def get_ts_ifreq(xcc, gcc, Fcc, E, tcommon):
ch, mtp, atonums, masses, mu = tcommon
ts = Molecule()
ts.setvar(xcc=xcc, gcc=gcc, Fcc=Fcc)
ts.setvar(atonums=atonums, masses=masses)
ts.setvar(ch=ch, mtp=mtp, V0=E)
ts.prepare()
ts.setup(mu)
ts.ana_freqs()
[(ifreq, evec)] = ts._ccimag
return ifreq, mu
def log_data(log, inpvars, fscal, folder="./"):
if inpvars._ts: fmode = -1
else: fmode = 0
# name from log
name = log.split(".")[-2]
point = TorPESpoint(name, inpvars._tlimit)
# Read log file
logdata = gau.read_gaussian_log(folder + log)
# prepare data
logdata = prepare_log_data(logdata)
ch, mtp, V0, symbols, symbols_wo, xcc_wo, gcc_wo, Fcc_wo, lzmat, zmatvals = logdata
# string for fccards
string_fccards = gau.get_fccards_string(gcc_wo, Fcc_wo)
# generate Molecule instance
molecule = Molecule()
molecule.setvar(xcc=xcc_wo, Fcc=Fcc_wo, V0=V0)
molecule.setvar(fscal=fscal)
molecule.setvar(symbols=symbols_wo)
molecule.setvar(ch=ch, mtp=mtp)
molecule.prepare()
molecule.setup()
molecule.ana_freqs()
# Calculate partition functions for the temperatures
qtot, V1, qis = molecule.calc_pfns(inpvars._temps, fmode=fmode)
qtr, qrot, qvib, qele = qis
Qrv = np.array([xx * yy for xx, yy in zip(qrot, qvib)])
# Calculate partition functions at target temperature
qtot, V1, qis = molecule.calc_pfns([inpvars._temp], fmode=fmode)
# remove rotsigma for Gibbs
gibbs = V1 - pc.KB * inpvars._temp * np.log(qtot[0] * molecule._rotsigma)
# imaginary frequency
if len(molecule._ccimag) == 0: ifreq = None
elif len(molecule._ccimag) == 1:
ifreq = [ifreq for ifreq, ivec in list(molecule._ccimag)][0]
else:
ifreq = None
# weight for this conformer
if inpvars._enantio and molecule._pgroup.lower() == "c1": weight = 2
else: weight = 1
# pack and return data
conf_tuple = (point, V0, V1, gibbs, weight, Qrv, ifreq, lzmat, zmatvals,
log)
return conf_tuple, symbols, string_fccards
def molecule_prep(gts, eslist=[], tiso=None, fscal=1.0):
# generate instance of Molecule
molecule = Molecule()
# read gts
molecule.set_from_gts(gts)
# masses
if tiso is not None:
imods, imasses = tiso
molecule.apply_imods(imods, imasses)
# electronic states
molecule.setvar(les=eslist)
# set frequency scaling
molecule.setvar(fscal=fscal)
# setup
molecule.setup()
molecule.ana_freqs("cc")
return molecule
def get_imag_freq(log, fscal):
try:
# Read log file
logdata = gau.read_gaussian_log(log)
logdata = prepare_log_data(logdata)
ch, mtp, V0, symbols, symbols_wo, xcc_wo, gcc_wo, Fcc_wo, lzmat, zmatvals = logdata
# diagonalize Fcc
molecule = Molecule()
molecule.setvar(xcc=xcc_wo, Fcc=Fcc_wo, V0=V0)
molecule.setvar(fscal=fscal)
molecule.setvar(symbols=symbols_wo)
molecule.setvar(ch=ch, mtp=mtp)
molecule.prepare()
molecule.setup()
molecule.ana_freqs()
ifreq = molecule._ccimag[0][0]
except:
ifreq = None
# return
return ifreq
def path2vadi(tcommon,drst,Eref=None,ics=None,boolint=False,lowfq={},freqscal=1.0,icsbw=None,icsfw=None,symmetry=None):
'''
lowfq: in case of imaginary frequencies
'''
# boolint as boolean
if boolint in [False,"no","No","n","N",None]: boolint = False
elif boolint in [True,"yes","YES","y","Y"] : boolint = True
# check there are internal coordinates if required
if boolint and ics in [None,False,[]]: raise Exc.NoICS(Exception)
# expand data in tcommon
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, Eref, Efw = sd.rstlimits(drst)
# Independent variable
data_x = [drst[label][0] for label in slabels]
# mep energy (relative value)
listV0 = [drst[label][1]-Eref for label in slabels]
# Initializing data
lcc_tzpe, lcc_frqs, lcc_Vadi = [], [], []
lic_tzpe, lic_frqs, lic_Vadi = [], [], []
dMols = {}
# Updating data
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 == 0.0: dlowfq = {}
elif s_i < 0.0: dlowfq = lowfq.get("bw",{})
elif s_i > 0.0: 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.setvar(xcc=xcc,gcc=gcc,Fcc=Fcc)
mol.setvar(atonums=atnums,masses=masses)
mol.setvar(ch=ch,mtp=mtp,V0=E_i)
mol.setvar(fscal=freqscal)
if symmetry is not None:
mol.setvar(pgroup=symmetry[0])
mol.setvar(rotsigma=symmetry[1])
mol.prepare()
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:
if s_i < 0.0 and icsbw is not None: mol.icfreqs(icsbw,bool_pg)
elif s_i > 0.0 and icsfw is not None: mol.icfreqs(icsfw,bool_pg)
else : 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)
# package data
tuple_cc = (data_x,lcc_frqs,lcc_tzpe)
tuple_ic = (data_x,lic_frqs,lic_tzpe)
# Generate splines
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
