class TestSuperCell(object):
def setUp(self):
alat = 1.42
sq3h = 3.**.5 * 0.5
self.sc = SuperCell(np.array(
[[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]], np.float64) *
alat,
nsc=[3, 3, 1])
def tearDown(self):
del self.sc
def test_repr(self):
repr(self.sc)
str(self.sc)
assert_false(self.sc == 'Not a SuperCell')
def test_nsc1(self):
sc = self.sc.copy()
sc.set_nsc([5, 5, 0])
assert_true(np.allclose([5, 5, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
def test_nsc2(self):
sc = self.sc.copy()
sc.set_nsc([0, 1, 0])
assert_true(np.allclose([1, 1, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
sc.set_nsc(a=3)
assert_true(np.allclose([3, 1, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
sc.set_nsc(b=3)
assert_true(np.allclose([3, 3, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
sc.set_nsc(c=5)
assert_true(np.allclose([3, 3, 5], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
def test_nsc3(self):
assert_raises(ValueError, self.sc.set_nsc, a=2)
assert_raises(ValueError, self.sc.set_nsc, b=2)
assert_raises(ValueError, self.sc.set_nsc, c=2)
assert_raises(ValueError, self.sc.set_nsc, [1, 2, 3])
def test_nsc4(self):
assert_true(self.sc.sc_index([0, 0, 0]) == 0)
for s in range(self.sc.n_s):
assert_true(self.sc.sc_index(self.sc.sc_off[s, :]) == s)
arng = np.arange(self.sc.n_s)
np.random.shuffle(arng)
sc_off = self.sc.sc_off[arng, :]
assert_true(np.all(self.sc.sc_index(sc_off) == arng))
def test_fill(self):
sc = self.sc.swapaxes(1, 2)
i = sc._fill([1, 1])
assert_true(i.dtype == np.int32)
i = sc._fill([1., 1.])
assert_true(i.dtype == np.float64)
for dt in [np.int32, np.int64, np.float32, np.float64, np.complex64]:
i = sc._fill([1., 1.], dt)
assert_true(i.dtype == dt)
i = sc._fill(np.ones([2], dt))
assert_true(i.dtype == dt)
def test_add_vacuum1(self):
sc = self.sc.copy()
for i in range(3):
s = sc.add_vacuum(10, i)
ax = self.sc.cell[i, :]
ax += ax / np.sum(ax**2)**.5 * 10
assert_true(np.allclose(ax, s.cell[i, :]))
def test_rotation1(self):
rot = self.sc.rotate(180, [0, 0, 1])
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = self.sc.rotate(m.pi, [0, 0, 1], radians=True)
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = rot.rotate(180, [0, 0, 1])
rot.cell[2, 2] *= -1
assert_true(np.allclose(rot.cell, self.sc.cell))
def test_rotation2(self):
rot = self.sc.rotatec(180)
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = self.sc.rotatec(m.pi, radians=True)
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = rot.rotatec(180)
rot.cell[2, 2] *= -1
assert_true(np.allclose(rot.cell, self.sc.cell))
def test_rotation3(self):
rot = self.sc.rotatea(180)
assert_true(np.allclose(rot.cell[0, :], self.sc.cell[0, :]))
assert_true(np.allclose(-rot.cell[2, 2], self.sc.cell[2, 2]))
rot = self.sc.rotateb(m.pi, radians=True)
assert_true(np.allclose(rot.cell[1, :], self.sc.cell[1, :]))
assert_true(np.allclose(-rot.cell[2, 2], self.sc.cell[2, 2]))
def test_swapaxes1(self):
sab = self.sc.swapaxes(0, 1)
assert_true(np.allclose(sab.cell[0, :], self.sc.cell[1, :]))
assert_true(np.allclose(sab.cell[1, :], self.sc.cell[0, :]))
def test_swapaxes2(self):
sab = self.sc.swapaxes(0, 2)
assert_true(np.allclose(sab.cell[0, :], self.sc.cell[2, :]))
