| c7899b2 | Nick Papior | 12 February 2016, 01:14:34 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 01:14:34 UTC |
| 13513ad | Nick Papior | 12 February 2016, 01:13:59 UTC | Added setupegg.py in hopes of correct installation of egg file Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 01:13:59 UTC |
| 7ce8017 | Nick Papior | 12 February 2016, 01:04:29 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 01:04:29 UTC |
| a4186c5 | Nick Papior | 12 February 2016, 01:04:14 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 01:04:14 UTC |
| 1a0cfbe | Nick Papior | 12 February 2016, 01:04:02 UTC | build: Added more compliance regarding the build system - Added a few statements ensuring setuptools loaded for wheel and trying to force numpy before setup. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 01:04:02 UTC |
| a646025 | Nick Papior | 12 February 2016, 00:53:23 UTC | Implemented access and several data members for TBTransSile - Several data objects in the TBTransSile are now accessible from the object directly. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 00:53:23 UTC |
| 56f84ad | Nick Papior | 12 February 2016, 00:52:35 UTC | Enhanced NCSile handling - Enabled "fast" access if the subsequent class implements easy access tables for often used variables in the NCSile. This is convenient for small arrays being used a lot. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 February 2016, 00:52:35 UTC |
| 3b37ca0 | Nick Papior | 05 January 2016, 08:08:45 UTC | enh: enabled geom import statements Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 January 2016, 08:08:45 UTC |
| 3b2fff4 | Nick Papior | 03 January 2016, 17:54:18 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 January 2016, 17:54:18 UTC |
| e1392f8 | Nick Papior | 03 January 2016, 17:54:09 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 January 2016, 17:54:09 UTC |
| 8bfe94d | Nick Papior | 03 January 2016, 17:40:58 UTC | enh: removed reading which does not always work. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 January 2016, 17:40:58 UTC |
| 1d78287 | Nick Papior | 03 January 2016, 17:36:57 UTC | enh: script change for sgeom Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 January 2016, 17:36:57 UTC |
| b88b508 | Nick Papior | 01 January 2016, 23:35:11 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 23:35:11 UTC |
| 0053ce1 | Nick Papior | 01 January 2016, 23:34:46 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 23:34:46 UTC |
| 26d37a0 | Nick Papior | 01 January 2016, 23:34:33 UTC | build: bug Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 23:34:33 UTC |
| 28d9ac7 | Nick Papior | 01 January 2016, 23:33:05 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 23:33:05 UTC |
| 3ded391 | Nick Papior | 01 January 2016, 23:33:05 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 23:33:05 UTC |
| 9f01b1d | Nick Papior | 01 January 2016, 23:32:59 UTC | build: fixes for pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 23:32:59 UTC |
| ceaf84f | Nick Papior | 01 January 2016, 16:42:46 UTC | build: fixed build Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 January 2016, 16:42:46 UTC |
| b88adcc | Nick Papior | 22 December 2015, 08:58:02 UTC | enh: added description for pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 December 2015, 08:58:02 UTC |
| e3fc511 | Nick Papior | 21 December 2015, 21:38:23 UTC | Added manifest for PYPI Signed-off-by: Nick Papior <nickpapior@gmail.com> | 21 December 2015, 21:38:23 UTC |
| b844e16 | Nick Papior | 17 December 2015, 23:12:19 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 December 2015, 23:12:19 UTC |
| 04b4ef0 | Nick Papior | 17 December 2015, 23:12:03 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 December 2015, 23:12:03 UTC |
| 15ae1fa | Nick Papior | 17 December 2015, 23:11:57 UTC | bug: fixed possibly missing overlap elements (sp2tb) - When creating a TightBinding model from a sparsity pattern we forgot to check both H and S, now this is enforced to ensure that all elements are there. - Small bug, when printing a warning message, has been corrected. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 December 2015, 23:11:57 UTC |
| 8231d97 | Nick Papior | 17 December 2015, 17:38:40 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 December 2015, 17:38:40 UTC |
| e5cb3ec | Nick Papior | 17 December 2015, 17:38:29 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 December 2015, 17:38:29 UTC |
| 13f8e66 | Nick Papior | 17 December 2015, 17:24:26 UTC | build: preparing for pypi release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 December 2015, 17:37:53 UTC |
| 42d1cda | Nick Papior | 12 December 2015, 11:49:22 UTC | enh: Enabled wrap-arounds for remove/sub - When removing atoms a wrap-around for negative numbers are useful. This is now enabled. Also larger quantities are wrapped to the unit-cell. - Added tests to check this. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 12 December 2015, 11:49:22 UTC |
