def readfile_xyz(fname):
string = ""
zmat, symbols, masses = ff.read_xyz_zmat(fname)
xcc = intl.zmat2xcc(zmat[0],zmat[1])
# Print more information
ndummy = symbols.count("XX")
natoms = len(symbols)-ndummy
# without dummies
symbols_wo , xcc_wo = fncs.clean_dummies(symbols,xcc=xcc)
symbols_wo , masses_wo = fncs.clean_dummies(symbols,masses=masses)
molecule = Molecule()
molecule.setvar(xcc=xcc_wo,symbols=symbols_wo,masses=masses_wo,ch=0,mtp=1)
molecule.prepare()
molecule.setup()
string += "Molecular formula : %s\n"%molecule._mform
string += "Number of atoms : %i\n"%natoms
string += "Number of dummy atoms : %i\n"%ndummy
string += "Vibrational d.o.f. : %i\n"%molecule._nvdof
string += "\n"
# Cartesian Coordinates
string += "Cartesian coordinates (in Angstrom):\n"
sidx = "%%%si"%len(str(len(symbols)))
at_wo = -1
dwithout = {}
for at,symbol in enumerate(symbols):
xi,yi,zi = [value*pc.ANGSTROM for value in xcc[3*at : 3*at+3]]
mass = masses[at]*pc.AMU
datainline = (sidx%(at+1),symbol,xi,yi,zi,mass)
if symbol != "XX": at_wo += 1; dwithout[at] = at_wo
else: dwithout[at] = None
string += "[%s] %-2s %+12.7f %+12.7f %+12.7f (%7.3f amu)\n"%datainline
string += "\n"
return xcc,zmat,symbols,masses,(dwithout,molecule,natoms,ndummy),string
def prepare_qrc(self,dchem,dctc,dimasses):
'''
also modifies self._qrccase:
self._qrccase == 0: everything is ok / qrc is not activated
self._qrccase == 1: no reaction is associated to the TS
self._qrccase == 2: reaction is not unimolecular
self._qrccase == 3: ctc for reactant not defined
self._qrccase == 4: gts file for reactant not found
self._qrccase == 5: unable to get energy of products
'''
# Will qrc be used?
if self._qrc is None: return
if self._reaction is None: self._qrccase = 1; return
# assert unimolecular
reactants = dchem[self._reaction][0]
products = dchem[self._reaction][2]
if self._exorgic:
if len(reactants) != 1: self._qrccase = 2; return
self._qrcname = reactants[0]
else:
if len(products ) != 1: self._qrccase = 2; return
self._qrcname = products[0]
if self._V1P is None: self._qrccase = 5; return
#---------------------------------#
# Now, generate Molecule instance #
#---------------------------------#
ctc, itc = PN.name2data(self._qrcname)
if ctc not in dctc.keys(): self._qrccase = 3; return
cluster = dctc[ctc]
if itc is None: itc = cluster._itcs[0][0]
if itc in cluster._diso.keys(): imods = cluster._diso[itc]
elif "*" in cluster._diso.keys(): imods = cluster._diso["*"]
else : imods = None
gtsfile = dctc[ctc].gtsfile(itc)
if not os.path.exists(gtsfile): self._qrccase = 4; return
# Generate Molecule instance
molecule = Molecule()
molecule.set_from_gts(gtsfile)
# apply fscal
molecule.setvar(fscal=cluster._fscal)
# apply isotopic masses
if imods is not None:
molecule.apply_imods(imods,dimasses)
# calculate frequencies
molecule.setup()
#------------------------------#
# Prepare list of QRC energies #
#------------------------------#
mode , nE = self._qrc
self._qrcafreq = molecule._ccfreqs[mode]
self._qrclE = [n*HBAR*self._qrcafreq for n in range(nE)]
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 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 generate_gts_file(esfile, gtsfile, read_method):
'''
Generate gts file (and molden & frozen files)
from given electronic structure (ES) file;
The ES file is read using read_method
'''
# Extra files that (maybe) will be generated
file_frozen = gtsfile + ".frozen" # only if any frozen atom
file_molden = gtsfile + ".molden" # molden file
# read file
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = read_method(
PN.UFOLDER + esfile)[0:9]
# clevel is not really clevel when using read_gtsfile as read_method
if read_method == read_gtsfile: clevel = ""
# symbols and atonums
symbols, atonums = fncs.symbols_and_atonums(atonums)
