Update docs

Author: xylar

docs/design_docs/cached_outputs.rst

@@ -35,7 +35,7 @@ Contributors: Xylar Asay-Davis
 Each ``compass`` step defines its output files in the ``compass.Step.outputs``
 attribute. For selected steps (see :ref:`req_select`), we require a mechanism
 to download cached files for each of these outputs and to use these cached
-files for the outputs of the step instead of computing them.  
+files for the outputs of the step instead of computing them.
 
 .. _req_select:
 
@@ -48,7 +48,7 @@ Contributors: Xylar Asay-Davis
 
 There needs to be a mechanism for developers and users to select which steps
 are run as normal and which use cached outputs.  For this mechanism to be
-practical, it should not be overly tedious or manual (e.g. manually setting a 
+practical, it should not be overly tedious or manual (e.g. manually setting a
 flag for each step).
 
 .. _req_update:
@@ -72,11 +72,11 @@ Date last modified: 2021/07/30
 
 Contributors: Xylar Asay-Davis
 
-There should be a mechanism for giving each cached output file a unique 
-identifier (such as a date stamp).  A given version (git hash or release) of 
+There should be a mechanism for giving each cached output file a unique
+identifier (such as a date stamp).  A given version (git hash or release) of
 ``compass`` should know which cached files to download.  Older cached files
 should be retained so that older versions of ``compass`` can still be used
-with these cached files.  
+with these cached files.
 
 .. note::
 
@@ -109,14 +109,14 @@ Date last modified: 2021/07/30
 
 Contributors: Xylar Asay-Davis
 
-``compass`` supports "databases" of input data files on the E3SM 
+``compass`` supports "databases" of input data files on the E3SM
 `LCRC server <https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/>`_.
-Files will be stored in a new ``compass_cache`` database within each MPAS 
+Files will be stored in a new ``compass_cache`` database within each MPAS
 core's space on that server.  If the "cached" version of a step is selected
-(see :ref:`des_select`), an appropriate "input" file will be added to the test 
+(see :ref:`des_select`), an appropriate "input" file will be added to the test
 case where the "target" is the file on the LCRC server to be cached locally for
 future use and the "filename" is the output file.  ``compass`` will know which
-files on the server correspond to which output files via a python dictionary, 
+files on the server correspond to which output files via a python dictionary,
 as described in :ref:`des_unique`.
 
 .. _des_select:
@@ -403,9 +403,9 @@ The implementation leans heavily on the assumption that a given step will
 either be run with cached outputs or as normal, so that both versions are not
 available in the same work directory or as part of the same test suite.
 
-Nevertheless, if a separate "cached" version of a step were desired, it would 
-be necessary to make symlinks from the cached files in the location of the 
-"uncached" version of the step to the location of the "cached" version.  For 
+Nevertheless, if a separate "cached" version of a step were desired, it would
+be necessary to make symlinks from the cached files in the location of the
+"uncached" version of the step to the location of the "cached" version.  For
 example, if the "uncached" step is
 
 .. code-block:: none
@@ -422,7 +422,7 @@ symlinks could be created on the LCRC server, e.g.
 
 .. code-block:: none
 
-    /lcrc/group/e3sm/public_html/mpas_standalonedata/mpas-ocean/compass_cache/global_ocean/QU240/cached/mesh/mesh/culled_mesh.210803.nc 
+    /lcrc/group/e3sm/public_html/mpas_standalonedata/mpas-ocean/compass_cache/global_ocean/QU240/cached/mesh/mesh/culled_mesh.210803.nc
       -> /lcrc/group/e3sm/public_html/mpas_standalonedata/mpas-ocean/compass_cache/global_ocean/QU240/mesh/mesh/culled_mesh.210803.nc
 
