside :literal:`/data`. From 968119a23844e2a706be4cd764b28e846bdf59b2 Mon Sep 17 00:00:00 2001 From: yuyao-cyber <64072369+yuyao-cyber@users.noreply.github.com> Date: Fri, 30 Jan 2026 16:57:50 -0600 Subject: [PATCH 83/86] Update index.rst --- docs/source/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/index.rst b/docs/source/index.rst index 2ecef3d88..2b1245f15 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -81,6 +81,7 @@ modifications to GEOS-Chem Classic source code. :caption: Supplemental guides :maxdepth: 4 + supplemental-guides/run-gcc-on-aws-ec2.rst supplemental-guides/directory-structure.rst supplemental-guides/horizontal-grids.rst supplemental-guides/vertical-grids.rst From bbec038be6e00e7f389b66c7ea68012193c7ae2d Mon Sep 17 00:00:00 2001 From: yuyao-cyber <64072369+yuyao-cyber@users.noreply.github.com> Date: Fri, 30 Jan 2026 17:36:32 -0600 Subject: [PATCH 84/86] fix typo --- docs/source/supplemental-guides/.DS_Store | Bin 0 -> 6148 bytes .../supplemental-guides/run-gcc-on-aws-ec2.rst | 6 +++--- 2 files changed, 3 insertions(+), 3 deletions(-) create mode 100644 docs/source/supplemental-guides/.DS_Store diff --git a/docs/source/supplemental-guides/.DS_Store b/docs/source/supplemental-guides/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..22169f3488a42070f14c6dcd76badcb537958190 GIT binary patch literal 6148 zcmeHK%TB{E5FD2Z6>+H$&|Z-81E~aG5UO(E%nv}DszeGcY6-7X?tBd2#|dWFR@J7d z1Q&$RuCyL|;~m@MD2@TRevzI6Z2&F0U}KL(jmdNI4QqtRF3~B+2oIQHju*rmy)Ez; z6_CB_AVtPq8)J3<7Tn7@3XK)|w8xUs%X~H(=CdI)<+VAd_deBF0}gSk??8rE;*=~m z$oW1@n4NK?1?qX;D?CTc9m{wu)0KQ-DwJtl&*V-jOvk#8sd9|Co>=DH|R<5(IU88%eupQu$z2{`e$o4Ir8j}hKn`WkfDPRix zPywFVVy%6TR+<8)fGMz4K)w$VT`&n)delz`3%vpmn+&V5EOHC;^ll^&NVtmsk9zH$_I>1vEeQXwV*OOK4u P>_ Date: Thu, 5 Feb 2026 10:56:41 -0500 Subject: [PATCH 85/86] Updated version numbers to 14.7.0 Updated version numbers in: - CHANGELOG.md - CMakeLists.txt - docs/source/conf.py 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 73cdc8afd..007e1b38b 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 +## [14.7.0] - 2026-02-05 ### Added - Added "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs - Added "GEOS-Chem Classic horiziontal grids" supplemental guide in ReadTheDocs diff --git a/CMakeLists.txt b/CMakeLists.txt index e1578db39..4eb8a32ce 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.13) project (geos-chem-classic - VERSION 14.6.3 + VERSION 14.7.0 LANGUAGES Fortran ) diff --git a/docs/source/conf.py b/docs/source/conf.py index 231bc35e1..07d7a7c03 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 = '14.6.3' +release = '14.7.0' # -- General configuration --------------------------------------------------- From c74bd2cba73372cc3f2530ec1139275690b87f55 Mon Sep 17 00:00:00 2001 From: Bob Yantosca Date: Fri, 6 Feb 2026 14:55:52 -0500 Subject: [PATCH 86/86] Updated submodules for GEOS-Chem Classic 14.7.0 release src/GEOS-Chem: - Now points to the GEOS-Chem (science codebase) 14.7.0 release src/HEMCO - Now points to the HEMCO 3.12.0 release CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca --- CHANGELOG.md | 5 ++++- src/GEOS-Chem | 2 +- src/HEMCO | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 007e1b38b..e5a57b2cd 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). -## [14.7.0] - 2026-02-05 +## [14.7.0] - 2026-02-06 ### Added - Added "GEOS-Chem Classic vertical grids" supplemental guide in ReadTheDocs - Added "GEOS-Chem Classic horiziontal grids" supplemental guide in ReadTheDocs @@ -20,6 +20,9 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Updated `lint-ci-workflows` to run on `main` and `dev/*` branches - Updated badges on `README.md` and `docs/source/index.rst` - Updated `geos-chem-shared-docs/editing_these_docs.rst` with instructions for using a Conda environment to build RTD doc +- Updated GEOS-Chem submodule to version 14.7.0 +- Updated HEMCO submodule to version 3.12.0 +- Updated geos-chem-shared-docs submodule to commit 03078d4 ### Fixed - Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail diff --git a/src/GEOS-Chem b/src/GEOS-Chem index dafdefa50..df4592e84 160000 --- a/src/GEOS-Chem +++ b/src/GEOS-Chem @@ -1 +1 @@ -Subproject commit dafdefa50adb77f01cab2c5ab3052bb02b218d2d +Subproject commit df4592e84561d3400950250e6fb57cd5b4bc90e7 diff --git a/src/HEMCO b/src/HEMCO index 16b499b6f..e23c43b89 160000 --- a/src/HEMCO +++ b/src/HEMCO @@ -1 +1 @@ -Subproject commit 16b499b6fc46a1d6f4b3ab8a80ce876fc848d005 +Subproject commit e23c43b89a754668d25744fa9827f8cfd7fa181f