def test_set_sc(self):
# Create new geometry with only the coordinates
# and atoms
s1 = SuperCell([2, 2, 2])
g1 = Geometry([[0, 0, 0], [1, 1, 1]], sc=[2, 2, 1])
g1.set_sc(s1)
assert_true(g1.sc == s1)
def hcp(a, atom, coa=1.63333, orthogonal=False):
"""
Returns a geometry with the FCC crystal structure (1 atom)
"""
# height of hcp structure
c = a * coa
a2sq = a / 2 ** .5
if orthogonal:
sc = SuperCell([[a + a * _c60 * 2, 0, 0],
[0, a * _c30 * 2, 0],
[0, 0, c / 2]])
gt = Geometry([[0, 0, 0],
[a, 0, 0],
[a * _s30, a * _c30, 0],
[a * (1 + _s30), a * _c30, 0]], atom, sc=sc)
# Create the rotated one on top
gr = gt.copy()
# mirror structure
gr.xyz[0, 1] += sc.cell[1, 1]
gr.xyz[1, 1] += sc.cell[1, 1]
gr = gr.translate(-np.amin(gr.xyz, axis=0))
# Now displace to get the correct offset
gr = gr.translate([0, a * _s30 / 2, 0])
g = gt.append(gr, 2)
else:
sc = SuperCell([a, a, c, 90, 90, 60],
nsc=[3, 3, 3])
g = Geometry(
[[0, 0, 0], [a2sq * _c30, a2sq * _s30, c / 2]], atom, sc=sc)
return g
def setUp(self):
bond = 1.42
sq3h = 3.0 ** 0.5 * 0.5
self.sc = SuperCell(
np.array([[1.5, sq3h, 0.0], [1.5, -sq3h, 0.0], [0.0, 0.0, 10.0]], np.float64) * bond, nsc=[3, 3, 1]
)
C = Atom(Z=6, R=bond * 1.01, orbs=2)
self.g = Geometry(np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]], np.float64) * bond, atom=C, sc=self.sc)
self.mol = Geometry([[i, 0, 0] for i in range(10)], sc=[50])
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.geometry.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 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.index(a)
except:
s = len(atoms.atom)
atoms._atom.append(a)
atoms._specie[i] = s
return Geometry(xyz, atoms, sc=sc)
def honeycomb(bond, atom, orthogonal=False):
""" Honeycomb lattice with 2 or 4 atoms per unit-cell, latter orthogonal cell
This enables creating BN lattices with ease, or graphene lattices.
Parameters
----------
bond : float
bond length between atoms (*not* lattice constant)
atom : Atom
the atom (or atoms) that the honeycomb lattice consists of
orthogonal : bool, optional
if True returns an orthogonal lattice
See Also
--------
graphene: the equivalent of this, but with default of Carbon atoms
bilayer: create bilayer honeycomb lattices
"""
sq3h = 3.**.5 * 0.5
if orthogonal:
sc = SuperCell(np.array(
[[3., 0., 0.], [0., 2 * sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
g = Geometry(np.array([[0., 0., 0.], [0.5, sq3h, 0.], [1.5, sq3h, 0.],
[2., 0., 0.]], np.float64) * bond,
atom,
sc=sc)
else:
sc = SuperCell(np.array(
[[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atom,
sc=sc)
return g
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 honeycomb(bond, atom, orthogonal=False):
"""
Returns a honeycomb geometry with the graphene unit-cell (2 atoms)
"""
sq3h = 3.**.5 * 0.5
if orthogonal:
sc = SuperCell(np.array(
[[3., 0., 0.], [0., 2 * sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
g = Geometry(np.array([[0., 0., 0.], [0.5, sq3h, 0.], [1.5, sq3h, 0.],
[2., 0., 0.]], np.float64) * bond,
atom,
sc=sc)
else:
sc = SuperCell(np.array(
[[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atom,
sc=sc)
return g
def _r_geometry_ase(self, na, header, sp, xyz, sc):
""" Read the geometry as though it was created with ASE """
# Convert F T to nsc
# F = 1
# T = 3
nsc = list(
map(lambda x: "FT".index(x) * 2 + 1,
header.pop("pbc").strip('"').split()))
cell = _a.fromiterd(header.pop("Lattice").strip('"').split()).reshape(
3, 3)
if sc is None:
sc = SuperCell(cell, nsc=nsc)
return Geometry(xyz, atoms=sp, 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])
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_spin1(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.int32, spin=Spin.POLARIZED)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
def test_imaginary_fail_geometry(sisl_tmp):
fr = sisl_tmp('GRID_real.cube', _dir)
fi = sisl_tmp('GRID_imag.cube', _dir)
geom = Geometry(np.random.rand(10, 3),
np.random.randint(1, 70, 10),
sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom, dtype=np.complex128)
grid.grid = np.random.rand(*grid.shape) + 1j * np.random.rand(*grid.shape)
grid.write(fr)
# Assert it fails on geometry
grid2 = Grid(0.3, dtype=np.complex128)
grid2.write(fi, imag=True)
grid.read(fr, imag=fi)
def test_grid_tile_geom():
grid = Grid([4, 5, 6], geometry=Geometry([0] * 3, Atom[4], sc=4.))
