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completely removed dtype in Spin class
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It does not belong there, and should have been removed
ages ago.

Signed-off-by: Nick Papior <[email protected]>
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@zerothi
zerothi committed Nov 26, 2024
1 parent c6253c8 commit 6dbd9d6
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Showing 10 changed files with 118 additions and 227 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ we hit release version 1.0.0.
This yield significant perf. improvements for DFT sparse matrices
with *many* edges in the sparse matrix, but a perf. hit for very
small TB matrices.
- dtype removed from `Spin` class


## [0.15.2] - 2024-11-06
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4 changes: 2 additions & 2 deletions src/sisl/io/siesta/binaries.py
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Expand Up @@ -610,7 +610,7 @@ def write_density_matrix(self, DM, **kwargs):
dm = csr._D[:, : DM.S_idx]

# Ensure shapes (say if only 1 spin)
dm.shape = (-1, len(DM.spin))
dm.shape = (-1, DM.spin.size(DM.dtype))

nsc = DM.geometry.lattice.nsc.astype(np.int32)

Expand Down Expand Up @@ -2583,7 +2583,7 @@ def write_header(self, bz, E, mu: float = 0.0, obj=None):
"""
if obj is None:
obj = bz.parent
nspin = len(obj.spin)
nspin = obj.spin.size(obj.dtype)
cell = obj.geometry.lattice.cell
na_u = obj.geometry.na
no_u = obj.geometry.no
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18 changes: 9 additions & 9 deletions src/sisl/io/siesta/siesta_nc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ def read_hamiltonian(self, **kwargs) -> Hamiltonian:
f"{self}.read_hamiltonian requires the stored matrix to be in Ry!"
)

for i in range(len(H.spin)):
for i in range(H.spin.size(H.dtype)):
H._csr._D[:, i] = sp.variables["H"][i, :] * Ry2eV

# fix siesta specific notation
Expand Down Expand Up @@ -281,7 +281,7 @@ def read_density_matrix(self, **kwargs) -> DensityMatrix:
DM = self._r_class_spin(DensityMatrix, **kwargs)

sp = self.groups["SPARSE"]
for i in range(len(DM.spin)):
for i in range(DM.spin.size(DM.dtype)):
DM._csr._D[:, i] = sp.variables["DM"][i, :]

# fix siesta specific notation
Expand All @@ -299,7 +299,7 @@ def read_energy_density_matrix(self, **kwargs) -> EnergyDensityMatrix:
Ef = np.tile(Ef, 2)

sp = self.groups["SPARSE"]
for i in range(len(EDM.spin)):
for i in range(EDM.spin.size(EDM.dtype)):
EDM._csr._D[:, i] = sp.variables["EDM"][i, :] * Ry2eV
if i < 2 and "DM" in sp.variables:
EDM._csr._D[:, i] -= sp.variables["DM"][i, :] * Ef[i]
Expand Down Expand Up @@ -629,7 +629,7 @@ def write_hamiltonian(self, H, **kwargs):
# Ensure that the geometry is written
self.write_geometry(H.geometry)

self._crt_dim(self, "spin", len(H.spin))
self._crt_dim(self, "spin", H.spin.size(H.dtype))

if H.dkind != "f":
raise NotImplementedError(
Expand Down Expand Up @@ -660,7 +660,7 @@ def write_hamiltonian(self, H, **kwargs):
)
v.info = "Hamiltonian"
v.unit = "Ry"
for i in range(len(H.spin)):
for i in range(H.spin.size(H.dtype)):
v[i, :] = csr._D[:, i] / Ry2eV

self._write_settings()
Expand Down Expand Up @@ -688,7 +688,7 @@ def write_density_matrix(self, DM, **kwargs):
# Ensure that the geometry is written
self.write_geometry(DM.geometry)

self._crt_dim(self, "spin", len(DM.spin))
self._crt_dim(self, "spin", DM.spin.size(DM.dtype))

