RTD update: Fixed more links/refs and text formatting issues

docs/source/gcclassic-user-guide/compile-cmake.rst - Add proper indentation to a ".. note::" block docs/source/gcclassic-user-guide/rundir-carbon.rst docs/source/gcclassic-user-guide/rundir-fullchem.rst docs/source/getting-started/quick-start.rst - Add "important" box about GEOS-FP convection issue - Trimmed trailing whitespace docs/source/gcclassic-user-guide/dry-run-download.rst - Fixed incorrect portal name "geoschem-s3" -> "geoschem+s3" docs/source/geos-chem-shared-docs - Submodule update to cd0f4ad (fix broken links & refs) docs/source/help-and-reference/known-bugs.rst - Renamed link text to avoid a "duplicate link" warning docs/source/index.rst - Removed geos-chem-input-data-on-aws.rst from toctree, as this is now moved to geos-chem-shared-docs/doc/gcid-portal-overview.rst Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Nov 5, 2024 · b81423c · b81423c
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diff --git a/docs/source/gcclassic-user-guide/compile-cmake.rst b/docs/source/gcclassic-user-guide/compile-cmake.rst
@@ -433,17 +433,16 @@ Classic contains code from the various repositories:
 
    .. note::
 
-   If you are cloning GEOS-Chem Classic between official releases, you
-   may the see :code:`Current status` reported like this:
+      If you are cloning GEOS-Chem Classic between official releases, you
+      may the see :code:`Current status` reported like this:
 
-   .. code-block:: console
+      .. code-block:: console
 		      
-      X.Y.Z-alpha.n-C-gabcd1234.dirty  or
+         X.Y.Z-alpha.n-C-gabcd1234.dirty  or
 
-      X.Y.Z.rc.n-C.gabcd1234.dirty
+         X.Y.Z.rc.n-C.gabcd1234.dirty
 
-   We will explain these formats below. |br|
-   |br|
+      We will explain these formats below.
 
 #. `HEMCO (Harmonized Emissions Component) submodule <https://github.com/geoschem/hemco.git>`_:
 

diff --git a/docs/source/gcclassic-user-guide/dry-run-download.rst b/docs/source/gcclassic-user-guide/dry-run-download.rst
@@ -133,13 +133,13 @@ where:
        - :command:`wget`
        - HTTP
 
-For example, to download data from the :ref:`dry-run-download-portal-gc`
-portal using the AWS CLI download (which is faster than HTTP
-download), use this command:
+For example, to download data from the :ref:`GEOS-Chem Input Data
+<gcid-data>` portal using the AWS CLI download (which is faster than
+HTTP download), use this command:
 
 .. code-block:: console
 
-   $ ./download_data.py log.dryrun geoschem-s3
+   $ ./download_data.py log.dryrun geoschem+s3
 
 .. note::
 

diff --git a/docs/source/gcclassic-user-guide/rundir-carbon.rst b/docs/source/gcclassic-user-guide/rundir-carbon.rst
@@ -136,6 +136,23 @@ simulation. We'll use the carbon gases simulation as an example.
    followed by :command:`ENTER`. |br|
    |br|
 
+   .. important::
+
+      The convection scheme used for GEOS-FP met generation changed
+      from RAS to Grell-Freitas with impact on GEOS-FP meteorology
+      files starting June 1, 2020, specifically enhanced vertical
+      transport. In addition, there is a bug in convective
+      precipitation flux following the switch where all values are
+      zero. While this bug is automatically fixed by computing fluxes
+      online for runs starting on or after June 1 2020, the fix
+      assumes meteorology year corresponds to simulation year. Due to
+      these issues we recommend splitting up GEOS-FP runs in time such
+      that a single simulation does not run across June
+      1, 2020. Instead. set one run to stop on June 1 2020 and then
+      restart a new run from there. If you wish to use a GEOS-FP
+      meteorology year different from your simulation year please
+      create a GEOS-Chem GitHub issue for assistance.
+
 #. The next menu will prompt you for the horizontal resolution that
    you wish to use:
 

diff --git a/docs/source/gcclassic-user-guide/rundir-fullchem.rst b/docs/source/gcclassic-user-guide/rundir-fullchem.rst
@@ -138,6 +138,23 @@ GEOS-Chem full-chemistry simulation.
    :command:`1` followed by :command:`ENTER`. |br|
    |br|
 
+   .. important::
+
+      The convection scheme used for GEOS-FP met generation changed
+      from RAS to Grell-Freitas with impact on GEOS-FP meteorology
+      files starting June 1, 2020, specifically enhanced vertical
+      transport. In addition, there is a bug in convective
+      precipitation flux following the switch where all values are
+      zero. While this bug is automatically fixed by computing fluxes
+      online for runs starting on or after June 1 2020, the fix
+      assumes meteorology year corresponds to simulation year. Due to
+      these issues we recommend splitting up GEOS-FP runs in time such
+      that a single simulation does not run across June
+      1, 2020. Instead. set one run to stop on June 1 2020 and then
+      restart a new run from there. If you wish to use a GEOS-FP
+      meteorology year different from your simulation year please
+      create a GEOS-Chem GitHub issue for assistance.
+
 #. The next menu will prompt you for the horizontal resolution that
    you wish to use:
 

diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs
diff --git a/docs/source/getting-started/quick-start.rst b/docs/source/getting-started/quick-start.rst
@@ -126,6 +126,23 @@ simulations follow the same pattern as the examples shown below.
    information to the `GEOS-Chem Users web page
    <https://geoschem.github.io/users.html>`_.
 
+.. important::
+
+   The convection scheme used for GEOS-FP met generation changed
+   from RAS to Grell-Freitas with impact on GEOS-FP meteorology
+   files starting June 1, 2020, specifically enhanced vertical
+   transport. In addition, there is a bug in convective
+   precipitation flux following the switch where all values are
+   zero. While this bug is automatically fixed by computing fluxes
+   online for runs starting on or after June 1 2020, the fix
+   assumes meteorology year corresponds to simulation year. Due to
+   these issues we recommend splitting up GEOS-FP runs in time such
+   that a single simulation does not run across June
+   1, 2020. Instead. set one run to stop on June 1 2020 and then
+   restart a new run from there. If you wish to use a GEOS-FP
+   meteorology year different from your simulation year please
+   create a GEOS-Chem GitHub issue for assistance.
+
 .. _quick-load:
 
 ========================

diff --git a/docs/source/help-and-reference/known-bugs.rst b/docs/source/help-and-reference/known-bugs.rst
@@ -44,4 +44,4 @@ are currently unresolved. We hope to fix these in future releases.
 Bugs that have been resolved
 ============================
 
-These `bug reports (on GitHub) <https://github.com/geoschem/geos-chem/issues?q=+label%3A%22category%3A+Bug+Fix%22+>`_ have been resolved.
+These `bugs (reported on GitHub) <https://github.com/geoschem/geos-chem/issues?q=+label%3A%22category%3A+Bug+Fix%22+>`_ have been resolved.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -84,7 +84,6 @@ modifications to GEOS-Chem Classic source code.
    geos-chem-shared-docs/supplemental-guides/parallel-guide.rst
    supplemental-guides/nested-grid-guide.rst
    geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.rst
-   geos-chem-shared-docs/supplemental-guides/geos-chem-input-data-on-aws.rst
    geos-chem-shared-docs/supplemental-guides/related-docs.rst
 
 .. toctree::