def read_geometry(self, primary=False, **kwargs):
""" Reads a geometry from the Sile """
# 1st line is number of supercells
nsc = _a.fromiteri(map(int, self.readline().split()[:3]))
na, ns = map(int, self.readline().split()[:2])
# Convert species to atom objects
try:
species = get_sile(self.file.rsplit('REF', 1)[0] + 'orbocc').read_atom()
except:
species = [Atom(s) for s in self.readline().split()[:ns]]
# Total number of super-cells
if primary:
# Only read in the primary unit-cell
ns = 1
else:
ns = np.prod(nsc)
cell = _a.fromiterd(map(float, self.readline().split()))
try:
cell.shape = (3, 3)
if primary:
cell[0, :] /= nsc[0]
cell[1, :] /= nsc[1]
cell[2, :] /= nsc[2]
except:
c = np.empty([3, 3], np.float64)
c[0, 0] = 1. + cell[0]
c[0, 1] = cell[5] / 2.
c[0, 2] = cell[4] / 2.
c[1, 0] = cell[5] / 2.
c[1, 1] = 1. + cell[1]
c[1, 2] = cell[3] / 2.
c[2, 0] = cell[4] / 2.
c[2, 1] = cell[3] / 2.
c[2, 2] = 1. + cell[2]
cell = c * Ang2Bohr
sc = SuperCell(cell * Bohr2Ang, nsc=nsc)
# Create list of coordinates and atoms
xyz = np.empty([na * ns, 3], np.float64)
atoms = [None] * na * ns
# Read the geometry
for ia in range(na * ns):
# Retrieve line
# ix iy iz ia is x y z
line = self.readline().split()
atoms[ia] = species[int(line[4]) - 1]
xyz[ia, :] = _a.fromiterd(map(float, line[5:8]))
return Geometry(xyz * Bohr2Ang, atoms, sc=sc)
def test_struct_reorder(sisl_tmp, sisl_system):
f = sisl_tmp('gr.STRUCT_IN', _dir)
g = sisl_system.g.copy()
g.atoms[0] = Atom(1)
g.write(structSileSiesta(f, 'w'))
g2 = structSileSiesta(f).read_geometry()
# Assert they are the same
assert np.allclose(g.cell, g2.cell)
assert np.allclose(g.xyz, g2.xyz)
assert g.atoms.equal(g2.atoms, R=False)
def test_set_nsc2(self, setup):
g = graphene(atom=Atom(6, R=1.43))
s = SparseAtom(g)
s.construct([[0.1, 1.43], [1, 2]])
s.finalize()
assert s.nnz == 8
s.set_nsc(a=1)
assert s.nnz == 6
s.set_nsc([None, 1, 1])
assert s.nnz == 4
assert s[0, 0] == 1
def test_sparse_atom_transpose_single(i):
""" This is problematic when the sparsity pattern is not *filled* """
g = fcc(1., Atom(1, R=1.5)) * 3
s = SparseAtom(g)
s[i, 2] = 1.
s[i, 0] = 2.
t = s.transpose()
assert t.nnz == s.nnz
assert t[2, i] == pytest.approx(1.)
assert t[0, i] == pytest.approx(2.)
