/usr/share/pyshared/ase/io/nwchem.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | from cStringIO import StringIO
from ase.atoms import Atoms
from ase.io.xyz import read_xyz
def read_nwchem(filename):
"""Method to read geometry from a nwchem output
"""
from ase import Atoms, Atom
if isinstance(filename, str):
f = open(filename)
lines = f.readlines()
i = 0
while i < len(lines):
if lines[i].find('XYZ format geometry') >=0:
natoms = int(lines[i + 2].split()[0])
string = ''
for j in range(2, natoms + 4):
xyzstring = lines[i + j]
symbol = xyzstring.split()[0].strip()
# replace bq ghost with X: MDTMP can we do better?
if symbol.startswith('bq'):
xyzstring = xyzstring.replace(symbol, 'X')
string += xyzstring
atoms = read_xyz(StringIO(string))
i += natoms + 4
else:
i += 1
if type(filename) == str:
f.close()
return atoms
def write_nwchem(filename, atoms, geometry=None):
"""Method to write nwchem coord file
"""
import numpy as np
if isinstance(filename, str):
f = open(filename, 'w')
else: # Assume it's a 'file-like object'
f = filename
# autosym and autoz are defaults
# http://www.nwchem-sw.org/index.php/Geometry
# geometry noautoz results in higher memory demand!
# http://www.emsl.pnl.gov/docs/nwchem/nwchem-support/2010/10/0060.RE:_NWCHEM_Geometry_problem_fwd_
if geometry is not None:
f.write('geometry ' + str(geometry) + '\n')
else:
f.write('geometry\n')
for atom in atoms:
if atom.tag == -71: # 71 is ascii G (Ghost)
symbol = 'bq' + atom.symbol
else:
symbol = atom.symbol
f.write(' ' + symbol + ' ' +
str(atom.position[0]) + ' ' +
str(atom.position[1]) + ' ' +
str(atom.position[2]) + '\n' )
f.write('end\n')
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