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)
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["-2"] = "ics will be removed"
msg["-1"] = "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)
print("")
#------------------#
# deal with target #
#------------------#
print(" Selected target is '%s'"%target)
systems = []
if target == "*": targets = [key for key in dctc.keys() if dctc[key]._type==1]
else : targets = [target]
for target in sorted(targets):
systems_i = []
if "." in target: ctc,itc = target.split(".")
else : ctc,itc = target, None
if ctc not in dctc.keys():
print(" - %s is NOT defined in '%s'\n"%(ctc,PN.IFILE1))
return
# itcs in dctc
dctc_itcs = [itc_i for itc_i,weight_i in dctc[ctc]._itcs]
# the itcs
if itc is None: itcs = dctc_itcs
elif itc in dctc_itcs: itcs = [itc]
else:
print(" - %s is NOT defined in '%s'\n"%(itc,PN.IFILE1))
return
# specific itcs
if "." in target:
systems_i.append( ([itc],itc) )
else:
dics = dctc[ctc]._dics
itcsB = [itc for itc in dics.keys() if itc != "*"]
itcsA = [itc for itc in itcs if itc not in itcsB]
# add data
if itcsA != []: systems_i.append( (itcsA,"*") )
for itc in sorted(itcsB): systems_i.append( ([itc],itc) )
# add data to total
systems.append( (ctc,systems_i) )
print("")
# print name of file to modify
print(" File to be updated: '%s'"%PN.IFILE1)
print("")
#--------------#
# Generate ics #
#--------------#
NEPL = 10
NOTVALID = [] # updated via global variable
for ctc,systems_i in systems:
# Print
print(" -------------------")
print(" System: %s"%ctc)
print(" -------------------")
print("")
for itcs,key in systems_i:
# print conformers
string = ""
for idx in range(0,len(itcs),NEPL):
str_i = ",".join(itcs[idx:idx+NEPL])
if idx == 0: string += " conformer(s): "+str_i
else : string += ",\n"+" "+str_i
print(string)
print("")
# gts files
gtsfiles = [dctc[ctc].gtsfile(itc) for itc in itcs]
# set of ics
ics = dctc[ctc]._dics.get(key,[])
# negative modes
if mode == "-2":
nics = count_ics(ics)
print(" * %i ics will be removed"%nics)
print("")
dctc[ctc]._dics[key] = []
continue
if mode == "-1":
valid,nvdof,nics = check_ics(ics,gtsfiles)
print(" * "+string_nics(nics,nvdof,valid))
print("")
# backward ics
ics_bw = dctc[ctc]._dicsbw.get(key,None)
if ics_bw is not None:
print(" -- checking backward ics --")
valid_bw,nvdof_bw,nics_bw = check_ics(ics_bw,gtsfiles)
print(" * "+string_nics(nics_bw,nvdof_bw,valid_bw))
print("")
# forward ics
ics_fw = dctc[ctc]._dicsfw.get(key,None)
if ics_fw is not None:
print(" -- checking forward ics --")
valid_fw,nvdof_fw,nics_fw = check_ics(ics_fw,gtsfiles)
print(" * "+string_nics(nics_fw,nvdof_fw,valid_fw))
print("")
continue
# ics already in file?
if len(ics) != 0:
valid,nvdof,nics = check_ics(ics,gtsfiles)
print(" * ics found!")
print(" "+string_nics(nics,nvdof,valid))
if not valid:
question = " remove set and generate new one (y/N)? "
answer = input(question).strip().lower()
if answer in ["y","yes"]: ics = []
else : print(""); continue
print("")
else:
nvdof = None
# is algorithm needed?
nics = count_ics(ics)
if nics != nvdof:
# positive modes
print(" * applying algorithm...")
if mode == "1" and len(ics) == 0:
ics,nvdof = mode1(gtsfiles)
if mode == "2":
ics,nvdof = mode2(gtsfiles,ics)
if mode == "3":
ics,nvdof = mode3(gtsfiles,ics)
# check final set after positive modes
if len(ics) == 0:
print(" algorithm failed!")
print("")
NOTVALID.append( (ctc,itcs) )
continue
valid,nvdof,nics = check_ics(ics,gtsfiles)
print(" "+string_nics(nics,nvdof,valid))
print("")
# update dictionary and rewrite
dctc[ctc]._dics[key] = ics
RW.write_ctc(dctc,dimasses)
else:
print(" * number(ics) = (vib.DOF); skypping...")
print("")
print(" -------------------")
print("")
print("")
# any fail?
if len(NOTVALID) != 0:
print(" The algorithm failed for:")
for ctc,itcs in NOTVALID:
# print conformers
string = ""
for idx in range(0,len(itcs),NEPL):
str_i = ",".join(itcs[idx:idx+NEPL])
if idx == 0: string += " * %s: "%ctc +str_i
else : string += ",\n"+" %s "%(" "*len(ctc))+str_i
print(string)
print("")
# rewrite again (for mode = -2)
if mode != "-1": RW.write_ctc(dctc,dimasses)
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
dall = RW.read_alldata(dof, ltemp)[0]
#--------------------------------#
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, dkmc, 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 = 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(dkmc)
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":
dkmc = add_kmc(val, dkmc, 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)
elif var == "kmc":
dkmc = mod_kmc(val, dkmc, dchem)
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)
elif var == "kmc": dkmc = rm_kmc(val, dkmc)
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(dkmc)
if dbool.get("dlevel", False):
print(" %s" % PN.IFILE7)
RW.write_dlevel(ddlevel)
print("")
break
# user ask for nothing
else:
continue