A python program for reading coordinates and gradients from a GAMESS output file

Some people liked the previous post on python, so I dusted off this python program for reading locating coordinates and gradients in a GAMESS log file and writing out and .xyz+vib file (to create this post).  I have only used it on this output file, but it should work for other files as well.

Even if you have no interest in .xyz+vib files, the program might be useful as an example of how to locate specific information in a file and read it in. If you have similar programs (or questions) please feel free to share them in the comments

	"""\
	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

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