def main(idata, status, mode=2, target="*"):
stat2check = [1]
mustexist = []
tocreate = []
#-------------------------------------------------------#
# Read Pilgrim input files and check file/folder status #
#-------------------------------------------------------#
# expand data
(dctc, dimasses), ltemp, dpath, dtes, 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()
#-------------------------------------------------------#
#----------------#
# deal with mode #
#----------------#
msg = {}
msg["-1"] = "ics will be removed"
msg["-2"] = "ics will be checked"
msg["1"] = "ics will be generated according to connectivity"
msg[ "2"] = "ics will be generated according to connectivity\n"+\
"and reduced"
msg[ "3"] = "ics will be generated according to connectivity\n"+\
"and reduced to a non-redundant set"
print " Selected mode is '%s'" % mode
if mode not in ["-2", "-1", "1", "2", "3"]:
print " - Unknown mode!"
print
return
for idx, line in enumerate(msg[mode].split("\n")):
if idx == 0: print " - " + line
else: print " " + line
#===============================================================#
def main(idata, status, case, targets="*"):
stat2check = [1, 2, 5]
mustexist = [PN.DIR1]
tocreate = [PN.DIR2, 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
#-------------------------------------------------------#
# 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
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)
def main(idata,status):
stat2check = []
mustexist = []
tocreate = []
#-------------------------------------------------------#
# Read Pilgrim input files and check file/folder status #
#-------------------------------------------------------#
# expand data
(dctc,dimasses), ltemp, dpath, (dtesLL,dtesHL), dchem, tkmc, ddlevel = idata
# status ok?
fstatus = status_check(status,[])
if fstatus == -1: exit()
# special warning
if status[0] == -1:
print " WARNING! '%s' file not found."%PN.IFILE1
print " In order to generate it, run"
print " pilgrim --gather"
# existency of folders
fstatus = ffchecking(mustexist=[],tocreate=[])
if fstatus == -1: exit()
#-------------------------------------------------------#
# print menu
print_string(MENU,1)
# setup dpath
for ctc in dpath.keys():
dpath[ctc].setup1()
dpath[ctc].setup2()
# interactive menu
dbool = {}
while True:
set_completer(1)
line = raw_input(ILINE1).split()
if len(line) == 0: continue
command = line[0].lower()
try : var = line[1].lower()
except: var = None
try : val = line[2:]
except: val = None
# update list of transition states
lts = [ctc for ctc in dctc.keys() if dctc[ctc]._type == 1]
# user ask for help
if command == "help":
if var is None : print_string(MENU,3)
elif var == "temp" : print_string(HELP_temp,6)
elif var == "path" : print_string(HELP_path,6)
elif var == "chem" : print_string(HELP_chem,6)
elif var == "kmc" : print_string(HELP_kmc ,6)
elif var == "dlevel" : print_string(HELP_dlevel,6)
elif var == "isomass": print_string(HELP_isomass,6)
elif var == "struc" : print_string(HELP_struc,6)
# user ask for list
elif command == "ls":
if var == "struc" : ls_struc(dctc)
elif var == "temp" : ls_temp(ltemp)
elif var == "path" : ls_path(dpath)
elif var == "chem" : ls_chem(dchem)
elif var == "kmc" : ls_kmc(tkmc)
elif var == "dlevel" : ls_dlevel(ddlevel)
elif var == "isomass": ls_isomass(dimasses)
else : continue
# add
elif command == "add":
if var == "temp" : ltemp = add_temp(val,ltemp)
elif var == "path" : dpath,dtesLL = add_path(val,dpath,dctc,dtesLL,lts)
elif var == "chem" : dchem = add_chem(val,dchem)
elif var == "kmc" : tkmc = add_kmc(val,tkmc,dchem)
elif var == "dlevel" : ddlevel,dtesHL = add_dlevel(val,ddlevel,dctc,dtesHL)
elif var == "isomass": dimasses = add_isomass(val,dimasses)
dbool[var] = True
# mod
elif command == "mod":
if var == "path" : dpath,dtesLL = add_path(val,dpath,dctc,dtesLL,lts,mod=True)
elif var == "struc" : dctc = mod_struc(val,dctc,dimasses)
dbool[var] = True
# rm
elif command == "rm":
if var == "temp" : ltemp = rm_temp(val,ltemp)
elif var == "path" : dpath = rm_path(val,dpath)
elif var == "chem" : dchem = rm_chem(val,dchem)
elif var == "dlevel" : ddlevel = rm_dlevel(val,ddlevel)
elif var == "struc" : dctc = rm_struc(val,dctc)
elif var == "isomass": dimasses = rm_isomass(val,dimasses)
dbool[var] = True
# user ask for finishing
elif command in END:
if dbool != {}:
print
print " (Re)Writing files:"
if dbool.get("isomass",False) or dbool.get("struc",False):
print " %s"%PN.IFILE1
RW.write_ctc(dctc,dimasses)
if dbool.get("temp",False):
print " %s"%PN.IFILE2
RW.write_temp(ltemp)
if dbool.get("path",False):
print " %s"%PN.IFILE3
RW.write_path(dpath)
if dbool.get("path",False) or dbool.get("dlevel",False):
print " %s"%PN.IFILE4
RW.write_tes(dtesLL,dtesHL)
if dbool.get("chem",False):
print " %s"%PN.IFILE5
RW.write_chem(dchem)
if dbool.get("kmc",False):
print " %s"%PN.IFILE6
RW.write_kmc(tkmc)
if dbool.get("dlevel",False):
print " %s"%PN.IFILE7
RW.write_dlevel(ddlevel)
print
break
# user ask for nothing
else: continue