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)
#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 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)
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)
print "Usage:"
print "%s <CHGCAR0,CHGCAR1...> <maxL0,maxL1,maxL2...> <[N,n]ormalize by total avg charge> <Ninterps: x,y,z>"%(sys.argv[0])
print "Note, CHGCAR must be part of a cubic/rectangular simulation"
if len(sys.argv)<3:
usage()
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)