| c9b3d06 | Nick Papior | 11 June 2017, 17:49:35 UTC | sisl release: 0.8.4 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 11 June 2017, 17:49:35 UTC |
| 228cb50 | Nick Papior | 11 June 2017, 17:46:23 UTC | doc: added DEPLOY file for description of release commands Signed-off-by: Nick Papior <nickpapior@gmail.com> | 11 June 2017, 17:46:23 UTC |
| 3a7fe1d | Nick Papior | 11 June 2017, 17:12:42 UTC | doc: trying to fix links (again) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 11 June 2017, 17:12:42 UTC |
| ecadccb | Nick Papior | 11 June 2017, 16:59:28 UTC | doc: fixed links in file formats Signed-off-by: Nick Papior <nickpapior@gmail.com> | 11 June 2017, 16:59:28 UTC |
| eb7c1e1 | Nick Papior | 06 June 2017, 15:25:50 UTC | test: added more tests Also fixed sparserij which is an atomic sparse pattern Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 June 2017, 15:25:50 UTC |
| b223af1 | Nick Papior | 05 June 2017, 19:56:13 UTC | bug: fixed atoms in Geometry Added more forms of the fdf sdata command. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 June 2017, 19:56:13 UTC |
| 1fe1550 | Nick Papior | 03 June 2017, 16:47:08 UTC | enh: added flags for TBT-info Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 June 2017, 16:47:08 UTC |
| 4674d0f | Nick Papior | 03 June 2017, 05:26:24 UTC | test: fixed tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 June 2017, 05:26:24 UTC |
| f0a24df | Nick Papior | 02 June 2017, 17:57:07 UTC | api: changed name of Path -> PathBZ for clarity Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 June 2017, 17:57:07 UTC |
| 4442715 | Nick Papior | 01 June 2017, 19:52:40 UTC | test: added test of BrillouinZone as arg to Ham Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 June 2017, 19:52:40 UTC |
| cab6272 | Nick Papior | 01 June 2017, 19:01:57 UTC | enh: enabled Hamiltonian to perform eigh on BZ Instead of passing a k-point to the Hamiltonian.eigh one may now pass a BZ object to retrieve eigenvalues for all the k-points in the BZ object. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 June 2017, 19:01:57 UTC |
| 5282f36 | Nick Papior | 01 June 2017, 18:41:34 UTC | enh: updated TBT.nc info Now the k-points has more information and the dE is also shown Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 June 2017, 18:41:34 UTC |
| b71151d | Nick Papior | 01 June 2017, 09:26:17 UTC | bug: fixed eliminate_zeros for bigger shapes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 June 2017, 09:26:17 UTC |
| 7c8f313 | Nick Papior | 01 June 2017, 09:17:56 UTC | enh: added eliminate_zeros() for sparse and Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 June 2017, 09:17:56 UTC |
| de5acd1 | Nick Papior | 31 May 2017, 17:10:30 UTC | test: added more tests of the shape Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 May 2017, 17:10:30 UTC |
| 71a1768 | Nick Papior | 31 May 2017, 10:47:04 UTC | bug: fixed iterations in iter_block_shape This fixes the too many iterations per shape. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 May 2017, 10:47:04 UTC |
| cc1512f | Nick Papior | 30 May 2017, 19:55:00 UTC | bug: fixed fdf writing of Chemical block Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 May 2017, 19:55:00 UTC |
| badb8f6 | Nick Papior | 30 May 2017, 11:20:01 UTC | bug: fixed within for the Cube shape Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 May 2017, 11:20:01 UTC |
| 2261302 | Nick Papior | 29 May 2017, 19:04:41 UTC | maint: added Hrepeat for benchmarks Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 May 2017, 19:04:41 UTC |
| 6fc750d | Nick Papior | 29 May 2017, 16:23:49 UTC | enh: enabled repeat for the Hamiltonian object Now one may use repeat and tile for the Hamiltonian object as well. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 May 2017, 16:23:49 UTC |
| 19783d9 | Nick Papior | 28 May 2017, 19:34:32 UTC | maint: pep8 update Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 May 2017, 19:34:32 UTC |
| 31fae3a | Nick Papior | 28 May 2017, 19:34:06 UTC | maint: trying to add repeat function for Hamiltonian Also speeded up the tile function a bit. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 May 2017, 19:34:06 UTC |
| 5bcaa3e | Nick Papior | 27 May 2017, 20:17:44 UTC | travis: removed unnecessary coverage flag Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 May 2017, 20:17:44 UTC |
| af146cf | Nick Papior | 27 May 2017, 19:56:16 UTC | enh: fixed tile for Hamiltonian to be faster and no limitations Fixed tile function to also work for long range orbitals (cross several cells). Added test for this. Speeded up tile function. However, the speedup with respect to construct is not that impressive. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 May 2017, 19:56:16 UTC |
