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=3)
self.g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) *
bond,
atom=C,
sc=self.sc)
self.D = DynamicalMatrix(self.g)
def func(D, ia, idxs, idxs_xyz):
idx = D.geom.close(ia, dR=(0.1, 1.44), idx=idxs, idx_xyz=idxs_xyz)
ia = ia * 3
i0 = idx[0] * 3
i1 = idx[1] * 3
print(ia, i0, i1)
# on-site
p = 1.
D.D[ia, i0] = p
D.D[ia + 1, i0 + 1] = p
D.D[ia + 2, i0 + 2] = p
# nn
p = 0.1
# on-site directions
D.D[ia, ia + 1] = p
D.D[ia, ia + 2] = p
D.D[ia + 1, ia] = p
D.D[ia + 1, ia + 2] = p
D.D[ia + 2, ia] = p
D.D[ia + 2, ia + 1] = p
D.D[ia, i1 + 1] = p
D.D[ia, i1 + 2] = p
D.D[ia + 1, i1] = p
D.D[ia + 1, i1 + 2] = p
D.D[ia + 2, i1] = p
D.D[ia + 2, i1 + 1] = p
self.func = func
def test_nc_dynamical_matrix(sisl_tmp, sisl_system):
f = sisl_tmp('grdyn.nc', _dir)
dm = DynamicalMatrix(sisl_system.gtb)
for _, ix in dm.iter_orbitals():
dm[ix, ix] = ix / 2.
dm.write(ncSileSiesta(f, 'w'))
ndm = ncSileSiesta(f).read_dynamical_matrix()
# Assert they are the same
assert np.allclose(dm.cell, ndm.cell)
assert np.allclose(dm.xyz, ndm.xyz)
dm.finalize()
assert np.allclose(dm._csr._D[:, 0], ndm._csr._D[:, 0])
assert sisl_system.g.atoms.equal(ndm.atoms, R=False)
class TestHamiltonian(object):
# Base test class for MaskedArrays.
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=3)
self.g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) *
bond,
atom=C,
sc=self.sc)
self.D = DynamicalMatrix(self.g)
def func(D, ia, idxs, idxs_xyz):
idx = D.geom.close(ia, dR=(0.1, 1.44), idx=idxs, idx_xyz=idxs_xyz)
ia = ia * 3
i0 = idx[0] * 3
i1 = idx[1] * 3
print(ia, i0, i1)
# on-site
p = 1.
D.D[ia, i0] = p
D.D[ia + 1, i0 + 1] = p
D.D[ia + 2, i0 + 2] = p
# nn
p = 0.1
# on-site directions
D.D[ia, ia + 1] = p
D.D[ia, ia + 2] = p
D.D[ia + 1, ia] = p
D.D[ia + 1, ia + 2] = p
D.D[ia + 2, ia] = p
D.D[ia + 2, ia + 1] = p
D.D[ia, i1 + 1] = p
D.D[ia, i1 + 2] = p
D.D[ia + 1, i1] = p
D.D[ia + 1, i1 + 2] = p
D.D[ia + 2, i1] = p
D.D[ia + 2, i1 + 1] = p
self.func = func
def tearDown(self):
del self.sc
del self.g
del self.D
def test_objects(self):
print(self.D)
assert_true(len(self.D.xyz) == 2)
assert_true(self.g.no == len(self.D))
def test_dtype(self):
assert_true(self.D.dtype == np.float64)
def test_ortho(self):
assert_true(self.D.orthogonal)
def test_set1(self):
self.D.D[0, 0] = 1.
assert_true(self.D[0, 0] == 1.)
assert_true(self.D[1, 0] == 0.)
self.D.empty()
def test_correct_newton(self):
self.D.construct(self.func)
assert_true(self.D[0, 0] == 1.)
assert_true(self.D[1, 0] == 0.1)
assert_true(self.D[0, 1] == 0.1)
self.D.correct_Newton()
self.D.empty()
