def test_nc_multiple_fail(sisl_tmp, sisl_system):
f = sisl_tmp('gr.nc', _dir)
H = Hamiltonian(sisl_system.gtb)
DM = DensityMatrix(sisl_system.gtb)
sile = ncSileSiesta(f, 'w')
H.construct([sisl_system.R, sisl_system.t])
H.write(sile)
DM[0, 0] = 1.
DM.write(sile)
def test_nc_multiple_fail(sisl_tmp, sisl_system):
# writing two different sparse matrices to the same
# file will fail
f = sisl_tmp('gr.nc', _dir)
H = Hamiltonian(sisl_system.gtb)
DM = DensityMatrix(sisl_system.gtb)
with ncSileSiesta(f, 'w') as sile:
H.construct([sisl_system.R, sisl_system.t])
H.write(sile)
DM[0, 0] = 1.
with pytest.raises(ValueError):
DM.write(sile)
def test_nc_density_matrix(sisl_tmp, sisl_system):
f = sisl_tmp('grDM.nc', _dir)
dm = DensityMatrix(sisl_system.gtb)
for _, ix in dm.iter_orbitals():
dm[ix, ix] = ix / 2.
dm.write(ncSileSiesta(f, 'w'))
ndm = ncSileSiesta(f).read_density_matrix()
# Assert they are the same
assert np.allclose(dm.cell, ndm.cell)
assert np.allclose(dm.xyz, ndm.xyz)
dm.finalize()
assert np.allclose(dm._csr._D[:, 0], ndm._csr._D[:, 0])
assert sisl_system.g.atoms.equal(ndm.atoms, R=False)
def test_nc_DM_non_colinear(sisl_tmp):
DM1 = DensityMatrix(sisl.geom.graphene(), spin=sisl.Spin('NC'))
DM1.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.4, 0.5]]))
f1 = sisl_tmp('DM1.nc', _dir)
f2 = sisl_tmp('DM2.nc', _dir)
DM1.write(f1)
DM1.finalize()
DM2 = sisl.get_sile(f1).read_density_matrix()
DM2.write(f2)
DM3 = sisl.get_sile(f2).read_density_matrix()
assert DM1._csr.spsame(DM2._csr)
assert np.allclose(DM1._csr._D, DM2._csr._D)
assert DM1._csr.spsame(DM3._csr)
assert np.allclose(DM1._csr._D, DM3._csr._D)
def test_nc_multiple_checks(sisl_tmp, sisl_system, sort):
f = sisl_tmp('gr.nc', _dir)
H = Hamiltonian(sisl_system.gtb)
DM = DensityMatrix(sisl_system.gtb)
sile = ncSileSiesta(f, 'w')
H.construct([sisl_system.R, sisl_system.t])
H.write(sile, sort=sort)
shuffle = np.random.shuffle
for io in range(len(H)):
edges = H.edges(io) # get all edges
shuffle(edges)
DM[io, edges] = 2.
DM.write(sile, sort=sort)
def test_nc_DM_spin_orbit_nc2dm2nc(sisl_tmp):
DM1 = DensityMatrix(sisl.geom.graphene(), orthogonal=False, spin=sisl.Spin('SO'))
DM1.construct(([0.1, 1.44],
[[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.],
[0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.]]))
f1 = sisl_tmp('DM1.nc', _dir)
f2 = sisl_tmp('DM2.DM', _dir)
DM1.finalize()
DM1.write(f1)
DM2 = sisl.get_sile(f1).read_density_matrix()
DM2.write(f2)
DM3 = sisl.get_sile(f2).read_density_matrix()
assert DM1._csr.spsame(DM2._csr)
assert np.allclose(DM1._csr._D, DM2._csr._D)
assert DM1._csr.spsame(DM3._csr)
assert np.allclose(DM1._csr._D, DM3._csr._D)
def test_nc_multiple_checks(sisl_tmp, sisl_system, sort):
f = sisl_tmp('gr.nc', _dir)
H = Hamiltonian(sisl_system.gtb)
DM = DensityMatrix(sisl_system.gtb)
with ncSileSiesta(f, 'w') as sile:
H.construct([sisl_system.R, sisl_system.t])
H.write(sile, sort=sort)
# fix seed
np.random.seed(42)
shuffle = np.random.shuffle
for io in range(len(H)):
edges = H.edges(io) # get all edges
shuffle(edges)
DM[io, edges] = 2.
if not sort:
with pytest.raises(ValueError):
DM.write(sile, sort=sort)
else:
DM.write(sile, sort=sort)