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 info_string(self, ib=0):
root_mass = sum(fncs.symbols2masses(self._symbols))
string = "Molecular formula : %s\n" % self._mform
string += "Number of atoms : %i\n" % self._natoms
string += "Number of electrons : %i\n" % self._nel
string += "Vibrational DOFs : %i\n" % self._nvdof
string += "Charge : %i\n" % self._ch
string += "Multiplicity : %i\n" % self._mtp
string += "Electronic energy (V0): %.8f hartree\n" % self._V0
string += "Total mass [root] : %.4f amu\n" % (root_mass * AMU)
string += "Total mass : %.4f amu\n" % (self._mass * AMU)
if self._pgroup is not None:
string += "Point group symmetry : %s\n" % (self._pgroup)
if self._rotsigma is not None:
string += "Rotational sym num : %i\n" % (self._rotsigma)
string += "Cartesian coordinates (Angstrom):\n"
for at, symbol in enumerate(self._symbols):
mass = self._masses[at] * AMU
x, y, z = fncs.xyz(self._xcc, at)
x *= ANGSTROM
y *= ANGSTROM
z *= ANGSTROM
string += " %2s %+12.8f %+12.8f %+12.8f [%7.3f amu]\n" % (
symbol, x, y, z, mass)
try:
str2 = "Moments and product of inertia (au):\n"
if len(self._imoms) == 1:
str2 += " %+10.3E\n" % self._imoms[0]
if len(self._imoms) == 3:
prodinert = self._imoms[0] * self._imoms[1] * self._imoms[2]
dataline = (self._imoms[0], self._imoms[1], self._imoms[2],
prodinert)
str2 += " %+10.3E %+10.3E %+10.3E [%10.3E]\n" % dataline
string += str2
except:
pass
try:
str2 = "Vibrational frequencies [1/cm] (scaled by %.3f):\n" % self._fscal
for idx in range(0, len(self._ccfreqs), 6):
str2 += " %s\n"%(" ".join("%8.2f"%fncs.afreq2cm(freq) \
for freq in self._ccfreqs[idx:idx+6]))
if len(self._ccfreqs) != 0: string += str2
except:
pass
try:
str2 = "Vibrational zero-point energies [kcal/mol]:\n"
for idx in range(0, len(self._cczpes), 6):
str2 += " %s\n"%(" ".join("%8.2f"%(zpe*KCALMOL) \
for zpe in self._cczpes[idx:idx+6]))
zpe_au = self._cczpe
zpe_kcal = self._cczpe * KCALMOL
zpe_eV = self._cczpe * EV
zpe_cm = self._cczpe * H2CM
str2 += "Vibrational zero-point energy: %+14.8f hartree = \n" % zpe_au
str2 += " %+14.2f kcal/mol = \n" % zpe_kcal
str2 += " %+14.2f eV = \n" % zpe_eV
str2 += " %+14.2f cm^-1 \n" % zpe_cm
str2 += "V0 + zero-point energy (V1) : %+14.8f hartree\n" % self._ccV1
if self._cczpe != 0.0: string += str2
except:
pass
# add blank spaces
string = "\n".join([" " * ib + line for line in string.split("\n")])
return string
(lzmat, zmatvals, zmatatoms), symbols = gau.convert_zmat(zmat)
# same current point
strconfs.append(str(point))
allconfs.append(point)
# correct symbols (just in case)
symbols, atonums = fncs.symbols_and_atonums(symbols)
# Data without dummies
symbols_wo, xcc_wo = fncs.clean_dummies(symbols, xcc=list(xcc))
symbols_wo, gcc_wo = fncs.clean_dummies(symbols, gcc=list(gcc))
symbols_wo, Fcc_wo = fncs.clean_dummies(symbols, Fcc=list(Fcc))
# calculate weight
atonums_wo = fncs.symbols2atonums(symbols_wo)
masses_wo = fncs.symbols2masses(symbols_wo)
pgroup, rotsigma = get_pgs(atonums_wo, masses_wo, xcc_wo)
if inpvars._enantio and pgroup.lower() == "c1":
weight = 2
enantio = tfh.enantiovec(lzmat, zmatvals, dcorr, inpvars)
allconfs.append(enantio)
denantio[str(enantio)] = str(point)
else:
weight = 1
