natalie-perlin · natalie-perlin · Jun 22, 2022 · Jun 22, 2022 · Jun 23, 2022 · Jun 23, 2022
diff --git a/Externals.cfg b/Externals.cfg
@@ -13,7 +13,7 @@ protocol = git
 repo_url = https://github.com/ufs-community/UFS_UTILS
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 31271f7
+hash = 1730d37
 local_path = src/UFS_UTILS
 required = True
 

diff --git a/README.md b/README.md
@@ -11,4 +11,4 @@ The UFS SRW App User's Guide associated with the development branch is at: https
 For instructions on how to clone the repository, build the code, and run the workflow, see:
 https://github.com/ufs-community/ufs-srweather-app/wiki/Getting-Started
 
-UFS Development Team. (2022, June 17). Unified Forecast System (UFS) Short-Range Weather (SRW) Application (Version v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.6505854
+UFS Development Team. (2022, June 23). Unified Forecast System (UFS) Short-Range Weather (SRW) Application (Version v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.6505854
diff --git a/docs/UsersGuide/source/BuildRunSRW.rst b/docs/UsersGuide/source/BuildRunSRW.rst
diff --git a/docs/UsersGuide/source/Components.rst b/docs/UsersGuide/source/Components.rst
@@ -19,10 +19,7 @@ These components are documented within this User's Guide and supported through a
 Pre-processor Utilities and Initial Conditions
 ==============================================
 
-The SRW Application includes a number of pre-processing utilities that initialize and prepare the model. Since the SRW App provides forecast predictions over a limited area (rather than globally), it is necessary to first generate a regional grid (``regional_esg_grid/make_hgrid``) along with :term:`orography` (``orog``) and surface climatology (``sfc_climo_gen``) files on that grid. Grids include a strip, or "halo," of six cells that surround the regional grid and feed in lateral boundary condition data. Since different grid and orography files require different numbers of :term:`halo` cells, additional utilities handle topography filtering and shave the number of halo points (based on downstream workflow component requirements). The pre-processing software :term:`chgres_cube` is used to convert the raw external model data into initial and lateral boundary condition files in :term:`netCDF` format. These are needed as input to the :term:`FV3`-:term:`LAM`. Additional information about the UFS pre-processor utilities can be found in the `UFS_UTILS User's Guide <https://noaa-emcufs-utils.readthedocs.io/en/ufs_utils_1_7_0/>`__.
-
-..
-   COMMENT: Update link!
+The SRW Application includes a number of pre-processing utilities that initialize and prepare the model. Since the SRW App provides forecast predictions over a limited area (rather than globally), it is necessary to first generate a regional grid (``regional_esg_grid/make_hgrid``) along with :term:`orography` (``orog``) and surface climatology (``sfc_climo_gen``) files on that grid. Grids include a strip, or "halo," of six cells that surround the regional grid and feed in lateral boundary condition data. Since different grid and orography files require different numbers of :term:`halo` cells, additional utilities handle topography filtering and shave the number of halo points (based on downstream workflow component requirements). The pre-processing software :term:`chgres_cube` is used to convert the raw external model data into initial and lateral boundary condition files in :term:`netCDF` format. These are needed as input to the :term:`FV3`-:term:`LAM`. Additional information about the UFS pre-processor utilities can be found in the `UFS_UTILS Technical Documentation <https://noaa-emcufs-utils.readthedocs.io/en/ufs_utils_1_7_0/>`__ and in the `UFS_UTILS Scientific Documentation <https://ufs-community.github.io/UFS_UTILS/ver-1.7.0/index.html>`__.
 
 The SRW Application can be initialized from a range of operational initial condition files. It is possible to initialize the model from the Global Forecast System (:term:`GFS`), North American Mesoscale (:term:`NAM`) Forecast System, Rapid Refresh (:term:`RAP`), and High-Resolution Rapid Refresh (:term:`HRRR`) files in Gridded Binary v2 (:term:`GRIB2`) format. GFS files also come in :term:`NEMSIO` format for past dates. 
 