if DM.dkind != "f":
raise NotImplementedError(
Expand Down Expand Up @@ -718,7 +718,7 @@ def write_density_matrix(self, DM, **kwargs):
**self._cmp_args,
)
v.info = "Density matrix"
for i in range(len(DM.spin)):
for i in range(DM.spin.size(DM.dtype)):
v[i, :] = csr._D[:, i]

self._write_settings()
Expand Down Expand Up @@ -746,7 +746,7 @@ def write_energy_density_matrix(self, EDM, **kwargs):
# Ensure that the geometry is written
self.write_geometry(EDM.geometry)

self._crt_dim(self, "spin", len(EDM.spin))
self._crt_dim(self, "spin", EDM.spin.size(EDM.dtype))

if EDM.dkind != "f":
raise NotImplementedError(
Expand Down Expand Up @@ -781,7 +781,7 @@ def write_energy_density_matrix(self, EDM, **kwargs):
)
v.info = "Energy density matrix"
v.unit = "Ry"
for i in range(len(EDM.spin)):
for i in range(EDM.spin.size(EDM.dtype)):
v[i, :] = csr._D[:, i] / Ry2eV

self._write_settings()
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6 changes: 3 additions & 3 deletions src/sisl/io/tbtrans/delta.py
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Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,7 @@ def write_delta(self, delta, **kwargs):
# Ensure that the geometry is written
self.write_geometry(delta.geometry)

self._crt_dim(self, "spin", len(delta.spin))
self._crt_dim(self, "spin", delta.spin.size(delta.dtype))

# Determine the type of delta we are storing...
k = kwargs.get("k", None)
Expand Down Expand Up @@ -583,7 +583,7 @@ def write_delta(self, delta, **kwargs):
attrs={"info": "Imaginary part of delta", "unit": "Ry"},
**self._cmp_args,
)
for i in range(len(delta.spin)):
for i in range(delta.spin.size(delta.dtype)):
sl[-2] = i
v1[sl] = csr._D[:, i].real * eV2Ry
v2[sl] = csr._D[:, i].imag * eV2Ry
Expand All @@ -598,7 +598,7 @@ def write_delta(self, delta, **kwargs):
attrs={"info": "delta", "unit": "Ry"},
**self._cmp_args,
)
for i in range(len(delta.spin)):
for i in range(delta.spin.size(delta.dtype)):
sl[-2] = i
v[sl] = csr._D[:, i] * eV2Ry

Expand Down
6 changes: 3 additions & 3 deletions src/sisl/physics/densitymatrix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ def close(a, v):
out._csr._D[:, [0, 1]] = out._csr._D[:, [1, 0]]

else:
spin = Spin("nc", dtype=self.dtype)
spin = Spin("nc")
out = self.__class__(
self.geometry,
dtype=self.dtype,
Expand Down Expand Up @@ -305,7 +305,7 @@ def spin_align(self, vec: SeqFloat, atoms: AtomsIndex = None):

elif self.spin.is_polarized:
if vec[:2] @ vec[:2] > 1e-6:
spin = Spin("nc", dtype=self.dtype)
spin = Spin("nc")
out = self.__class__(
self.geometry,
dtype=self.dtype,
Expand Down Expand Up @@ -768,7 +768,7 @@ def density(

