def obtain_cvt(dMols,
points,
VadiSpl,
temps,
pathvars,
si=-float("inf"),
sj=+float("inf"),
dcfs={}):
print("")
fncs.print_string("Calculating CVT variational coefficient...", 4)
print("")
useics = pathvars._useics
if len(temps) == 0: raise Exc.NoTemps(Exception)
# Only points between si and sj
points = [pp for pp in points if si <= dMols[pp][0] <= sj]
lcvt_s, lcvt_gamma, gibbs_matrix, gibbsTS, lnew = cv.get_cvt(
dMols, points, VadiSpl, temps, useics)
# print gibbs
svals = [dMols[point][0] for point in points]
fncs.print_string(
PS.scvt_gibbs(svals, temps, gibbs_matrix.copy(), pathvars, gibbsTS), 8)
# print cvt coefs
fncs.print_string(PS.scvt_coefs(lcvt_s, lcvt_gamma, temps), 8)
# save data
dcfs["cvt"] = lcvt_gamma
return dcfs, lcvt_s, gibbs_matrix, lnew
def obtain_sct(dMols, points, VadiSpl, temps, dv1, pathvars, dcfs={}):
print("")
fncs.print_string("Calculating SCT transmission coefficient...", 4)
print("")
# data from pathvars
useics = pathvars._useics
v1mode = pathvars._v1mode
# E0 value
if pathvars._e0 is None:
V1bw = pathvars._eref + VadiSpl.get_alpha()[1]
V1fw = pathvars._eref + VadiSpl.get_omega()[1]
if pathvars._V1R is not None: E0bw = pathvars._V1R
else: E0bw = V1bw
if pathvars._V1P is not None: E0fw = pathvars._V1P
else: E0fw = V1fw
E0 = max(E0bw, E0fw) - pathvars._eref
else:
E0 = pathvars._e0 - pathvars._eref
# some checks
if len(temps) == 0: raise Exc.NoTemps(Exception)
if useics in ["yes", True]: case = "ic"
else: case = "cc"
# MEP LIMITS
sbw, sfw = VadiSpl.get_alpha()[0], VadiSpl.get_omega()[0]
# Part I - Get E0 and VAG
E0 = sct.get_sct_part1(points, VadiSpl, E0)
sAG, VAG = VadiSpl.get_max()
fncs.print_string(PS.ssct_init(E0, VadiSpl, pathvars, v1mode), 8)
# Part II - Calculate tbar, bmfs and mueff
tuple_part2 = (dMols, points, dv1, case, pathvars._muintrpl)
svals, lkappa, ltbar, ldtbar, mu, lmueff, toignore = sct.get_sct_part2(
*tuple_part2)
fncs.print_string(
PS.ssct_mueff(svals, VadiSpl, lkappa, ltbar, lmueff, mu, toignore), 8)
#----------#
# E0 < VAG #
#----------#
if E0 < VAG:
# Part III - Quantum reaction coordinate
fncs.print_string(PS.ssct_E0VAG(E0, VAG), 8)
if pathvars._qrc is not None:
afreq = pathvars._qrcafreq
lEquant = [E0 + E_i for E_i in pathvars._qrclE]
fncs.print_string(PS.ssct_qrc(pathvars), 8)
if pathvars._qrccase != 0: return dcfs, None, E0, VAG
qrc_ZCT = sct.get_sct_part3(svals, mu, VadiSpl, afreq, lEquant, E0,
VAG, temps)
qrc_SCT = sct.get_sct_part3(svals, lmueff, VadiSpl, afreq, lEquant,
E0, VAG, temps)
fncs.print_string(
PS.ssct_probs(qrc_SCT[1], qrc_ZCT[2], qrc_SCT[2], qrc_SCT[3],
sbw, sfw), 12)
kappaI1_zct = qrc_ZCT[0]
kappaI1_sct = qrc_SCT[0]
qrc_Elim = lEquant[1]
else:
