def add_path(targets,dpath,dctc,dtesLL,lts,mod=False):
set_completer(2)
# defaults
if "*" in targets or targets == []:
if mod: targets = dpath.keys()
else : targets = lts
targets = [target for target in targets if target in lts]
# no targets? Finish
if len(targets) == 0: return dpath, dtesLL
# Generate PathVars object for all of them
for target in targets:
ctc, itc = PN.name2data(target)
if ctc not in dctc.keys(): return dpath, dtesLL
if mod and (ctc in dpath.keys()): continue
if ctc in dpath.keys(): continue
dpath[ctc] = PathVars("mep")
# get fwdir (this may take some time...)
gtsfile = dctc[ctc].gtsfiles()[0]
try : fwdir = calc_fwdir(gtsfile)
except: continue
dpath[ctc]._fwdir = fwdir
# print path(s)
ls_path(dpath,targets)
# modify them
while True:
try:
line = input(ILINE2).strip()
if line.split()[0] in END: break
if "=" not in line:
line = line.split()
else:
line = [ string.strip() for string in line.split("=")]
if len(line) != 2: raise Exception
var, val = line
var = var.lower()
if var not in ["sbw","sfw","ds","hsteps","paral","scterr","sctmns"]: raise Exception
for target in targets:
dpath[target].setvar(var,val)
except KeyboardInterrupt:
print("")
break
except:
print(IBLANK2+"invalid line...")
print("")
ls_path(dpath,targets)
continue
# print
ls_path(dpath,targets)
# update dtesLL
for ctc in dpath.keys():
try : ch,mtp = dctc[ctc]._ch, dctc[ctc]._mtp
except: ch,mtp = 0, 1
# templates by default
default_templates = get_templates(ch,mtp,"LL")
# add default?
for software,string in default_templates.items():
dtesLL[software] = dtesLL.get(software,{})
if ctc in dtesLL[software].keys(): continue
dtesLL[software][ctc] = string
return dpath, dtesLL
def get_itargets(targets, dpath, dctc):
'''
get individual targets
'''
# Targets?
if (len(targets) == 0) or ("*" in targets): targets = dpath.keys()
# generate list of individual targets
itargets = []
for target in targets:
ctc, itc = PN.name2data(target)
# check ctc
if ctc not in dctc.keys():
fncs.print_string("* '%s' not in '%s'" % (target, PN.IFILE1), 3)
print("")
continue
if ctc not in dpath.keys():
fncs.print_string("* '%s' not in '%s'" % (target, PN.IFILE3), 3)
print("")
continue
# list of itcs for the ctc
itclist = [itc_i for itc_i, weight_i in dctc[ctc]._itcs]
# add itc
if itc is None:
itargets += [
PN.struckey(ctc, itc) for itc, weight in dctc[ctc]._itcs
]
elif itc in itclist:
itargets += [PN.struckey(ctc, itc)]
return sorted(itargets)
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 get_masses(target, dctc, dimasses):
ctc, itc = PN.name2data(target)
diso = dctc[ctc]._diso
if itc in diso.keys(): imod = diso[itc]
elif "*" in diso.keys(): imod = diso["*"]
else: imod = None
if imod is None: return None
gtsTS = dctc[ctc].gtsfile(itc)
TS = Molecule()
TS.set_from_gts(gtsTS)
TS.apply_imods(imod, dimasses)
masses = list(TS._masses)
return masses
def get_itcs(target,dctc):
if target is None: return None
# ctc and itc name
ctc, itc = PN.name2data(target)
# multi-structural? (True even with one conformer if itc is not defined)
if itc is None: ms = True
else : ms = False
# list of itcs
if itc is not None : itcs = [(itc,1)]
elif ctc in dctc.keys(): itcs = list(dctc[ctc]._itcs)
