def chgcarBondAnalysis(chgcarfile,bondLengths,normalize=False,verbose=False,Ninterps=None,loc=None):
BLs=bondLengths
nBLs=len(BLs)
#Parse CHGCAR
chgcar=open(chgcarfile,"r").readlines()
(v1,v2,v3,atypes,axs,ays,azs,header),chg = chgcarIO.read(chgcar)
gridSize = chg.shape
basis=asarray([v1,v2,v3])
lengths=array([v1[0],v2[1],v3[2]])
atoms=array(zip(axs,ays,azs))
#Grid properties
nGridPoints=reduce(operator.mul,gridSize)
#Neighbors
halfNeighbors=voronoiNeighbors(atoms,basis,atypes,style='half')
a=chg.shape
AvgChg=sum([sum([sum(line) for line in plane]) for plane in chg])/a[0]/a[1]/a[2]
if verbose:
print "Average CHG value:",AvgChg
#Evaluate the CHG between each nieghbor pair
if Ninterps==None:
Ninterps=array([1,50,50])
avgGrids,grids,bondcounts=fieldNeighbors3D(atoms,atypes,basis,chg,gridSize,halfNeighbors,cutoffs=bondLengths,loc=loc)
else:
Ninterps=array([1]+Ninterps)
avgGrids,grids,bondcounts=fieldNeighbors3D(atoms,atypes,basis,chg,gridSize,halfNeighbors,cutoffs=bondLengths,Ninterps=Ninterps,loc=loc)
#Normalize if necessary
if normalize:
avgGrids=[avgGrid/AvgChg for avgGrid in avgGrids]
return avgGrids,grids,bondcounts
"""
if len(sys.argv) < 2:
print "Usage:"
print sys.argv[0] + " <poscar> <opt: max bond length>"
exit(0)
poscar = open(sys.argv[1], "r").readlines()
mbl = -1.
if len(sys.argv) == 3:
mbl = float(sys.argv[2])
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
bounds = array([basis[0][0], basis[1][1], basis[2][2]])
#Generate neighbor lists, half and full
vhalfNeighbors = voronoiNeighbors(atoms, basis, atypes, style='half')
vfullNeighbors = half2full(vhalfNeighbors)
#Check lengths of bonds
if mbl > 0:
ls = list()
for ai, neighbs in enumerate(vfullNeighbors):
ls.append(
[dist_periodic(atoms[ai], atoms[aj], bounds) for aj in neighbs])
vfullNeighbors = [[
vfullNeighbors[i][j] for j, dist in enumerate(dists) if dist <= mbl
] for i, dists in enumerate(ls)]
for i, j in zip(vfullNeighbors, ls):
print len(i), len(j)
for i in sys.argv[2:]:
try:
maxls.append(float(i))
except ValueError:
if i[0] in ["v","V"]:
voronEnable=True
voronCap=float(i.split(",")[1])
else:
raise ValueError
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
atoms=array(atoms)
lengths=array([basis[0][0],basis[1][1],basis[2][2]])
atLFullNeighbors=[neighbors(atoms,array([[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]),maxlen,style='full') for maxlen in maxls]
vFullNeighbors=voronoiNeighbors(atoms,basis,atypes,style='full')
vFullNeighbors=[[j for j in vFullNeighbors[i] if dist_periodic(atoms[i],atoms[j],lengths)<voronCap] for i in range(len(vFullNeighbors))]
atLCoordNumbers=map(lambda x:map(len,x),atLFullNeighbors)
vCoordNumbers=map(len,vFullNeighbors)
#To include Voronoi (capped at max length) uncomment:
if voronEnable:
atLCoordNumbers.append(vCoordNumbers)
absMin=0
absMax=50
mncn=max(min(map(min,atLCoordNumbers))-3,absMin)
mxcn=min(max(map(max,atLCoordNumbers))+4,absMax)
colors=["red","blue","green","purple","yellow"]
if len(sys.argv)<2:
print "Usage:"
print sys.argv[0]+" <poscar> <opt: max bond length>"
exit(0)
poscar = open(sys.argv[1],"r").readlines()
mbl=-1.
