https://github.com/zerothi/sisl

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Revision Author Date Message Commit Date
8663bdd sisl release: 0.9.5 Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 November 2018, 20:03:35 UTC
305080f doc: fixed minor things in the documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 November 2018, 19:44:28 UTC
c91c8d8 enh: enabled spin-argument in self-energy routines Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 November 2018, 18:26:04 UTC
dc38986 bug: fixed defusedxml usage in 3.7 (bug in defusedxml) Thanks to Nils Wittemeier and Zeila Zanolli for finding the bug. Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 November 2018, 10:42:21 UTC
d2f712a enh: changed k_axis to k_axes to clarify multiple axes Also updated documentation for the RSE Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 November 2018, 09:24:35 UTC
c3069f8 test: added 3 more tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 November 2018, 21:03:51 UTC
08f7c76 enh: enabled 3D expansions for real-spaceSE Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 November 2018, 20:46:14 UTC
98d538d bug: fixed eigenstate retrieval for the projection output Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 November 2018, 12:13:04 UTC
60a35a7 enh: added printing out the moleculs and the projections Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 November 2018, 11:39:47 UTC
f952a03 enh: added density_matrix, COOP, COHP for projected TBT Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 November 2018, 20:11:07 UTC
bc3e9c2 maint: removed deprecated class and fixed lots of XPASS faults Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 November 2018, 16:47:06 UTC
3c4bc05 test: added test for TBT.Proj Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 November 2018, 12:39:51 UTC
ca3237a bug: fixed many minor details related to the sdata command and TBT.Proj Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 November 2018, 12:23:39 UTC
63b7016 maint: small help change Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 November 2018, 22:24:51 UTC
855c116 enh: almost finished the TBT.Proj implementation Now the tbtprojnc sile implements: - transmission retrieval - transmission eigenvalue retrieval - spectral DOS retrieval - Argument parser which re-uses the tbtncSileTBtrans This means that sdata may be used to extract information! Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 November 2018, 22:23:33 UTC
eb604ac bug: fixed eta value Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 November 2018, 15:56:42 UTC
6f0ecf5 maint: ensured phonon methods are removed (in pht*ncSileTBtrans Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 November 2018, 15:51:40 UTC
54d2148 maint: trying to fix documentation for PHT Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 November 2018, 15:04:01 UTC
5bb5fc2 enh: added projection output files to docs and info Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 November 2018, 12:50:09 UTC
e654da2 enh: performance increase for pyamg insertion The BC setup for the sparse matrices is still horribly slow, but for now it should be fine. Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 November 2018, 10:06:14 UTC
a4cec41 bug: fixed fdf-reading of grid files Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 November 2018, 13:52:06 UTC
08cc991 doc: updated objects.inv links, intersphinx Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 November 2018, 11:15:21 UTC
b5b1f5e doc: another try at fixing links Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 November 2018, 11:08:17 UTC
82d37df doc: added more documentation (testing Bloch matrix stuff Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 November 2018, 10:55:01 UTC
650055c maint: updated XML like printing of objects Now Geometry also prints SuperCell, and Grid also does the same Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 November 2018, 09:56:00 UTC
bfba4ce bug: fixed geometry origo Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 17:59:13 UTC
6cee4ec maint: silence error when passed coefficients *is* 1D Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 13:49:37 UTC
3cdf917 bug: fixed plotting wavefunction in skewed cells Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 13:47:02 UTC
243ee85 doc: added more documentation for wavefunction Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 12:53:38 UTC
f03f8dd doc: added explanations for some states Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 12:42:47 UTC
ca43a81 maint: added same bug for density, however still untested Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 10:34:12 UTC
76b0629 bug: finally fixed wavefunction for arbitrary positions of SuperCell Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 November 2018, 10:32:00 UTC
956cd79 bug: small fix (but still a problem) for wavefunctions Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 November 2018, 20:53:25 UTC
d8ef8ca enh: added area calculation of lattice vectors Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 November 2018, 14:30:44 UTC
