def test_op3(self, setup):
g = Geometry([[i, 0, 0] for i in range(100)],
Atom(6, R=1.01),
sc=[100])
H = Hamiltonian(g, dtype=np.int32)
Hc = H.copy()
del Hc
# Create initial stuff
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = i
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert h.dtype == np.int32
h = func(1.)
assert h.dtype == np.float64
if op != 'pow':
h = func(1.j)
assert h.dtype == np.complex128
H = H.copy(dtype=np.float64)
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert h.dtype == np.float64
h = func(1.)
assert h.dtype == np.float64
if op != 'pow':
h = func(1.j)
assert h.dtype == np.complex128
H = H.copy(dtype=np.complex128)
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert h.dtype == np.complex128
h = func(1.)
assert h.dtype == np.complex128
if op != 'pow':
h = func(1.j)
assert h.dtype == np.complex128
def test_op3(self):
g = Geometry([[i, 0,0] for i in range(100)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32)
# Create initial stuff
for i in range(10):
j = range(i*4, i*4+3)
H[0, j] = i
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert_equal(h.dtype, np.int32)
h = func(1.)
assert_equal(h.dtype, np.float64)
if op != 'pow':
h = func(1.j)
assert_equal(h.dtype, np.complex128)
H = H.copy(dtype=np.float64)
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert_equal(h.dtype, np.float64)
h = func(1.)
assert_equal(h.dtype, np.float64)
if op != 'pow':
h = func(1.j)
assert_equal(h.dtype, np.complex128)
H = H.copy(dtype=np.complex128)
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert_equal(h.dtype, np.complex128)
h = func(1.)
assert_equal(h.dtype, np.complex128)
if op != 'pow':
h = func(1.j)
assert_equal(h.dtype, np.complex128)
def test_set_nsc1(self, setup):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
H = Hamiltonian(setup.g.copy())
H.construct([R, param])
h = H.copy()
H.set_nsc(nsc=[None, 1, 1])
assert H.nnz == 6
H.set_nsc(nsc=[1, None, 1])
assert H.nnz == 4
h.set_nsc(nsc=[1, None, 1])
assert h.nnz == 6
g = setup.g.copy()
g.set_nsc([1] * 3)
Hg = Hamiltonian(g)
Hg.construct([R, param])
assert Hg.nnz == 4
assert Hg.spsame(H)
class TestHamiltonian(object):
def setUp(self):
bond = 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) *
bond,
nsc=[3, 3, 1])
C = Atom(Z=6, R=bond * 1.01, orbs=1)
self.g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) *
bond,
atom=C,
sc=self.sc)
self.H = Hamiltonian(self.g)
self.HS = Hamiltonian(self.g, orthogonal=False)
C = Atom(Z=6, R=bond * 1.01, orbs=2)
self.g2 = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) *
bond,
atom=C,
sc=self.sc)
self.H2 = Hamiltonian(self.g2)
self.HS2 = Hamiltonian(self.g2, orthogonal=False)
def tearDown(self):
del self.sc
del self.g
del self.H
del self.HS
del self.g2
del self.H2
del self.HS2
def test_objects(self):
assert_true(len(self.H.xyz) == 2)
assert_true(self.g.no == len(self.H))
assert_true(len(self.HS.xyz) == 2)
assert_true(self.g.no == len(self.HS))
assert_true(len(self.H2.xyz) == 2)
assert_true(self.g2.no == len(self.H2))
assert_true(len(self.HS2.xyz) == 2)
assert_true(self.g2.no == len(self.HS2))
def test_dtype(self):
assert_true(self.H.dtype == np.float64)
assert_true(self.HS.dtype == np.float64)
assert_true(self.H2.dtype == np.float64)
assert_true(self.HS2.dtype == np.float64)
def test_ortho(self):
assert_true(self.H.orthogonal)
assert_false(self.HS.orthogonal)
def test_set1(self):
self.H.H[0, 0] = 1.
assert_true(self.H[0, 0] == 1.)
assert_true(self.H[1, 0] == 0.)
self.H.empty()
self.HS.H[0, 0] = 1.
assert_true(self.HS.H[0, 0] == 1.)
assert_true(self.HS.H[1, 0] == 0.)
assert_true(self.HS.S[0, 0] == 0.)
assert_true(self.HS.S[1, 0] == 0.)
self.HS.S[0, 0] = 1.
assert_true(self.HS.H[0, 0] == 1.)
assert_true(self.HS.H[1, 0] == 0.)
assert_true(self.HS.S[0, 0] == 1.)
assert_true(self.HS.S[1, 0] == 0.)