else : itcs = None
# save data?
return ctc,itcs,ms
def execute_pfn(itargets, dchem, idata, status, case):
reactions = set([])
for target in itargets:
ctc1, itc1 = PN.name2data(target)
the_reaction = None
for reaction, (Rs, TS, Ps) in dchem.items():
try:
ctc2, itc2 = PN.name2data(TS)
except:
continue
if ctc1 == ctc2:
the_reaction = reaction
if itc1 == itc2: break
if the_reaction is not None: reactions.add(the_reaction)
if len(reactions) == 0: return
reactions = sorted(list(reactions))
fncs.print_string(
"The selected transitions states are involved in defined reactions!",
3)
pfn_targets = set([])
for reaction in reactions:
fncs.print_string("* %s" % reaction, 6)
Rs, TS, Ps = dchem[reaction]
for xx in Rs + [TS] + Ps:
pfn_targets.add(PN.name2data(xx)[0])
if len(pfn_targets) == 0: return
pfn_targets = sorted(list(pfn_targets))
print("")
import opt_pfn as pfn
fncs.print_string("Calculating partition functions for the next targets:",
3)
for target in pfn_targets:
fncs.print_string("* %s" % target, 6)
print("")
pfn.main(idata, status, case, targets=pfn_targets)
def calc_mep(itarget, gtsTS, pathvars, tsoftware, TMP):
# data in name
ctc, itc = PN.name2data(itarget)
# Low-Level
if pathvars._dlevel is None:
tcommon, drst, pathvars = obtain_mep(itarget, gtsTS, pathvars,
tsoftware, TMP)
fncs.print_string(PS.smep_table(drst, pathvars._eref), 4)
# Dual-Level
else:
rstfile = PN.get_rst(ctc, itc)
xyzfile = PN.get_rstxyz(ctc, itc)
software, tes = tsoftware
fncs.print_string(PS.smep_init(itarget,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
tpath, tcommon, drst = ff.read_rst(rstfile)
fncs.print_string(PS.smep_rst(rstfile, drst), 4)
fncs.print_string("Applying Dual-Level...", 4)
print("")
dlevel_xy = [(find_label_in_rst(x, drst)[0], y)
for x, y in pathvars._dlevel.items()]
dlevel_xy = [(x, y) for x, y in dlevel_xy if x is not None]
# Print points (sorted by s value)
dummy = [(drst[xx][0], idx) for idx, (xx, yy) in enumerate(dlevel_xy)]
dummy.sort()
for s_i, idx_i in dummy:
xx_i, yy_i = dlevel_xy[idx_i]
fncs.print_string(
"%+8.4f bohr (%-6s) --> %.7f hartree" % (s_i, xx_i, yy_i), 13)
print("")
# interpolation
drst, points, xx, yyll, yyhl = ispe.ispe(tcommon,
drst,
dlevel_xy,
tension=0.0)
tdleveldata = (points, xx, yyll, yyhl)
# table new values
fncs.print_string(
PS.smep_tableDLEVEL(drst, tdleveldata, pathvars._eref), 4)
return tcommon, drst, pathvars
def set_eref_from_reaction(self,tsname,dchem,dof):
thebool = self._eref in [None,"auto","default"]
ctc, itc = PN.name2data(tsname)
# Get data from reactions
rname, V0R, V0P, V1R, V1P, GibbsR = get_reaction_energies(tsname,dchem,dof)
self._V1R = V1R
self._V1P = V1P
if None not in (self._V1R,self._V1P) and self._V1P > self._V1R: self._exorgic = False
# save GibbsR for CVT gibbs
self._GibbsR = GibbsR
# go case by case
if thebool and V0R is not None: self._eref = V0R
# save reaction name and check if beyond mep
self._reaction = rname
if self._eref in [None,"auto","default"]: self._beyondmep = False
try:
Rs,TS,Ps = dchem[self._reaction]
self._reactioneq = '%s --> %s --> %s'%("+".join(Rs),TS,"+".join(Ps))
except: self._reactioneq = None
def __init__(self, rcname, reacts, ts, prods, ltemp, dctc):
# save input data
self._rcname = rcname
self._ltemp = ltemp
self._beta = 1.0 / (np.array(ltemp) * KB)
self._reacts = reacts
self._ts = ts
self._prods = prods
#---------------------------------------#
# Some basic operations with input data #
#---------------------------------------#
remove = []
self._itcs = {}
self._gtsfile = {} # name of gts files
self._anhfile = {} # name of anh files
self._disos = {} # isotopic modifications
self._weight = {}
for target in self._reacts + [self._ts] + self._prods:
ctc, itcs, ms = None, None, None
# get itcs
if target is not None:
ctc, itc = PN.name2data(target)
# list of itcs
if itc is not None: itcs = [(itc, 1)]
elif ctc in dctc.keys(): itcs = list(dctc[ctc]._itcs)
