edit Tutorial & misc; chg CCPP update location

docs/UsersGuide/source/BuildingRunningTesting/BuildSRW.rst

@@ -205,7 +205,13 @@ where valid values are ``intel`` or ``gnu``.
 
 The last few lines of the console output should include ``[100%] Built target ufs-weather-model``, indicating that the UFS Weather Model executable has been built successfully. 
 
-After running ``devbuild.sh``, the executables listed in :numref:`Table %s <ExecDescription>` should appear in the ``ufs-srweather-app/exec`` directory. If the application built properly, users may continue to :numref:`Section %s <RunSRW>` to configure and run an experiment. If the ``devbuild.sh`` build method does *not* work, or if users are not on a supported machine, they will have to manually set up the environment and build the SRW App binaries with CMake as described in :numref:`Section %s <CMakeApproach>`.
+After running ``devbuild.sh``, the executables listed in :numref:`Table %s <ExecDescription>` should appear in the ``ufs-srweather-app/exec`` directory. If the application built properly, users may configure and run an experiment. Users have a few options: 
+
+#. Proceed to :numref:`Section %s: Quick Start Guide <NCQuickstart>` for a quick overview of the workflow steps. 
+#. Try the :ref:`SRW App Tutorials <Tutorial>` (good for new users!). 
+#. For detailed information on running the SRW App, including optional tasks like plotting and verification, users can refer to :numref:`Section %s: Running the SRW App <RunSRW>`.
+
+If the ``devbuild.sh`` build method did *not* work, or if users are not on a supported machine, they will have to manually set up the environment and build the SRW App binaries with CMake as described in :numref:`Section %s <CMakeApproach>`.
 
 .. _ExecDescription:
 
@@ -383,4 +389,8 @@ Proceed to building the executables using the process outlined in :numref:`Step
 Run an Experiment
 =====================
 
-To configure and run an experiment, users should proceed to :numref:`Chapter %s <RunSRW>`.
+To configure and run an experiment, users have a few options: 
+
+#. Proceed to :numref:`Section %s: Quick Start Guide <NCQuickstart>` for a quick overview of the workflow steps. 
+#. Try the :ref:`SRW App Tutorials <Tutorial>` (good for new users!). 
+#. For detailed information on running the SRW App, including optional tasks like plotting and verification, users can refer to :numref:`Section %s: Running the SRW App <RunSRW>`.

docs/UsersGuide/source/BuildingRunningTesting/Tutorial.rst

@@ -160,6 +160,9 @@ should be included in the ``rocoto:tasks:taskgroups:`` section, like this:
            walltime: 02:00:00
       taskgroups: '{{ ["parm/wflow/prep.yaml", "parm/wflow/coldstart.yaml", "parm/wflow/post.yaml", "parm/wflow/plot.yaml"]|include }}'
 
+For more information on how to turn on/off tasks in the workflow, please
+see :numref:`Section %s <ConfigTasks>`.
+
 In the ``task_get_extrn_ics:`` section, add ``USE_USER_STAGED_EXTRN_FILES`` and ``EXTRN_MDL_SOURCE_BASEDIR_ICS``. Users will need to adjust the file path to reflect the location of data on their system (see :numref:`Section %s <Data>` for locations on `Level 1 <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__ systems). 
 
 .. code-block:: console
@@ -239,7 +242,7 @@ Once the control case is running, users can return to the ``config.yaml`` file (
      EXPT_SUBDIR: test_expt
      CCPP_PHYS_SUITE: FV3_RRFS_v1beta
 
-``EXPT_SUBDIR:`` This name must be different than the ``EXPT_SUBDIR`` name used in the previous forecast experiment. Otherwise, the first forecast experiment will be overwritten. ``test_expt`` is used here, but the user may select a different name if desired. 
+``EXPT_SUBDIR:`` This name must be different than the ``EXPT_SUBDIR`` name used in the previous forecast experiment. Otherwise, the first forecast experiment will be renamed, and the new experiment will take its place (see :numref:`Section %s <preexisting-dirs>` for details). To avoid this issue, this tutorial uses ``test_expt`` as the second experiment's name, but the user may select a different name if desired. 
 
 ``CCPP_PHYS_SUITE:`` The FV3_RRFS_v1beta physics suite was specifically created for convection-allowing scales and is the precursor to the operational physics suite that will be used in the Rapid Refresh Forecast System (:term:`RRFS`). 
 
