def pilgrim_spc(xcc,symbols,bhessian,mname,eargs):
atonums = fncs.symbols2atonums(symbols)
ch, mtp = None, None
masses = None
# expand extra-args
if len(eargs) == 1:
asurf = eargs[0]
folder, clean = None, False
elif len(eargs) == 2:
asurf, folder = eargs
clean = False
elif len(eargs) == 3:
asurf, folder, clean = eargs
# create folder
if folder is not None:
if not os.path.exists(folder): os.mkdir(folder)
# names of files
wname, ifile, ofile, err = ITF.iofiles(mname,folder)
# write ifile
ITF.write_input(ifile,xcc)
# calculate gradient/hessian
if bhessian: E, gcc, Fcc = ITF.calculate_hessian(ifile,ofile,err,asurf)
else : E, gcc, Fcc = ITF.calculate_gcc(ifile,ofile,err,asurf)+[None]
# Remove files
if clean:
files = os.listdir(folder)
for fff in files: os.remove(folder+fff)
return xcc, atonums, ch, mtp, E, gcc, Fcc, masses
def read_gauout(filename):
# read gaussian file
data_gaulog = read_gaussian_log(filename)
# split data
ch = data_gaulog[2]
mtp = data_gaulog[3]
symbols = data_gaulog[4]
xcc = data_gaulog[5]
gcc = data_gaulog[6]
Fcc = data_gaulog[7]
V0 = data_gaulog[8]
level = data_gaulog[11]
# symbols to atomic numbers
atonums = symbols2atonums(symbols)
# atomic mass
atomasses = atonums2masses(atonums)
# return data
return xcc, atonums, ch, mtp, V0, gcc, Fcc, atomasses, level
def prepare(self):
# check atnums
if self._atnums is not None and type(self._atnums[0]) == str:
self._symbols = list(self._atnums)
# check symbols
if self._symbols is not None and type(self._symbols[0]) == int:
self._atnums = list(self._symbols)
# Get both atnums and symbols if None
if self._atnums is None: self._atnums = fncs.symbols2atonums(self._symbols)
if self._symbols is None: self._symbols = fncs.atonums2symbols(self._atnums)
# check masses
if self._masses is None:
self._masses = fncs.atonums2masses(self._atnums)
# derivated magnitudes
self.genderivates()
# check Fcc
if self._Fcc not in (None,[]) and len(self._Fcc) != 3*self._natoms:
self._Fcc = fncs.lowt2matrix(self._Fcc)
zmat = gau.zmat_from_loginp(folder + log)
(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()
#----------------------------#
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)