grid2 = grid.tile(2, 2)
assert grid.shape[:2] == grid2.shape[:2]
assert grid.shape[2] == grid2.shape[2] // 2
assert grid.volume * 2 == pytest.approx(grid2.volume)
assert grid.geometry.na * 2 == grid2.geometry.na
grid4 = grid2.tile(2, 1)
assert grid.shape[0] == grid4.shape[0]
assert grid.shape[1] == grid4.shape[1] // 2
assert grid.shape[2] == grid4.shape[2] // 2
assert grid.volume * 4 == pytest.approx(grid4.volume)
assert grid.geometry.na * 4 == grid4.geometry.na
def diamond(alat=3.57, atom=None):
"""
Returns a geometry with the diamond unit-cell (2 atoms)
"""
dist = alat * 3.**.5 / 4
if atom is None:
atom = Atom(Z=6, R=dist * 1.01)
sc = SuperCell(np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], np.float64) *
alat / 2,
nsc=[3, 3, 3])
dia = Geometry(np.array([[0, 0, 0], [1, 1, 1]], np.float64) * alat / 4,
atom,
sc=sc)
return dia
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(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 * 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(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)
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_non_colinear_non_orthogonal(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, orthogonal=False, spin=Spin.NONCOLINEAR)
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
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*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.
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)
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 bcc(alat, atoms, orthogonal=False):
""" Body centered cubic lattice with 1 (non-orthogonal) or 2 atoms (orthogonal)
Parameters
----------
alat : float
lattice parameter
atoms : Atom
the atom(s) in the BCC lattice
orthogonal : bool, optional
whether the lattice is orthogonal (2 atoms)
"""
if orthogonal:
sc = SuperCell(
np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], np.float64) * alat)
ah = alat / 2
g = Geometry([[0, 0, 0], [ah, ah, ah]], atoms, sc=sc)
else:
sc = SuperCell(
np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]], np.float64) * alat /
2)
g = Geometry([0, 0, 0], atoms, sc=sc)
geometry_define_nsc(g)
return g
def sc(alat, atom):
""" Simple cubic lattice with 1 atom
Parameters
----------
alat : float
lattice parameter
atom : Atom
the atom in the SC lattice
"""
sc = SuperCell(
np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], np.float64) * alat)
g = Geometry([0, 0, 0], atom, sc=sc)
geometry_define_nsc(g)
return g
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 hcp(a, atoms, coa=1.63333, orthogonal=False):
""" Hexagonal closed packed lattice with 2 (non-orthogonal) or 4 atoms (orthogonal)
Parameters
----------
a : float
lattice parameter for 1st and 2nd lattice vectors
atoms : Atom
the atom(s) in the HCP lattice
coa : float, optional
c over a parameter where c is the 3rd lattice vector length
orthogonal : bool, optional
whether the lattice is orthogonal (4 atoms)
"""
# height of hcp structure
c = a * coa
a2sq = a / 2**.5
if orthogonal:
sc = SuperCell([[a + a * _c60 * 2, 0, 0], [0, a * _c30 * 2, 0],
[0, 0, c / 2]])
gt = Geometry([[0, 0, 0], [a, 0, 0], [a * _s30, a * _c30, 0],
[a * (1 + _s30), a * _c30, 0]],
atoms,
sc=sc)
# Create the rotated one on top
gr = gt.copy()
# mirror structure
gr.xyz[0, 1] += sc.cell[1, 1]
gr.xyz[1, 1] += sc.cell[1, 1]
gr = gr.translate(-np.amin(gr.xyz, axis=0))
# Now displace to get the correct offset
gr = gr.translate([0, a * _s30 / 2, 0])
g = gt.append(gr, 2)
else:
sc = SuperCell([a, a, c, 90, 90, 60])
g = Geometry([[0, 0, 0], [a2sq * _c30, a2sq * _s30, c / 2]],
atoms,
sc=sc)
if np.all(g.maxR(True) > 0.):
g.optimize_nsc()
return g
def test_non_colinear1(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.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.
eig1 = H.eigh()
# Check TimeSelector
for i in range(4):
assert np.allclose(H.eigh(), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, 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.
assert H1.spsame(H)
eig1 = H1.eigh()
# Check TimeSelector
for i in range(4):
assert np.allclose(H1.eigh(), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H1.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 test_non_collinear1(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.
assert_true(len(H.eigh()) == len(H) * 2)
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.S = Overlap(self.g)
def read_geom(self):
""" Returns `Geometry` object from the CUBE file """
na, sc = self.read_sc(na=True)
# Start reading the geometry
xyz = np.empty([na, 3], np.float64)
atom = []
for ia in range(na):
tmp = self.readline().split()
atom.append(Atom(int(tmp[0])))
xyz[ia, 0] = float(tmp[2])
xyz[ia, 1] = float(tmp[3])
xyz[ia, 2] = float(tmp[4])
xyz /= Ang2Bohr
return Geometry(xyz, atom, sc=sc)
def test_orbital_momentum(self, setup):
bond = 1.42
sq3h = 3.**.5 * 0.5
sc = SuperCell(np.array([[1.5, sq3h, 0.],
[1.5, -sq3h, 0.],
[0., 0., 10.]], np.float64) * bond, nsc=[3, 3, 1])
orb = AtomicOrbital('px', R=bond * 1.001)
C = Atom(6, orb)
g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * bond,
atoms=C, sc=sc)
D = DensityMatrix(g, spin=Spin('SO'))
D.construct([[0.1, bond + 0.01], [(1., 0.5, 0.01, 0.01, 0.01, 0.01, 0., 0.), (0.1, 0.1, 0.1, 0.1, 0., 0., 0., 0.)]])