 and the ``cached`` attribute could be set to ``True`` in the constructor of the
@@ -452,8 +452,8 @@ using test-case runs on Chrysalis.
     ocean/global_ocean/QUwISC240/PHC/init/ssh_adjustment/
     ocean/global_ocean/EC30to60/mesh/mesh/
     ocean/global_ocean/EC30to60/PHC/init/initial_state/
-    ocean/global_ocean/WC14/mesh/mesh/
-    ocean/global_ocean/WC14/PHC/init/initial_state/
+    ocean/global_ocean/NARRM14/mesh/mesh/
+    ocean/global_ocean/NARRM14/PHC/init/initial_state/
     ocean/global_ocean/ECwISC30to60/mesh/mesh/
     ocean/global_ocean/ECwISC30to60/PHC/init/initial_state/
     ocean/global_ocean/ECwISC30to60/PHC/init/ssh_adjustment/

docs/design_docs/compass_package.rst

@@ -1550,7 +1550,7 @@ metadata to include in the output files:
     forward_max_disk = 1000
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = EC
     # a description of the mesh and initial condition
     mesh_description = MPAS Eddy Closure mesh for E3SM version ${e3sm_version} with

docs/developers_guide/ocean/api.rst

@@ -236,8 +236,8 @@ test cases and steps
    mesh.so12to60.SO12to60BaseMesh
    mesh.so12to60.SO12to60BaseMesh.build_cell_width_lat_lon
 
-   mesh.wc14.WC14BaseMesh
-   mesh.wc14.WC14BaseMesh.build_cell_width_lat_lon
+   mesh.narrm14.NARRM14BaseMesh
+   mesh.narrm14.NARRM14BaseMesh.build_cell_width_lat_lon
 
    performance_test.PerformanceTest
    performance_test.PerformanceTest.configure

docs/developers_guide/ocean/test_groups/global_ocean.rst

@@ -46,7 +46,7 @@ The values of some of the metadata are given in config options:
     ## metadata related to the mesh
     # whether to add metadata to output files
     add_metadata = True
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = PREFIX
     # a description of the mesh
     mesh_description = <<<Missing>>>
@@ -87,7 +87,7 @@ defines:
     ...
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = EC
     # a description of the mesh and initial condition
     mesh_description = MPAS Eddy Closure mesh for E3SM version ${e3sm_version} with
@@ -371,7 +371,7 @@ The default config options for these meshes are:
     approx_cell_count = 7400
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = QU
     # a description of the mesh
     mesh_description = MPAS quasi-uniform mesh for E3SM version ${e3sm_version} at
@@ -454,7 +454,7 @@ The default config options for these meshes are:
     [global_ocean]
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = QU
 
     # a description of the mesh
@@ -486,7 +486,7 @@ corresponding QU config options above:
     [global_ocean]
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = Icos
 
     # a description of the mesh
@@ -552,7 +552,7 @@ The default config options for these meshes are:
     approx_cell_count = 240000
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = EC
     # a description of the mesh and initial condition
     mesh_description = MPAS Eddy Closure mesh for E3SM version ${e3sm_version} with
@@ -612,7 +612,7 @@ module:
     [global_ocean]
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO, Kuroshio)
+    # the prefix (e.g. QU, EC, NARRM, SO, Kuroshio)
     prefix = Kuroshio
     # a description of the mesh and initial condition
     mesh_description = MPAS Kuroshio regionally refined mesh for E3SM version
@@ -694,7 +694,7 @@ The default config options for these meshes are:
     approx_cell_count = 3700000
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = RRS
     # a description of the mesh and initial condition
     mesh_description = MPAS Eddy Closure mesh for E3SM version ${e3sm_version} with
@@ -820,7 +820,7 @@ The default config options for these meshes are:
     approx_cell_count = 570000
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = SO
     # a description of the mesh and initial condition
     mesh_description = MPAS Southern Ocean regionally refined mesh for E3SM version
@@ -855,19 +855,19 @@ The vertical grid is an ``index_tanh_dz`` profile (see
 :ref:`dev_ocean_framework_vertical`) with 64 vertical levels ranging in
 thickness from 10 to 250 m.
 
