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 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 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