def unFractional(posfile):
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=True)
xs,ys,zs = zip(*atoms)
if sum(xs)/len(xs)>1.0 or sum(ys)/len(ys)>1.0 or sum(zs)/len(zs)>1.0:
print "Error: it appears these are already unfractional coordinates. %s"%posfile
exit(0)
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=False)
poscarIO.write(posfile,basis, atoms,atypes,head,frac=True,autoFrac=False)
def poscar2dump(pcarFile, lmpFile, scale=None):
try:
poscar = open(pcarFile, "r").readlines()
lammps = open(lmpFile, "w")
except IOError:
print "Error: %s Unable to open POSCAR/Lammps file." % sys.argv[0].split("/")[-1]
usage()
exit(0)
if scale == None:
scale = 1.0
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
# Convert from POSCAR style basis vectors to LAMMPS style boundaries.
xhi, yhi, zhi, xy, xz, yz = basis2lohi(basis)
basis = matrix([[xhi, 0, 0], [xy, yhi, 0], [xz, yz, zhi]])
N = sum(atypes)
Ntypes = len(atypes)
types = [i for i in flatten([[i] * v for i, v in enumerate(atypes)])]
data = "#Generated by %s from %s\n\n" % (sys.argv[0].split("/")[-1], pcarFile)
data += "%d atoms\n" % N
data += "%d atom types\n\n" % Ntypes
data += "0.0000 %4f xlo xhi\n" % xhi
data += "0.0000 %4f ylo yhi\n" % yhi
data += "0.0000 %4f zlo zhi\n" % zhi
data += "% 4f % 4f % 4f xy xz yz\n\n" % (xy, xz, yz)
data += "Atoms\n\n"
for i, (t, atom) in enumerate(zip(types, atoms)):
x, y, z = atom # (atom*basis).tolist()[0]
data += "\t %d \t %d \t % 5f\t% 5f\t% 5f\n" % (i + 1, t + 1, x, y, z)
lammps.write(data)
lammps.close()
def fractional(posfile):
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=True)
fraced=False
xs,ys,zs = zip(*atoms)
if sum(xs)/len(xs)>1.0 or sum(ys)/len(ys)>1.0 or sum(zs)/len(zs)>1.0:
fraced=True
if not fraced:
print "Error: it appears these are already fractional coordiantes. %s"%posfile
exit(0)
poscarIO.write(posfile,basis,atoms,atypes,head,frac=True)
def unFractional(posfile):
[basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
"r").readlines(),
frac_coord=True)
xs, ys, zs = zip(*atoms)
if sum(xs) / len(xs) > 1.0 or sum(ys) / len(ys) > 1.0 or sum(zs) / len(
zs) > 1.0:
print "Error: it appears these are already unfractional coordinates. %s" % posfile
exit(0)
[basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
"r").readlines(),
frac_coord=False)
poscarIO.write(posfile,
basis,
atoms,
atypes,
head,
frac=True,
autoFrac=False)
def fractional(posfile):
[basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
"r").readlines(),
frac_coord=True)
fraced = False
xs, ys, zs = zip(*atoms)
if sum(xs) / len(xs) > 1.0 or sum(ys) / len(ys) > 1.0 or sum(zs) / len(
zs) > 1.0:
fraced = True
if not fraced:
print "Error: it appears these are already fractional coordiantes. %s" % posfile
exit(0)
poscarIO.write(posfile, basis, atoms, atypes, head, frac=True)
def read(elfcar,swapxz=True):
basis,types,atoms,header,elfcar=poscarIO.read(elfcar)
atoms=asarray(atoms)
basis=asarray(basis)
poscardata=(basis,types,atoms,header)
elfcar.pop(0)
gridsz=[int(i) for i in elfcar.pop(0).split()]
if swapxz:
gridsz=[gridsz[2],gridsz[1],gridsz[0]]
Tot_pnts = reduce(operator.mul,gridsz)
elfdata=asarray(map(float,"".join(elfcar).split()[:Tot_pnts]))
elfdata.shape=gridsz
if swapxz:
elfdata=elfdata.swapaxes(0,2)
return poscardata,elfdata
def read(elfcar, swapxz=True):
basis, types, atoms, header, elfcar = poscarIO.read(elfcar)
