def get_ts_ifreq(xcc, gcc, Fcc, E, tcommon):
ch, mtp, atonums, masses, mu = tcommon
ts = Molecule()
ts.set(xcc, atonums, ch, mtp, E, gcc, Fcc, masses)
ts.prep()
ts.setup(mu)
ts.ana_freqs()
[(ifreq, evec)] = ts._ccimag
return ifreq, mu
def path2vadi(tcommon,
drst,
Eref=None,
ics=None,
boolint=False,
lowfq={},
freqscal=1.0):
'''
lowfq in case of imaginary frequencies
'''
if boolint in [False, "no", "No", "n", "N", None]: boolint = False
elif boolint in [True, "yes", "YES", "y", "Y"]: boolint = True
if boolint and ics in [None, False, []]: raise Exc.NoICS(Exception)
ch, mtp, atnums, masses, mu = tcommon
# Sorted labels (by s)
slabels = sd.sorted_points(drst, hess=True)
# Reference energy
if Eref is None:
lbw, lfw, sbw, sfw, Ebw, Efw = sd.rstlimits(drst)
Eref = Ebw
# Independent variable
data_x = [drst[label][0] for label in slabels]
# mep energy
listV0 = [drst[label][1] - Eref for label in slabels]
# Dependent variable (cc)
lcc_tzpe, lcc_frqs, lcc_Vadi = [], [], []
lic_tzpe, lic_frqs, lic_Vadi = [], [], []
dMols = {}
for label in slabels:
# data in drst
s_i, E_i, xms_i, gms_i, Fms_i, v0_i, v1_i, t_i = drst[label]
# project gradient
if s_i == 0.0: bool_pg = False
else: bool_pg = True
# lowfq
if s_i == 0: dlowfq = {}
elif s_i < 0: dlowfq = lowfq.get("bw", {})
elif s_i > 0: dlowfq = lowfq.get("fw", {})
# mass-scaled --> Cartesian coords
xcc = fncs.ms2cc_x(xms_i, masses, mu)
gcc = fncs.ms2cc_g(gms_i, masses, mu)
Fcc = fncs.ms2cc_F(Fms_i, masses, mu)
# create Molecule instance
mol = Molecule()
mol.set(xcc, atnums, ch, mtp, E_i, gcc, Fcc, masses)
mol.prep()
mol.set_fscal(freqscal)
mol.setup(mu, projgrad=bool_pg)
mol.clean_freqs("cc") # it may be needed with orca
mol.deal_lowfq(dlowfq, "cc") # deal with low frequencies
mol.ana_freqs("cc") # calculate zpe
# append data
lcc_tzpe.append(float(mol._cczpe))
lcc_Vadi.append(mol._ccV1 - Eref)
lcc_frqs.append(list(mol._ccfreqs))
# internal coordinates
if boolint:
mol.icfreqs(ics, bool_pg)
mol.deal_lowfq(dlowfq, "ic")
mol.ana_freqs("ic")
# append data
lic_tzpe.append(float(mol._iczpe))
lic_Vadi.append(mol._icV1 - Eref)
lic_frqs.append(list(mol._icfreqs))
# save instance
dMols[label] = (s_i, mol)
tuple_cc = (data_x, lcc_frqs, lcc_tzpe)
tuple_ic = (data_x, lic_frqs, lic_tzpe)
# Generate splines and setup
Vadi_cc = VadiSpline(data_x, lcc_Vadi)
if boolint: Vadi_ic = VadiSpline(data_x, lic_Vadi)
else: Vadi_ic = None
# Return data
return dMols, Vadi_cc, Vadi_ic, tuple_cc, tuple_ic, listV0