| b8006bd | Nick Papior | 26 May 2017, 21:04:39 UTC | enh: added remove and sub to Hamiltonian Now the Hamiltonian object may remove and retain certain atoms. This seems to work very well. However, I have not tried on very big systems to see how well it performs. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 May 2017, 21:04:39 UTC |
| b8fa651 | Nick Papior | 26 May 2017, 18:02:25 UTC | enh: added tiling Hamiltonian for simple systems Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 May 2017, 18:02:25 UTC |
| cf76e19 | Nick Papior | 26 May 2017, 11:47:31 UTC | bug: trying to fix test bugs Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 May 2017, 11:47:31 UTC |
| 6efffa7 | Nick Papior | 26 May 2017, 11:35:24 UTC | bug: removed fromstring which seems to not function properly in P3 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 May 2017, 11:35:24 UTC |
| b98209c | Nick Papior | 25 May 2017, 20:39:41 UTC | enh: added more tests for write_geometry and for Argparser Signed-off-by: Nick Papior <nickpapior@gmail.com> | 25 May 2017, 20:39:41 UTC |
| 833d5ed | Nick Papior | 25 May 2017, 20:13:42 UTC | doc: updated a tutorial Signed-off-by: Nick Papior <nickpapior@gmail.com> | 25 May 2017, 20:13:42 UTC |
| 25f5f87 | Nick Papior | 24 May 2017, 19:52:55 UTC | fmt: updated pep format Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 May 2017, 19:52:55 UTC |
| 719527a | Nick Papior | 24 May 2017, 19:38:13 UTC | enh: added orbocc from ScaleUp Now the geometry tries to read in the orbocc to correctly set the number of orbitals. Secondly, if the geometry used when creating the rham Hamiltonian does not have the correct orbitals it will try and read the orbocc file and automatically correct the atomic species. This should capture the majority of use cases. Reverted the rham to read the entire file into memory. This sadly has the effect that we need to parse it twice. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 May 2017, 19:38:13 UTC |
| d55392c | Nick Papior | 23 May 2017, 20:05:57 UTC | bug: fixed refscaleup read Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 20:05:57 UTC |
| 5427c69 | Nick Papior | 23 May 2017, 19:55:27 UTC | bug: forced scaleup to always use supercell of 3, 3, 3 Perhaps this may be changed later on, but it should suffice for nearly all cases. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 19:55:27 UTC |
| 3cb3618 | Nick Papior | 23 May 2017, 17:39:30 UTC | enh: added rham from ScaleUp, fixed fromsp with multiple spin components It should now work, I need to create the band-structure of the system sent by Pablo. Fixed Hamiltonian.fromsp to be able to read from a list of Hamiltonian sparse matrices each accounting for a spin-component. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 17:39:30 UTC |
| b7b1b61 | Nick Papior | 23 May 2017, 11:32:33 UTC | api: changed read_sc to read_supercell Updated all code to reflect this and also added a test of REF and restart (from ScaleUp) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 11:32:33 UTC |
| 2ee9b21 | Nick Papior | 23 May 2017, 11:15:51 UTC | bug: fixed map in scaleup Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 11:15:51 UTC |
| 5b5c89f | Nick Papior | 23 May 2017, 09:47:41 UTC | bug: fixed map in python3 (return iterator) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 09:47:41 UTC |
| 2a2fe48 | Nick Papior | 23 May 2017, 09:43:21 UTC | bug: fixed *args, **kwargs in Geometry.read Also fixed representation of the Geometry to not have too many {} Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 09:43:21 UTC |
| 1cfa2cd | Nick Papior | 23 May 2017, 09:34:34 UTC | enh: added ScaleUp REF and restart file Also added iterator to the supercell to iterate on the supercells. Currently this is an enumerate iterator. I think this is the general usage. So even though the iterator could simply yield the sc_off[i, :], it will hardly be used (I guess) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 09:34:34 UTC |
| 79d1bb4 | Nick Papior | 23 May 2017, 07:05:02 UTC | doc: updated documentation list Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 May 2017, 07:05:02 UTC |
| 473ec0f | Nick Papior | 19 May 2017, 20:23:52 UTC | test: ensured test of interp function for grid It still does not work, but at least it works if all values are the same Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 May 2017, 20:23:52 UTC |
| 0436494 | Nick Papior | 19 May 2017, 19:23:10 UTC | bug: added __repr__ for sparsecsr Fixed native Ham format for text file representation. It should now work as expected. One thing to note is that sparse matrices written will automatically remove 0's. This may be a problem in case the on-site energies are 0. In which case they wont be written. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 May 2017, 19:23:10 UTC |