atoms = asarray(atoms)
basis = asarray(basis)
poscardata = (basis, types, atoms, header)
elfcar.pop(0)
gridsz = [int(i) for i in elfcar.pop(0).split()]
if swapxz:
gridsz = [gridsz[2], gridsz[1], gridsz[0]]
Tot_pnts = reduce(operator.mul, gridsz)
elfdata = asarray(map(float, "".join(elfcar).split()[:Tot_pnts]))
elfdata.shape = gridsz
if swapxz:
elfdata = elfdata.swapaxes(0, 2)
return poscardata, elfdata
def read(chgcar, SP=False, frac_coord=True, swapxz=True):
basis, types, atoms, header, chgcar = poscarIO.read(chgcar, frac_coord)
poscardata = (basis, types, atoms, header)
chgcar.pop(0)
gridsz = map(int, chgcar.pop(0).split())
Tot_pnts = reduce(operator.mul, gridsz)
npline = len(chgcar[0].split())
cur = Tot_pnts / npline
if cur * npline < Tot_pnts:
cur += 1
#Divices by Tot_pnts to get absolute Charge (e.g. total # electrons)
chgdata = array(
map(lambda x: float(x) / Tot_pnts, "".join(chgcar[:cur]).split()))
if swapxz:
gridsz = [gridsz[2], gridsz[1], gridsz[0]]
chgdata.shape = gridsz
chgcar = chgcar[cur:]
#Spin polarized chgcar, first half is chgdata-summed, second is subtracted
if SP:
if len(chgcar) > 0:
chgdata_add = chgdata
chgcar = chgcar[2:]
chgdata_sub = array(
map(lambda x: float(x) / Tot_pnts,
"".join(chgcar[:cur]).split()))
chgdata_sub.shape = gridsz
else:
print "WARNING: Requested Spin-Polarized CHGCAR read from a non-spin polarized CHGCAR file."
SP = False
#To eliminate points that step outside a reasonable range
#avg = sum(chgdata)/len(chgdata)
#chgdata[where(chgdata > 3*avg)[0]]=avg
#Some chgcars seem to need their axes swapped, possible bug in VASP
if swapxz:
chgdata = swapaxes(chgdata, 0, 2)
if SP:
return poscardata, chgdata_add, chgdata_sub
return poscardata, chgdata
def read(chgcar,SP=False,frac_coord=True,swapxz=True):
basis,types,atoms,header,chgcar=poscarIO.read(chgcar,frac_coord)
poscardata=(basis,types,atoms,header)
chgcar.pop(0)
gridsz=map(int,chgcar.pop(0).split())
Tot_pnts = reduce(operator.mul,gridsz)
npline=len(chgcar[0].split())
cur=Tot_pnts/npline
if cur*npline<Tot_pnts:
cur+=1
#Divices by Tot_pnts to get absolute Charge (e.g. total # electrons)
chgdata=array(map(lambda x:float(x)/Tot_pnts,"".join(chgcar[:cur]).split()))
if swapxz:
gridsz=[gridsz[2],gridsz[1],gridsz[0]]
chgdata.shape=gridsz
chgcar=chgcar[cur:]
#Spin polarized chgcar, first half is chgdata-summed, second is subtracted
if SP:
if len(chgcar)>0:
chgdata_add=chgdata
chgcar = chgcar[2:]
chgdata_sub=array(map(lambda x:float(x)/Tot_pnts,"".join(chgcar[:cur]).split()))
chgdata_sub.shape=gridsz
else:
print "WARNING: Requested Spin-Polarized CHGCAR read from a non-spin polarized CHGCAR file."
SP=False
#To eliminate points that step outside a reasonable range
#avg = sum(chgdata)/len(chgdata)
#chgdata[where(chgdata > 3*avg)[0]]=avg
#Some chgcars seem to need their axes swapped, possible bug in VASP
if swapxz:
chgdata=swapaxes(chgdata,0,2)
if SP:
return poscardata,chgdata_add,chgdata_sub
return poscardata,chgdata
def poscar2dump(pcarFile, lmpFile, scale=None):
try:
poscar = open(pcarFile, "r").readlines()
lammps = open(lmpFile, "w")
except IOError:
print "Error: %s Unable to open POSCAR/Lammps file." % sys.argv[
0].split("/")[-1]
usage()
exit(0)
if scale == None:
scale = 1.0
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
#Convert from POSCAR style basis vectors to LAMMPS style boundaries.