DM = _a.emptyz([self.nnz, 2, 2])
idx = _a.array_arange(csr.ptr[:-1], n=csr.ncol)
if self.spin.kind == Spin.NONCOLINEAR:
if self.spin.is_noncolinear:
# non-collinear
DM[:, 0, 0] = csr._D[idx, 0]
DM[:, 0, 1] = csr._D[idx, 2] + 1j * csr._D[idx, 3]
Expand Down
70 changes: 36 additions & 34 deletions src/sisl/physics/sparse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,21 +53,21 @@ def _get_spin(M, spin, what: Literal["trace", "box", "vector"] = "box"):
if spin.is_polarized:
m[..., :2] = 0.0
elif spin.is_noncolinear:
if spin.dkind in ("f", "i"):
m[..., 0] = 2 * M[..., 2]
m[..., 1] = -2 * M[..., 3]
else:
if np.iscomplexobj(M):
m[..., 0] = 2 * M[..., 2].real
m[..., 1] = -2 * M[..., 2].imag
else:
m[..., 0] = 2 * M[..., 2]
m[..., 1] = -2 * M[..., 3]
else:
# spin-orbit
if spin.dkind in ("f", "i"):
m[..., 0] = M[..., 2] + M[..., 6]
m[..., 1] = -M[..., 3] + M[..., 7]
else:
if np.iscomplexobj(M):
tmp = M[..., 2].conj() + M[..., 3]
m[..., 0] = tmp.real
m[..., 1] = tmp.imag
else:
m[..., 0] = M[..., 2] + M[..., 6]
m[..., 1] = -M[..., 3] + M[..., 7]
return m

if what == "box":
Expand All @@ -82,27 +82,27 @@ def _get_spin(M, spin, what: Literal["trace", "box", "vector"] = "box"):
m[..., 0, 0] = M[..., 0]
m[..., 1, 1] = M[..., 1]
elif spin.is_noncolinear:
if spin.dkind in ("f", "i"):
if np.iscomplexobj(M):
m[..., 0, 0] = M[..., 0]
m[..., 1, 1] = M[..., 1]
m[..., 0, 1] = M[..., 2]
m[..., 1, 0] = M[..., 2].conj()
else:
m[..., 0, 0] = M[..., 0]
m[..., 1, 1] = M[..., 1]
m[..., 0, 1] = M[..., 2] + 1j * M[..., 3]
m[..., 1, 0] = m[..., 0, 1].conj()
else:
else:
if np.iscomplexobj(M):
m[..., 0, 0] = M[..., 0]
m[..., 1, 1] = M[..., 1]
m[..., 0, 1] = M[..., 2]
m[..., 1, 0] = M[..., 2].conj()
else:
if spin.dkind in ("f", "i"):
m[..., 1, 0] = M[..., 3]
else:
m[..., 0, 0] = M[..., 0] + 1j * M[..., 4]
m[..., 1, 1] = M[..., 1] + 1j * M[..., 5]
m[..., 0, 1] = M[..., 2] + 1j * M[..., 3]
m[..., 1, 0] = M[..., 6] + 1j * M[..., 7]
else:
m[..., 0, 0] = M[..., 0]
m[..., 1, 1] = M[..., 1]
m[..., 0, 1] = M[..., 2]
m[..., 1, 0] = M[..., 3]

return m

Expand Down Expand Up @@ -828,6 +828,8 @@ def __init__(
if isinstance(dim, Spin):
spin = dim
else:
# Back conversion, actually this should depend
# on dtype
spin = {
1: Spin.UNPOLARIZED,
2: Spin.POLARIZED,
Expand All @@ -836,17 +838,17 @@ def __init__(
}.get(dim)
else:
spin = kwargs.pop("spin")
self._spin = Spin(spin, dtype)
self._spin = Spin(spin)

super().__init__(geometry, len(self.spin), self.spin.dtype, nnzpr, **kwargs)
super().__init__(geometry, self.spin.size(dtype), dtype, nnzpr, **kwargs)
self._reset()

def _reset(self):
r"""Reset object according to the options, please refer to `SparseOrbital.reset` for details"""
super()._reset()

