| 851d78c | Nick Papior | 18 January 2023, 10:43:32 UTC | rel: updating to next release | 18 January 2023, 10:43:32 UTC |
| 3a7d140 | Nick Papior | 18 January 2023, 10:39:25 UTC | ci: removed 311 for macos | 18 January 2023, 10:39:25 UTC |
| 81b411c | Nick Papior | 18 January 2023, 10:15:56 UTC | rel: new release to check workflow | 18 January 2023, 10:15:56 UTC |
| d14618d | Nick Papior | 18 January 2023, 10:14:52 UTC | bug: fixed tabs in workflow | 18 January 2023, 10:14:52 UTC |
| f73eab3 | Nick Papior | 18 January 2023, 10:13:24 UTC | rel: new release to check workflow | 18 January 2023, 10:13:24 UTC |
| c23e26b | Nick Papior | 18 January 2023, 10:11:36 UTC | ci: added 311 on wheel creation | 18 January 2023, 10:11:36 UTC |
| a288bef | Nick Papior | 18 January 2023, 10:03:06 UTC | mnt: preparation for next rel | 18 January 2023, 10:03:06 UTC |
| 5e509f1 | Nick Papior | 18 January 2023, 10:02:27 UTC | bug: ensured head could create proper changelog | 18 January 2023, 10:02:27 UTC |
| 5bed5d6 | Nick Papior | 18 January 2023, 09:36:50 UTC | doc: fixed v0.9.6 changelog | 18 January 2023, 09:36:50 UTC |
| 322196d | Nick Papior | 18 January 2023, 08:17:44 UTC | doc: fixes for sphinx running Fixed changelog.py to replace all tabs to 2 spaces. Trying to add another colon to make references in items work. They all produced errors. | 18 January 2023, 08:17:44 UTC |
| e839be6 | Nick Papior | 17 January 2023, 14:36:04 UTC | mnt: added fdf possibility of reading geometry This applies to tshs file for H and S reads. | 17 January 2023, 14:36:04 UTC |
| 62bfe10 | Nick Papior | 17 January 2023, 14:34:48 UTC | Merge pull request #526 from pfebrer/edm_bug bug: reading the EDM from fdf did not read geometry automatically | 17 January 2023, 14:34:48 UTC |
| 944b2e6 | Pol Febrer | 17 January 2023, 14:31:23 UTC | bug: reading the EDM from fdf did not read geometry automatically | 17 January 2023, 14:31:23 UTC |
| 2d961a6 | Nick Papior | 17 January 2023, 11:16:59 UTC | ci: fixed requirements and removed fetch-depth No need to explicitly write fetch-depth in ci actions, that is the default. | 17 January 2023, 11:16:59 UTC |
| 1928efa | Nick Papior | 17 January 2023, 10:56:46 UTC | req: fixed requirements in pyproject and setup.cfg | 17 January 2023, 10:56:46 UTC |
| 6039537 | Nick Papior | 17 January 2023, 10:49:21 UTC | fix: fixed deprecated use in vis showcase | 17 January 2023, 10:49:21 UTC |
| 7a429d3 | Nick Papior | 17 January 2023, 10:35:37 UTC | doc: fixed documentation to use viz Also fixed changes introduced by 7441209a. | 17 January 2023, 10:35:37 UTC |
| 26fdcd7 | Nick Papior | 17 January 2023, 10:25:56 UTC | feat: added Geometry.apply A function was necessary to apply operations on segmented data in such a way to easily change from, say orbital data to atomic data. This could be either mean/sum/diff calculations. This is now enabled via the Geometry.apply function. It will be moved to somewhere more clean in the future. | 17 January 2023, 10:25:56 UTC |
| 49d3e1c | Nick Papior | 17 January 2023, 08:29:38 UTC | ci: workflow fix for documentation | 17 January 2023, 08:29:38 UTC |
| 17bb762 | Nick Papior | 17 January 2023, 08:24:00 UTC | doc: updated link sizes for publications This should make it easier for end-users to press links for the respective articles. | 17 January 2023, 08:24:00 UTC |
| afa5cce | Nick Papior | 16 January 2023, 10:20:42 UTC | doc: added link and copyright notice | 16 January 2023, 10:20:42 UTC |
| b16a6f7 | Nick Papior | 16 January 2023, 08:20:57 UTC | mnt: added suggestions from Pol The tutorial now is cleaner to read. | 16 January 2023, 08:20:57 UTC |
| 71316ef | Nick Papior | 11 January 2023, 09:34:58 UTC | mnt: changed first tutorial to use viz Almost done on that one. | 11 January 2023, 09:34:58 UTC |