139a51a maint: cleaned str printing of states Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 November 2018, 08:57:48 UTC
8714922 doc: added remark on siesta grid files Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 November 2018, 08:45:44 UTC
060a6b8 test: added tests for NamedIndex Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 November 2018, 08:13:20 UTC
521539b maint: conversion of few zeros/ones to full Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 November 2018, 21:37:42 UTC
6cd6ea6 maint: moved import statement to where it is used Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 November 2018, 13:31:08 UTC
0f874f2 maint: added warning for PDOS reads without E_F Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 November 2018, 10:39:25 UTC
f057a08 maint: changed default eta values to 1e-4 Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 November 2018, 08:56:21 UTC
e55f1dd doc: added installation of development version using pip Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 November 2018, 13:49:59 UTC
07eb95e doc: added another citation Signed-off-by: Nick Papior <nickpapior@gmail.com> 31 October 2018, 20:48:02 UTC
f465d85 enh: added W90 tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 31 October 2018, 19:20:41 UTC
6ddc8b8 bug: fixed W90 reads and added tests for reading geometry Signed-off-by: Nick Papior <nickpapior@gmail.com> 31 October 2018, 19:01:02 UTC
68e4458 bug: fixed table-IO and 1D data write/read Signed-off-by: Nick Papior <nickpapior@gmail.com> 31 October 2018, 08:33:00 UTC
e2faa7a bug: fixed table writes of 1D arrays Signed-off-by: Nick Papior <nickpapior@gmail.com> 29 October 2018, 19:54:06 UTC
2f5c72a maint: forced the use of Cython 0.29 When using Py3.7 we need a more recent version of Cython. Now everything has been recreated using Cython 0.29. Hence 0.9.4 will not work for Py3.7. Signed-off-by: Nick Papior <nickpapior@gmail.com> 29 October 2018, 12:39:45 UTC
05216fe doc: fixed documentation of GF Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 October 2018, 20:05:01 UTC
e5a8ffe enh: enabled Geometries to correct for displaced atoms This should allow geometries which are initially displaced to be aligned when appending/prepending. Simply pass align='min' to align the minimum of self. Fixes #86 Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 October 2018, 19:43:13 UTC
4eb889c enh: enabled TSGF with spin-polarized calculations, fixed #88 Now TSGF/TBTGF files enable writing/reading spin-polarized files. Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 October 2018, 18:28:42 UTC
c9b3bda bug: fixed reading TSGF files Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 October 2018, 18:18:34 UTC
e720dce build: fixed year in git revisions Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 October 2018, 07:39:27 UTC
238ffcb enh: performance increase for bloch-expansions along one dimension Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 October 2018, 07:29:28 UTC
03208df bug: fixed energy-density matrix reading from TSDE file Now the EDM is correctly shifted according to the Fermi-level Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 October 2018, 08:24:07 UTC
3917642 enh: added reading overlap matrix from the fdf Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 October 2018, 09:07:51 UTC
53faeea dist: added year to citation (and setup.py) Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 October 2018, 07:20:21 UTC
4457c38 maint: moved siesta/src to siesta/_src Signed-off-by: Nick Papior <nickpapior@gmail.com> 22 October 2018, 17:55:28 UTC
4a57eee maint: no code-changes, simply re-ordered _bloch.pyx Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 October 2018, 20:13:09 UTC
1fd17e9 maint: streamlining the memoryview Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 October 2018, 18:21:24 UTC
63fe545 test: added test for both dtypes Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 October 2018, 12:32:37 UTC
3055e00 maint: small change in bloch-pyx Signed-off-by: Nick Papior <nickpapior@gmail.com> 21 October 2018, 12:24:23 UTC
563aa76 enh: moved Bloch expansion to Cython This means at least a factor 2. However, I am a bit puzzled why not more? Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 October 2018, 19:38:21 UTC
7498388 maint: changed unit-specification TBT-output when electrode is part of name Signed-off-by: Nick Papior <nickpapior@gmail.com> 19 October 2018, 09:49:38 UTC
a0882dd maint: RSSE updates Calculating real-space SE is now a bit faster because of sign removals Also, I have added two tests which checks that the real-space G/SE is equivalent in the folded (unfolded in RSE) and full unfolded (no unfold in RSE) cases. Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2018, 12:41:01 UTC
9716fd7 maint: small performance increase for RSSE for very large systems Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2018, 10:12:46 UTC
9f4f9b4 maint: eased write_header in TSGF Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2018, 09:47:50 UTC
