def read_hamiltonian(self, **kwargs):
""" Returns the electronic structure from the siesta.TSHS file """
tshs_g = self.read_geometry()
geom = _geometry_align(tshs_g, kwargs.get('geometry', tshs_g),
self.__class__, 'read_hamiltonian')
# read the sizes used...
sizes = _siesta.read_tshs_sizes(self.file)
_bin_check(self, 'read_hamiltonian', 'could not read sizes.')
isc = _siesta.read_tshs_cell(self.file, sizes[3])[2].T
_bin_check(self, 'read_hamiltonian', 'could not read cell.')
spin = sizes[0]
no = sizes[2]
nnz = sizes[4]
ncol, col, dH, dS = _siesta.read_tshs_hs(self.file, spin, no, nnz)
_bin_check(self, 'read_hamiltonian',
'could not read Hamiltonian and overlap matrix.')
# Check whether it is an orthogonal basis set
orthogonal = np.abs(dS).sum() == geom.no
# Create the Hamiltonian container
H = Hamiltonian(geom, spin, nnzpr=1, orthogonal=orthogonal)
# 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)
if orthogonal:
H._csr._D = _a.emptyd([nnz, spin])
H._csr._D[:, :] = dH[:, :]
else:
H._csr._D = _a.emptyd([nnz, spin + 1])
H._csr._D[:, :spin] = dH[:, :]
H._csr._D[:, spin] = dS[:]
_mat_spin_convert(H)
# Convert to sisl supercell
_csr_from_sc_off(H.geometry, isc, H._csr)
# Find all indices where dS == 1 (remember col is in fortran indices)
idx = col[np.isclose(dS, 1.).nonzero()[0]]
if np.any(idx > no):
print('Number of orbitals: {}'.format(no))
print(idx)
raise SileError(
str(self) + '.read_hamiltonian could not assert '
'the supercell connections in the primary unit-cell.')
return H
def unfold_points(self, k):
r""" Return a list of k-points to be evaluated for this objects unfolding
The k-point `k` is with respect to the unfolded geometry.
The return list of `k` points are the k-points required to be sampled in the
folded geometry.
Parameters
----------
k : (3,) of float
k-point evaluation corresponding to the unfolded unit-cell
Returns
-------
k_unfold
a list of ``np.prod(self.bloch)`` k-points used for the unfolding
"""
k = _a.arrayd(k)
# Create expansion points
B = self._bloch
unfold = _a.emptyd([B[2], B[1], B[0], 3])
# Use B-casting rules (much simpler)
unfold[:, :, :, 0] = (aranged(B[0]).reshape(1, 1, -1) + k[0]) / B[0]
unfold[:, :, :, 1] = (aranged(B[1]).reshape(1, -1, 1) + k[1]) / B[1]
unfold[:, :, :, 2] = (aranged(B[2]).reshape(-1, 1, 1) + k[2]) / B[2]
# Back-transform shape
return unfold.reshape(-1, 3)
def read_overlap(self, **kwargs):
""" Returns the overlap matrix from the TranSiesta file """
tshs_g = self.read_geometry()
geom = _geometry_align(tshs_g, kwargs.get('geometry', tshs_g),
self.__class__, 'read_overlap')
# read the sizes used...
sizes = _siesta.read_tshs_sizes(self.file)
_bin_check(self, 'read_overlap', 'could not read sizes.')
isc = _siesta.read_tshs_cell(self.file, sizes[3])[2].T
_bin_check(self, 'read_overlap', 'could not read cell.')
no = sizes[2]
nnz = sizes[4]
ncol, col, dS = _siesta.read_tshs_s(self.file, no, nnz)
_bin_check(self, 'read_overlap', 'could not read overlap matrix.')
# Create the Hamiltonian container
S = SparseOrbitalBZ(geom, nnzpr=1)
# Create the new sparse matrix
S._csr.ncol = ncol.astype(np.int32, copy=False)
S._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
S._csr.col = col.astype(np.int32, copy=False) - 1
S._csr._nnz = len(col)
S._csr._D = _a.emptyd([nnz, 1])
S._csr._D[:, 0] = dS[:]
# Convert to sisl supercell
_csr_from_sc_off(S.geometry, isc, S._csr)
return S
def lineark(self, ticks=False):
""" A 1D array which corresponds to the delta-k values of the path
This is meant for plotting
Examples
--------
>>> p = BandStructure(...) # doctest: +SKIP
>>> eigs = Hamiltonian.eigh(p) # doctest: +SKIP
>>> for i in range(len(Hamiltonian)): # doctest: +SKIP
... plt.plot(p.lineark(), eigs[:, i]) # doctest: +SKIP
>>> p = BandStructure(...) # doctest: +SKIP
>>> eigs = Hamiltonian.eigh(p) # doctest: +SKIP
>>> lk, kt, kl = p.lineark(True) # doctest: +SKIP
>>> plt.xticks(kt, kl) # doctest: +SKIP
>>> for i in range(len(Hamiltonian)): # doctest: +SKIP
... plt.plot(lk, eigs[:, i]) # doctest: +SKIP
Parameters
----------
ticks : bool, optional
if `True` the ticks for the points are also returned
lk, xticks, label_ticks, lk = BandStructure.lineark(True)
Returns
-------
linear_k : The positions in reciprocal space determined by the distance between points
k_tick : Linear k-positions of the points, only returned if `ticks` is ``True``
k_label : Labels at `k_tick`, only returned if `ticks` is ``True``
"""
# Calculate points
k = [self.tocartesian(pnt) for pnt in self.point]
# Get difference between points
dk = np.diff(k, axis=0)
# Calculate the cumultative distance between points
k_len = np.insert(_a.cumsumd((dk ** 2).sum(1) ** .5), 0, 0.)
