def main(idata,status,case):
stat2check = [2,5]
mustexist = []
tocreate = []
#-------------------------------------------------------#
# 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
#-------------------------------------------------------#
# read dofs
dall, ltemp = RW.read_alldata(dof)
# get saved reactions
print_string(PS.skies_summary(dchem,dall),5)
# Ask user which reactions
count = 0
while True:
# Ask user for reactions
bool_end,bool_cont,reaction1,reaction2 = ask_for_reactions(dchem)
print("")
print("")
if bool_end : break
if bool_cont: continue
kies_from_pair_of_reactions(reaction1,reaction2,ltemp,dchem,dctc,dall)
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(" " * NINIT + "Analytic expressions:")
print("")
print(" " * NINIT + "(1) k = A exp(-B/T) ")
print(" " * NINIT + "(2) k = A*T^n*exp(-B/T) ")
print(" " * NINIT + "(3) k = A*(T/Tr)^n*exp(-B/T) ")
print(" " * NINIT + "(4) k = A*(T/Tr)^n*exp(-B*(T+T0)/(T^2+T0^2))")
print(" " * NINIT + "(5) k = A*((T+T0)/Tr)^n*exp(-B*(T+T0)/(T^2+T0^2))")
print("")
LINES, plotdata = {}, {}
ml = max(len(rcname) for rcname in targets) + 3
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