Index: branches/UKMO/dev_r5518_GO6_package/NEMOGCM/TOOLS/REBUILD_NEMO/icb_combrest.py
===================================================================
--- branches/UKMO/dev_r5518_GO6_package/NEMOGCM/TOOLS/REBUILD_NEMO/icb_combrest.py	(revision 6491)
+++ branches/UKMO/dev_r5518_GO6_package/NEMOGCM/TOOLS/REBUILD_NEMO/icb_combrest.py	(revision 6491)
@@ -0,0 +1,255 @@
+from netCDF4 import Dataset
+from argparse import ArgumentParser
+import numpy as np
+import sys
+
+#
+# Basic iceberg trajectory restart post-processing python script.
+# This script collects iceberg information from the distributed restarts written
+# out by each processing region and writes the information into a global restart file.
+# The global restart file must already exist and contain the collated 2D spatial fields
+# as prepared by utilities such as rebuild_nemo. This python script simply adds the
+# iceberg position and state data that is held using the unlimited dimension 'n' which
+# has been ignored by rebuild_nemo. Each processing region that contains icebergs will
+# (probably) have a different number of icebergs (indicated by differing values for the
+# current size of the unlimited dimension). This script collects all icebergs into a 
+# single unordered list.
+#
+
+parser = ArgumentParser(description='produce a global trajectory restart file from distributed output\
+                                     files, e.g. \n python ./icb_pp.py \
+                                     -f  icebergs_00692992_restart_ -n 480 -o icebergs_restart.nc [-O]')
+
+parser.add_argument('-f',dest='froot',help='fileroot_of_distrbuted_data; root name of \
+                     distributed trajectory restart file (usually completed with XXXX.nc, where \
+                     XXXX is the 4 digit processor number)', 
+                     default='icebergs_00692992_restart_')
+
+parser.add_argument('-n',dest='fnum',help='number of distributed files to process', 
+                     type=int, default=None)
+
+parser.add_argument('-o',dest='fout',help='global_iceberg_restart; file name to append the \
+                     global iceberg restart data to.', default='icebergs_restart.nc')
+
+parser.add_argument('-O',dest='fcre',help='Create the output file from scratch rather than \
+                     append to an existing file.', \
+                     action='store_true', default=False)
+
+args = parser.parse_args()
+
+default_used = 0
+if args.froot is None:
+    pathstart = 'icebergs_00692992_restart_'
+    default_used = 1
+else:
+    pathstart = args.froot
+
+if args.fnum is None:
+    procnum = 0
+    default_used = 1
+else:
+    procnum = args.fnum
+
+if args.fout is None:
+    pathout = 'icebergs_restart.nc'
+    default_used = 1
+else:
+    pathout = args.fout
+
+if default_used == 1:
+   print('At least one default value will be used; command executing is:')
+   print('icb_combrest.py -f ',pathstart,' -n ',procnum,' -o ',pathout)
+
+if procnum < 1:
+   print('Need some files to collate! procnum = ',procnum)
+   sys.exit()
+
+icu = []
+times = []
+ntraj = 0
+nk = 0
+#
+# Loop through all distributed datasets to obtain the total number 
+# of icebergs to transfer
+#
+for n in range(procnum):
+ nn = '%4.4d' % n
+ try:
+   fw = Dataset(pathstart+nn+'.nc')
+ except:
+   print 'Error: unable to open input file: ' + pathstart+nn+'.nc'
+   sys.exit()
+ for d in fw.dimensions :
+  if d == 'n' :
+   if len(fw.dimensions['n']) > 0:
+#    print 'icebergs found in: ' + pathstart+nn+'.nc' 
+     if len(fw.dimensions['k']) > nk :
+       nk = len(fw.dimensions['k'])
+     ntraj = ntraj + len(fw.dimensions['n'])
+ fw.close()
+#
+print(ntraj, ' icebergs found across all datasets')
+#
+# Declare 2-D arrays to receive the data from all files
+#
+lons = np.zeros(ntraj)
+lats = np.zeros(ntraj)
+xis  = np.zeros(ntraj)
+yjs  = np.zeros(ntraj)
+uvs  = np.zeros(ntraj)
+vvs  = np.zeros(ntraj)
+mas  = np.zeros(ntraj)
+ths  = np.zeros(ntraj)
+wis  = np.zeros(ntraj)
+les  = np.zeros(ntraj)
+dys  = np.zeros(ntraj)
+mss  = np.zeros(ntraj)
+msb  = np.zeros(ntraj)
+hds  = np.zeros(ntraj)
+yrs  = np.zeros(ntraj      , dtype=int)