| ff3672c | Nick Papior | 08 December 2015, 09:37:21 UTC | bug: bugfixes when rotating structure (non-copy) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 08 December 2015, 09:37:21 UTC |
| de61120 | Nick Papior | 07 December 2015, 21:41:25 UTC | doc: update Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 21:41:25 UTC |
| d7066ee | Nick Papior | 07 December 2015, 20:46:09 UTC | doc: update Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 20:46:09 UTC |
| 6de527f | Nick Papior | 07 December 2015, 20:16:32 UTC | doc: updated Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 20:16:32 UTC |
| 40d1d35 | Nick Papior | 07 December 2015, 19:45:44 UTC | doc: small update Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 19:45:44 UTC |
| cfed310 | Nick Papior | 07 December 2015, 19:11:07 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 19:11:07 UTC |
| 8d822ac | Nick Papior | 07 December 2015, 19:11:07 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 19:11:07 UTC |
| 3614d99 | Nick Papior | 07 December 2015, 19:10:21 UTC | doc: Updated documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 19:10:21 UTC |
| 73fc5e8 | Nick Papior | 07 December 2015, 14:50:38 UTC | enh: faster GULP read, faster IO Sile - Changed the way the step_to and step_either reads lines. Now the checks for case and lists are done at a higher level reducing the checks considerably for large files. - Enhanced throughput for GULP TB models. The enhancement is due to only setting the elements on a per row basis, instead of element wise. This means that the lil_matrix only gets updated once per row, no times, instead of noXno times with alot of zeroes. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 07 December 2015, 14:50:38 UTC |
| bbccc85 | Nick Papior | 06 December 2015, 19:51:55 UTC | bug: fixed usage of _cmp_args from NCSile Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 December 2015, 19:51:55 UTC |
| bf7dd50 | Nick Papior | 04 December 2015, 11:25:22 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 December 2015, 11:25:22 UTC |
| 575399d | Nick Papior | 04 December 2015, 11:25:22 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 December 2015, 11:25:22 UTC |
| beef56c | Nick Papior | 04 December 2015, 11:23:27 UTC | bug: fixed non-found element in step_either Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 December 2015, 11:23:27 UTC |
| e4ff099 | Nick Papior | 04 December 2015, 10:16:17 UTC | build: enhanced the build travis job for different settings Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 December 2015, 10:16:17 UTC |
| 6dace89 | Nick Papior | 03 December 2015, 14:55:21 UTC | bug: Fixed, setup should be called before creating mode Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 December 2015, 14:55:21 UTC |
| 4773420 | Nick Papior | 03 December 2015, 14:49:10 UTC | bug: Fixed Mutable constants in class methods - The Mutable constants are now created via a setup script. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 December 2015, 14:49:10 UTC |
| c0a7ccd | Nick Papior | 03 December 2015, 10:36:22 UTC | doc: Added link to API documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 December 2015, 10:36:22 UTC |
| ad2aa88 | Nick Papior | 02 December 2015, 23:47:55 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 December 2015, 23:47:55 UTC |
| c6796d2 | Nick Papior | 02 December 2015, 23:47:55 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 December 2015, 23:47:55 UTC |
| 22c7348 | Nick Papior | 02 December 2015, 23:38:20 UTC | doc: Updated documentation of atom.py Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 December 2015, 23:38:20 UTC |
| 406bffc | Nick Papior | 02 December 2015, 18:27:21 UTC | enh: removed wiki from the repo Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 December 2015, 18:27:21 UTC |
| 825cc32 | Nick Papior | 01 December 2015, 15:40:22 UTC | enh: tag.sh now prints out the current sids version. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 December 2015, 15:40:22 UTC |
| 6ea4aae | Nick Papior | 01 December 2015, 15:39:51 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 December 2015, 15:39:51 UTC |
| 10752ec | Nick Papior | 01 December 2015, 15:39:51 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 December 2015, 15:39:51 UTC |
| 993a9db | Nick Papior | 01 December 2015, 15:38:30 UTC | enh: Enabled full control of GULP reading - The gulp output has several different ways of writing the information. Hence we now allow the user full control via setting lookup keys. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 December 2015, 15:38:30 UTC |
