def parse_molcas(file_path, momatrix=None, overlap=None, occvec=None, density=None, **kwargs):
"""
Will parse a Molcas output file. Optionally it will attempt
to parse additional information obtained from the same directory
from specified Orb files or the AO overlap matrix and density matrix.
If density keyword is specified, the momatrix keyword is ignored.
Args
file_path (str): Path to output file
momatrix (str): file name of the C matrix of interest
overlap (str): file name of the overlap matrix
density (str): file name of the density matrix
Returns
parsed (Editor): contains many attributes similar to the
exatomic universe
"""
uni1 = Output(file_path, **kwargs)
dirtree = sep.join(file_path.split(sep)[:-1])
if density is not None:
fp = sep.join([dirtree, density])
if os.path.isfile(fp):
dens = DensityMatrix(_parse_ovl(fp))
uni1.density = dens
else:
print('Is {} in the same directory as {}?'.format(density, file_path))
if momatrix is not None and density is None:
fp = sep.join([dirtree, momatrix])
if os.path.isfile(fp):
orbs = Orb(fp)
orbs.parse_momatrix()
if occvec is not None:
dens = DensityMatrix.from_momatrix(orbs.momatrix, occvec)
else:
dens = DensityMatrix.from_momatrix(orbs.momatrix, orbs.occupation_vector)
uni1.momatrix = orbs.momatrix
uni1.occupation_vector = orbs.occupation_vector
uni1.density = dens
else:
print('Is {} in the same directory as {}?'.format(momatrix, file_path))
if overlap is not None:
fp = sep.join([dirtree, overlap])
if os.path.isfile(fp):
ovl = _parse_ovl(fp)
uni1.overlap = ovl
else:
print('Is {} in the same directory as {}?'.format(overlap, file_path))
return uni1
def compute_density(self):
"""Compute density from momatrix and occupation vector."""
if not hasattr(self, 'occupation_vector'):
raise Exception('Universe must have momatrix and occupation_vector attributes')
self.density = DensityMatrix.from_momatrix(self.momatrix, self.occupation_vector)