| 0b8f052 | Nick Papior | 19 May 2017, 14:23:19 UTC | test: added more tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 May 2017, 14:23:19 UTC |
| 318634a | Nick Papior | 18 May 2017, 13:50:46 UTC | enh: implemented direct slice notation in additions This should speed up slightly the sparse generation of matrices but only slightly. Also added more tests to the SparseCSR matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 May 2017, 13:50:46 UTC |
| c881ed5 | Nick Papior | 17 May 2017, 13:39:10 UTC | test: added more tests to supercell Now testing for supercell is complete only read misses. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 May 2017, 13:39:10 UTC |
| 2c9960c | Nick Papior | 16 May 2017, 15:15:34 UTC | test: added tests of the Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 May 2017, 15:15:34 UTC |
| 78c7652 | Nick Papior | 16 May 2017, 09:01:51 UTC | test: added more tests to sparse module Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 May 2017, 09:01:51 UTC |
| 8aee8a2 | Nick Papior | 16 May 2017, 08:33:43 UTC | doc: updated doc strings and added link to RTD Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 May 2017, 08:33:43 UTC |
| 1add8b3 | Nick Papior | 16 May 2017, 08:28:51 UTC | doc: updated documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 May 2017, 08:28:51 UTC |
| f2d667d | Nick Papior | 16 May 2017, 08:26:24 UTC | enh: changed name_spec to str_spec Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 May 2017, 08:26:24 UTC |
| f68ad69 | Nick Papior | 09 May 2017, 20:17:09 UTC | enh: updated README Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 20:17:09 UTC |
| 298e23c | Nick Papior | 09 May 2017, 13:00:46 UTC | doc: updated documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 13:00:46 UTC |
| 48560e8 | Nick Papior | 09 May 2017, 12:48:15 UTC | api: moved quantity to physics As this module has never been used before it makes sense to update it to something more tangible. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 12:48:15 UTC |
| b567f82 | Nick Papior | 09 May 2017, 12:43:52 UTC | enh: enabled slice deletion for the sparse matrix and Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 12:43:52 UTC |
| 7787449 | Nick Papior | 09 May 2017, 08:17:01 UTC | api: changed read/write_es to read/write_hamiltonian for consistency The API is cleaned up a bit to make use more intuitive. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 08:17:01 UTC |
| c45ce4d | Nick Papior | 09 May 2017, 08:11:09 UTC | api: changed read/write_geom to read/write_geometry for consistency The API is cleaned up a bit to make use more intuitive. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 08:11:09 UTC |
| ef7eba9 | Nick Papior | 09 May 2017, 08:03:01 UTC | enh: added possibility of updating the geometry of a TBT.nc file This is to get the correct species when printing to out-files with species information. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 May 2017, 08:03:01 UTC |
| 7138e78 | Nick Papior | 03 May 2017, 13:24:09 UTC | enh: added supercell index specification and supercell fill In case one only has a 2D system sisl can now figure out the dimensions, but only when the number of supercells is explicitly set corresponding to the dimensions. I.e. if >>> s = SuperCell(..., [1, 3, 1]) >>> s._fill_sc((1,)) (0, 1, 0) so where 1's are present in the supercell it is filled with zeroes. Secondly this is used with the Hamiltonian object which now enables: >>> H[0, 1, (0, 1, 0)] = ... which sets the Hamiltonian element between the first orbital in the unit cell and the second orbital in the (0, 1, 0) supercell. This makes it easier to set the coupling constants along axis. This fixes #27. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 May 2017, 13:24:09 UTC |
| a9667d6 | Nick Papior | 07 April 2017, 12:16:50 UTC | enh: added BrillouinZone Implementation of BrillouinZone and Path to construct paths in the Brillouin zone. I am not sure that the API is stable for this code, so I will not encourage a heavy usage of it. We'll see. Fixes #26 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 April 2017, 12:16:50 UTC |
| 4e75db1 | Nick Papior | 06 April 2017, 09:06:24 UTC | doc: added default tutorial setup for tex Moved figures to not clutter the directory Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 April 2017, 09:06:24 UTC |
| fa31488 | Nick Papior | 06 April 2017, 08:41:20 UTC | doc: re-ordered tutorial and examples Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 April 2017, 08:41:20 UTC |
| 27f0566 | Nick Papior | 06 April 2017, 08:27:41 UTC | doc: updated pictures and script Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 April 2017, 08:27:41 UTC |
