Merge remote-tracking branch 'ufs-fork/develop' into bugfix_tisfc_202…

…40213

LICENSE.md

@@ -10,19 +10,32 @@ This project includes a mix of the following:
 
 This project utilizes the following unmodified works under various licenses, as shown below.
 
-- Atmos cube sphere dycore: [GNU Lesser General Public License 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html) (LGPL)
+- [atmos_cubed_sphere dycore](https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
 
-- FV3 Atm: [GNU Lesser General Public License 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html) (LGPL)
+- [fv3atm](https://github.com/NOAA-EMC/fv3atm): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
 
-- NEMS: [GNU Lesser General Public License 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html) (LGPL)
+- [Stochastic Physics](https://github.com/NOAA-PSL/stochastic_physics): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
 
-- FMS: [GNU Lesser General Public License 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html) (LGPL)
+- [CCPP Physics](https://github.com/ufs-community/ccpp-physics): [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0)
 
-- Stochastic Physics: [GNU Lesser General Public License 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html) (LGPL)
+- [CCPP Framework](https://github.com/NCAR/ccpp-framework): [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0)
 
-- CCPP Physics: [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0)
+- [AQM](https://github.com/NOAA-EMC/AQM): GNU General Public License 3.0 ([GPL](https://www.gnu.org/licenses/gpl-3.0.en.html))
+
+- [CICE](https://github.com/NOAA-EMC/CICE): CICE Consortium license ([LICENSE.pdf](https://github.com/NOAA-EMC/CICE/blob/emc/develop/LICENSE.pdf))
+
+- [CMakeModules](https://github.com/NOAA-EMC/CMakeModules): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
+
+- [GOCART](https://github.com/GEOS-ESM/GOCART): [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0)
+
+- [HYCOM](https://github.com/NOAA-EMC/HYCOM-src): [MIT License](https://opensource.org/license/mit/)
+
+- [MOM6](https://github.com/NOAA-EMC/MOM6): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
+
+- [WW3](https://github.com/NOAA-EMC/WW3): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
+
+- [Unified Post Processor](https://github.com/NOAA-EMC/UPP): GNU Lesser General Public License 3.0 ([LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html))
 
-- CCPP Framework: [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0)
 
 ## The rest of this project is in the worldwide public domain
 

README.md

@@ -18,18 +18,21 @@ The top level directory structure groups source code and input files as follow:
 | --------------            | ------- |
 | ```LICENSE.md```          | A copy of the GNU Lesser General Public License, Version 3. |
 | ```README.md```           | This file with basic pointers to more information. |
-| ```NEMS/```               | Contains NOAA Environmental Modeling System source code and nems compset run scripts. |
+| ```AQM/```                | Contains air quality modeling component |
 | ```CMEPS-interface/```    | Contains CMEPS mediator |
+| ```CICE-interface/```     | Contains CICE sea-ice model component including CICE6 and Icepack |
+| ```CDEPS-interface/```    | Contains CDEPS data components, including data-atmosphere (DATM) and data-ocean (DOCN) model components|
 | ```FV3/```                | Contains FV3 atmosphere model component including FV3 dynamical core, dynamics to physics driver, physics and IO. |
-| ```DATM/```               | Contains Data Atmosphere model component |
-| ```WW3/```                | Contains community wave modeling framework WW3. |
+| ```GOCART/```             | Contains GOCART aerosol model component |
+| ```HYCOM-interface/```    | Contains HYCOM ocean model component |
 | ```MOM6-interface/```     | Contains MOM6 ocean model component |
-| ```CICE-interface/```     | Contains CICE sea-ice model component including CICE6 and Icepack |
-| ```stochastic_physics/``` | Contains the stochastic physics source code. |
+| ```NOAHMP-interface/```   | Contains Noah-MP land model component |
+| ```WW3/```                | Contains community wave modeling framework WW3 |
+| ```stochastic_physics/``` | Contains the stochastic physics source code |
 | ```cmake/```              | Contains compile option files on various platforms. |
 | ```modulefiles/```        | Contains module files on various platforms. |
 | ```tests/```              | Regression and unit testing framework scripts. |
-| ```build.sh```            | Script to build the model executable. (also used by `tests/`) |
+| ```build.sh```            | Script to build the model executable (also used by `tests/`) |
 