# save data
geoms.append((V0, xcc_wo, gcc_wo, Fcc_wo, str(point)))
weights[str(point)] = weight
geoms.sort()
#----------------------------#
# calculate M_{j,tau} values #
def write_mstorinp(geoms,symbols,mtp,freqscal,inpvars,dMj,nrics,folder,lCH3=[]):
str_inp = ""
str_inp += "#--------------------------------------------#\n"
str_inp += "# Ms-Tor input file generated with TorsiFlex #\n"
str_inp += "#--------------------------------------------#\n"
str_inp += "\n"
torsions = inpvars._tatoms
ntorsions = inpvars._ntorsions
Lenantio = inpvars._enantio
natoms = len(symbols)
atonums = fncs.symbols2atonums(symbols)
masses = fncs.symbols2masses(symbols)
Eref = geoms[0][0]
#-----------------#
# general section #
#-----------------#
str_inp += "$general\n"
str_inp += " natoms %i\n"%natoms
str_inp += " nstr %i\n"%len(geoms)
str_inp += " ntor %i\n"%(ntorsions+len(lCH3))
str_inp += " freqscale %.4f\n"%freqscal
str_inp += " deltat 0.5\n"
str_inp += " elec\n"
str_inp += " %i 0.0\n"%mtp
str_inp += " end\n"
str_inp += "end\n"
str_inp += "\n"
#---------------------#
# temperature section #
#---------------------#
str_inp += "$temp\n"
for idx in range(0,len(inpvars._temps),6):
str_inp += " ".join("%7.2f"%T for T in inpvars._temps[idx:idx+6])+"\n"
str_inp += "end\n"
str_inp += "\n"
#----------------------#
# internal coordinates #
#----------------------#
str_inp += "$intdef\n"
if nrics is not None:
for ic in nrics:
ictype,icatoms = ic
# which torsion?
dtorX = ""
if ictype == "pt":
for X,tatoms in inpvars._tatoms.items():
if icatoms in (tuple(tatoms),tuple(tatoms[::-1])):
dtorX = "# torsion%s"%X
break
for CH3 in lCH3:
if icatoms in (tuple(CH3),tuple(CH3[::-1])):
dtorX = "# CH3"
break
# add to string
str_inp += " %s %s\n"%(intl.ic2string(ic).replace("_","-"),dtorX)
str_inp += "end\n"
str_inp += "\n"
#---------------------#
# coordinates&hessian #
#---------------------#
count = 0
str_hess = ""
for E,xcc,gcc,Fcc,point in geoms:
count += 1
# relative energy
erel = (E-Eref)*pc.KCALMOL
# rotational symmetry number
pgroup, rotsigma = get_pgs(atonums,masses,xcc)
if Lenantio and pgroup.lower() == "c1": weight = 2
else : weight = 1
# The string
str_inp += "$structure %i\n"%count
str_inp += "geom\n"
for idx,at in enumerate(atonums):
x,y,z = [coord*pc.ANGSTROM for coord in xcc[3*idx:3*idx+3]]
str_inp += "%-2s %15.8E %15.8E %15.8E\n"%(at,x,y,z)
str_inp += "end\n"
# M_j,tau values
str_inp += "mtor\n"
part_ttorsions = " ".join(["%.4f"%dMj[str(point)] for torsion in inpvars._ttorsions])
part_ch3 = " ".join("3.0000" for CH3 in lCH3)
str_inp += " %s %s \n"%(part_ttorsions,part_ch3)
str_inp += "end\n"
# weight, rel energy and rotsigma
str_inp += "weight %i\n"%weight
str_inp += "energy %.5f\n"%erel
str_inp += "rotsigma %i # point group: %s\n"%(rotsigma,pgroup)
str_inp += "end\n"
str_inp += "\n"
# hessian
str_hess += "$hess %2i\n"%count
for idx in range(0,len(Fcc),6):
values = "".join([" %+11.8f"%value for value in Fcc[idx:idx+6]])
str_hess += values + "\n"
str_hess += "end\n\n"
# write files
print(tvars.IBS2+" - %s"%(folder+tvars.MSTORIF1))
with open(folder+tvars.MSTORIF1,"w") as asdf: asdf.write(str_inp)
print(tvars.IBS2+" - %s"%(folder+tvars.MSTORIF2))
with open(folder+tvars.MSTORIF2,"w") as asdf: asdf.write(str_hess)