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
"""
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
"""
exit(0)
chgcarfiles = sys.argv[1].split(",")
bondLengths = map(float, sys.argv[2].split(","))
normalize = False
if len(sys.argv) > 3:
if sys.argv[3][0] in ["n", "N"]:
normalize = True
verbose = True
Ninterps = [15, 15, 15]
if len(sys.argv) > 4:
Ninterps = map(int, sys.argv[4].split(","))
for chgcarfile in chgcarfiles:
avgGrids, bondCounts = chgcarBondAnalysis(chgcarfile,
bondLengths,
normalize,
verbose,
Ninterps=Ninterps)
chgcar = open(chgcarfile, "r").readlines()
poscardata, gridSize, chg = chgcarIO.read(chgcar)
for avgGrid, bondCount, cutoff in zip(avgGrids, bondCounts,
bondLengths):
vtkfname = chgcarfile + "_cut%2.2f_NBond%d.vtk" % (cutoff,
bondCount)
chgcarIO.writeVTK(vtkfname, poscardata, avgGrid.shape, avgGrid)
def usage():
print "Usage:"
print "%s <chgfile> <charge cutoff (eV)> <plotting style: 0,1,2>"%sys.argv[0]
print "Plotting Styles: 0=none, 1=chg contours, 2=vacancy contours"
sys.exit()
if not(len(sys.argv) in [3,4]):
usage()
chgcar = open(sys.argv[1],"r").readlines()
cutev = float(sys.argv[2])
pstyle = int(sys.argv[3])
global dataset
(basis,types,atoms,header),gridsz,dataset = chgcarIO.read(chgcar)
#dataset.shape=gridsz[0]*gridsz[1]*gridsz[2]
Tot_pnts = reduce(operator.mul,gridsz)
#dataset=vclearout(dataset,avgval*3)
#dataset=array([log(i/avgval) for i in dataset])
#dataset is 1d
#dhist=pl.hist(dataset,bins=10000,range=(0,1000),normed=True,histtype='step')[0]
#f=open("CHGDENS_HIST","w")
#pickle.dump(dhist,f)
#f.close()
#Convert the dataset from charge density to vacancy
#def vval(a,b): return 1 if a<b else 0
#vacData=[vval(i,cutev) for i in dataset]
print "Usage:"
print "%s <chgfile> <charge cutoff (eV)> <plotting style: 0,1,2>" % sys.argv[
0]
print "Plotting Styles: 0=none, 1=chg contours, 2=vacancy contours"
sys.exit()
if not (len(sys.argv) in [3, 4]):
usage()
chgcar = open(sys.argv[1], "r").readlines()
cutev = float(sys.argv[2])
pstyle = int(sys.argv[3])
global dataset
(basis, types, atoms, header), gridsz, dataset = chgcarIO.read(chgcar)
#dataset.shape=gridsz[0]*gridsz[1]*gridsz[2]
Tot_pnts = reduce(operator.mul, gridsz)
#dataset=vclearout(dataset,avgval*3)
#dataset=array([log(i/avgval) for i in dataset])
#dataset is 1d
#dhist=pl.hist(dataset,bins=10000,range=(0,1000),normed=True,histtype='step')[0]
#f=open("CHGDENS_HIST","w")
#pickle.dump(dhist,f)
#f.close()
#Convert the dataset from charge density to vacancy
#def vval(a,b): return 1 if a<b else 0
#vacData=[vval(i,cutev) for i in dataset]
from vtk import *
#mine
import chgcarIO
def usage():
print "Usage:"
print "%s <chg-vtk-file>"%sys.argv[0]
sys.exit()
if not(len(sys.argv) in [2]):
usage()
fname=sys.argv[1]
vtkfile=fname+".vtk"
poscarData,chgcarData=chgcarIO.read(open(fname,"r").readlines(),swapxz=False)
chgcarIO.writeVTK(vtkfile,poscarData,chgcarData)
#---------------------------------
#Below is taken from website
#x---------------------------------
# Interaction with an Isosurface visualization
# A reader
reader = vtkStructuredPointsReader()
reader.SetFileName(vtkfile)
renWin = vtkRenderWindow()
renWin.SetWindowName("%s"%vtkfile)
renWin.SetPolygonSmoothing(1)
#renWin.SetAAFrames(2)
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
if clean==True:
chgdata=chgdata.ravel()
def clearoutlier(i,a): return 1.0 if i>a else i/a
avgval=scipy.sum(chgdata)/Tot_pnts
vclearout=vectorize(clearoutlier)
chgdata=vclearout(chgdata,avgval)
#chgdata=array([i/avgval for i in chgdata])
chgdata.shape=gridsz
#chgdata=chgdata.ravel()
for i in range(gridsz[0]):
for j in range(gridsz[1]):
vtkfile.write(" ".join(map(lambda x:str(x),chgdata[i][j]))+"\n")
"""
def usage():