if len(sys.argv)==3:
mbl=float(sys.argv[2])
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
bounds=array([basis[0][0],basis[1][1],basis[2][2]])
#Generate neighbor lists, half and full
vhalfNeighbors=voronoiNeighbors(atoms,basis,atypes,style='half')
vfullNeighbors=half2full(vhalfNeighbors)
#Check lengths of bonds
if mbl>0:
ls=list()
for ai,neighbs in enumerate(vfullNeighbors):
ls.append([dist_periodic(atoms[ai],atoms[aj],bounds) for aj in neighbs])
vfullNeighbors= [[vfullNeighbors[i][j] for j,dist in enumerate(dists) if dist<=mbl] for i,dists in enumerate(ls)]
for i,j in zip(vfullNeighbors,ls):
print len(i),len(j)
coordNumbers=map(len,vfullNeighbors)
CNhist=zeros(200)
voronEnable = True
voronCap = float(i.split(",")[1])
else:
raise ValueError
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
atoms = array(atoms)
lengths = array([basis[0][0], basis[1][1], basis[2][2]])
atLFullNeighbors = [
neighbors(atoms,
array([[0, basis[0][0]], [0, basis[1][1]], [0, basis[2][2]]]),
maxlen,
style='full') for maxlen in maxls
]
vFullNeighbors = voronoiNeighbors(atoms, basis, atypes, style='full')
vFullNeighbors = [[
j for j in vFullNeighbors[i]
if dist_periodic(atoms[i], atoms[j], lengths) < voronCap
] for i in range(len(vFullNeighbors))]
atLCoordNumbers = map(lambda x: map(len, x), atLFullNeighbors)
vCoordNumbers = map(len, vFullNeighbors)
#To include Voronoi (capped at max length) uncomment:
if voronEnable:
atLCoordNumbers.append(vCoordNumbers)
absMin = 0
absMax = 50
mncn = max(min(map(min, atLCoordNumbers)) - 3, absMin)
def chgcarBondAnalysis(chgcarfile,
bondLengths,
normalize=False,
verbose=False):
BLs = bondLengths
nBLs = len(BLs)
#Parse CHGCAR
chgcar = open(chgcarfile, "r").readlines()
(v1, v2, v3, atypes, axs, ays, azs,
header), gridSize, chg = chgcarIO.read(chgcar)
basis = asarray([v1, v2, v3])
lengths = array([v1[0], v2[1], v3[2]])
atoms = array(zip(axs, ays, azs))
#Grid properties
nGridPoints = reduce(operator.mul, gridSize)
#Neighbors
halfNeighbors = voronoiNeighbors(atoms, basis, atypes, style='half')
a = chg.shape
AvgChg = sum([sum([sum(line) for line in plane])
for plane in chg]) / a[0] / a[1] / a[2]
if verbose:
print "Average CHG value:", AvgChg
#Evaluate the CHG between each nieghbor pair
avgchgline, xchglines, ychglines, halfNeighbors = fieldNeighbors1D(
atoms, atypes, basis, chg, gridSize, halfNeighbors)
#Cutoff neighbors that fall below the thresh-hold
Ninterp = len(avgchgline)
avgIBL = zeros([nBLs, Ninterp]) #avg line inside the bond length
avgOBL = zeros([nBLs, Ninterp]) #avg line outside the bond length
nibl = zeros(nBLs)
nobl = zeros(nBLs)
cnt = 0
for a, jNeighbors in enumerate(halfNeighbors):
atoma = atoms[a]
for b, jNeighb in enumerate(jNeighbors):
atomb = atoms[jNeighb]
d = dist_periodic(atoma, atomb, lengths)
vals = ychglines[a][b]
xx = xchglines[a][b]
for j, bl in enumerate(BLs):
if normalize:
avals = array(vals) / AvgChg
else:
avals = array(vals)
if d < bl:
nibl[j] += 2
avgIBL[j] += avals
avgIBL[j] += avals[::-1]
else:
cnt += 1
nobl[j] += 2
avgOBL[j] += avals
avgOBL[j] += avals[::-1]
for i in range(nBLs):
if nibl[i] == 0:
nibl[i] = 1
if nobl[i] == 0:
nobl[i] = 1
avgOBL = [avgOBL[i] / nobl[i] for i in range(nBLs)]
avgIBL = [avgIBL[i] / nibl[i] for i in range(nBLs)]
return avgOBL, nobl, avgIBL, nibl
def outcarCoordination(outcarfile, maxls, voronoiEnable):
outcar = open(outcarfile, "r")
#Grab ion types
while True:
line = outcar.readline()
if "ions per type" in line:
break
atypes = map(int, line.split("=")[1].split())
tCoordNumbers = zeros([len(maxls), sum(atypes)])
#Grab basis vectors
while True:
line = outcar.readline()
if "direct lattice vectors" in line:
break
basis = array(
[map(float,
outcar.readline().split()[:3]) for i in range(3)])