| d941e49 | Nick Papior | 06 April 2017, 08:24:05 UTC | doc: added tutorial images for supercell Also added script to easily convert all pdf to pngs in the tutorial dir Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 April 2017, 08:24:05 UTC |
| 5ad351f | Nick Papior | 05 April 2017, 08:42:00 UTC | maint: added gitter badges in docs and README.md Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 08:42:00 UTC |
| 0466f2c | Nick Papior | 05 April 2017, 08:31:52 UTC | maint: added gitter support Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 08:31:52 UTC |
| 058edeb | Nick Papior | 05 April 2017, 07:48:21 UTC | doc: added doi link Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 07:48:21 UTC |
| 473e5b3 | Nick Papior | 05 April 2017, 07:12:10 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 07:12:10 UTC |
| f7cb00e | Nick Papior | 05 April 2017, 07:11:11 UTC | sisl release: 0.8.3 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 07:11:11 UTC |
| cd21d25 | Nick Papior | 05 April 2017, 07:09:09 UTC | maint: trying to fix tag.sh Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 07:09:09 UTC |
| 4df8ef3 | Nick Papior | 05 April 2017, 07:07:31 UTC | bug: fixed multiplication and power of SparseCSR I think the math of __mul__ and __pow__ are now correct. I.e. we should have checked for zeros everywhere and ensured correct values: 0 * <> = 0 float ** 0 = 1 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 07:07:31 UTC |
| 9167eb0 | Nick Papior | 05 April 2017, 06:55:40 UTC | bug: fixed TableSile writeout My implementation of the __write_default should have used _write_default. Obviously. Fixes #25. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 April 2017, 06:55:40 UTC |
| a8be1ea | Nick Papior | 04 April 2017, 19:38:19 UTC | doc: minor update in documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2017, 19:38:19 UTC |
| e2cdd6f | Nick Papior | 04 April 2017, 12:40:56 UTC | api: changed ret_coord => ret_xyz, ret_dist => ret_rij for consistency Changed keyword names for close and related functions in Geometry. Also added a sparserij which returns a sparse matrix with all non-zero distances (note the diagonal elements are not defined). Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2017, 12:40:56 UTC |
| 063f7cf | Nick Papior | 04 April 2017, 06:20:49 UTC | enh: vectorized searching for indices in SparseCSR Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2017, 06:20:49 UTC |
| 06ff4e0 | Nick Papior | 03 April 2017, 20:27:47 UTC | maint: updated .gitignore Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 April 2017, 20:27:47 UTC |
| 847f7d1 | Nick Papior | 03 April 2017, 20:20:41 UTC | doc: added API documentation link in side-bar Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 April 2017, 20:20:41 UTC |
| 465de5e | Nick Papior | 03 April 2017, 20:07:57 UTC | doc: added tutorials for RTD Basic tutorials on creating a geometry and supercell has been added. Now I need to create figures with tikz-code (shipped with sisl) to complete and make it understandable. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 April 2017, 20:07:57 UTC |
| 35e05d7 | Nick Papior | 03 April 2017, 19:55:51 UTC | bug: added sparse matrix operations with each other Sparse matrices may now be added, multiplied, subtracted, etc. This is uncharted territority and the code have not been tested yet. The idea is that people may easily add two Hamiltonian objects together to ease certain operations. Especially for multiplications are the routines fast because of zero elements making many operations needless (unless they have the same sparsity pattern). Added spsame, checks whether two sparse matrices are equivalent with respect to the sparse elements, no more, no less. Added spalign, make the sparse matrix it operates on contain all elements in the sparse matrix argument. A geometry with no supercell and no orbital radii will create a molecule box (10 ang vacuum along each Cartesian vector). Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 April 2017, 19:55:51 UTC |
| d1f50b3 | Nick Papior | 02 April 2017, 20:30:21 UTC | doc: reverted conf.py for path Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 April 2017, 20:30:21 UTC |
| 8ce8753 | Nick Papior | 02 April 2017, 19:38:13 UTC | doc: trying to fix RTD Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 April 2017, 19:38:13 UTC |
| 3e8c59c | Nick Papior | 02 April 2017, 18:12:29 UTC | doc: trying to fix RTD documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 April 2017, 18:12:29 UTC |
| 6a1fe44 | Nick Papior | 01 April 2017, 09:12:27 UTC | doc: added initial examples to documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 April 2017, 09:12:27 UTC |