@@ -321,7 +324,7 @@ Users should substitute ``/path/to/expt_dirs/test_expt`` with the actual path on
 Compare and Analyze Results
 -----------------------------
 
-Navigate to ``test_expt/2019061518/postprd``. This directory contains the post-processed data generated by the :term:`UPP` from the forecast. After the ``plot_allvars`` task completes, this directory will contain ``.png`` images for several forecast variables including 2-m temperature, 2-m dew point temperature, 10-m winds, accumulated precipitation, composite reflectivity, and surface-based CAPE/CIN. Plots with a ``_diff`` label in the file name are plots that compare the ``control`` forecast and the ``test_expt`` forecast. 
+Navigate to ``test_expt/2019061518/postprd``. This directory contains the post-processed data generated by the :term:`UPP` from the ``test_expt`` forecast. After the ``plot_allvars`` task completes, this directory will contain ``.png`` images for several forecast variables including 2-m temperature, 2-m dew point temperature, 10-m winds, accumulated precipitation, composite reflectivity, and surface-based CAPE/CIN. Plots with a ``_diff`` label in the file name are plots that compare the ``control`` forecast and the ``test_expt`` forecast. 
 
 Copy ``.png`` Files onto Local System
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -386,20 +389,23 @@ In the Sea Level Pressure (SLP) plots, the ``control`` and ``test_expt`` plots a
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/slp_diff_regional_f000.png
       :align: center
+      :width: 75%
 
       *Difference Plot for Sea Level Pressure at f000*
 
 As the forecast continues, the results begin to diverge, as evidenced by the spattering of light blue dispersed across the f006 SLP difference plot. 
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/slp_diff_regional_f006.png
       :align: center
+      :width: 75%
 
       *Difference Plot for Sea Level Pressure at f006*
 
 The predictions diverge further by f012, where a solid section of light blue in the top left corner of the difference plot indicates that to the northwest of Indianapolis, the SLP predictions for the ``control`` forecast were slightly lower than the predictions for the ``test_expt`` forecast. 
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/slp_diff_regional_f012.png
       :align: center
+      :width: 75%
 
       *Difference Plot for Sea Level Pressure at f012*
 
@@ -414,6 +420,7 @@ At f000, the ``test_expt`` plot (top left) is showing more severe weather than t
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/refc_diff_regional_f000.png
       :align: center
+      :width: 75%
 
       *Composite Reflectivity at f000*
 
@@ -423,13 +430,15 @@ As the forecast progresses, the radar images resemble each other more (see :numr
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/refc_diff_regional_f006.png
       :align: center
+      :width: 75%
 
       *Composite reflectivity at f006 shows storm gathering strength*
 
 At forecast hour 12, the plots for each forecast show a similar evolution of the storm with both resolving a squall line. The ``test_expt`` plot shows a more intense squall line with discrete cells (areas of high composite reflectivity in dark red), which could lead to severe weather. The ``control`` plot shows an overall decrease in composite reflectivity values compared to f006. It also orients the squall line more northward with less intensity, possibly due to convection from the previous forecast runs cooling the atmosphere. In short, ``test_expt`` suggests that the storm will still be going strong at 06z on June 15, 2019, whereas the ``control`` suggests that the storm will begin to let up. 
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/refc_diff_regional_f012.png
       :align: center
+      :width: 75%
 
       *Composite Reflectivity at f012*
 
@@ -441,7 +450,7 @@ Surface-Based CAPE/CIN
 Background
 """"""""""""
 
-The National Weather Service (:term:`NWS`) defines Surface-Based Convective Available Potential Energy (CAPE) as "the amount of fuel available to a developing thunderstorm." According to NWS, CAPE "describes the instabilily of the atmosphere and provides an approximation of updraft strength within a thunderstorm. A higher value of CAPE means the atmosphere is more unstable and would therefore produce a stronger updraft" (see `NWS, What is CAPE? <https://www.weather.gov/ilx/swop-severetopics-CAPE>`__ for further explanation). 
+The National Weather Service (:term:`NWS`) defines Surface-Based Convective Available Potential Energy (CAPE) as "the amount of fuel available to a developing thunderstorm." According to NWS, CAPE "describes the instabilily of the atmosphere and provides an approximation of updraft strength within a thunderstorm. A higher value of CAPE means the atmosphere is more unstable and would therefore produce a stronger updraft" (see `NWS: What is CAPE? <https://www.weather.gov/ilx/swop-severetopics-CAPE>`__ for further explanation). 
 
 According to the NWS `Storm Prediction Center <https://www.spc.noaa.gov/exper/mesoanalysis/help/begin.html>`__, Convective Inhibition (CIN) "represents the 'negative' area on a sounding that must be overcome for storm initiation." In effect, it measures negative buoyancy (-B) --- the opposite of CAPE, which measures positive buoyancy (B or B+) of an air parcel. 
 
