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
def fieldNeighbors3D(atoms,atypes,basis,field,fieldSize,halfNeighbors=None,Ninterps=[7,7,15],cutoffs=None,loc=None):
#loc=["center","bond","half"]
[v1,v2,v3]=basis
latoms=array(atoms)
if loc==None:
loc="bond"
#Ensure simulation box is orthorhombic
if sum(map(fabs,v1))-fabs(v1[0]) > 1e-10 or \
sum(map(fabs,v2))-fabs(v2[1]) > 1e-10 or \
sum(map(fabs,v3))-fabs(v3[2]) > 1e-10:
print "Error: simulation axes are not sufficiently orthogonal. Use script poscarRectify.py and regenerate doscar"
exit(0)
cutFlag=True
if cutoffs==None:
cutFlag=False
else: #ensure cutoffs is a list and not just a float
cutoffs=list(cutoffs)
bounds=[[0.,v1[0]],[0.,v2[1]],[0.,v3[2]]]
simSize=asarray([v1[0],v2[1],v3[2]])
if halfNeighbors==None:
halfNeighbors=voronoiNeighbors(atoms=latoms,basis=basis,atypes=atypes,style='half')
#Interpolation and summation properties
grids=list()
if cutFlag:
avgGrids=[zeros(Ninterps) for i in range(len(cutoffs))]
bondcnts=zeros(len(cutoffs))
else:
avgGrid=zeros(Ninterps)
bondcnt=0
nlines=float(sum(map(len,halfNeighbors)))
delx=2.0/Ninterps[0]
dely=2.0/Ninterps[1]
#Local Grid size
delGrids=simSize/fieldSize
lGridSize=fieldSize
nlGridPoints=reduce(operator.mul,lGridSize)
for iNeighb,jNeighbors in enumerate(halfNeighbors):
if len(jNeighbors)==0:
continue
atomi=latoms[iNeighb]
for i,ai in enumerate(atomi):
if ai < 0.0:
atomi[i]+=simSize[i]
if ai > simSize[i]:
atomi[i]-=simSize[i]
#Make the local grid about the central atom
lGridCenter = map(int,atomi/simSize*fieldSize)
lGridBounds = [[lGridCenter[i]-lGridSize[i]/2,lGridCenter[i]+lGridSize[i]/2] for i in range(3)]
lGridBoundPoints = array([[lGridBounds[i][0]*delGrids[i],lGridBounds[i][1]*delGrids[i]] for i in range(3)])
lGridPoints = array( [ \
map(lambda x: x*delGrids[i],range(lGridCenter[i]-lGridSize[i]/2,lGridCenter[i]+lGridSize[i]/2)) \
for i in range(3) ] )
bnds=list()
lbnds=list()
bnds.append(list(lGridBounds))
lbnds.append(map(list,zip([0,0,0],lGridSize)))
while outOfBounds(bnds,fieldSize):
a=whichBounds(bnds,fieldSize)
bnds.append(map(list,bnds[a]))
lbnds.append(map(list,lbnds[a]))
for i in range(3):
if bnds[-1][i][1] > fieldSize[i]:
lbnds[a][i][1] = lGridSize[i]-(bnds[-1][i][1]-fieldSize[i])
lbnds[-1][i][0] = lGridSize[i]-(bnds[-1][i][1]-fieldSize[i])
lbnds[-1][i][1] = lbnds[-1][i][0]+(bnds[-1][i][1]-fieldSize[i])
bnds[-1][i][0] = 0
bnds[-1][i][1] -= fieldSize[i]
bnds[a][i][1] = fieldSize[i]
break
elif bnds[-1][i][0] < 0:
lbnds[-1][i][0] = 0
lbnds[-1][i][1] = -bnds[-1][i][0]
lbnds[a][i][0] = -bnds[-1][i][0]
bnds[-1][i][1] = fieldSize[i]
bnds[-1][i][0] += fieldSize[i]
bnds[a][i][0] = 0
break
#Now make the field
lfield=zeros(lGridSize)
for lbnd,bnd in zip(lbnds,bnds):
[[lxa,lxb],[lya,lyb],[lza,lzb]]=lbnd
[[xa,xb],[ya,yb],[za,zb]]=bnd
lfield[lxa:lxb, lya:lyb, lza:lzb]=field[xa:xb, ya:yb, za:zb]
#Loop over Neighboring atoms within the local grid
for jNeighb in jNeighbors:
atomj=latoms[jNeighb]
for i,aj in enumerate(atomj):
if aj < lGridPoints[i][0]:
atomj[i]+=simSize[i]
if aj > lGridPoints[i][-1]:
atomj[i]-=simSize[i]
d=dist(atomj,atomi)
#If this bond is longer than all the cutoffs than don't bother with it
if cutFlag and len([1 for i in cutoffs if d<=i])==0:
continue
#Change the location as requested
if loc=="bond":
delz=mag(atomj-atomi)/Ninterps[2]
Tran=(atomj-atomi)/2.+atomi
if loc=="half":
delz=mag(atomj-atomi)/(Ninterps[2]*2.)
Tran=(atomj-atomi)/4.+atomi
if loc=="center":
delz=dely
Tran=atomi
#Change of coordinate systems into atomj-atomi basis.
Rota=rotmatx(array([0.,0.,1.]),atomj-atomi)
xps=array([(i-Ninterps[0]/2)*delx for i in range(Ninterps[0])]*Ninterps[1]*Ninterps[2]).ravel()
yps=array([[(i-Ninterps[1]/2)*dely]*Ninterps[0] for i in range(Ninterps[1])]*Ninterps[2]).ravel()
zps=array([[(i-Ninterps[2]/2)*delz]*Ninterps[0]*Ninterps[1] for i in range(Ninterps[2])]).ravel()
ipnts=array([dot(Rota,array(pnt))+Tran for pnt in zip(xps,yps,zps)])
#Do the interpolation
if cutFlag:
for j,cut in enumerate(cutoffs):
if d <= cut:
bondcnts[j]+=1
if Ninterps[0]!=1:
grid=array([interp3d(ipnts[i],lGridBoundPoints,lGridPoints,lfield) for i in range(len(ipnts))]).reshape(Ninterps)
else:
grid=array([interp3d(ipnts[i],lGridBoundPoints,lGridPoints,lfield) for i in range(len(ipnts))]).reshape(Ninterps[1:])
grids.append(grid)
avgGrids[j]+=grid
else:
grid=array([interp3d(ipnts[i],lGridBoundPoints,lGridPoints,lfield) for i in range(len(ipnts))]).reshape(Ninterps)
grids.append(grid)
avgGrid+=grid
bondcnt+=1
if cutFlag:
for i,v in enumerate(bondcnts):
if v==0:
bondcnts[i]=1
return [avgGrid/bc for bc,avgGrid in zip(bondcnts,avgGrids)],grids,bondcnts
return avgGrid/bondcnt,grids,bondcnt
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
