Comments (7)
Perhaps there are other places:
~/codes/sisl/src % grep "nsc > 1" **/*.py main
sisl/_core/geometry.py: axes = (self.lattice.nsc > 1).nonzero()[0]
sisl/_core/geometry.py: elif np.any(self.nsc > 1):
sisl/_core/geometry.py: periodic system (where ``self.nsc > 1`` or `periodic` is true).
sisl/_core/geometry.py: directions are only where ``self.nsc > 1 & self.pbc``.
sisl/_core/geometry.py: periodic = np.logical_and(self.pbc, self.nsc > 1)
sisl/_core/geometry.py: pbc=geom.nsc > 1,
sisl/_core/lattice.py: if changed.any() and (~bc).all() and nsc > 1:
sisl/_core/sparse_geometry.py: axes = (self.lattice.nsc > 1).nonzero()[0]
sisl/_core/tests/test_geometry.py: # Even if the geometry has nsc > 1, if we set periodic=False
sisl/io/dftb/realdat.py: if np.any(nsc > 1):
sisl/io/siesta/binaries.py: if all(nsc > 1):
sisl/io/siesta/fdf.py: # periodic = geom.nsc > 1
sisl/io/siesta/tests/test_orb_indx.py: assert np.all(nsc > 1)
sisl/physics/brillouinzone.py: The default value is `(self.parent.nsc > 1).nonzero()[0]`.
sisl/physics/brillouinzone.py: periodic = (self.parent.nsc > 1).nonzero()[0]
sisl/physics/brillouinzone.py: if self.points.shape[1] != np.sum(self.parent.nsc > 1):
sisl/viz/data/pdos.py: kgrid = [3 if nsc > 1 else 1 for nsc in H.geometry.nsc]
~/codes/sisl/src % grep "nsc == 1" **/*.py main
sisl/_core/geometry.py: if all(self.nsc == 1):
sisl/_core/sparse_geometry.py: # since we may have nsc == 1 and cut it X times.
sisl/_core/sparse_geometry.py: Untiling structures with ``nsc == 1`` along `axis` are assumed to have periodic boundary
sisl/_core/sparse_geometry.py: When untiling structures with ``nsc == 1`` along `axis` it is important to
sisl/_core/sparse_geometry.py: Untiling structures with ``nsc == 1`` along `axis` are assumed to have periodic boundary
sisl/_core/sparse_geometry.py: When untiling structures with ``nsc == 1`` along `axis` it is important to
sisl/io/siesta/binaries.py: # we will never have all(nsc == 1) since that is
sisl/io/siesta/tests/test_orb_indx.py: assert np.all(nsc == 1)
sisl/io/xsf.py: if all(lattice.nsc == 1):
from sisl.
Even more so because
nsc
is many times [1,1,1] because it is simply unset, but we know that there is periodicity. For example when a geometry is read from a SIESTA file.
But... ;) When PSolver
can be used, then we will not have periodicity. And the all hell breaks loose. ;)
Half-joke aside. Do we know if all geometries read from Siesta actually have periodicity along all directions?
from sisl.
Indeed, however, I am not sure whether it should be a default of both merged?
Consider a case where a user has done pbc = (T, T, F)
but then set nsc = [3, 1, 1]
?
However, I can see that the documentation specifies periodic direction, so if this is clarified in the doc-string, that pbc
is used, then fine!
from sisl.
This goes back to the never ending discussion 😄
My view is that as long as you have periodicity, it makes sense to translate to the unit cell regardless of nsc
.
from sisl.
Ok, lets do that then :)
from sisl.
Even more so because nsc
is many times [1,1,1] because it is simply unset, but we know that there is periodicity. For example when a geometry is read from a SIESTA file.
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For the moment they should, right? SIESTA assumes that everything is periodic when it calculates things.
But yeah when the PSolver makes it possible to not treat things periodically I can see that this will become more complicated 😅 Maybe one could check Psolver options then, I don't know.
But that is a problem of how to determine boundary conditions. I think that once you have established that the boundaries are periodic I believe it makes sense to use that fact here.
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Related Issues (20)
- use tocartesian HOT 11
- Change neighborfinder returns to a tuple of indices and supercell indices HOT 21
- Sisl files not available in readthedocs documentation HOT 18
- Ufuncs could support external classes HOT 4
- `Geometry ` coordinates as f-contiguous array HOT 4
- Streamlining spin/index arguments on `read_grid` methods
- Writing Hamiltonian with sisl from Wannier HOT 3
- Transport routines within the kubo approach HOT 16
- Disentangle overlap matrix and *other matrices*
- Merging Atom/Orbital etc. HOT 1
- eigenvalues from hamiltonian in presence of magnetic field HOT 2
- Listify breaks documentation HOT 8
- Custom colormaps for 3D plots HOT 3
- numpy 2.0 released -- need to bump stuff HOT 1
- sisl release policy HOT 6
- Docs formatting issue: Missing argument for `\mathbf` HOT 2
- sisl.viz.FatBandsPlot error in fatbands_mode = 'line/scatter' HOT 16
- #496 seems broken on 3.12 HOT 3
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