# delete before creating the same content
self.HS.empty()
# THIS IS A CHECK FOR BACK_WARD COMPATIBILITY!
with warnings.catch_warnings():
warnings.simplefilter('ignore')
self.HS[0, 0] = 1., 1.
assert_true(self.HS.H[0, 0] == 1.)
assert_true(self.HS.S[0, 0] == 1.)
self.HS.empty()
def test_set2(self):
self.H.construct([(0.1, 1.5), (1., 0.1)])
assert_true(self.H[0, 0] == 1.)
assert_true(self.H[1, 0] == 0.1)
assert_true(self.H[0, 1] == 0.1)
self.H.empty()
def test_set3(self):
self.HS.construct([(0.1, 1.5), ((1., 2.), (0.1, 0.2))])
assert_true(self.HS.H[0, 0] == 1.)
assert_true(self.HS.S[0, 0] == 2.)
assert_true(self.HS.H[1, 1] == 1.)
assert_true(self.HS.S[1, 1] == 2.)
assert_true(self.HS.H[1, 0] == 0.1)
assert_true(self.HS.H[0, 1] == 0.1)
assert_true(self.HS.S[1, 0] == 0.2)
assert_true(self.HS.S[0, 1] == 0.2)
assert_true(self.HS.nnz == len(self.HS) * 4)
self.HS.empty()
def test_set4(self):
for ia, io in self.H:
# Find atoms close to 'ia'
idx = self.H.geom.close(ia, R=(0.1, 1.5))
self.H[io, idx[0]] = 1.
self.H[io, idx[1]] = 0.1
assert_true(self.H.H[0, 0] == 1.)
assert_true(self.H.H[1, 1] == 1.)
assert_true(self.H.H[1, 0] == 0.1)
assert_true(self.H.H[0, 1] == 0.1)
assert_true(self.H.nnz == len(self.H) * 4)
self.H.empty()
@attr('slow')
def test_set5(self):
# Test of HUGE construct
g = self.g.tile(10, 0).tile(10, 1).tile(10, 2)
H = Hamiltonian(g)
H.construct([(0.1, 1.5), (1., 0.1)])
assert_true(H.H[0, 0] == 1.)
assert_true(H.H[1, 1] == 1.)
assert_true(H.H[1, 0] == 0.1)
assert_true(H.H[0, 1] == 0.1)
# This is graphene
# on-site == len(H)
# nn == 3 * len(H)
assert_true(H.nnz == len(H) * 4)
del H
def test_iter1(self):
self.HS.construct([(0.1, 1.5), ((1., 2.), (0.1, 0.2))])
nnz = 0
for io, jo in self.HS.iter_nnz():
nnz = nnz + 1
assert_equal(nnz, self.HS.nnz)
nnz = 0
for io, jo in self.HS.iter_nnz(0):
nnz = nnz + 1
# 3 nn and 1 onsite
assert_equal(nnz, 4)
self.HS.empty()
def test_iter2(self):
self.HS.H[0, 0] = 1.