 E.g. use of `build.sh` to build the coupled model with `FV3_GFS_v15p2` as the CCPP suite.
 ```

cmake/GNU.cmake

@@ -10,7 +10,7 @@ endif()
 
 if(DEBUG)
     add_definitions(-DDEBUG)
-    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check")
+    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check -mcmodel=medium")
     set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
 else()
     set(CMAKE_Fortran_FLAGS_RELEASE "-O2")

doc/UsersGuide/Makefile

@@ -3,16 +3,20 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
+SPHINXOPTS    = -a -n
+SPHINXBUILD   = sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
+LINKCHECKDIR  = $(BUILDDIR)/linkcheck
 
 # Put it first so that "make" without argument is like "make help".
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+.PHONY: help Makefile linkcheck
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(SPHINXOPTS) $(SOURCEDIR) $(LINKCHECKDIR)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

doc/UsersGuide/requirements.in

@@ -0,0 +1,3 @@
+sphinx>=6.0.0
+sphinx_rtd_theme
+sphinxcontrib-bibtex

doc/UsersGuide/requirements.txt

@@ -1,3 +1,82 @@
-sphinxcontrib-bibtex
-sphinx_rtd_theme
-docutils==0.16
+#
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
+#
+#    pip-compile requirements.in
+#
+alabaster==0.7.16
+    # via sphinx
+babel==2.14.0
+    # via sphinx
+certifi==2024.2.2
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+docutils==0.20.1
+    # via
+    #   pybtex-docutils
+    #   sphinx
+    #   sphinx-rtd-theme
+    #   sphinxcontrib-bibtex
+idna==3.6
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+importlib-metadata==7.0.1
+    # via
+    #   sphinx
+    #   sphinxcontrib-bibtex
+jinja2==3.1.3
+    # via sphinx
+latexcodec==2.0.1
+    # via pybtex
+markupsafe==2.1.5
+    # via jinja2
+packaging==23.2
+    # via sphinx
+pybtex==0.24.0
+    # via
+    #   pybtex-docutils
+    #   sphinxcontrib-bibtex
+pybtex-docutils==1.0.3
+    # via sphinxcontrib-bibtex
+pygments==2.17.2
+    # via sphinx
+pyyaml==6.0.1
+    # via pybtex
+requests==2.31.0
+    # via sphinx
+six==1.16.0
+    # via
+    #   latexcodec
+    #   pybtex
+snowballstemmer==2.2.0
+    # via sphinx
+sphinx==7.2.6
+    # via
+    #   -r requirements.in
+    #   sphinx-rtd-theme
+    #   sphinxcontrib-bibtex
+    #   sphinxcontrib-jquery
+sphinx-rtd-theme==2.0.0
+    # via -r requirements.in
+sphinxcontrib-applehelp==1.0.8
+    # via sphinx
+sphinxcontrib-bibtex==2.6.2
+    # via -r requirements.in
+sphinxcontrib-devhelp==1.0.6
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.5
+    # via sphinx
+sphinxcontrib-jquery==4.1
+    # via sphinx-rtd-theme
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.7
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.10
+    # via sphinx
+urllib3==2.2.1
+    # via requests
+zipp==3.17.0
+    # via importlib-metadata

doc/UsersGuide/source/CodeOverview.rst

@@ -67,7 +67,7 @@ The UFS :term:`WM` repository supports the :term:`UFS` short- and medium-range w
   * - :term:`FV3` dynamical core
     - https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere
   * - Stochastic physics pattern generator
-    - https://github.com/noaa-psd/stochastic_physics
+    - https://github.com/NOAA-PSL/stochastic_physics
   * - Modular Ocean Model (:term:`MOM6`)
     - https://github.com/NOAA-EMC/MOM6
   * - HYbrid Coordinate Ocean Model (:term:`HYCOM`)

doc/UsersGuide/source/Configurations.rst

@@ -335,7 +335,7 @@ Each test file lists the input files required for a given test. Input files requ
 
 Information on ``ufs.configure`` files is available in :numref:`Section %s <ufs-conf>`. The supported RRFS WM RTs use the same ``ufs.configure`` file that ATM-only tests do (``ufs.configure.atm.IN``). This file can be viewed in the ``ufs-weather-model/tests/parm`` `directory <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.atm.IN>`__. 
 
-Additionally, users can find examples of various RRFS configuration files in the ``ufs-weather-model/tests/parm`` `directory <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/>`__. These files include ``model_configure_*``, ``*_run.IN`` (input run), ``*.nml.IN`` (input namelist), ``field_table_*``, and ``diag_table_*`` files.  
+Additionally, users can find examples of various RRFS configuration files in the ``ufs-weather-model/tests/parm`` `directory <https://github.com/ufs-community/ufs-weather-model/tree/develop/tests/parm>`__. These files include ``model_configure_*``, ``*_run.IN`` (input run), ``*.nml.IN`` (input namelist), ``field_table_*``, and ``diag_table_*`` files.  
 
 .. _lnd-documented:
 

doc/UsersGuide/source/Glossary.rst

@@ -120,7 +120,7 @@ Glossary
 
    NCEPLIBS
       The software libraries created and maintained by :term:`NCEP` that are required for running 
-      :term:`chgres_cube`, the UFS Weather Model, and the :term:`UPP`. They are included in `spack-stack <https://github.com/NOAA-EMC/spack-stack>`__ and `HPC-Stack <https://github.com/NOAA-EMC/hpc-stack>`__. 
+      :term:`chgres_cube`, the UFS Weather Model, and the :term:`UPP`. They are included in `spack-stack <https://github.com/JCSDA/spack-stack>`__ and `HPC-Stack <https://github.com/NOAA-EMC/hpc-stack>`__. 
 
    NCEPLIBS-external
       A collection of third-party libraries required to build :term:`NCEPLIBS`, :term:`chgres_cube`, 
@@ -167,7 +167,7 @@ Glossary
