def ls_struc(dctc):
'''
extra option to show what's in .ctc file
to show: ls ctc
'''
ib = " "
htable = [
"struc name", "m.form.", "num.ifreqs.", "ch", "mtp", "num.confs."
]
# some numbers and list for nice formatting
ml1 = max([len(ctc) for ctc in dctc.keys()] + [len(htable[0])])
ml2 = max([len(CTC._mformu) for CTC in dctc.values()] + [len(htable[1])])
ll = [ml1, ml2, len(htable[2]), 3, 3, len(htable[5])]
# fill strings in htable
htable = [fill_string(string, ml) for ml, string in zip(ll, htable)]
# start loop
htable = " " + " | ".join(htable) + " "
divis = "-" * len(htable)
stable = "\n"
stable += ib + divis + "\n"
stable += ib + htable + "\n"
stable += ib + divis + "\n"
# separate minima from saddle point and from other (xx)
ctc_min = sorted([ctc for ctc in dctc.keys() if dctc[ctc]._type == 0])
ctc_ts = sorted([ctc for ctc in dctc.keys() if dctc[ctc]._type == 1])
ctc_xx = sorted(
[ctc for ctc in dctc.keys() if dctc[ctc]._type not in [0, 1]])
for ctcs in [ctc_min, ctc_ts, ctc_xx]:
if ctcs == []: continue
for ctc in ctcs:
mformu = dctc[ctc]._mformu
itcs = dctc[ctc]._itcs
ch = dctc[ctc]._ch
mtp = dctc[ctc]._mtp
sptype = dctc[ctc]._type
# variable to string
ncnfs = "%i" % int(sum([weight for itc, weight in itcs]))
ch = "%i" % ch
mtp = "%i" % mtp
nif = "%i" % sptype
# fill strings
ltable = [ctc, mformu, nif, ch, mtp, ncnfs]
ltable = [
fill_string(string, ml) for ml, string in zip(ll, ltable)
]
# add to table
ltable = " " + " | ".join(ltable) + " "
stable += ib + ltable + "\n"
stable += ib + divis + "\n"
print stable
# Analyze point by point
wrongconn = []
repeated = []
outofdomain = []
norestr = []
wimag = []
iii = len(str(len(dataconfs)))
jjj = max(len(str(vec0)),len("angles"))
kkk = max(inpvars._ntorsions*2+2,len("conf"))
if inpvars._ts:
lengths = (iii,jjj,kkk,6,7,7,7,7,8)
head = ("","angles","conf","weight","E","E+ZPE","Gibbs","X","ifreq")
else:
lengths = (iii,jjj,kkk,6,7,7,7,7)
head = ("","angles","conf","weight","E","E+ZPE","Gibbs","X")
table_head = " "+" | ".join(fncs.fill_string(col,length) for col,length in zip(head,lengths))+" "
print(IBS2+"-"*len(table_head))
print(IBS2+table_head)
print(IBS2+"-"*len(table_head))
nomenclatures = []
QMSHO = np.array([0.0 for temp in inpvars._temps])
QMSHO_pre = np.array([0.0 for temp in inpvars._temps])
QMSHO_sto = np.array([0.0 for temp in inpvars._temps])
count_pre = 0
count_sto = 0
# calculate quotient of Xj
xj_quo = 0.0
beta = 1.0/pc.KB/inpvars._temp
for idx_j,conftuple_j in enumerate(dataconfs):
vec_j,V0_j,V1_j,Gj,weight_j,Qrv_j,ifreq_j,lzmat_j,zmatvals_j,log_j = conftuple_j
xj_quo += weight_j*np.exp(-(Gj-minG)*beta)
def ls_struc(dctc):
'''
extra option to show what's in .ctc file
to show: ls ctc
'''
ib = " "
htable = [
"species name", "m.form.", "num.ifreqs.", "ch", "mtp", "num.confs.",
"iso.mod."
]
# some numbers and list for nice formatting
ml1 = max([len(ctc) for ctc in dctc.keys()] + [len(htable[0])])
ml2 = max([len(CTC._mformu) for CTC in dctc.values()] + [len(htable[1])])
ll = [ml1, ml2, len(htable[2]), 3, 3, len(htable[5]), len(htable[6])]
# fill strings in htable
htable = [fill_string(string, ml) for ml, string in zip(ll, htable)]
# start loop
htable = " " + " | ".join(htable) + " "
divis = "-" * len(htable)
stable = "\n"
stable += ib + divis + "\n"
stable += ib + htable + "\n"
stable += ib + divis + "\n"
# separate minima from saddle point and from other (xx)
ctc_root_min = sorted([
ctc for ctc in dctc.keys()
if dctc[ctc]._type == 0 and dctc[ctc]._diso == {}
])
ctc_root_ts = sorted([
ctc for ctc in dctc.keys()
if dctc[ctc]._type == 1 and dctc[ctc]._diso == {}
])
ctc_isoX_min = sorted([
ctc for ctc in dctc.keys()
if dctc[ctc]._type == 0 and dctc[ctc]._diso != {}
])
ctc_isoX_ts = sorted([
ctc for ctc in dctc.keys()
if dctc[ctc]._type == 1 and dctc[ctc]._diso != {}
])
ctc_xx = sorted(
[ctc for ctc in dctc.keys() if dctc[ctc]._type not in [0, 1]])
numSP0, numSP0all = 0, 0
numSP1, numSP1all = 0, 0
numSPX, numSPXall = 0, 0
for idx, ctcs in enumerate(
[ctc_root_min + ctc_isoX_min, ctc_root_ts + ctc_isoX_ts, ctc_xx]):
if ctcs == []: continue
for ctc in ctcs:
mformu = dctc[ctc]._mformu
itcs = dctc[ctc]._itcs
ch = dctc[ctc]._ch
mtp = dctc[ctc]._mtp
sptype = dctc[ctc]._type
diso = dctc[ctc]._diso
if diso == {}:
isostr = "none"
else:
try:
isostr = " ".join(diso["*"])
except:
isostr = "yes"
# count conformers
num1 = len(itcs)
num2 = int(sum([weight for itc, weight in itcs]))
# variable to string
ncnfs = "%i (%i)" % (num2, num1)
ch = "%i" % ch
mtp = "%i" % mtp
nif = "%i" % sptype
# fill strings
ltable = [
"%%-%is" % ml1 % ctc,
"%%-%is" % ml2 % mformu, nif, ch, mtp, ncnfs, isostr
]
ltable = [
fill_string(string, ml) for ml, string in zip(ll, ltable)
]
# add to table
ltable = " " + " | ".join(ltable) + " "
stable += ib + ltable + "\n"
if sptype == 0:
numSP0 += num1
numSP0all += num2
elif sptype == 1:
numSP1 += num1
numSP1all += num2
else:
numSPX += num1
numSPXall += num2
stable += ib + divis + "\n"
stable += ib + " * num(minimum) = %i (%i)\n" % (numSP0all, numSP0)
stable += ib + " * num(saddle ) = %i (%i)\n" % (numSP1all, numSP1)
print(stable)