# is masses available?
if masses is None or len(masses) == 0 or sum(masses) == 0.0:
masses = atonums2masses(atonums)
# is Fcc available?
if len(atonums) != 1 and (Fcc is None or len(Fcc) == 0):
status = -1
cache = None
molec = None
else:
# Generate Molecule instance
molec = Molecule()
molec.setvar(xcc=xcc, gcc=gcc, Fcc=Fcc)
molec.setvar(atonums=atonums, masses=masses)
molec.setvar(ch=ch, mtp=mtp, V0=E)
molec.prepare()
# Deal with frozen atoms [atom i is frozen if Fij=0 forall j)
frozen_xcc, frozen_symbols = molec.remove_frozen()
# Calculate point group (must be done after remove frozen)
molec.calc_pgroup(force=True)
# Deal with Hessian
molec.setup()
# write gts file
molec.genfile_gts(PN.DIR1 + gtsfile, level=clevel)
status = 1
# write frozen (if there are frozen atoms)
RW.write_frozen(PN.DIR1 + file_frozen, frozen_xcc, frozen_symbols)
# write molden file
idata = (PN.DIR1 + file_molden, molec._xcc, molec._symbols,
molec._ccfreqs, molec._ccFevecs)
write_molden(*idata)
# save to cache
nimag = int(fncs.numimag(molec._ccfreqs))
pgroup = str(molec._pgroup)
mform = str(molec._mform)
cache = [esfile, gtsfile, E, ch, mtp, nimag, mform, pgroup]
# delete variable, just in case
del xcc, gcc, Fcc
del symbols, atonums, masses
del molec
# return
return status, cache
def get_rotcons(lzmat,zmatvals,symbols):
xcc = zmat2xcc(lzmat,zmatvals)
# 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))
# generate Molecule instance
molecule = Molecule()
molecule.setvar(xcc=xcc_wo)
molecule.setvar(symbols=symbols_wo)
molecule.setvar(V0=0)
molecule.setvar(ch=0,mtp=1)
molecule.prepare()
molecule.setup()
# in freq units (GHz)
imoms = [Ii * pc.KG*pc.METER**2 for Ii in molecule._imoms]
rotcons = [pc.H_SI/(Ii*8*np.pi**2)/1E9 for Ii in imoms]
return rotcons
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 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 userfile_to_gtsfile(filename, gtsfile):
'''
Read a file given by the user and generate gts file
if possible
'''
gtsfile = gtsname(gtsfile, "full")
read_methods = []
read_methods.append(read_gtsfile) #(a) a gts file
read_methods.append(read_fchk) #(b) a fchk file
read_methods.append(read_gauout_v1) #(c.1) a Gaussian output file (ramos)
read_methods.append(read_gauout_v2) #(c.2) a Gaussian output file (ferro)
read_methods.append(read_orca) #(d) an Orca output file
for read_method in read_methods:
try:
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = read_method(
filename)[0:9]
if read_method == read_gtsfile: clevel = ""
# in case no data in masses
if masses is None or len(masses) == 0 or sum(masses) == 0.0:
masses = atonums2masses(atonums)
# Some checking
if len(atonums) != 1 and Fcc in ([], None):
#raise Exc.FccNotFound
return -1, None
# Generate Molecule instance
molecule = Molecule()
molecule.setvar(xcc=xcc, gcc=gcc, Fcc=Fcc)
molecule.setvar(atonums=atonums, masses=masses)
molecule.setvar(ch=ch, mtp=mtp, V0=E)
molecule.prepare()
# Deal with frozen atoms
ffrozen = gtsfile + ".frozen"
frozen_xcc, frozen_symbols = molecule.remove_frozen()
RW.write_frozen(ffrozen, frozen_xcc, frozen_symbols)
# write gts
molecule.calc_pgroup(force=True)
molecule.genfile_gts(gtsfile, level=clevel)
return 1, E
except Exc.FileType:
continue
except:
continue
return 0, None
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
def obtain_mep(target, gtsTS, pathvars, tsoftware, TMP):
ctc, itc = PN.name2data(target)
# create folder now and not in the parallel process
if not os.path.exists(TMP):
try:
os.mkdir(TMP)
except:
pass
# Files
rstfile = PN.get_rst(ctc, itc)
xyzfile = PN.get_rstxyz(ctc, itc)
# print
software, tes = tsoftware
fncs.print_string(PS.smep_init(target,software,pathvars._paral,pathvars.tuple_first(),\
pathvars.tuple_sdbw(),pathvars.tuple_sdfw()),4)
fncs.print_string(PS.smep_ff(TMP, PN.DIR4, PN.DIR5, rstfile, xyzfile), 4)
# read rst
try:
tpath2, tcommon2, drst = ff.read_rst(rstfile)
except:
exception = Exc.RstReadProblem(Exception)
exception._var = rstfile
raise exception
fncs.print_string(PS.smep_rst(rstfile, drst), 4)
