def rdfCriteria(atoms,basis,cr,criteria=None,perTS=False):
atoms = array(atoms)
basis = array(basis)
nTime = atoms.shape[0]
nAtom = atoms.shape[1]
nDel=0
ltFlag = False
if "lt" in criteria:
ltFlag=True
cutoff = float(criteria[2:])
if perTS:
pass
else:
for i,r in enumerate(cr):
if ltFlag:
if r>cutoff:
atoms = delete(atoms,i-nDel,1)
nAtom -= 1
nDel += 1
else:
if r<cutoff:
atoms = delete(atoms,i-nDel,1)
nAtom -= 1
nDel += 1
print "nAtom=%d atoms meet criteria %s"%(nAtom,criteria)
nbins = 1000
rcut = 10.0
rdf = zeros(nbins)
for i in range(nTime):
if perTS:
if ltFlag:
atomCR = atoms[i][ where( cr[i] < cutoff)[0] ]
else:
atomCR = atoms[i][ where( cr[i] > cutoff)[0] ]
print "nAtom=%d atoms meet criteria %s"%(len(atomCR),criteria)
rbins,rdist = rdf_periodic(atomCR,basis,rcut,nbins)
else:
rbins,rdist = rdf_periodic(atoms[i],basis,rcut,nbins)
rdf += rdist
rdf /= nTime
return rbins,rdf
rdistavg=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
[rbins,rdist]=rdf_periodic(array(atoms),array(bounds),cutoff=cutoff,nbins=nbins)
if avg==0:
if smooth==1:
smdist=rdist[:]
smdist = wsmooth(smdist,nbins/10)
plotting(rbins,smdist)
else:
plotting(rbins,rdist)
else:
rdistavg+=rdist
if avg>=1 and cnt%avg==0 and cnt>0:
plotting(rbins,rdistavg/avg)
rdistavg=zeros(nbins)
lengths = array(map(lambda x: float(x) * 1E10, xdatcar[1].split()[1:4]))
xdatcar = xdatcar[5:]
delr = float(cutoff) / numbins
pcors = list()
i = 0
cnt = 0
atomconfigs = list()
while i < len(xdatcar):
i += 1
cnt += 1
atoms = map(lambda x: map(float, x.split()), xdatcar[i:i + Natoms])
i += Natoms
pcors.append(
rdf_periodic(array(atoms), basis, cutoff=cutoff, nbins=numbins)[1])
print "=" * 50
print "=" * 50
print "%d Configurations found." % len(pcors)
print "=" * 50
print "=" * 50
print "Writing rdf of these configurations to %s" % pcfile
head = "\nCreated by %s, from %s\n" % (sys.argv[0].split(
"/")[-1], xdatfile) + "\n" * 4 + str(numbins) + "\n" * 2 + str(
delr / 1E10) + "\n" * 4
pcdat = open(pcfile, "w")
pcdat.write(head)
for pcor in pcors:
dat = "\n".join(map(str, pcor))
pcdat.write(dat + "\n\n")
nbins=int(sys.argv[3])
if len(sys.argv)==5:
pcfile=sys.argv[4]
dumpfile=sys.argv[1]
dump=open(dumpfile,"r").readlines()
delr=float(cutoff)/nbins
pcors=list()
i=0
cnt=0
while True:
try:
dump,bounds,types,atoms,head = dumpReadNext(dump)
cnt+=1
except Exception as inst:
#last of the configurations
break
pcors.append(rdf_periodic(array(atoms),array(bounds),cutoff=cutoff,nbins=nbins)[1])
print cnt
print "Found %d configurations."%cnt
print "Writing RDF of these configurations to %s"%pcfile
head="\nCreated by %s, from %s\n"%(sys.argv[0].split("/")[-1],dumpfile)+"\n"*4+str(nbins)+"\n"*2+str(delr/1E10)+"\n"*4
pcdat=open(pcfile,"w")
pcdat.write(head)
for pcor in pcors:
dat="\n".join(map(str,pcor))
pcdat.write(dat+"\n\n")
Natoms = int(xdatcar[0].split()[0])
lengths = array(map(lambda x: float(x) * 1e10, xdatcar[1].split()[1:4]))
xdatcar = xdatcar[5:]
delr = float(cutoff) / numbins
pcors = list()
i = 0
cnt = 0
atomconfigs = list()
while i < len(xdatcar):
i += 1
cnt += 1
atoms = map(lambda x: map(float, x.split()), xdatcar[i : i + Natoms])
i += Natoms
pcors.append(rdf_periodic(array(atoms), basis, cutoff=cutoff, nbins=numbins)[1])
print "=" * 50
print "=" * 50
print "%d Configurations found." % len(pcors)
print "=" * 50
print "=" * 50
print "Writing radial distribution function of these configurations to %s" % pcfile
head = (
"\nCreated by %s, from %s\n" % (sys.argv[0].split("/")[-1], xdatfile)
+ "\n" * 4
+ str(numbins)
+ "\n" * 2
+ str(delr / 1e10)
+ "\n" * 4
)
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
[rbins, rdist] = rdf_periodic(array(atoms),
array(bounds),
cutoff=cutoff,
nbins=nbins)
if avg == 0:
if smooth == 1:
smdist = rdist[:]
smdist = wsmooth(smdist, nbins / 10)
plotting(rbins, smdist)
else:
plotting(rbins, rdist)
else:
rdistavg += rdist
if avg >= 1 and cnt % avg == 0 and cnt > 0:
plotting(rbins, rdistavg / avg)
rdistavg = zeros(nbins)
dumpfile = sys.argv[1]
dump = open(dumpfile, "r").readlines()
delr = float(cutoff) / nbins
pcors = list()
i = 0
cnt = 0
while True:
try:
dump, bounds, types, atoms, head = dumpReadNext(dump)
cnt += 1
except Exception as inst:
#last of the configurations
break
pcors.append(
rdf_periodic(array(atoms), array(bounds), cutoff=cutoff,
nbins=nbins)[1])
print cnt
print "Found %d configurations." % cnt
print "Writing RDF of these configurations to %s" % pcfile
head = "\nCreated by %s, from %s\n" % (sys.argv[0].split(
"/")[-1], dumpfile) + "\n" * 4 + str(nbins) + "\n" * 2 + str(
delr / 1E10) + "\n" * 4
pcdat = open(pcfile, "w")
pcdat.write(head)
for pcor in pcors:
dat = "\n".join(map(str, pcor))
pcdat.write(dat + "\n\n")