def test_cdse_supercell(self):
"""check supercell expansion for CdSe.
"""
cdse_222 = supercell(self.stru_cdse, (2, 2, 2))
# new atoms should be grouped together
elems = sum([8*[a.element] for a in self.stru_cdse], [])
elems_222 = [a.element for a in cdse_222]
self.assertEqual(elems, elems_222)
return
def superCell(self, mno, stru=None, replace=False):
from diffpy.Structure.expansion import supercell
if stru == None:
stru = self.convertDiffpyStru('xyz')
newstru = supercell(stru, mno)
if replace:
self.rawstru = newstru
self.rawstype = 'diffpy'
self.parseDiffpyStru(newstru)
return self.addProp(newstru)
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 test_ni_supercell(self):
"""check supercell expansion for Ni.
"""
ni_123 = supercell(self.stru_ni, (1, 2, 3))
self.assertEqual(6*len(self.stru_ni), len(ni_123))
a, b, c = self.stru_ni.lattice.abcABG()[:3]
a1, b2, c3 = ni_123.lattice.abcABG()[:3]
self.assertAlmostEqual(a, a1, 8)
self.assertAlmostEqual(b*2, b2, 8)
self.assertAlmostEqual(c*3, c3, 8)
x, y, z = self.stru_ni[-1].xyz
x1, y2, z3 = ni_123[-1*2*3].xyz
self.assertAlmostEqual(x/1, x1, 8)
self.assertAlmostEqual(y/2, y2, 8)
self.assertAlmostEqual(z/3, z3, 8)
return
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
--------------------Raman Spectroscopy and Neutron Scattering Laboratory
--------------------Professor Dmitry Reznik
Description: You have to go down to where 'masses' is introduced and enter the
masses of the atoms corresponding to the atoms in 'types'
"""
import numpy as np
from diffpy.Structure import loadStructure
from diffpy.Structure.expansion import supercell
infile = 'C_mp-667273_conventional_standard.cif'
outfile = 'c60'
c60 = loadStructure(infile)
c60_2x2x2 = supercell(c60, [12, 2, 2])
c60.write(outfile + '.xyz', 'xyz')
c60_2x2x2.write(outfile + '_2x2x2.xyz', 'xyz')
struct = c60_2x2x2
with open(outfile + '_2x2x2.xyz', 'r') as fid:
nat = int(fid.readline()) # number of atoms
fid.readline() # skip comment line
pos = np.zeros((nat, 4))
types = []
for i in range(nat):
tmp = fid.readline().strip().split()
if tmp[0] not in types:
types.append(tmp[0])
pos[i, 0] = types.index(tmp[0]) + 1