       The `Short-Range Weather Application <https://github.com/ufs-community/ufs-srweather-app>`__ is a UFS Application that targets predictions of atmospheric behavior on a limited spatial domain and on time scales from minutes out to about two days. It packages a prognostic atmospheric model (the UFS Weather Model), pre- and post-processing tools, and a community workflow.
 
    spack-stack
-      The `spack-stack <https://github.com/NOAA-EMC/spack-stack>`__ is a collaborative effort between the NOAA Environmental Modeling Center (EMC), the UCAR Joint Center for Satellite Data Assimilation (JCSDA), and the Earth Prediction Innovation Center (EPIC). *spack-stack* is a repository that provides a Spack-based method for building the software stack required for numerical weather prediction (NWP) tools such as the `Unified Forecast System (UFS) <https://ufscommunity.org/>`__ and the `Joint Effort for Data assimilation Integration (JEDI) <https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/>`__ framework. *spack-stack* uses the Spack package manager along with custom Spack configuration files and Python scripts to simplify installation of the libraries required to run various applications. The *spack-stack* can be installed on a range of platforms and comes pre-configured for many systems. Users can install the necessary packages for a particular application and later add the missing packages for another application without having to rebuild the entire stack.
+      The `spack-stack <https://github.com/JCSDA/spack-stack>`__ is a collaborative effort between the NOAA Environmental Modeling Center (EMC), the UCAR Joint Center for Satellite Data Assimilation (JCSDA), and the Earth Prediction Innovation Center (EPIC). *spack-stack* is a repository that provides a Spack-based method for building the software stack required for numerical weather prediction (NWP) tools such as the `Unified Forecast System (UFS) <https://ufscommunity.org/>`__ and the `Joint Effort for Data assimilation Integration (JEDI) <https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/>`__ framework. *spack-stack* uses the Spack package manager along with custom Spack configuration files and Python scripts to simplify installation of the libraries required to run various applications. The *spack-stack* can be installed on a range of platforms and comes pre-configured for many systems. Users can install the necessary packages for a particular application and later add the missing packages for another application without having to rebuild the entire stack.
 
    Suite Definition File (SDF)
      An external file containing information about the 

doc/UsersGuide/source/InputsOutputs.rst

@@ -1639,7 +1639,7 @@ A sample of the file contents is shown below:
 However, ``ufs.configure`` files for other configurations of the Weather Model are more complex. A full set of ``ufs.configure`` templates is available in the ``ufs-weather-model/tests/parm/`` directory `here <https://github.com/ufs-community/ufs-weather-model/tree/develop/tests/parm>`__. Template names follow the pattern ``ufs.configure.*.IN``. A number of samples are available below: 
 
    * `ATMAQ <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.atmaq.IN>`__ configuration
-   * `S2S <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.s2s_aoflux.IN>`__ (fully coupled ``S2S`` configuration that receives atmosphere-ocean fluxes from a mediator)
+   * `S2S <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.s2s_aoflux_esmf.IN>`__ (fully coupled ``S2S`` configuration that receives atmosphere-ocean fluxes from a mediator)
    * `S2SW <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.s2sw.IN>`__ (fully coupled ``S2SW`` configuration)
    * `S2SWA <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.s2swa.IN>`__ (coupled GOCART in the S2SAW configuration)
    * `ATM-LND <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/ufs.configure.atm_lnd.IN>`__ (ATML configuration)

doc/UsersGuide/source/conf.py

@@ -69,12 +69,9 @@
 # The master toctree document.
 master_doc = 'index'
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
+# The language for content autogenerated by Sphinx. 
+# Not set because default is 'en'.
+# language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -84,6 +81,15 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
+# Avoid a 403 Forbidden error when accessing certain links (e.g., noaa.gov)
+user_agent = "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/121.0.0.0 Safari/537.36"
+
+# Ignore anchor tags for links that show Not Found even when they exist.
+linkcheck_anchors_ignore = [r"L\d*",
+                            ]
+# Ignore working links that cause a linkcheck 403 error.
+linkcheck_ignore = [r'https://agupubs\.onlinelibrary\.wiley\.com/doi/10\.1029/2020MS002260',
+                   ]
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -100,6 +106,7 @@
 #
 # html_theme_options = {}
 html_theme_options = {"body_max_width": "none"}
+html_logo="https://github.com/ufs-community/ufs/wiki/images/ufs-epic-logo.png"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

doc/UsersGuide/source/references.bib

@@ -16,6 +16,6 @@ @article{BengtssonEtAl2020
   title={A Stochastic Parameterization of Organized Tropical Convection Using Cellular Automata for Global Forecasts in NOAA's Unified Forecast System},
   author={L. Bengtsson and J. Dias and S. Tulich and M. Gehne and J. Bao},
   journal={Journal of Advances in Modeling Earth Systems},
-  url={https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020MS002260},
+  url={https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020MS002260},
   year={2020},
 }