lengths = array([basis[0][0], basis[1][1], basis[2][2]])
absMax = 50
if voronoiEnable:
avgCNhist = zeros([len(maxls) + 1, absMax])
else:
avgCNhist = zeros([len(maxls), absMax])
#Grab atom positions and perform adf calculation
count = 0
posit = False
for line in outcar:
if posit:
if "--" in line:
if len(atoms) == 0:
continue
else:
#Analysis
if max(zip(*atoms)[0]) < 1.01:
atoms = dot(array(atoms), basis)
else:
atoms = array(atoms)
atLFullNeighbors = [
neighborOrtho(
atoms,
array([basis[0][0], basis[1][1], basis[2][2]]),
6.0,
style='full') for maxlen in maxls
]
atLCoordNumbers = map(lambda x: map(len, x),
atLFullNeighbors)
if voronoiEnable:
vFullNeighbors = voronoiNeighbors(atoms,
basis,
atypes,
style='full')
vFullNeighbors = [[
j for j in vFullNeighbors[i] if dist_periodic(
atoms[i], atoms[j], lengths) < voronCap
] for i in range(len(vFullNeighbors))]
vCoordNumbers = map(len, vFullNeighbors)
atLCoordNumbers.append(vCoordNumbers)
hist = [[i.count(j) for j in range(absMax)]
for i in atLCoordNumbers]
avgCNhist += array(hist)
print count
posit = False
else:
atoms.append(map(float, line.split()[:3]))
elif "POSITION" in line:
atoms = list()
posit = True
count += 1
avgCNhist /= count
return avgCNhist.tolist()
def elfcarNeighborAnalysis(elfcarfile,
verbose=False,
minELF=0.5,
maxBondLength=4.0):
#Loads up an ELFCAR, generates a starting neighbor list from voronoi tesselation
#Initial neighbors are dropped if bondlength is greater than maxBondLength
#Generates a bunch of points on a cylinder
#Maps the cylinder points across each neighbor pair
#If the average ELF is always above minELF accross this cylinder, atoms are bonded.
#Parse ELFCAR
elfcar = open(elfcarfile, "r").readlines()
(basis, atypes, atoms, header), elf = elfcarIO.read(elfcar)
lengths = array([basis[0][0], basis[1][1], basis[2][2]])
#Neighbors
bounds = [[0, basis[0][0]], [0, basis[1][1]], [0, basis[2][2]]]
halfNeighbs = voronoiNeighbors(atoms, basis, style="half")
a = elf.shape
AvgElf = sum([sum([sum(line) for line in plane])
for plane in elf]) / a[0] / a[1] / a[2]
if verbose:
print elfcarfile
print "Average ELF value:", AvgElf
#Evaluate the ELF between each nieghbor pair
#creates a bunch of points on a circle in the x-y plane
def circlePoints(center, radius):
N = 4
ps = [float(p) / N * radius for p in range(-N, N + 1)]
r2 = radius * radius
points = list()
for x in ps:
for y in ps:
if (x**2 + y**2) <= r2:
points.append(asarray([x, y]))
return asarray(points)
atoms = asarray([lengths[i] - v for i, v in enumerate(atoms.T)]).T
#Flip the ELF because its off, thanks a lot VASP.
elf = elf[::-1, ::-1, ::-1]
#Loop over atom pairs, generate cylinders
cylSlices = 10
cylRadius = 0.7
cirPoints = circlePoints(a, cylRadius).T
cylPoints = [
vstack([cirPoints, zeros(cirPoints.shape[1]) + float(z)])
for z in range(cylSlices + 1)
]
coordination = zeros(len(atoms))
neighborsELF = [list() for i in range(len(atoms))]
for i, ineighbs in enumerate(halfNeighbs):
a = atoms[i]
for j in ineighbs:
#copy the cylinder points so you can play with them...
localCyl = array(cylPoints)
#Find the minimum image atom
b = minImageAtom(a, atoms[j], basis)
l = minImageDist(a, b, basis)
if l > maxBondLength or l == 0.0: continue
#How to map your cylinder onto the local atom
R = rotmatx([0, 0, l], b - a)
#Loop over each cylinder slice
sliceParam = list()
for cir in localCyl:
#cir is stretched and rotated cylinder
cir[2] /= cylSlices / l
cir = asarray([dot(R, p) + a for p in cir.T]).T
#cir2 is cir with periodic boundary conditions applied and mapped to index space
cir2 = asarray([((c / lengths[ind] * elf.shape[ind]) %
(elf.shape[ind] - 1))
for ind, c in enumerate(cir)])
#Interpolation across cylinder
z = ndimage.map_coordinates(elf, cir2)
#Average ELF value across each slice.
