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
print "Usage:" print "%s <ELFCAR> <bond-ELF-cutoff=0.5>" % (sys.argv[0]) print "Note ELFCAR must be part of a cubic/rectangular simulation" if len(sys.argv) < 2: usage() exit(0) 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., basis[0][0]], [0., basis[1][1]], [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])
import numpy as np def usage(): print "%s CHGCARfiles"%sys.argv[0].split("/")[-1] if len(sys.argv)<2: usage() exit(0) chgelfcarfiles = sorted(sys.argv[1:],key=lambda x:str(x.split("_")[-1])) m=0 for chgelfcarfile in chgelfcarfiles: car=open(chgelfcarfile,"r").readlines() if "CHG" in chgelfcarfile: pcar,field = chgcarIO.read(car) if "ELF" in chgelfcarfile: pcar,field = elfcarIO.read(car) (basis,atypes,atoms,head)=pcar volume=np.dot(np.cross(basis[0],basis[1]),basis[2])/len(atoms) field=field.ravel() field=map(float,field.tolist()) #field.sort() vals,bins,dummy=pl.hist(field,100,alpha=0.5,visible=False) s=sum(vals) vals=[v/s*100 for v in vals] m=max(m,max(vals)) bins=map(lambda x:(x[0]+x[1])/2.,zip(bins[:-1],bins[1:])) pl.plot(bins,vals,label="Step: %s"%chgelfcarfile.split("_")[-1].split("/")[0]+" Vol:%4.4f"%volume) #pl.xticks([x/20.*2.5 - 0.5 for x in range(20)]) pl.ylabel("Percent Volume") pl.xlabel("Charge (meV)") pl.ylim([0,m*1.1])
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
print "Usage:" print "%s <ELFCAR> <bond-ELF-cutoff=0.5>" % (sys.argv[0]) print "Note ELFCAR must be part of a cubic/rectangular simulation" if len(sys.argv) < 2: usage() exit(0) 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]
if len(sys.argv) < 3: usage() elfcar = open(sys.argv[1],"r").readlines() pstyle = int(sys.argv[2]) #If saving a picture, assume remote use which requires Agg if pstyle==0: fname=sys.argv[3] matplotlib.use("Agg") else: from matplotlib import pyplot as P import pylab as pl global dataset (basis,types,atoms,header),gridsz,dataset = elfcarIO.read(elfcar) Npnts = reduce(operator.mul,gridsz) #VASP outputs CHGCAR/ELFCARs in the order Z,Y,X. Transfrom this to X,Y,Z dataset=array(dataset).reshape(list(reversed(gridsz))) #[x,y,z] dataset=dataset.swapaxes(0,2) #dataset=log(dataset) global atoms,atomcolors,atombounds #Ge: 1.22 #Sb: 1.4 #Te: 1.4 #Au: 1.35 #Cu: 1.4 #Ce: 1.8 radii=[0.7]
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