assert_true(np.allclose(sab.cell[2, :], self.sc.cell[0, :]))
def test_swapaxes3(self):
sab = self.sc.swapaxes(1, 2)
assert_true(np.allclose(sab.cell[1, :], self.sc.cell[2, :]))
assert_true(np.allclose(sab.cell[2, :], self.sc.cell[1, :]))
def test_offset1(self):
off = self.sc.offset()
assert_true(np.allclose(off, [0, 0, 0]))
off = self.sc.offset([1, 1, 1])
cell = self.sc.cell[:, :]
assert_true(np.allclose(off, cell[0, :] + cell[1, :] + cell[2, :]))
def test_sc_index1(self):
sc_index = self.sc.sc_index([0, 0, 0])
assert_equal(sc_index, 0)
assert_raises(Exception, self.sc.sc_index, [100, 100, 100])
sc_index = self.sc.sc_index([0, 0, None])
assert_equal(len(sc_index), self.sc.nsc[2])
def test_sc_index2(self):
sc_index = self.sc.sc_index([[0, 0, 0], [1, 1, 0]])
assert_equal(len(sc_index), 2)
def test_cut1(self):
cut = self.sc.cut(2, 0)
assert_true(np.allclose(cut.cell[0, :] * 2, self.sc.cell[0, :]))
assert_true(np.allclose(cut.cell[1, :], self.sc.cell[1, :]))
def test_creation1(self):
# full cell
tmp1 = SuperCell([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# diagonal cell
tmp2 = SuperCell([1, 1, 1])
# cell parameters
tmp3 = SuperCell([1, 1, 1, 90, 90, 90])
tmp4 = SuperCell([1])
assert_true(np.allclose(tmp1.cell, tmp2.cell))
assert_true(np.allclose(tmp1.cell, tmp3.cell))
assert_true(np.allclose(tmp1.cell, tmp4.cell))
def test_creation2(self):
# full cell
class P(SuperCellChild):
def copy(self):
a = P()
a.set_supercell(self.sc)
return a
tmp1 = P()
tmp1.set_supercell([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# diagonal cell
tmp2 = P()
tmp2.set_supercell([1, 1, 1])
# cell parameters
tmp3 = P()
tmp3.set_supercell([1, 1, 1, 90, 90, 90])
tmp4 = P()
tmp4.set_supercell([1])
assert_true(np.allclose(tmp1.cell, tmp2.cell))
assert_true(np.allclose(tmp1.cell, tmp3.cell))
assert_true(np.allclose(tmp1.cell, tmp4.cell))
assert_true(len(tmp1._fill([0, 0, 0])) == 3)
assert_true(len(tmp1._fill_sc([0, 0, 0])) == 3)
assert_true(tmp1.is_orthogonal())
for i in range(3):
t2 = tmp2.add_vacuum(10, i)
assert_true(tmp1.cell[i, i] + 10 == t2.cell[i, i])
def test_creation3(self):
assert_raises(ValueError, self.sc.tocell, [3, 6])
assert_raises(ValueError, self.sc.tocell, [3, 4, 5, 6])
assert_raises(ValueError, self.sc.tocell, [3, 4, 5, 6, 7])
assert_raises(ValueError, self.sc.tocell, [3, 4, 5, 6, 7, 6, 7])
def test_rcell(self):
# LAPACK inverse algorithm implicitly does
# a transpose.
rcell = sli.inv(self.sc.cell) * 2. * np.pi
assert_true(np.allclose(rcell.T, self.sc.rcell))
def test_translate1(self):
sc = self.sc.translate([0, 0, 10])
assert_true(np.allclose(sc.cell[2, :2], self.sc.cell[2, :2]))
assert_true(np.allclose(sc.cell[2, 2], self.sc.cell[2, 2] + 10))
def test_center1(self):
assert_true(
np.allclose(self.sc.center(),
np.sum(self.sc.cell, axis=0) / 2))
for i in [0, 1, 2]:
assert_true(np.allclose(self.sc.center(i), self.sc.cell[i, :] / 2))
def test_pickle(self):
import pickle as p
s = p.dumps(self.sc)
n = p.loads(s)
assert_true(self.sc == n)
assert_false(self.sc != n)
s = SuperCell([1, 1, 1])
assert_false(self.sc == s)
def test_orthogonal(self):
assert_false(self.sc.is_orthogonal())
def test_fit1(self):
g = graphene()
gbig = g.repeat(40, 0).repeat(40, 1)