else: itcs = None
# multi-structural?
ms = itc is None # (True also with 1 conformer if itc is None)
# itcs NOT found
if itcs is None:
remove.append(target)
continue
# save data
self._anhfile[ctc] = dctc[ctc]._anh
self._disos[ctc] = dctc[ctc]._diso
self._itcs[target] = (ctc, itcs, ms)
for itc, weight in itcs:
self._weight[(ctc, itc)] = weight
self._gtsfile[(ctc, itc)] = dctc[ctc].gtsfile(itc)
# clean up
self._reacts = [
target for target in self._reacts if target not in remove
]
self._prods = [
target for target in self._prods if target not in remove
]
if self._ts in remove: self._ts = None
# number of reactants/product and correction weight
self._nR, self._wfw = len(self._reacts), 1
self._nP, self._wbw = len(self._prods), 1
if self._nR == 2 and self._reacts[0] == self._reacts[1]: self._wfw = 2
if self._nP == 2 and self._prods[0] == self._prods[1]: self._wbw = 2
#------------------------------#
# initialize rest of variables #
#------------------------------#
self._dall = {}
self._massch = {}
self._massR = 0.0
self._massTS = 0.0
self._massP = 0.0
self._chR = 0
self._chTS = 0
self._chP = 0
self._V0R = 0.0
self._V1R = 0.0
self._V0P = 0.0
self._V1P = 0.0
self._V0TS = 0.0
self._V1TS = 0.0
self._QtR = np.array([1.0 for t in self._ltemp])
self._QtP = np.array([1.0 for t in self._ltemp])
self._QtTS = np.array([1.0 for t in self._ltemp])
self._chi0 = {
} # contribution of most stable conformer [considering V0]
self._tsitc0 = None # for ctc of ts [considering V0]
self._tschi = {
X: {}
for X in "tst,tstzct,tstsct,cvt,cvtzct,cvtsct".split(",")
}
self._dtcoef = {
X: {}
for X in "tstzct,tstsct,cvt,cvtzct,cvtsct".split(",")
}
self._anhctcs = set([])
self._FMSQH = np.array([1.0 for t in self._ltemp]) # SS considering V0
self._ANHR = np.array([1.0 for t in self._ltemp])
self._ANHP = np.array([1.0 for t in self._ltemp])
self._ANHTS = np.array([1.0 for t in self._ltemp])
self._ANHKeq = np.array([1.0 for t in self._ltemp])
self._ANHkfw = np.array([1.0 for t in self._ltemp])
self._ANHkbw = np.array([1.0 for t in self._ltemp])
self._Keq = np.array([1.0 for t in self._ltemp])
self._kfw = {X: None for X in RCONS}
self._kbw = {X: None for X in RCONS}
self._problem = False
def get_reaction_energies(TS,dchem,dof):
'''
* checks the reactions which involved the target transition
state (TS) in order to extract V0 and V1 for reactants
and products
'''
# initialize variables
reaction = None
Eref = None
V0R = None
V0P = None
V1R = None
V1P = None
GibbsR = None
# select reaction
ctc, itc = PN.name2data(TS)
for rname in dchem.keys():
Rs, ts, Ps = dchem[rname]
ctc2, itc2 = PN.name2data(ts)
if ctc == ctc2:
