| 1f429c3 | Nick Papior | 04 April 2024, 18:10:25 UTC | small refactor of in [ to in ( Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2024, 18:10:25 UTC |
| 19ae8dd | Nick Papior | 04 April 2024, 12:07:14 UTC | removed cell and ensured move had a shorter doc Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2024, 12:07:14 UTC |
| 00b8afa | Nick Papior | 04 April 2024, 09:01:29 UTC | enabled to using ase and DataFrame classes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2024, 09:01:29 UTC |
| 16c55d0 | Nick Papior | 04 April 2024, 06:56:04 UTC | Merge branch 'license_precommit' | 04 April 2024, 06:56:04 UTC |
| 97b434e | Nick Papior | 04 April 2024, 06:55:48 UTC | moved LICENSE_header to .LICENSE_header Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 April 2024, 06:55:48 UTC |
| 7c2ea72 | Nick Papior | 04 April 2024, 06:24:46 UTC | Merge pull request #736 from pfebrer/nodes_registry Some polishing of `sisl.nodes` | 04 April 2024, 06:24:46 UTC |
| a91c788 | Pol Febrer | 03 April 2024, 15:28:04 UTC | Pre-commit hook to add license | 03 April 2024, 15:28:04 UTC |
| 74a6de6 | Pol Febrer | 03 April 2024, 15:23:21 UTC | Some polishing of sisl.nodes | 03 April 2024, 15:23:21 UTC |
| 44286a5 | Nick Papior | 03 April 2024, 10:19:17 UTC | documentation fixes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 April 2024, 10:19:17 UTC |
| 9ab5c2c | Nick Papior | 02 April 2024, 11:06:26 UTC | Merge pull request #734 from tfrederiksen/grid-bc-dep Remove deprecated `bc` argument to `Grid` | 02 April 2024, 11:06:26 UTC |
| a6f12a8 | Nick Papior | 27 March 2024, 14:07:49 UTC | enabled logging, cleaned logging scheme Now SISL_LOG_FILE and SISL_LOG_LEVEL can be used to automatically create the logging environment. Also moved the CLI of the toolboxes to their respective imports. This should make it simpler for end-users to adapt a toolbox parser. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 March 2024, 14:07:49 UTC |
| 24aa8ba | Nick Papior | 27 March 2024, 11:30:26 UTC | removed things to report in coverage report Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 March 2024, 11:30:26 UTC |
| 9d7ac3b | Thomas Frederiksen | 27 March 2024, 11:22:10 UTC | removed deprecated bc argument to Grid | 27 March 2024, 11:22:10 UTC |
| 267d63f | Nick Papior | 27 March 2024, 11:04:08 UTC | changed last eps in code to atol Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 March 2024, 11:04:08 UTC |
| 3fec2ba | Nick Papior | 27 March 2024, 07:42:11 UTC | internal refactor Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 March 2024, 07:42:11 UTC |
| 8df4402 | Nick Papior | 26 March 2024, 08:42:29 UTC | added comment for PropertyDict Basically what I did is similar to the addict class (pypi package). Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 March 2024, 08:42:29 UTC |
| 5951ce8 | Nick Papior | 26 March 2024, 05:26:52 UTC | added read_basis to simple files Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 March 2024, 05:26:52 UTC |
| 07abcef | Nick Papior | 26 March 2024, 05:14:32 UTC | lots of documentation fixes Mainly with respect to typing. Also changed a few `geom` arguments to `geometry` for consistency. Changed velocity to ret_velocity. Others have changed as well. For siesta, a xv and struct files had species_Z, which was not fully clear. Now the flag is called species_as_Z. Which is more telling. Changed all specie references to species. This is the general convention that species is also a singular form. A few code segments had in_place. These got changed to inplace. Changed HFI in orca to use species for atomic specie name. Major refactoring of the siesta read_basis functions. A read_basis function should in principle read the Atoms object as though all atoms are present. So this is what is happening now. fdf siles will read all atoms and associate the basis with each atom. The former implementation only returned unique species. This is a rather drastic change, but should make things simpler as one does not need to adapt the basis to how many atoms are there after. It also makes more sense for the actual file. I.e. an XV file contains many atoms, why shouldn't the basis contain the information about how many atoms were there? Signed-off-by: Nick Papior <nickpapior@gmail.com> | 26 March 2024, 05:14:32 UTC |
| 269a174 | Nick Papior | 25 March 2024, 09:36:14 UTC | upgraded workflows, also testing for 3.9 removed annotations where it broke with future Signed-off-by: Nick Papior <nickpapior@gmail.com> | 25 March 2024, 10:44:19 UTC |
| 5c9316d | Nick Papior | 25 March 2024, 08:26:35 UTC | fixing typing view, and some doc improvements Now all files should contain the license and the future annotations import. This should allow autodoc some flexibility. Also added more citations. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 25 March 2024, 09:03:25 UTC |
| c02b256 | Nick Papior | 24 March 2024, 06:50:07 UTC | fixed units argument data-type With type-hinting it is more obvious what is allowed. Also fixed all ORCA and VASP return types. Moved all units serializations to the top of the method. I tend to prefer to do options parsing first, to sustain a better overview of what the method is doing. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 March 2024, 06:50:46 UTC |
| 7460295 | Thomas Frederiksen | 24 March 2024, 06:12:42 UTC | improved some docstrings etc (#729) | 24 March 2024, 06:12:42 UTC |
| 47a90a9 | Nick Papior | 23 March 2024, 09:06:01 UTC | dispatch for 3.8 does not work with unions Reverted Union register. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 March 2024, 09:06:01 UTC |
| 3448041 | Nick Papior | 23 March 2024, 08:52:37 UTC | the permutation list was not needed removed it from typing Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 March 2024, 08:52:37 UTC |
| 786325c | Nick Papior | 23 March 2024, 08:19:53 UTC | final clean-up of doc strings etc Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 March 2024, 08:19:53 UTC |
| fd72155 | Nick Papior | 23 March 2024, 07:53:52 UTC | fixed tuple unpacking in typing added simple doc strings and cleaned typing doc page Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 March 2024, 07:53:52 UTC |
| 6a60423 | Nick Papior | 22 March 2024, 20:41:04 UTC | upgraded sisl.typing Changed names and how the Axis/Axes types were defined. They are now explicit in which elements are allowed. E.g. Literal is used. Fixed a few left-over bugs with plural axes not used where axis were used. For places where axis/axes specifications are allowed, we now transfer any kind. E.g. geometry.tile(2, "a") is allowed. But since "x" is cartesian, geometry.tile(2, "x") shouldn't be allowed (it is by chance, but shouldn't be encouraged). Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 20:41:04 UTC |
| 359a99c | Nick Papior | 22 March 2024, 19:13:52 UTC | fixed changelog ordering Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 19:13:52 UTC |
| 3799396 | Nick Papior | 22 March 2024, 19:11:59 UTC | added tb.dat reading to changelog Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 19:11:59 UTC |
| b9c50da | Thomas Frederiksen | 22 March 2024, 19:11:34 UTC | `units` as parameter in `read_*` (#726) * energy unit as parameter * units argument to dict * introduced units argument in sisl.io.vasp | 22 March 2024, 19:11:34 UTC |
| 328816f | Nick Papior | 22 March 2024, 18:59:22 UTC | fixed removal of netcdf files Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 18:59:22 UTC |
| 5cac580 | Nick Papior | 22 March 2024, 18:55:25 UTC | implemented parse_order in w90 And fixed a lot of details in the w90 code. Enabled reading lattice from TB file. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 18:55:25 UTC |
| f9497d1 | Nils Wittemeier | 22 March 2024, 18:31:52 UTC | Resolve Issue #716 (#727) * Split Wannier90 sile types. Expose new siles and associate file types add reading of lattice from win as fallback - Reading geometry in read_hamiltonian explicitly requestes order=["centres"] - Crash reading of Hamiltonian from <>_hr.dat file if neither lattice nor geometry is available include new siles in docuementation --------- Signed-off-by: Nick Papior <nickpapior@gmail.com> Co-authored-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 18:31:52 UTC |
| 02de8b1 | Nick Papior | 22 March 2024, 18:30:02 UTC | made parse_order generic for sisl This is a method to more consistently select variables for siles Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 18:30:02 UTC |
| 3d85f12 | Nick Papior | 22 March 2024, 07:44:24 UTC | reverted ipr in BandsData (double adding) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 07:44:24 UTC |
| ffc5539 | Nick Papior | 22 March 2024, 06:54:18 UTC | moved orca files to new directories Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 06:54:18 UTC |
