elif option == "fit":
fit.main(idata, status, case, dargs["fit"])
elif option == "plot":
plot.main(case, dargs["plot"])
print("")
print(" ===========================================================")
break
# User asked for nothing. Print help!
if not IN_OPTS:
print_string(HELP_main, 2)
return
# Print elapsed time
t2 = time.time()
timeline = "| Total Elapsed Time: %5.1f %5s |" % time2human(
t2 - t1, "secs")
print(" " * 25 + "-" * len(timeline))
print(" " * 25 + timeline)
print(" " * 25 + "-" * len(timeline))
print("")
#==========================================================#
#==========================================================#
if __name__ == '__main__':
try:
main()
except Exception as exception:
deal_with_exception(exception)
#==========================================================#
def print_elapsed(delta_time, nibs):
t, units = time2human(delta_time)
sprint("--------------------------------", NIBS)
sprint("Elapsed time: %.2f %s" % (t, units), nibs)
sprint("--------------------------------", NIBS)
sprint()
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(target,data,fratios,volume,timeunits))
write_plotfile(plotfile,plotdata)
#kmc_savedata(kmcof,data)
# print end of file
t2 = time.time()
etime = time2human(t2-t1,"secs")
sys.stdout.writeinfile(PS.end_txt(*etime))
# End logger
sys.stdout = Logger(None)
#---------------------------------------------------------------#
def main():
date = time.strftime("%Y/%m/%d %H:%M")
t1 = time.time()
# Read user arguments
user_args = sys.argv[1:]
if len(user_args) == 0:
print PROGNAME
print AUTHORINFO
print_string(HELP_main,2)
return
dargs = classify_args(user_args)
# User asked for version
if "version" in dargs.keys():
print "Current version: %s"%VERSION
return
# User asked for help
elif "help" in dargs.keys():
print PROGNAME
print AUTHORINFO
if len(dargs["help"]) == 0 : print_string(HELP_main ,2)
if "gather" in dargs["help"]: print_string(HELP_gather,1)
if "input" in dargs["help"]: print_string(HELP_input ,1)
if "ics" in dargs["help"]: print_string(HELP_ics ,1)
if "pfn" in dargs["help"]: print_string(HELP_pfn ,1)
if "path" in dargs["help"]: print_string(HELP_path ,1)
if "hlcalc" in dargs["help"]: print_string(HELP_hlcalc,1)
if "rcons" in dargs["help"]: print_string(HELP_rcons ,1)
if "fit" in dargs["help"]: print_string(HELP_fit ,1)
if "kmc" in dargs["help"]: print_string(HELP_kmc ,1)
if "plot" in dargs["help"]: print_string(HELP_plot ,1)
return
# Print logo and current date
print PROGNAME
print AUTHORINFO
print
print " -----------------------------------------------------------"
print " Current date: %s"%date
print " -----------------------------------------------------------"
print
# check some arguments
dargs = check_ics(dargs)
software = check_sft(dargs)
dlevel = check_dlevel(dargs)
# --software used properly
if software is None:
print " Software option has to be followed by an argument!"
print
exit()
# Act according user argument
IN_OPTS = False
for option in "ls,gather,input,ics,pfn,path,hlcalc,rcons,kmc,fit,plot".split(","):
if option not in dargs.keys(): continue
IN_OPTS = True
# read input files and print table
idata, status, string = get_input_data()
print_string(string,nbs=3)
# data files according to case
datafiles,string = dlevel_to_files(dlevel)
if option in "pfn,path,hlcalc,rcons,kmc,fit,plot".split(","):
print_string(string,nbs=3)
case = (datafiles,dlevel,software)
# execute pilgrim with option
print " ==========================================================="
print " || EXECUTING PILGRIM WITH --%-6s ||"%option
print " ==========================================================="
print
if option == "ls" : gather.ls_struc(idata[0][0])
elif option == "gather": gather.main(idata,status )
elif option == "input" : inpmenu.main(idata,status )
elif option == "ics" : ics.main(idata,status,*dargs["ics" ] )
elif option == "pfn" : pfn.main(idata,status,case, dargs["pfn" ])
elif option == "path" : path.main(idata,status,case, dargs["path" ])
elif option == "hlcalc": hlcalc.main(idata,status,case, dargs["hlcalc"])
elif option == "rcons" : rcons.main(idata,status,case, dargs["rcons" ])
elif option == "kmc" : kmc.main(idata,status,case )
elif option == "fit" : fit.main(idata,status,case, dargs["fit" ])
elif option == "plot" : plot.main( case, dargs["plot" ])
print
print " ===========================================================\n"
break
# User asked for nothing. Print help!
if not IN_OPTS: print_string(HELP_main,2); return
# Print elapsed time
t2 = time.time()
timeline = "Total Elapsed Time: %5.1f %5s |"%time2human(t2-t1,"secs")
print " "+timeline
print " "+"-"*len(timeline)
pathvars = copy.deepcopy(dpath[ctc])