| 71b7636 | Nick Papior | 29 November 2015, 11:59:12 UTC | enh: enabled pickling Atom,SuperCell,Geometry - Also enabled __eq__ and __ne__ for comparisons Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 November 2015, 11:59:12 UTC |
| 24a4157 | Nick Papior | 29 November 2015, 09:50:23 UTC | Revert "enh: Implemented siesta grid scaling for correct units" This reverts commit 747c2d8e99b521f167bbbdbfdf25a23a6ef95808. | 29 November 2015, 09:50:23 UTC |
| 747c2d8 | Nick Papior | 24 November 2015, 20:11:55 UTC | enh: Implemented siesta grid scaling for correct units - The grids are now scaled with the volume and the units Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 November 2015, 20:11:55 UTC |
| 3eb59c5 | Nick Papior | 18 November 2015, 17:18:08 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 November 2015, 17:18:08 UTC |
| cf6e943 | Nick Papior | 18 November 2015, 17:18:08 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 November 2015, 17:18:08 UTC |
| d9854e1 | Nick Papior | 18 November 2015, 17:14:59 UTC | enh: Added TightBinding no field, converted Error to Warning - The TightBinding.no was grabbed from the geometry, however, in the unlikely event that a user changes the geometry without calling reset then that value is wrong. We now error out when calling finalize if the two does not equal. - An error when cutting a TightBinding model failed due to geometry failing has been changed to a warning. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 November 2015, 17:14:59 UTC |
| db36688 | Nick Papior | 17 November 2015, 12:27:16 UTC | doc: Added six dependency on documentation. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 November 2015, 12:27:16 UTC |
| ad20f4a | Nick Papior | 16 November 2015, 08:43:18 UTC | Taking average is faster Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 November 2015, 08:43:18 UTC |
| 5fa2cd2 | Nick Papior | 16 November 2015, 08:33:58 UTC | enh: faster dcell calculation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 November 2015, 08:33:58 UTC |
| 1caa12f | Nick Papior | 15 November 2015, 22:06:03 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 November 2015, 22:06:03 UTC |
| 78cf661 | Nick Papior | 15 November 2015, 22:06:02 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 November 2015, 22:06:02 UTC |
| 4e01e5f | Nick Papior | 15 November 2015, 12:44:57 UTC | bug: fixed grid operations with non-grid operand Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 November 2015, 12:44:57 UTC |
| 8ded1df | Nick Papior | 15 November 2015, 09:19:47 UTC | bug: fixed type of rotation vector Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 November 2015, 09:19:47 UTC |
| 7fbcb7d | Nick Papior | 15 November 2015, 00:38:48 UTC | fix: build fix for passing lists Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 November 2015, 00:38:48 UTC |
| 6c46990 | Nick Papior | 14 November 2015, 22:42:10 UTC | bug: ensured normalization of rotation vector Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 November 2015, 22:42:10 UTC |
| d97bcd9 | Nick Papior | 06 November 2015, 12:35:00 UTC | bug: For TB with one atom we should do linear creation (construct) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 06 November 2015, 12:35:00 UTC |
| d7b3726 | Nick Papior | 05 November 2015, 18:27:14 UTC | travis Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 November 2015, 18:27:14 UTC |
| 42a5a22 | Nick Papior | 05 November 2015, 18:24:21 UTC | fixed nose requirement in travis test. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 November 2015, 18:24:21 UTC |
| e0fa6e0 | Nick Papior | 05 November 2015, 18:18:40 UTC | try travis Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 November 2015, 18:18:40 UTC |
| 17a19d6 | Nick Papior | 05 November 2015, 18:09:25 UTC | enh: added construct for creating simple tight-binding setups - you simply pass down the radii and the parameters for the radii and it will create the tight-binding model. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 November 2015, 18:09:25 UTC |
| 2e6bfec | Nick Papior | 30 October 2015, 10:39:40 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 October 2015, 10:39:40 UTC |
| 401e77c | Nick Papior | 30 October 2015, 10:39:40 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 October 2015, 10:39:40 UTC |
| 16e3a00 | Nick Papior | 30 October 2015, 10:39:30 UTC | bug: sparse matrix requires tuple, not list Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 October 2015, 10:39:30 UTC |
| 055ced6 | Nick Papior | 30 October 2015, 10:34:09 UTC | enh: enabled fractional coordinates in fdf - The fractional keyword is not accepted in fdf files. You are still limited to writing files in Ang format - Unrolled loops when correcting the Newton laws for the phonon-tightbinding model. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 October 2015, 10:34:09 UTC |
