def elfcarBondAnalysis(elfcarFile,elfcarNeighbsFile,verbose=True):
#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.
ELFlevel=0.5
#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
elfcarNeighbs=open(elfcarNeighbsFile,"r").readlines()
neighbors=[map(int,line.split()) for line in elfcarNeighbs[1:]]
halfNeighbs=full2half(neighbors)
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=11
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
cylRadius = 2.0
cirPoints = circlePoints(a,cylRadius).T
cirPoints = vstack([cirPoints,zeros(cirPoints.shape[1])])
coordination=zeros(len(atoms))
gridx,gridy=np.mgrid[0:1:20j,0:1:20j]*4.2-2.1
cirPoints2=array(cirPoints)
cirPoints2=cirPoints2[:2].T
f,ax =plt.subplots(1,1)
rs=[list() for i in halfNeighbs]
rsFlat=list()
for i,ineighbs in enumerate(halfNeighbs):
a=atoms[i]
for j in ineighbs:
#copy the cylinder points so you can play with them...
localCir=array(cirPoints)
#Find the minimum image atom
b=minImageAtom(a,atoms[j],basis)
l=minImageDist(a,b,basis)
#How to map your cylinder onto the local atom
R=rotmatx([0,0,l],b-a)
#Loop over each cylinder slice
sliceParam=list()
localCir[2]=l/2.
cir=asarray([dot(R,p)+a for p in localCir.T]).T
#cir2 is circle 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)
#Generate a grid and find the desired contour on the bond crosssection
gridz=interpolate.griddata(cirPoints2,z,(gridx,gridy),fill_value=0)
ac=ax.contour(gridx,gridy,gridz,levels=[ELFlevel],linewidths=5,colors="black")
#take the longest list (this is the bond)
m=0
if len(ac.collections[0].get_paths()):
m=np.asarray([len(v.vertices) for v in ac.collections[0].get_paths()]).argmax()
midCircle= ac.collections[0].get_paths()[m].vertices.T
n=midCircle.shape[1]
#Find the center of the bond and calculate the radius
com=[midCircle[0].sum()/n,midCircle[1].sum()/n]
midCircle[0]-=com[0]
midCircle[1]-=com[1]
r=0
for m in midCircle.T:
r+=(m[0]**2+m[1]**2)**(0.5)
r/=n
rs[i].append(r)
rs[j].append(r)
rsFlat.append(r)
# pl.contour(gridx,gridy,gridz,levels=[0.5],linewidths=5,colors="black")
# pl.show()
#avgCircle+=jCircle
#avgCircle/=sum(map(len,neighbors))/2.
#pl.show()
return rs,rsFlat,atoms,neighbors,basis
pl.hist(rsFlat,bins=[i/35.+0.5 for i in range(100)])
pl.show()
"""
#Plotting of atoms with bond radius.
from mayavi import mlab
fig=mlab.figure(bgcolor=(1.0,1.0,1.0))
#coordination of atoms
coord=map(lambda x: float(x.split()[0]), open(elfcarfile+".Coord","r").readlines()[1:])
mx=max(coord)
mn=min(coord)
dl=mx-mn
coord=map(lambda x: (x-mn)/dl,coord)
mlab.points3d(atoms[:,0],atoms[:,1],atoms[:,2],coord,scale_factor=1.0,scale_mode='none')
#bond radius
mx=max(rsFlat)
mn=min(rsFlat)
dl=mx-mn
for i,ineighbs in enumerate(neighbors):
a=atoms[i]
for i2,j in enumerate(ineighbs):
b=minImageAtom(a,atoms[j],basis)
c=(rs[i][i2]-mn)/dl
mlab.plot3d([a[0],b[0]],[a[1],b[1]],[a[2],b[2]],color=(c,1-c,1-c),tube_radius=0.1,tube_sides=10)
mlab.show()
#need to do this plot separately
pl.plot([a[0],b[0]],[a[1],b[1]],[a[2],b[2]],c=r/1.6,lw=10)
rlen.append(r)
if r<3.2:
mxLen=max(mxLen,rlen[-1])
mnLen=min(mnLen,rlen[-1])
mnSoft,mxSoft=0.15,4.0
mnLen,mxLen = 2.40,2.9
pairs=list()
ds=list()
cs=list()
for i in range(nIon):
d=0
n=0
for v,j in enumerate(neighbs[i]):
r=dist_periodic(atoms[i],atoms[j],lengths)
b=minImageAtom(atoms[i],atoms[j],basis)
#if r<3.2:
#Based on softness (blue is soft, red is not-soft)
cSoft=(s2[i][v]-mnSoft)/(mxSoft-mnSoft)
#Based on bond length
cLen=(r-mnLen)/(mxLen-mnLen)
#mlab.plot3d([atoms[i,0],b[0]],[atoms[i,1],b[1]],[atoms[i,2],b[2]],color=(1-cSoft,cSoft,cSoft),tube_radius=0.1,tube_sides=10)
#mlab.plot3d([atoms[i,0],b[0]],[atoms[i,1],b[1]],[atoms[i,2],b[2]],color=(1-cLen,cLen,cLen),tube_radius=0.1,tube_sides=10)
#mlab.plot3d([atoms[i,0],b[0]],[atoms[i,1],b[1]],[atoms[i,2],b[2]],color=(0.8,0.8,0.8),tube_radius=0.1,tube_sides=10)
d+=cSoft
n+=1
rlen.append(r)
if r < 3.2:
mxLen = max(mxLen, rlen[-1])
mnLen = min(mnLen, rlen[-1])
mnSoft, mxSoft = 0.15, 4.0
mnLen, mxLen = 2.40, 2.9
pairs = list()
ds = list()
cs = list()
for i in range(nIon):
d = 0
n = 0
for v, j in enumerate(neighbs[i]):
r = dist_periodic(atoms[i], atoms[j], lengths)
b = minImageAtom(atoms[i], atoms[j], basis)
#if r<3.2:
#Based on softness (blue is soft, red is not-soft)
cSoft = (s2[i][v] - mnSoft) / (mxSoft - mnSoft)
#Based on bond length
cLen = (r - mnLen) / (mxLen - mnLen)
#mlab.plot3d([atoms[i,0],b[0]],[atoms[i,1],b[1]],[atoms[i,2],b[2]],color=(1-cSoft,cSoft,cSoft),tube_radius=0.1,tube_sides=10)
#mlab.plot3d([atoms[i,0],b[0]],[atoms[i,1],b[1]],[atoms[i,2],b[2]],color=(1-cLen,cLen,cLen),tube_radius=0.1,tube_sides=10)
#mlab.plot3d([atoms[i,0],b[0]],[atoms[i,1],b[1]],[atoms[i,2],b[2]],color=(0.8,0.8,0.8),tube_radius=0.1,tube_sides=10)
d += cSoft
n += 1
if n == 0:
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 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