xtick = [None] * len(k)
# Prepare output array
dK = _a.emptyd(len(self))
# short-hand
ls = np.linspace
xtick = np.insert(_a.cumsumi(self.division), 0, 0)
for i in range(len(dk)):
n = self.division[i]
end = i == len(dk) - 1
dK[xtick[i]:xtick[i+1]] = ls(k_len[i], k_len[i+1], n, dtype=np.float64, endpoint=end)
xtick[-1] -= 1
# Get label tick, in case self.name is a single string 'ABCD'
label_tick = [a for a in self.name]
if ticks:
return dK, dK[xtick], label_tick
return dK
def __init__(self, parent, nkpt, displacement=None, size=None, trs=True):
super(MonkhorstPack, self).__init__(parent)
if isinstance(nkpt, Integral):
nkpt = np.diag([nkpt] * 3)
elif isinstance(nkpt[0], Integral):
nkpt = np.diag(nkpt)
# Now we have a matrix of k-points
if np.any(nkpt - np.diag(np.diag(nkpt)) != 0):
raise NotImplementedError(
self.__class__.__name__ +
" with off-diagonal components is not implemented yet")
if displacement is None:
displacement = np.zeros(3, np.float64)
elif isinstance(displacement, Real):
displacement = np.zeros(3, np.float64) + displacement
if size is None:
size = _a.onesd(3)
elif isinstance(size, Real):
size = _a.zerosd(3) + size
# Retrieve the diagonal number of values
Dn = np.diag(nkpt).astype(np.int32)
if np.any(Dn) == 0:
raise ValueError(self.__class__.__name__ +
' *must* be initialized with '
'diagonal elements different from 0.')
i_trs = -1
if trs:
# Figure out which direction to TRS
nmax = 0
for i in [0, 1, 2]:
if displacement[i] == 0. and Dn[i] > nmax:
nmax = Dn[i]
i_trs = i
# Calculate k-points and weights along all directions
kw = [
self.grid(Dn[i], displacement[i], size[i], i == i_trs)
for i in (0, 1, 2)
]
self._k = _a.emptyd((kw[0][0].size, kw[1][0].size, kw[2][0].size, 3))
self._w = _a.onesd(self._k.shape[:-1])
for i in (0, 1, 2):
k = kw[i][0].reshape(-1, 1, 1)
w = kw[i][1].reshape(-1, 1, 1)
self._k[..., i] = np.rollaxis(k, 0, i + 1)
self._w[...] *= np.rollaxis(w, 0, i + 1)
del kw
self._k.shape = (-1, 3)
self._k = np.where(self._k > .5, self._k - 1, self._k)
self._w.shape = (-1, )
def _index_shape_ellipsoid(self, ellipsoid):
""" Internal routine for ellipsoid shape-indices """
# Figure out the points on the ellipsoid
rad1 = pi / 180
theta, phi = ogrid[-pi:pi:rad1, 0:pi:rad1]
rxyz = _a.emptyd([theta.size, phi.size, 3])
rxyz[..., 2] = cos(phi)
sin(phi, out=phi)
rxyz[..., 0] = cos(theta) * phi
rxyz[..., 1] = sin(theta) * phi
rxyz = dot(rxyz, ellipsoid._v) + ellipsoid.center.reshape(1, 3)
del theta, phi
# Get all indices of the ellipsoid circumference
return self.index(rxyz)
def solve_lagrange(self):
r""" Calculate the coefficients according to Pulay's method, return everything + Lagrange multiplier """
hist = self.history
n_h = len(hist)
metric = self._metric
if n_h == 0:
# Externally the coefficients should reflect the weight per previous iteration.
# The mixing weight is an additional parameter
return _a.arrayd([1.]), 100.
elif n_h == 1:
return _a.arrayd([1.]), metric(hist[0][-1], hist[0][-1])
# Initialize the matrix to be solved against
B = _a.emptyd([n_h + 1, n_h + 1])
# Fill matrix B
for i in range(n_h):
ei = hist[i][-1]
B[i, i] = metric(ei, ei)
for j in range(i + 1, n_h):
ej = hist[j][-1]
B[i, j] = metric(ei, ej)
B[j, i] = B[i, j]
B[:, n_h] = 1.
B[n_h, :] = 1.
B[n_h, n_h] = 0.
# Although B contains 1 and a number on the order of
# number of elements (self._hist.size), it seems very
# numerically stable.
# Create RHS
RHS = _a.zerosd(n_h + 1)
RHS[-1] = 1
try:
