def write_data(self,file):
from Util import cleansym
from Element import sym2no
file.write(' $DATA\n')
file.write('%s GAMESS job generated automatically by gamess.py\n'
% self.name)
file.write('C1\n')
for atom in self.atomlist:
name,x,y,z = atom
sym = cleansym(name)
atno = sym2no[sym]
file.write('%s %5.1f %12.6f %12.6f %12.6f\n' %\
(name,atno,x,y,z))
file.write(' $END\n')
return
def read_xyz(xyz_name):
'Takes the last structure from an xyz file'
xyz_file = open(xyz_name,'r')
while 1:
line = xyz_file.readline()
if not line: break
words = string.split(line)
if not words: break
nat = int(words[0])
title = xyz_file.readline()
atoms = []
for i in range(nat):
line = xyz_file.readline()
words = string.split(line)
sym = words[0]
sym = cleansym(sym)
x,y,z = float(words[1]),float(words[2]),float(words[3])
atoms.append((sym,x,y,z))
xyz_file.close()
return atoms
def read(filename,do_center=0):
"Read all the frames from an XYZ file. Optionally center each frame"
file = open(filename)
geometries = []
while 1:
line = file.readline()
if not line: break
try:
nat = int(line.split()[0])
except:
break
title = file.readline()
atoms = []
for i in range(nat):
line = file.readline()
words = line.split()
atno = sym2no[cleansym(words[0])]
x,y,z = map(float,words[1:4])
atoms.append((atno,(x,y,z)))
if do_center: atoms = center(atoms)
geometries.append(atoms)
return geometries