| ab05887 | Nick Papior | 09 January 2023, 21:17:40 UTC | mnt: removed all _* definitions in state.py Also updated conftest for new marks. | 09 January 2023, 21:17:40 UTC |
| c3b836c | Nick Papior | 09 January 2023, 19:23:09 UTC | mnt: updated linalg routines to prepare for scipy>1.12 scipy will remove the turbo argument, and change to driver. Also, giving wrong driver argument will cause failures. For instance we cannot default "gvd" argument, since for non-generalized calculations, it will fail. We can only recommend users to do H.eigenstate(driver="evr") for orthogonal basis sets. | 09 January 2023, 19:23:09 UTC |
| 06c6b66 | Nick Papior | 09 January 2023, 18:57:07 UTC | Merge pull request #498 from zerothi/495-deprecation 495 deprecation | 09 January 2023, 18:57:07 UTC |
| 7441209 | Nick Papior | 09 January 2023, 18:55:53 UTC | mnt: removed deprecated test | 09 January 2023, 18:55:53 UTC |
| 1d7ff6e | Nick Papior | 09 January 2023, 11:04:49 UTC | mnt: removed final deprecation notices | 09 January 2023, 13:47:19 UTC |
| 01492f0 | Nick Papior | 09 January 2023, 10:51:06 UTC | mnt: removed velocity and velocity matrix | 09 January 2023, 13:47:19 UTC |
| 87fffad | Nick Papior | 12 October 2022, 11:04:15 UTC | mnt: removed non-used imports | 09 January 2023, 13:47:19 UTC |
| 04723ff | Nick Papior | 12 October 2022, 10:38:28 UTC | mnt: removed Z deprecation of orbital argument | 09 January 2023, 13:47:19 UTC |
| c90d858 | Nick Papior | 05 October 2022, 11:07:33 UTC | mnt: removed deprecated routines This means that uses of bz.DOS will have to be changed to wrap the eigenstate. We should consider whether this needs to be eased, possibly with fixing __getattr__. | 09 January 2023, 13:47:19 UTC |
| fa3d91c | Pol Febrer | 07 January 2023, 21:18:10 UTC | mnt: make viz work with new spin conventions | 09 January 2023, 12:37:54 UTC |
| 764f3f8 | Nick Papior | 09 January 2023, 11:54:11 UTC | mnt: cleaned BZ tests | 09 January 2023, 11:54:11 UTC |
| 4782e61 | Nick Papior | 09 January 2023, 11:25:41 UTC | bug: fixed #524 This was introduced in 384d7e2f86 (I think) | 09 January 2023, 11:25:41 UTC |
| 9f9a5e2 | Nick Papior | 09 January 2023, 09:21:10 UTC | ci: trying to fix basic test ci | 09 January 2023, 09:21:10 UTC |
| 1198ada | Nick Papior | 09 January 2023, 09:14:16 UTC | Merge pull request #516 from zerothi/501-spin-charge mnt: changed index ordering of spin-charge quantities | 09 January 2023, 09:14:16 UTC |
| f823a45 | Nick Papior | 09 January 2023, 09:13:53 UTC | bug: fixed test after rebase | 09 January 2023, 09:13:53 UTC |
| cd28858 | Nick Papior | 07 January 2023, 19:57:32 UTC | bug: fixed shape of nspin=1 for pdosSile | 09 January 2023, 08:57:21 UTC |
| d871083 | Nick Papior | 05 January 2023, 20:37:12 UTC | mnt: trying to fix viz | 09 January 2023, 08:57:21 UTC |
| 27a15e4 | Nick Papior | 05 January 2023, 10:12:51 UTC | mnt: finalized the 501 PR All routines has been reworked and ordered to have the Cartesian directions as the first dimension. This might be a bit weird at first, but the benefit is simpler internal code and a coherence between all routines. Specifically the PDOS was troublesome since it had varying dimensions and for polarized it was up/down, whereas now it is total/z. This will require end-users to accommodate, which is annoying, but needed. Also fixed bug in displacement calculation. | 09 January 2023, 08:57:20 UTC |
| cb12836 | Nick Papior | 22 November 2022, 20:04:02 UTC | mnt: moved last spin dimension to the first index | 09 January 2023, 08:56:33 UTC |