# Apparently we cannot use assume_a='sym'
# Is this because sym also implies positive definitiness?
# However, these are matrices of order ~30, so we don't care
c = solve(B, RHS)
return c[:-1], -c[-1]
except np.linalg.LinAlgError as e:
# We have a LinalgError
return _a.arrayd([1.]), metric(hist[-1][-1], hist[-1][-1])
def spher2cart(r, theta, phi):
r""" Convert spherical coordinates to cartesian coordinates
Parameters
----------
r : array_like
radius
theta : array_like
azimuthal angle in the :math:`x-y` plane
phi : array_like
polar angle from the :math:`z` axis
"""
rx = r * cos(theta) * sin(phi)
R = _a.emptyd(rx.shape + (3, ))
R[..., 0] = rx
del rx
R[..., 1] = r * sin(theta) * sin(phi)
R[..., 2] = r * cos(phi)
return R
def _index_shape_cuboid(self, cuboid):
""" Internal routine for cuboid shape-indices """
# Construct all points on the outer rim of the cuboids
min_d = fnorm(self.dcell).min()
# Retrieve cuboids edge-lengths
v = cuboid.edge_length
# Create normalized cuboid vectors (because we expan via the lengths below
vn = cuboid._v / fnorm(cuboid._v).reshape(-1, 1)
LL = (cuboid.center - cuboid._v.sum(0) / 2).reshape(1, 3)
UR = (cuboid.center + cuboid._v.sum(0) / 2).reshape(1, 3)
# Create coordinates
a = vn[0, :].reshape(1, -1) * _a.aranged(0, v[0] + min_d, min_d).reshape(-1, 1)
b = vn[1, :].reshape(1, -1) * _a.aranged(0, v[1] + min_d, min_d).reshape(-1, 1)
c = vn[2, :].reshape(1, -1) * _a.aranged(0, v[2] + min_d, min_d).reshape(-1, 1)
# Now create all sides
sa = a.shape[0]
sb = b.shape[0]
sc = c.shape[0]
def plane(v1, v2):
return (v1.reshape(-1, 1, 3) + v2.reshape(1, -1, 3)).reshape(1, -1, 3)
# Allocate for the 6 faces of the cuboid
rxyz = _a.emptyd([2, sa * sb + sa * sc + sb * sc, 3])
# Define the LL and UR
rxyz[0, :, :] = LL
rxyz[1, :, :] = UR
i = 0
rxyz[:, i:i + sa * sb, :] += plane(a, b)
i += sa * sb
rxyz[:, i:i + sa * sc, :] += plane(a, c)
i += sa * sc
rxyz[:, i:i + sb * sc, :] += plane(b, c)
del a, b, c, sa, sb, sc
rxyz.shape = (-1, 3)
# Get all indices of the cuboid planes
return self.index(rxyz)
def _index_shape(self, shape):
""" Internal routine for shape-indices """
# First grab the sphere, subsequent indices will be reduced
# by the actual shape
cuboid = shape.toCuboid()
ellipsoid = shape.toEllipsoid()
if ellipsoid.volume() > cuboid.volume():
idx = self._index_shape_cuboid(cuboid)
else:
idx = self._index_shape_ellipsoid(ellipsoid)
# Get min/max
imin = idx.min(0)
imax = idx.max(0)
del idx
dc = self.dcell
# Now to find the actual points inside the shape
# First create all points in the square and then retrieve all indices
# within.
ix = _a.aranged(imin[0], imax[0] + 0.5)
iy = _a.aranged(imin[1], imax[1] + 0.5)
iz = _a.aranged(imin[2], imax[2] + 0.5)
output_shape = (ix.size, iy.size, iz.size, 3)
rxyz = _a.emptyd(output_shape)
ao = add.outer
ao(ao(ix * dc[0, 0], iy * dc[1, 0]), iz * dc[2, 0], out=rxyz[:, :, :, 0])
ao(ao(ix * dc[0, 1], iy * dc[1, 1]), iz * dc[2, 1], out=rxyz[:, :, :, 1])
ao(ao(ix * dc[0, 2], iy * dc[1, 2]), iz * dc[2, 2], out=rxyz[:, :, :, 2])
idx = shape.within_index(rxyz.reshape(-1, 3))
del rxyz
i = _a.emptyi(output_shape)
i[:, :, :, 0] = ix.reshape(-1, 1, 1)
i[:, :, :, 1] = iy.reshape(1, -1, 1)
i[:, :, :, 2] = iz.reshape(1, 1, -1)
del ix, iy, iz
i.shape = (-1, 3)
i = take(i, idx, axis=0)
del idx
return i
def fermi_level(self,
bz=None,
q=None,
distribution='fermi_dirac',
q_tol=1e-10):
""" Calculate the Fermi-level using a Brillouinzone sampling and a target charge
The Fermi-level will be calculated using an iterative approach by first calculating all eigenvalues
and subsequently fitting the Fermi level to the final charge (`q`).
Parameters
----------
bz : Brillouinzone, optional
sampled k-points and weights, the ``bz.parent`` will be equal to this object upon return
default to Gamma-point
q : float, list of float, optional
seeked charge, if not set will be equal to ``self.geometry.q0``. If a list of two is passed
there will be calculated a Fermi-level per spin-channel. If the Hamiltonian is not spin-polarized
the sum of the list will be used and only a single fermi-level will be returned.
distribution : str, func, optional
used distribution, must accept the keyword ``mu`` as parameter for the Fermi-level
q_tol : float, optional
tolerance of charge for finding the Fermi-level
Returns
-------
float or array_like
the Fermi-level of the system (or two if two different charges are passed)
"""
if bz is None:
# Gamma-point only
from .brillouinzone import BrillouinZone
bz = BrillouinZone(self)
else:
# Overwrite the parent in bz
bz.set_parent(self)
if q is None:
if self.spin.is_unpolarized:
q = self.geometry.q0 * 0.5
else:
q = self.geometry.q0
# Ensure we have an "array" in case of spin-polarized calculations
q = _a.asarrayd(q)
if np.any(q <= 0.):
raise ValueError(
f"{self.__class__.__name__}.fermi_level cannot calculate the Fermi level "
"for 0 electrons.")
if isinstance(distribution, str):
distribution = get_distribution(distribution)
# B-cast for easier weights
w = bz.weight.reshape(-1, 1)
# Internal class to calculate the Fermi-level
def _Ef(q, eig):
# We could reduce it depending on the temperature,
# however the distribution does not have the kT
# parameter available.
min_Ef, max_Ef = eig.min(), eig.max()
nextafter = np.nextafter
while nextafter(min_Ef, max_Ef) < max_Ef:
Ef = (min_Ef + max_Ef) * 0.5
# Calculate guessed charge
qt = (distribution(eig, mu=Ef) * w).sum()
if abs(qt - q) < q_tol:
return Ef
if qt >= q:
max_Ef = Ef
elif qt <= q:
min_Ef = Ef
return Ef
# Retrieve dispatcher for averaging
eigh = bz.apply.array.eigh
if self.spin.is_polarized and q.size == 2:
if np.any(q >= len(self)):
raise ValueError(
f"{self.__class__.__name__}.fermi_level cannot calculate the Fermi level "
"for electrons ({q}) equal to or above number of orbitals ({len(self)})."
