[develop]: Updated ConfigWorkflow.rst to reflect changes to config_defaults.yaml (PI13)

doc/UsersGuide/source/CustomizingTheWorkflow/ConfigWorkflow.rst

@@ -159,6 +159,9 @@ These settings define platform-specific run commands. Users should set run comma
 ``RUN_CMD_AQM``: (Default: "")
   The run command for some AQM tasks.
 
+``RUN_CMD_NEXUS``: (Default: "")
+  The run command for the AQM NEXUS tasks.
+
 ``RUN_CMD_AQMLBC``: (Default: "")
   The run command for the ``aqm_lbcs`` task.
 
@@ -271,6 +274,12 @@ These parameters are associated with the fixed (i.e., static) files. On :srw-wik
 ``FIXshp``: (Default: "")
    System directory containing the graphics shapefiles. On Level 1 systems, these are set within the machine files. Users on other systems will need to provide the path to the directory that contains the *Natural Earth* shapefiles.
 
+``FIXaqm``: (Default: "")
+   System directory where AQM data files are located.
+
+``FIXemis``: (Default: "")
+   System directory where AQM emission data files are located.
+
 ``FIXcrtm``: (Default: "")
    Path to system directory containing CRTM fixed files. 
 
@@ -287,7 +296,7 @@ WORKFLOW Configuration Parameters
 
 If non-default parameters are selected for the variables in this section, they should be added to the ``workflow:`` section of the ``config.yaml`` file. 
 
-``WORKFLOW_ID``: (Default: ``!nowtimestamp ''``)
+``WORKFLOW_ID``: (Default: "")
    Unique ID for the workflow run that will be set in ``setup.py``.
 
 ``RELATIVE_LINK_FLAG``: (Default: "--relative")
@@ -389,6 +398,9 @@ Set File Name Parameters
 ``NEMS_CONFIG_FN``: (Default: "nems.configure")
    Name of a file that contains information about the various :term:`NEMS` components and their run sequence. In general, users should not set this variable in their configuration file (see :ref:`note <tmpl-fn-warning>`).
 
+``UFS_CONFIG_FN``: (Default: "ufs.configure")
+  Name of a template file that contains information about the various UFS components and their run sequence (ufs-weather-model: ufs.configure). Its default value is the name of the file that the ufs weather model expects to read in.
+
 ``AQM_RC_FN``: (Default: "aqm.rc")
    Name of resource file for NOAA Air Quality Model (AQM). 
 
@@ -422,6 +434,9 @@ Set File Path Parameters
 ``NEMS_CONFIG_TMPL_FP``: (Default: ``'{{ [user.PARMdir, NEMS_CONFIG_FN]|path_join }}'``) 
    Path to the ``NEMS_CONFIG_FN`` file. 
 
+``UFS_CONFIG_TMPL_FP:``: (Default: ``'{{ [user.PARMdir, UFS_CONFIG_FN]|path_join }}'``)
+   Path to the ``UFS_CONFIG_FN`` file.
+
 ``AQM_RC_TMPL_FP``: (Default: ``'{{ [user.PARMdir, AQM_RC_TMPL_FN]|path_join }}'``) 
    Path to the ``AQM_RC_TMPL_FN`` file. 
 
@@ -440,6 +455,9 @@ This section contains files and paths to files that are staged in the experiment
 ``NEMS_CONFIG_FP``: (Default: ``'{{ [EXPTDIR, NEMS_CONFIG_FN]|path_join }}'``)
    Path to the ``NEMS_CONFIG_FN`` file in the experiment directory. 
 
+``UFS_CONFIG_FP``: (Default: ``'{{ [EXPTDIR, UFS_CONFIG_FN]|path_join }}'``)
+   Path to the ``UFS_CONFIG_FN`` file in the experiment directory. 
+
 ``FV3_NML_FP``: (Default: ``'{{ [EXPTDIR, FV3_NML_FN]|path_join }}'``)
    Path to the ``FV3_NML_FN`` file in the experiment directory.
 
@@ -452,8 +470,8 @@ This section contains files and paths to files that are staged in the experiment
 ``WFLOW_XML_FN``: (Default: "FV3LAM_wflow.xml")
    Name of the Rocoto workflow XML file that the experiment generation script creates. This file defines the workflow for the experiment.
 
-``GLOBAL_VAR_DEFNS_FN``: (Default: "var_defns.sh")
-   Name of the file (a shell script) containing definitions of the primary and secondary experiment variables (parameters). This file is sourced by many scripts (e.g., the J-job scripts corresponding to each workflow task) in order to make all the experiment variables available in those scripts. The primary variables are defined in the default configuration file (``config_defaults.yaml``) and in the user configuration file (``config.yaml``). The secondary experiment variables are generated by the experiment generation script. 
+``GLOBAL_VAR_DEFNS_FN``: (Default: "var_defns.yaml")
+   Name of the experiment configuration file. It contains the primary experiment variables defined in this default configuration script and in the user-specified configuration as well as secondary experiment variables generated by the experiment generation script. This file is the primary source of information used in the scripts at run time. The primary variables are defined in the default configuration file (``config_defaults.yaml``) and in the user configuration file (``config.yaml``). The secondary experiment variables are generated by the experiment generation script. 
 
 ``ROCOTO_YAML_FN``: (Default: "rocoto_defns.yaml")
    Name of the YAML file containing the YAML workflow definition from which the Rocoto XML file is created.
@@ -532,13 +550,13 @@ CCPP Parameter
 ``CCPP_PHYS_SUITE_FP``: (Default: ``'{{ [workflow.EXPTDIR, CCPP_PHYS_SUITE_FN]|path_join }}'``)
    The full path to the suite definition file (SDF) in the experiment directory. 
 
-``CCPP_PHYS_DIR``: (Default: ``'{{ [user.UFS_WTHR_MDL_DIR, "FV3", "ccpp", "physics", "physics"] |path_join }}'``)
+``CCPP_PHYS_DIR``: (Default: ``'{{ [user.UFS_WTHR_MDL_DIR, "FV3", "ccpp", "physics", "physics", "SFC_models", "Land", "Noahmp"] |path_join }}'``)
    The directory containing the CCPP physics source code. This is needed to link table(s) contained in that repository. 
 
 Field Dictionary Parameters
 ------------------------------
 
-``FIELD_DICT_FN``: (Default: "fd_nems.yaml")
+``FIELD_DICT_FN``: (Default: "fd_ufs.yaml")
    The name of the field dictionary file. This file is a community-based dictionary for shared coupling fields and is automatically generated by the :term:`NUOPC` Layer. 
 
 ``FIELD_DICT_IN_UWM_FP``: (Default: ``'{{ [user.UFS_WTHR_MDL_DIR, "tests", "parm", FIELD_DICT_FN]|path_join }}'``)
@@ -1108,10 +1126,10 @@ For each workflow task, certain parameter values must be passed to the job sched
 
       For more information, see the `Intel Development Reference Guide <https://www.intel.com/content/www/us/en/docs/cpp-compiler/developer-guide-reference/2021-10/thread-affinity-interface.html>`__. 
 
-``OMP_NUM_THREADS_RUN_FCST``: (Default: 1)
+``OMP_NUM_THREADS_RUN_FCST``: (Default: 2)
    The number of OpenMP threads to use for parallel regions. Corresponds to the ``ATM_omp_num_threads`` value in ``nems.configure``.
 
-``OMP_STACKSIZE_RUN_FCST``: (Default: "512m")
+``OMP_STACKSIZE_RUN_FCST``: (Default: "1024m")
    Controls the size of the stack for threads created by the OpenMP implementation.
 
 .. _ModelConfigParams: