2d65fc3 | Nick Papior | 18 September 2023, 12:55:19 UTC | added pinv and pinvh to the linalg lib Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 September 2023, 12:55:19 UTC |
0e7ad14 | Nick Papior | 18 September 2023, 12:55:00 UTC | updated wheels for macos, trying Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 September 2023, 12:55:00 UTC |
a912196 | Nick Papior | 14 September 2023, 08:58:23 UTC | fixed cases where the arguments to BandStructure were wrong Now an error is raised Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 September 2023, 08:58:23 UTC |
99dc6c3 | Nick Papior | 12 September 2023, 07:51:01 UTC | added now wheel for a different binutils Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 September 2023, 07:51:01 UTC |
21978de | Nick Papior | 12 September 2023, 07:42:20 UTC | fixed order negation test Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 September 2023, 07:42:20 UTC |
addf8f1 | Nick Papior | 12 September 2023, 07:34:44 UTC | added a new publication using sisl Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 September 2023, 07:34:44 UTC |
1f705f5 | Nick Papior | 12 September 2023, 07:32:54 UTC | fixed wrong mulliken calculation for polarized calculations, #611 This happened because we were forgetting to do a copy of the element matrix. This resulted in creating a view, but calculating on the same array leaving the exact calculation wrong. Essentially the old Mulliken was non-sense M[0] was M[0] + M[0] - M[1] Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 September 2023, 07:32:59 UTC |
6935c06 | Nick Papior | 12 September 2023, 07:20:44 UTC | enabled negating order arguments for fdf sile Now doing read_geometry(order='^fdf') will use the default arguments, but remove fdf from the default list (if present). This will allow one to omit specific siles, but retain compatibility with future additions of siles. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 September 2023, 07:20:44 UTC |
e75613f | Nick Papior | 06 September 2023, 07:09:07 UTC | removed branch of reading that should not be needed (hsx) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 September 2023, 07:09:07 UTC |
5eae9dd | Nick Papior | 30 August 2023, 11:37:17 UTC | amended units to effective_mass Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 August 2023, 11:37:17 UTC |
d7a2ca1 | Nick Papior | 11 August 2023, 08:06:54 UTC | bumped rc candidate Signed-off-by: Nick Papior <nickpapior@gmail.com> | 11 August 2023, 08:06:54 UTC |
fe0bdf4 | Nick Papior | 11 August 2023, 08:06:09 UTC | fixed index checks for cylinders Signed-off-by: Nick Papior <nickpapior@gmail.com> | 11 August 2023, 08:06:09 UTC |
5b4c872 | Nick Papior | 10 August 2023, 09:19:08 UTC | fixes for arm removal (workflow) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 09:19:08 UTC |
243e362 | Nick Papior | 10 August 2023, 09:00:35 UTC | bumped to new rc Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 09:00:35 UTC |
964fc10 | Nick Papior | 10 August 2023, 09:00:06 UTC | removing arm (for now) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 09:00:06 UTC |
8635a3b | Nick Papior | 10 August 2023, 08:38:48 UTC | added flags to mac Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 08:38:48 UTC |
9cb9593 | Nick Papior | 10 August 2023, 08:21:03 UTC | fixed needs in upload target Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 08:21:03 UTC |
22a25c3 | Nick Papior | 10 August 2023, 08:19:43 UTC | bumped build matrix again Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 08:19:43 UTC |
5d6f661 | Nick Papior | 10 August 2023, 07:29:49 UTC | trying again Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 07:29:49 UTC |
4539a5c | Nick Papior | 10 August 2023, 07:27:57 UTC | new wheel matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 07:27:57 UTC |
e960882 | Nick Papior | 10 August 2023, 07:25:09 UTC | testing again Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 07:25:09 UTC |
ed4ffae | Nick Papior | 10 August 2023, 07:15:12 UTC | trying to make an rc release This is mainly for testing, but could be useful as it should be uploaded to pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 07:15:12 UTC |
86afb76 | Nick Papior | 10 August 2023, 07:14:37 UTC | fixed erroneous matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 07:14:37 UTC |
def4ce4 | Nick Papior | 10 August 2023, 07:12:03 UTC | trying to make an rc release This is mainly for testing, but could be useful as it should be uploaded to pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 August 2023, 07:12:03 UTC |
e868903 | Nick Papior | 09 August 2023, 19:55:11 UTC | simplified the matrix structure in wheels.yaml This is a maintenance workflow update. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 09 August 2023, 19:55:11 UTC |
7da586a | Nick Papior | 08 August 2023, 20:09:58 UTC | Added a new shape, EllipticalCylinder This shape is a simple cylinder with elliptical base. It can be oriented in any direction. Currently there is no simple CircularCylinder which might be a handy one, this could be added later. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 08 August 2023, 20:09:58 UTC |
ad88dc3 | Nick Papior | 08 August 2023, 10:39:59 UTC | removed 37 references in pyproject.toml Signed-off-by: Nick Papior <nickpapior@gmail.com> | 08 August 2023, 10:39:59 UTC |
1205771 | Nick Papior | 05 August 2023, 19:17:33 UTC | fixed #604 and #605 It was a result of a leftover check since close_sc did not return isc, and hence the check. It should now work. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 August 2023, 19:17:33 UTC |
9b1cc67 | Nick Papior | 18 July 2023, 11:02:26 UTC | adding sub-energies to the automatic energy-min Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 July 2023, 11:02:26 UTC |
aa3a012 | Nick Papior | 18 July 2023, 10:59:20 UTC | removed custom single dispatch method Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 July 2023, 10:59:20 UTC |
35ad6e2 | Nick Papior | 18 July 2023, 09:14:00 UTC | isort fixes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 July 2023, 09:14:00 UTC |
645e3c0 | Nick Papior | 18 July 2023, 09:02:55 UTC | removed custom single dispatch method Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 July 2023, 09:02:55 UTC |
2754537 | Nick Papior | 17 July 2023, 19:15:22 UTC | Merge pull request #421 from pfebrer/heteroribbons Function to build heteroribbons | 17 July 2023, 19:15:22 UTC |
e086e20 | Nick Papior | 16 July 2023, 20:06:00 UTC | removed reference to spmatrix, now using issparse Fixes #599. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 July 2023, 20:06:00 UTC |
eefa952 | Nick Papior | 16 July 2023, 20:01:00 UTC | added CompositeGeometrySection to docs Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 July 2023, 20:01:00 UTC |
1915527 | Nick Papior | 10 July 2023, 20:29:02 UTC | renamed section class names Now they are exposed Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2023, 19:01:12 UTC |
22c51e1 | Nick Papior | 10 July 2023, 20:23:02 UTC | rebase isort fixes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2023, 19:01:12 UTC |
628cee4 | Nick Papior | 10 July 2023, 19:31:23 UTC | fixed tests and docs Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2023, 19:01:12 UTC |
076e18d | Nick Papior | 10 July 2023, 09:18:11 UTC | fixed tests after rebasing Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2023, 19:01:12 UTC |
331d3e4 | Pol Febrer | 26 January 2022, 20:33:15 UTC | bug: corrected some bugs on valid shifts | 15 July 2023, 19:01:12 UTC |
201c953 | Pol Febrer | 26 January 2022, 17:20:42 UTC | bug: less buggy way of shifting the cell | 15 July 2023, 19:01:12 UTC |
0dafb02 | Pol Febrer | 18 January 2022, 00:02:45 UTC | new paradigm | 15 July 2023, 19:01:12 UTC |
579de54 | Nick Papior | 15 July 2023, 19:00:56 UTC | ensured workflows has correct requirements This ensures the installation also installs netCDF4 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2023, 19:00:56 UTC |
8d725ed | Nick Papior | 14 July 2023, 04:44:22 UTC | removed debug statements Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 July 2023, 04:44:22 UTC |
01e705d | Nick Papior | 13 July 2023, 20:46:26 UTC | ensured that wavefunctions do not translate coordinates Now if a translation would have shifted the atoms, an information notice will be shown. Users should in this case try and shift everything into the primary unit cell which should disable the warning and ensure proper function. Ideally this should be solved otherwise, and will probably be solved later, but for now this seems like the most appropriate thing to do. Fixes #592. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 July 2023, 20:46:26 UTC |
8d2a675 | Nick Papior | 13 July 2023, 13:44:22 UTC | removed unneeded functions Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 July 2023, 13:44:22 UTC |
d10f112 | Nick Papior | 13 July 2023, 13:40:10 UTC | added vacuum addition to the orthogonal direction of planes This could be used in wavefunction/densities to reduce the search space for very hexagonal cells. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 July 2023, 13:40:10 UTC |
708e494 | Nick Papior | 13 July 2023, 12:28:11 UTC | Merge pull request #598 from pfebrer/sparse_fixes maint: Adapt to breaking changes in scipy.sparse.isspmatrix | 13 July 2023, 12:28:11 UTC |
3b6a434 | Pol Febrer | 13 July 2023, 11:09:40 UTC | maint: Adapt to breaking changes in scipy.sparse.isspmatrix This used to return True with sparse arrays as well, but now it only returns True for sparse matrices. To keep the old behavior, we use `scipy.sparse.issparse` instead. | 13 July 2023, 11:09:40 UTC |
1ef16ed | Nick Papior | 13 July 2023, 08:09:28 UTC | fixed lattice handling in Grid Previously one could tile non-commensurate grids. A commensurate grid has a lattice and a geometry that are integer repetitions of the original geometry. This is now checked before one can tile the grid. The Grid.__str__ has been updated to highlight this configuration where the commensurability is shown (instead of lattice). However, when they are not commensurate, the full lattice + full geometry is shown. Removed some set_lattice when calling this on LatticeChild. It had the side-effect of setting the lattice for some hamiltonians etc when calling wavefunction. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 July 2023, 08:10:07 UTC |
3a9a946 | Nick Papior | 10 July 2023, 20:23:38 UTC | removed APPLICATION from isort, not needed Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 20:23:38 UTC |
72a78ee | Nick Papior | 10 July 2023, 20:18:41 UTC | Merge branch 'isort-2' | 10 July 2023, 20:18:41 UTC |
8f7c0bb | Nick Papior | 10 July 2023, 20:18:35 UTC | isort amendment for PR Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 20:18:35 UTC |
56f10c0 | Nick Papior | 10 July 2023, 19:45:05 UTC | isort is now fully functional The recommended way to produce PR's is also to run isort at the top-directory. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 20:16:52 UTC |
4cad90b | Nick Papior | 10 July 2023, 19:42:52 UTC | changed fallback version shouldn't be needed Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 19:42:52 UTC |
1f1f0ef | Nick Papior | 10 July 2023, 19:34:47 UTC | typing for nodes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 19:34:47 UTC |
a6ba1f8 | Nick Papior | 10 July 2023, 13:49:43 UTC | removed unused assignments Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 13:49:43 UTC |
3ce018d | Nick Papior | 10 July 2023, 10:11:01 UTC | deleted netCDF4 from requirements.txt Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 10:11:01 UTC |
0298005 | Nick Papior | 10 July 2023, 09:34:55 UTC | changed casing of code-of-conduct Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 09:34:55 UTC |
2af10b6 | Nick Papior | 10 July 2023, 08:47:22 UTC | moved error raising into the respective codes This makes security detection better. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 08:47:22 UTC |