)
# We need to do Fermi-level separately since the user requests
# separate fillings
Ef = _a.emptyd(2)
Ef[0] = _Ef(q[0], eigh(spin=0))
Ef[1] = _Ef(q[1], eigh(spin=1))
else:
# Ensure a single charge
q = q.sum()
if q >= len(self):
raise ValueError(
f"{self.__class__.__name__}.fermi_level cannot calculate the Fermi level "
"for electrons ({q}) equal to or above number of orbitals ({len(self)})."
)
if self.spin.is_polarized:
Ef = _Ef(q, np.concatenate(
[eigh(spin=0), eigh(spin=1)], axis=1))
else:
Ef = _Ef(q, eigh())
return Ef
def read_energy_density_matrix(self, **kwargs):
""" Returns the energy density matrix from the siesta.DM file """
# Now read the sizes used...
spin, no, nsc, nnz = _siesta.read_tsde_sizes(self.file)
_bin_check(self, 'read_energy_density_matrix',
'could not read energy density matrix sizes.')
ncol, col, dEDM = _siesta.read_tsde_edm(self.file, spin, no, nsc, nnz)
_bin_check(self, 'read_energy_density_matrix',
'could not read energy density matrix.')
# Try and immediately attach a geometry
geom = kwargs.get('geometry', kwargs.get('geom', None))
if geom is None:
# We truly, have no clue,
# Just generate a boxed system
xyz = [[x, 0, 0] for x in range(no)]
sc = SuperCell([no, 1, 1], nsc=nsc)
geom = Geometry(xyz, Atom(1), sc=sc)
if nsc[0] != 0 and np.any(geom.nsc != nsc):
# We have to update the number of supercells!
geom.set_nsc(nsc)
if geom.no != no:
raise SileError(
str(self) + '.read_energy_density_matrix could '
'not use the passed geometry as the number of atoms or orbitals '
'is inconsistent with DM file.')
# Create the energy density matrix container
EDM = EnergyDensityMatrix(geom,
spin,
nnzpr=1,
dtype=np.float64,
orthogonal=False)
# Create the new sparse matrix
EDM._csr.ncol = ncol.astype(np.int32, copy=False)
EDM._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
EDM._csr.col = col.astype(np.int32, copy=False) - 1
EDM._csr._nnz = len(col)
EDM._csr._D = _a.emptyd([nnz, spin + 1])
EDM._csr._D[:, :spin] = dEDM[:, :]
# EDM file does not contain overlap matrix... so neglect it for now.
EDM._csr._D[:, spin] = 0.
_mat_spin_convert(EDM)
# Convert the supercells to sisl supercells
if nsc[0] != 0 or geom.no_s >= col.max():
_csr_from_siesta(geom, EDM._csr)
else:
warn(
str(self) +
'.read_energy_density_matrix may result in a wrong sparse pattern!'
)
return EDM
def fermi_level(self,
bz=None,
q=None,
distribution='fermi_dirac',
q_tol=1e-12):
""" Calculate the Fermi-level using a Brillouinzone sampling and a target charge
The Fermi-level will be calculated using an iterative approach by first calculating all eigenvalues
and subsequently fitting the Fermi level to the final charge (`q`).
Parameters
----------
bz : Brillouinzone, optional
sampled k-points and weights, the ``bz.parent`` will be equal to this object upon return
default to Gamma-point
q : float, list of float, optional
seeked charge, if not set will be equal to ``self.geometry.q0``. If a list of two is passed
there will be calculated a Fermi-level per spin-channel. If the Hamiltonian is not spin-polarized
the sum of the list will be used and only a single fermi-level will be returned.
distribution : str, func, optional
used distribution, must accept the keyword ``mu`` as parameter for the Fermi-level
q_tol : float, optional
tolerance of charge for finding the Fermi-level
Returns
-------
fermi-level : the Fermi-level of the system (or two if two different charges are passed)
"""
if bz is None:
# Gamma-point only
from .brillouinzone import BrillouinZone
bz = BrillouinZone(self)
else:
# Overwrite the parent in bz
bz.set_parent(self)
# Ensure we are using asarray
bz.asarray()
if q is None:
q = self.geometry.q0
# Ensure we have an "array" in case of spin-polarized calculations
q = np.asarray(q)
if isinstance(distribution, str):
distribution = get_distribution(distribution)
# B-cast for easier weights
w = bz.weight.reshape(-1, 1)
# Internal class to calculate the Fermi-level
def _Ef(q, eig):
# We could reduce it depending on the temperature,
# however the distribution does not have the kT
# parameter available.
Ef = np.average(eig[:, int(q)])
l_Ef = []
l_q = []
def list_append(q, Ef):
l_q.append(q)
l_Ef.append(Ef)
# Calculate guessed charge
qt = (distribution(eig, mu=Ef) * w).sum()
while abs(qt - q) > q_tol:
# Add to cubic-spline
list_append(qt, Ef)
# Estimate new Fermi-level
if len(l_q) > 1:
# We can do a spline interpolation
lq = np.array(l_q)
idx = np.argsort(lq)
lEf = np.array(l_Ef)
Ef = CubicSpline(lq[idx], lEf[idx], extrapolate=True)(q)
else:
# Update limits
if qt > q:
Ef = Ef - 0.5
elif qt < q:
Ef = Ef + 0.5
# Calculate new guessed charge
qt = (distribution(eig, mu=Ef) * w).sum()
return Ef
if self.spin.is_polarized and q.size == 2:
# We need to do Fermi-level separately since the user requests
# separate fillings
Ef = _a.emptyd(2)
Ef[0] = _Ef(q[0], bz.eigh(spin=0))
Ef[1] = _Ef(q[1], bz.eigh(spin=1))
else:
# Ensure a single charge
q = q.sum()
if self.spin.is_polarized:
Ef = _Ef(
q,
np.concatenate(
[bz.eigh(spin=0), bz.eigh(spin=1)], axis=1))
else:
Ef = _Ef(q, bz.eigh())
return Ef
def __init__(self, parent, nkpt, displacement=None, size=None, centered=True, trs=True):
super(MonkhorstPack, self).__init__(parent)
if isinstance(nkpt, Integral):
nkpt = np.diag([nkpt] * 3)
elif isinstance(nkpt[0], Integral):
nkpt = np.diag(nkpt)
# Now we have a matrix of k-points
if np.any(nkpt - np.diag(np.diag(nkpt)) != 0):
raise NotImplementedError(self.__class__.__name__ + " with off-diagonal components is not implemented yet")
if displacement is None:
displacement = np.zeros(3, np.float64)
elif isinstance(displacement, Real):
displacement = np.zeros(3, np.float64) + displacement
if size is None:
size = _a.onesd(3)
elif isinstance(size, Real):
size = _a.zerosd(3) + size
else:
size = _a.arrayd(size)
# Retrieve the diagonal number of values
Dn = np.diag(nkpt).astype(np.int32)
if np.any(Dn) == 0:
raise ValueError(self.__class__.__name__ + ' *must* be initialized with '
'diagonal elements different from 0.')
i_trs = -1
if trs:
# Figure out which direction to TRS
nmax = 0
for i in [0, 1, 2]:
if displacement[i] in [0., 0.5] and Dn[i] > nmax:
nmax = Dn[i]
i_trs = i
if nmax == 1:
i_trs = -1
if i_trs == -1:
# If we still haven't decided (say for weird displacements)
# simply take the one with the maximum number of k-points.
i_trs = np.argmax(Dn)
# Calculate k-points and weights along all directions
kw = [self.grid(Dn[i], displacement[i], size[i], centered, i == i_trs) for i in (0, 1, 2)]
self._k = _a.emptyd((kw[0][0].size, kw[1][0].size, kw[2][0].size, 3))
self._w = _a.onesd(self._k.shape[:-1])
for i in (0, 1, 2):
k = kw[i][0].reshape(-1, 1, 1)
w = kw[i][1].reshape(-1, 1, 1)
self._k[..., i] = np.rollaxis(k, 0, i + 1)
self._w[...] *= np.rollaxis(w, 0, i + 1)
del kw
self._k.shape = (-1, 3)
self._k = np.where(self._k > .5, self._k - 1, self._k)
self._w.shape = (-1,)
# Store information regarding size and diagonal elements
# This information is basically only necessary when
# we want to replace special k-points
self._diag = Dn # vector
self._displ = displacement # vector
self._size = size # vector
self._centered = centered
self._trs = i_trs
def param_circle(self, sc, N_or_dk, kR, normal, origo, loop=False):
r""" Create a parameterized k-point list where the k-points are generated on a circle around an origo
The generated circle is a perfect circle in the reciprocal space (Cartesian coordinates).
To generate a perfect circle in units of the reciprocal lattice vectors one can
generate the circle for a diagonal supercell with side-length :math:`2\pi`, see
example below.
Parameters
----------
sc : SuperCell, or SuperCellChild
the supercell used to construct the k-points
N_or_dk : int
number of k-points generated using the parameterization (if an integer),
otherwise it specifies the discretization length on the circle (in 1/Ang),
If the latter case will use less than 4 points a warning will be raised and
the number of points increased to 4.
kR : float
radius of the k-point. In 1/Ang
normal : array_like of float
normal vector to determine the circle plane
origo : array_like of float
origo of the circle used to generate the circular parameterization
loop : bool, optional
whether the first and last point are equal
Examples
--------
>>> sc = SuperCell([1, 1, 10, 90, 90, 60])
>>> bz = BrillouinZone.param_circle(sc, 10, 0.05, [0, 0, 1], [1./3, 2./3, 0])
To generate a circular set of k-points in reduced coordinates (reciprocal
>>> sc = SuperCell([1, 1, 10, 90, 90, 60])
>>> bz = BrillouinZone.param_circle(sc, 10, 0.05, [0, 0, 1], [1./3, 2./3, 0])
>>> bz_rec = BrillouinZone.param_circle(2*np.pi, 10, 0.05, [0, 0, 1], [1./3, 2./3, 0])
>>> bz.k[:, :] = bz_rec.k[:, :]
Returns
-------
BrillouinZone : with the parameterized k-points.
"""
if isinstance(N_or_dk, Integral):
N = N_or_dk
else:
# Calculate the required number of points
N = int(kR ** 2 * np.pi / N_or_dk + 0.5)
if N < 4:
N = 4
info('BrillouinZone.param_circle increased the number of circle points to 4.')
# Conversion object
bz = BrillouinZone(sc)
normal = _a.arrayd(normal)
origo = _a.arrayd(origo)
k_n = bz.tocartesian(normal)
k_o = bz.tocartesian(origo)
# Generate a preset list of k-points on the unit-circle
if loop:
radians = _a.aranged(N) / (N-1) * 2 * np.pi
else:
radians = _a.aranged(N) / N * 2 * np.pi
k = _a.emptyd([N, 3])
k[:, 0] = np.cos(radians)
k[:, 1] = np.sin(radians)
k[:, 2] = 0.
