zerothi/sisl: v0.8.5

Added the following routines:

• SuperCell.fit routine to determine a new supercell object such that a given set of coordinates are all within AND periodic in the new supercell.
• SuperCell.parallel to check whether two objects have parallel latticevectors.
• Geometry.distance returns a list of distances from a given set of atoms. I.e. to determine a set of distances required for a subsequent close call. This routine can also be used to group neighbouring atoms in a common fashion.
• Geometry.optimize_nsc loops all atoms and minimizes nsc in case one is not sure of the interaction range.
• Hamiltonian.shift enables the shift of the entire electronic structure Fermi-level.
• Added new flag to Hamiltonian.Hk routines format={'csr', 'array', 'dense', ...} to ensure a consistent return of the data-type.

Bug fix for dHncSileSiesta for multiple levels.

Performance boost for the sub and remove functions for the Hamiltonian objects. Instead of creating the geometry first, it may now be much faster to generate the small Hamiltonian, tile -> repeat -> sub -> remove.

Performance boost for the tile and repeat functions for the Hamiltonian objects. They are now the preferred method for creating large systems.

Bug fixed when having extremely long atomic ranges and using tile/repeat. The number of supercells was too large. It did not affect anything, but it was inconsistent.

Enabled reading the density matrix and energy density matrix from siesta.

Addition of a PerformanceSelector class which enables a dynamic selection of the best routine.

Currently this is enabled in the SparseOrbitalBZ class where constructing a matrix @ k can be done in numerous ways.

Bug fixed in supercell specification of the Hamiltonian:

now works in all cases.

Spin-orbit H(k) has been enabled

Fixed reading the <>.nc file from SIESTA, the non-zero elements count was wrong.

Now H(k) has been tested for non-colinear and spin-orbit coupling and one can now use sisl to perform non-colinear and spin-orbit coupling calculations.

API change, all dR keywords has been changed to R for consistency and reduction of ambiguity. Also the Atoms.dR is now referred to as Atoms.maxR() to indicate its meaning.

This may break old scripts if one use the dR keyword in arguments.