@@ -38,7 +35,7 @@ The prognostic atmospheric model in the UFS SRW Application is the Finite-Volume
 
 Supported model resolutions in this release include 3-, 13-, and 25-km predefined contiguous U.S. (:term:`CONUS`) domains, each with 127 vertical levels. Preliminary tools for users to define their own domain are also available in the release with full, formal support of these tools to be provided in future releases. The Extended Schmidt Gnomonic (ESG) grid is used with the FV3-LAM, which features relatively uniform grid cells across the entirety of the domain. Additional information about the FV3 dynamical core can be found in the `scientific documentation <https://repository.library.noaa.gov/view/noaa/30725>`__, the `technical documentation <https://noaa-emc.github.io/FV3_Dycore_ufs-v2.0.0/html/index.html>`__, and on the `NOAA Geophysical Fluid Dynamics Laboratory website <https://www.gfdl.noaa.gov/fv3/>`__.
 
-Interoperable atmospheric physics, along with various land surface model options, are supported through the Common Community Physics Package (CCPP), described `here <https://dtcenter.org/community-code/common-community-physics-package-ccpp>`__. Atmospheric physics are a set of numerical methods describing small-scale processes such as clouds, turbulence, radiation, and their interactions. There will be four physics suites supported for the SRW App v2.0.0 release. The first is the FV3_RRFS_v1beta physics suite, which is being tested for use in the future operational implementation of the Rapid Refresh Forecast System (RRFS) planned for 2023-2024, and the second is an updated version of the physics suite used in the operational Global Forecast System (GFS) v16. Additionally, FV3_WoFS and FV3_HRRR will be supported. A scientific description of the CCPP parameterizations and suites can be found in the `CCPP Scientific Documentation <https://dtcenter.ucar.edu/GMTB/v6.0.0p/sci_doc/html/index.html>`__, and CCPP technical aspects are described in the `CCPP Technical Documentation <https://ccpp-techdoc.readthedocs.io/en/v6.0.0/>`__. The model namelist has many settings beyond the physics options that can optimize various aspects of the model for use with each of the supported suites. Additional information on Stochastic Physics options is available `here <https://stochastic-physics.readthedocs.io/en/release-public-v3/>`__.
+Interoperable atmospheric physics, along with various land surface model options, are supported through the Common Community Physics Package (CCPP), described `here <https://dtcenter.org/community-code/common-community-physics-package-ccpp>`__. Atmospheric physics are a set of numerical methods describing small-scale processes such as clouds, turbulence, radiation, and their interactions. There will be four physics suites supported for the SRW App v2.0.0 release. The first is the FV3_RRFS_v1beta physics suite, which is being tested for use in the future operational implementation of the Rapid Refresh Forecast System (RRFS) planned for 2023-2024, and the second is an updated version of the physics suite used in the operational Global Forecast System (GFS) v16. Additionally, FV3_WoFS and FV3_HRRR will be supported. A scientific description of the CCPP parameterizations and suites can be found in the `CCPP Scientific Documentation <https://dtcenter.ucar.edu/GMTB/v6.0.0/sci_doc/index.html>`__, and CCPP technical aspects are described in the `CCPP Technical Documentation <https://ccpp-techdoc.readthedocs.io/en/v6.0.0/>`__. The model namelist has many settings beyond the physics options that can optimize various aspects of the model for use with each of the supported suites. Additional information on Stochastic Physics options is available `here <https://stochastic-physics.readthedocs.io/en/release-public-v3/>`__.
 
 The SRW App supports the use of both :term:`GRIB2` and :term:`NEMSIO` input data. The UFS Weather Model ingests initial and lateral boundary condition files produced by :term:`chgres_cube` and outputs files in netCDF format on a specific projection (e.g., Lambert Conformal) in the horizontal direction and model levels in the vertical direction.
 

diff --git a/docs/UsersGuide/source/ConfigWorkflow.rst b/docs/UsersGuide/source/ConfigWorkflow.rst
@@ -48,6 +48,8 @@ Platform Environment
 ``WFLOW_MOD_FN``: (Default: "")
    Name of alternative workflow module file to use if running on an unsupported platform. Is set automatically for supported machines.
 