# Now generate the rotation
_, theta, phi = cart2spher(k_n)
if theta != 0:
pv = _a.arrayd([k_n[0], k_n[1], 0])
pv /= fnorm(pv)
q = Quaternion(phi, pv, rad=True) * Quaternion(theta, [0, 0, 1], rad=True)
else:
q = Quaternion(0., [0, 0, k_n[2] / abs(k_n[2])], rad=True)
# Calculate k-points
k = q.rotate(k)
k *= kR / fnorm(k).reshape(-1, 1)
k = bz.toreduced(k + k_o)
# The sum of weights is equal to the BZ area
W = np.pi * kR ** 2
w = np.repeat([W / N], N)
return BrillouinZone(sc, k, w)
def read_geometry(self, ret_dynamic=False):
r""" Returns Geometry object from the CONTCAR/POSCAR file
Possibly also return the dynamics (if present).
Parameters
----------
ret_dynamic : bool, optional
also return selective dynamics (if present), if not, None will
be returned.
"""
sc = self.read_supercell()
# The species labels are not always included in *CAR
line1 = self.readline().split()
opt = self.readline().split()
try:
species = line1
species_count = np.array(opt, np.int32)
except:
species_count = np.array(line1, np.int32)
# We have no species...
# We default to consecutive elements in the
# periodic table.
species = [i + 1 for i in range(len(species_count))]
err = '\n'.join([
"POSCAR best format:", " <Specie-1> <Specie-2>",
" <#Specie-1> <#Specie-2>",
"Format not found, the species are defaulted to the first elements of the periodic table."
])
warn(err)
# Create list of atoms to be used subsequently
atom = [
Atom[spec] for spec, nsp in zip(species, species_count)
for i in range(nsp)
]
# Number of atoms
na = len(atom)
# check whether this is Selective Dynamics
opt = self.readline()
if opt[0] in 'Ss':
dynamics = True
# pre-create the dynamic list
dynamic = np.empty([na, 3], dtype=np.bool_)
opt = self.readline()
else:
dynamics = False
dynamic = None
# Check whether this is in fractional or direct
# coordinates (Direct == fractional)
cart = False
if opt[0] in 'CcKk':
cart = True
xyz = _a.emptyd([na, 3])
for ia in range(na):
line = self.readline().split()
xyz[ia, :] = list(map(float, line[:3]))
if dynamics:
dynamic[ia] = list(map(lambda x: x.lower() == 't', line[3:6]))
if cart:
# The unit of the coordinates are cartesian
xyz *= self._scale
else:
xyz = xyz.dot(sc.cell)
# The POT/CONT-CAR does not contain information on the atomic species
geom = Geometry(xyz=xyz, atom=atom, sc=sc)
if ret_dynamic:
return geom, dynamic
return geom
def read_data(self, as_dataarray=False):
""" Returns data associated with the bands file
Parameters
--------
as_dataarray: boolean, optional
if `True`, the information is returned as an `xarray.DataArray`
Ticks (if read) are stored as an attribute of the DataArray
(under `array.ticks` and `array.ticklabels`)
"""
band_lines = False
# Luckily the data is in eV
Ef = float(self.readline())
# Read the total length of the path (not used)
_, _ = map(float, self.readline().split())
l = self.readline()
try:
_, _ = map(float, l.split())
band_lines = True
except:
# We are dealing with a band-points file
pass
# orbitals, n-spin, n-k
if band_lines:
l = self.readline()
no, ns, nk = map(int, l.split())
# Create the data to contain all band points
b = _a.emptyd([nk, ns, no])
# for band-lines
if band_lines:
k = _a.emptyd([nk])
for ik in range(nk):
l = [float(x) for x in self.readline().split()]
k[ik] = l[0]
del l[0]
# Now populate the eigenvalues
while len(l) < ns * no:
l.extend([float(x) for x in self.readline().split()])
l = _a.arrayd(l)
l.shape = (ns, no)
b[ik, :, :] = l[:, :] - Ef
# Now we need to read the labels for the points
xlabels = []
labels = []
nl = int(self.readline())
for _ in range(nl):
l = self.readline().split()
xlabels.append(float(l[0]))
labels.append((' '.join(l[1:])).replace("'", ''))
vals = (xlabels, labels), k, b
else:
k = _a.emptyd([nk, 3])
for ik in range(nk):
l = [float(x) for x in self.readline().split()]
k[ik, :] = l[0:3]
del l[2]
del l[1]
del l[0]
# Now populate the eigenvalues
while len(l) < ns * no:
l.extend([float(x) for x in self.readline().split()])
l = _a.arrayd(l)
l.shape = (ns, no)
b[ik, :, :] = l[:, :] - Ef
vals = k, b
if as_dataarray:
from xarray import DataArray
ticks = {
"ticks": xlabels,
"ticklabels": labels
} if band_lines else {}
return DataArray(b,
name="Energy",
attrs=ticks,
coords=[("k", k),
("spin", _a.arangei(0, b.shape[1])),
("band", _a.arangei(0, b.shape[2]))])
return vals
def wavefunction(v,
grid,
geometry=None,
k=None,
spinor=0,
spin=None,
eta=False):
r""" Add the wave-function (`Orbital.psi`) component of each orbital to the grid
This routine calculates the real-space wave-function components in the
specified grid.
This is an *in-place* operation that *adds* to the current values in the grid.
It may be instructive to check that an eigenstate is normalized:
>>> grid = Grid(...) # doctest: +SKIP
>>> psi(state, grid) # doctest: +SKIP
>>> (np.abs(grid.grid) ** 2).sum() * grid.dvolume == 1. # doctest: +SKIP
Note: To calculate :math:`\psi(\mathbf r)` in a unit-cell different from the
originating geometry, simply pass a grid with a unit-cell smaller than the originating
supercell.
