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.mod_les(eslist)
# set frequency scaling
molecule.set_fscal(fscal)
# setup
molecule.setup()
molecule.ana_freqs("cc")
return molecule
def prepare_qrc(self, dchem, dctc, dimasses):
# Will qrc be used?
if self._reaction is None: return
if self._qrc is None: return
reactants = dchem[self._reaction][0]
if len(reactants) != 1: return
# generate Molecule instance
reactant = reactants[0]
ctc, itc = PN.name2data(reactant)
if ctc not in dctc.keys(): 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 = PN.get_gts(ctc, itc)
if not os.path.exists(gtsfile): raise Exception
# Generate Molecule instance
reactant = Molecule()
reactant.set_from_gts(gtsfile)
# apply fscal
reactant.set_fscal(fscal=cluster._fscal)
# apply isotopic masses
if imods is not None:
reactant.apply_imods(imods, dimasses)
# calculate frequencies
reactant.setup()
mode, nE = self._qrc
Vadi = reactant._V0
for idx, afreq in enumerate(reactant._ccfreqs):
if idx == mode: continue
Vadi += afreq2zpe(afreq)
afreq = reactant._ccfreqs[mode]
listE = [
Vadi + (n + 0.5) * HBAR * afreq - self._eref for n in range(nE)
]
self._qrclE = listE
self._qrcafreq = afreq
def obtain_mep(target, gtsTS, pathvars, tsoftware, TMP):
ctc, itc = PN.name2data(target)
# 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)
# data for single-point calculation
spc_args = (tes, TMP, False)
spc_fnc = get_spc_fnc(software)
# read rst
tpath2, tcommon2, drst = ff.read_rst(rstfile)
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]):
print " 'fwdir' variable differs from MEP direction in rst file!"
print " * modifying rst internal dictionary..."
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
print " * rewriting rst file..."
ff.write_rst(rstfile, tpath2, tcommon2, drst)
# Extension of MEP in rst is bigger
if drst != {}:
lbw, lfw, sbw, sfw, Ebw, Efw = 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.set_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)
#------------#
# First step #
#------------#
print
print " Performing first step of MEP..."
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)
fncs.print_string(PS.smep_first(ts._symbols, ts._xms, v0, v1), 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
print " Calculating MEP..."
print
print " * REMEMBER: data of each step will be saved at %s" % rstfile
print " a summary will be printed when finished"
# 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
print " * FINISHED!"
print
drst.update(drstbw)
drst.update(drstfw)
points = [TSLABEL] + pointsbw + pointsfw
# empty variables
del drstbw, pointsbw
del drstfw, pointsfw
# Rewrite rst
print " * (re)writing file: %s (sorted version)" % rstfile
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, Ebw, Efw = sd.rstlimits(drst)
convbw, l1bw, l2bw = convbw
convfw, l1fw, l2fw = convfw
if l1bw + l1fw != "":
print " * EPS criteria (epse and epsg):"
print
if l1bw != "": print " %s" % l1bw
if l2bw != "": print " %s" % l2bw
if l1fw != "": print " %s" % l1fw
if l2fw != "": print " %s" % l2fw
print
if convbw:
pathvars.converged_in_bw(sbw)
print " CRITERIA FULFILLED in backward dir.!"
print " path stopped at sbw = %+8.4f bohr" % sbw
print
if convfw:
pathvars.converged_in_fw(sfw)
print " CRITERIA FULFILLED in forward dir.!"
print " path stopped at sfw = %+8.4f bohr" % sfw
print
# write molden file
print " * writing file: %s" % xyzfile
ff.rst2xyz(rstfile, xyzfile, onlyhess=True)
print
# reference energy
if pathvars._eref is None: pathvars._eref = Ebw
# return data
return tcommon, drst, pathvars