Merge pull request #578 from matthewhoffman/ocean/add_scrip_depth_mas…

…k_script

Add script for adding map of sufficiently deep ocean bathymetry to a scrip file

This PR adds a script for adding a mask to a scrip file needed for ocn-glc fjord coupling. This script defines a mask of ocean cells that are deeper than a threshold. This is to be used for updating a scrip file so that it only remaps from ocean cells deeper than that threshold. The resulting mapping file can be used as an OCN2GLC_TF_SMAPNAME mapping file in E3SM. Note that config_2d_thermal_forcing_depth in the MPAS-Ocean namelist needs to match the depth used here.

This PR is needed for generating a mapping file to support E3SM PR:
E3SM-Ocean-Discussion/E3SM#94

mesh_tools/create_SCRIP_files/create_scrip_mask_for_sufficiently_deep_ocean_mapping.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+"""
+Script for defining mask of ocean cells that are deeper than a threshold.
+To be used for updating a scrip file so that it only remaps
+from ocean cells deeper than that threshold.
+The resulting mapping file can be used as an OCN2GLC_TF_SMAPNAME
+mapping file in E3SM.
+Note that config_2d_thermal_forcing_depth in the MPAS-Ocean namelist
+needs to match the depth used here!
+"""
+
+import argparse
+import sys
+from datetime import datetime
+from netCDF4 import Dataset
+
+parser = argparse.ArgumentParser(
+                    description=__doc__)
+parser.add_argument("-s", dest="scrip",
+                    required=True,
+                    help="scrip file to which to add mask")
+parser.add_argument("-m", dest="mpas",
+                    required=True,
+                    help="MPAS-Ocean mesh file")
+parser.add_argument("-d", dest="depth",
+                    required=True,
+                    help="depth threshold (m), should be a positive value",
+                    type=float)
+args = parser.parse_args()
+
+assert args.depth > 0.0, "'depth' argument should be a positive value"
+
+# open mesh file
+fmesh = Dataset(args.mpas, 'r')
+nCells = len(fmesh.dimensions['nCells'])
+bottomDepth = fmesh.variables['bottomDepth'][:]
+
+# identify cells shallower than target depth
+mask = bottomDepth > args.depth
+
+# insert mask into scrip file
+fscrip = Dataset(args.scrip, 'r+')
+if 'grid_imask' not in fscrip.variables:
+    fscrip.createVariable('grid_imask', 'i', ('nCells',))
+fscrip.variables['grid_imask'][:] = mask
+
+# Update history attribute of scrip netCDF file
+thiscommand = datetime.now().strftime("%a %b %d %H:%M:%S %Y") + ": " + " ".join(sys.argv[:])
+if hasattr(fscrip, 'history'):
+   newhist = '\n'.join([thiscommand, getattr(fscrip, 'history')])
+else:
+   newhist = thiscommand
+setattr(fscrip, 'history', newhist )
+
+fmesh.close()
+fscrip.close()