xhi, yhi, zhi, xy, xz, yz = basis2lohi(basis)
basis = matrix([[xhi, 0, 0], [xy, yhi, 0], [xz, yz, zhi]])
N = sum(atypes)
Ntypes = len(atypes)
types = [i for i in flatten([[i] * v for i, v in enumerate(atypes)])]
data = "#Generated by %s from %s\n\n" % (sys.argv[0].split("/")[-1],
pcarFile)
data += "%d atoms\n" % N
data += "%d atom types\n\n" % Ntypes
data += "0.0000 %4f xlo xhi\n" % xhi
data += "0.0000 %4f ylo yhi\n" % yhi
data += "0.0000 %4f zlo zhi\n" % zhi
data += "% 4f % 4f % 4f xy xz yz\n\n" % (xy, xz, yz)
data += "Atoms\n\n"
for i, (t, atom) in enumerate(zip(types, atoms)):
x, y, z = atom #(atom*basis).tolist()[0]
data += "\t %d \t %d \t % 5f\t% 5f\t% 5f\n" % (i + 1, t + 1, x, y, z)
lammps.write(data)
lammps.close()
#Reading in the options and preparing for file reading
if len(sys.argv) < 2:
usage()
exit(0)
if path.isdir(sys.argv[1]):
outcar = open(sys.argv[1] + "/OUTCAR", "r")
poscar = open(sys.argv[1] + "/POSCAR",
"r") #need to use the poscar to fetch the atom types
elif path.isfile(sys.argv[1]):
outcar = False
poscar = open(sys.argv[1], "r")
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar.readlines())
[v1, v2, v3] = basis
atoms = zip(*atoms)
ax, ay, az = atoms[0], atoms[1], atoms[2]
afx, afy, afz = [0] * len(ax), [0] * len(ay), [0] * len(az)
types = [i for i in flatten([[i] * num for i, num in enumerate(atypes)])]
startconfig = 0
plotdisabled = False
if outcar:
if (len(sys.argv) >= 3):
startconfig = int(sys.argv[2])
if (len(sys.argv) >= 4):
if int(sys.argv[3]) == 0:
plotdisabled = True
if not (plotdisabled):
numbins = 1000
pcfile = "PCDAT_fromX"
if len(sys.argv) < 3:
usage()
exit(0)
if len(sys.argv) >= 4:
cutoff = float(sys.argv[3])
if len(sys.argv) >= 5:
numbins = int(sys.argv[4])
if len(sys.argv) == 6:
pcfile = sys.argv[5]
xdatfile = sys.argv[1]
pcarfile = sys.argv[2]
basis = poscarIO.read(open(pcarfile, "r").readlines())[0]
xdatcar = open(xdatfile, "r").readlines()
Natoms = int(xdatcar[0].split()[0])
lengths = array(map(lambda x: float(x) * 1e10, xdatcar[1].split()[1:4]))
xdatcar = xdatcar[5:]
delr = float(cutoff) / numbins
pcors = list()
i = 0
cnt = 0
atomconfigs = list()
while i < len(xdatcar):
i += 1
cnt += 1
atoms = map(lambda x: map(float, x.split()), xdatcar[i : i + Natoms])
iQ = array([simps([Q[abs(ir-it)]*dQ[it] for it,t in enumerate(rads[ir:])],x=rads[ir:]) for ir,r in enumerate(rads)])
return (-dQ + 2.0*pi*density*iQ)/rads
def sq_calc(rads,cr,qs):
dx = rads[1]-rads[0]
cq = array([ 4*pi*simps(rads*cr*np.sin(q*rads)/q,dx=dx) for q in qs])
return 1./(1. - density*cq)
def residual_qhr(coefs,y,x):
Q = interp(dx,coefs,x)
hr = y
return x*hr - hrq_calc(dr,Q,hr,x)
basis,atypes,atoms,head,poscar = poscarIO.read(open(sys.argv[1]).readlines())
atoms=array(atoms)
basis=array(basis)
rads,gr = radialDistribution(atoms,basis)
rads = array(rads)
hr = wsmooth(gr)[:-1] - 1#superSmooth(rads,gr)[:-20] - 1
#hr = gr - 1
dr=rads[1]-rads[0]
density = atoms.shape[0]/dot(cross(basis[0],basis[1]),basis[2])
rcut = rads[-1]
radsCut = [i for i in rads if i <= rcut]
hrCut = [hr[i] for i in range(len(rads)) if rads[i] <= rcut]
Nknots=70
print "Usage:"
print "%s <directory containing OUTCAR & POSCAR, or just POSCAR file> <optional: starting config #> <optional 0: disables plotting>"%(sys.argv[0].split("/")[-1])
#Reading in the options and preparing for file reading
if len(sys.argv)<2:
usage()
exit(0)
if path.isdir(sys.argv[1]):
outcar = open(sys.argv[1]+"/OUTCAR","r")
poscar = open(sys.argv[1]+"/POSCAR","r") #need to use the poscar to fetch the atom types
elif path.isfile(sys.argv[1]):
outcar = False
poscar = open(sys.argv[1],"r")
[basis,atypes,atoms,head,poscar]=poscarIO.read(poscar.readlines())
[v1,v2,v3]=basis
atoms=zip(*atoms)
ax,ay,az=atoms[0],atoms[1],atoms[2]
afx,afy,afz=[0]*len(ax),[0]*len(ay),[0]*len(az)
types=[i for i in flatten([[i]*num for i,num in enumerate(atypes)])]
startconfig=0
plotdisabled=False
if outcar:
if (len(sys.argv)>=3):
startconfig=int(sys.argv[2])
if (len(sys.argv)>=4):
if int(sys.argv[3])==0:
plotdisabled=True
if not(plotdisabled):
import poscarIO
def usage():
print "Usage:"
print "%s <elfcarfile> <elf cutoff [0-1]>"%sys.argv[0]
print "Plotting Styles: 0=none, 1=chg contours, 2=vacancy contours, 3=make a bunch of plots for a movie,\n4=chg contours with atoms, 5=make a bunch of plots for a movie with spheres"
exit(0)
if not(len(sys.argv) in [3,4]):
usage()
elfcar = open(sys.argv[1],"r").readlines()
cutev = float(sys.argv[2])
pstyle = int(sys.argv[3])
basis,types,catoms,header,elfcar = poscarIO.read(elfcar)
elfcar.pop(0)
gridsz=[int(i) for i in elfcar.pop(0).split()]
Tot_pnts = reduce(operator.mul,gridsz)
dataset=list()
for line in elfcar:
dataset+=[float(i) for i in line.split()]
dataset=dataset[:Tot_pnts] #chop off extra, invalid values
#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]
#nvacays=sum(vacData)
def usage():
print "Usage:"
print "%s <elfcarfile> <elf cutoff [0-1]>" % sys.argv[0]
print "Plotting Styles: 0=none, 1=chg contours, 2=vacancy contours, 3=make a bunch of plots for a movie,\n4=chg contours with atoms, 5=make a bunch of plots for a movie with spheres"
exit(0)
if not (len(sys.argv) in [3, 4]):
usage()
elfcar = open(sys.argv[1], "r").readlines()
cutev = float(sys.argv[2])
pstyle = int(sys.argv[3])
basis, types, catoms, header, elfcar = poscarIO.read(elfcar)
elfcar.pop(0)
gridsz = [int(i) for i in elfcar.pop(0).split()]
Tot_pnts = reduce(operator.mul, gridsz)
dataset = list()
for line in elfcar:
dataset += [float(i) for i in line.split()]
dataset = dataset[:Tot_pnts] #chop off extra, invalid values
#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]
#nvacays=sum(vacData)
lammpsFlag=False
xdatcarFlag=False
if "OUTCAR" in filename:
outcarFlag=True
elif "XDATCAR" in filename:
xdatcarFlag=True
poscarFile = sys.argv[3]
else:
lammpsFlag=True
neighbsfile=filename+".neighb"
header=["Spaces Seperate Neighbs, Commas Seperate Atoms, Lines Seperate Arrangements\n"]
lines=header
if xdatcarFlag:
basis,dummy,atoms,dummy,dummy = poscarIO.read(poscarFile)
nAtoms = len(atoms)
bounds = [[0,1],[0,1],[0,1]]
rcut /= basis[0][0]
for i,atoms in enumerate(xdatcarIO.read2(filename)):
neighbs = neighbors.neighbors(atoms,bounds,rcut)
lines += [",".join([" ".join(map(str,atomn)) for atomn in neighbs])+"\n"]
if outcarFlag:
nAtoms = outcarIO.nAtoms(filename)
basis = array(map(array,outcarIO.basis(filename)))
bounds = [[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
#Find the starting locations of atomic data in outcarfile
grepResults = subprocess.check_output("grep -b POSITION %s"%filename,shell=True).split("\n")
bytenums=[int(i.split(":")[0]) for i in grepResults if len(i)>2]
op = sys.argv[1]
if op[:2]=="BO":
lval=int(op[-1])
op="BO"
opFlag = True
configFile=sys.argv[2]
else:
usage()
exit(0)
#Parse POSCAR
j=0
if "POSCAR" in configFile or "CONTCAR" in configFile:
poscar=open(configFile,"r").readlines()
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
types=list()
for i in atypes:
types+=[j+1]*i
j+=1
elif "OUTCAR" in configFile:
TE,stress,basis,atoms,forces,types = outcarIO.outcarReadConfig(configFile,Nconfig)
#Parse LAMMPS DUMP
else:
basis,types,atoms = lammpsIO.readConfig(configFile,Nconfig)
ax,ay,az=map(np.array,zip(*atoms))
v1,v2,v3=basis
cutoff = 10.0
numbins = 1000
pcfile = "PCDAT_fromX"
if len(sys.argv) < 3:
usage()
exit(0)
if len(sys.argv) >= 4:
cutoff = float(sys.argv[3])
if len(sys.argv) >= 5:
numbins = int(sys.argv[4])
if len(sys.argv) == 6:
pcfile = sys.argv[5]
xdatfile = sys.argv[1]
pcarfile = sys.argv[2]
basis = poscarIO.read(open(pcarfile, "r").readlines())[0]
xdatcar = open(xdatfile, "r").readlines()
Natoms = int(xdatcar[0].split()[0])
lengths = array(map(lambda x: float(x) * 1E10, xdatcar[1].split()[1:4]))
xdatcar = xdatcar[5:]
delr = float(cutoff) / numbins
pcors = list()
i = 0
cnt = 0
atomconfigs = list()
while i < len(xdatcar):
i += 1
cnt += 1
atoms = map(lambda x: map(float, x.split()), xdatcar[i:i + Natoms])
def sq_calc(rads, cr, qs):
dx = rads[1] - rads[0]
cq = array(
[4 * pi * simps(rads * cr * np.sin(q * rads) / q, dx=dx) for q in qs])
return 1. / (1. - density * cq)
def residual_qhr(coefs, y, x):
Q = interp(dx, coefs, x)
hr = y
return x * hr - hrq_calc(dr, Q, hr, x)
basis, atypes, atoms, head, poscar = poscarIO.read(
open(sys.argv[1]).readlines())
atoms = array(atoms)
basis = array(basis)
rads, gr = radialDistribution(atoms, basis)
rads = array(rads)
hr = wsmooth(gr)[:-1] - 1 #superSmooth(rads,gr)[:-20] - 1
#hr = gr - 1
dr = rads[1] - rads[0]
density = atoms.shape[0] / dot(cross(basis[0], basis[1]), basis[2])
rcut = rads[-1]
radsCut = [i for i in rads if i <= rcut]
hrCut = [hr[i] for i in range(len(rads)) if rads[i] <= rcut]
Nknots = 70
v0_0 ...
...
vMN_0 ...
#instead of vertices, writing vertex coordinates
"""
if len(sys.argv)<4:
usage()
exit(0)
qvodata=open(sys.argv[1],"r").readlines()
qvfidata=open(sys.argv[2],"r").readlines()
poscar=open(sys.argv[3],"r").readlines()
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
basis=array(basis)
bounds=array([basis[0][0],basis[1][1],basis[2][2]])
polyverts=readQVo(qvodata)#,bounds)
polyplanes,neighbors=readQVFi(qvfidata)
#Chop off polyhedra of points outside simulation
polyplanes=polyplanes[:len(atoms)]
polyhedra=[points2polyhedron(verts,planes,plotting=False) for verts,planes in zip(polyverts,polyplanes)]
polyverts=readQVo(qvodata)
polyplanes,neighbors=readQVFi(qvfidata)
polyhedra=[points2polyhedron(verts,planes,plotting=False) for verts,planes in zip(polyverts[0:100],polyplanes[0:100])]
def poscarGrow(poscarName,outputName,cx,cy,cz):
poscar=open(poscarName,"r").readlines()
nCopies=cx*cy*cz
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar,frac_coord=True)
natoms=len(atoms)
v1,v2,v3=map(array,basis)
ax,ay,az=map(array,zip(*atoms))
#duplicate and tile
ax=array(split(tile(ax,nCopies),nCopies))
ay=array(split(tile(ay,nCopies),nCopies))
az=array(split(tile(az,nCopies),nCopies))
#Shift tiles in x dirn
shift=array([1]*natoms)
shiftfull=array([shift*j for j in range(cx)])
for i in range(cy*cz):
ax[i*cx+array(range(cx))]+=shiftfull
#Shift tiles in y dirn
shift=array([1]*natoms)
shiftfull=array([shift*(j/cx) for j in range(cy*cx)])
for i in range(cz):
ay[i*cx*cy+array(range(cy*cx))]+=shiftfull
#Shift tiles in z dirn
shift=array([1]*natoms)
shiftfull=array([shift*(j/cx/cy) for j in range(cy*cx*cz)])
az+=shiftfull
ax=ax.reshape([nCopies*natoms])
ay=ay.reshape([nCopies*natoms])
az=az.reshape([nCopies*natoms])
#need to normalize with new positions with respect to duplicated lattice params
v1*=cx
v2*=cy
v3*=cz
basis=[v1,v2,v3]
A=matrix([[float(cx),0.0,0.0],[0.0,float(cy),0.0],[0.0,0.0,float(cz)]])
ax,ay,az=zip(*[linalg.solve(A,array(p).T)[:] for p in zip(ax,ay,az)])
# if max(ax)>1.0 or max(ay)>1.0 or max(az)>1.0:
# continue
# exit(0)
atoms=zip(ax,ay,az)
#Sort atoms by type, as required by POSCAR
types=list()
j=0
for i in atypes:
types+=[j+1]*i
j+=1
newtypes=types*cx*cy*cz
atoms,types=zip(*sorted(zip(atoms,newtypes),key=lambda x:x[1]))
atypes=[i*nCopies for i in atypes]
poscarIO.write(outputName,basis,atoms,atypes,head)
return len(atoms),basis
qvfp.write("% 6.6f % 6.6f % 6.6f\n"%(atom[0],atom[1],atom[2]))
qvfp.flush()
qvfp.close()
return qvfile,basis,datoms,NRealAtoms
if __name__=="__main__":
def usage():
print "Usage: %s <poscar/contcar> <QV filename>"%sys.argv[0]
print "Makes a QV_input file from the poscar/contcar file. Employs periodic boundary conditions."
if len(sys.argv)<2:
usage()
exit(0)
poscarFile=open(sys.argv[1],"r").readlines()
basis,atypes,atoms,head,poscar = poscarIO.read(poscarFile)
qvfile=None
if len(sys.argv)>=3:
qvfile=sys.argv[2]
dummy,basis,datoms,nreal=poscar2qvoronoi(atoms,basis,atypes,qvfile)
else:
dummy,basis,datoms,nreal=poscar2qvoronoi(atoms,basis,atypes)
print "Bounds of simulation area are:"
for i in basis:
print i
print "Make sure to remove excess atoms outside these bounds after analysis."
if __name__ == "__main__":
def usage():
print "Usage:"
print "%s <POSCAR> //prints volume and atomic volume"
print "%s <POSCAR> <frac/unfrac>" % sys.argv[0].split("/")[-1]
print "%s <POSCAR> <ratio value>" % sys.argv[0].split("/")[-1]
if len(sys.argv) not in [2, 3]:
usage()
exit(0)
if len(sys.argv) == 2:
[basis, atypes, atoms, head,
poscar] = poscarIO.read(open(sys.argv[1], "r").readlines())
v = volume(basis)
print "Total Volume in AA^3 = %f" % v
print "Atomic Volume in AA^3 = %f" % (v / len(atoms))
elif sys.argv[2] == "frac":
fractional(sys.argv[1])
elif sys.argv[2] == "unfrac":
unFractional(sys.argv[1])
else:
try:
r = float(sys.argv[2])
ratio(sys.argv[1], r)
except:
print "Error, unrecognized volume arguement: %s" % sys.argv[2]
usage()
exit(0)