decf913 bug: wrong variable name usage Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2018, 09:14:58 UTC
56a3446 bug: fixed RealSpaceSE for coupling matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2018, 09:13:17 UTC
c0199fa maint: toSparseAtom now returns a matrix with 0s Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2018, 06:20:01 UTC
98a8fbc maint: small clean-up of minor details, and also added branch test Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 October 2018, 07:58:34 UTC
9f81805 Merge pull request #84 from tfrederiksen/master Zak phase from closed-loop integration 16 October 2018, 07:50:56 UTC
2773ac9 tests: namespace fix for Zak phase test 16 October 2018, 07:13:45 UTC
f8a73ff enh: updates according to review comments for Zak phase 16 October 2018, 07:07:38 UTC
0926ec7 enh: calculation of Zak phase as option to electron.berry_phase(..., method='zak') 16 October 2018, 06:42:57 UTC
172bbd0 maint: updated changelog Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 October 2018, 18:32:00 UTC
f2a7647 maint: removed several superfluous calls to _elec in tbt Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 October 2018, 13:10:14 UTC
34226f0 enh: final changes to the inner product and berry-phase Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 October 2018, 12:10:24 UTC
8ac4232 enh: added sufficient inner/outer products for states The State objects now correctly implements inner/outer products which may be used with other State objects. This required some changes: - .outer/.inner does not accept indices, for this one should do .sub(idx).outer/.inner - When the outer/inner products are performed we now rotate the states to be aligned (as much as possible) This will typically change signs of the resulting matrices, but otherwise not do anything - Added notes that inner/outer does not work correctly for non-orthogonal basis-sets. - Added calculation of phases (for all states-sites or just maximum) Fixed a dtype in RealSpaceSE. Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 October 2018, 11:26:17 UTC
f5a13ab enh: removed optional argument _gauge and cleaned some things from #82 Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2018, 09:32:49 UTC
5947241 Merge pull request #82 from tfrederiksen/master Introduced option for berry_phase(...) to not close the integration contour 11 October 2018, 09:24:14 UTC
d87b43a maint: interchanged determinant and product in description 10 October 2018, 10:09:31 UTC
9d5c497 enh: made closing of loop optional, e.g., to compute the Zak phase 10 October 2018, 10:07:54 UTC
8218112 test: fixed test for self-energy Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 October 2018, 08:36:24 UTC
19f2d77 maint: added dtype to RealSpaceSE and tests Added tests for checking dtype returns of the real-space SE method. Also updated documentation here and there. Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 October 2018, 08:18:29 UTC
83edbf9 maint: fixed real_space_coupling and documentation for TSGF Signed-off-by: Nick Papior <nickpapior@gmail.com> 07 October 2018, 12:18:30 UTC
e95d847 bug: removed matplotlib dependency Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2018, 19:38:59 UTC
9ac47cb test: fixed test Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2018, 19:10:36 UTC
23380ac test: added trs=false for one of the RSE Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2018, 18:58:05 UTC
c850dbb test: added test for undfolded real-space Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2018, 18:51:24 UTC
5f3ce67 enh: added real-space self-energy calculation The real-space self-energy will be used to calculate the self-energy for a given system. Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2018, 18:47:36 UTC
dfb296e maint: cleaned the Bloch class and made a small performance increase for linalg.* Currently removed Bloch expansion using repetitions, only tiling is allowed. Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2018, 17:42:46 UTC
4a0c034 travis: reverted git-lfs Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 October 2018, 11:05:57 UTC
582dfc4 enh: performance increase for BZ without wrap functions Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 October 2018, 10:36:14 UTC
685982e bug: fixed reading TSHS with fdf and passed geometries Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 October 2018, 13:04:34 UTC
5fc11b1 travis: reverted submodule update Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 October 2018, 09:31:05 UTC
23cf801 travis: try LFS 2nd Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 October 2018, 08:49:19 UTC
1285af8 travis: added caching for LFS Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 October 2018, 07:29:12 UTC
2ab0d6f maint: changed uniq to unique Signed-off-by: Nick Papior <nickpapior@gmail.com> 30 September 2018, 05:53:08 UTC
1201739 test: fixed test Signed-off-by: Nick Papior <nickpapior@gmail.com> 29 September 2018, 18:04:47 UTC
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