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

tools/eff/VMD-input.py

@@ -0,0 +1,67 @@
+#!/usr/local/bin/python-2.5/bin/python
+
+import sys, os
+from getopt import gnu_getopt as getopt
+
+Info="""
+Module name: VMD-input.py 
+
+Author: (c) Andres Jaramillo-Botero
+California Institute of Technology
+ajaramil@wag.caltech.edu
+Project: pEFF
+Version: August 2009
+
+Usage: python VMD-input.py lammps_dump_filename radii_column_number
+Example: python VMD-input.py dump.lammpstrj 6
+
+1. Extracts the electron radii from a lammps trajectory dump into %s.out
+2. Creates %s.xyz file
+3. Creates appropriate %.vmd file which can be sourced using TCL/TK in VMD
+
+"""
+
+from lmp2radii_col import makeradii 
+from lmp2xyz import lmp2xyz
+ 
+def printHelp(input):
+  Info%(input,input,input)
+
+if __name__ == '__main__':
+
+   # if no input, print help and exit
+    if len(sys.argv) < 2:
+        print "Usage: python VMD-input.py lammps_dump_filename radii_column_number\n"
+        sys.exit(1)
+    else:
+        infile=sys.argv[1]
+
+    # set defaults
+    outfile = infile.split('.')[0]
+    if len(sys.argv) == 2:
+      column = int(sys.argv[2])
+    else:
+      column=6    # default = radius for dump -> id type x y z spin radius
+
+    # check for input:
+    opts, argv = getopt(sys.argv[1:], 'c:o:ha')
+
+    # read options
+    for opt, arg in opts:
+        if opt == '-h':             # -h: print help
+          Info%(input,input,input)
+        if opt == '-o':         # output file name
+          outfile=arg
+        if opt == '-c':         # select column from lammpstrj file to tabulate
+          column=int(arg)
+
+    makeradii(infile,outfile+".out",column,True)
+    lmp2xyz(infile,outfile+".xyz")
+    print "Creating %s file ..."%(outfile+".vmd")
+    os.system("cat %s | sed 's/xyzfile/%s/' > %s"%("radii.vmd",outfile+".xyz","temp"))
+    os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",outfile+".vmd"))
+    print "Done !! (you can now source %s using VMD's console) \n"%(outfile+".vmd")
+
+    print "NOTE: In VMD, set graphics representation for electrons to transparency,"
+    print "and change the atom types in the xyz file according to your values,"
+    print "for simplicity, they are set using the same mass sequence definition\nfrom your lammps data file\n"