Merge pull request #3 from NOAA-EMC/community_develop

Community develop

Externals.cfg

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+[ufs_utils]
+protocol = git
+repo_url = https://github.com/NCAR/UFS_UTILS
+# Specify either a branch name or a hash but not both.
+#branch = dtc/develop
+hash = 22d9e6ad
+local_path = sorc/UFS_UTILS_develop
+required = True
+
+[ufs_utils_chgres]
+protocol = git
+repo_url = https://github.com/NCAR/UFS_UTILS
+# Specify either a branch name or a hash but not both.
+#branch = feature/chgres_grib2
+hash = b47bc84c
+local_path = sorc/UFS_UTILS_chgres_grib2
+required = True
+
+[ufs_weather_model]
+protocol = git
+repo_url = https://github.com/NCAR/ufs-weather-model
+# Specify either a branch name or a hash but not both.
+#branch = dtc/develop
+hash = 4c2d541b
+local_path = sorc/ufs_weather_model
+required = True
+
+[EMC_post]
+protocol = git
+repo_url = https://github.com/NOAA-EMC/EMC_post
+# Specify either a branch name or a hash but not both.
+#branch = develop
+hash = 78078f62
+local_path = sorc/EMC_post
+required = True
+
+#[gsi]
+#protocol = git
+#repo_url = gerrit:ProdGSI
+## Specify either a branch name or a hash but not both.
+#branch = regional
+##hash =
+#local_path = sorc/regional_gsi.fd
+#required = True
+
+[externals_description]
+schema_version = 1.0.0

README.md

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+# Regional workflow
+
+This is the community\_develop branch of the regional\_workflow used to run the stand-alone regional (SAR) version of FV3.
+
+## Check out and build the regional workflow:
+
+1. Check out the regional workflow external components:
+
+`./manage_externals/checkout_externals`
+
+This step will checkout EMC\_post, NEMSfv3gfs and its submodules, UFS\_UTILS\_chgres\_grib2 and UFS\_UTILS\_develop in the sorc directory.
+
+2. Build the utilities, post and FV3:
+```
+cd sorc
+./build_all.sh
+```
+This step will also copy the executables to the `exec` directory and link the fix files.
+4. Create a `config.sh` file in the `ush` directory (see Users Guide).
+5. Generate a workflow:
+```
+cd ush
+generate_FV3SAR_wflow.sh
+```
+This will create an experiment directory in `$EXPT_SUBDIR` with a rocoto xml file FV3SAR_wflow.xml. It will also output information specific to your experiment.
+
+6. Launch and monitor the workflow:
+```
+module load rocoto/1.3.1`
+cd $EXPTDIR
+rocotorun -w FV3SAR_wflow.xml -d FV3SAR_wflow.db -v 10
+rocotostat -w FV3SAR_wflow.xml -d FV3SAR_wflow.db -v 10
+```
+7.  For automatic resubmission of the workflow, the following can be added to your crontab:
+```
+*/3 * * * * cd $EXPTDIR && rocotorun -w FV3SAR_wflow.xml -d FV3SAR_wflow.db -v 10
+```

docs/user_guide_sphinx/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/user_guide_sphinx/README

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+Steps to build and use the Sphinx documentation tool:
+
+1) Get Sphinx and sphinxcontrib-bibtex installed on your desktop from
+    http://www.sphinx-doc.org/en/master/usage/installation.html
+    https://sphinxcontrib-bibtex.readthedocs.io/en/latest/quickstart.html#installation
+
+2) Create a Sphinx documentation root directory:
+   % mkdir docs
+   % cd docs
+
+3) Initialize your Sphinx project (set up an initial directory structure) using
+   % sphinx-quickstart
+
+   See http://www.sphinx-doc.org/en/master/usage/quickstart.html or
+       https://sphinx-rtd-tutorial.readthedocs.io/en/latest/sphinx-quickstart.html
+
+    for help.  You can answer (ENTER) to most of the questions.
+
+To build html:
+
+From the directory above source and build, the sphinx project directory:
+
+make html
+
+Sphinx uses Latex to export the documentation as a PDF file.  To build pdf:
+
+make latexpdf
+
+It will generate a PDF file in ./build/latex/<sphinx-project-name>.pdf

docs/user_guide_sphinx/build/.gitignore

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+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

docs/user_guide_sphinx/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/user_guide_sphinx/source/Acknowledgement.rst

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+.. _acknowledgement:
+.. include:: prolog.inc 
+
+---------------
+Acknowledgement
+---------------
+
+This user's guide is constructed with contributions from distributed developers. We give our special acknowledgement to these contributors and reviewers, including, but not limited to:
+
+National Centers for Environmental Prediction (NCEP) Environmental Modeling Center (EMC): |br|
+*Jim Abeles, Eric Aligo, Tom Black, Benjamin Blake, Jacob Carley, Dusan Jovic, Jim Purser, Eric Rogers, Ed Strobach, and Fanglin Yang*
+
+National Center for Atmospheric Research (NCAR) and Developmental Testbed Center (DTC): |br|
+*Laurie Carson, Michael Kavulich, Julie Schramm, Don Stark, and Jamie Wolff*
+
+National Oceanic and Atmospheric Administration (NOAA) Earth System Research Laboratory (ESRL): |br|
+*Jeff Beck, Gerard Ketefian, and Linlin Pan*
+
+The community support and code management effort is sponsored by NOAA's Office of Oceanic and Atmospheric Research (OAR).  This work is also facilitated by NCAR. NCAR is supported by the National Science Foundation (NSF).
+

docs/user_guide_sphinx/source/Chapter1.rst

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+***************************************
+Summary of the FV3SAR model
+***************************************
+
+========================
+Basics of the FV3 Solver
+========================
+
+===========================================
+Handling of Boundary and Initial Conditions
+===========================================
+
+=======================
+The Gnomonic Projection
+=======================
+
+------------------------
+Grid Space Heterogeneity
+------------------------
+
+------------------------------------------------------------
+Optimization of the Gnomonic Projection for Regional Domains
+------------------------------------------------------------
+
+=================================
+Available Preset Regional Domains
+=================================