The wavefunctions are calculated in real-space via:
.. math::
\psi(\mathbf r) = \sum_i\phi_i(\mathbf r) |\psi\rangle_i \exp(-i\mathbf k \mathbf R)
While for non-collinear/spin-orbit calculations the wavefunctions are determined from the
spinor component (`spinor`)
.. math::
\psi_{\alpha/\beta}(\mathbf r) = \sum_i\phi_i(\mathbf r) |\psi_{\alpha/\beta}\rangle_i \exp(-i\mathbf k \mathbf R)
where ``spinor in [0, 1]`` determines :math:`\alpha` or :math:`\beta`, respectively.
Notes
-----
Currently this method only works for :math:`\Gamma` states
Parameters
----------
v : array_like
coefficients for the orbital expansion on the real-space grid.
If `v` is a complex array then the `grid` *must* be complex as well.
grid : Grid
grid on which the wavefunction will be plotted.
If multiple eigenstates are in this object, they will be summed.
geometry : Geometry, optional
geometry where the orbitals are defined. This geometry's orbital count must match
the number of elements in `v`.
If this is ``None`` the geometry associated with `grid` will be used instead.
k : array_like, optional
k-point associated with wavefunction, by default the inherent k-point used
to calculate the eigenstate will be used (generally shouldn't be used unless the `EigenstateElectron` object
has not been created via `Hamiltonian.eigenstate`).
spinor : int, optional
the spinor for non-collinear/spin-orbit calculations. This is only used if the
eigenstate object has been created from a parent object with a `Spin` object
contained, *and* if the spin-configuration is non-collinear or spin-orbit coupling.
Default to the first spinor component.
spin : Spin, optional
specification of the spin configuration of the orbital coefficients. This only has
influence for non-collinear wavefunctions where `spinor` choice is important.
eta : bool, optional
Display a console progressbar.
"""
if geometry is None:
geometry = grid.geometry
warn(
'wavefunction was not passed a geometry associated, will use the geometry associated with the Grid.'
)
if geometry is None:
raise SislError(
'wavefunction did not find a usable Geometry through keywords or the Grid!'
)
# In case the user has passed several vectors we sum them to plot the summed state
if v.ndim == 2:
v = v.sum(0)
if spin is None:
if len(v) // 2 == geometry.no:
# We can see from the input that the vector *must* be a non-collinear calculation
v = v.reshape(-1, 2)[:, spinor]
info(
'wavefunction assumes the input wavefunction coefficients to originate from a non-collinear calculation!'
)
elif spin.kind > Spin.POLARIZED:
# For non-collinear cases the user selects the spinor component.
v = v.reshape(-1, 2)[:, spinor]
if len(v) != geometry.no:
raise ValueError(
"wavefunction require wavefunction coefficients corresponding to number of orbitals in the geometry."
)
# Check for k-points
k = _a.asarrayd(k)
kl = (k**2).sum()**0.5
has_k = kl > 0.000001
if has_k:
raise NotImplementedError(
'wavefunction for k != Gamma does not produce correct wavefunctions!'
)
# Check that input/grid makes sense.
# If the coefficients are complex valued, then the grid *has* to be
# complex valued.
# Likewise if a k-point has been passed.
is_complex = np.iscomplexobj(v) or has_k
if is_complex and not np.iscomplexobj(grid.grid):
raise SislError(
"wavefunction input coefficients are complex, while grid only contains real."
)
if is_complex:
psi_init = _a.zerosz
else:
psi_init = _a.zerosd
# Extract sub variables used throughout the loop
shape = _a.asarrayi(grid.shape)
dcell = grid.dcell
ic = grid.sc.icell * shape.reshape(1, -1)
geom_shape = dot(ic, geometry.cell.T).T
# In the following we don't care about division
# So 1) save error state, 2) turn off divide by 0, 3) calculate, 4) turn on old error state
old_err = np.seterr(divide='ignore', invalid='ignore')
addouter = add.outer
def idx2spherical(ix, iy, iz, offset, dc, R):
""" Calculate the spherical coordinates from indices """
rx = addouter(addouter(ix * dc[0, 0], iy * dc[1, 0]),
iz * dc[2, 0] - offset[0]).ravel()
ry = addouter(addouter(ix * dc[0, 1], iy * dc[1, 1]),
iz * dc[2, 1] - offset[1]).ravel()
rz = addouter(addouter(ix * dc[0, 2], iy * dc[1, 2]),
iz * dc[2, 2] - offset[2]).ravel()
# Total size of the indices
n = rx.shape[0]
# Reduce our arrays to where the radius is "fine"
idx = indices_le(rx**2 + ry**2 + rz**2, R**2)
rx = rx[idx]
ry = ry[idx]
rz = rz[idx]
xyz_to_spherical_cos_phi(rx, ry, rz)
return n, idx, rx, ry, rz
# Figure out the max-min indices with a spacing of 1 radian
rad1 = pi / 180
theta, phi = ogrid[-pi:pi:rad1, 0:pi:rad1]
cphi, sphi = cos(phi), sin(phi)
ctheta_sphi = cos(theta) * sphi
stheta_sphi = sin(theta) * sphi
del sphi
nrxyz = (theta.size, phi.size, 3)
del theta, phi, rad1
# First we calculate the min/max indices for all atoms
idx_mm = _a.emptyi([geometry.na, 2, 3])
rxyz = _a.emptyd(nrxyz)
rxyz[..., 0] = ctheta_sphi
rxyz[..., 1] = stheta_sphi
rxyz[..., 2] = cphi
# Reshape
rxyz.shape = (-1, 3)
idx = dot(ic, rxyz.T)
idxm = idx.min(1).reshape(1, 3)
idxM = idx.max(1).reshape(1, 3)
del ctheta_sphi, stheta_sphi, cphi, idx, rxyz, nrxyz
origo = grid.sc.origo.reshape(1, -1)
for atom, ia in geometry.atom.iter(True):
if len(ia) == 0:
continue
R = atom.maxR()
