def read_basis(self):
""" Returns a set of atoms corresponding to the basis-sets in the ORB_INDX file
The specie names have a short field in the ORB_INDX file, hence the name may
not necessarily be the same as provided in the species block
"""
# First line contains no no_s
line = self.readline().split()
no = int(line[0])
self.readline()
self.readline()
pt = PeriodicTable()
def crt_atom(spec, orbs):
i = pt.Z(spec)
if isinstance(i, int):
return Atom(i, orbs)
else:
return Atom(-1, orbs, tag=spec)
# Now we begin by reading the atoms
atom = []
orbs = []
specs = []
ia = 1
for _ in range(no):
line = self.readline().split()
i_a = int(line[1])
if i_a != ia:
if i_s not in specs:
atom.append(crt_atom(spec, orbs))
specs.append(i_s)
ia = i_a
orbs = []
i_s = int(line[2]) - 1
if i_s in specs:
continue
spec = line[3]
nlmz = list(map(int, line[5:9]))
P = line[9] == 'T'
rc = float(line[11]) * Bohr2Ang
# Create the orbital
o = AtomicOrbital(n=nlmz[0],
l=nlmz[1],
m=nlmz[2],
Z=nlmz[3],
P=P,
spherical=Orbital(rc))
orbs.append(o)
if i_s not in specs:
atom.append(crt_atom(spec, orbs))
specs.append(i_s)
# Now re-arrange the atoms and create the Atoms object
return Atoms([atom[i] for i in specs])
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 test_spin_rotate_so(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, 0.2, 0.2), (0.1, 0.2, 0.1, 0.1, 0., 0.1, 0.2, 0.3)]])
D_mull = D.mulliken()
d = D.spin_rotate([45, 60, 90], rad=False)
d_mull = d.mulliken()
assert not np.allclose(D_mull, d_mull)
assert np.allclose(D_mull[:, 0], d_mull[:, 0])
def test_spin_align_pol(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('p'))
D.construct([[0.1, bond + 0.01], [(1., 0.5), (0.1, 0.2)]])
D_mull = D.mulliken()
v = np.array([1, 2, 3])
d = D.spin_align(v)
d_mull = d.mulliken()
assert D_mull.shape == (len(D), 2)
assert d_mull.shape == (len(D), 4)
assert not np.allclose(-np.diff(D_mull, axis=1), d_mull[:, 3])
assert np.allclose(D_mull.sum(1), d_mull[:, 0])
def test_spin_align_nc(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,
atom=C,
sc=sc)
D = DensityMatrix(g, spin=Spin('nc'))
D.construct([[0.1, bond + 0.01],
[(1., 0.5, 0.01, 0.01), (0.1, 0.2, 0.1, 0.1)]])
D_mull = D.mulliken()
v = np.array([1, 2, 3])
d = D.spin_align(v)
d_mull = d.mulliken()
assert not np.allclose(D_mull, d_mull)
assert np.allclose(D_mull[:, 0], d_mull[:, 0])
def read_basis(self, atoms=None):
""" Returns a set of atoms corresponding to the basis-sets in the ORB_INDX file
The specie names have a short field in the ORB_INDX file, hence the name may
not necessarily be the same as provided in the species block
Parameters
----------
atoms : Atoms, optional
list of atoms used for the species index
"""
# First line contains no no_s
line = self.readline().split()
no = int(line[0])
self.readline()
self.readline()
pt = PeriodicTable()
def crt_atom(i_s, spec, orbs):
if atoms is None:
# The user has not specified an atomic basis
i = pt.Z(spec)
if isinstance(i, int):
return Atom(i, orbs)
else:
return Atom(-1, orbs, tag=spec)
# Get the atom and add the orbitals
return atoms[i_s].copy(orbitals=orbs)
# Now we begin by reading the atoms
atom = []
orbs = []
specs = []
ia = 1
for _ in range(no):
line = self.readline().split()
i_a = int(line[1])
if i_a != ia:
if i_s not in specs:
atom.append(crt_atom(i_s, spec, orbs))
specs.append(i_s)
ia = i_a
orbs = []
i_s = int(line[2]) - 1
if i_s in specs:
continue
spec = line[3]
nlmz = list(map(int, line[5:9]))
P = line[9] == 'T'
rc = float(line[11]) * Bohr2Ang
# Create the orbital
o = AtomicOrbital(n=nlmz[0],
l=nlmz[1],
m=nlmz[2],
zeta=nlmz[3],
P=P,
R=rc)
orbs.append(o)
if i_s not in specs:
atom.append(crt_atom(i_s, spec, orbs))
specs.append(i_s)
# Now re-arrange the atoms and create the Atoms object
return Atoms([atom[i] for i in specs])