nnz = 0
for io, jo in self.HS.iter_nnz():
nnz = nnz + 1
assert_equal(nnz, self.HS.nnz)
assert_equal(nnz, 1)
self.HS.empty()
@raises(ValueError)
def test_construct_raise(self):
# Test that construct fails with more than one
# orbital
self.H2.construct([(0.1, 1.5), (1., 0.1)])
def test_getitem1(self):
H = self.H
# graphene Hamiltonian
H.construct([(0.1, 1.5), (0.1, 0.2)])
# Assert all connections
assert_equal(H[0, 0], 0.1)
assert_equal(H[0, 1], 0.2)
assert_equal(H[0, 1, (-1, 0)], 0.2)
assert_equal(H[0, 1, (0, -1)], 0.2)
assert_equal(H[1, 0], 0.2)
assert_equal(H[1, 1], 0.1)
assert_equal(H[1, 0, (1, 0)], 0.2)
assert_equal(H[1, 0, (0, 1)], 0.2)
H[0, 0, (0, 1)] = 0.3
assert_equal(H[0, 0, (0, 1)], 0.3)
H[0, 1, (0, 1)] = -0.2
assert_equal(H[0, 1, (0, 1)], -0.2)
H.empty()
def test_delitem1(self):
H = self.H
H.construct([(0.1, 1.5), (0.1, 0.2)])
assert_equal(H[0, 1], 0.2)
del H[0, 1]
assert_equal(H[0, 1], 0.0)
H.empty()
def test_sp2HS(self):
csr = self.H.tocsr(0)
H = Hamiltonian.fromsp(self.H.geom, csr)
assert_true(H.spsame(self.H))
def test_op1(self):
g = Geometry([[i, 0, 0] for i in range(100)],
Atom(6, R=1.01),
sc=[100])
H = Hamiltonian(g, dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = i
# i+
H += 1
for jj in j:
assert_equal(H[0, jj], i + 1)
assert_equal(H[1, jj], 0)
# i-
H -= 1
for jj in j:
assert_equal(H[0, jj], i)
assert_equal(H[1, jj], 0)
# i*
H *= 2
for jj in j:
assert_equal(H[0, jj], i * 2)
assert_equal(H[1, jj], 0)
# //
H //= 2
for jj in j:
assert_equal(H[0, jj], i)
assert_equal(H[1, jj], 0)
# i**
H **= 2
for jj in j:
assert_equal(H[0, jj], i**2)
assert_equal(H[1, jj], 0)
def test_op2(self):
g = Geometry([[i, 0, 0] for i in range(100)],
Atom(6, R=1.01),
sc=[100])
H = Hamiltonian(g, dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = i
# +
s = H + 1
for jj in j:
assert_equal(s[0, jj], i + 1)
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
# -
s = H - 1
for jj in j:
assert_equal(s[0, jj], i - 1)
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
# -
s = 1 - H
for jj in j:
assert_equal(s[0, jj], 1 - i)
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
# *
s = H * 2
for jj in j:
assert_equal(s[0, jj], i * 2)
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
# //
s = s // 2
for jj in j:
assert_equal(s[0, jj], i)
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
# **
s = H**2
for jj in j:
assert_equal(s[0, jj], i**2)
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
# ** (r)
s = 2**H
for jj in j:
assert_equal(s[0, jj], 2**H[0, jj])
assert_equal(H[0, jj], i)
assert_equal(s[1, jj], 0)
def test_op3(self):
g = Geometry([[i, 0, 0] for i in range(100)],
Atom(6, R=1.01),
sc=[100])
H = Hamiltonian(g, dtype=np.int32)
Hc = H.copy()
del Hc
# Create initial stuff
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = i
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert_equal(h.dtype, np.int32)
h = func(1.)
assert_equal(h.dtype, np.float64)
if op != 'pow':
h = func(1.j)
assert_equal(h.dtype, np.complex128)
H = H.copy(dtype=np.float64)
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert_equal(h.dtype, np.float64)
h = func(1.)
assert_equal(h.dtype, np.float64)
if op != 'pow':
h = func(1.j)
assert_equal(h.dtype, np.complex128)
H = H.copy(dtype=np.complex128)
for op in ['add', 'sub', 'mul', 'pow']:
func = getattr(H, '__{}__'.format(op))
h = func(1)
assert_equal(h.dtype, np.complex128)
h = func(1.)