| 8cdcaec | Nick Papior | 31 March 2017, 20:37:14 UTC | doc: fixed docs for code-block Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 20:37:14 UTC |
| b8c6772 | Nick Papior | 31 March 2017, 20:25:55 UTC | conda: fixed conda-build with new version names Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 20:25:55 UTC |
| c7075b7 | Nick Papior | 31 March 2017, 19:18:08 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 19:18:08 UTC |
| 374140b | Nick Papior | 31 March 2017, 19:17:44 UTC | sisl release: 0.8.2 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 19:17:44 UTC |
| d3d8ba2 | Nick Papior | 31 March 2017, 19:09:52 UTC | doc: fixed links Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 19:09:52 UTC |
| ae2e990 | Nick Papior | 31 March 2017, 18:57:21 UTC | doc: added documentation for introduction and installation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 18:57:21 UTC |
| 276cd17 | Nick Papior | 31 March 2017, 17:34:40 UTC | enh: enabled added a geometry with integers Now one may use add, prepend and append functions by adding a geometry by a tuple of a Geometry or simply another geometry: >>> 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) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 March 2017, 17:34:40 UTC |
| bca4483 | Nick Papior | 30 March 2017, 13:55:15 UTC | enh: enabled multiplying a geometry with integers Now one may use repeat and tile functions by multiplying a geometry by a tuple, or an integer: >>> 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 makes it very easy to use a repetitive function to create bigger structures. It may, however, be considered an advanced use of the repeat/tile functions Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 March 2017, 13:55:15 UTC |
| 6c096bb | Nick Papior | 30 March 2017, 11:53:18 UTC | enh: added atom to rotate functions, and various bug-fixes Now rotate can take an optional atom argument to only rotate a subset of atoms. Note that origo is still default [0, 0, 0]. Also, origo may take an integer which corresponds to the atomic index's coordinate. Bug-fix for get_sile when a {XYZSile} specification was present. Added documentation for winSileW90. Bug-fix for ensure array in self-energy. Possible speed-up of quaternion due to C-indexing. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 March 2017, 11:53:18 UTC |
| 5c5faf3 | Nick Papior | 30 March 2017, 06:43:36 UTC | bug: fixed wannier90 interface for reading _hr.dat files The band-structure can now be reproduced easily. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 March 2017, 06:43:36 UTC |
| dc4bdf1 | Nick Papior | 28 March 2017, 13:55:45 UTC | enh: added origo argument to rotate functions This makes it much easier to rotate about a certain point in space Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 March 2017, 13:55:45 UTC |
| bba7196 | Nick Papior | 28 March 2017, 11:15:36 UTC | enh: added sparse elements to __init__ Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 March 2017, 11:15:36 UTC |
| 1216ec5 | Nick Papior | 28 March 2017, 06:33:40 UTC | enh: added default scale to XSF When using xcrysden it is nice to re-scale the data such that the largest data is show as a length of 1. To disable this default behaviour use flag --no-scale-vector (-nsv) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 March 2017, 06:33:40 UTC |
| 4446c79 | Nick Papior | 27 March 2017, 06:20:00 UTC | bug: fixed bugs introduced by returning array sizes Added a new ensure_dtype method which allows ensure_array to return single numbers (in cases where one requests a single digit) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 March 2017, 06:20:00 UTC |
| 57c50e0 | Nick Papior | 26 March 2017, 19:55:48 UTC | enh: implemented new iterable for the sparse matrices The new iterable has been renamed from iter_spmatrix to two new functions: ispmatrix, yields row, column ispmatrixd, yields row, column, Matrix[row, column] The new algorithms are extremely fast and enables much more interaction with the matrices in an easy fashion. Changed interfaces for tbtrans.py routines such that the orbital currents are forced to return an energy orbital current. One cannot return *ALL*. Changed tbtrans.py routines to use the new routines for the atom_current and bond_current. This results in huge speed-ups for even small systems. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 March 2017, 19:55:48 UTC |
| ace69a1 | Nick Papior | 26 March 2017, 19:07:10 UTC | bug: added arguments to XSF read_* function Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 March 2017, 19:07:10 UTC |
| 806e22d | Nick Papior | 24 March 2017, 20:45:57 UTC | maint: updated documentation placement Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 March 2017, 20:45:57 UTC |
