GAMESS#1

"""\
From Jan Jensen's public repo**
This python program extracts coordinates and gradients from a GAMESS output
file and creates a .xzy+vib file.  Note that the sign of the gradient is chaged to produce the force

To use it type (assuming opt.py and the output file is in the same directory):

python opt.py x xx > xxx.xyz

where x is the number of atoms in the molecule and xx is the name of the GAMESS output file. xxx is whatever you want to call your xyz file.

Written by Jan H. Jensen, released under the GNU GPL license
"""

import string,sys

atoms = eval(sys.argv[1]) # convert x to number

filename = sys.argv[2]
file = open(filename,'r')

coord = []
grad = []

while 1:
    line = file.readline() # read a line from he file
    if not line: break # if end-of-file: quit
    words = string.split(line) # split line into words

# equilibrium coordinates are printed out a second time and should not be read
    if len(words) > 1 and words[1] == 'EQUILIBRIUM': break

# find and read coordniates

    if len(words) > 0 and words[0] == 'COORDINATES': # find line with EQUILIRBIUM as the 1st word
        file.readline() # skip a line
        file.readline() # skip a line
        for i in range(atoms): # read in x, y, z coordinates 
            line = file.readline()
            words = string.split(line)
            coord.append((words[0],words[2],words[3],words[4]))

# find and read gradient

    if len(words) > 0 and words[0] == 'NSERCH=': # find line with NSERCH= as the 1st word
        for i in range(6):
            file.readline() # skip 6 lines
        for i in range(atoms): # read x, y, z component of gradient
             line = file.readline()
             words = string.split(line)
             grad.append((eval(words[3]),eval(words[4]),eval(words[5]))) # gradients to be multiplied by -1, so convert to number

# print in .xyz+vib format and change sign of gradient

scale =  -1.
for i in range( len(coord) ):
    if i%atoms == 0: print atoms
    if i%atoms == 0: print 'title'
    tog = (coord[i][0],coord[i][1],coord[i][2],coord[i][3],scale*grad[i][0],scale*grad[i][1],scale*grad[i][2])
    print '%s %s %s %s %f %f %f' % tog