ReadTheDocs updates for GEOS-Chem Classic 14.5.0 #68
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Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/geos-chem-shared-docs - Fixed broken links in supplemental-guides/spack-guide.rst docs/source/getting-started/login-env-files-gnu.rst - Changed label from env-files-gnu10 to env-files-gnu - Added tip box to build software with Spack if necessary docs/source/getting-started/login-env-files-intel.rst - Changed label from _env-files-intel19 to _env-files-intel - Added tip box to build software with Spack if necessary docs/source/getting-started/login-env-compilers.rst docs/source/getting-started/login-env-parallel.rst - Updated references accordingly docs/source/getting-started/login-env.rst - Updated references accordingly - Added tip box to build software with Spack if necessary Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCClassic superproject about the following commits pushed to the geos-chem-shared-docs submodule: a68981b Update gcc@10.2.0 -> gcc@12.2.0 in load-libraries-guide.rst This updates the GCC compiler version from 10.2.0 to 12.2.0 in the various documentation pages. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/requirements.txt - Use jinja 3.1.4 as there is a dependabot security warning for the previous version 3.1.3. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/gcclassic-user-guide/geoschem-config.rst docs/source/gcclassic-user-guide/hemco-config.rst docs/source/gcclassic-user-guide/hemco-diagn.rst docs/source/gcclassic-user-guide/phot-chem.rst docs/source/gcclassic-user-guide/spec-db.rst - Moved to geos-chem-shared-docs/doc docs/source/gcclassic-user-guide/config-overview.rst - Now points to relocated files docs/source/geos-chem-shared-docs - Submodule update to CHANGELOG.md - Updated accordingly
docs/source/gcclassic-user-guide/run-speedup.rst - Changed "Use coarser timesteps" to "Use a coarser chemistry timestep" - Added table of recommended GEOS-Chem Classic timesteps - Cite Philip et al. 2016 - Added section "Use the Rosenbrock solver w/ auto-reduction" - Added section "Reduce the amount of files that need to be read" - Added section "Speeding up GEOS-Chem Classic nested-grid simulations" - Added subsection "Crop nested-grid meteorology inputs" - Added subsection "Increase the size of the transport buffer zone" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/geos-chem-shared-docs: - Added documentation to doc/geoschem-config.rst and doc/hemco-config.rst to make the differences between GCHP and GCClassic more explicit. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/geos-chem-shared-docs - Fixed typo in doc/geoschem-config.rst - Added GCHP vs. GCC usage difference section in the documentation for HEMCO_Diagn.rc Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca
added
TODO: Documentation
This was referenced Oct 2, 2024
yantosca
changed the title
This commit informs the GCClassic superproject about the following commits that were pushed to the geos-chem-shared-docs repository: 65b2a35 Merge "docs/update_guides_for_gchp" into "main" 7f0cfbb Merge PR #3 (Add doc/tutorial for GEOS-Chem input data on AWS) These are documentation updates for the 14.5.0 release. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/gcclassic-user-guide/download-data.rst - Removed input-overview.rst from toctree - Added gcid-repository-overview.rst to toctree - Added gcid-special-repos.rst to toctree docs/source/gcclassic-user-guide/dry-run-download.rst - Add references to pages in geos-chem-shared-docs/doc folder pertaining to the GEOS-Chem input data - Renamed "Choose a data portal" section to "Choose a data repository", and updated the data repository descriptions docs/source/gcclassic-user-guide/gcid-special-repos.rst - New page describing GEOS-Chem Nested Input Data and GCAP 2.0 @ Rochester repositories docs/source/geos-chem-shared-docs - Updated submodule hash to commit 09a2f03 Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/gcclassic-user-guide/download-data.rst - Updated toctree docs/source/gcclassic-user-guide/dry-run-download.rst - Terminology change: "repository" -> "portal" - Simplified "Choose a data portal" section with table docs/source/gcclassic-user-guide/dry-run.rst - Removed tip box - Text formatting update docs/source/gcclassic-user-guide/gcid-special-repos.rst -> renamed to docs/source/gcclassic-user-guide/gcid-special-portals.rst docs/source/gcclassic-user-guide/input-overview.rst - Removed (now obsolete) docs/source/gcclassic-user-guide/restart-files-gc.rst docs/source/gcclassic-user-guide/restart-files-what.rst docs/source/gcclassic-user-guide/run-checklist.rst docs/source/getting-started/disk-space.rst - Fixed broken links & references - Text formatting updates docs/source/getting-started/quick-start.rst - Fixed broken links & references - Text formatting updates - Added attention box for resetting the time cycle flag for SPC_ in HEMCO_Config.rc docs/source/geos-chem-shared-docs - Submodule update with further updates for GEOS-Chem data portals Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
lizziel
reviewed
Nov 5, 2024
docs/source/gcclassic-user-guide/dry-run-download.rst - Reduce indentation for GEOS-Chem data portals & access methods - Update log.dryrun.unique output to remove obsolete file listings docs/source/gcclassic-user-guide/run-checklist.rst docs/source/help-and-reference/known-bugs.rst - Add "important" box with warning about GEOS-FP convection switch Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/gcclassic-user-guide/gcid-special-portals.rst - Moved to geos-chem-shared-docs/doc/gcid-special-portals.rst docs/source/gcclassic-user-guide/download-data.rst - Toctree now points to geoschem-shared-docs/doc/gcid-special-portals.rst docs/source/gcclassic/dry-run-run.rst - Add warning box about GEOS-FP convection switch docs/source/geos-chem-shared-docs - Submodule update to 54890ed Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
lizziel
reviewed
Nov 5, 2024
docs/source/gcclassic-user-guide/compile-cmake.rst - Add proper indentation to a ".. note::" block docs/source/gcclassic-user-guide/rundir-carbon.rst docs/source/gcclassic-user-guide/rundir-fullchem.rst docs/source/getting-started/quick-start.rst - Add "important" box about GEOS-FP convection issue - Trimmed trailing whitespace docs/source/gcclassic-user-guide/dry-run-download.rst - Fixed incorrect portal name "geoschem-s3" -> "geoschem+s3" docs/source/geos-chem-shared-docs - Submodule update to cd0f4ad (fix broken links & refs) docs/source/help-and-reference/known-bugs.rst - Renamed link text to avoid a "duplicate link" warning docs/source/index.rst - Removed geos-chem-input-data-on-aws.rst from toctree, as this is now moved to geos-chem-shared-docs/doc/gcid-portal-overview.rst Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/gcclassic-user-guide/dry-run-run.rst docs/source/gcclassic-user-guide/rundir-carbon.rst docs/source/gcclassic-user-guide/rundir-fullchem.rst - Edit the "important" box with the warning about GEOS-FP convection to make it more clear that the user should choose MERRA-2 to avoid discontinuities across June 1, 2020. docs/source/geos-chem-shared-docs - Submodule update, now link to GCClassic & HEMCO dry-run-instructions from the GEOS-Chem Input Data portal documentation
CHANGELOG.md CMakeLists.txt docs/source/conf.py - Updated version number to 14.5.0, in anticipation of the GEOS-Chem Classic 14.5.0 release Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
8 tasks
lizziel
approved these changes
Nov 8, 2024
msulprizio
approved these changes
Nov 8, 2024
8 tasks
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Name and Institution (Required)
Name: Bob Yantosca
Institution: Harvard + GCST
Describe the update
This PR seeks to merge documentation updates for GEOS-Chem 14.5.0 into the dev/14.5.0 branch. We have made the following general updates:
geoschem_config.yml,HEMCO_Diagn.rc,HEMCO_Config.rc,species_database.yml, and the aerosol/chemistry/photolysis configuration files to the https://github.com/geoschem/geos-chem-shared-docs repo... option::tags, etc)Related Github Issue
NOTES
Tagging @msulprizio @lizziel @yidant