assert_equal(h.dtype, np.complex128)
if op != 'pow':
h = func(1.j)
assert_equal(h.dtype, np.complex128)
def test_op4(self):
g = Geometry([[i, 0, 0] for i in range(100)],
Atom(6, R=1.01),
sc=[100])
H = Hamiltonian(g, dtype=np.int32)
# Create initial stuff
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = i
h = 1 + H
assert_equal(h.dtype, np.int32)
h = 1. + H
assert_equal(h.dtype, np.float64)
h = 1.j + H
assert_equal(h.dtype, np.complex128)
h = 1 - H
assert_equal(h.dtype, np.int32)
h = 1. - H
assert_equal(h.dtype, np.float64)
h = 1.j - H
assert_equal(h.dtype, np.complex128)
h = 1 * H
assert_equal(h.dtype, np.int32)
h = 1. * H
assert_equal(h.dtype, np.float64)
h = 1.j * H
assert_equal(h.dtype, np.complex128)
h = 1**H
assert_equal(h.dtype, np.int32)
h = 1.**H
assert_equal(h.dtype, np.float64)
h = 1.j**H
assert_equal(h.dtype, np.complex128)
def test_cut1(self):
# Test of eigenvalues using a cut
# Hamiltonian
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g)
Hg.construct([R, param])
g = self.g.tile(2, 0).tile(2, 1)
H = Hamiltonian(g)
H.construct([R, param])
# Create cut Hamiltonian
Hc = H.cut(2, 1).cut(2, 0)
eigc = Hc.eigh()
eigg = Hg.eigh()
assert_true(np.allclose(eigc, eigg))
assert_true(np.allclose(Hg.eigh(), Hc.eigh()))
del Hc, H
def test_cut2(self):
# Test of eigenvalues using a cut
# Hamiltonian
R, param = [0.1, 1.5], [(1., 1.), (0.1, 0.1)]
# Create reference
Hg = Hamiltonian(self.g, orthogonal=False)
Hg.construct([R, param])
g = self.g.tile(2, 0).tile(2, 1)
H = Hamiltonian(g, orthogonal=False)
H.construct([R, param])
# Create cut Hamiltonian
Hc = H.cut(2, 1).cut(2, 0)
eigc = Hc.eigh()
eigg = Hg.eigh()
assert_true(np.allclose(Hg.eigh(), Hc.eigh()))
del Hc, H
def test_eig1(self):
# Test of eigenvalues
R, param = [0.1, 1.5], [1., 0.1]
g = self.g.tile(2, 0).tile(2, 1).tile(2, 2)
H = Hamiltonian(g)
H.construct((R, param), eta=True)
eig1 = H.eigh()
for i in range(2):
assert_true(np.allclose(eig1, H.eigh()))
H.eigsh(n=4)
H.empty()
del H
def test_eig2(self):
# Test of eigenvalues
HS = self.HS.copy()
HS.construct([(0.1, 1.5), ((1., 1.), (0.1, 0.1))])
eig1 = HS.eigh()
for i in range(2):
assert_true(np.allclose(eig1, HS.eigh()))
self.HS.empty()
def test_eig3(self):
self.HS.construct([(0.1, 1.5), ((1., 1.), (0.1, 0.1))])
BS = PathBZ(self.HS, [[0, 0, 0], [0.5, 0.5, 0]], 10)
eigs = BS.array().eigh()
assert_equal(len(BS), eigs.shape[0])
assert_equal(len(self.HS), eigs.shape[1])
eig2 = np.array([eig for eig in BS.yields().eigh()])
assert_true(np.allclose(eigs, eig2))
self.HS.empty()
def test_spin1(self):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32, spin=2)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
def test_spin2(self):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32, spin=2)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
H2 = Hamiltonian(g, Spin(2), dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
H2 = Hamiltonian(g, Spin('polarized'), dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
def test_non_colinear1(self):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=4)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(2):
assert_true(np.allclose(H.eigh(), eig1))
assert_true(len(eig1) == len(H))
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('non-colinear'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
assert_true(H1.spsame(H))
eig1 = H1.eigh()
# Check TimeSelector
for i in range(2):
assert_true(np.allclose(H1.eigh(), eig1))
assert_true(np.allclose(H.eigh(), H1.eigh()))
def test_so1(self):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=8)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
H[i, i, 4] = 0.1
H[i, i, 5] = 0.1
H[i, i, 6] = 0.1
H[i, i, 7] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(2):
assert_true(np.allclose(H.eigh(), eig1))
assert_true(len(H.eigh()) == len(H))
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
assert_true(H1.spsame(H))
eig1 = H1.eigh()
# Check TimeSelector
for i in range(2):
assert_true(np.allclose(H1.eigh(), eig1))
assert_true(np.allclose(H.eigh(), H1.eigh()))
def test_finalized(self):
assert_false(self.H.finalized)
self.H.H[0, 0] = 1.
self.H.finalize()
assert_true(self.H.finalized)
assert_true(self.H.nnz == 1)
self.H.empty()
assert_false(self.HS.finalized)
self.HS.H[0, 0] = 1.
self.HS.S[0, 0] = 1.
self.HS.finalize()
assert_true(self.HS.finalized)
assert_true(self.HS.nnz == 1)
self.HS.empty()
@attr('slow')
def test_tile1(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g.tile(2, 0).tile(2, 1).tile(2, 2))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(self.g)
H.construct([R, param])
H = H.tile(2, 0).tile(2, 1).tile(2, 2, eta=True)
assert_true(Hg.spsame(H))
@attr('slow')
def test_tile2(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g.tile(2, 0))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(self.g)
H.construct([R, param])
H = H.tile(2, 0)
assert_true(Hg.spsame(H))
@attr('slow')
def test_tile3(self):
R, param = [0.1, 1.1, 2.1, 3.1], [1., 2., 3., 4.]