D.orbital_momentum("atom")
D.orbital_momentum("orbital")
def read_hamiltonian(self, **kwargs):
""" Returns the electronic structure from the siesta.TSHS file """
# Now read the sizes used...
Gamma, spin, no, no_s, nnz = _siesta.read_hsx_sizes(self.file)
ncol, col, dH, dS, dxij = _siesta.read_hsx_hsx(self.file, Gamma, spin,
no, no_s, nnz)
# Try and immediately attach a geometry
geom = kwargs.get('geometry', kwargs.get('geom', None))
if geom is None:
# We have *no* clue about the
if np.allclose(dxij, 0.):
# We truly, have no clue,
# Just generate a boxed system
xyz = [[x, 0, 0] for x in range(no)]
geom = Geometry(xyz, Atom(1), sc=[no, 1, 1])
else:
# Try to figure out the supercell
warn(
self.__class__.__name__ +
".read_hamiltonian (currently we can not calculate atomic positions from"
" xij array)")
if geom.no != no:
raise ValueError(
"Reading HSX files requires the input geometry to have the "
"correct number of orbitals {} / {}.".format(no, geom.no))
# Create the Hamiltonian container
H = Hamiltonian(geom,
spin,
nnzpr=1,
dtype=np.float32,
orthogonal=False)
# Create the new sparse matrix
H._csr.ncol = ncol.astype(np.int32, copy=False)
H._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
H._csr.col = col.astype(np.int32, copy=False) - 1
H._csr._nnz = len(col)
H._csr._D = np.empty([nnz, spin + 1], np.float32)
H._csr._D[:, :spin] = dH[:, :]
H._csr._D[:, spin] = dS[:]
return H
def _read_geometry(self, sc, *args, **kwargs):
""" Defered routine """
is_frac = True
f, _ = self.step_to('atoms_frac', case=False)
if not f:
is_frac = False
self.fh.seek(0)
f, _ = self.step_to('atoms_cart', case=False)
if not f:
raise ValueError(
"The geometry coordinates (atoms_frac/cart) could not be found in the seed-file."
)
# Species and coordinate list
s = []
xyz = []
# Read the next line to determine the units
if is_frac:
unit = 1.
else:
unit = self.readline()
if len(unit.split()) > 1:
l = unit.split()
s.append(l[0])
xyz.append(list(map(float, l[1:4])))
unit = 1.
else:
unit = unit_convert(unit.strip().capitalize(), 'Ang')
l = self.readline()
while not 'end' in l:
# Get the species and
l = l.split()
s.append(l[0])
xyz.append(list(map(float, l[1:4])))
l = self.readline()
# Convert
xyz = np.array(xyz, np.float64) * unit
if is_frac:
xyz = np.dot(sc.cell.T, xyz.T).T
return Geometry(xyz, atoms=s, sc=sc)
def read_geometry(self):
""" Returns Geometry object from the XV file
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
atms = [None] * na
xyz = np.empty([na, 3], np.float64)
line = np.empty(8, np.float64)
for ia in range(na):
line[:] = list(map(float, self.readline().split()[:8]))
atms[ia] = Atom[int(line[1])]
xyz[ia, :] = line[2:5]
xyz *= Bohr2Ang
return Geometry(xyz, atms, sc=sc)
def read_geom(self):
""" Returns Geometry object from the XV file
"""
sc = self.read_sc()
# Read number of atoms
na = int(self.readline())
atms = [None] * na
xyz = np.empty([na, 3], np.float64)
line = np.empty(8, np.float64)
for ia in range(na):
line[:] = np.fromstring(self.readline(), dtype=float, sep=' ')[0:8]
atms[ia] = Atom[int(line[1])]
xyz[ia, :] = line[2:5]
xyz *= Bohr2Ang
return Geometry(xyz, atms, sc=sc)
def test_rho2(self, setup):
bond = 1.42
sq3h = 3.**.5 * 0.5
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)
g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atom=C,
sc=sc)
D = DensityMatrix(g)
D.construct([[0.1, bond + 0.01], [1., 0.1]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
D = DensityMatrix(g, spin=Spin('P'))
D.construct([[0.1, bond + 0.01], [(1., 0.5), (0.1, 0.1)]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
D.density(grid, [1., -1])
D.density(grid, 0)
D.density(grid, 1)
D = DensityMatrix(g, spin=Spin('NC'))
D.construct([[0.1, bond + 0.01],
[(1., 0.5, 0.01, 0.01), (0.1, 0.1, 0.1, 0.1)]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
D.density(grid, [[1., 0.], [0., -1]])
D = DensityMatrix(g, spin=Spin('SO'))
D.construct([[0.1, bond + 0.01],
[(1., 0.5, 0.01, 0.01, 0.01, 0.01, 0., 0.),
(0.1, 0.1, 0.1, 0.1, 0., 0., 0., 0.)]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
D.density(grid, [[1., 0.], [0., -1]])
D.density(grid, Spin.X)
D.density(grid, Spin.Y)
D.density(grid, Spin.Z)
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)
func = self.H.create_construct([0.1, bond+0.1], [0., -2.7])
self.H.construct(func)
self.HS = Hamiltonian(self.g, orthogonal=False)
func = self.HS.create_construct([0.1, bond+0.1], [(0., 1.), (-2.7, 0.)])
self.HS.construct(func)
def test_sparse_orbital_sub_orbital():
a0 = Atom(1, R=(1.1, 1.4, 1.6))
a1 = Atom(2, R=(1.3, 1.1))
g = Geometry([[0, 0, 0], [1, 1, 1]], [a0, a1],
sc=SuperCell(2, nsc=[3, 1, 1]))
assert g.no == 5
spo = SparseOrbital(g)
for io in range(g.no):
spo[io, io] = io + 1
spo[io, io + g.no - 1] = io - 2
spo[io, io + 1] = io + 2
# Ensure we have a Hermitian matrix
spo = spo + spo.transpose()
# Ensure sub and remove does the same
for i in [0, a0]:
spo_rem = spo.remove_orbital(i, 0)
spo_sub = spo.sub_orbital(i, [1, 2])
assert spo_rem.spsame(spo_sub)
spo_rem = spo.remove_orbital(i, [0, 2])
spo_sub = spo.sub_orbital(i, 1)
assert spo_rem.spsame(spo_sub)
spo_rem = spo.remove_orbital(i, 2)
spo_sub = spo.sub_orbital(i, [0, 1])
assert spo_rem.spsame(spo_sub)
spo_rem = spo.remove_orbital(i, a0[0])
spo_sub = spo.sub_orbital(i, [1, 2])
assert spo_rem.spsame(spo_sub)
for i in [1, a1]:
spo_rem = spo.remove_orbital(i, a1[0])
spo_sub = spo.sub_orbital(i, a1[1])
assert spo_rem.spsame(spo_sub)
spo_rem = spo.remove_orbital([0, 1], 0)
spo_sub = spo.sub_orbital(0, [1, 2]).sub_orbital(1, 1)
assert spo_rem.spsame(spo_sub)
spo_rem = spo.remove_orbital([0, 1], 1)
spo_sub = spo.sub_orbital(0, [0, 2]).sub_orbital(1, 0)
assert spo_rem.spsame(spo_sub)
def read_geometry(self, species_Z=False):
""" Returns a `Geometry` object from the STRUCT file
Parameters
----------
species_Z : bool, optional
if ``True`` the atomic numbers are the species indices (useful when
reading the ChemicalSpeciesLabel block simultaneously).
Returns
-------
Geometry
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
xyz = np.empty([na, 3], np.float64)
atms = [None] * na
sp = np.empty([na], np.int32)
for ia in range(na):
line = self.readline().split()
sp[ia] = int(line[0])
if species_Z:
atms[ia] = Atom(sp[ia])
else:
atms[ia] = Atom(int(line[1]))
xyz[ia, :] = line[2:5]
xyz = xyz @ sc.cell
# Ensure correct sorting
max_s = sp.max()
sp -= 1
# Ensure we can remove the atom after having aligned them
atms2 = Atoms(AtomUnknown(1000), na=na)
for i in range(max_s):
idx = (sp[:] == i).nonzero()[0]
if len(idx) == 0:
# Always ensure we have "something" for the unoccupied places
atms2[idx] = AtomUnknown(1000 + i)
else:
atms2[idx] = atms[idx[0]]
return Geometry(xyz, atms2.reduce(), sc=sc)
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)
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=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):
print(self.H)
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()
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, dR=(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_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)
# 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_eig1(self):
# Test of eigenvalues
g = self.g.tile(2, 0).tile(2, 1).tile(2, 2)
H = Hamiltonian(g)
H.construct((0.1,1.5), (1.,0.1))
H.eigh()
H.eigsh(n=4)
H.empty()
del H
def test_eig2(self):
# Test of eigenvalues
self.HS.construct((0.1,1.5), ((1.,1.), (0.1,0.1)))
self.HS.eigh()
self.HS.empty()
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)
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[0,0] = 1., 1.
self.HS.finalize()
assert_true(self.HS.finalized)
assert_true(self.HS.nnz == 1)
self.HS.empty()
class TestGeometry(object):
def setUp(self):
bond = 1.42
sq3h = 3.0 ** 0.5 * 0.5
self.sc = SuperCell(
np.array([[1.5, sq3h, 0.0], [1.5, -sq3h, 0.0], [0.0, 0.0, 10.0]], np.float64) * bond, nsc=[3, 3, 1]
)
C = Atom(Z=6, R=bond * 1.01, orbs=2)
self.g = Geometry(np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]], np.float64) * bond, atom=C, sc=self.sc)
self.mol = Geometry([[i, 0, 0] for i in range(10)], sc=[50])
def tearDown(self):
del self.g
del self.sc
del self.mol
def test_objects(self):
# just make sure __repr__ works
print(self.g)
assert_true(len(self.g) == 2)
assert_true(len(self.g.xyz) == 2)
assert_true(np.allclose(self.g[0, :], np.zeros([3])))
i = 0
for ia in self.g:
i += 1
assert_true(i == len(self.g))
assert_true(self.g.no_s == 2 * len(self.g) * np.prod(self.g.sc.nsc))
def test_iter1(self):
i = 0
for ia in self.g:
i += 1
assert_true(i == 2)
def test_iter2(self):
for ia in self.g:
assert_true(np.allclose(self.g[ia, :], self.g.xyz[ia, :]))
def test_tile1(self):
cell = np.copy(self.g.sc.cell)
cell[0, :] *= 2
t = self.g.tile(2, 0)
assert_true(np.allclose(cell, t.sc.cell))
cell[1, :] *= 2
t = t.tile(2, 1)
assert_true(np.allclose(cell, t.sc.cell))
cell[2, :] *= 2
t = t.tile(2, 2)
assert_true(np.allclose(cell, t.sc.cell))
def test_tile2(self):
cell = np.copy(self.g.sc.cell)
cell[:, :] *= 2
t = self.g.tile(2, 0).tile(2, 1).tile(2, 2)
assert_true(np.allclose(cell, t.sc.cell))
def test_repeat1(self):
cell = np.copy(self.g.sc.cell)
cell[0, :] *= 2
t = self.g.repeat(2, 0)
assert_true(np.allclose(cell, t.sc.cell))
cell[1, :] *= 2
t = t.repeat(2, 1)
assert_true(np.allclose(cell, t.sc.cell))
cell[2, :] *= 2
t = t.repeat(2, 2)
assert_true(np.allclose(cell, t.sc.cell))
def test_repeat2(self):
cell = np.copy(self.g.sc.cell)
cell[:, :] *= 2
t = self.g.repeat(2, 0).repeat(2, 1).repeat(2, 2)
assert_true(np.allclose(cell, t.sc.cell))
def test_a2o1(self):
assert_true(0 == self.g.a2o(0))
assert_true(self.g.atom[0].orbs == self.g.a2o(1))
assert_true(self.g.no == self.g.a2o(self.g.na))
def test_sub1(self):
assert_true(len(self.g.sub([0])) == 1)
assert_true(len(self.g.sub([0, 1])) == 2)
assert_true(len(self.g.sub([-1])) == 1)
def test_sub2(self):
assert_true(len(self.g.sub(range(1))) == 1)
assert_true(len(self.g.sub(range(2))) == 2)
def test_cut(self):
assert_true(len(self.g.cut(1, 1)) == 2)
assert_true(len(self.g.cut(2, 1)) == 1)
assert_true(len(self.g.cut(2, 1, 1)) == 1)
def test_cut2(self):
c1 = self.g.cut(2, 1)
c2 = self.g.cut(2, 1, 1)
assert_true(np.allclose(c1.xyz[0, :], self.g.xyz[0, :]))
assert_true(np.allclose(c2.xyz[0, :], self.g.xyz[1, :]))
def test_remove1(self):
assert_true(len(self.g.remove([0])) == 1)
assert_true(len(self.g.remove([])) == 2)
assert_true(len(self.g.remove([-1])) == 1)
assert_true(len(self.g.remove([-0])) == 1)
def test_remove2(self):
assert_true(len(self.g.remove(range(1))) == 1)
assert_true(len(self.g.remove(range(0))) == 2)
def test_copy(self):
assert_true(self.g == self.g.copy())
def test_nsc1(self):
nsc = np.copy(self.g.nsc)
self.g.sc.set_nsc([5, 5, 0])
assert_true(np.allclose([5, 5, 1], self.g.nsc))
assert_true(len(self.g.sc_off) == np.prod(self.g.nsc))
def test_nsc2(self):
nsc = np.copy(self.g.nsc)
self.g.sc.set_nsc([0, 1, 0])
assert_true(np.allclose([1, 1, 1], self.g.nsc))
assert_true(len(self.g.sc_off) == np.prod(self.g.nsc))
def test_rotation1(self):
rot = self.g.rotate(180, [0, 0, 1])
rot.sc.cell[2, 2] *= -1
assert_true(np.allclose(-rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(-rot.xyz, self.g.xyz))
rot = self.g.rotate(np.pi, [0, 0, 1], radians=True)
rot.sc.cell[2, 2] *= -1
assert_true(np.allclose(-rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(-rot.xyz, self.g.xyz))
rot = rot.rotate(180, [0, 0, 1])
rot.sc.cell[2, 2] *= -1
assert_true(np.allclose(rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(rot.xyz, self.g.xyz))
def test_rotation2(self):
rot = self.g.rotate(180, [0, 0, 1], only="abc")
rot.sc.cell[2, 2] *= -1
assert_true(np.allclose(-rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(rot.xyz, self.g.xyz))
rot = self.g.rotate(np.pi, [0, 0, 1], radians=True, only="abc")
rot.sc.cell[2, 2] *= -1
assert_true(np.allclose(-rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(rot.xyz, self.g.xyz))
rot = rot.rotate(180, [0, 0, 1], only="abc")
rot.sc.cell[2, 2] *= -1
assert_true(np.allclose(rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(rot.xyz, self.g.xyz))
def test_rotation3(self):
rot = self.g.rotate(180, [0, 0, 1], only="xyz")
assert_true(np.allclose(rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(-rot.xyz, self.g.xyz))
rot = self.g.rotate(np.pi, [0, 0, 1], radians=True, only="xyz")
assert_true(np.allclose(rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(-rot.xyz, self.g.xyz))
rot = rot.rotate(180, [0, 0, 1], only="xyz")
assert_true(np.allclose(rot.sc.cell, self.g.sc.cell))
assert_true(np.allclose(rot.xyz, self.g.xyz))
def test_translate(self):
t = self.g.translate([0, 0, 1])
assert_true(np.allclose(self.g[:, 0], t[:, 0]))
assert_true(np.allclose(self.g[:, 1], t[:, 1]))
assert_true(np.allclose(self.g[:, 2] + 1, t[:, 2]))
t = self.g.move([0, 0, 1])
assert_true(np.allclose(self.g[:, 0], t[:, 0]))
assert_true(np.allclose(self.g[:, 1], t[:, 1]))
assert_true(np.allclose(self.g[:, 2] + 1, t[:, 2]))
def test_iter(self):
for i, iaaspec in enumerate(self.g.iter_species()):
ia, a, spec = iaaspec
assert_true(i == ia)
assert_true(self.g.atom[ia] == a)
for ia in self.g:
assert_true(ia >= 0)
i = 0
for ias, idx in self.g.iter_block():
for ia in ias:
i += 1
assert_true(i == len(self.g))
def test_swap(self):
s = self.g.swap(0, 1)
for i in [0, 1, 2]:
assert_true(np.allclose(self.g[::-1, i], s[:, i]))
def test_append1(self):
for axis in [0, 1, 2]:
s = self.g.append(self.g, axis)
assert_equal(len(s), len(self.g) * 2)
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
s = self.g.prepend(self.g, axis)
assert_equal(len(s), len(self.g) * 2)
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
s = self.g.append(self.g.sc, axis)
assert_equal(len(s), len(self.g))
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
s = self.g.prepend(self.g.sc, axis)
assert_equal(len(s), len(self.g))
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
assert_true(np.allclose(s.cell[axis, :], self.g.cell[axis, :] * 2))
def test_swapaxes(self):
s = self.g.swapaxes(0, 1)
assert_true(np.allclose(self.g[:, 0], s[:, 1]))
assert_true(np.allclose(self.g[:, 1], s[:, 0]))
assert_true(np.allclose(self.g.cell[0, :], s.cell[1, :]))
assert_true(np.allclose(self.g.cell[1, :], s.cell[0, :]))
def test_center(self):
one = self.g.center(atom=[0])
assert_true(np.allclose(self.g[0, :], one))
al = self.g.center()
assert_true(np.allclose(np.mean(self.g.xyz, axis=0), al))
def test_add(self):
double = self.g.add(self.g)
assert_equal(len(double), len(self.g) * 2)
assert_true(np.allclose(self.g.cell, double.cell))
def test_insert(self):
double = self.g.insert(0, self.g)
assert_equal(len(double), len(self.g) * 2)
assert_true(np.allclose(self.g.cell, double.cell))
def test_a2o(self):
# There are 2 orbitals per C atom
assert_equal(self.g.a2o(1), self.g.atom[0].orbs)
def test_o2a(self):
# There are 2 orbitals per C atom
assert_equal(self.g.o2a(2), 1)
def test_reverse(self):
rev = self.g.reverse()
assert_true(len(rev) == 2)
assert_true(np.allclose(rev.xyz[::-1, :], self.g.xyz))
rev = self.g.reverse(atom=list(range(len(self.g))))
assert_true(len(rev) == 2)
assert_true(np.allclose(rev.xyz[::-1, :], self.g.xyz))
def test_close1(self):
three = range(3)
for ia in self.mol:
i = self.mol.close(ia, dR=(0.1, 1.1), idx=three)
if ia < 3:
assert_equal(len(i[0]), 1)
else:
assert_equal(len(i[0]), 0)
# Will only return results from [0,1,2]
# but the fourth atom connects to
# the third
if ia in [0, 2, 3]:
assert_equal(len(i[1]), 1)
elif ia == 1:
assert_equal(len(i[1]), 2)
else:
assert_equal(len(i[1]), 0)
def test_close2(self):
mol = range(3, 5)
for ia in self.mol:
i = self.mol.close(ia, dR=(0.1, 1.1), idx=mol)
assert_equal(len(i), 2)
i = self.mol.close([100, 100, 100], dR=0.1)
assert_equal(len(i), 0)
i = self.mol.close([100, 100, 100], dR=0.1, ret_dist=True)
for el in i:
assert_equal(len(el), 0)
i = self.mol.close([100, 100, 100], dR=0.1, ret_dist=True, ret_coord=True)
for el in i:
assert_equal(len(el), 0)
def test_close_sizes(self):
point = 0
# Return index
idx = self.mol.close(point, dR=0.1)
assert_equal(len(idx), 1)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1))
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 1)
assert_false(isinstance(idx[0], list))
