def test_NaI(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Na', [0.0, 0.0, 0.0])
at2 = Atom('Na', [0.0, 0.5, 0.5])
at3 = Atom('Na', [0.5, 0.0, 0.5])
at4 = Atom('Na', [0.5, 0.5, 0.0])
at5 = Atom('I', [0.5, 0.5, 0.5])
at6 = Atom('I', [0.0, 0.0, 0.5])
at7 = Atom('I', [0.0, 0.5, 0.0])
at8 = Atom('I', [0.5, 0.0, 0.0])
naI = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8],
lattice = Lattice(6.482, 6.482, 6.482, 90, 90, 90),
sgid = 225 )
lines = []
for sym,pos in zip(naI.symbols, naI.xyz_cartn):
lines.append( sym+' %f %f %f' % tuple(pos) )
lines.append('\n')
naI_sup = supercell(naI, (2,2,2))
for sym,pos in zip(naI_sup.symbols, naI_sup.xyz_cartn):
lines.append(sym+' %f %f %f' % tuple(pos))
expected = open('expected-test_NaI-TestSuperCell').readlines()
self.assertEqual(len(lines), len(expected))
for l1, l2 in zip(lines, expected):
self.assertEqual(l1.strip(), l2.strip())
return
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.symbol] for a in self.stru_cdse], [])
elems_222 = [a.symbol for a in cdse_222]
self.assertEqual(elems, elems_222)
return
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.symbol] for a in self.stru_cdse], [])
elems_222 = [a.symbol for a in cdse_222]
self.assertEqual(elems, elems_222)
return
def test_writeStr_xyz_Supercell(self):
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure([at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid=225)
from matter.expansion import supercell
al_333 = supercell(self.stru4, (3, 3, 3))
s1 = al_333.writeStr(self.format)
def test_writeStr_xyz_Supercell(self):
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure( [ at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid = 225 )
from matter.expansion import supercell
al_333 = supercell(self.stru4, (3, 3, 3))
s1 = al_333.writeStr(self.format)
def test_al_supercell(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure( [ at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid = 225 )
al_sup = supercell(self.stru4, (3,3,3))
#print al_sup
return
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 matter.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 matter.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 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 test_naI_supercell(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Na', [0.0, 0.0, 0.0])
at2 = Atom('Na', [0.0, 0.5, 0.5])
at3 = Atom('Na', [0.5, 0.0, 0.5])
at4 = Atom('Na', [0.5, 0.5, 0.0])
at5 = Atom('I', [0.5, 0.5, 0.5])
at6 = Atom('I', [0.0, 0.0, 0.5])
at7 = Atom('I', [0.0, 0.5, 0.0])
at8 = Atom('I', [0.5, 0.0, 0.0])
naI = Structure([at1, at2, at3, at4, at5, at6, at7, at8],
lattice=Lattice(6.482, 6.482, 6.482, 90, 90, 90),
sgid=225)
for sym, pos in zip(naI.symbols, naI.xyz_cartn):
print sym + ' %f %f %f' % tuple(pos)
print
naI_sup = supercell(naI, (2, 2, 2))
for sym, pos in zip(naI_sup.symbols, naI_sup.xyz_cartn):
print sym + ' %f %f %f' % tuple(pos)
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 matter.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 matter.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
from matter.Lattice import Lattice
from matter.orm.BigStructure import Structure
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
hexag = Lattice(2.456, 2.456, 6.696, 90, 90, 120)
graphite = Structure( [ at1, at2], lattice = hexag, sgid = 194)
graphite.id = 'graphite'
print graphite
#lattice=Lattice(a=2.456, b=2.456, c=6.696, alpha=90, beta=90, gamma=120)
#C 0.333333 0.666667 0.000000 1.0000
#C 0.666667 0.333333 0.000000 1.0000
from matter.expansion import supercell
graphite_sheet = supercell(graphite, (10,10,1))
graphite_sheet.id = 'sheet'
print graphite_sheet.getChemicalFormula()
#C200
orm.save(graphite_sheet)
#orm.destroyAllTables()
from dsaw.db import connect
db = connect(db='postgres:///test', echo=True)
db.autocommit(True)
from dsaw.model.visitors.OrmManager import OrmManager
orm = OrmManager(db)
from matter.Atom import Atom
from matter.Lattice import Lattice
from matter.orm.BigStructure import Structure
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
hexag = Lattice(2.456, 2.456, 6.696, 90, 90, 120)
graphite = Structure([at1, at2], lattice=hexag, sgid=194)
graphite.id = 'graphite'
print graphite
#lattice=Lattice(a=2.456, b=2.456, c=6.696, alpha=90, beta=90, gamma=120)
#C 0.333333 0.666667 0.000000 1.0000
#C 0.666667 0.333333 0.000000 1.0000
from matter.expansion import supercell
graphite_sheet = supercell(graphite, (10, 10, 1))
graphite_sheet.id = 'sheet'
print graphite_sheet.getChemicalFormula()
#C200
orm.save(graphite_sheet)
#orm.destroyAllTables()