reaction = rname
if itc == itc2: break
# no reaction?
if reaction is None: return reaction, V0R, V0P, V1R, V1P, GibbsR
# read dof
dall = RW.read_alldata(dof)[0]
# get energy from reaction
Rs = dchem[reaction][0]
Ps = dchem[reaction][2]
# reactants
if len(Rs) != 0:
V0R, V1R = 0.0, 0.0
for R in Rs:
ctc, itc = PN.name2data(R)
if itc is None: key = PN.struckey(ctc,"msho")
else : key = R
data = dall["pfn"].get(key,None)
if data is None:
V0R, V1R = None, None
break
V0, V1, pfns = data
V0R += V0
V1R += V1
# Gibbs energy
if key in dall["gibbs1cm3"].keys():
gibbs = dall["gibbs1cm3"][key]
if GibbsR is None: GibbsR = gibbs
else : GibbsR = [ gi+gj for gi,gj in zip(GibbsR,gibbs)]
# products
if len(Ps) != 0:
V0P, V1P = 0.0, 0.0
for P in Ps:
ctc, itc = PN.name2data(P)
if itc is None: key = PN.struckey(ctc,"msho")
else : key = P
data = dall["pfn"].get(key,None)
if data is None:
V0P, V1P = None, None
break
V0, V1, pfns = data
V0P += V0
V1P += V1
# Output
return reaction, V0R, V0P, V1R, V1P, GibbsR
if fstatus == -1: exit()
# expand case
(dof,hlf,plotfile),dlevel,software = case
#-------------------------------------------------------#
print(" Selected software: %s"%software)
print("")
targets = get_targets(targets,dctc)
# Print targets
if len(targets) != 0:
print(" High-level (HL) calculations will be carried out for:")
ml = max([len(target) for target in targets]+[1])
for target in targets:
ctc,itc = PN.name2data(target)
TMP = PN.TMPHLi%PN.struckey(ctc,itc)
print(" %s (TMP folder: %s)"%("%%-%is"%ml%target,TMP))
print("")
else:
print(" No valid target(s) for High-level (HL) calculations")
print("")
return
# read high-level output file
dhighlvl = RW.read_highlevelfile(hlf)
# loop over each target
print(" Carrying out HL-calculations:")
print("")
ml = max([len(target) for target in targets])
def deal_with_path(target, dlevel, software, ltemp, dctc, pathvars, dtes,
dchem, dhighlvl, dimasses):
dof = PN.get_dof(dlevel)
plotfile = PN.get_plf(dlevel)
# gts file for this TS
ctc, itc = PN.name2data(target)
gtsTS = dctc[ctc].gtsfile(itc)
# rotational symmetry
moleculeTS = Molecule()
moleculeTS.set_from_gts(gtsTS)
symmetry = str(moleculeTS._pgroup), int(moleculeTS._rotsigma)
# temporal folder
TMP = PN.TMPi % (target)
# if exists,remove content (unless keeptmp is activated)
# (to avoid reading old files from different levels of calculation)
if os.path.exists(TMP) and not pathvars._keeptmp:
shutil.rmtree(TMP, ignore_errors=True)
# split target
ctc, itc = PN.name2data(target)
# name of rst file
rstfile = PN.get_rst(ctc, itc)
# tuple software
tes = dtes.get(software, {}).get(ctc, None)
tsoftw = (software, tes)
# internal coordinates
if itc in dctc[ctc]._dics.keys(): ics = dctc[ctc]._dics[itc]
elif "*" in dctc[ctc]._dics.keys(): ics = dctc[ctc]._dics["*"]
else: ics = None
if itc in dctc[ctc]._dicsbw.keys(): icsbw = dctc[ctc]._dicsbw[itc]
elif "*" in dctc[ctc]._dicsbw.keys(): icsbw = dctc[ctc]._dicsbw["*"]
else: icsbw = None
if itc in dctc[ctc]._dicsfw.keys(): icsfw = dctc[ctc]._dicsfw[itc]
elif "*" in dctc[ctc]._dicsfw.keys(): icsfw = dctc[ctc]._dicsfw["*"]
else: icsfw = None
# path variables
pathvars.set_ics(ics, icsbw, icsfw) # before setup3!!
