[develop]: Minor updates to documentation

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "hpc-stack-mod"]
-	path = hpc-stack-mod
-	url = https://github.com/NOAA-EMC/hpc-stack.git

docs/UsersGuide/source/Components.rst

@@ -35,7 +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_v0 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/latest/>`__. 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_v0 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/latest/>`__. 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/latest/>`__.
 
 .. note::
    SPP is currently only available for specific physics schemes used in the RAP/HRRR physics suite. Users need to be aware of which physics suite definition file (:term:`SDF`) is chosen when turning this option on. Among the supported physics suites, the full set of parameterizations can only be used with the ``FV3_HRRR`` option for ``CCPP_PHYS_SUITE``.
@@ -79,7 +79,7 @@ Build System and Workflow
 
 The SRW Application has a portable build system and a user-friendly, modular, and expandable workflow framework.
 
-An umbrella CMake-based build system is used for building the components necessary for running the end-to-end SRW Application, including the UFS Weather Model and the pre- and post-processing software. Additional libraries necessary for the application (e.g., :term:`NCEPLIBS-external` and :term:`NCEPLIBS`) are not included in the SRW Application build system but are available pre-built on pre-configured platforms. On other systems, they can be installed via the HPC-Stack (see :numref:`Chapter %s: Installing the HPC-Stack <InstallHPCStack>`). There is a small set of system libraries and utilities that are assumed to be present on the target computer: the CMake build software, a Fortran, C, and C++ compiler, and an :term:`MPI` library.
+An umbrella CMake-based build system is used for building the components necessary for running the end-to-end SRW Application, including the UFS Weather Model and the pre- and post-processing software. Additional libraries necessary for the application (e.g., :term:`NCEPLIBS-external` and :term:`NCEPLIBS`) are not included in the SRW Application build system but are available pre-built on pre-configured platforms. On other systems, they can be installed via the HPC-Stack (see :doc:`HPC-Stack Documentation <hpc-stack:index>`). There is a small set of system libraries and utilities that are assumed to be present on the target computer: the CMake build software, a Fortran, C, and C++ compiler, and an :term:`MPI` library.
 
 Once built, the provided experiment generator script can be used to create a Rocoto-based
 workflow file that will run each task in the system in the proper sequence (see :numref:`Chapter %s <RocotoInfo>` or the `Rocoto documentation <https://github.com/christopherwharrop/rocoto/wiki/Documentation>`_ for more information on Rocoto). If Rocoto and/or a batch system is not present on the available platform, the individual components can be run in a stand-alone, command line fashion with provided run scripts. The generated namelist for the atmospheric model can be modified in order to vary settings such as forecast starting and ending dates, forecast length hours, the :term:`CCPP` physics suite, integration time step, history file output frequency, and more. It also allows for configuration of other elements of the workflow; for example, users can choose whether to run some or all of the pre-processing, forecast model, and post-processing steps.

docs/UsersGuide/source/ConfigWorkflow.rst

@@ -205,7 +205,7 @@ File Name Parameters
    Name of the file specifying the fields that the forecast model will output.
 
 ``FIELD_TABLE_FN``: (Default: "field_table")
-   Name of the file specifying the :term:`tracers` that the forecast model will read in from the :term:`IC/LBC` files.
+   Name of the file specifying the :term:`tracers <tracer>` that the forecast model will read in from the :term:`IC/LBC <IC/LBCs>` files.
 
 ``DATA_TABLE_FN``: (Default: "data_table")
    Name of the file containing the data table read in by the forecast model.
@@ -413,7 +413,7 @@ CCPP Parameter
 Stochastic Physics Parameters
 ================================
 
-For the most updated and detailed documentation of these parameters, see the `UFS Stochastic Physics Documentation <https://stochastic-physics.readthedocs.io/en/release-public-v3/namelist_options.html>`__.
+For the most updated and detailed documentation of these parameters, see the `UFS Stochastic Physics Documentation <https://stochastic-physics.readthedocs.io/en/latest/namelist_options.html>`__.
 
 ``NEW_LSCALE``: (Default: "TRUE") 
    Use correct formula for converting a spatial legnth scale into spectral space. 
@@ -508,7 +508,7 @@ Stochastic Kinetic Energy Backscatter (SKEB) Parameters
 Parameters for Stochastically Perturbed Parameterizations (SPP)
 ------------------------------------------------------------------
 
-SPP perturbs specific tuning parameters within a physics :term:`parameterization` (unlike :ref:`SPPT <SPPT>`, which multiplies overall physics tendencies by a random perturbation field *after* the call to the physics suite). Each SPP option is an array, applicable (in order) to the :term:`RAP`/:term:`HRRR`-based parameterization listed in ``SPP_VAR_LIST``. Enter each value of the array in ``config.sh`` as shown below without commas or single quotes (e.g., ``SPP_VAR_LIST=( "pbl" "sfc" "mp" "rad" "gwd"`` ). Both commas and single quotes will be added by Jinja when creating the namelist.
+SPP perturbs specific tuning parameters within a physics :term:`parameterization <parameterizations>` (unlike :ref:`SPPT <SPPT>`, which multiplies overall physics tendencies by a random perturbation field *after* the call to the physics suite). Each SPP option is an array, applicable (in order) to the :term:`RAP`/:term:`HRRR`-based parameterization listed in ``SPP_VAR_LIST``. Enter each value of the array in ``config.sh`` as shown below without commas or single quotes (e.g., ``SPP_VAR_LIST=( "pbl" "sfc" "mp" "rad" "gwd"`` ). Both commas and single quotes will be added by Jinja when creating the namelist.
 
 .. note::
    SPP is currently only available for specific physics schemes used in the RAP/HRRR physics suite. Users need to be aware of which :term:`SDF` is chosen when turning this option on. Among the supported physics suites, the full set of parameterizations can only be used with the ``FV3_HRRR`` option for ``CCPP_PHYS_SUITE``.

docs/UsersGuide/source/ContainerQuickstart.rst

@@ -31,7 +31,7 @@ Install Singularity
 To build and run the SRW App using a Singularity container, first install the Singularity package according to the `Singularity Installation Guide <https://sylabs.io/guides/3.2/user-guide/installation.html#>`__. This will include the installation of dependencies and the installation of the Go programming language. SingularityCE Version 3.7 or above is recommended. 
 
 .. warning:: 
-   Docker containers can only be run with root privileges, and users cannot have root privileges on :term:`HPCs`. Therefore, it is not possible to build the SRW App, which uses the HPC-Stack, inside a Docker container on an HPC system. However, a Singularity image may be built directly from a Docker image for use on the system.
+   Docker containers can only be run with root privileges, and users cannot have root privileges on :term:`HPCs <HPC>`. Therefore, it is not possible to build the SRW App, which uses the HPC-Stack, inside a Docker container on an HPC system. However, a Singularity image may be built directly from a Docker image for use on the system.
 
 Working in the Cloud or on HPC Systems
 -----------------------------------------