def gen_enantio_and_correlate(xcc,
symbols,
masses=None,
fconnect=1.3,
pp=False):
# generate list of masses
if masses is None: masses = fncs.symbols2masses(symbols)
# xcc1: center and reorient
xcc1 = center_and_orient(xcc, None, None, masses)[0]
# xcc2: xcc for enantiomer
xcc2 = generate_enantio(xcc1)
xcc2 = center_and_orient(xcc2, None, None, masses)[0]
# correlate enantiomer
dcorr = correlate_enantio(xcc1, xcc2, symbols, fconnect=fconnect, pp=pp)
# non-assigned?
if get_not_assigned(dcorr) != 0: return None
# Generate xcc for enantiomer
try:
xcc_enantio = [0.0 for ii in range(len(xcc))]
for node2, node1 in dcorr.items():
xcc_enantio[3 * node1:3 * node1 + 3] = xcc2[3 * node2:3 * node2 +
3]
return xcc_enantio
except:
return None
def correlate(symbols_t,xcc_t,symbols_0,xcc_0,fconnect=1.3):
'''
reference geometry: symbols_0,xcc_0
target geometry: symbols_t,xcc_t
'''
# prepare reference geometry
masses_0 = fncs.symbols2masses(symbols_0)
xcc_0 = center_and_orient(xcc_0,None,None,masses_0)[0]
# prepare target geometry
masses_t = fncs.symbols2masses(symbols_t)
xcc_t = center_and_orient(xcc_t,None,None,masses_t)[0]
# correlate enantiomer
dcorr = correlate_xccs(xcc_t,symbols_t,xcc_0,symbols_0,fconnect=fconnect,pp=False)
# non-assigned?
if get_num_of_not_assigned(dcorr) != 0: return None
# Re-order xcc_t
symbols,xcc = reorder_xcc(symbols_t,xcc_t,dcorr)
return symbols,xcc
def setup(self, mu=1.0 / AMU, projgrad=False):
self._mu = mu
# derivated magnitudes (again, in case sth was modified)
# for example, when set from gts and masses are added latter
self.genderivates()
# shift to center of mass and reorientate molecule
idata = (self._xcc, self._gcc, self._Fcc, self._masses)
self._xcc, self._gcc, self._Fcc = fncs.center_and_orient(*idata)
# symmetry
self.calc_pgroup(force=False)
# Generate mass-scaled arrays
self._xms = fncs.cc2ms_x(self._xcc, self._masses, self._mu)
self._gms = fncs.cc2ms_g(self._gcc, self._masses, self._mu)
self._Fms = fncs.cc2ms_F(self._Fcc, self._masses, self._mu)
#-------------#
# Atomic case #
#-------------#
if self._natoms == 1:
self._nvdof = 0
self._linear = False
#self._xms = list(self._xcc)
#self._gms = list(self._gcc)
#self._Fms = list(self._Fcc)
self._ccfreqs = []
self._ccFevals = []
self._ccFevecs = []
#----------------#
# Molecular case #
#----------------#
else:
# Calculate inertia
self._itensor = fncs.get_itensor_matrix(self._xcc, self._masses)
self._imoms, self._rotTs, self._rtype, self._linear = \
fncs.get_itensor_evals(self._itensor)
# Vibrational degrees of freedom
if self._linear: self._nvdof = 3 * self._natoms - 5
else: self._nvdof = 3 * self._natoms - 6
# calculate frequencies
if self._Fcc is None: return
if len(self._Fcc) == 0: return
if self._ccfreqs is not None: return
v0 = self._gms if projgrad else None
data = fncs.calc_ccfreqs(self._Fcc,
self._masses,
self._xcc,
self._mu,
v0=v0)
self._ccfreqs, self._ccFevals, self._ccFevecs = data
# Scale frequencies
self._ccfreqs = fncs.scale_freqs(self._ccfreqs, self._fscal)