| b9c3fca | Nick Papior | 22 March 2024, 06:46:57 UTC | Merge pull request #722 from tfrederiksen/orca-hfi Add `read_gtensor` and `read_hyperfine_coupling` to `txtSileORCA` | 22 March 2024, 06:46:57 UTC |
| b7ea782 | Nick Papior | 22 March 2024, 06:36:27 UTC | adding spaces for clarity and only return list Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 06:46:36 UTC |
| 8036e53 | Thomas Frederiksen | 21 March 2024, 14:48:25 UTC | added read_gtensor and read_hyperfine_coupling to txtSileORCA | 22 March 2024, 06:46:34 UTC |
| 809633b | Nick Papior | 22 March 2024, 06:45:19 UTC | Merge pull request #725 from tfrederiksen/units Additional energy units | 22 March 2024, 06:45:19 UTC |
| bb5adca | Nick Papior | 22 March 2024, 06:44:55 UTC | added cm^-1 for future, added xfail for class Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 March 2024, 06:44:55 UTC |
| a04a6ff | Thomas Frederiksen | 21 March 2024, 23:34:55 UTC | additional energy units | 21 March 2024, 23:34:55 UTC |
| aeb6084 | Nick Papior | 21 March 2024, 14:11:58 UTC | enabled ipr data fetching in eigenstate stuff Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 14:11:58 UTC |
| d93919a | Nils Wittemeier | 21 March 2024, 13:13:16 UTC | add test for reading Hamiltonian from wannier90 output (#723) * add test for reading Hamiltonian from wannier90 output Signed-off-by: Nick Papior <nickpapior@gmail.com> --------- Signed-off-by: Nick Papior <nickpapior@gmail.com> Co-authored-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 13:13:16 UTC |
| 29aba13 | Nick Papior | 21 March 2024, 13:12:20 UTC | added more notes to eigsh Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 13:12:20 UTC |
| 53aaa64 | Nick Papior | 21 March 2024, 12:45:40 UTC | doc: fixed links to external resources We now have proper links to scipy.sparse.linalg.eigsh etc. Also added some typing. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 12:45:40 UTC |
| 518d492 | Nils Wittemeier | 21 March 2024, 11:59:02 UTC | Remove 'run' argument from pytest.xfail calls | 21 March 2024, 12:19:12 UTC |
| db35e31 | Nick Papior | 21 March 2024, 11:42:34 UTC | added link to orbitals section Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 11:42:34 UTC |
| 483c2bd | Nick Papior | 21 March 2024, 11:22:28 UTC | bug: fixed isinstance call Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 11:22:28 UTC |
| 0079f28 | Nick Papior | 21 March 2024, 11:21:28 UTC | fixed documentation stuff, links to ipynb and also split orbitals into a separate heading. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 11:21:28 UTC |
| 4c8eb7a | Nick Papior | 21 March 2024, 09:25:09 UTC | fixed thumbnails in more showcase plots Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 09:25:09 UTC |
| 4641145 | Nick Papior | 21 March 2024, 08:45:56 UTC | bug fix for f31669a5b Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 March 2024, 08:45:56 UTC |
| e8da022 | Nick Papior | 20 March 2024, 20:26:19 UTC | created an xfail test that is to be fixed Also ensured correct module path for SuperCell and LatticeChild. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 20:26:19 UTC |
| f31669a | Nick Papior | 20 March 2024, 19:53:16 UTC | moved apply into a functional form Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 19:53:16 UTC |
| f50bd7e | Nick Papior | 20 March 2024, 13:13:20 UTC | added hidden classes to the API (for completeness) This is necessary for the end-user to see the sources. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 13:13:20 UTC |
| 23fab98 | Nick Papior | 20 March 2024, 13:03:14 UTC | typing: removed Optional for AtomsArgument Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 13:03:14 UTC |
| 5fb3c43 | Nick Papior | 20 March 2024, 10:47:50 UTC | enabled bool in sanitize_* Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 10:47:50 UTC |
| 851f60f | Nick Papior | 20 March 2024, 10:19:09 UTC | updated the contributing document Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 10:19:09 UTC |
| 2c6c154 | Nick Papior | 20 March 2024, 09:10:27 UTC | added literal typing for some methods Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 09:10:27 UTC |
| 1b3855d | Nick Papior | 20 March 2024, 08:14:35 UTC | preparing for numpy 2.0.0 Used ruff check src --select NPY201 and resolved them Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 08:14:35 UTC |
| f6195fe | Nick Papior | 20 March 2024, 07:40:04 UTC | Merge branch '719-outcar' | 20 March 2024, 07:40:04 UTC |
