def mode3(gtsfiles,ics=[]):
# mode 2
ics, nvdof = mode2(gtsfiles,ics)
nics = count_ics(ics)
# mode 3
if nics > nvdof:
ics2, valid = nonredundant_gtsfiles(gtsfiles,ics)
if valid: return ics2,nvdof
return ics,nvdof
def check_ics(ics,gtsfiles):
# counting
nics = count_ics(ics)
# checking
valid = True
for gts in gtsfiles:
valid, nvdof = check_ics_gtsfile(gts,ics)
if not valid: break
# return
return valid, nvdof, nics
def check_ics_gtsfile(gtsfile,ics):
# number of internal coordinates
nics = count_ics(ics)
# read gts and prepare Molecule
molecule = Molecule()
molecule.set_from_gts(gtsfile)
molecule.setup()
# number of vibrational degrees of freedom
nvdof = len(molecule._ccfreqs)
# enough internal coordinates
if nics < nvdof: return False, nvdof
# calc ic-freqs
molecule.icfreqs(ics)
# comparison
valid = same_freqs(molecule._ccfreqs,molecule._icfreqs)
return valid, nvdof
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)
# Update torsions with CH3s
torsions = torsions + lCH3
sprint()
# (a) generate redundant internal coordinates
sprint(
"Trying to generate valid redundant set of internal coordinates...",
NIBS2)
nvdof = len(list_ccfrqs[0])
sprint("number of vib. degrees of freedom: %i" % nvdof, NIBS2 + 4)
idata_rics = (list_xcc, list_gcc, list_Fcc, list_ccfrqs, symbols,
masses, torsions)
rics = valid_redundant_set(*idata_rics)
nrics = None
num_ics = None
if rics is not None:
num_ics = intl.count_ics(rics)
sprint("number of internal coordinates : %i" % num_ics,
NIBS2 + 4)
sprint()
# (b) generate non-redundant internal coordinates
if num_ics == nvdof: nrics = rics
elif rics is not None:
sprint(
"Trying to generate valid non-redundant set of internal coordinates...",
NIBS2)
sprint("number of vib. degrees of freedom: %i" % nvdof, NIBS2 + 4)
idata_nrics = (rics, list_xcc, list_gcc, list_Fcc, list_ccfrqs,
symbols, masses, torsions)
nrics = valid_nonredundant_set(*idata_nrics)
if nrics is not None:
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
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: