def makeEllipsoid(S, a, b=None, c=None):
"""Cut a structure out of another one.
Arguments
S -- A Structure instance
a -- primary equatorial radius (along x-axis)
b -- secondary equatorial radius (along y-axis). If b is None
(default) then it is set equal to a
c -- polar radius (along z-axis). If c is None (default), then it is
set equal to a.
Returns a new structure instance
"""
if b is None: b = a
if c is None: c = a
sabc = array([a, b, c])
# Create a supercell large enough for the ellipsoid
frac = S.lattice.fractional(sabc)
mno = map(ceil, 2*frac)
mno = max(map(ceil, 2*frac))*array([1,1,1])
# Make the supercell
from diffpy.Structure.expansion import supercell
newS = supercell(S, mno)
lat = newS.lattice
# Find the central atom
ncenter = findCenter(newS)
cxyz = lat.cartesian(newS[ncenter].xyz)
delList = []
N = len(newS)
j = N
for i in xrange(N):
j -= 1
# Calculate (x/a)**2 + (y/b)**2 + (z/c)**2
xyz = lat.cartesian(newS[j].xyz)
darray = ((xyz-cxyz)/sabc)**2
d = sum(darray)**0.5
# Discard atom if (x/a)**2 + (y/b)**2 + (z/c)**2 > 1
if d > 1:
delList.append(j)
for i in delList:
newS.pop(i)
return newS
def makeEllipsoid(S, a, b=None, c=None):
"""Cut a structure out of another one.
Arguments
S -- A Structure instance
a -- primary equatorial radius (along x-axis)
b -- secondary equatorial radius (along y-axis). If b is None
(default) then it is set equal to a
c -- polar radius (along z-axis). If c is None (default), then it is
set equal to a.
Returns a new structure instance
"""
if b is None: b = a
if c is None: c = a
sabc = array([a, b, c])
# Create a supercell large enough for the ellipsoid
frac = S.lattice.fractional(sabc)
mno = map(ceil, 2 * frac)
mno = max(map(ceil, 2 * frac)) * array([1, 1, 1])
# Make the supercell
from diffpy.Structure.expansion import supercell
newS = supercell(S, mno)
lat = newS.lattice
# Find the central atom
ncenter = findCenter(newS)
cxyz = lat.cartesian(newS[ncenter].xyz)
delList = []
N = len(newS)
j = N
for i in xrange(N):
j -= 1
# Calculate (x/a)**2 + (y/b)**2 + (z/c)**2
xyz = lat.cartesian(newS[j].xyz)
darray = ((xyz - cxyz) / sabc)**2
d = sum(darray)**0.5
# Discard atom if (x/a)**2 + (y/b)**2 + (z/c)**2 > 1
if d > 1:
delList.append(j)
for i in delList:
newS.pop(i)
return newS
def makeCuboctahedron(S, dist):
"""Make a cuboctahedron nanoparticle.
Arguments
S -- A Structure instance
dist -- Distance from center to nearest face
Returns a new structure instance
"""
# Create a supercell large enough for the ellipsoid
frac = S.lattice.fractional((dist, dist, dist))
mno = map(ceil, 2 * frac)
# Make the supercell
from diffpy.Structure.expansion import supercell
newS = supercell(S, mno)
lat = newS.lattice
# Find the central atom
ncenter = findCenter(newS)
# Make the cuboctahedron template
from geometry.composites import cuboctahedron
from geometry.operations import translate, rotate
c0 = translate(cuboctahedron(dist), lat.cartesian(newS[ncenter].xyz))
# Cut out an octahedron
from geometry import locate
N = len(newS)
j = N
for i in xrange(N):
xyz = lat.cartesian(newS[N - 1 - i].xyz)
if locate(xyz, c0) == 1:
newS.pop(N - 1 - i)
return newS
def makeCuboctahedron(S, dist):
"""Make a cuboctahedron nanoparticle.
Arguments
S -- A Structure instance
dist -- Distance from center to nearest face
Returns a new structure instance
"""
# Create a supercell large enough for the ellipsoid
frac = S.lattice.fractional((dist, dist, dist))
mno = map(ceil, 2*frac)
# Make the supercell
from diffpy.Structure.expansion import supercell
newS = supercell(S, mno)
lat = newS.lattice
# Find the central atom
ncenter = findCenter(newS)
# Make the cuboctahedron template
from geometry.composites import cuboctahedron
from geometry.operations import translate, rotate
c0 = translate(cuboctahedron(dist), lat.cartesian(newS[ncenter].xyz))
# Cut out an octahedron
from geometry import locate
N = len(newS)
j = N
for i in xrange(N):
xyz = lat.cartesian(newS[N-1-i].xyz)
if locate(xyz, c0) == 1:
newS.pop(N-1-i)
return newS