| a32a893 | Nick Papior | 20 March 2024, 07:39:31 UTC | fixed documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 March 2024, 07:39:53 UTC |
| 91dfd27 | Thomas Frederiksen | 19 March 2024, 21:50:54 UTC | rename stdoutSileVASP to outcarSileVASP | 20 March 2024, 07:39:49 UTC |
| b00d5e6 | Thomas Frederiksen | 20 March 2024, 07:33:19 UTC | Fix for reading spinful CHG/CHGCAR (#717) bugfix for reading spinful CHG/CHGCAR files added more tests distinguish CHG and CHGCAR by number of data columns | 20 March 2024, 07:33:19 UTC |
| 9aa6228 | Nick Papior | 19 March 2024, 21:24:20 UTC | Merge branch 'ci312' | 19 March 2024, 21:24:20 UTC |
| 92a9c0e | Nick Papior | 19 March 2024, 20:23:44 UTC | fixed dropna how= usage Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 21:14:59 UTC |
| f5b1f0f | Nick Papior | 22 February 2024, 16:32:44 UTC | cleaned wheels creation Added 3.12 moved to fortran-lang/setup-fortran Enabled running on macos-14 (arm64) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 21:14:11 UTC |
| 99879bb | Nick Papior | 19 March 2024, 14:55:14 UTC | changed scale_atoms to scale_basis Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 14:55:14 UTC |
| 64197db | Nick Papior | 19 March 2024, 12:05:38 UTC | added pyx for add_license.bash code Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 12:05:38 UTC |
| e83107b | Nick Papior | 19 March 2024, 11:53:56 UTC | added license clause to all files missing Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 11:53:56 UTC |
| d11dc6a | Nick Papior | 19 March 2024, 10:00:42 UTC | Merge pull request #706 from zerothi/neighbor-test cleaned finder and removed pbc (getting it from Lattice) | 19 March 2024, 10:00:42 UTC |
| 97e3544 | Nick Papior | 19 March 2024, 09:56:06 UTC | fixed formatting of bibtex stuff Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:56:06 UTC |
| 32ec229 | Nick Papior | 19 March 2024, 09:46:02 UTC | removed to be filled Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:46:02 UTC |
| 10260c5 | Nick Papior | 19 March 2024, 09:40:08 UTC | added matplotlib to imports Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:40:08 UTC |
| 345b418 | Nick Papior | 12 March 2024, 19:15:30 UTC | cleaned finder and removed pbc (getting it from Lattice) The neighbor finder got an overhaul to check for PBC and friends. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:35:22 UTC |
| e5f622a | Nick Papior | 19 March 2024, 09:29:31 UTC | Merge pull request #714 from zerothi/675-documentation 675 documentation | 19 March 2024, 09:29:31 UTC |
| a6667eb | Nick Papior | 18 March 2024, 21:08:41 UTC | renamed sisl introduction changed header for publications fixed lists and definition lists created better alignment for noise_power Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:28:42 UTC |
| fcc3656 | Nick Papior | 23 February 2024, 21:47:29 UTC | first step towards a better documentation also cleaned up some details when adding more documentation for the basic things. added more to the first tutorial which are now in an nbgallery restructure of the docs Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:27:57 UTC |
| 0542661 | Nick Papior | 22 February 2024, 16:38:44 UTC | removed epilog, and added sphinx-design Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 March 2024, 09:27:49 UTC |
| 7dfe0ea | Nils Wittemeier | 18 March 2024, 19:22:28 UTC | Optimize nsc after reading Hamiltonian from wann90 output (#697) * Optimize nsc after reading Hamiltonian from wann90 output * reformat * Revert "reformat" This reverts commit d5e6d0bf558c9c88d0eaa66925b5b90405b75e0c. * Revert "Optimize nsc after reading Hamiltonian from wann90 output" This reverts commit be3c50523cfb7a68ff391afc47151ebc94512883. * Re-implement read_hamiltonian for wannier90 output * remove duplicate definition of isc * refactored the seed reading of the Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> * final optimizations Signed-off-by: Nick Papior <nickpapior@gmail.com> * final amendment Signed-off-by: Nick Papior <nickpapior@gmail.com> --------- Signed-off-by: Nick Papior <nickpapior@gmail.com> Co-authored-by: Nick Papior <nickpapior@gmail.com> | 18 March 2024, 19:22:28 UTC |
| 463b53d | dependabot[bot] | 18 March 2024, 13:39:41 UTC | Bump pypa/cibuildwheel from 2.16 to 2.17 (#715) Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.16 to 2.17. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](https://github.com/pypa/cibuildwheel/compare/v2.16...v2.17) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 18 March 2024, 13:39:41 UTC |