# Longer
idx = self.mol.close(point, dR=(0.1, 1.1, 2.1))
assert_equal(len(idx), 3)
assert_equal(len(idx[0]), 1)
# Return index
idx = self.mol.close(point, dR=0.1, ret_coord=True)
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 1)
assert_equal(len(idx[1]), 1)
assert_equal(idx[1].shape[0], 1) # equivalent to above
assert_equal(idx[1].shape[1], 3)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1), ret_coord=True)
# [[idx-1, idx-2], [coord-1, coord-2]]
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 2)
assert_equal(len(idx[1]), 2)
# idx-1
assert_equal(len(idx[0][0].shape), 1)
assert_equal(idx[0][0].shape[0], 1)
# idx-2
assert_equal(idx[0][1].shape[0], 1)
# coord-1
assert_equal(len(idx[1][0].shape), 2)
assert_equal(idx[1][0].shape[1], 3)
# coord-2
assert_equal(idx[1][1].shape[1], 3)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1), ret_coord=True, ret_dist=True)
# [[idx-1, idx-2], [coord-1, coord-2], [dist-1, dist-2]]
assert_equal(len(idx), 3)
assert_equal(len(idx[0]), 2)
assert_equal(len(idx[1]), 2)
# idx-1
assert_equal(len(idx[0][0].shape), 1)
assert_equal(idx[0][0].shape[0], 1)
# idx-2
assert_equal(idx[0][1].shape[0], 1)
# coord-1
assert_equal(len(idx[1][0].shape), 2)
assert_equal(idx[1][0].shape[1], 3)
# coord-2
assert_equal(idx[1][1].shape[1], 3)
# dist-1
assert_equal(len(idx[2][0].shape), 1)
assert_equal(idx[2][0].shape[0], 1)
# dist-2
assert_equal(idx[2][1].shape[0], 1)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1), ret_dist=True)
# [[idx-1, idx-2], [dist-1, dist-2]]
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 2)
assert_equal(len(idx[1]), 2)
# idx-1
assert_equal(len(idx[0][0].shape), 1)
assert_equal(idx[0][0].shape[0], 1)
# idx-2
assert_equal(idx[0][1].shape[0], 1)
# dist-1
assert_equal(len(idx[1][0].shape), 1)
assert_equal(idx[1][0].shape[0], 1)
# dist-2
assert_equal(idx[1][1].shape[0], 1)
def test_close_sizes_none(self):
point = [100.0, 100.0, 100.0]
# Return index
idx = self.mol.close(point, dR=0.1)
assert_equal(len(idx), 0)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1))
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 0)
assert_false(isinstance(idx[0], list))
# Longer
idx = self.mol.close(point, dR=(0.1, 1.1, 2.1))
assert_equal(len(idx), 3)
assert_equal(len(idx[0]), 0)
# Return index
idx = self.mol.close(point, dR=0.1, ret_coord=True)
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 0)
assert_equal(len(idx[1]), 0)
assert_equal(idx[1].shape[0], 0) # equivalent to above
assert_equal(idx[1].shape[1], 3)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1), ret_coord=True)
# [[idx-1, idx-2], [coord-1, coord-2]]
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 2)
assert_equal(len(idx[1]), 2)
# idx-1
assert_equal(len(idx[0][0].shape), 1)
assert_equal(idx[0][0].shape[0], 0)
# idx-2
assert_equal(idx[0][1].shape[0], 0)
# coord-1
assert_equal(len(idx[1][0].shape), 2)
assert_equal(idx[1][0].shape[1], 3)
# coord-2
assert_equal(idx[1][1].shape[1], 3)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1), ret_coord=True, ret_dist=True)
# [[idx-1, idx-2], [coord-1, coord-2], [dist-1, dist-2]]
assert_equal(len(idx), 3)
assert_equal(len(idx[0]), 2)
assert_equal(len(idx[1]), 2)
# idx-1
assert_equal(len(idx[0][0].shape), 1)
assert_equal(idx[0][0].shape[0], 0)
# idx-2
assert_equal(idx[0][1].shape[0], 0)
# coord-1
assert_equal(len(idx[1][0].shape), 2)
assert_equal(idx[1][0].shape[0], 0)
assert_equal(idx[1][0].shape[1], 3)
# coord-2
assert_equal(idx[1][1].shape[0], 0)
assert_equal(idx[1][1].shape[1], 3)
# dist-1
assert_equal(len(idx[2][0].shape), 1)
assert_equal(idx[2][0].shape[0], 0)
# dist-2
assert_equal(idx[2][1].shape[0], 0)
# Return index of two things
idx = self.mol.close(point, dR=(0.1, 1.1), ret_dist=True)
# [[idx-1, idx-2], [dist-1, dist-2]]
assert_equal(len(idx), 2)
assert_equal(len(idx[0]), 2)
assert_equal(len(idx[1]), 2)
# idx-1
assert_equal(len(idx[0][0].shape), 1)
assert_equal(idx[0][0].shape[0], 0)
# idx-2
assert_equal(idx[0][1].shape[0], 0)
# dist-1
assert_equal(len(idx[1][0].shape), 1)
assert_equal(idx[1][0].shape[0], 0)
# dist-2
assert_equal(idx[1][1].shape[0], 0)
def test_bond_correct(self):
# Create ribbon
rib = self.g.tile(2, 1)
# Convert the last atom to a H atom
rib.atom[-1] = Atom[1]
ia = len(rib) - 1
# Get bond-length
idx, d = rib.close(ia, dR=(0.1, 1000), ret_dist=True)