-.. _dev_ocean_global_ocean_wc14:
+.. _dev_ocean_global_ocean_narrm14:
 
-WC14 and WCwISC14
+NARRM14 and NARRMwISC14
 +++++++++++++++++
 
-The ``WC14`` and ``WCwISC14`` meshes are the Water Cycle regionally refined
+The ``NARRM14`` and ``NARRMwISC14`` meshes are the Water Cycle regionally refined
 meshes for E3SM v3.  They have higher resolution (~14-km) around the continental
 US, the Arctic Ocean, and a section of the North Atlantic containing the Gulf
 Stream. The resolution is uniformly about 30 km elsewhere.
 
-The class :py:class:`compass.ocean.tests.global_ocean.mesh.wc14.WC14BaseMesh`
+The class :py:class:`compass.ocean.tests.global_ocean.mesh.narrm14.NARRM14BaseMesh`
 defines the resolution for the meshes. The
-``compass.ocean.tests.global_ocean.mesh.wc14`` module includes namelist options
+``compass.ocean.tests.global_ocean.mesh.narrm14`` module includes namelist options
 appropriate for forward simulations with split-explicit (but not RK4) time
 integration on these meshes.  These set the time step and default run duration for
 short runs with these meshes.
@@ -906,8 +906,8 @@ The default config options for these meshes are:
     approx_cell_count = 410000
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
-    prefix = WC
+    # the prefix (e.g. QU, EC, NARRM, SO)
+    prefix = NARRM
     # a description of the mesh and initial condition
     mesh_description = MPAS North America and Arctic Focused Water Cycle mesh for E3SM version
                        ${e3sm_version}, with a focused ${min_res}-km resolution

docs/users_guide/config_files.rst

@@ -347,7 +347,7 @@ looks like:
     add_metadata = True
 
     ## metadata related to the mesh
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     # source: /home/xylar/code/compass/customize_config_parser/compass/ocean/tests/global_ocean/mesh/qu240/qu240.cfg
     prefix = QU
 

docs/users_guide/ocean/test_groups/global_ocean.rst

@@ -102,7 +102,7 @@ Note that meshes and test cases may modify these options, as noted below.
     ## metadata related to the mesh
     # whether to add metadata to output files
     add_metadata = True
-    # the prefix (e.g. QU, EC, WC, SO)
+    # the prefix (e.g. QU, EC, NARRM, SO)
     prefix = PREFIX
     # a description of the mesh
     mesh_description = <<<Missing>>>
@@ -452,20 +452,20 @@ in the North Pacific, and 35 km in the Arctic.  The mesh includes the
    :width: 500 px
    :align: center
 
-.. _global_ocean_mesh_wc14:
+.. _global_ocean_mesh_narrm14:
 
-WC14 and WCwISC14
+NARRM14 and NARRMwISC14
 ^^^^^^^^^^^^^^^^^
 
-The Water Cycle 14- to 30-km mesh (WC14) is a regionally refined mesh for
+The Water Cycle 14- to 30-km mesh (NARRM14) is a regionally refined mesh for
 several
 `E3SM v3 Science Campaigns <https://e3sm.org/research/science-campaigns/v3-v4-campaign-goals/>`_.
 
 The mesh has 14 km resolution around the continental US, Arctic Ocean and parts
 of the North Atlantic, with 30 km uniform resolution elsewhere around the
 globe.
 
-.. image:: images/wc14.png
+.. image:: images/narrm14.png
    :width: 500 px
    :align: center
 

docs/users_guide/quick_start.rst

@@ -430,8 +430,8 @@ The output is:
       -c ocean -t quwisc240_for_e3sm
       -c ocean -t so12to60
       -c ocean -t sowisc12to60
-      -c ocean -t wc14
-      -c ocean -t wcwisc14
+      -c ocean -t narrm14
+      -c ocean -t narrmwisc14
       -c ocean -t wetdry
 
 You can set up a suite as follows:

docs/users_guide/test_suites.rst

@@ -43,8 +43,8 @@ the current set of available test suites is:
       -c ocean -t quwisc240_for_e3sm
       -c ocean -t so12to60
       -c ocean -t sowisc12to60
-      -c ocean -t wc14
-      -c ocean -t wcwisc14
+      -c ocean -t narrm14
+      -c ocean -t narrmwisc14
       -c ocean -t wetdry
 
 As an example, the ocean ``nightly`` test suite includes the test cases used