sliceParam.append(sum(z) / len(z))
if min(sliceParam) > minELF:
#neighbor pair is bonded, count it!
neighborsELF[i].append(j)
neighborsELF[j].append(i)
return neighborsELF
def chgcarBondAnalysis(chgcarfile,bondLengths,normalize=False,verbose=False):
BLs=bondLengths
nBLs=len(BLs)
#Parse CHGCAR
chgcar=open(chgcarfile,"r").readlines()
(v1,v2,v3,atypes,axs,ays,azs,header),gridSize,chg = chgcarIO.read(chgcar)
basis=asarray([v1,v2,v3])
lengths=array([v1[0],v2[1],v3[2]])
atoms=array(zip(axs,ays,azs))
#Grid properties
nGridPoints=reduce(operator.mul,gridSize)
#Neighbors
halfNeighbors=voronoiNeighbors(atoms,basis,atypes,style='half')
a=chg.shape
AvgChg=sum([sum([sum(line) for line in plane]) for plane in chg])/a[0]/a[1]/a[2]
if verbose:
print "Average CHG value:",AvgChg
#Evaluate the CHG between each nieghbor pair
avgchgline,xchglines,ychglines,halfNeighbors=fieldNeighbors1D(atoms,atypes,basis,chg,gridSize,halfNeighbors)
#Cutoff neighbors that fall below the thresh-hold
Ninterp=len(avgchgline)
avgIBL=zeros([nBLs,Ninterp]) #avg line inside the bond length
avgOBL=zeros([nBLs,Ninterp]) #avg line outside the bond length
nibl=zeros(nBLs)
nobl=zeros(nBLs)
cnt=0
for a,jNeighbors in enumerate(halfNeighbors):
atoma=atoms[a]
for b,jNeighb in enumerate(jNeighbors):
atomb=atoms[jNeighb]
d=dist_periodic(atoma,atomb,lengths)
vals=ychglines[a][b]
xx=xchglines[a][b]
for j,bl in enumerate(BLs):
if normalize:
avals=array(vals)/AvgChg
else:
avals=array(vals)
if d<bl:
nibl[j]+=2
avgIBL[j]+=avals
avgIBL[j]+=avals[::-1]
else:
cnt+=1
nobl[j]+=2
avgOBL[j]+=avals
avgOBL[j]+=avals[::-1]
for i in range(nBLs):
if nibl[i]==0:
nibl[i]=1
if nobl[i]==0:
nobl[i]=1
avgOBL=[avgOBL[i]/nobl[i] for i in range(nBLs)]
avgIBL=[avgIBL[i]/nibl[i] for i in range(nBLs)]
return avgOBL,nobl,avgIBL,nibl
bondCutoffs = [float(i) / 10 for i in range(2, 7)]
if len(sys.argv) == 3:
bondCutoffs = [float(sys.argv[2])]
# Parse ELFCAR
elfcar = open(sys.argv[1], "r").readlines()
(basis, atypes, atoms, header), gridSize, elf = elfcarIO.read(elfcar)
basis = array(basis)
bounds = [[0.0, basis[0][0]], [0.0, basis[1][1]], [0.0, basis[2][2]]]
atoms = array(atoms)
# Grid properties
nGridPoints = reduce(operator.mul, gridSize)
# Neighbors
halfNeighbors = voronoiNeighbors(atoms=atoms, basis=basis, atypes=atypes, style="half")
print "Number of Neighbors before elimination:", sum([len(i) for i in halfNeighbors])
a = elf.shape
print "Average ELF value:", sum([sum([sum(line) / a[2] for line in plane]) / a[1] for plane in elf]) / a[0]
# Evaluate the ELF between each nieghbor pair
avgelfline, elflines, halfNeighbors = fieldNeighbors(atoms, atypes, basis, elf, gridSize, halfNeighbors)
# Cutoff neighbors that fall below the thresh-hold
Ninterp = len(avgelfline)
avgbig = zeros([len(bondCutoffs), Ninterp])
avgsmall = zeros([len(bondCutoffs), Ninterp])
nab = zeros(len(bondCutoffs))
nas = zeros(len(bondCutoffs))
def outcarCoordination(outcarfile,maxls,voronoiEnable):
outcar=open(outcarfile,"r")
#Grab ion types
while True:
line=outcar.readline()
if "ions per type" in line:
break
atypes=map(int,line.split("=")[1].split())
tCoordNumbers=zeros([len(maxls),sum(atypes)])
#Grab basis vectors
while True:
line=outcar.readline()
if "direct lattice vectors" in line:
break