761f808 | Nick Papior | 10 July 2023, 08:43:06 UTC | added code-of-conduct.md Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 08:43:06 UTC |
8f45d78 | Nick Papior | 10 July 2023, 08:27:11 UTC | Merge pull request #596 from zerothi/595-netcdf4-removall netCDF4 is now an optional dependency | 10 July 2023, 08:27:11 UTC |
e0e9be4 | Nick Papior | 10 July 2023, 08:10:36 UTC | netCDF4 is now an optional dependency An import error will be raised with explanation on how to mitigate the problem. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 July 2023, 08:10:36 UTC |
fc1da2c | Nick Papior | 07 July 2023, 12:58:32 UTC | copied netCDF4 to the optional dependencies Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 July 2023, 12:58:32 UTC |
e9f8818 | Nick Papior | 07 July 2023, 12:46:54 UTC | added importorskips for netCDF4 module missing Still now sisl depends on netCDF4, while it actually doesn't. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 July 2023, 12:46:54 UTC |
300592e | Nick Papior | 07 July 2023, 10:17:56 UTC | small clean-up fo the documentation process Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 July 2023, 10:17:56 UTC |
8f0c55a | Nick Papior | 07 July 2023, 09:47:47 UTC | Merge pull request #594 from juijan/missing_import_siesta_grid Fix missing import in siesta_grid. | 07 July 2023, 09:47:47 UTC |
ed0a6aa | Nils Wittemeier | 07 July 2023, 09:39:37 UTC | Fix missing import in siesta_grid. This import is needed when the `read_grid` routine receives an array of floats for the kwarg `spin`. | 07 July 2023, 09:40:27 UTC |
10d1da3 | Nick Papior | 06 July 2023, 16:10:13 UTC | Merge pull request #585 from pfebrer/583-t2uc-matrix `translate2uc` for sparse matrices with associated geometries. | 06 July 2023, 16:10:13 UTC |
98af2b8 | Nick Papior | 06 July 2023, 13:59:56 UTC | trying to hide the __doc__ to the __call__ method as well this is for silebinder stuff Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 July 2023, 13:59:56 UTC |
7e8006f | Nick Papior | 06 July 2023, 11:34:41 UTC | fixed SileBinder for documentation problems Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 July 2023, 11:34:41 UTC |
d3fe31f | Nick Papior | 06 July 2023, 11:17:49 UTC | updated docs to reflect removed objects Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 July 2023, 11:17:49 UTC |
cd99581 | Nick Papior | 06 July 2023, 11:06:21 UTC | added tab for config-settings flag for cmake defines Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 July 2023, 11:06:21 UTC |
9862512 | Nick Papior | 06 July 2023, 10:59:09 UTC | added test for sparseorbital Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 July 2023, 10:59:09 UTC |
b107ebc | Nick Papior | 06 July 2023, 10:21:41 UTC | minor fixes here and there Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 July 2023, 10:21:41 UTC |
cb7e3cb | Nick Papior | 04 July 2023, 13:43:20 UTC | performance improvement for Sparse*.nonzero, also changed interface Now uses pure array functions, should be much faster! Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 July 2023, 13:43:20 UTC |
08f50fe | Nick Papior | 04 July 2023, 12:56:04 UTC | bumped to 0.14.0 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 July 2023, 12:56:04 UTC |
e641677 | Nick Papior | 21 June 2023, 06:47:03 UTC | bug fixed numpy>=1.25 handling of stack stack and friends now forces tuple/list, no generators Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 June 2023, 06:47:03 UTC |
1a06052 | Nick Papior | 21 June 2023, 06:33:31 UTC | fixed bug with __slots__ behaviour A missing _D was present in the SparseCSR. Weirdly enough it was never caught, but has been present, basically for ever. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 June 2023, 06:33:31 UTC |
2971430 | Nick Papior | 21 June 2023, 06:01:30 UTC | Merge pull request #589 from zerothi/del-collection removed Collection + GeometryCollection | 21 June 2023, 06:01:30 UTC |
