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["gibbs"].keys():
gibbs = dall["gibbs"][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()
# existency of folders
fstatus = ffchecking(mustexist, tocreate)
if fstatus == -1: exit()
# expand case
(dof, hlf, plotfile), dlevel, software = case
#-------------------------------------------------------#
# no specific target selected
if "*" in targets or len(targets) == 0: targets = dchem.keys()
# clean targets
targets = sorted([target for target in targets if target in dchem.keys()])
# read dof
dall = RW.read_alldata(dof, ltemp)[0]
#--------------------------------#
# Calculations for each reaction #
#--------------------------------#
print " Analytic expressions:"
print
print " (1) k = A exp(-B/T) "
print " (2) k = A*T^n*exp(-B/T) "
print " (3) k = A*(T/Tr)^n*exp(-B/T) "
print " (4) k = A*(T/Tr)^n*exp(-B*(T+T0)/(T^2+T0^2))"
print
plotdata = {}
LINES = {}
for rcname in targets:
Rs, TS, Ps = dchem[rcname]
def main(idata, status, case):
stat2check = [2, 5, 6]
mustexist = []
tocreate = [PN.DIR3, PN.DIR6]
#-------------------------------------------------------#
# Read Pilgrim input files, check file/folder status #
# and expand tuple 'case' #
#-------------------------------------------------------#
# expand data
(dctc, dimasses), ltemp, dpath, (dtesLL,
dtesHL), dchem, tkmc, ddlevel = idata
# status ok?
fstatus = status_check(status, stat2check)
if fstatus == -1: exit()
# existency of folders
fstatus = ffchecking(mustexist, tocreate)
if fstatus == -1: exit()
# expand case
(dof, hlf, plotfile), dlevel, software = case
#-------------------------------------------------------#
#---------------------------------#
# files with data and output file #
#---------------------------------#
pof = PN.get_pof(dlevel, "kmc")
print " Pilgrim output file: %s" % pof
print
sys.stdout = Logger(pof, "w", True)
# expand KMC tuple
ipops, rcs, psteps, volume, timeunits, excess = tkmc
valid_tu = "fs,ps,mcs,ms,s,min,hr".split()
if timeunits not in valid_tu: valid_tu = "ps"
# reactivo limitante
try:
POP0 = min(
[ipop for species, ipop in sorted(ipops.items()) if ipop != 0.0])
except:
POP0 = 0
print_string(
PS.skmc_init(ipops, POP0, excess, rcs, psteps, volume, timeunits, dof),
5)
# continue?
if POP0 == 0:
print " All initial populations are zero..."
print
return
if rcs == {}:
print " No reactions considered in %s" % PN.IFILE6
print
return
# read dof
dall = RW.read_alldata(dof, ltemp)[0]
# perform KMC for each temperature
data = []
fratios = {}
ftimes = []
for idx, temp in enumerate(ltemp):
# title
title = " T = %.3f Kelvin " % temp
division = "-" * len(title)
string = " " + division + "\n"
string += " " + title + "\n"
string += " " + division + "\n"
print string
# get rate constants
processes = get_ratecons(rcs, dchem, dall, idx, temp)
# print initial information before simulation
print_string(PS.skmc_processes(temp, processes), 9)
# perform kmc simulation
xvalues, yvalues = kmc(ipops, processes, excess, volume, psteps)
fratios["%7.2f" % temp] = {}
for species in yvalues.keys():
fratios["%7.2f" % temp][species] = yvalues[species][-1] / POP0
# print data from simulation
print_string(PS.skmc_results(xvalues, yvalues, timeunits), 9)
# save data needed for txt and pdf files
data += [("%.2f" % temp, xvalues, yvalues)]
ftimes.append(xvalues[-1])
# print final ratios
species = sorted(yvalues.keys())
print_string(PS.skmc_finaltimes(ltemp, ftimes, timeunits), 5)
print_string(PS.skmc_finalratio(ltemp, species, fratios), 5)
# save data for plotting
if plotfile is not None:
plotdata = {}
plotdata.update(
manage_data_for_plot_kmc(data, fratios, volume, timeunits))
write_plotfile(plotfile, plotdata)