def test_geom_category():
hBN = honeycomb(1.42, [Atom(5, R=1.43), Atom(7, R=1.43)]) * (10, 11, 1)
B = AtomZ([5, 6])
B2 = AtomNeighbours(2, neighbour=B)
N = AtomZ(7)
N2 = AtomNeighbours(2, neighbour=N)
B3 = AtomNeighbours(3, neighbour=B)
N3 = AtomNeighbours(3, neighbour=N)
assert B != N
n2 = AtomNeighbours(2)
n3 = AtomNeighbours(3)
n3n2 = AtomNeighbours(1, 3, neighbour=n2) & n3
n3n3n2 = AtomNeighbours(1, 3, neighbour=n3n2) & n3
category = (B & B2) ^ (N & N2) ^ (B & B3) ^ (N & N3) ^ n2
cat = category.categorize(hBN)
def __init__(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]*2)
self.g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * bond,
atom=C, sc=self.sc)
self.mol = Geometry([[i, 0, 0] for i in range(10)], sc=[50])
def test_bilayer():
a = bilayer(1.42)
a = bilayer(1.42, stacking='AA')
a = bilayer(1.42, stacking='BA')
a = bilayer(1.42, stacking='AB')
for m in range(7):
a = bilayer(1.42, twist=(m, m + 1))
a = bilayer(1.42, twist=(6, 7), layer='bottom')
a = bilayer(1.42, twist=(6, 7), layer='TOP')
a = bilayer(1.42, bottom_atoms=(Atom['B'], Atom['N']), twist=(6, 7))
a = bilayer(1.42, top_atoms=(Atom(5), Atom(7)), twist=(6, 7))
a, th = bilayer(1.42, twist=(6, 7), ret_angle=True)
with pytest.raises(ValueError):
bilayer(1.42, twist=(6, 7), layer='undefined')
with pytest.raises(ValueError):
bilayer(1.42, twist=(6, 7), stacking='undefined')
with pytest.raises(ValueError):
bilayer(1.42, twist=('str', 7), stacking='undefined')
def test_wavefunction1():
N = 50
o1 = SphericalOrbital(0, (np.linspace(0, 2, N), np.exp(-np.linspace(0, 100, N))))
G = Geometry([[1] * 3, [2] * 3], Atom(6, o1), sc=[4, 4, 4])
H = Hamiltonian(G)
R, param = [0.1, 1.5], [1., 0.1]
H.construct([R, param])
ES = H.eigenstate(dtype=np.float64)
# Plot in the full thing
grid = Grid(0.1, geometry=H.geom)
grid.fill(0.)
ES.sub(0).wavefunction(grid)
def test_non_colinear_non_orthogonal(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g,
dtype=np.float64,
orthogonal=False,
spin=Spin.NONCOLINEAR)
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.
H.S[i, i] = 1.
eig1 = H.eigh(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g,
dtype=np.float64,
orthogonal=False,
spin=Spin('non-collinear'))
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.
H1.S[i, i] = 1.
assert H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(dtype=np.complex64),
H1.eigh(dtype=np.complex128))
es = H1.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_spin1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32, spin=Spin.POLARIZED)
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 H.spsame(H2)
def test_get1():
atoms = Atoms(['C', 'C', 'Au'])
assert atoms[2] == Atom('Au')
assert atoms[0] == Atom('C')
assert atoms[1] == Atom('C')
assert atoms[0:2] == [Atom('C')]*2
assert atoms[1:] == [Atom('C'), Atom('Au')]
def test_sparse_orbital_replace_hole_norbs():
""" Create a big graphene flake remove a hole (multiple orbitals) """
a1 = Atom(5, R=(1.44, 1.44))
a2 = Atom(7, R=(1.44, 1.44, 1.44))
g = graphene(atoms=[a1, a2], orthogonal=True)
spo = SparseOrbital(g)
def func(self, ia, atoms, atoms_xyz=None):
geom = self.geometry
def a2o(idx):
return geom.a2o(idx, True)
io = a2o(ia)
idx = self.geometry.close(ia, R=[0.1, 1.44], atoms=atoms, atoms_xyz=atoms_xyz)
idx = list(map(a2o, idx))
self[io, idx[0]] = 0
for i in io:
self[i, idx[1]] = 2.7
# create the sparse-orbital
spo.construct(func)
# create 10x10 geoemetry
nx, ny = 10, 10
big = spo.tile(10, 0).tile(10, 1)
hole = spo.tile(6, 0).tile(6, 1)
hole = hole.remove(hole.close(hole.center(), R=3))
def create_sp(geom):
spo = SparseOrbital(geom)
# create the sparse-orbital
spo.construct(func)
return spo
# now replace every position that can be replaced
for y in [0, 3]:
for x in [1, 3]:
cube = Cuboid(hole.sc.cell, origin=g.sc.offset([x, y, 0]) - 0.1)
atoms = big.within(cube)
assert len(atoms) == 4 * 6 * 6
new = big.replace(atoms, hole)
new_copy = create_sp(new.geometry)
assert np.fabs((new - new_copy)._csr._D).sum() == 0.