ead65f7 | Nick Papior | 21 June 2023, 06:00:05 UTC | removed Collection + GeometryCollection Basically reverted #546 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 June 2023, 06:00:05 UTC |
9852fbf | Thomas Frederiksen | 20 June 2023, 19:31:28 UTC | VASP forces from OUTCAR (#573) added read_trajectory for VASP OUTCAR This will now use the SileBinder approach --------- Co-authored-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 19:31:28 UTC |
853a9b7 | Nick Papior | 20 June 2023, 19:27:24 UTC | amended changelog for txt orca sile Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 19:27:24 UTC |
2f840ce | Nick Papior | 20 June 2023, 19:22:36 UTC | updated orca/txt to use SileBinder Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 19:22:36 UTC |
0e04bf0 | Pol Febrer | 20 June 2023, 19:21:51 UTC | added tests | 20 June 2023, 19:21:51 UTC |
3068d32 | Pol Febrer | 20 June 2023, 15:14:37 UTC | fix annotations | 20 June 2023, 15:14:37 UTC |
3782251 | Nick Papior | 20 June 2023, 12:26:54 UTC | enabled deleting an argument Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 12:26:54 UTC |
974026e | Pol Febrer | 20 June 2023, 11:26:22 UTC | add atoms and axes arguments | 20 June 2023, 11:26:22 UTC |
dcbd9a6 | Pol Febrer | 20 June 2023, 08:02:54 UTC | moved functionality to _SparseGeometry so that it works for SparseAtom | 20 June 2023, 11:17:55 UTC |
4d4219a | Pol Febrer | 19 June 2023, 09:38:58 UTC | removed geometry_coords argument | 20 June 2023, 11:17:55 UTC |
29bd643 | Pol Febrer | 15 June 2023, 22:54:26 UTC | enh: first sketch of translate2uc for matrices | 20 June 2023, 11:17:55 UTC |
0b17eec | Nick Papior | 20 June 2023, 08:12:23 UTC | Merge pull request #586 from zerothi/584-sile-slicer Slicing IO read_ routines | 20 June 2023, 08:12:23 UTC |
34a265e | Nick Papior | 17 June 2023, 06:16:56 UTC | removed parameters from xyz Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:12:06 UTC |
6eb605c | Nick Papior | 17 June 2023, 06:09:45 UTC | converted orca.stdout to use SileBinder This makes the read-functionalities more useable to retain other parts of the information. All tests are functional again. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:12:06 UTC |
0552845 | Nick Papior | 16 June 2023, 18:17:42 UTC | added last/next in the slicer Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:12:06 UTC |
1a56852 | Nick Papior | 16 June 2023, 12:02:34 UTC | added default slice to the patched documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:12:06 UTC |
3665e05 | Nick Papior | 16 June 2023, 11:31:31 UTC | added negative test and reversing elements Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:12:06 UTC |
5203e9d | Nick Papior | 16 June 2023, 09:59:39 UTC | removed try..except if the file reads raises something, then announce Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:12:06 UTC |
e00a557 | Nick Papior | 14 June 2023, 20:33:49 UTC | preliminary test-bed for slicing io stuff Fixed documentation issues and enabled this. Storing sliced objects will also work. Currently nested slicing is not possible. enabled nested with of a sile and changed to SileBinder The sile_read_multiple has been deleted, now the way to do it is SileBinder. This is more versatile and allows better handling. It also patches the documentation. This changes the behaviour of all files using this. By default a read_* with the SileBinder will only read the next entry, however to read multiple one should use read_*[...] for slicing the data. The bound method will try and be smart about only reading the needed elements, there is a bit of overhead, but largely it should be fast. All tests are functional again. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 June 2023, 08:11:22 UTC |
a8665e9 | Nick Papior | 19 June 2023, 06:51:07 UTC | enabled True for translate2uc for all axes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 June 2023, 06:51:07 UTC |