+.. _sched:
+
 ``SCHED``: (Default: "")
    The job scheduler to use (e.g., Slurm) on the specified ``MACHINE``. Leaving this an empty string allows the experiment generation script to set it automatically depending on the machine the workflow is running on. Valid values: ``"slurm"`` | ``"pbspro"`` | ``"lsf"`` | ``"lsfcray"`` | ``"none"``
 
@@ -397,7 +399,7 @@ CCPP Parameter
    | ``"FV3_GFS_v16"`` 
    | ``"FV3_RRFS_v1beta"`` 
    | ``"FV3_HRRR"``
-   | ``"FV3_WoFS"``
+   | ``"FV3_WoFS_v0"``
 
    **Other valid values include:**
 

diff --git a/docs/UsersGuide/source/InputOutputFiles.rst b/docs/UsersGuide/source/InputOutputFiles.rst
@@ -27,10 +27,7 @@ The data format for these files can be :term:`GRIB2` or :term:`NEMSIO`. More inf
 
 Pre-processing (UFS_UTILS)
 ---------------------------
-When a user generates the regional workflow, as described in :numref:`Section %s <GenerateWorkflow>`, the workflow generation script links the input data for the pre-processing utilities to the experiment directory. The pre-processing utilities use many different datasets to create grids and to generate model input datasets from the external model files. A detailed description of the input files for the pre-processing utilities can be found in the `UFS_UTILS Documentation <https://noaa-emcufs-utils.readthedocs.io/en/ufs_utils_1_7_0/>`__.
-
-..
-   COMMENT: Update link! (UFS_UTILS)
+When a user generates the regional workflow, as described in :numref:`Section %s <GenerateWorkflow>`, the workflow generation script links the input data for the pre-processing utilities to the experiment directory. The pre-processing utilities use many different datasets to create grids and to generate model input datasets from the external model files. A detailed description of the input files for the pre-processing utilities can be found in the UFS_UTILS `Technical Documentation <https://noaa-emcufs-utils.readthedocs.io/en/ufs_utils_1_7_0/>`__ and `Scientific Documentation <https://ufs-community.github.io/UFS_UTILS/ver-1.7.0/index.html>`__.
 
 UFS Weather Model
 -----------------
@@ -100,10 +97,7 @@ and are shown in :numref:`Table %s <TemplateFiles>`.
    | README.xml_templating.md    | Instructions for Rocoto XML templating with Jinja.           |
    +-----------------------------+--------------------------------------------------------------+
 
-Additional information related to ``diag_table_[CCPP]``, ``field_table_[CCPP]``, ``input.nml.FV3``, ``model_conigure``, and ``nems.configure`` can be found in the `UFS Weather Model User's Guide <https://ufs-weather-model.readthedocs.io/en/release-public-v3/InputsOutputs.html#model-configuration-files>`__, while information on ``regional_grid.nml`` can be found in the `UFS_UTILS User's Guide <https://noaa-emcufs-utils.readthedocs.io/en/ufs_utils_1_7_0/>`__.
-
-..
-   COMMENT: Update links! (for UFS_UTILS)
+Additional information related to ``diag_table_[CCPP]``, ``field_table_[CCPP]``, ``input.nml.FV3``, ``model_conigure``, and ``nems.configure`` can be found in the `UFS Weather Model User's Guide <https://ufs-weather-model.readthedocs.io/en/release-public-v3/InputsOutputs.html#model-configuration-files>`__, while information on ``regional_grid.nml`` options can be found in the `UFS_UTILS Technical Documentation <https://noaa-emcufs-utils.readthedocs.io/en/ufs_utils_1_7_0/ufs_utils.html#regional-esg-grid>`__.
 
 Migratory Route of the Input Files in the Workflow
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^