Update global workflow info (#29)

* add HTF section

* update indexes

* Update Intro to reflect HTF work`

* add info about how to change checkout version and physics suite during build step

* update global workflow script change

docs/source/2018Michael.rst

@@ -49,13 +49,13 @@ Model Configuration and Datasets
         :download:`Download initial condition files: 2018100700.gfs.nemsio.tar.gz <https://ufs-case-studies.s3.amazonaws.com/2018100700.gfs.nemsio.tar.gz>`
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case was initialized at 00z Oct 07, 2018 and forecast out to 120 hours. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot Michael --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2018100700 --edate 2018100700 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot Michael --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2018100700 --edate 2018100700 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/Michael/config.base`` file. 
 

docs/source/2019Barry.rst

@@ -52,13 +52,13 @@ Model Configuration and Datasets
 
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 00z Jul 11, 2019 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot Barry --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019071100 --edate 2019071100 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot Barry --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019071100 --edate 2019071100 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/Barry/config.base`` file. 
 

docs/source/2019HaloweenStorm.rst

@@ -38,13 +38,13 @@ Model Configuration and Datasets
 
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 12z Oct 25, 2019 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2019Halloween --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019102512 --edate 2019102512 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2019Halloween --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019102512 --edate 2019102512 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2019Halloween/config.base`` file. 
 

docs/source/2019Lorenzo.rst

@@ -49,13 +49,13 @@ Model Configuration and Datasets
         :download:`Download initial condition files: 2019092512.gfs.nemsio.tar.gz <https://ufs-case-studies.s3.amazonaws.com/2019092512.gfs.nemsio.tar.gz>`
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 12z Sep 25, 2019 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot Lorenzo --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019092512 --edate 2019092512 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot Lorenzo --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019092512 --edate 2019092512 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/Lorenzo/config.base`` file. 
 

docs/source/2019MemHeat.rst

@@ -35,13 +35,13 @@ Model Configuration and Datasets
         :download:`Download initial condition files: 2019052300.gfs.nemsio.tar.gz <https://ufs-case-studies.s3.amazonaws.com/2019052300.gfs.nemsio.tar.gz>`
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 00z May 23, 2019 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2019MemHeat --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019052300 --edate 2019052300 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2019MemHeat --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2019052300 --edate 2019052300 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2019MemHeat/config.base`` file. 
 

docs/source/2020CAD.rst

@@ -35,13 +35,13 @@ Model Configuration and Datasets
         :download:`Download initial condition files: 2020020312.gfs.nemsio.tar.gz <https://ufs-case-studies.s3.amazonaws.com/2020020312.gfs.nemsio.tar.gz>`
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 12z Feb 03, 2020 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2020CAD --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020020312 --edate 2020020312 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2020CAD --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020020312 --edate 2020020312 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2020CAD/config.base`` file. 
 

docs/source/2020CAPE.rst

@@ -35,13 +35,13 @@ Model Configuration and Datasets
         :download:`Download initial condition files: 2020072300.gfs.nemsio.tar.gz <https://ufs-case-studies.s3.amazonaws.com/2020072300.gfs.nemsio.tar.gz>`
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 00z Jul 23, 2020 with a 24 hour forecast length. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2020CAPE --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020072300 --edate 2020072300 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2020CAPE --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020072300 --edate 2020072300 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2020CAPE/config.base`` file. 
 

docs/source/2020ColdBlast.rst

@@ -35,13 +35,13 @@ Model Configuration and Datasets
         :download:`Download initial condition files: 2020011712.gfs.nemsio.tar.gz <https://ufs-case-studies.s3.amazonaws.com/2020011712.gfs.nemsio.tar.gz>`
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 12z Jan 17, 2020 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2020ColdBias --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020011712 --edate 2020011712 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2020ColdBias --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020011712 --edate 2020011712 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2020ColdBias/config.base`` file. 
 

docs/source/2020DNRInversion.rst

@@ -35,13 +35,13 @@ Model Configuration and Datasets
 
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 12z Apr 29, 2020 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2020DNRInversion --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020042912 --edate 2020042912 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2020DNRInversion --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020042912 --edate 2020042912 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2020DNRInversion/config.base`` file. 
 

docs/source/2020EasterStorm.rst

@@ -36,13 +36,13 @@ Model Configuration and Datasets
 
   .. group-tab:: GFS.v16.0.10
 
-    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt_fcstonly.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
+    The GFS model EMC global workflow points to the most up-to-date GFS model development code. The GFS.v16.0.10 is tested in C768 (~13km) resolution and in 128 vertical levels. It uses two scripts, ``setup_expt.py`` and ``setup_workflow_fcstonly.py`` to set up the mode simulation date and case directories.
 
     The case runs are initialized at 12z Apr 07, 2020 with 120 hours forecasting. The settings that need to be modified to set up the start date and directories are listed below. 
 
     .. code-block:: bash
  
-      ./setup_expt_fcstonly.py --pslot 2020Easter --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020040712 --edate 2020040712 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
+      ./setup_expt.py forecast-only --pslot 2020Easter --configdir /PATH/TO/YOUR/GLOBAL/WORKFLOW/parm/config --idate 2020040712 --edate 2020040712 --res 768 --comrot /PATH/TO/YOUR/EXP/DIR/comrot --expdir /PATH/TO/YOUR/EXP/OUTPUT/expdir 
 
     The account and simulation duration time can be set up in ``/expdir/2020Easter/config.base`` file.