0.8.2

Released 31 of March 2017.

Contributors

A total of 1 people contributed to this release. People with a “+” by their names contributed a patch for the first time.

Nick Papior

Pull requests merged

A total of 0 pull requests were merged for this release.

Fixed reading _hr.dat from Wannier90, now the band-structure of SrTiO3 (Junquera’s test example) is correct.
Speeded up tbtrans.py analyzing methods enourmously by introducing faster sparse iterators. Now one can easily perform data-analysis on systems in excess of 10.000 atoms very fast.
Added the TBT.AV.nc file which is meant to be created by sisl from the TBT.nc files (i.e. create the k-averaged output). This enables users to run tbtrans, create the k-averaged output, and then delete the old file to heavily reduce disk-usage.

An example:

tbtrans RUN.fdf > TBT.out sdata siesta.TBT.nc –tbt-av rm siesta.TBT.nc

after this siesta.TBT.AV.nc exists will all k-averaged quantites. If one is not interested in k-resolved quantities this may be very interesting.
Updated the TBT.nc sile for improved readability.
Easier script data-extraction from TBT.nc files due to easier conversion between atomic indices and pivoting orbitals.

For this:
- a2p returns the pivoting indices for the given atoms (complete set)
- o2p returns the pivoting indices for the given orbitals
- Added atom keyword for retrieving DOS for a given set of atoms
- sdata and TBT.nc files now enable the creation of the TBT.AV.nc file which is the k-averaged file of TBT.nc
Faster bond-current algorithms (faster iterator)
Initial template for TBT.Proj files for sdata processing
Geometry:
- Enabled multiplying geometries with integers to emulate repeat or tile functions:
```
>>> geometry * 2 == geometry.tile(2, 0).tile(2, 1).tile(2, 2)
>>> geometry * [2, 1, 2] == geometry.tile(2, 0).tile(2, 2)
>>> geometry * [2, 2] == geometry.tile(2, 2)
>>> geometry * ([2, 1, 2], 'repeat') == geometry.repeat(2, 0).repeat(2, 2)
>>> geometry * ([2, 1, 2], 'r') == geometry.repeat(2, 0).repeat(2, 2)
>>> geometry * ([2, 0], 'r') == geometry.repeat(2, 0)
>>> geometry * ([2, 2], 'r') == geometry.repeat(2, 2)
```
  This may be considered an advanced feature but useful nonetheless.
- Enabled “adding” geometries in a similar way as multiplication I.e. the following applies:
```
>>> A + B == A.add(B)
>>> A + (B, 1) == A.append(B, 1)
>>> A + (B, 2) == A.append(B, 2)
>>> (A, 1) + B == A.prepend(B, 1)
```
- Added origo and atom argument to rotation functions. Previously this could be accomblished by:
  
  rotated = geometry.move(-origo).rotate(…).move(origo)
  
  while now it is:
  
  rotated = geometry.rotate(…, origo=origo)
  
  The origo argument may also be a single integer in which case the rotation is around atom origo.
  
  Lastly the atom argument enables only rotating a sub-set of atoms.
- Geometry[..] is now calling axyz if is pure indices, if it is a slice it does not work with super-cell indices
- Added rij functions to the Geometry for retrieving distances between two atoms (orij for orbitals)
- Renamed iter_linear to iter
- Added argument to iter_species for only looping certain atomic indices
- Added iter_orbitals which returns an iterator with atomic _and_ associated orbitals. The orbitals are with respect to the local orbital indices on the given atom
  
  ` >>> for ia, io in Geometry.iter_orbitals(): >>> Geometry.atom[ia].R[io] `
  
  works, while
  
  ` >>> for ia, io in Geometry.iter_orbitals(local=False): >>> Geometry.atom[ia].R[io] `
  
  does not work because io is globally defined.
- Changed argument name for coords, atom instead of the old idx.
- Renamed function axyzsc to axyz
SparseCSR:
- Added iter_nnz(i=None) which loops on sparse elements connecting to row i (or default to loop on all rows and columns).
- ispmatrix to iterate through a scipy.sparse.*_matrix (and the SparseCSR matrix).
Hamiltonian:
- Added iter_nnz which is the Hamiltonian equivalent of SparseCSR.iter_nnz. It enables explicit looping on atomic couplings, or orbital couplings. I.e. one may specify a subset of atoms or orbitals to loop over.
- Preliminary implementation of the non-collinear spin-case. Needs testing.