@@ -465,23 +474,23 @@ In general, the higher the CIN values are (i.e., the closer they are to zero), t
 At the 0th forecast hour, the ``test_expt`` plot (below, left) shows lower values of CAPE and higher values of CIN than in the ``control`` plot (below, right). This means that ``test_expt`` is projecting lower potential energy available for a storm but also lower inhibition, which means that less energy would be required for a storm to develop. The difference between the two plots is particularly evident in the southwest corner of the difference plot, which shows a 1000+ J/kg difference between the two plots. 
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/sfcape_diff_regional_f000.png
-      :width: 1200
+      :width: 75%
       :align: center
 
       *CAPE/CIN Difference Plot at f000*
 
 At the 6th forecast hour, both ``test_expt`` and ``control`` plots are forecasting higher CAPE values overall. Both plots also predict higher CAPE values to the southwest of Indianapolis than to the northeast. This makes sense because the storm was passing from west to east. However, the difference plot shows that the ``control`` forecast is predicting higher CAPE values primarily to the southwest of Indianapolis, whereas ``test_expt`` is projecting a rise in CAPE values throughout the region. The blue region of the difference plot indicates where ``test_expt`` predictions are higher than the ``control`` predictions; the red/orange region shows places where ``control`` predicts significantly higher CAPE values than ``test_expt`` does. 
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/sfcape_diff_regional_f006.png
-      :width: 1200
+      :width: 75%
       :align: center
 
       *CAPE/CIN Difference Plot at f006*
 
 At the 12th forecast hour, the ``control`` plot indicates that CAPE may be decreasing overall. ``test_expt``, however, shows that areas of high CAPE remain and continue to grow, particularly to the east. The blue areas of the difference plot indicate that ``test_expt`` is predicting higher CAPE than ``control`` everywhere but in the center of the plot. 
 
 .. figure:: https://github.com/ufs-community/ufs-srweather-app/wiki/Tutorial/fcst1_plots/sfcape_diff_regional_f012.png
-      :width: 1200
+      :width: 75%
       :align: center
 
       *CAPE/CIN Difference Plot at f012*

docs/UsersGuide/source/CustomizingTheWorkflow/ConfigWorkflow.rst

@@ -646,6 +646,8 @@ Forecast Parameters
 
    By setting ``FCST_LEN_HRS: -1``, the experiment will derive the values of ``FCST_LEN_HRS`` (18) and ``LONG_FCST_LEN_HRS`` (48) for each cycle date. 
 
+.. _preexisting-dirs:
+
 Pre-Existing Directory Parameter
 ------------------------------------
 ``PREEXISTING_DIR_METHOD``: (Default: "delete")
@@ -1173,7 +1175,7 @@ Write-Component (Quilting) Parameters
 
    .. math::
       
-      LAYOUT_X * LAYOUT_Y + WRTCMP\_write\_groups * WRTCMP_write_tasks_per_group 
+      LAYOUT\_X * LAYOUT\_Y + WRTCMP\_write\_groups * WRTCMP\_write\_tasks\_per\_group 
 
 ``WRTCMP_write_groups``: (Default: "")
    The number of write groups (i.e., groups of :term:`MPI` tasks) to use in the write component. Each write group will write to one set of output files (a ``dynf${fhr}.nc`` and a ``phyf${fhr}.nc`` file, where ``${fhr}`` is the forecast hour). Each write group contains ``WRTCMP_write_tasks_per_group`` tasks. Usually, one write group is sufficient. This may need to be increased if the forecast is proceeding so quickly that a single write group cannot complete writing to its set of files before there is a need/request to start writing the next set of files at the next output time.

docs/UsersGuide/source/Reference/FAQ.rst

@@ -66,9 +66,9 @@ However, users can choose from a variety of predefined grids listed in :numref:`
 How can I select which workflow tasks to run? 
 ===============================================
 
-:numref:`Section %s <_ConfigTasks>` provides a full description of how to set which workflow tasks and task groups run. 
+:numref:`Section %s <ConfigTasks>` provides a full description of how to set which workflow tasks and task groups run. 
 
-The default workflow tasks are defined in ``ufs-srweather-app/parm/wflow/default_workflow.yaml``. However, the ``/parm/wflow`` directory contains several ``YAML`` files that configure different workflow task groups. Each file contains a number of tasks that are typically run together (see :numref:`Table %s <task-group-files>` for a description of each task group). To add or remove workflow tasks, users will need to alter the user configuration file (``config.yaml``) as described in :numref:`Section %s <_ConfigTasks>` to override the default workflow and run the selected tasks and task groups.   
+The default workflow tasks are defined in ``ufs-srweather-app/parm/wflow/default_workflow.yaml``. However, the ``/parm/wflow`` directory contains several ``YAML`` files that configure different workflow task groups. Each file contains a number of tasks that are typically run together (see :numref:`Table %s <task-group-files>` for a description of each task group). To add or remove workflow tasks, users will need to alter the user configuration file (``config.yaml``) as described in :numref:`Section %s <ConfigTasks>` to override the default workflow and run the selected tasks and task groups.   
 
 .. _CycleInd:
 

docs/UsersGuide/source/conf.py

@@ -111,7 +111,7 @@
 # html_theme_options = {}
 html_theme_options = {
     "body_max_width": "none", 
-    'navigation_depth': 5,
+    'navigation_depth': 6,
     }
 
 # Add any paths that contain custom static files (such as style sheets) here,