def test_get1(self):
atoms = Atoms(['C', 'C', 'Au'])
assert_true(atoms[2] == Atom('Au'))
assert_true(atoms[0] == Atom('C'))
assert_true(atoms[1] == Atom('C'))
assert_true(atoms[0:2] == [Atom('C')] * 2)
assert_true(atoms[1:] == [Atom('C'), Atom('Au')])
def test6(self):
assert_true(Atom(Z=1, orbs=3).orbs == 3)
assert_true(len(Atom(Z=1, orbs=3)) == 3)
assert_true(Atom(Z=1, R=1.4).R == 1.4)
assert_true(Atom(Z=1, R=1.4).maxR() == 1.4)
assert_true(Atom(Z=1, R=[1.4, 1.8]).orbs == 2)
assert_true(Atom(Z=1, R=[1.4, 1.8]).maxR() == 1.8)
def test_so1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=Spin.SPINORBIT)
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 np.allclose(H.eigh(), eig1)
assert 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 H1.spsame(H)
eig1 = H1.eigh()
# Check TimeSelector
for i in range(2):
assert np.allclose(H1.eigh(), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H.eigenstate()
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def __init__(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] * 3)
self.g = Geometry(
np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atoms=C,
sc=self.sc)
self.E = EnergyDensityMatrix(self.g)
self.ES = EnergyDensityMatrix(self.g, orthogonal=False)
def func(E, ia, idxs, idxs_xyz):
idx = E.geometry.close(ia,
R=(0.1, 1.44),
atoms=idxs,
atoms_xyz=idxs_xyz)
ia = ia * 3
i0 = idx[0] * 3
i1 = idx[1] * 3
# on-site
p = 1.
E.E[ia, i0] = p
E.E[ia + 1, i0 + 1] = p
E.E[ia + 2, i0 + 2] = p
# nn
p = 0.1
# on-site directions
E.E[ia, ia + 1] = p
E.E[ia, ia + 2] = p
E.E[ia + 1, ia] = p
E.E[ia + 1, ia + 2] = p
E.E[ia + 2, ia] = p
E.E[ia + 2, ia + 1] = p
E.E[ia, i1 + 1] = p
E.E[ia, i1 + 2] = p
E.E[ia + 1, i1] = p
E.E[ia + 1, i1 + 2] = p
E.E[ia + 2, i1] = p
E.E[ia + 2, i1 + 1] = p
self.func = func
def test_optimize_nsc1(self):
# Create a 1D chain
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc(), [3, 3, 3]))
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc(1), [77, 3, 77]))
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc([0, 2]), [3, 77, 3]))
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc([0, 2], R=2), [5, 77, 5]))
geom.set_nsc([1, 1, 1])
assert_true(np.allclose(geom.optimize_nsc([0, 2], R=2), [5, 1, 5]))
def test_geometry_sort_func_sort():
bi = sisl_geom.bilayer().tile(2, 0).repeat(2, 1)
# Sort according to another cell fractional coordinates
fcc = sisl_geom.fcc(2.4, Atom(6))
def fcc_fracs(axis):
def _(geometry):
return np.dot(geometry.xyz, fcc.icell.T)[:, axis]
return _
out = bi.sort(func_sort=(fcc_fracs(0), fcc_fracs(2)))
def test_berry_phase_method_fail(self):
g = Geometry([[-.6, 0, 0], [0.6, 0, 0]],
Atom(1, 1.001),
sc=[2, 10, 10])
g.set_nsc([3, 1, 1])
H = Hamiltonian(g)
H.construct([(0.1, 1.0, 1.5), (0, 1., 0.5)])
# Contour
k = np.linspace(0.0, 1.0, 101)
K = np.zeros([k.size, 3])
K[:, 0] = k
bz = BrillouinZone(H, K)
berry_phase(bz, method='unknown')
def test_wavefunction_eta():
N = 50
o1 = SphericalOrbital(0, (np.linspace(0, 2, N), np.exp(-np.linspace(0, 100, N))))
G = Geometry([[1] * 3, [2] * 3], Atom(6, o1), sc=[4, 4, 4])
H = Hamiltonian(G, spin=Spin('nc'))
R, param = [0.1, 1.5], [[0., 0., 0.1, -0.1],
[1., 1., 0.1, -0.1]]
H.construct([R, param])
ES = H.eigenstate()
# Plot in the full thing
grid = Grid(0.1, dtype=np.complex128, sc=SuperCell([2, 2, 2], origo=[-1] * 3))
grid.fill(0.)
ES.sub(0).wavefunction(grid, eta=True)
def test_wavefunction2():
N = 50
o1 = SphericalOrbital(0, (np.linspace(0, 2, N), np.exp(-np.linspace(0, 100, N))))
G = Geometry([[1] * 3, [2] * 3], Atom(6, o1), sc=[4, 4, 4])
H = Hamiltonian(G)
R, param = [0.1, 1.5], [1., 0.1]
H.construct([R, param])
ES = H.eigenstate(dtype=np.float64)
# This is effectively plotting outside where no atoms exists
# (there could however still be psi weight).
grid = Grid(0.1, sc=SuperCell([2, 2, 2], origo=[2] * 3))
grid.fill(0.)
ES.sub(0).wavefunction(grid)
def read_geometry(self):
""" Read geometry from the contained file """
# First we read in the geometry
sc = self.read_supercell()
# Try and go to the first model record
in_model, l = self._step_record('MODEL')
idx = []
tags = []
xyz = []
Z = []
if in_model:
l = self.readline()
def is_atom(line):
return l.startswith('ATOM') or l.startswith('HETATM')
def is_end_model(line):
return l.startswith('ENDMDL') or l == ''
while not is_end_model(l):
if is_atom(l):
idx.append(int(l[6:11]))
tags.append(l[12:16].strip())
xyz.append(
[float(l[30:38]),
float(l[38:46]),
float(l[46:54])])
Z.append(l[76:78].strip())
l = self.readline()
# First sort all atoms according to the idx array
idx = np.array(idx)
idx = np.argsort(idx)
xyz = np.array(xyz)[idx, :]
tags = [tags[i] for i in idx]
Z = [Z[i] for i in idx]
# Create the atom list
atoms = Atoms(Atom(Z[0], tag=tags[0]), na=len(Z))
for i, a in enumerate(map(Atom, Z, tags)):
try:
s = atoms.specie_index(a)
except:
s = len(atoms.atom)
atoms._atom.append(a)
atoms._specie[i] = s
return Geometry(xyz, atoms, sc=sc)
def __init__(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])
n = 60
rf = np.linspace(0, bond * 1.01, n)
rf = (rf, rf)
orb = SphericalOrbital(1, rf, 2.)
C = Atom(6, orb.toAtomicOrbital())
self.g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * bond,
atoms=C, sc=self.sc)
self.D = DensityMatrix(self.g)
self.DS = DensityMatrix(self.g, orthogonal=False)
def func(D, ia, atoms, atoms_xyz):
idx = D.geometry.close(ia, R=(0.1, 1.44), atoms=atoms, atoms_xyz=atoms_xyz)
ia = ia * 3
i0 = idx[0] * 3
i1 = idx[1] * 3
# 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 __init__(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] * 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,
R=(0.1, 1.44),
idx=idxs,
idx_xyz=idxs_xyz)
ia = ia * 3
i0 = idx[0] * 3
i1 = idx[1] * 3
# 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_so1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.float64, spin=Spin.SPINORBIT)
for i in range(10):
j = range(i*2, i*2+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(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert len(H.eigh()) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i*2, i*2+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 H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(dtype=np.complex64), H1.eigh(dtype=np.complex128))
es = H.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
sm = es.spin_moment()
om = es.spin_orbital_moment()
assert np.allclose(sm, om.sum(1))
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_sparse_orbital_transpose_more(i):
g = fcc(1., Atom(1, R=(1.5, 2.1))) * 3
s = SparseOrbital(g)
s[i, 2] = 1.
s[i, 0] = 2.
s[i + 3, 4] = 1.
s[i + 2, 4] = 2.
t = s.transpose()
assert t.nnz == s.nnz
assert t[2, i] == pytest.approx(1.)
