git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1691 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/python/pizza/xyz.py

@@ -0,0 +1,121 @@
+# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+#
+# Copyright (2005) Sandia Corporation.  Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software.  This software is distributed under 
+# the GNU General Public License.
+
+# xyz tool
+
+oneline = "Convert LAMMPS snapshots to XYZ format"
+
+docstr = """
+x = xyz(d)		d = object containing atom coords (dump, data)
+
+x.one()                 write all snapshots to tmp.xyz
+x.one("new")            write all snapshots to new.xyz
+x.many()                write snapshots to tmp0000.xyz, tmp0001.xyz, etc
+x.many("new")           write snapshots to new0000.xyz, new0001.xyz, etc
+x.single(N)             write snapshot for timestep N to tmp.xyz 
+x.single(N,"file")      write snapshot for timestep N to file.xyz 
+"""
+
+# History
+#   8/05, Steve Plimpton (SNL): original version
+
+# ToDo list
+
+# Variables
+#   data = data file to read from
+
+# Imports and external programs
+
+import sys
+
+# Class definition
+
+class xyz:
+
+  # --------------------------------------------------------------------
+
+  def __init__(self,data):
+    self.data = data
+   
+  # --------------------------------------------------------------------
+
+  def one(self,*args):
+    if len(args) == 0: file = "tmp.xyz"
+    elif args[0][-4:] == ".xyz": file = args[0]
+    else: file = args[0] + ".xyz"
+
+    f = open(file,"w")
+    n = flag = 0
+    while 1:
+      which,time,flag = self.data.iterator(flag)
+      if flag == -1: break
+      time,box,atoms,bonds,tris,lines = self.data.viz(which)
+
+      print >>f,len(atoms)
+      print >>f,"Atoms"
+      for atom in atoms:
+        itype = int(atom[1])
+        print >>f,itype,atom[2],atom[3],atom[4]
+      
+      print time,
+      sys.stdout.flush()
+      n += 1
+      
+    f.close()
+    print "\nwrote %d snapshots to %s in XYZ format" % (n,file)
+      
+  # --------------------------------------------------------------------
+
+  def many(self,*args):
+    if len(args) == 0: root = "tmp"
+    else: root = args[0]
+
+    n = flag = 0
+    while 1:
+      which,time,flag = self.data.iterator(flag)
+      if flag == -1: break
+      time,box,atoms,bonds,tris,lines = self.data.viz(which)
+      
+      if n < 10:
+        file = root + "000" + str(n)
+      elif n < 100:
+        file = root + "00" + str(n)
+      elif n < 1000:
+        file = root + "0" + str(n)
+      else:
+        file = root + str(n)  
+      file += ".xyz"
+      f = open(file,"w")
+      print >>f,len(atoms)
+      print >>f,"Atoms"
+      for atom in atoms:
+        itype = int(atom[1])
+        print >>f,itype,atom[2],atom[3],atom[4]
+      print time,
+      sys.stdout.flush()
+      f.close()
+      n += 1
+  
+    print "\nwrote %s snapshots in XYZ format" % n
+  
+  # --------------------------------------------------------------------
+
+  def single(self,time,*args):
+    if len(args) == 0: file = "tmp.xyz"
+    elif args[0][-4:] == ".xyz": file = args[0]
+    else: file = args[0] + ".xyz"
+
+    which = self.data.findtime(time)
+    time,box,atoms,bonds,tris,lines = self.data.viz(which)
+    f = open(file,"w")
+    print >>f,len(atoms)
+    print >>f,"Atoms"
+    for atom in atoms:
+      itype = int(atom[1])
+      print >>f,itype,atom[2],atom[3],atom[4]
+    f.close()