basis=array([map(float,outcar.readline().split()[:3]) for i in range(3)])
lengths=array([basis[0][0],basis[1][1],basis[2][2]])
absMax=50
if voronoiEnable:
avgCNhist=zeros([len(maxls)+1,absMax])
else:
avgCNhist=zeros([len(maxls),absMax])
#Grab atom positions and perform adf calculation
count=0
posit=False
for line in outcar:
if posit:
if "--" in line:
if len(atoms)==0:
continue
else:
#Analysis
if max(zip(*atoms)[0])<1.01:
atoms=dot(array(atoms),basis)
else:
atoms=array(atoms)
atLFullNeighbors=[neighborOrtho(atoms,array([basis[0][0],basis[1][1],basis[2][2]]),6.0,style='full') for maxlen in maxls]
atLCoordNumbers=map(lambda x:map(len,x),atLFullNeighbors)
if voronoiEnable:
vFullNeighbors=voronoiNeighbors(atoms,basis,atypes,style='full')
vFullNeighbors=[[j for j in vFullNeighbors[i] if dist_periodic(atoms[i],atoms[j],lengths)<voronCap] for i in range(len(vFullNeighbors))]
vCoordNumbers=map(len,vFullNeighbors)
atLCoordNumbers.append(vCoordNumbers)
hist=[[i.count(j) for j in range(absMax)] for i in atLCoordNumbers]
avgCNhist+=array(hist)
print count
posit=False
else:
atoms.append(map(float,line.split()[:3]))
elif "POSITION" in line:
atoms=list()
posit=True
count+=1
avgCNhist/=count
return avgCNhist.tolist()
def outcarADF(outcarfile,nbins,bl=-1.0,bw=-1.0):
outcar=open(outcarfile,"r")
tbinvals=list()
#Grab ion types
while True:
line=outcar.readline()
if "ions per type" in line:
break
atypes=map(int,line.split("=")[1].split())
#Grab basis vectors
while True:
line=outcar.readline()
if "direct lattice vectors" in line:
break
basis=array([map(float,outcar.readline().split()[:3]) for i in range(3)])
lengths=array([basis[0][0],basis[1][1],basis[2][2]])
#Grab atom positions and perform adf calculation
count=0
posit=False
for line in outcar:
if posit:
if "--" in line:
if len(atoms)==0:
continue
else:
#Analysis
if max(zip(*atoms)[0])<1.01:
atoms=dot(array(atoms),basis)
else:
atoms=array(atoms)
neighbs=voronoiNeighbors(atoms,basis,atypes,style='full')
if bl!=-1 and bw!=-1:
specbonds=[list() for i in range(len(atoms))]
for i in range(len(atoms)):
ai=atoms[i]#dot(atoms[i],basis)
for j in neighbs[i]:
aj=atoms[j]#dot(atoms[j],basis)
d=dist_periodic(ai,aj,lengths)
if fabs(d-bl)<bw:
if d<1.0:
print d
print dist_periodic(ai,aj,lengths)
print ai
print aj
exit(0)
specbonds[i].append(j)
else:
specbonds=neighbs
[angs,abins]=adf(atoms,specbonds,basis,nbins=nbins)
tbinvals.append(abins)
print count
posit=False
else:
atoms.append(map(float,line.split()[:3]))
elif "POSITION" in line:
atoms=list()
posit=True
count+=1
return angs,tbinvals
def outcarADF(outcarfile, nbins, bl=-1.0, bw=-1.0):
outcar = open(outcarfile, "r")
tbinvals = list()
#Grab ion types
while True:
line = outcar.readline()
if "ions per type" in line:
break
atypes = map(int, line.split("=")[1].split())
#Grab basis vectors
while True:
line = outcar.readline()
if "direct lattice vectors" in line:
break
basis = array(
[map(float,
outcar.readline().split()[:3]) for i in range(3)])
lengths = array([basis[0][0], basis[1][1], basis[2][2]])
#Grab atom positions and perform adf calculation
count = 0
posit = False
for line in outcar:
if posit:
if "--" in line:
if len(atoms) == 0:
continue
else:
#Analysis
if max(zip(*atoms)[0]) < 1.01:
atoms = dot(array(atoms), basis)
else:
atoms = array(atoms)