assert t[0, i] == pytest.approx(2.)
assert t[4, i + 3] == pytest.approx(1.)
assert t[4, i + 2] == pytest.approx(2.)
def test_op_numpy_scalar(self, setup):
g = graphene(atoms=Atom(6, R=1.43))
S = SparseAtom(g)
I = np.ones(1, dtype=np.complex128)[0]
# Create initial stuff
for i in range(10):
j = range(i, i * 2)
S[0, j] = i
S.finalize()
Ssum = S._csr._D.sum()
s = S + I
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum + S.nnz
s = S - I
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum - S.nnz
s = I + S
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum + S.nnz
s = S * I
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum
s = I * S
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum
s = S / I
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum
s = S**I
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
assert s._csr._D.sum() == Ssum
s = I**S
assert isinstance(s, SparseAtom)
assert s.dtype == np.complex128
def read_basis(self):
""" Reads the basis as found in the output file
This parses 3 things:
1. At the start of the file there are some initatom output
specifying which species in the calculation.
2. Reading the <basis_specs> entries for the masses
3. Reading the PAO.Basis block output for orbital information
"""
found, line = self.step_to("Species number:")
if not found:
return []
atoms = {}
order = []
while 'Species number:' in line:
ls = line.split()
if ls[3] == 'Atomic':
atoms[ls[7]] = {'Z': int(ls[5]), 'tag': ls[7]}
order.append(ls[7])
else:
atoms[ls[4]] = {'Z': int(ls[7]), 'tag': ls[4]}
order.append(ls[4])
line = self.readline()
# Now go down to basis_specs
found, line = self.step_to("<basis_specs>")
while found:
# =====
self.readline()
# actual line
line = self.readline().split("=")
tag = line[0].split()[0]
atoms[tag]["mass"] = float(line[2].split()[0])
found, line = self.step_to("<basis_specs>", reread=False)
block = []
found, line = self.step_to("%block PAO.Basis")
line = self.readline()
while not line.startswith("%endblock PAO.Basis"):
block.append(line)
line = self.readline()
from .fdf import fdfSileSiesta
atom_orbs = fdfSileSiesta._parse_pao_basis(block)
for atom, orbs in atom_orbs.items():
atoms[atom]["orbitals"] = orbs
return [Atom(**atoms[tag]) for tag in order]
def __init__(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])
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] * 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 test_rocksalt_slab():
rocksalt_slab(5.64, [Atom(11, R=3), Atom(17, R=4)], 100)
assert (rocksalt_slab(5.64, ['Na', 'Cl'], 100, layers=5).equal(
rocksalt_slab(5.64, ['Na', 'Cl'], 100, layers="ABABA")))
rocksalt_slab(5.64, ['Na', 'Cl'], 110, vacuum=None)
rocksalt_slab(5.64, ['Na', 'Cl'], 111, orthogonal=False)
rocksalt_slab(5.64, ['Na', 'Cl'], 111, orthogonal=True)
rocksalt_slab(5.64, 'Na', 100)
with pytest.raises(ValueError):
rocksalt_slab(5.64, ['Na', 'Cl'], 100, start=0, end=0)
with pytest.raises(ValueError):
rocksalt_slab(5.64, ['Na', 'Cl'], 1000)
with pytest.raises(NotImplementedError):
rocksalt_slab(5.64, ['Na', 'Cl'], 200)
with pytest.raises(ValueError):
rocksalt_slab(5.64, ['Na', 'Cl'], 100, start=0, layers='BABAB')
rocksalt_slab(5.64, ['Na', 'Cl'], 100, start=1, layers='BABAB')
with pytest.raises(ValueError):
rocksalt_slab(5.64, ['Na', 'Cl'], 100, end=0, layers='BABAB')
rocksalt_slab(5.64, ['Na', 'Cl'], 100, end=1, layers='BABAB')
assert not np.allclose(
rocksalt_slab(5.64, ['Na', 'Cl'], 100, end=1, layers='BABAB').xyz,
rocksalt_slab(5.64, ['Na', 'Cl'], 100, end=1, layers=' BABAB ').xyz)