if avg==1:
cntavg=zeros(nbins)
cnt=0
while True:
try:
dump,bounds,types,atoms,head = dumpReadNext(dump)
cnt+=1
except Exception as inst:
#last of the configurations
if avg==0:
print "No more configs in dump file."
else:
print "Found %d configurations."%cnt
break
bounds=[[0,bounds[0][0]],[0,bounds[1][1]],[0,bounds[2][2]]]
Qis=orderParam.bondOrientation(array(atoms),array(bounds),l,neighbCut=cutoff,ortho=True)
(cnts,bins) = histogram(Qis,bins=nbins,range=(0,cutoff))
if avg==0:
if smooth==1:
smCnts = wsmooth(cnts,nbins/10)
plotting(bins,smCnts)
else:
plotting(bins,cnts)
else:
cntavg+=cnts
if avg==1:
plotting(bins,cntavg/cnt)
outcar = open(filename, "r")
bondOrderOut = open(filename + ".BO%d" % lval, "w")
if sh2:
bondOrderOut = open(filename + ".BO%dsh2" % lval, "w")
bondOrderOut.write("AverageBO%d PerAtomBO%d\n" % (lval, lval))
for i, b in enumerate(bytenums):
outcar.seek(b)
outcar.readline()
outcar.readline()
atoms = [map(float, outcar.readline().split()[:3]) for a in range(nAtoms)]
if sh2:
q, rcut = orderParam.bondOrientation2sh(atoms, basis, lval)
else:
q, rcut = orderParam.bondOrientation(atoms, basis, lval)
qAvg = sum(q) / len(q)
qs = " ".join(map(str, q))
bondOrderOut.write(str(qAvg) + " " + qs + "\n")
# print i
if lammpsFlag:
nAtoms = lammpsIO.nAtoms(filename)
basisByteNums = lammpsIO.basisBytes(filename)
atomsByteNums = lammpsIO.atomsBytes(filename)
bondOrderOut = open(filename + ".BO%d" % lval, "w")
if sh2:
bondOrderOut = open(filename + ".BO%dsh2" % lval, "w")
while True:
try:
dump, bounds, types, atoms, head = dumpReadNext(dump)
cnt += 1
except Exception as inst:
#last of the configurations
if avg == 0:
print "No more configs in dump file."
else:
print "Found %d configurations." % cnt
break
bounds = [[0, bounds[0][0]], [0, bounds[1][1]], [0, bounds[2][2]]]
Qis = orderParam.bondOrientation(array(atoms),
array(bounds),
l,
neighbCut=cutoff,
ortho=True)
(cnts, bins) = histogram(Qis, bins=nbins, range=(0, cutoff))
if avg == 0:
if smooth == 1:
smCnts = wsmooth(cnts, nbins / 10)
plotting(bins, smCnts)
else:
plotting(bins, cnts)
else:
cntavg += cnts
if avg == 1:
plotting(bins, cntavg / cnt)