# isotopic modification?
masses = get_masses(target, dctc, dimasses)
pathvars.set_masses(masses)
# calculate path + coefficients
idata = (target, dlevel, software, ltemp, dctc, pathvars, dtesLL,
dchem, dhighlvl, dimasses)
try:
dcoefs, pathvars = deal_with_path(*idata)
except Exception as exception:
deal_with_exception(exception)
sys.stdout = Logger(None)
continue
# print end of file
t2 = time.time()
etime = fncs.time2human(t2 - t1, "secs")
sys.stdout.writeinfile(PS.end_txt(*etime))
# update file (read, check ltemp, update, write)
sys.stdout = Logger(None)
fncs.print_string("Updating data file: %s" % dof, 3)
dall = RW.read_alldata(dof, ltemp)[0]
for coef in dcoefs.keys():
dall[coef][target] = dcoefs[coef]
RW.write_alldata(dof, ltemp, dall)
print("")
# collect garbage
gc.collect()
# print WARNINGS
if len(WARNINGS) != 0:
fncs.print_string("WARNINGS:", 3)
def main():
cdate = time.strftime("%Y-%m-%d")
ctime = time.strftime("%H:%M:%S")
t1 = time.time()
# Read user arguments
user_args = sys.argv[1:]
if len(user_args) == 0:
print(PROGNAME)
print(PROGHEAD)
print(AUTHORINFO)
print_string(HELP_main,2)
return
dargs = classify_args(user_args)
# User asked for version
if "version" in dargs.keys() or "-v" in user_args:
print("Current version: %s"%VERSION)
return
# User asked for help
elif "help" in dargs.keys():
print(PROGNAME)
print(PROGHEAD)
print(AUTHORINFO)
if len(dargs["help"]) == 0 : print_string(HELP_main ,2)
if "gather" in dargs["help"]: print_string(HELP_gather ,1)
if "input" in dargs["help"]: print_string(HELP_input ,1)
if "ics" in dargs["help"]: print_string(HELP_ics ,1)
if "pfn" in dargs["help"]: print_string(HELP_pfn ,1)
if "path" in dargs["help"]: print_string(HELP_path ,1)
if "hlcalc" in dargs["help"]: print_string(HELP_hlcalc ,1)
if "rcons" in dargs["help"]: print_string(HELP_rcons ,1)
if "fit" in dargs["help"]: print_string(HELP_fit ,1)
if "kmc" in dargs["help"]: print_string(HELP_kmc ,1)
if "plot" in dargs["help"]: print_string(HELP_plot ,1)
if "kies" in dargs["help"]: print_string(HELP_kies ,1)
if "summary" in dargs["help"]: print_string(HELP_summary,1)
return
# Print logo and current date
string_head = PROGNAME+"\n"+PROGHEAD+"\n"+AUTHORINFO+"\n"+"\n"
string_head += " -----------------------------------------------------------\n"
string_head += exe_info()
string_head += " -----------------------------------------------------------\n\n"
print(string_head)
# check some arguments
dargs = check_ics(dargs)
software = check_sft(dargs)
dlevel = check_dlevel(dargs)
boolms = check_boolms(dargs)
# --software used properly
if software is None:
print(" Software option has to be followed by an argument!")
print("")
exit()
# Act according user argument
IN_OPTS = False
for option in OPTIONS.split(","):
if option not in dargs.keys(): continue
IN_OPTS = True
# read input files and print table
idata, status, string = get_input_data()
print_string(string,nbs=3)
# data files according to case
datafiles,string = dlevel_to_files(dlevel)
if option in OPTIONS1.split(","): print_string(string,nbs=3)
case = (datafiles,dlevel,software)
# execute pilgrim with option
print(" ===========================================================")
print(" || EXECUTING PILGRIM WITH --%-6s ||"%option)
print(" ===========================================================")
print("")
if option == "ls" : gather.ls_struc(idata[0][0])
elif option == "gather" : gather.main(idata,status )
elif option == "input" : inpmenu.main(idata,status )
elif option == "ics" : ics.main(idata,status,*dargs["ics" ] )
elif option == "pfn" : pfn.main(idata,status,case,dargs["pfn" ])
elif option == "path" : path.main(idata,status,case,dargs["path" ],boolms)
elif option == "hlcalc" : hlcalc.main(idata,status,case,dargs["hlcalc"])
elif option == "rcons" : rcons.main(idata,status,case,dargs["rcons" ])
elif option == "kmc" : kmc.main(idata,status,case,dargs["kmc" ])
elif option == "kies" : kies.main(idata,status,case )
elif option == "fit" : fit.main(idata,status,case,dargs["fit" ])
elif option == "plot" : plot.main( case,dargs["plot" ])
elif option == "summary": summary.main(idata,status,case,dargs["summary"])
print("")
print(" ===========================================================")
break
# User asked for nothing. Print help!
if not IN_OPTS: print_string(HELP_main,2); return
# Print elapsed time
t2 = time.time()
timeline = "| Total Elapsed Time: %5.1f %5s |"%time2human(t2-t1,"secs")
print(" "*25+"-"*len(timeline))
print(" "*25+ timeline)
print(" "*25+"-"*len(timeline))
print("")