| 8d82dca | Nick Papior | 21 November 2022, 13:02:09 UTC | mnt: changed index ordering of spin-charge quantities Before the resulting charge arrays were not strictly the same order. Now we always have indices such as: states, spin, orbitals which means that spin is not the last index anymore. Furthermore for polarized calculations we will return spin dimension as: total, Sz to make it more compatible with the SOC cases. This will perhaps confuse users in the beginning (those who were used to the old ordering), but in the long run this should be easier to handle since users don't need to put in checks for polarized vs non-colinear calculations. | 09 January 2023, 08:56:31 UTC |
| e6de9af | Nick Papior | 09 January 2023, 08:13:34 UTC | ci: removed coverage upload for reduced tests | 09 January 2023, 08:13:34 UTC |
| 0886011 | Nick Papior | 06 January 2023, 21:18:53 UTC | mnt: changed oplist to enable generators in loops This will reduce memory requirements for COP curves since we do not need to hold all energy-points, only 1 at a time. This change is now used in COP method and is much easier on memory (a factor len(E)). Additionally a tolerance argument to COP has been added to reduce calculations on energy points where the contribution is negligeble. This further improves performance for large systems since there are many states. | 06 January 2023, 21:18:53 UTC |
| 2021d3b | Nick Papior | 06 January 2023, 10:33:37 UTC | Merge branch 'gto-sto-orbs' | 06 January 2023, 10:33:37 UTC |
| b9fc1b1 | Nick Papior | 06 January 2023, 10:33:31 UTC | mnt: moved global funcs to class funcs These funcs were thought to be good for general usage. However, they cannot easily be used if orbitals have m internally defined. To not clutter with lots of if-statements we duplicate the code currently... :( | 06 January 2023, 10:33:31 UTC |
| 384d7e2 | Nick Papior | 05 May 2022, 07:00:43 UTC | enh: added all functionality of the GTO and STO types The GTO and STO are new orbitals that utilize the Gaussian and Slater type orbitals. These rely on a set of coefficients and exponents used to calculate the radial part of the orbitals. | 06 January 2023, 10:23:08 UTC |
| 6c82200 | Nick Papior | 05 January 2023, 13:39:04 UTC | doc: updated documentation and publication list | 05 January 2023, 13:39:04 UTC |
| 80aca09 | Nick Papior | 05 January 2023, 13:22:52 UTC | mnt: major performance boost for COOP curves Now the sparse matrices are much better utilized. The new implementation actually uses sparse matrices, whereas the old expanded the matrices to the full supercell picture, which meant that a large fraction of the orbital space was never used. This is now fixed and for regular systems it is easily a factor 100 faster. For very small systems, it is now much slower, but should be acceptable since COOP curves are primarily interesting for sizes > 400 orbitals. | 05 January 2023, 13:22:52 UTC |
| be19d66 | Nick Papior | 05 January 2023, 11:39:26 UTC | ci: updated all action versions (nodejs problems) | 05 January 2023, 11:39:26 UTC |
| ec239ff | Nick Papior | 05 January 2023, 11:28:06 UTC | ci: trying to update test workflow | 05 January 2023, 11:28:06 UTC |
| 32fca39 | Nick Papior | 05 January 2023, 11:27:04 UTC | ci: trying to update test workflow | 05 January 2023, 11:27:04 UTC |
| 038aa30 | Nick Papior | 05 January 2023, 11:16:40 UTC | bug: fixed ufunc handling for numpy >= 1.24 | 05 January 2023, 11:16:40 UTC |
| 4e198b1 | Nick Papior | 05 January 2023, 10:22:30 UTC | doc: clarified documentation on convert usage (unit) | 05 January 2023, 10:22:30 UTC |
| 116712d | Nick Papior | 06 December 2022, 10:56:05 UTC | Merge pull request #521 from tfrederiksen/io-api Minor fixes for IO-API | 06 December 2022, 10:56:05 UTC |
| 7c46f7c | Thomas Frederiksen | 06 December 2022, 10:49:10 UTC | doc: PHtrans as entry | 06 December 2022, 10:49:10 UTC |
| 48d9149 | Thomas Frederiksen | 06 December 2022, 10:48:54 UTC | doc: remove tbtrans double entry | 06 December 2022, 10:48:54 UTC |
