git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4549 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/eff/lmp2xyz.py

@@ -0,0 +1,81 @@
+Info="""
+Module name: lmp2xyz.py 
+
+Author: (c) Andres Jaramillo-Botero
+California Institute of Technology
+ajaramil@caltech.edu
+Project: pEFF
+Version: August 2009
+
+Extracts the xyz from a lammps trajectory dump of style custom:
+dump    1 all custom period dump_file id type x y z spin radius ...
+
+Usage: python lmp2xyz.py lammps_dump_filename xyz_filename
+
+"""
+
+import os, sys
+from math import log10
+from numpy import zeros
+
+mass={"1.00794":"H","4.002602":"He","6.941":"Li","9.012182":"Be","10.811":"B","12.0107":"C","1.00":"Au","0.0005486":"Au"}
+
+def lmp2xyz(lammps,xyz):
+  print "\nGenerating %s file"%(xyz)
+  fin=open(lammps,'r')
+  fout=open(xyz,'w')
+  header=9
+  lines=fin.readlines()
+  numatoms=lines[3].split()[0]
+  fsize=os.system("wc -l %s> lines"%(lammps))
+  tmp=open('lines','r')
+  tlines=tmp.readline()
+  tmp.close()
+  flines=int(tlines.split()[0])
+  snaps=flines/(int(numatoms)+header)
+  countsnap=1
+  coords=zeros((int(numatoms),4),dtype=float)
+  sys.stdout.write("Writing [%d]: "%(snaps))
+  sys.stdout.flush()
+  read_atoms=1
+  for line in lines:
+    if line.find('ITEM: TIMESTEP')==0:
+      read_atom_flag=False
+      sys.stdout.write("%d "%(countsnap))
+      sys.stdout.flush()
+      fout.writelines("%s\nAtoms\n"%(numatoms))
+      countsnap+=1
+      continue
+    if line.find('ITEM: ATOMS')==0:
+      read_atom_flag=True
+      continue
+    if read_atom_flag==True:
+      read_atoms+=1
+      parse=line.split()
+      if parse[0]!="":
+        coords[int(parse[0])-1][0]=int(parse[1])
+        coords[int(parse[0])-1][1]=float(parse[2])
+        coords[int(parse[0])-1][2]=float(parse[3])
+        coords[int(parse[0])-1][3]=float(parse[4])
+      if read_atoms==int(numatoms):
+        read_atoms=0
+        for i in range(int(numatoms)):
+          fout.writelines("%d %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
+
+  print "\nDone converting to xyz!!\n"
+  fin.close()
+  fout.close()
+  return
+
+if __name__ == '__main__':
+
+    # if no input, print help and exit
+    if len(sys.argv) < 2:
+        print Info()
+        sys.exit(1)
+
+    inputfile=sys.argv[1]
+    outfile=sys.argv[2]
+
+    lmp2xyz(inputfile,outfile.split()[0])
+