Merge pull request MPAS-Dev#37 from xylar/add_SOwISC12to60E2r4

New Mesh: SOwISC12to60E2r4
Long name: SOwISC12to60kmL60E3SMv2r4

This version of the Southern Ocean Regionally Refined Mesh (SORRM) includes:
* 12 km resolution around Antarctica, about 1000 km farther north than in revision 3 of the mesh
* 45 km resolution at southern mid-latitudes
* 30 km resolution at the equator and the north Atlantic
* 60 km resolution in the north Pacific
* 35 km resolution in the Arctic

It matches the EC30to60 mesh except in the Southern Ocean and north Atlantic.

The merge includes some reorganization of the SOwISC test cases within COMPASS:
* the "resolution" has been renamed from `SO10to60wISC` to `SOwISC12to60`
* a new test case `files_for_e3sm` has been added to create the initial condition, graph files, analysis region masks and mapping files, etc.

The script that produces files for E3SM has been modified to use the short name of the mesh in output file names, rather than the long name.

Initial condition, spin-up and files for E3SM are on Anvil at:
```
lcrc/group/e3sm/ac.xylar/mpas/spinup_expand_hr_SOwISC12to60E2r4/ocean/global_ocean/SOwISC12to60/
```

ocean/global_ocean/SOwISC12to60/files_for_e3sm/config_driver.xml

@@ -0,0 +1,5 @@
+<driver_script name="run.py">
+	<case name="files_for_e3sm">
+		<step executable="./run.py" quiet="true" pre_message=" * Creating ocean and sea-ice initial conditions and supporting files for E3SM" post_message=" - Complete"/>
+	</case>
+</driver_script>

ocean/global_ocean/SO60to10wISC/init/config_E3SM_coupling_files.ini → ocean/global_ocean/SOwISC12to60/files_for_e3sm/config_files_for_e3sm.ini

@@ -15,18 +15,18 @@ description = MPAS Southern Ocean regionally refined mesh for E3SM version
               ${e3sm_version} with enhanced resolution (${min_res} km) around
               Antarctica, 45-km resolution in the mid southern latitudes,
               30-km resolution in a 15-degree band around the equator, 60-km
-              resolution in northern mid latitudes, and a region transitioning
-              from 35-km resolution at the Arctic and North-Atlantic margins to
-              15 km near Greenland.  This mesh has ${levels} vertical levels and
-              includes cavities under the ice shelves in the Antarctic.
+              resolution in northern mid latitudes, 30 km in the north
+              Atlantic and 35 km in the Arctic.  This mesh has ${levels}
+              vertical levels and includes cavities under the ice shelves
+              around Antarctica. The mesh is described in the following pull
+              request: https://github.com/MPAS-Dev/compass/pull/37
 e3sm_version = 2
-mesh_version = 03
+mesh_version = 4
 creation_date = autodetect
 min_res = 12
 max_res = 60
 max_depth = autodetect
 levels = autodetect
-runoff_description = <<<Spreading function described here>>>
 
 # The following options are detected from .gitconfig if not explicitly entered
 author = autodetect
@@ -76,6 +76,3 @@ enable = false
 
 [prescribed_ismf]
 enable = false
-# path to the Rignot2013 data set.
-# The default is a symlink to the initial conditions database
-rignot_2013_file = ../MeltRatesRignot2013.nc

ocean/global_ocean/SOwISC12to60/files_for_e3sm/config_files_for_e3sm.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<config case="files_for_e3sm">
+
+	<add_link source="../../init/initial_state/initial_state.nc" dest="mesh_before_metadata.nc"/>
+	<add_link source="../../init/initial_state/graph.info" dest="graph.info"/>
+	<add_link source_path="script_configuration_dir" source="scripts/create_E3SM_coupling_files.py" dest="create_files_for_e3sm.py"/>
+	<add_link source_path="script_configuration_dir" source="scripts/config_E3SM_coupling_files.ini" dest="defaults.ini"/>
+    <copy_file source_path="script_test_dir" source="config_files_for_e3sm.ini" dest="config_files_for_e3sm.ini"/>
+	<add_link source_path="script_configuration_dir" source="scripts/readme_E3SM_coupling_files" dest="readme"/>
+
+	<run_script name="run.py">
+		<step executable="./create_files_for_e3sm.py">
+			<argument flag="--config">config_files_for_e3sm.ini</argument>
+		</step>
+	</run_script>
+</config>

ocean/global_ocean/SOwISC12to60/init/atlantic.geojson

@@ -0,0 +1,97 @@
+{
+  "type": "FeatureCollection",
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "name": "Atlantic region",
+        "component": "ocean",
+        "object": "region",
+        "author": "Xylar Asay-Davis"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [
+              -97.3828125,
+              85.05112877979998
+            ],
+            [
+              -102.3046875,
+              40.17887331434696
+            ],
+            [
+              -102.3046875,
+              23.241346102386135
+            ],
+            [
+              -93.1640625,
+              15.623036831528264
+            ],
+            [
+              -85.78125,
+              13.581920900545844
+            ],
+            [
+              -83.583984375,
+              9.535748998133627
+            ],
+            [
+              -81.2109375,
+              8.059229627200192
+            ],
+            [
+              -79.013671875,
+              9.795677582829743
+            ],
+            [
+              -75.9375,
+              5.61598581915534
+            ],
+            [
+              -77.6953125,
+              0
+            ],
+            [
+              16.171875,
+              0
+            ],
+            [
+              27.773437499999996,
+              26.745610382199022
+            ],
+            [
+              37.96875,
+              32.24997445586331
+            ],
+            [
+              39.7265625,
+              39.36827914916014
+            ],
+            [
+              32.6953125,
+              53.9560855309879
+            ],
+            [
+              37.6171875,
+              61.438767493682825
+            ],
+            [
+              25.664062500000004,
+              68.26938680456564
+            ],
+            [
+              24.609375,
+              85.05112877979998
+            ],
+            [
+              -97.3828125,
+              85.05112877979998
+            ]
+          ]
+        ]
+      }
+    }
+  ]
+}

ocean/global_ocean/SO60to10wISC/init/build_base_mesh.py → ocean/global_ocean/SOwISC12to60/init/build_base_mesh.py