# correct MEP direction?
if TSLABEL in drst.keys():
ii_s, ii_V, ii_x, ii_g, ii_F, ii_v0, ii_v1, ii_t = drst[TSLABEL]
ii_ic, ii_sign = pathvars._fwdir
if not intl.ics_correctdir(ii_x, ii_v0, ii_ic, ii_sign, tcommon2[3],
tcommon2[4]):
fncs.print_string(
"'fwdir' variable differs from MEP direction in rst file!", 4)
fncs.print_string("* modifying rst internal dictionary...", 8)
new_drst = {}
for key in drst.keys():
ii_s, ii_V, ii_x, ii_g, ii_F, ii_v0, ii_v1, ii_t = drst[key]
ii_s = -ii_s
if ii_v0 is not None: ii_v0 = [-ii for ii in ii_v0]
if ii_v1 is not None: ii_v1 = [-ii for ii in ii_v1]
if "bw" in key: newkey = key.replace("bw", "fw")
else: newkey = key.replace("fw", "bw")
new_drst[newkey] = (ii_s, ii_V, ii_x, ii_g, ii_F, ii_v0, ii_v1,
ii_t)
drst = new_drst
del new_drst
fncs.print_string("* rewriting rst file...", 8)
ff.write_rst(rstfile, tpath2, tcommon2, drst)
# Extension of MEP in rst is bigger
if drst != {}:
lbw, lfw, sbw, sfw, V0bw, V0fw = sd.rstlimits(drst)
pathvars._sbw = min(pathvars._sbw, sbw)
pathvars._sfw = max(pathvars._sfw, sfw)
# Read gts
ts = Molecule()
ts.set_from_gts(gtsTS)
# scaling of frequencies
ts.setvar(fscal=pathvars._freqscal)
# apply iso mod
if pathvars._masses is not None: ts.mod_masses(pathvars._masses)
# setup
ts.setup(mu=pathvars._mu)
ts.ana_freqs(case="cc")
fncs.print_string(PS.smep_ts(ts), 4)
tcommon = (ts._ch, ts._mtp, ts._atnums, ts._masses, ts._mu)
compare_tpath(pathvars.tuple_rst(), tpath2, rstfile)
compare_tcommon(tcommon, tcommon2, rstfile)
# data for single-point calculation
frozen = RW.read_frozen(gtsTS + ".frozen")
oniom_layers = (list(pathvars._oniomh), list(pathvars._oniomm),
list(pathvars._onioml))
spc_args = (tes, TMP, False, frozen, oniom_layers)
spc_fnc = get_spc_fnc(software)
#------------#
# First step #
#------------#
print("")
fncs.print_string("Performing first step of MEP...", 4)
print("")
inputvars = (ts._xcc,ts._gcc,ts._Fcc,ts._symbols,ts._masses,pathvars.tuple_first(),\
spc_fnc,spc_args,drst,pathvars._paral)
(xms, gms, Fms), (v0, v1), (xms_bw, xms_fw) = sd.mep_first(*inputvars)
s1bw = -float(pathvars._ds)
s1fw = +float(pathvars._ds)