| 5b67913 | Nick Papior | 05 December 2022, 13:13:06 UTC | Merge pull request #520 from tfrederiksen/orca-api ORCA API | 05 December 2022, 13:13:06 UTC |
| 99fc8d6 | Thomas Frederiksen | 05 December 2022, 13:09:20 UTC | doc: added orca api | 05 December 2022, 13:09:20 UTC |
| 4a68e0c | Nick Papior | 02 December 2022, 12:05:53 UTC | doc: extended replace documentation | 02 December 2022, 12:05:53 UTC |
| a07997c | Nick Papior | 29 November 2022, 20:09:18 UTC | mnt: bumped files | 29 November 2022, 20:09:18 UTC |
| eba4dec | Nick Papior | 29 November 2022, 19:56:30 UTC | Merge pull request #519 from juijan/read-basis-fix Fix reading of basis | 29 November 2022, 19:56:30 UTC |
| 9b7d872 | Nick Papior | 29 November 2022, 19:55:24 UTC | mtn: added new test for the next added file It has 2 species | 29 November 2022, 19:55:24 UTC |
| 3108137 | Nils Wittemeier | 29 November 2022, 14:36:52 UTC | Fix reading of basis | 29 November 2022, 14:40:44 UTC |
| db0fc67 | Nick Papior | 22 November 2022, 20:16:33 UTC | mnt: changed E, M order for COP | 22 November 2022, 20:16:33 UTC |
| 014353b | Nick Papior | 22 November 2022, 13:26:10 UTC | mnt: additional codeql configuration | 22 November 2022, 13:26:10 UTC |
| baa6274 | Nick Papior | 21 November 2022, 13:19:26 UTC | bug: fixed build bug for distutils and numpy Numpy officially does not support setuptools >=60, so currently we shouldn't either. We need to move to meson | 21 November 2022, 13:19:26 UTC |
| 51b57c7 | Thomas Frederiksen | 17 November 2022, 16:22:51 UTC | doc: fixed indices in sums (#515) | 17 November 2022, 16:22:51 UTC |
| 724a820 | Thomas Frederiksen | 17 November 2022, 14:27:51 UTC | doc: clarified how a vacuum gap can be avoided (#514) | 17 November 2022, 14:27:51 UTC |
| df234f4 | Nick Papior | 17 November 2022, 13:08:01 UTC | mnt: enabled using str for filenames in merge | 17 November 2022, 13:08:01 UTC |
| 980af87 | Nick Papior | 17 November 2022, 13:04:12 UTC | enh: enabled merging delta siles This will make it easier to merge several files. | 17 November 2022, 13:04:12 UTC |
| ecd42bd | Nick Papior | 15 November 2022, 19:56:35 UTC | bug: fixed #512 due to compiler bug A compiler bug has been found when doing: Gamma .neqv. no_u == no_s I have tried to create a small report: program t integer :: n, m logical :: Gam call wrt() open(238, form="unformatted", status="old") call rd(Gam, n, m) print *, Gam, n == m, Gam .neqv. n == m call rd(Gam, n, m) print *, Gam, n == m, Gam .neqv. n == m call rd(Gam, n, m) print *, Gam, n == m, Gam .neqv. n == m call rd(Gam, n, m) print *, Gam, n == m, Gam .neqv. n == m close(238) contains subroutine wrt() open(238, form="unformatted") write(238) .true. write(238) 14, 352 write(238) .true. write(238) 14, 14 write(238) .false. write(238) 14, 352 write(238) .false. write(238) 14, 14 close(238) end subroutine wrt subroutine rd(Gam, n, m) logical, intent(out) :: Gam integer, intent(out) :: n, m read(238) Gam read(238) n, m end subroutine rd end program t But it still works there... So I guess it has something to do with the way f2py makes changes, or whatever. It is at least a little difficult to debug and I frankly don't think that the GNU gcc will accept a bug-report when it goes through f2py. It would require more digging. | 15 November 2022, 19:56:35 UTC |
| 730155d | Nick Papior | 14 November 2022, 12:19:44 UTC | doc: updated changelog | 14 November 2022, 12:19:44 UTC |
| 9973c46 | pfebrer | 14 November 2022, 12:08:01 UTC | bug: within_inf non periodic had bug for nsc > 1 (#511) | 14 November 2022, 12:08:01 UTC |
| c5f7d5d | Nick Papior | 11 November 2022, 19:32:10 UTC | doc: updated publication list | 11 November 2022, 19:32:10 UTC |
| 36f9f65 | Nick Papior | 11 November 2022, 08:01:05 UTC | rel: bumped rc | 11 November 2022, 08:01:05 UTC |
