def vanHoveTotal(atoms,basis,steps,cutr=10.0,nBin=1000,norm=False):
atoms = array(atoms)
basis = array(basis)
if type(steps) != type(list()): #handle the case where steps is just a single step
steps = list(steps)
steps = array(steps)
nTime = atoms.shape[0]
nAtom = atoms.shape[1]
nStep = steps.shape[0]
atoms = atoms.ravel()
b = basis.ravel()
dr = cutr/nBin
rbins = [i*dr for i in range(nBin)]
bins = zeros(nStep*nBin)
weave.inline(vhTotalRefCode,['atoms','nTime','nAtom','steps','nStep','b','bins','nBin','dr'])
bins.shape = [nStep,nBin]
atoms.shape = [nTime,nAtom,3]
if norm:
Ndensity=nAtom/volume(basis)
for i,r in enumerate(rbins):
if i==0:
vol=4.0*pi*dr*dr*dr/3.0
else:
vol=4.0*pi*r*r*dr
for k in range(nStep):
bins[k][i] /= vol*Ndensity
return rbins,bins
def rdf_periodic(atoms,basis,cutoff=10.0,nbins=1000):
#atoms: list of atoms[N][3]
#cutoff: float, max radius to measure radial distro out to
#nbins: number of bins to store in radial distro
basis=array(basis)
atoms=array(atoms)
bt=basis.T
rdist=zeros(nbins)
dr=float(cutoff)/nbins
N=len(atoms)
rdist=rdfperHelper(atoms,rdist,cutoff,basis)
rbins=[i*dr for i in range(nbins)] #the central point of each bin (x-axis on plot)
Ndensity=N/volume(basis)
for i,r in enumerate(rbins):
if i==0:
vol=4.0*pi*dr*dr*dr/3.0
else:
vol=4.0*pi*r*r*dr
rdist[i]/=vol*(Ndensity*N)
return [rbins,rdist]
open(posfile,"w").writelines(posdata)
if __name__=="__main__":
def usage():
print "Usage:"
print "%s <POSCAR> //prints volume and atomic volume"
print "%s <POSCAR> <frac/unfrac>"%sys.argv[0].split("/")[-1]
print "%s <POSCAR> <ratio value>"%sys.argv[0].split("/")[-1]
if len(sys.argv) not in [2,3]:
usage()
exit(0)
if len(sys.argv)==2:
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(sys.argv[1],"r").readlines())
v = volume(basis)
print "Total Volume in AA^3 = %f"%v
print "Atomic Volume in AA^3 = %f"%(v/len(atoms))
elif sys.argv[2]=="frac":
fractional(sys.argv[1])
elif sys.argv[2]=="unfrac":
unFractional(sys.argv[1])
else:
try:
r=float(sys.argv[2])
ratio(sys.argv[1],r)
except:
print "Error, unrecognized volume arguement: %s"%sys.argv[2]
usage()
exit(0)
if __name__ == "__main__":
def usage():
print "Usage:"
print "%s <POSCAR> //prints volume and atomic volume"
print "%s <POSCAR> <frac/unfrac>" % sys.argv[0].split("/")[-1]
print "%s <POSCAR> <ratio value>" % sys.argv[0].split("/")[-1]
if len(sys.argv) not in [2, 3]:
usage()
exit(0)
if len(sys.argv) == 2:
[basis, atypes, atoms, head,
poscar] = poscarIO.read(open(sys.argv[1], "r").readlines())
v = volume(basis)
print "Total Volume in AA^3 = %f" % v
print "Atomic Volume in AA^3 = %f" % (v / len(atoms))
elif sys.argv[2] == "frac":
fractional(sys.argv[1])
elif sys.argv[2] == "unfrac":
unFractional(sys.argv[1])
else:
try:
r = float(sys.argv[2])
ratio(sys.argv[1], r)
except:
print "Error, unrecognized volume arguement: %s" % sys.argv[2]
usage()
exit(0)
