def bondOrientation2sh(atoms,basis,l,neighbs=None,rcut=None,debug=False):
atoms = array(atoms)
basis = array(basis)
atoms = rectify(atoms,basis)
if neighbs==None:
bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
if rcut==None:
rcut = generateRCut(atoms,basis,debug=debug)
#print "Automatically generating r-cutoff=",rcut
neighbs = secondShell( neighbors(atoms,bounds,rcut) )
#sum the spherical harmonic over ever neighbor pair
a = 4*np.pi / (2*l+1.)
Ql=list()
for i,ineighbs in enumerate(neighbs):
n=len(ineighbs)
shij = np.vectorize(complex)(zeros(2*l+1)) #spherical harmonic for bond i-j
for j in ineighbs:
shij += pairSphereHarms(atoms[i],minImageAtom(atoms[i],atoms[j],basis),l)/n
shi = a * sum( scipy.real( scipy.multiply(shij,scipy.conj(shij)) ) )
Ql.append(shi**0.5)
return Ql,rcut
lmpFile = inputFile
atomByteNums = lammpsIO.atomsBytes(lmpFile)
nAtom = lammpsIO.nAtoms(lmpFile)
basis = lammpsIO.basis(lmpFile)
bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
configIterator = parserGens.parseLammpsAtoms(atomByteNums,lmpFile,nAtom)
atomsTime = [array(atoms) for atoms in configIterator]
bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
if len(crTime)+1 == nAtom:
crTime=crTime[1:] #chop off the average if necessary
if sh2Enable:
rcut = 3.1
neighbs = secondShell( neighbors(array(atomsTime[-1]),bounds,rcut) )
ns = map(len,neighbs)
crTime = [sum([crTime[j] for j in neighbs[i]])/ns[i] if ns[i]>0 else crTime[i] for i in range(len(neighbs))]
if isfType == "total":
steps,isfs = ISFFull(atomsTime,basis,crTime,nqVecs=3,nStep=nStep,criteria=criteria)
elif isfType == "self":
steps,isfs = ISFSelf(atomsTime,basis,crTime,nqVecs=3,nStep=nStep,criteria=criteria)
scale /= 1E-12 #picosecond conversion
steps = [i*scale for i in steps]
if logtEnable:
steps=log10(steps)
#Write Data
outputFile = criteFile + ".isf" + isfType[0].upper() + "_" + criteria
