git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4988 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/python/neb_final.py

@@ -0,0 +1,71 @@
+#!/usr/local/bin/python
+
+# make new dump file from final snapshots from multiple NEB replica dumps
+# Syntax: neb_final.py -switch arg(s) -switch arg(s) ...
+#         -o outfile = new dump file
+#            snapshots numbered 1 to M = # of replicas
+#         -r dump1 dump2 ... = replica dump files of NEB atoms
+#            must be in correct sequence
+#         -b dumpfile = background atoms (optional)
+#            last snapshot in this file used as static non-NEB atoms
+
+import sys,os
+path = os.environ["LAMMPS_PYTHON_TOOLS"]
+sys.path.append(path)
+from dump import dump
+
+# parse args
+
+outfile = ""
+backfile = ""
+rfiles = []
+
+argv = sys.argv
+iarg = 1
+narg = len(argv)
+while iarg < narg:
+  if argv[iarg] == "-o":
+    outfile = argv[iarg+1]
+    iarg += 2
+  elif argv[iarg] == "-b":
+    backfile = argv[iarg+1]
+    iarg += 2
+  elif argv[iarg] == "-r":
+    ilast = iarg + 1
+    while ilast < narg and argv[ilast][0] != '-': ilast += 1
+    rfiles = argv[iarg+1:ilast]
+    iarg = ilast
+  else: break
+
+if iarg < narg or not outfile or not rfiles:
+  print "Syntax: neb_final.py -o outfile -b backfile -r dump1 dump2 ..."
+  sys.exit()
+
+if os.path.exists(outfile): os.remove(outfile)
+
+# nback = additional atoms in each snapshot
+
+if backfile:
+  back = dump(backfile)
+  t = back.time()
+  back.tselect.one(t[-1])
+  nback = back.snaps[-1].nselect
+else: nback = 0
+
+# write out each snapshot
+# time = replica #
+# natoms = ntotal, by overwriting nselect
+# add background atoms if requested
+
+n = 1
+for file in rfiles:
+  neb = dump(file)
+  t = neb.time()
+  neb.tselect.one(t[-1])
+  hold = neb.snaps[-1].nselect
+  neb.snaps[-1].nselect = hold + nback
+  neb.snaps[-1].time = n
+  neb.write(outfile,1,1)
+  neb.snaps[-1].nselect = hold
+  if backfile: back.write(outfile,0,1)
+  n += 1