0.9.6
Released 18 of June 2019.
Contributors
A total of 2 people contributed to this release. People with a “+” by their names contributed a patch for the first time.
Jonas Lundholm Bertelsen +
Nick Papior
Pull requests merged
A total of 7 pull requests were merged for this release.
#94: Added option to plot atom indices in sisl.plot(Geometry)
#105: Minor fix on rotate documentation: degrees/rads
#107: Sub orbital
#108: travis: fixing build-system
#111: Added rudimentary support for Path objects in get_sile
#113: Added some noisy files to gitignore
#116: Adding geometries preserves named regions
Officially added real-space self-energy calculations
Cleaned TBT vs. PHT for class name structures
Bugfix for reading MD output from Siesta out-files #130
Bugfix for tbtse files when requesting pivoting indices using this combination
in_device=True, sort=False
which in most cases return wrong indices, thanks to J. Bertelsen for bug-find!Added several routines for retrieving transposed coupling elements. When having connections i -> j it may be beneficial to easily get the transposed connection j -> i by taking into account the supercell. Geometry.a2transpose enables this functionality making construct functions much simpler when having edges/boundaries.
Bug-fix for reading white-space prefixed keywords in XSF files, #127
Performance increase for self-energy calculations for very small systems
Huge memory reduction for Geometry.o2a with very large system
Enabled pickling on BrillouinZone objects
Added spin_moment to Hamiltonian
Removed
rotate[abc]
methods since they were cluttering the name-space Codes should simply replace with:>>> geometry.rotate(angle, geometry.cell[{012}, :], *)
for the same effect.
Finally removed deprecated write_geom from the API
Enabled calculation of
<S^2>
for spin-polarized calculations, this may be used for calculating spin-contaminationsadded checks for SparseCSR to disallow out-of-bounds keys
Bug fixed for reading POSCAR files from VASP (only when multiple species are used in a non-ordered fashion)
added
sisl
command line utility, it is exactly the same as sdataEnabled pickling sparse matrices, this allows dask usage of sparse matrices
Performance increase for sparse matrix handling
Fixed a problem with Fortran IO + Jupyter notebooks, now the file-handles are re-used if a code block is terminated before closing the file
Added SparseOrbital append + transpose This enables appending Hamiltonian’s (append) and makes hermiticity checks possible (transpose)
Enabled complex averaged calculations using oplist The oplist object is a container allowing inter-element operations
>>> l1 = oplist([0, 1]) >>> l2 = oplist([2, 3]) >>> l = l1 + l2 >>> print(l) [2, 4]
This is extremely handy for BrillouinZone.asaverage/assum when calculating multiple values using eigenstate objects.
Added reflection calculation to tbtncSileTBtrans
Added more distribution functions (step and heaviside)
Removed numpy deprecated class numpy.matrix, now everything is array
Removed possibility of using kavg=list(…) due to complexity, now single kavg requests are not k-averaged.
Bugfix in calculating shot_noise, noise_power and fano factors in tbtncSileSiesta They were only correct for Gamma-point calculations
Fixed *.EIG sdata processing when using –dos
Fixed reading geometries from grids from VASP (grid values were correct)
Toolboxes:
Added a toolbox to calculate the Poisson solution for arbitrary electrodes for TranSiesta