print "Usage: %s <input chgcar> <optional:output vtk filename>"%sys.argv[0].split("/")[-1]
if len(sys.argv)<2:
usage()
exit(0)
chgfname=sys.argv[1]
if len(sys.argv)==3:
vtkfname=sys.argv[2]
else:
vtkfname=chgfname+".vtk"
poscardata,chgdata=chgcarIO.read(open(chgfname,"r").readlines())
chgcarIO.writeVTK(vtkfname,poscardata,chgdata,clean=True)
chgcarfiles=sys.argv[1].split(",")
bondLengths=map(float,sys.argv[2].split(","))
normalize=False
if len(sys.argv)>3:
if sys.argv[3][0] in ["n","N"]:
normalize=True
verbose=True
Ninterps=[50,50]
if len(sys.argv)>4:
Ninterps=map(int,sys.argv[5].split(","))
for chgcarfile in chgcarfiles:
avgGrids,grids,bondCounts=chgcarBondAnalysis(chgcarfile,bondLengths,normalize,verbose,Ninterps=Ninterps,loc="center")
chgcar=open(chgcarfile,"r").readlines()
poscardata,gridSize,chg = chgcarIO.read(chgcar)
"""
for avgGrid,bondCount,cutoff in zip(avgGrids,bondCounts,bondLengths):
#vtkfname=chgcarfile+"_cut%2.2f_NBond%d.vtk"%(cutoff,bondCount)
#chgcar.writeVTK(vtkfname,poscardata,avgGrid.shape,avgGrid)
pl.imshow(avgGrid[0])
pl.show()
"""
for i,grid in enumerate(grids):
pl.savetxt("grid%d_%s.data"%(i,chgcarfile),grid)
pl.imshow(grid)
pl.show()
def clearoutlier(i,a): return 1.0 if i>a else i/a
avgval=scipy.sum(chgdata)/Tot_pnts
vclearout=vectorize(clearoutlier)
chgdata=vclearout(chgdata,avgval)
#chgdata=array([i/avgval for i in chgdata])
chgdata.shape=gridsz
#chgdata=chgdata.ravel()
for i in range(gridsz[0]):
for j in range(gridsz[1]):
vtkfile.write(" ".join(map(lambda x:str(x),chgdata[i][j]))+"\n")
"""
def usage():
print "Usage: %s <input chgcar> <optional:output vtk filename>" % sys.argv[
0].split("/")[-1]
if len(sys.argv) < 2:
usage()
exit(0)
chgfname = sys.argv[1]
if len(sys.argv) == 3:
vtkfname = sys.argv[2]
else:
vtkfname = chgfname + ".vtk"
poscardata, chgdata = chgcarIO.read(open(chgfname, "r").readlines())
chgcarIO.writeVTK(vtkfname, poscardata, chgdata, clean=True)
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
usage()
exit(0)
rVals = None
if len(sys.argv) == 3:
chgcarfile = sys.argv[1]
rVals = [float(sys.argv[2])]
if len(sys.argv) == 5:
chgcarfile = sys.argv[1]
rStart = float(sys.argv[2])
rStop = float(sys.argv[3])
rSteps = int(sys.argv[4])
rVals = [(rStop - rStart) * i / rSteps + rStart for i in range(rSteps)]
chgcar = open(chgcarfile, "r").readlines()
pcar, chg = chgcarIO.read(chgcar)
(basis, atypes, atoms, head) = pcar
#R space distance between grid points
delR = sum([np.linalg.norm(basis[i]) / chg.shape[i] for i in range(3)]) / 3.0
bounds = chg.shape
xGrids, yGrids, zGrids = [range(i) for i in bounds]
gridCoords = [i for i in itertools.product(xGrids, yGrids, zGrids)]
for rCut in rVals:
chgs = list()
coordShifts = sphereCoords(delR, rCut)
N = coordShifts.shape[0]
a = 0
for gc in gridCoords:
x, y, z = np.split(gen2BCoords(gc, coordShifts, bounds), 3, axis=1)
import sys
import pylab as pl
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")
usage()
exit(0)
rVals=None
if len(sys.argv)==3:
chgcarfile = sys.argv[1]
rVals = [float(sys.argv[2])]
if len(sys.argv)==5:
chgcarfile = sys.argv[1]
rStart = float(sys.argv[2])
rStop = float(sys.argv[3])
rSteps = int(sys.argv[4])
rVals = [(rStop-rStart)*i/rSteps+rStart for i in range(rSteps)]
chgcar=open(chgcarfile,"r").readlines()
pcar,chg = chgcarIO.read(chgcar)
(basis,atypes,atoms,head)=pcar
#R space distance between grid points
delR = sum([np.linalg.norm(basis[i])/chg.shape[i] for i in range(3)])/3.0
bounds=chg.shape
xGrids,yGrids,zGrids=[range(i) for i in bounds]
gridCoords=[i for i in itertools.product(xGrids,yGrids,zGrids)]
for rCut in rVals:
chgs=list()
coordShifts=sphereCoords(delR,rCut)
N=coordShifts.shape[0]
a=0
for gc in gridCoords:
x,y,z=np.split(gen2BCoords(gc,coordShifts,bounds),3,axis=1)
