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 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)
# temporal folder
TMP = PN.TMPi % (target)
# if exists,remove content
# (to avoid reading old files from different levels of calculation)
if os.path.exists(TMP): 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
dics = dctc[ctc]._dics
if itc in dics.keys(): ics = dics[itc]
elif "*" in dics.keys(): ics = dics["*"]
else: ics = None
# path variables
pathvars.set_ics(ics) # 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._sctmns = 0
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)
#string
fncs.print_string(PS.smep_title(target, pathvars, pof), 2)
#----------------#
# calculate path #
#----------------#
# 1. MEP
if not pathvars._beyondmep:
common, drst, pathvars = calc_mep(target,
gtsTS,
pathvars,
tsoftw,
TMP,
decrease=False)
dcoefs = {}
del drst
# raise error
raise Exc.OnlyMEP(Exception)
# 2. MEP + coefs
else:
# 2.1 MEP expanded till SCT convergence
if pathvars.sct_convergence():
dcoefs = get_path_sctconv(target, gtsTS, pathvars, tsoftw, ltemp,
TMP, plotfile)
# 2.2 Coefs with the current MEP extension
else:
tcommon, drst, pathvars = calc_mep(target,
gtsTS,
pathvars,
tsoftw,
TMP,
decrease=False)
dcoefs, pathvars = calc_coefs(target, tcommon, drst, pathvars,
ltemp, plotfile)
del drst
# print summary with the coefficients
fncs.print_string(PS.spath_allcoefs(ltemp, dcoefs), 3)
# return data
return dcoefs, pathvars