From 0d0fd0afac96790d2d0eaaa98439e635e60930ce Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 30 Sep 2010 21:24:52 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4913
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 examples/README      |  1 +
 src/Makefile         |  2 +-
 tools/python/neb1.py | 54 ++++++++++++++++++++++++++++++++++++++++++++
 tools/python/neb2.py | 31 +++++++++++++++++++++++++
 4 files changed, 87 insertions(+), 1 deletion(-)
 create mode 100755 tools/python/neb1.py
 create mode 100755 tools/python/neb2.py

diff --git a/examples/README b/examples/README
index 0af97f5d38..e476df30f4 100644
--- a/examples/README
+++ b/examples/README
@@ -39,6 +39,7 @@ melt:	  rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:	  energy minimization of 2d LJ melt
 msst:	  MSST shock dynamics
+neb:	  nudged elastic band (NEB) calculation for barrier finding
 nemd:	  non-equilibrium MD of 2d sheared system
 obstacle: flow around two voids in a 2d channel
 peptide:  dynamics of a small solvated peptide chain (5-mer)
diff --git a/src/Makefile b/src/Makefile
index 7b32442c39..686d4a53d7 100755
--- a/src/Makefile
+++ b/src/Makefile
@@ -14,7 +14,7 @@ OBJ = 	$(SRC:.cpp=.o)
 # Package variables
 
 PACKAGE = asphere class2 colloid dipole dsmc gpu granular \
-	  kspace manybody meam molecule opt peri poems prd reax shock xtc
+	  kspace manybody meam molecule opt peri poems reax replica shock xtc
 
 PACKUSER = user-ackland user-atc user-cd-eam user-cg-cmm user-eff \
 	   user-ewaldn user-imd user-smd
diff --git a/tools/python/neb1.py b/tools/python/neb1.py
new file mode 100755
index 0000000000..065f511e2e
--- /dev/null
+++ b/tools/python/neb1.py
@@ -0,0 +1,54 @@
+#!/usr/local/bin/python
+
+# combine multiple NEB dump files into 1 dump file
+# Syntax: neb1.py dfinal itype dfile1 dfile2 ...
+#         dfinal = new combined dump file
+#         itype = atoms of this type are added to each snapshot
+#         dfile1, dfile2, ... = NEB output dump files from each replica
+
+# assumes all N input files have same # of snapshots
+# for each snapshot time:
+#   all dfile1 atoms are added to dfinal
+#   only atoms of itype in dfile2,...,dfileN are added to dfinal
+
+import sys,os
+from dump import dump
+if not globals().has_key("argv"): argv = sys.argv
+
+if len(argv) < 5:
+  print "Syntax: neb1.py dfinal itype dfile1 dfile2 ..."
+  sys.exit()
+
+dfinal = argv[1]
+itype = int(argv[2])
+files = argv[3:]
+
+tstr = "$type == %d" % itype
+
+ntotal = 0
+d = []
+for file in files:
+  one = dump(file)
+  one.sort()
+  if d:
+    one.aselect.test(tstr)
+    nnew = one.snaps[0].nselect
+    idvec = range(ntotal+1,ntotal+nnew+1)
+    one.setv("id",idvec)
+  ntotal += one.snaps[0].nselect
+  d.append(one)
+
+if os.path.exists(dfinal): os.remove(dfinal)
+
+times = d[0].time()
+for time in times:
+  d[0].tselect.one(time)
+  i = d[0].findtime(time)
+  hold = d[0].snaps[i].nselect
+  d[0].snaps[i].nselect = ntotal
+  d[0].write(dfinal,1,1)
+  d[0].snaps[i].nselec = hold
+  for one in d[1:]:
+    one.tselect.one(time)
+    one.aselect.test(tstr)
+    one.write(dfinal,0,1)
diff --git a/tools/python/neb2.py b/tools/python/neb2.py
new file mode 100755
index 0000000000..3cf6de09e1
--- /dev/null
+++ b/tools/python/neb2.py
@@ -0,0 +1,31 @@
+#!/usr/local/bin/python
+
+# combine final snapshots from multiple NEB dump files into 1 dump file
+# Syntax: neb2.py dfinal dfile1 dfile2 ...
+#         dfinal = new combined dump file
+#         dfile1, dfile2, ... = NEB output dump files from each replica,
+#                               in correct order
+
+# for M replicas, final snapshots are renumbered in final file from 1 to M
+
+import sys,os
+from dump import dump
+if not globals().has_key("argv"): argv = sys.argv
+
+if len(argv) < 5:
+  print "Syntax: neb2.py dfinal dfile1 dfile2 ..."
+  sys.exit()
+
+dfinal = argv[1]
+files = argv[2:]
+
+if os.path.exists(dfinal): os.remove(dfinal)
+
+n = 1
+for file in files:
+  one = dump(file)
+  t = one.time()
+  one.tselect.one(t[-1])
+  one.snaps[-1].time = n
+  one.write(dfinal,1,1)
+  n += 1