Add some grid info

Author: zmoon

02-run.md

@@ -9,6 +9,7 @@ subtitle: Running MPAS on NSF NCAR Derecho
 
 Limited-area domain as in:
 
+- https://doi.org/10.1029/2023MS004070
 - https://doi.org/10.1029/2024GL112341
 - https://doi.org/10.22541/essoar.174547926.68665522/v1
 - https://doi.org/10.22541/essoar.174547944.43729039/v1

03-viz.ipynb

@@ -13,20 +13,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "478e135b-116c-41c1-8397-0880936dc908",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "yes\n"
-     ]
-    }
-   ],
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "id": "06e6dfea-99c3-42dc-bc96-4c06da842ace",
+   "metadata": {},
    "source": [
-    "print(\"yes\")"
+    "With unstructured-grid data, the grid/coordinate information is usually stored in a separate file from the model output fields. Considerably more information is needed to reconstruct the grid than in the case of a rectangular lat/lon grid, for example, which can be expressed with 1-D coordinate variables.\n",
+    "\n",
+    "With MPAS-A, the necessary grid variables are available in multiple files:\n",
+    "\n",
+    "* the **grid** file (usually ends in `.grid.nc`)\n",
+    "  - agnostic to simulation\n",
+    "  - note that with the standard limited-area workflow, which involves cutting out a section of a global grid, this can't be used\n",
+    "* the **static** file (usually ends in `.static.nc`)\n",
+    "  - produced as part of the model initialization/prep preocess, contains static fields like terrain height\n",
+    "* **initial conditions** (usually ends in `.init.nc`)\n",
+    "  - easier to work with since the connectivity for the primal mesh uses zeros for padding\n",
+    " \n",
+    "Some example grid and static files are available at: <https://mpas-dev.github.io/atmosphere/atmosphere_meshes.html>\n",
+    "\n",
+    "Or on Casper/Derecho at:\n",
+    "```\n",
+    "/glade/campaign/mmm/wmr/duda/mesh/\n",
+    "```"
    ]
   },
   {
@@ -90,7 +105,9 @@
    "source": [
     "# GeoVista\n",
     "\n",
-    "Built on PyVista/VTK, [GeoVista](https://geovista.readthedocs.io/) provides GPU-accelerated interactive visualization of geospatial data and has [builtin support](https://geovista.readthedocs.io/en/v0.5.3/reference/generated/api/geovista/bridge/#geovista.bridge.Transform.from_unstructured) for unstructured meshes."
+    "Built on PyVista/VTK, [GeoVista](https://geovista.readthedocs.io/) provides GPU-accelerated interactive visualization of geospatial data and has [builtin support](https://geovista.readthedocs.io/en/v0.5.3/reference/generated/api/geovista/bridge/#geovista.bridge.Transform.from_unstructured) for unstructured meshes.\n",
+    "\n",
+    "It will still work if a GPU is not available/detected, but it may be much slower to first plot and to respond."
    ]
   },
   {