def __init__(self, filename):
"""
Constructor.
filename -- filename to get info from, either Gaussian (out, g03) or netCDF file (nc)
"""
self.file = filename
if os.path.exists(filename):
ext = filename.split('.')[-1]
self.complex = filename.split('.')[-2]
#print ext
if ext == 'nc':
self.type = 'nc'
# read directly from nc to avoid calculation
#self.data = netCDF(filename,'r')
self.data = Jacapo.read_atoms(filename)
elif ext == 'out' or ext == 'g03' or ext == 'log':
gout = Gaussian(filename)
gout.logger.setLevel(logging.ERROR)
self.type = 'gau'
self.data = gout.parse()
else:
raise Exception, 'File is not of identifiable format'
mol = 'NH3'
atoms = Atoms(mol, positions=molecules.data[mol]['positions'])
sg = SYMMOL(atoms)
print(sg.get_point_group())
print(sg.get_moments_of_inertia())
print(atoms.get_moments_of_inertia())
print(sg.get_symmetry_operators())
if __name__ == '__main__':
from ase.calculators.jacapo import Jacapo
from optparse import OptionParser
parser = OptionParser(usage='symmol.py ncfile', version='0.1')
parser.add_option('-f', nargs=0, help='print full output')
parser.add_option('-o', nargs=1, help='save output in filename')
options, args = parser.parse_args()
for ncfile in args:
sy = SYMMOL(Jacapo.read_atoms(ncfile), outfile=options.o)
print('Point group = ', sy.get_point_group())
print('Moments of inertia = ', sy.get_moments_of_inertia())
print('Symmetry operators = ', sy.get_symmetry_operators())
if options.f is not None:
print(sy)
cmd = 'bader -p all_atom %s' % (self.densityfile)
print(cmd)
os.system(cmd)
def write_all_bader(self):
'''
-p all_bader Write all Bader volumes (containing charge above
threshold of 0.0001) to a file. The charge distribution in
each volume is written to a separate file, named
Bvolxxxx.dat. It will either be of a CHGCAR format or a CUBE
file format, depending on the format of the initial charge
density file. These files can be quite large, so this option
should be used with caution.
'''
cmd = 'bader -p all_bader %s' % (self.densityfile)
print(cmd)
os.system(cmd)
if __name__ == '__main__':
from ase.calculators.jacapo import Jacapo
atoms = Jacapo.read_atoms('ethylene.nc')
b = Bader(atoms)
print(b.get_bader_charges())
print(b.get_bader_volumes())
b.write_atom_volume([3, 4])
return string.join(self.output)
def get_space_group(self):
regexp = re.compile('^Space Group')
for line in self.output:
if regexp.search(line):
return line
if __name__ == '__main__':
from ase.calculators.jacapo import Jacapo
from optparse import OptionParser
parser = OptionParser(usage='findsym.py ncfile', version='0.1')
parser.add_option('-f', nargs=0, help='print full output')
parser.add_option('-o', nargs=1, help='save output in filename')
options, args = parser.parse_args()
for ncfile in args:
sg = FINDSYM(Jacapo.read_atoms(ncfile), outfile=options.o)
print(sg.get_space_group())
if options.f is not None:
print(sg)
'''
cmd = 'bader -p all_atom %s' % (self.densityfile)
print cmd
os.system(cmd)
def write_all_bader(self):
'''
-p all_bader Write all Bader volumes (containing charge above
threshold of 0.0001) to a file. The charge distribution in
each volume is written to a separate file, named
Bvolxxxx.dat. It will either be of a CHGCAR format or a CUBE
file format, depending on the format of the initial charge
density file. These files can be quite large, so this option
should be used with caution.
'''
cmd = 'bader -p all_bader %s' % (self.densityfile)
print cmd
os.system(cmd)
if __name__ == '__main__':
from ase.calculators.jacapo import Jacapo
atoms = Jacapo.read_atoms('ethylene.nc')
b = Bader(atoms)
print b.get_bader_charges()
print b.get_bader_volumes()
b.write_atom_volume([3, 4])
index += 5
symmetry_operators.append(temparray)
taus.append(array(temptau))
return symmetry_operators, taus
if __name__ == '__main__':
from ase.calculators.jacapo import Jacapo
from optparse import OptionParser
parser = OptionParser(usage='sgroup.py ncfile', version='0.1')
parser.add_option('-f', nargs=0, help='print full output')
parser.add_option('-o', nargs=1, help='save output in filename')
options, args = parser.parse_args()
#print options
for ncfile in args:
sg = SGROUP(Jacapo.read_atoms(ncfile), outfile=options.o)
print(sg.get_space_group())
if options.f is not None:
print(sg)