kappaI1_zct = None
kappaI1_sct = None
qrc_Elim = None
# apply QRC always?
if not pathvars._qrcauto: qrc_Elim = None
# Part IV - calculate thetas and probs
fncs.print_string(
"Transmission probabilities for Kappa^SAG calculation:", 8)
print("")
outZCT = sct.get_sct_part4(svals, mu, VadiSpl, E0)
outSCT = sct.get_sct_part4(svals, lmueff, VadiSpl, E0)
weights_ZCT, lE_ZCT, probs_ZCT, rpoints_ZCT, diffs_ZCT, (
pZCT0, rpZCT0) = outZCT
weights_SCT, lE_SCT, probs_SCT, rpoints_SCT, diffs_SCT, (
pSCT0, rpSCT0) = outSCT
# include also prob at E=E0 (pZCT0 and pSCT0)
fncs.print_string(PS.ssct_probs( [E0]+lE_SCT ,\
[pZCT0 ]+probs_ZCT,\
[pSCT0 ]+probs_SCT,\
[rpSCT0]+rpoints_SCT,sbw,sfw),8)
fncs.print_string(PS.ssct_diffs(lE_SCT, diffs_SCT), 8)
# Part V - calculate coefficients
ZCTdata = sct.get_sct_part5(lE_ZCT, probs_ZCT, weights_ZCT, E0, VAG,
temps, kappaI1_zct, qrc_Elim)
SCTdata = sct.get_sct_part5(lE_SCT, probs_SCT, weights_SCT, E0, VAG,
temps, kappaI1_sct, qrc_Elim)
ZCT, lIi_ZCT, RTE_ZCT, INTG_ZCT, bqrcZCT = ZCTdata
SCT, lIi_SCT, RTE_SCT, INTG_SCT, bqrcSCT = SCTdata
fncs.print_string(
PS.ssct_kappa(temps,
ZCT,
lIi_ZCT,
RTE_ZCT,
E0,
bqrcZCT,
case="zct"), 8)
fncs.print_string(
PS.ssct_kappa(temps,
SCT,
lIi_SCT,
RTE_SCT,
E0,
bqrcSCT,
case="sct"), 8)
#----------#
# E0 > VAG #
#----------#
else:
ZCT = [1.0 for T in temps]
SCT = [1.0 for T in temps]
INTG_ZCT = None
INTG_SCT = None
RTE_ZCT = None
RTE_SCT = None
fncs.print_string(PS.ssct_E0_above_VAG(E0, VAG), 8)
fncs.print_string(PS.ssct_onlykappa(temps, ZCT, SCT), 8)
# data for the plot
forplot = (svals, lmueff, temps, INTG_ZCT, INTG_SCT, RTE_ZCT, RTE_SCT, E0,
VAG)
# save data
dcfs["zct"] = ZCT
dcfs["sct"] = SCT
return dcfs, forplot, E0, VAG
def obtain_sct(dMols, points, VadiSpl, temps, dv1, pathvars, dcfs={}):
print
print " Calculating SCT transmission coefficient..."