# Create reference
g = Geometry([[0] * 3], Atom('H', R=[4.]), sc=[1.] * 3)
g.set_nsc([7] * 3)
# Now create bigger geometry
G = g.tile(2, 0).tile(2, 1).tile(2, 2)
HG = Hamiltonian(G.tile(2, 0).tile(2, 1).tile(2, 2))
HG.construct([R, param])
HG.finalize()
H = Hamiltonian(G)
H.construct([R, param])
H.finalize()
H = H.tile(2, 0).tile(2, 1).tile(2, 2)
assert_true(HG.spsame(H))
def test_tile4(self):
def func(self, ia, idxs, idxs_xyz=None):
idx = self.geom.close(ia, R=[0.1, 1.43], idx=idxs)
io = self.geom.a2o(ia)
# Set on-site on first and second orbital
odx = self.geom.a2o(idx[0])
self[io, odx] = -1.
self[io + 1, odx + 1] = 1.
# Set connecting
odx = self.geom.a2o(idx[1])
self[io, odx] = 0.2
self[io, odx + 1] = 0.01
self[io + 1, odx] = 0.01
self[io + 1, odx + 1] = 0.3
self.H2.construct(func)
Hbig = self.H2.tile(3, 0).tile(3, 1)
gbig = self.H2.geom.tile(3, 0).tile(3, 1)
H = Hamiltonian(gbig)
H.construct(func)
assert_true(H.spsame(Hbig))
self.H2.empty()
@attr('slow')
def test_repeat1(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g.repeat(2, 0))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(self.g)
H.construct([R, param])
H = H.repeat(2, 0)
assert_true(Hg.spsame(H))
@attr('slow')
def test_repeat2(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
Hg = Hamiltonian(self.g.repeat(2, 0).repeat(2, 1).repeat(2, 2))
Hg.construct([R, param])
Hg.finalize()
H = Hamiltonian(self.g)
H.construct([R, param])
H = H.repeat(2, 0).repeat(2, 1).repeat(2, 2, eta=True)
assert_true(Hg.spsame(H))
@attr('slow')
def test_repeat3(self):
R, param = [0.1, 1.1, 2.1, 3.1], [1., 2., 3., 4.]
# Create reference
g = Geometry([[0] * 3], Atom('H', R=[4.]), sc=[1.] * 3)
g.set_nsc([7] * 3)
# Now create bigger geometry
G = g.repeat(2, 0).repeat(2, 1).repeat(2, 2)
HG = Hamiltonian(G.repeat(2, 0).repeat(2, 1).repeat(2, 2))
HG.construct([R, param])
HG.finalize()
H = Hamiltonian(G)
H.construct([R, param])
H.finalize()
H = H.repeat(2, 0).repeat(2, 1).repeat(2, 2)
assert_true(HG.spsame(H))
@attr('slow')
def test_repeat4(self):
def func(self, ia, idxs, idxs_xyz=None):
idx = self.geom.close(ia, R=[0.1, 1.43], idx=idxs)
io = self.geom.a2o(ia)
# Set on-site on first and second orbital
odx = self.geom.a2o(idx[0])
self[io, odx] = -1.
self[io + 1, odx + 1] = 1.
# Set connecting
odx = self.geom.a2o(idx[1])
self[io, odx] = 0.2
self[io, odx + 1] = 0.01
self[io + 1, odx] = 0.01
self[io + 1, odx + 1] = 0.3
self.H2.construct(func)
Hbig = self.H2.repeat(3, 0).repeat(3, 1)
gbig = self.H2.geom.repeat(3, 0).repeat(3, 1)
H = Hamiltonian(gbig)
H.construct(func)
assert_true(H.spsame(Hbig))
self.H2.empty()
def test_sub1(self):
R, param = [0.1, 1.5], [1., 0.1]
# Create reference
H = Hamiltonian(self.g)
H.construct([R, param])
H.finalize()
# Tiling in this direction will not introduce
# any new connections.
# So tiling and removing is a no-op (but
# increases vacuum in 3rd lattice vector)
Hg = Hamiltonian(self.g.tile(2, 2))
Hg.construct([R, param])
Hg = Hg.sub(range(len(self.g)))
Hg.finalize()
assert_true(Hg.spsame(H))