pathvars.apply_specific(itc)
pathvars.setup1()
pathvars.setup2()
pathvars.setup3()
# Set Eref (from reaction)
pathvars.set_eref_from_reaction(target, dchem, dof)
# Quantum reaction coordinate qrc
pathvars.prepare_qrc(dchem, dctc, dimasses)
# frequency scaling factor
pathvars._freqscal = float(dctc[ctc]._fscal)
# if dlevel --> no convergence and dlevel data
if dlevel:
exception = Exc.NoDLEVELdata(Exception)
pathvars._scterr = None
keydhl = "%s.%s.path" % (ctc, itc)
if keydhl not in dhighlvl.keys():
# maybe only TS
keydhl = "%s.%s" % (dctc[ctc]._root, itc)
if keydhl in dhighlvl.keys():
dictE = {0.0: dhighlvl[keydhl]}
else:
global WARNINGS
WARNINGS.append("No high-level data for %s" % target)
raise exception
else:
dictE = dhighlvl[keydhl]
pathvars._dlevel = dictE
# LOGGER
pof = PN.get_pof(dlevel, "path", target)
sys.stdout = Logger(pof, "w", True)
sys.stdout.writeinfile(PS.init_txt())
#string
fncs.print_string(PS.smep_title(target, pathvars, pof), 2)
# Was previously converged???
ffloat = "%.3f"
drstconv = RW.read_rstconv()
if target in drstconv.keys() and not dlevel and os.path.exists(rstfile):
lowtemp, useics, scterr, converged = drstconv[target]
b0 = (converged == "yes")
b1 = (pathvars._useics == useics)
b2 = (ffloat % pathvars._scterr == ffloat % scterr)
b3 = (ffloat % min(ltemp) == ffloat % lowtemp)
if b0 and b1 and b2 and b3:
pathvars._scterr = None
fncs.print_string("THIS PATH IS STORED AS CONVERGED!\n", 4)
tpath, tcommon, drst = ff.read_rst(rstfile)
lbw, lfw, sbw, sfw, V0bw, V0fw = sd.rstlimits(drst)
pathvars._sbw = sbw
pathvars._sfw = sfw
del drst
#----------------#
# calculate path #
#----------------#
# 1. Only MEP
if not pathvars._beyondmep:
common, drst, pathvars = calc_mep(target, gtsTS, pathvars, tsoftw, TMP)
dcoefs = {}
del drst
# raise error
raise Exc.OnlyMEP(Exception)
# 2. MEP expanded till SCT convergence
elif pathvars.sct_convergence():
dcoefs, converged = get_path_sctconv(target, gtsTS, pathvars, tsoftw,
ltemp, TMP, symmetry, plotfile)
# save convergence in file!
drstconv = RW.read_rstconv()
if converged:
drstconv[target] = (min(ltemp), pathvars._useics, pathvars._scterr,
"yes")
else:
drstconv[target] = (min(ltemp), pathvars._useics, pathvars._scterr,
"no")
RW.write_rstconv(drstconv)
# 3. Coefs with the current MEP extension
else:
tcommon, drst, pathvars = calc_mep(target, gtsTS, pathvars, tsoftw,
TMP)
dcoefs, pathvars, palpha, pomega = calc_coefs(target, tcommon, drst,
pathvars, ltemp,
symmetry, plotfile)
del drst
# print summary with the coefficients
fncs.print_string(PS.spath_allcoefs(ltemp, dcoefs), 3)
# return data
return dcoefs, pathvars
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