neighbs = voronoiNeighbors(atoms,
basis,
atypes,
style='full')
if bl != -1 and bw != -1:
specbonds = [list() for i in range(len(atoms))]
for i in range(len(atoms)):
ai = atoms[i] #dot(atoms[i],basis)
for j in neighbs[i]:
aj = atoms[j] #dot(atoms[j],basis)
d = dist_periodic(ai, aj, lengths)
if fabs(d - bl) < bw:
if d < 1.0:
print d
print dist_periodic(ai, aj, lengths)
print ai
print aj
exit(0)
specbonds[i].append(j)
else:
specbonds = neighbs
[angs, abins] = adf(atoms, specbonds, basis, nbins=nbins)
tbinvals.append(abins)
print count
posit = False
else:
atoms.append(map(float, line.split()[:3]))
elif "POSITION" in line:
atoms = list()
posit = True
count += 1
return angs, tbinvals
def elfcarNeighborAnalysis(elfcarfile,verbose=False,minELF=0.5,maxBondLength=4.0):
#Loads up an ELFCAR, generates a starting neighbor list from voronoi tesselation
#Initial neighbors are dropped if bondlength is greater than maxBondLength
#Generates a bunch of points on a cylinder
#Maps the cylinder points across each neighbor pair
#If the average ELF is always above minELF accross this cylinder, atoms are bonded.
#Parse ELFCAR
elfcar=open(elfcarfile,"r").readlines()
(basis,atypes,atoms,header),elf = elfcarIO.read(elfcar)
lengths=array([basis[0][0],basis[1][1],basis[2][2]])
#Neighbors
bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
halfNeighbs = voronoiNeighbors(atoms,basis,style="half")
a=elf.shape
AvgElf=sum([sum([sum(line) for line in plane]) for plane in elf])/a[0]/a[1]/a[2]
if verbose:
print elfcarfile
print "Average ELF value:",AvgElf
#Evaluate the ELF between each nieghbor pair
#creates a bunch of points on a circle in the x-y plane
def circlePoints(center,radius):
N=4
ps=[float(p)/N*radius for p in range(-N,N+1)]
r2=radius*radius
points=list()
for x in ps:
for y in ps:
if (x**2+y**2)<=r2:
points.append(asarray([x,y]))
return asarray(points)
atoms=asarray([lengths[i]-v for i,v in enumerate(atoms.T)]).T
#Flip the ELF because its off, thanks a lot VASP.
elf=elf[::-1,::-1,::-1]
#Loop over atom pairs, generate cylinders
cylSlices = 10
cylRadius = 0.7
cirPoints = circlePoints(a,cylRadius).T
cylPoints = [vstack([cirPoints,zeros(cirPoints.shape[1])+float(z)]) for z in range(cylSlices+1)]
coordination=zeros(len(atoms))
neighborsELF=[list() for i in range(len(atoms))]
for i,ineighbs in enumerate(halfNeighbs):
a=atoms[i]
for j in ineighbs:
#copy the cylinder points so you can play with them...
localCyl=array(cylPoints)
#Find the minimum image atom
b=minImageAtom(a,atoms[j],basis)
l=minImageDist(a,b,basis)
if l>maxBondLength or l==0.0: continue
#How to map your cylinder onto the local atom
R=rotmatx([0,0,l],b-a)
#Loop over each cylinder slice
sliceParam=list()
for cir in localCyl:
#cir is stretched and rotated cylinder
cir[2]/=cylSlices/l
cir=asarray([dot(R,p)+a for p in cir.T]).T
#cir2 is cir with periodic boundary conditions applied and mapped to index space
cir2=asarray([((c/lengths[ind]*elf.shape[ind])%(elf.shape[ind]-1)) for ind,c in enumerate(cir)])
#Interpolation across cylinder
z=ndimage.map_coordinates(elf,cir2)
#Average ELF value across each slice.
sliceParam.append(sum(z)/len(z))
if min(sliceParam)>minELF:
#neighbor pair is bonded, count it!
neighborsELF[i].append(j)
neighborsELF[j].append(i)
return neighborsELF