+num  = np.zeros((ntraj, nk), dtype=int)
+#
+# loop through distributed datasets again, this time
+# collecting all trajectory data
+#
+nt = 0
+for n in range(procnum):
+ nn = '%4.4d' % n
+ fw = Dataset(pathstart+nn+'.nc')
+ for d in fw.dimensions :
+  if d == 'n' :
+# Note many distributed datafiles will contain no iceberg data
+# so skip quickly over these
+    m  = len(fw.dimensions['n'])
+    if m > 0:
+#     print pathstart+nn+'.nc'
+      lons[nt:nt+m]  = fw.variables['lon'][:]
+      lats[nt:nt+m]  = fw.variables['lat'][:]
+      xis[nt:nt+m]   = fw.variables['xi'][:]
+      yjs[nt:nt+m]   = fw.variables['yj'][:]
+      uvs[nt:nt+m]   = fw.variables['uvel'][:]
+      vvs[nt:nt+m]   = fw.variables['vvel'][:]
+      mas[nt:nt+m]   = fw.variables['mass'][:]
+      ths[nt:nt+m]   = fw.variables['thickness'][:]
+      wis[nt:nt+m]   = fw.variables['width'][:]
+      les[nt:nt+m]   = fw.variables['length'][:]
+      dys[nt:nt+m]   = fw.variables['day'][:]
+      mss[nt:nt+m]   = fw.variables['mass_scaling'][:]
+      msb[nt:nt+m]   = fw.variables['mass_of_bits'][:]
+      hds[nt:nt+m]   = fw.variables['heat_density'][:]
+      yrs[nt:nt+m]   = fw.variables['year'][:]
+      num[nt:nt+m,:] = fw.variables['number'][:,:]
+      nt = nt + m
+ fw.close()
+
+# Finally create the output file and write out the collated sets
+#
+if args.fcre :
+  try:
+    fo = Dataset(pathout, 'w', format='NETCDF4')
+  except:
+    print 'Error accessing output file: ' + pathout
+    print 'Check it is a writable location.'
+    sys.exit()
+else :
+  try:
+    fo = Dataset(pathout, 'r+', format='NETCDF4')
+  except:
+    print 'Error accessing output file: ' + pathout
+    print 'Check it exists and is writable.'
+    print 'Or run adding the -O option to create an output file which will'
+    print 'contain the iceberg state data only.'
+    sys.exit()
+#
+add_k = 1
+for d in fo.dimensions :
+  if d == 'n' :
+    print 'Error: dimension n already exists in output file'
+    sys.exit()
+  if d == 'k' :
+    add_k = 0
+onn  = fo.createDimension('n', None)
+if add_k > 0 :
+ onk = fo.createDimension('k', nk)
+olon = fo.createVariable('lon', 'f8',('n'))
+olat = fo.createVariable('lat', 'f8',('n'))
+oxis = fo.createVariable('xi', 'f8',('n'))
+oyjs = fo.createVariable('yj', 'f8',('n'))
+ouvs = fo.createVariable('uvel', 'f8',('n'))
+ovvs = fo.createVariable('vvel', 'f8',('n'))
+omas = fo.createVariable('mass', 'f8',('n'))
+oths = fo.createVariable('thickness', 'f8',('n'))
+owis = fo.createVariable('width', 'f8',('n'))
+oles = fo.createVariable('length', 'f8',('n'))
+odys = fo.createVariable('day', 'f8',('n'))
+omss = fo.createVariable('mass_scaling', 'f8',('n'))
+omsb = fo.createVariable('mass_of_bits', 'f8',('n'))
+ohds = fo.createVariable('heat_density', 'f8',('n'))
+oyrs = fo.createVariable('year', 'i4',('n'))
+onum = fo.createVariable('number', 'i4',('n','k'))
+#
+olon[:] = lons
+olon.long_name = "longitude"
+olon.units = "degrees_E" 
+#
+olat[:] = lats
+olat.long_name = "latitude"
+olat.units = "degrees_N"
+#
+oxis[:] = xis
+oxis.long_name = "x grid box position"
+oxis.units = "fractional"
+#
+oyjs[:] = yjs
+oyjs.long_name = "y grid box position"
+oyjs.units = "fractional"
+#
+ouvs[:] = uvs
+ouvs.long_name = "zonal velocity"
+ouvs.units = "m/s"
+#
+ovvs[:] = vvs
+ovvs.long_name = "meridional velocity"
+ovvs.units = "m/s"
+#
+omas[:] = mas
+omas.long_name = "mass"
+omas.units = "kg"
+#
+oths[:] = ths
+oths.long_name = "thickness"
+oths.units = "m"
+#
+owis[:] = wis
+owis.long_name = "width"
+owis.units = "m"
+#
+oles[:] = les
+oles.long_name = "length"
+oles.units = "m"
+#
+odys[:] = dys
+odys.long_name = "year day of calving event"
+odys.units = "days"
+#
+omss[:] = mss
+omss.long_name = "scaling factor for mass of calving berg"
+omss.units = "none"
+#
+omsb[:] = msb
+omsb.long_name = "mass of bergy bits"
+omsb.units = "kg"
+#
+ohds[:] = hds
+ohds.long_name = "heat density"
+ohds.units = "J/kg"
+#
+oyrs[:] = yrs
+oyrs.long_name = "calendar year of calving event"
+oyrs.units = "years"
+#
+onum[:,:] = num
+onum.long_name = "iceberg number on this processor"
+onum.units = "count"
+#
+fo.close()