@@ -37,11 +37,12 @@ def cellWidthVsLatLon():
                                            cellWidthPole=45.,
                                            latPosEq=7.5, latWidthEq=3.0)
 
-    # Transition at Equator
     cellWidthNorth = mdt.EC_CellWidthVsLat(lat, cellWidthEq=30.,
                                            cellWidthMidLat=60.,
-                                           cellWidthPole=60.,
+                                           cellWidthPole=35.,
                                            latPosEq=7.5, latWidthEq=3.0)
+
+    # Transition at Equator
     latTransition = 0.0
     latWidthTransition = 2.5
     cellWidthVsLat = mdt.mergeCellWidthVsLat(
@@ -53,51 +54,47 @@ def cellWidthVsLatLon():
 
     _, cellWidth = np.meshgrid(lon, cellWidthVsLat)
 
-    # now, add the high-res region
-    fc = read_feature_collection('high_res_region.geojson')
+    cellWidthAtlantic = mdt.EC_CellWidthVsLat(lat, cellWidthEq=30.,
+                                              cellWidthMidLat=30.,
+                                              cellWidthPole=35.,
+                                              latPosEq=7.5, latWidthEq=3.0)
 
-    so_signed_distance = signed_distance_from_geojson(fc, lon, lat,
-                                                      earth_radius,
-                                                      max_length=0.25)
+    cellWidthAtlantic = mdt.mergeCellWidthVsLat(
+        lat,
+        cellWidthSouth,
+        cellWidthAtlantic,
+        latTransition,
+        latWidthTransition)
 
-    # Equivalent to 20 degrees latitude
-    trans_width = 1600e3
-    trans_start = -500e3
-    dx_min = 12.
+    _, cellWidthAtlantic = np.meshgrid(lon, cellWidthAtlantic)
 
-    weights = 0.5 * (1 + np.tanh((so_signed_distance - trans_start) /
-                                 trans_width))
+    fc = read_feature_collection('atlantic.geojson')
 
-    cellWidth = dx_min * (1 - weights) + cellWidth * weights
+    atlantic_signed_distance = signed_distance_from_geojson(
+        fc, lon, lat, earth_radius, max_length=0.25)
 
-    fc = read_feature_collection('north_mid_res_region.geojson')
+    trans_width = 400e3
+    trans_start = 0.
+    weights = 0.5 * (1 + np.tanh((atlantic_signed_distance - trans_start) /
+                                 trans_width))
 
-    ar_signed_distance = signed_distance_from_geojson(fc, lon, lat,
-                                                      earth_radius,
-                                                      max_length=0.25)
+    cellWidth = cellWidthAtlantic * (1 - weights) + cellWidth * weights
 
-    fc = read_feature_collection('greenland.geojson')
+    fc = read_feature_collection('high_res_region.geojson')
 
-    gr_signed_distance = signed_distance_from_geojson(fc, lon, lat,
+    so_signed_distance = signed_distance_from_geojson(fc, lon, lat,
                                                       earth_radius,
                                                       max_length=0.25)
 
-    frac = (-ar_signed_distance/(-ar_signed_distance + gr_signed_distance))
-
-    frac = np.maximum(0., np.minimum(1., frac))
-
-    dx_min = 15.
-    dx_max = 35.
-
-    arctic_widths = dx_max + (dx_min - dx_max)*frac
-
-    trans_width = 1000e3
-    trans_start = 0.
+    # Equivalent to 20 degrees latitude
+    trans_width = 1600e3
+    trans_start = 500e3
+    dx_min = 12.
 
-    weights = 0.5 * (1 + np.tanh((ar_signed_distance - trans_start) /
+    weights = 0.5 * (1 + np.tanh((so_signed_distance - trans_start) /
                                  trans_width))
 
-    cellWidth = arctic_widths * (1 - weights) + cellWidth * weights
+    cellWidth = dx_min * (1 - weights) + cellWidth * weights
 
     return cellWidth, lon, lat
 

ocean/global_ocean/SO60to10wISC/init/config_base_mesh.xml → ocean/global_ocean/SOwISC12to60/init/config_base_mesh.xml

@@ -3,8 +3,7 @@
 
 	<add_link source_path="script_test_dir" source="build_base_mesh.py" dest="build_base_mesh.py"/>
 	<add_link source_path="script_test_dir" source="high_res_region.geojson" dest="high_res_region.geojson"/>
-	<add_link source_path="script_test_dir" source="north_mid_res_region.geojson" dest="north_mid_res_region.geojson"/>
-	<add_link source_path="script_test_dir" source="greenland.geojson" dest="greenland.geojson"/>
+	<add_link source_path="script_test_dir" source="atlantic.geojson" dest="atlantic.geojson"/>
 
 	<run_script name="run.py">
 		<step executable="./build_base_mesh.py">