print
# data from pathvars
useics = pathvars._useics
v1mode = pathvars._v1mode
# E0 value
if pathvars._e0 is None:
V1bw = pathvars._eref + VadiSpl.get_alpha()[1]
V1fw = pathvars._eref + VadiSpl.get_omega()[1]
if pathvars._V1R is not None: E0bw = pathvars._V1R
else: E0bw = V1bw
if pathvars._V1P is not None: E0fw = pathvars._V1P
else: E0fw = V1fw
E0 = max(E0bw, E0fw) - pathvars._eref
else:
E0 = pathvars._e0 - pathvars._eref
# some checks
if len(temps) == 0: raise Exc.NoTemps(Exception)
if useics in ["yes", True]: case = "ic"
else: case = "cc"
# Part I - Get E0 and VAG
E0 = sct.get_sct_part1(points, VadiSpl, E0)
sAG, VAG = VadiSpl.get_max()
fncs.print_string(PS.ssct_init(E0, VadiSpl, pathvars, v1mode), 8)
# Part II - Calculate tbar, bmfs and mueff
tuple_part2 = (dMols, points, dv1, case, pathvars._muintrpl)
svals, lkappa, ltbar, ldtbar, mu, lmueff, toignore = sct.get_sct_part2(
*tuple_part2)
fncs.print_string(
PS.ssct_mueff(svals, VadiSpl, lkappa, ltbar, lmueff, toignore), 8)
# Part III - Quantum reaction coordinate
fncs.print_string(PS.ssct_E0VAG(E0, VAG), 8)
if pathvars._qrc is not None:
afreq = pathvars._qrcafreq
lEquant = pathvars._qrclE
print " Quantum reaction coordinate keyword (qrc) activated!"
print
mode = pathvars._qrc[0] + 1
numst = pathvars._qrc[1]
print " * reactant mode : %i (%.2f cm^-1)" % (
mode, fncs.afreq2cm(afreq))
print " * number of states : %i" % numst
print " * contribution to kappa_SCT from E0 to VAG will"
print " be obtained from discrete set of energies"
print
print " * calculating transmission probabilities..."
print
qrc_ZCT = sct.get_sct_part3(svals, mu, VadiSpl, afreq, lEquant, E0,
VAG, temps)
qrc_SCT = sct.get_sct_part3(svals, lmueff, VadiSpl, afreq, lEquant, E0,
VAG, temps)
nE = len(qrc_SCT[1])
fncs.print_string(
PS.ssct_probs(qrc_SCT[1], qrc_ZCT[2], qrc_SCT[2], qrc_SCT[3]), 12)
print " * number of included states : %i" % nE
print
kappaI1_zct = qrc_ZCT[0]
kappaI1_sct = qrc_SCT[0]
else:
kappaI1_zct = None
kappaI1_sct = None
# Part IV - calculate thetas and probs
print " Transmission probabilities for kappa_SCT calculation:"
print
weights_ZCT, lE_ZCT, probs_ZCT, rpoints_ZCT, diffs_ZCT = sct.get_sct_part4(
svals, mu, VadiSpl, E0)
weights_SCT, lE_SCT, probs_SCT, rpoints_SCT, diffs_SCT = sct.get_sct_part4(
svals, lmueff, VadiSpl, E0)
fncs.print_string(PS.ssct_probs(lE_SCT, probs_ZCT, probs_SCT, rpoints_SCT),
8)
fncs.print_string(PS.ssct_diffs(lE_SCT, diffs_SCT), 8)
# Part V - calculate coefficients
ZCTdata = sct.get_sct_part5(lE_ZCT, probs_ZCT, weights_ZCT, E0, VAG, temps,
kappaI1_zct)
SCTdata = sct.get_sct_part5(lE_SCT, probs_SCT, weights_SCT, E0, VAG, temps,
kappaI1_sct)
ZCT, lIi_ZCT, RTE_ZCT, INTG_ZCT = ZCTdata
SCT, lIi_SCT, RTE_SCT, INTG_SCT = SCTdata
fncs.print_string(
PS.ssct_kappa(temps, ZCT, lIi_ZCT, RTE_ZCT, E0, case="zct"), 8)
fncs.print_string(
PS.ssct_kappa(temps, SCT, lIi_SCT, RTE_SCT, E0, case="sct"), 8)
#fncs.print_string(PS.ssct_kappa(temps,ZCT,SCT,RTE_ZCT,RTE_SCT,E0),8)
# save data
dcfs["zct"] = ZCT
dcfs["sct"] = SCT
# data for the plot
forplot = (svals, lmueff, temps, INTG_ZCT, INTG_SCT, RTE_ZCT, RTE_SCT, E0,
VAG)
return dcfs, forplot
