def obtain_adipot(tcommon, drst, pathvars, symmetry):
print("")
fncs.print_string("Calculating adiabatic potential...", 4)
print()
ics = pathvars.get_ics()
icsbw = pathvars._icsbw
icsfw = pathvars._icsfw
if pathvars._useics == "yes" and (ics is None or len(ics) == 0):
raise Exc.NoICS(Exception)
# calculate adiabatic potential
idata = (tcommon, drst, pathvars._eref, ics, pathvars._useics,
pathvars._lowfq, pathvars._freqscal, icsbw, icsfw, symmetry)
dMols, ccVadi, icVadi, tuple_cc, tuple_ic, listV0 = ap.path2vadi(*idata)
# expand tuples
data_x, lcc_frqs, lcc_tzpe = tuple_cc
data_x, lic_frqs, lic_tzpe = tuple_ic
# check data
fncs.print_string(PS.sadipot_ics(ics, pathvars._useics, icsbw, icsfw), 8)
if pathvars._useics == "yes":
ok1 = ap.ccvsic_checknfreqs(lcc_frqs, lic_frqs)
ok2 = ap.ccvsic_checkts(data_x, lcc_frqs, lic_frqs)
ok3 = ap.ccvsic_checkzpe(lcc_tzpe, lic_tzpe)
checks = (ok1, ok2, ok3)
# select spline
if not ok1 or not ok2: Vadi, pathvars._useics = ccVadi, "no"
elif pathvars._useics == "yes": Vadi, pathvars._useics = icVadi, "yes"
else: Vadi, pathvars._useics = ccVadi, "no"
else:
ok1, ok2, ok3 = True, True, True
Vadi, pathvars._useics = ccVadi, "no"
# Any imag freq along the MEP?
if pathvars._useics == "yes": lfqs = list(lic_frqs)
else: lfqs = list(lcc_frqs)
nfreqs = min([len(xx) for xx in lcc_frqs])
allfqreal = True
for lfq in lfqs:
if len(lfq) > nfreqs: lfq = lfq[1:]
if True in [fq < 0.0 for fq in lfq]: allfqreal = False
del lfqs
# print checks
fncs.print_string(
PS.sadipot_checks(ok1, ok2, ok3, pathvars._useics, allfqreal), 8)
# setup spline
Vadi.setup()
data4print = (Vadi.xx(), Vadi.yy(), Vadi._sAG, Vadi._VAG, listV0, lcc_tzpe,
lic_tzpe, pathvars._eref)
fncs.print_string(PS.sadipot_table(*data4print), 8)
# print freqs
fncs.print_string("- Vibrational frequencies summary: cc (ic) [in cm^-1]:",
8)
print("")
fncs.print_string(PS.sadipot_freqs(Vadi.xx(), lcc_frqs, lic_frqs), 8)
return dMols, Vadi, pathvars
def setup3(self):
'''
apply default value to those not defined!
'''
# use ics but no ics?
if self._useics == "yes" and (self._ics is None
or len(self._ics) == 0):
raise Exc.NoICS(Exception)
# path variables (via input) - advanced
if self._fwdir == "default": self._fwdir = None # ("1-2","++")
if self._cvt == "default": self._cvt = "yes"
if self._sct == "default": self._sct = "yes"
if self._mtype == "default": self._mtype = "pm"
if self._mu == "default": self._mu = 1.0 / AMU
if self._cubic == "default": self._cubic = "no"
if self._eref in ["default", "auto"]: self._eref = None
if self._paral == "default": self._paral = "no"
if self._epse == "default": self._epse = 1e-8
if self._epsg == "default": self._epsg = 1e-4
if self._useics == "default": self._useics = "yes"
if self._v1mode == "default": self._v1mode = "grad"
if self._scterr == "default": self._scterr = 0.0
if self._e0 in ["default", "auto"]: self._e0 = None
if self._lowfq == "default": self._lowfq = {}
if self._muintrpl == "default": self._muintrpl = ("linear", 0)
if self._qrc == "default": self._qrc = None
if self._onioml == "default": self._onioml = []
if self._oniomm == "default": self._oniomm = []
if self._oniomh == "default": self._oniomh = []
# setup parallel
self._paral = do_parallel(self._paral)
# setup cag
self.set_cag()
# useics = yes but there are no ics?
if self._useics == "yes" and (self._ics is None
or len(self._ics) == 0):
self._useics = "no"
def obtain_adipot(tcommon, drst, pathvars):
print
print " Calculating adiabatic potential..."
print
ics = pathvars.get_ics()
if pathvars._useics == "yes" and (ics is None or len(ics) == 0):
raise Exc.NoICS(Exception)
# calculate adiabatic potential
idata = (tcommon, drst, pathvars._eref, ics, pathvars._useics,
pathvars._lowfq, pathvars._freqscal)
dMols, ccVadi, icVadi, tuple_cc, tuple_ic, listV0 = ap.path2vadi(*idata)
# expand tuples
data_x, lcc_frqs, lcc_tzpe = tuple_cc
data_x, lic_frqs, lic_tzpe = tuple_ic
# check data
fncs.print_string(PS.sadipot_ics(ics, pathvars._useics), 8)
if pathvars._useics == "yes":
ok1 = ap.ccvsic_checknfreqs(lcc_frqs, lic_frqs)
ok2 = ap.ccvsic_checkts(data_x, lcc_frqs, lic_frqs)
ok3 = ap.ccvsic_checkzpe(lcc_tzpe, lic_tzpe)
checks = (ok1, ok2, ok3)
fncs.print_string(PS.sadipot_checks(checks), 8)
# select spline
if not ok1 or not ok2: Vadi, pathvars._useics = ccVadi, "no"
elif pathvars._useics == "yes": Vadi, pathvars._useics = icVadi, "yes"
else: Vadi, pathvars._useics = ccVadi, "no"
else:
Vadi, pathvars._useics = ccVadi, "no"
# setup spline
Vadi.setup()
data4print = (Vadi.xx(), Vadi.yy(), Vadi._sAG, Vadi._VAG, listV0, lcc_tzpe,
lic_tzpe, pathvars._eref)
fncs.print_string(PS.sadipot_table(*data4print), 8)
# print freqs
print " Vibrational frequencies summary: cc (ic) [in cm^-1]:"
fncs.print_string(PS.sadipot_freqs(Vadi.xx(), lcc_frqs, lic_frqs), 8)
return dMols, Vadi, pathvars
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