def parse_overlap(self):
if 'symmetrized' not in self.meta: self.parse_atom()
key = 'AO_OVERLAP_MATRIX'
if not self.meta['symmetrized']:
self.overlap = Overlap.from_column(
_flat_square_to_triangle(np.array(self._hdf[key])))
else:
print('Symmetrized overlap indices not set correctly.')
self.overlap = Overlap.from_dict({
'coef': np.array(self._hdf[key]),
'chi0': 0, 'chi1': 0, 'frame': 0
})
def parse_molcas(fp, momatrix=None, overlap=None, occvec=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:
fp (str): Path to output file
momatrix (str): file name of the C matrix of interest
overlap (str): file name of the overlap matrix
occvec (str): an occupation vector
Returns:
parsed (Editor): contains many attributes similar to the
exatomic universe
"""
uni = Output(fp, **kwargs)
adir = os.sep.join(fp.split(os.sep)[:-1])
if momatrix is not None:
fp = os.sep.join([adir, momatrix])
if os.path.isfile(fp):
orb = Orb(fp)
uni.momatrix = orb.momatrix
uni.occupation_vector = orb.occupation_vector
occvec = occvec if occvec is not None else orb.occupation_vector
d = DensityMatrix.from_momatrix(orb.momatrix, occvec)
uni.density = d
else:
print('Is {} in the same directory as {}?'.format(momatrix, fp))
if overlap is not None:
fp = os.sep.join([adir, overlap])
if os.path.isfile(fp): uni.overlap = Overlap.from_file(fp)
else: print('Is {} in the same directory as {}?'.format(overlap, fp))
return uni
def integrals(self):
"""Compute the overlap matrix using primitive cartesian integrals."""
from exatomic.core.basis import Overlap
ovl = _cartesian_shell_pairs(len(self), self._ptrs.astype(np.int64),
self._xyzs, *self._shells)
ovl = _triangle(ovl)
chi0, chi1 = _tri_indices(ovl)
return Overlap.from_dict({'chi0': chi0, 'chi1': chi1,
'frame': 0, 'coef': ovl})
def integrals(self):
"""Compute the overlap matrix using primitive cartesian integrals."""
from exatomic.core.basis import Overlap
ovl = _cartesian_shell_pairs(len(self), self._ptrs.astype(np.int64),
self._xyzs, *self._shells)
ovl = _triangle(ovl)
chi0, chi1 = _tri_indices(ovl)
return Overlap.from_dict({
'chi0': chi0,
'chi1': chi1,
'frame': 0,
'coef': ovl
})
def parse_overlap(self):
self._init()
start = self.find_next("$OVERLAP", keys_only=True) + 1
stop = self.find_next("$END", start=start, keys_only=True)
ovl = self.pandas_dataframe(start, stop, range(len(
self[start].split()))).stack().values
if ovl.shape[0] != self._nbas * (self._nbas + 1) // 2:
ovl = _flat_square_to_triangle(ovl.stack().values)
chi0, chi1 = _tri_indices(ovl)
self.overlap = Overlap.from_dict({
'coef': ovl,
'chi0': chi0,
'chi1': chi1,
'frame': 0
})
def add_overlap(self, path):
try: # If it's an ASCII text file
self.overlap = Overlap.from_column(path)
except ParserError: # If it's an HDF5 file
hdf = HDF(path)
if 'DESYM_CENTER_CHARGES' not in hdf._hdf:
self.overlap = hdf.overlap
return
if 'irrep' not in self.momatrix:
raise Exception("Trying to set symmetrized overlap with "
"desymmetrized MOMatrix data.")
ovl = pd.DataFrame(np.array(hdf._hdf['AO_OVERLAP_MATRIX']),
columns=('coef',))
ovl['irrep'] = self.momatrix['irrep']
ovl['chi0'] = self.momatrix['chi']
ovl['chi1'] = self.momatrix['orbital']
ovl['frame'] = 0
self.overlap = ovl