gbig.xyz[:, :] += (np.random.rand(len(gbig), 3) - 0.5) * 0.01
sc = g.sc.fit(gbig)
assert_true(np.allclose(sc.cell, gbig.cell))
def test_fit2(self):
g = graphene(orthogonal=True)
gbig = g.repeat(40, 0).repeat(40, 1)
gbig.xyz[:, :] += (np.random.rand(len(gbig), 3) - 0.5) * 0.01
sc = g.sc.fit(gbig)
assert_true(np.allclose(sc.cell, gbig.cell))
def test_fit3(self):
g = graphene(orthogonal=True)
gbig = g.repeat(40, 0).repeat(40, 1)
gbig.xyz[:, :] += (np.random.rand(len(gbig), 3) - 0.5) * 0.01
sc = g.sc.fit(gbig, axis=0)
assert_true(np.allclose(sc.cell[0, :], gbig.cell[0, :]))
assert_true(np.allclose(sc.cell[1:, :], g.cell[1:, :]))
def test_fit4(self):
g = graphene(orthogonal=True)
gbig = g.repeat(40, 0).repeat(40, 1)
gbig.xyz[:, :] += (np.random.rand(len(gbig), 3) - 0.5) * 0.01
sc = g.sc.fit(gbig, axis=[0, 1])
assert_true(np.allclose(sc.cell[0:2, :], gbig.cell[0:2, :]))
assert_true(np.allclose(sc.cell[2, :], g.cell[2, :]))
def test_parallel1(self):
g = graphene(orthogonal=True)
gbig = g.repeat(40, 0).repeat(40, 1)
assert_true(g.sc.parallel(gbig.sc))
assert_true(gbig.sc.parallel(g.sc))
g = g.rotatea(90)
assert_false(g.sc.parallel(gbig.sc))
def test_sc_indices():
sc = SuperCell([1] * 3, nsc=[3, 5, 7])
for i in range(sc.n_s):
assert i == sc.sc_index(sc.sc_off[i])
class TestSuperCell(object):
def setUp(self):
alat = 1.42
sq3h = 3.**.5 * 0.5
self.sc = SuperCell(np.array([[1.5, sq3h, 0.],
[1.5, -sq3h, 0.],
[0., 0., 10.]], np.float64) * alat, nsc=[3, 3, 1])
def tearDown(self):
del self.sc
def test_repr(self):
print(self.sc)
assert_false(self.sc == 'Not a SuperCell')
def test_nsc1(self):
sc = self.sc.copy()
sc.set_nsc([5, 5, 0])
assert_true(np.allclose([5, 5, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
def test_nsc2(self):
sc = self.sc.copy()
sc.set_nsc([0, 1, 0])
assert_true(np.allclose([1, 1, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
sc.set_nsc(a=3)
assert_true(np.allclose([3, 1, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
sc.set_nsc(b=3)
assert_true(np.allclose([3, 3, 1], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
sc.set_nsc(c=5)
assert_true(np.allclose([3, 3, 5], sc.nsc))
assert_true(len(sc.sc_off) == np.prod(sc.nsc))
def test_nsc3(self):
assert_raises(ValueError, self.sc.set_nsc, a=2)
assert_raises(ValueError, self.sc.set_nsc, b=2)
assert_raises(ValueError, self.sc.set_nsc, c=2)
assert_raises(ValueError, self.sc.set_nsc, [1, 2, 3])
def test_nsc4(self):
assert_true(self.sc.sc_index([0, 0, 0]) == 0)
def test_rotation1(self):
rot = self.sc.rotate(180, [0, 0, 1])
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = self.sc.rotate(m.pi, [0, 0, 1], radians=True)
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = rot.rotate(180, [0, 0, 1])
rot.cell[2, 2] *= -1
assert_true(np.allclose(rot.cell, self.sc.cell))
def test_rotation2(self):
rot = self.sc.rotatec(180)
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = self.sc.rotatec(m.pi, radians=True)
rot.cell[2, 2] *= -1
assert_true(np.allclose(-rot.cell, self.sc.cell))
rot = rot.rotatec(180)
rot.cell[2, 2] *= -1
assert_true(np.allclose(rot.cell, self.sc.cell))
def test_rotation3(self):
rot = self.sc.rotatea(180)
assert_true(np.allclose(rot.cell[0, :], self.sc.cell[0, :]))
assert_true(np.allclose(-rot.cell[2, 2], self.sc.cell[2, 2]))