# Now do it for all the atoms to get indices of the middle of
# the atoms
# The coordinates are relative to origo, so we need to shift (when writing a grid
# it is with respect to origo)
xyz = geometry.xyz[ia, :] - origo
idx = dot(ic, xyz.T).T
# Get min-max for all atoms
idx_mm[ia, 0, :] = idxm * R + idx
idx_mm[ia, 1, :] = idxM * R + idx
# Now we have min-max for all atoms
# When we run the below loop all indices can be retrieved by looking
# up in the above table.
# Before continuing, we can easily clean up the temporary arrays
del origo, idx
aranged = _a.aranged
# In case this grid does not have a Geometry associated
# We can *perhaps* easily attach a geometry with the given
# atoms in the unit-cell
sc = grid.sc.copy()
if grid.geometry is None:
# Create the actual geometry that encompass the grid
ia, xyz, _ = geometry.within_inf(sc)
if len(ia) > 0:
grid.set_geometry(Geometry(xyz, geometry.atom[ia], sc=sc))
# Instead of looping all atoms in the supercell we find the exact atoms
# and their supercell indices.
add_R = _a.zerosd(3) + geometry.maxR()
# Calculate the required additional vectors required to increase the fictitious
# supercell by add_R in each direction.
# For extremely skewed lattices this will be way too much, hence we make
# them square.
o = sc.toCuboid(True)
sc = SuperCell(o._v, origo=o.origo) + np.diag(2 * add_R)
sc.origo -= add_R
# Retrieve all atoms within the grid supercell
# (and the neighbours that connect into the cell)
IA, XYZ, ISC = geometry.within_inf(sc)
r_k = dot(geometry.rcell, k)
r_k_cell = dot(r_k, geometry.cell)
phase = 1
# Retrieve progressbar
eta = tqdm_eta(len(IA), 'wavefunction', 'atom', eta)
# Loop over all atoms in the grid-cell
for ia, xyz, isc in zip(IA, XYZ - grid.origo.reshape(1, 3), ISC):
# Get current atom
atom = geometry.atom[ia]
# Extract maximum R
R = atom.maxR()
if R <= 0.:
warn("Atom '{}' does not have a wave-function, skipping atom.".
format(atom))
eta.update()
continue
# Get indices in the supercell grid
idx = (isc.reshape(3, 1) * geom_shape).sum(0)
idxm = floor(idx_mm[ia, 0, :] + idx).astype(int32)
idxM = ceil(idx_mm[ia, 1, :] + idx).astype(int32) + 1
# Fast check whether we can skip this point
if idxm[0] >= shape[0] or idxm[1] >= shape[1] or idxm[2] >= shape[2] or \
idxM[0] <= 0 or idxM[1] <= 0 or idxM[2] <= 0:
eta.update()
continue
# Truncate values
if idxm[0] < 0:
idxm[0] = 0
if idxM[0] > shape[0]:
idxM[0] = shape[0]
if idxm[1] < 0:
idxm[1] = 0
if idxM[1] > shape[1]:
idxM[1] = shape[1]
if idxm[2] < 0:
idxm[2] = 0
if idxM[2] > shape[2]:
idxM[2] = shape[2]
# Now idxm/M contains min/max indices used
# Convert to spherical coordinates
n, idx, r, theta, phi = idx2spherical(aranged(idxm[0], idxM[0]),
aranged(idxm[1], idxM[1]),
aranged(idxm[2], idxM[2]), xyz,
dcell, R)
# Get initial orbital
io = geometry.a2o(ia)
if has_k:
phase = np.exp(-1j * (dot(r_k_cell, isc)))
# TODO
# Possibly the phase should be an additional
# array for the position in the unit-cell!
# + np.exp(-1j * dot(r_k, spher2cart(r, theta, np.arccos(phi)).T) )
# Allocate a temporary array where we add the psi elements
psi = psi_init(n)
# Loop on orbitals on this atom, grouped by radius
for os in atom.iter(True):
# Get the radius of orbitals (os)
oR = os[0].R
if oR <= 0.:
warn(
"Orbital(s) '{}' does not have a wave-function, skipping orbital!"
.format(os))
# Skip these orbitals
io += len(os)
continue
# Downsize to the correct indices
if R - oR < 1e-6:
idx1 = idx.view()
r1 = r.view()
theta1 = theta.view()
phi1 = phi.view()
else:
idx1 = indices_le(r, oR)
# Reduce arrays
r1 = r[idx1]
theta1 = theta[idx1]
phi1 = phi[idx1]
idx1 = idx[idx1]
# Loop orbitals with the same radius
for o in os:
# Evaluate psi component of the wavefunction and add it for this atom
psi[idx1] += o.psi_spher(r1, theta1, phi1,
cos_phi=True) * (v[io] * phase)
io += 1
# Clean-up
del idx1, r1, theta1, phi1, idx, r, theta, phi
# Convert to correct shape and add the current atom contribution to the wavefunction
psi.shape = idxM - idxm
grid.grid[idxm[0]:idxM[0], idxm[1]:idxM[1], idxm[2]:idxM[2]] += psi
# Clean-up
del psi
# Step progressbar
eta.update()
eta.close()
# Reset the error code for division
np.seterr(**old_err)