# oniom layers?
oniom_ok = pathvars.isONIOMok(ts._natoms, software)
layers = pathvars.get_layers()
fncs.print_string(PS.smep_oniom(layers, ts._natoms, software), 8)
if not oniom_ok: raise Exc.WrongONIOMlayers(Exception)
# Print MEP info
fncs.print_string(PS.smep_first(ts._symbols, ts._xms, v0, v1, layers), 8)
# write rst file
if TSLABEL not in drst.keys():
drst[TSLABEL] = (0.0, ts._V0, xms, gms, Fms, v0, v1, None)
ff.write_rst_head(rstfile, pathvars.tuple_rst(), tcommon)
ff.write_rst_add(rstfile, TSLABEL, drst[TSLABEL])
#------------#
# The MEP #
#------------#
print("")
fncs.print_string("Calculating MEP...", 4)
print("")
fncs.print_string(
"* REMEMBER: data of each step will be saved at %s" % rstfile, 7)
fncs.print_string(" a summary will be printed when finished", 7)
# preparation
xcc_bw = fncs.ms2cc_x(xms_bw, ts._masses, pathvars._mu)
xcc_fw = fncs.ms2cc_x(xms_fw, ts._masses, pathvars._mu)
args_bw = ((xcc_bw,s1bw,ts._symbols,ts._masses,pathvars.tuple_sdbw(),\
spc_fnc,spc_args,drst,ts._Fms,"bw%i") , rstfile,drst)
args_fw = ((xcc_fw,s1fw,ts._symbols,ts._masses,pathvars.tuple_sdfw(),\
spc_fnc,spc_args,drst,ts._Fms,"fw%i") , rstfile,drst)
# execution
if pathvars._paral:
import multiprocessing
pool = multiprocessing.Pool()
out = [
pool.apply_async(onesidemep, args=args)
for args in [args_bw, args_fw]
]
drstbw, pointsbw, convbw = out[0].get()
drstfw, pointsfw, convfw = out[1].get()
del out
# clean up pool
pool.close()
pool.join()
else:
drstbw, pointsbw, convbw = onesidemep(*args_bw)
drstfw, pointsfw, convfw = onesidemep(*args_fw)
# update drst
fncs.print_string("* FINISHED!", 7)
print("")
drst.update(drstbw)
drst.update(drstfw)
points = [TSLABEL] + pointsbw + pointsfw
# empty variables
del drstbw, pointsbw
del drstfw, pointsfw
# Rewrite rst
fncs.print_string("* (re)writing file: %s (sorted version)" % rstfile, 7)
ff.write_rst(rstfile, pathvars.tuple_rst(), tcommon, drst)
print("")
## restrict drst to points
#if restrict: drst = {point:drst[point] for point in points}
# Get limits of rst
lbw, lfw, sbw, sfw, V0bw, V0fw = sd.rstlimits(drst)
convbw, l1bw, l2bw = convbw
convfw, l1fw, l2fw = convfw
if l1bw + l1fw != "":
fncs.print_string("* MEP convergence criteria (epse and epsg):", 7)
print("")
if l1bw != "": fncs.print_string("%s" % l1bw, 9)
if l2bw != "": fncs.print_string("%s" % l2bw, 9)
if l1fw != "": fncs.print_string("%s" % l1fw, 9)
if l2fw != "": fncs.print_string("%s" % l2fw, 9)
print("")
if convbw:
pathvars.converged_in_bw(sbw)
fncs.print_string("CRITERIA FULFILLED in backward dir.!", 9)
fncs.print_string("path stopped at sbw = %+8.4f bohr" % sbw, 9)
print("")
if convfw:
pathvars.converged_in_fw(sfw)
fncs.print_string("CRITERIA FULFILLED in forward dir.!", 9)
fncs.print_string("path stopped at sfw = %+8.4f bohr" % sfw, 9)
print("")
# write molden file
fncs.print_string("* writing file: %s" % xyzfile, 7)
ff.rst2xyz(rstfile, xyzfile, onlyhess=True)
print("")
# reference energy
if pathvars._eref is None: pathvars._eref = V0bw
# return data
return tcommon, drst, pathvars