rot = self.sc.rotateb(m.pi, radians=True)
assert_true(np.allclose(rot.cell[1, :], self.sc.cell[1, :]))
assert_true(np.allclose(-rot.cell[2, 2], self.sc.cell[2, 2]))
def test_swapaxes1(self):
sab = self.sc.swapaxes(0, 1)
assert_true(np.allclose(sab.cell[0, :], self.sc.cell[1, :]))
assert_true(np.allclose(sab.cell[1, :], self.sc.cell[0, :]))
def test_swapaxes2(self):
sab = self.sc.swapaxes(0, 2)
assert_true(np.allclose(sab.cell[0, :], self.sc.cell[2, :]))
assert_true(np.allclose(sab.cell[2, :], self.sc.cell[0, :]))
def test_swapaxes3(self):
sab = self.sc.swapaxes(1, 2)
assert_true(np.allclose(sab.cell[1, :], self.sc.cell[2, :]))
assert_true(np.allclose(sab.cell[2, :], self.sc.cell[1, :]))
def test_offset1(self):
off = self.sc.offset()
assert_true(np.allclose(off, [0, 0, 0]))
off = self.sc.offset([1, 1, 1])
cell = self.sc.cell[:, :]
assert_true(np.allclose(off, cell[0, :] + cell[1, :] + cell[2, :]))
def test_sc_index1(self):
sc_index = self.sc.sc_index([0, 0, 0])
assert_equal(sc_index, 0)
assert_raises(Exception, self.sc.sc_index, [100, 100, 100])
sc_index = self.sc.sc_index([0, 0, None])
assert_equal(len(sc_index), self.sc.nsc[2])
def test_cut1(self):
cut = self.sc.cut(2, 0)
assert_true(np.allclose(cut.cell[0, :] * 2, self.sc.cell[0, :]))
assert_true(np.allclose(cut.cell[1, :], self.sc.cell[1, :]))
def test_creation(self):
# full cell
tmp1 = SuperCell([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# diagonal cell
tmp2 = SuperCell([1, 1, 1])
# cell parameters
tmp3 = SuperCell([1, 1, 1, 90, 90, 90])
tmp4 = SuperCell([1])
assert_true(np.allclose(tmp1.cell, tmp2.cell))
assert_true(np.allclose(tmp1.cell, tmp3.cell))
assert_true(np.allclose(tmp1.cell, tmp4.cell))
def test_creation2(self):
# full cell
class P(SuperCellChild):
pass
tmp1 = P()
tmp1.set_supercell([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# diagonal cell
tmp2 = P()
tmp2.set_supercell([1, 1, 1])
# cell parameters
tmp3 = P()
tmp3.set_supercell([1, 1, 1, 90, 90, 90])
tmp4 = P()
tmp4.set_supercell([1])
assert_true(np.allclose(tmp1.cell, tmp2.cell))
assert_true(np.allclose(tmp1.cell, tmp3.cell))
assert_true(np.allclose(tmp1.cell, tmp4.cell))
def test_creation3(self):
assert_raises(ValueError, self.sc.tocell, [3, 6])
assert_raises(ValueError, self.sc.tocell, [3, 4, 5, 6])
assert_raises(ValueError, self.sc.tocell, [3, 4, 5, 6, 7])
assert_raises(ValueError, self.sc.tocell, [3, 4, 5, 6, 7, 6, 7])
def test_rcell(self):
# LAPACK inverse algorithm implicitly does
# a transpose.
rcell = sli.inv(self.sc.cell) * 2. * np.pi
assert_true(np.allclose(rcell.T, self.sc.rcell))
def test_translate1(self):
sc = self.sc.translate([0, 0, 10])
assert_true(np.allclose(sc.cell[2, :2], self.sc.cell[2, :2]))
assert_true(np.allclose(sc.cell[2, 2], self.sc.cell[2, 2]+10))
def test_center1(self):
assert_true(np.allclose(self.sc.center(), np.sum(self.sc.cell, axis=0) / 2))
for i in [0, 1, 2]:
assert_true(np.allclose(self.sc.center(i), self.sc.cell[i, :] / 2))
def test_pickle(self):
import pickle as p
s = p.dumps(self.sc)
n = p.loads(s)
assert_true(self.sc == n)
assert_false(self.sc != n)
s = SuperCell([1, 1, 1])
assert_false(self.sc == s)
def test_orthogonal(self):
assert_false(self.sc.is_orthogonal())