| ab5ffdc | Nick Papior | 11 November 2022, 07:53:51 UTC | test: fixed orca tests with pytest.approx | 11 November 2022, 07:53:51 UTC |
| 29242f6 | Nick Papior | 11 November 2022, 07:53:43 UTC | mnt: fixed codata Hz unit | 11 November 2022, 07:53:43 UTC |
| 1d5665a | lgtm-com[bot] | 10 November 2022, 15:21:48 UTC | Add CodeQL workflow for GitHub code scanning (#510) Co-authored-by: LGTM Migrator <lgtm-migrator@users.noreply.github.com> | 10 November 2022, 15:21:48 UTC |
| 96f02f7 | Nick Papior | 10 November 2022, 12:14:25 UTC | mnt: rc | 10 November 2022, 12:14:25 UTC |
| 7021eb1 | Nick Papior | 10 November 2022, 11:41:48 UTC | mnt: added codata.py script to parse ascii file | 10 November 2022, 11:41:48 UTC |
| 2a7bede | Nick Papior | 10 November 2022, 11:40:12 UTC | test: bumped files | 10 November 2022, 11:40:12 UTC |
| f6cb734 | Nick Papior | 10 November 2022, 11:39:34 UTC | Merge branch 'codata' | 10 November 2022, 11:39:34 UTC |
| 0032a9c | Nick Papior | 10 November 2022, 11:39:23 UTC | mnt: changed all unit-values to CODATA-2018 values Also did this for the constants. | 10 November 2022, 11:39:23 UTC |
| 17700e2 | Thomas Frederiksen | 10 November 2022, 11:13:46 UTC | Reading output from ORCA (#500) Both property.txt and output files has been added. Multiple methods are available for reading: - energies - orbital energies - charges and geometry information. Tests are also added. | 10 November 2022, 11:13:46 UTC |
| 73f15f4 | Nick Papior | 09 November 2022, 19:46:48 UTC | mnt: added forcefully reopen to out sile for read_* | 09 November 2022, 19:46:48 UTC |
| 31a761e | Nick Papior | 09 November 2022, 11:42:41 UTC | doc: added links to testing | 09 November 2022, 11:42:41 UTC |
| 4036539 | Nick Papior | 09 November 2022, 11:33:16 UTC | doc: fixed indexing for mulliken | 09 November 2022, 11:33:16 UTC |
| 647e000 | Nick Papior | 09 November 2022, 11:28:15 UTC | bug: fixed tuple indexing | 09 November 2022, 11:28:15 UTC |
| ec98e9e | Nick Papior | 08 November 2022, 20:31:59 UTC | test: fixed test after cell2length change | 08 November 2022, 20:31:59 UTC |
| a3bad60 | Thomas Frederiksen | 08 November 2022, 19:39:24 UTC | enh: new keywords in sile.step_to() (#508) | 08 November 2022, 19:39:24 UTC |
| 7914930 | Nick Papior | 08 November 2022, 12:39:59 UTC | mnt: changed cell_length to cell2length This clarifies that it can use cells as convertion. Also enabled sub-set axes to be converted. | 08 November 2022, 12:39:59 UTC |
| b537cb5 | Nick Papior | 07 November 2022, 20:52:00 UTC | mnt: removed deprecation of zeta argument (was Z) | 07 November 2022, 20:52:00 UTC |
| 06d8e63 | pfebrer | 07 November 2022, 13:58:53 UTC | enh: allow reading forces from transiesta in output file (#504) | 07 November 2022, 13:58:53 UTC |
| 76bca48 | pfebrer | 06 November 2022, 14:06:09 UTC | Plotly is incompatible with ipywidgets 8.x (#503) Apparently plotly is incompatible with ipywidgets 8.x and this is making the plots in the docs not display properly. | 06 November 2022, 14:06:09 UTC |
| c7f88bb | Nick Papior | 03 November 2022, 12:04:12 UTC | enh: cleaned a few last things for the HydrogenicOrbital Amended documentation and added pickling possibility. | 03 November 2022, 12:04:12 UTC |
| 9115510 | Thomas Frederiksen | 03 November 2022, 11:56:39 UTC | Easy construction of hydrogenic orbitals (#499) * enh: added HydrogenicOrbital tests: check normalizations test: HydrogenicOrbital.copy() | 03 November 2022, 11:56:39 UTC |
| e168a81 | Nick Papior | 03 November 2022, 11:56:06 UTC | mnt: moved doubly occuring code in AtomicOrbital | 03 November 2022, 11:56:06 UTC |
| 5525009 | Nick Papior | 02 November 2022, 11:49:20 UTC | mnt: added Bohr radius to constants | 02 November 2022, 11:49:20 UTC |