i = np.argmin(d[1])
d = d[1][i]
rib.bond_correct(ia, idx[1][i])
idx, d2 = rib.close(ia, dR=(0.1, 1000), ret_dist=True)
i = np.argmin(d2[1])
d2 = d2[1][i]
assert_false(d == d2)
# Calculate actual radius
assert_true(d2 == (Atom[1].radius() + Atom[6].radius()))
def test_unit_cell_estimation1(self):
# Create new geometry with only the coordinates
# and atoms
geom = Geometry(self.g.xyz, Atom[6])
# Only check the two distances we know have sizes
for i in range(2):
# It cannot guess skewed axis
assert_false(np.allclose(geom.cell[i, :], self.g.cell[i, :]))
def test_unit_cell_estimation2(self):
# Create new geometry with only the coordinates
# and atoms
s1 = SuperCell([2, 2, 2])
g1 = Geometry([[0, 0, 0], [1, 1, 1]], sc=s1)
g2 = Geometry(np.copy(g1.xyz))
assert_true(np.allclose(g1.cell, g2.cell))
# Assert that it correctly calculates the bond-length in the
# directions of actual distance
g1 = Geometry([[0, 0, 0], [1, 1, 0]], atom="H", sc=s1)
g2 = Geometry(np.copy(g1.xyz))
for i in range(2):
assert_true(np.allclose(g1.cell[i, :], g2.cell[i, :]))
assert_false(np.allclose(g1.cell[2, :], g2.cell[2, :]))
def test_argumentparser(self):
self.g.ArgumentParser()
def test_set_sc(self):
# Create new geometry with only the coordinates
# and atoms
s1 = SuperCell([2, 2, 2])
g1 = Geometry([[0, 0, 0], [1, 1, 1]], sc=[2, 2, 1])
g1.set_sc(s1)
assert_true(g1.sc == s1)
def test_attach1(self):
g = self.g.attach(0, self.mol, 0, dist=1.42, axis=2)
g = self.g.attach(0, self.mol, 0, dist="calc", axis=2)
g = self.g.attach(0, self.mol, 0, dist=[0, 0, 1.42])
def test_mirror1(self):
for plane in ["xy", "xz", "yz"]:
self.g.mirror(plane)
def test_pickle(self):
import pickle as p
s = p.dumps(self.g)
n = p.loads(s)
assert_true(n == self.g)
assert_false(n != self.g)
def nanotube(bond, atom=None, chirality=(1, 1)):
"""
Create a nano-tube geometry
This routine is implemented as in ``ASE`` with few changes.
Parameters
----------
bond: float
length between atoms in nano-tube
atom: Atom(6)
nanotube atoms
chirality: (int, int)
chirality of nanotube (n, m)
"""
if atom is None:
atom = Atom[6]
# Correct the input...
n, m = chirality
if n < m:
m, n = n, m
sign = -1
else:
sign = 1
sq3 = 3.0 ** .5
a = sq3 * bond
l2 = n * n + m * m + n * m
l = l2 ** .5
def gcd(a, b):
while a != 0:
a, b = b % a, a
return b
nd = gcd(n, m)
if (n - m) % (3 * nd) == 0:
ndr = 3 * nd
else:
ndr = nd
nr = (2 * m + n) // ndr
ns = -(2 * n + m) // ndr
nn = 2 * l2 // ndr
ichk = 0
if nr == 0:
n60 = 1
else:
n60 = nr * 4
absn = abs(n60)
nnp = []
nnq = []
for i in range(-absn, absn + 1):
for j in range(-absn, absn + 1):
j2 = nr * j - ns * i
if j2 == 1:
j1 = m * i - n * j
if j1 > 0 and j1 < nn:
ichk += 1
nnp.append(i)
nnq.append(j)
if ichk == 0:
raise RuntimeError('not found p, q strange!!')
if ichk >= 2:
raise RuntimeError('more than 1 pair p, q strange!!')
nnnp = nnp[0]
nnnq = nnq[0]
lp = nnnp * nnnp + nnnq * nnnq + nnnp * nnnq
r = a * lp ** .5
c = a * l
t = sq3 * c / ndr
rs = c / (2.0 * np.pi)
q1 = np.arctan((sq3 * m) / (2 * n + m))
q2 = np.arctan((sq3 * nnnq) / (2 * nnnp + nnnq))
q3 = q1 - q2
q4 = 2.0 * np.pi / nn
q5 = bond * np.cos((np.pi / 6.0) - q1) / c * 2.0 * np.pi
h1 = abs(t) / abs(np.sin(q3))
h2 = bond * np.sin((np.pi / 6.0) - q1)
xyz = np.empty([nn*2, 3], np.float64)
for i in range(nn):
ix = i * 2
k = np.floor(i * abs(r) / h1)
xyz[ix,0] = rs * np.cos(i * q4)
xyz[ix,1] = rs * np.sin(i * q4)
z = (i * abs(r) - k * h1) * np.sin(q3)
kk2 = abs(np.floor((z + 0.0001) / t))
if z >= t - 0.0001:
z -= t * kk2
elif z < 0:
z += t * kk2
xyz[ix,2] = z * sign
# Next
ix += 1
xyz[ix, 0] = rs * np.cos(i * q4 + q5)
xyz[ix, 1] = rs * np.sin(i * q4 + q5)
z = (i * abs(r) - k * h1) * np.sin(q3) - h2
if z >= 0 and z < t:
pass
else:
z -= h1 * np.sin(q3)
kk = abs(np.floor(z / t))
if z >= t - 0.0001:
z -= t * kk
elif z < 0:
z += t * kk
xyz[ix, 2] = z * sign
# Sort the atomic coordinates according to z
idx = np.argsort(xyz[:,2])
xyz = xyz[idx,:]
sc = SuperCell([rs * 4, rs * 4, t], nsc=[1,1,3])
geom = Geometry(xyz, atom, sc=sc)
# Return a geometry with the first atom at (0,0,0)
return geom.translate(-np.amin(geom.xyz, axis=0))
def ArgumentParser(self, *args, **kwargs):
""" Returns the arguments that is available for this Sile """
newkw = Geometry._ArgumentParser_args_single()
newkw.update(kwargs)
return self.read_geom().ArgumentParser(*args, **newkw)