| b01ae00 | Nick Papior | 29 October 2015, 15:02:06 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 October 2015, 15:02:06 UTC |
| 342aaee | Nick Papior | 29 October 2015, 15:02:06 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 October 2015, 15:02:06 UTC |
| 11b9f5a | Nick Papior | 29 October 2015, 14:57:00 UTC | bug: Fixed gulp reading - The cell was erroneously referenced Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 October 2015, 14:57:00 UTC |
| a72f1e8 | Nick Papior | 23 October 2015, 19:35:35 UTC | enh: Allowed passing down arguments for SileIO - When saving information using siles directly from objects it is now possible to pass down arguments to the underlying routines. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 October 2015, 19:35:35 UTC |
| 43815b8 | Nick Papior | 20 October 2015, 22:14:56 UTC | enh: Enabled ASE interface - ASE interface can be passed to the sids.Geometry to return sids geometry. TODO enable the reverse operation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 October 2015, 22:14:56 UTC |
| 7973f95 | Nick Papior | 16 October 2015, 11:50:28 UTC | pushed wiki id | 16 October 2015, 11:50:28 UTC |
| a24de64 | Nick Papior | 16 October 2015, 11:37:29 UTC | doc: Updated doc to denote bigdft support | 16 October 2015, 11:37:29 UTC |
| a7ebced | Nick Papior | 16 October 2015, 11:32:02 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 October 2015, 11:32:02 UTC |
| 07667d1 | Nick Papior | 16 October 2015, 11:32:02 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 October 2015, 11:32:02 UTC |
| 80dfaa2 | Nick Papior | 16 October 2015, 11:31:58 UTC | build: Enhanced setup.py to construct a version tag - sids.__version__ now exists sids.__major/minor/micro__ also exists. - If non released the version will have the git-rev tag attached. - Updated tag.sh to also update release tag. This means that any release is processed as two commits. One with the actual release, and one fake to re-create the ISRELEASED = False variable. - Added keyword for bigdft ascii file, not important. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 October 2015, 11:31:58 UTC |
| 4d58658 | Nick Papior | 16 October 2015, 11:31:21 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 October 2015, 11:31:21 UTC |
| 185d016 | Nick Papior | 16 October 2015, 09:41:10 UTC | enh: Added BigDFT ASCII format for geometry - Enabled reading the ASCII format for BigDFT - Bugfix for Bohr coordinates in FDF files. - Added explicit mention of the units of the angles in the `tocell` function of supercell. - Added tests for the bigdft ascii format. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 16 October 2015, 09:41:10 UTC |
| 47cf4b6 | Nick Papior | 13 October 2015, 14:17:24 UTC | Prepping for release | 13 October 2015, 14:17:24 UTC |
| 2c63457 | Nick Papior | 13 October 2015, 14:17:18 UTC | bug: Fixed test to reflect recent changes Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 October 2015, 14:17:18 UTC |
| f36c523 | Nick Papior | 13 October 2015, 14:09:06 UTC | Prepping for release | 13 October 2015, 14:09:06 UTC |
| 8432b08 | Nick Papior | 13 October 2015, 14:09:01 UTC | enh: Created short-hands for rotate - Routines for rotating along certain cell vectors have been enabled through: rotate[a-c] which rotates around the lattice vector [a-c]. - Enabled the reduction of rotation axes when rotating a cell. Doing SuperCell.rotate(only='a') will only rotate the first cell vector. This is handy when certain directions needs fixed This is also enabled in the geometry rotation where abc is defaulting to rotaing the entire cell. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 October 2015, 14:09:01 UTC |
| c4d1924 | Nick Papior | 13 October 2015, 11:43:25 UTC | Prepping for release | 13 October 2015, 11:43:25 UTC |
| f47b2e9 | Nick Papior | 13 October 2015, 11:43:19 UTC | Merged Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 October 2015, 11:43:19 UTC |
| 39bbedc | Nick Papior | 13 October 2015, 11:42:36 UTC | Prepping for release | 13 October 2015, 11:42:36 UTC |
| 3462f8f | Nick Papior | 13 October 2015, 11:42:17 UTC | Reduced nsc when at least doubling the cell size - Added representation of SuperCell object. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 13 October 2015, 11:42:17 UTC |
| b617917 | Nick Papior | 09 October 2015, 13:07:35 UTC | Prepping for release | 09 October 2015, 13:07:35 UTC |
| 5a1a2a9 | Nick Papior | 09 October 2015, 13:07:33 UTC | enh: Allowed grid-reduce/grid-part - Added -grid-remove as option for the sgrid to remove parts of the grid. Note that grid-remove is exactly opposite to grid-part - Cleanup in data structures of the quanternion. | 09 October 2015, 13:07:33 UTC |
| eebadff | Nick Papior | 09 October 2015, 08:03:49 UTC | Prepping for release | 09 October 2015, 08:03:49 UTC |