# Update the dtype of the spin
self._spin = Spin(self.spin, dtype=self.dtype)
self._spin = Spin(self.spin)

if self.spin.is_unpolarized:
self.UP = 0
Expand All @@ -865,7 +867,7 @@ def _reset(self):
self.dSk = self._dSk

elif self.spin.is_noncolinear:
if self.spin.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
self.M11 = 0
self.M22 = 1
self.M12r = 2
Expand All @@ -882,7 +884,7 @@ def _reset(self):
self.ddSk = self._ddSk_non_colinear

elif self.spin.is_spinorbit:
if self.spin.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
self.SX = np.array([0, 0, 1, 0, 0, 0, 1, 0], self.dtype)
self.SY = np.array([0, 0, 0, -1, 0, 0, 0, 1], self.dtype)
self.SZ = np.array([1, -1, 0, 0, 0, 0, 0, 0], self.dtype)
Expand Down Expand Up @@ -1509,7 +1511,7 @@ def transpose(self, hermitian: bool = False, spin: bool = True, sort: bool = Tru
if sp.is_spinorbit:
if hermitian and spin:
# conjugate the imaginary value and transpose spin-box
if sp.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
# imaginary components (including transposing)
# 12,11,22,21
D[:, [3, 4, 5, 7]] = -D[:, [7, 4, 5, 3]]
Expand All @@ -1519,15 +1521,15 @@ def transpose(self, hermitian: bool = False, spin: bool = True, sort: bool = Tru
D[:, [0, 1, 2, 3]] = np.conj(D[:, [0, 1, 3, 2]])
elif hermitian:
# conjugate the imaginary value
if sp.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
# imaginary components
# 12,11,22,21
D[:, [3, 4, 5, 7]] *= -1.0
else:
D[:, :] = np.conj(D[:, :])
elif spin:
# transpose spin-box, 12 <-> 21
if sp.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
D[:, [2, 3, 6, 7]] = D[:, [6, 7, 2, 3]]
else:
D[:, [2, 3]] = D[:, [3, 2]]
Expand All @@ -1544,7 +1546,7 @@ def transpose(self, hermitian: bool = False, spin: bool = True, sort: bool = Tru
# So for transposing we should negate the sign
# to ensure we put the opposite value in the
# correct place.
if sp.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
D[:, 3] = -D[:, 3]
else:
D[:, 2] = np.conj(D[:, 2])
Expand All @@ -1568,7 +1570,7 @@ def trs(self):

# Apply Pauli-Y on the left and right of each spin-box
if sp.is_spinorbit:
if sp.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
# [R11, R22, R12, I12, I11, I22, R21, I21]
# [R11, R22] = [R22, R11]
# [I12, I21] = [I21, I12] (conj + Y @ Y[sign-changes conj])
Expand All @@ -1579,7 +1581,7 @@ def trs(self):
else:
raise NotImplementedError
elif sp.is_noncolinear:
if sp.dkind in ("f", "i"):
if self.dkind in ("f", "i"):
# [R11, R22, R12, I12]
D[:, 2] = -D[:, 2]
else:
Expand Down Expand Up @@ -1648,16 +1650,16 @@ def transform(self, matrix=None, dtype=None, spin=None, orthogonal=None):
if spin is None:
spin = self.spin
else:
spin = Spin(spin, dtype)
spin = Spin(spin)

if orthogonal is None:
orthogonal = self.orthogonal

# get dimensions to check
N = n = self.spin.size
N = n = self.spin.size(self.dtype)
if not self.orthogonal:
N += 1
M = m = spin.size
M = m = spin.size(dtype)
if not orthogonal:
M += 1

Expand All @@ -1673,10 +1675,10 @@ def transform(self, matrix=None, dtype=None, spin=None, orthogonal=None):
# ensure the overlap matrix is carried over
matrix[-1, -1] = 1.0

if spin.is_unpolarized and self.spin.size > 1:
if spin.is_unpolarized and self.spin.size(self.dtype) > 1:
# average up and down components
matrix[0, [0, 1]] = 0.5
elif spin.size > 1 and self.spin.is_unpolarized:
elif spin.size(dtype) > 1 and self.spin.is_unpolarized:
# set up and down components to unpolarized value
matrix[[0, 1], 0] = 1.0

Expand Down
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