| 54e0c14 | Nick Papior | 15 March 2024, 21:39:01 UTC | added no/na to the stdoutSiesta file Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 21:39:01 UTC |
| cd7d2da | Nick Papior | 15 March 2024, 21:19:25 UTC | fixed typos in doc Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 21:19:25 UTC |
| d19a111 | Nick Papior | 15 March 2024, 17:46:25 UTC | fixed typo Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 17:46:25 UTC |
| 6d65989 | Nick Papior | 15 March 2024, 17:38:27 UTC | typos in doc for Geometry Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 17:38:27 UTC |
| 72be186 | Nick Papior | 15 March 2024, 17:35:51 UTC | more typing and clarifications Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 17:35:51 UTC |
| 1bf866e | Nick Papior | 15 March 2024, 11:18:04 UTC | removed txtSileOrca.no/info.no since it was never present (#710) * bumped files to test info.no for txtOrca * ensured orca raises error when not found na/no Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 11:18:04 UTC |
| 296ace4 | Nick Papior | 15 March 2024, 11:02:04 UTC | bug fix, wrong argument Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 11:02:04 UTC |
| b8cd81e | Nick Papior | 15 March 2024, 10:51:37 UTC | reduced number of eigenvalues calculated in eigsh (to 1) This was to ensure that users explicitly request it. Also added lots of typing. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 10:51:37 UTC |
| 8e33ecd | Nick Papior | 15 March 2024, 10:12:57 UTC | Merge pull request #711 from zerothi/709-isosurface-complex added warning for complex grids and isosurface | 15 March 2024, 10:12:57 UTC |
| dedb88f | Nick Papior | 15 March 2024, 10:08:40 UTC | added warning for complex grids and isosurface Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 10:12:24 UTC |
| af0fda3 | Nick Papior | 15 March 2024, 07:55:29 UTC | mnt: changed _read_* to _r_* methods in Siles Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 March 2024, 07:55:29 UTC |
| 13a67c7 | Nick Papior | 14 March 2024, 14:43:50 UTC | enabled Sile attributes to warn/info/raise/ignore Some info.<attribute> may raise problems if they are not available. For instance if the stdout file does not contain the completed signal, then it might signal something went wrong. Now it has some control over this. Fixed lots of tests with catches for pytest.warns. Fixed remaining calls to read_force_constant (changed to read_hessian). When calculating spherical angles, it now checks for non-valid divisions (r / rr with rr == 0). Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 March 2024, 14:43:50 UTC |
| c8e2a6e | Nick Papior | 14 March 2024, 12:36:14 UTC | fixed mark for density matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 March 2024, 12:36:14 UTC |
| d51cba3 | Nick Papior | 14 March 2024, 12:14:38 UTC | added atoms argument to DensityMatrix.spin_align enables aligning subset of atoms to specific directions. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 March 2024, 12:14:38 UTC |
| a8c743c | Nick Papior | 14 March 2024, 12:06:02 UTC | cleaned docs for Geometry.center Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 March 2024, 12:06:02 UTC |
| 51a0825 | Nick Papior | 14 March 2024, 12:05:36 UTC | lots of small updates/fixes Fixed #708, in cases where the argument was a string and wasn't part of the Z-tables, then it saved a str as the Z value. It should *always* be an integer. Anything beyond the periodic table should be considered AtomUnknown/AtomGhost. Removed deprecated set_sc method in LatticeChild (due for 0.14). Fixed parsing HSX files due to it handling the Geometry.atoms wrongly, this was partly due to #708, but also a bug had sneaked in. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 March 2024, 12:05:36 UTC |
| c4550dc | Nick Papior | 13 March 2024, 11:23:23 UTC | cleaned stdout and densitymatrix projection Now projection argument in DensityMatrix.* allows plural s (simpler to use). Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 March 2024, 11:23:23 UTC |
| d2b7455 | Nick Papior | 13 March 2024, 11:21:19 UTC | changed minimizer energy to basis.enthalpy And also cleaned outSileSiesta usage to stdoutSileSiesta. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 March 2024, 11:21:19 UTC |
| 910a8c8 | Nick Papior | 13 March 2024, 08:43:13 UTC | Merge branch 'fc-hessian' | 13 March 2024, 08:43:13 UTC |
