| 8f2a1a0 | Nick Papior | 24 October 2016, 13:30:14 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 October 2016, 13:30:14 UTC |
| c1ee436 | Nick Papior | 24 October 2016, 08:42:10 UTC | bug: Gamma-only made weights 0, fixed to 1 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 October 2016, 08:42:10 UTC |
| 10936d6 | Nick Papior | 24 October 2016, 06:51:58 UTC | bug: fixed sgeom and the reading of the lattice parameters and geometry The read_sc and read_geom sections in the fdf file should not be forced open, we have to re-read the entire file in case the key isn't found. The sgeom script did take the arguments from the input file (which is not desirable). Instead we now take the inputfile and read the geometry and retain the argumenst from that. tbt.nc fixes: - Fixed k-points in tbtrans for Gamma-only calculations - Change Arng to Orng to reflect that it is an orbital range and not atomic. Reformatted the xyz file to also contain the nsc fields Signed-off-by: Nick Papior <nickpapior@gmail.com> | 24 October 2016, 06:51:58 UTC |
| 6ecf6d4 | Nick Papior | 19 October 2016, 14:15:19 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 October 2016, 14:15:19 UTC |
| 66ad03a | Nick Papior | 19 October 2016, 14:15:11 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 October 2016, 14:15:11 UTC |
| 9e3b9df | Nick Papior | 19 October 2016, 14:12:11 UTC | bug: fixed package creation for the python wheels Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 October 2016, 14:12:11 UTC |
| fc915d3 | Nick Papior | 18 October 2016, 14:29:51 UTC | bug: lots of small bugfixes Vector currents had a bug related to geom.na_u Added representation to BaseSile Fixed vector output in xsf files, now it enables the passing of arguments. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 October 2016, 14:29:51 UTC |
| 823f584 | Nick Papior | 18 October 2016, 09:35:32 UTC | enh: moved the geometry in Hamiltonian to a property Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 October 2016, 09:35:32 UTC |
| 918b704 | Nick Papior | 18 October 2016, 08:01:22 UTC | bug: fixed printing of non-zero elements in Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> | 18 October 2016, 08:01:22 UTC |
| ab5df03 | Nick Papior | 17 October 2016, 14:55:57 UTC | enh: enabled out dependent options for sdata and sgeom. Basically sgeom is now a wrapper for sdata with different standard desription. I am not quite confident that the current way is scalable, however it works and is at the top of the food chain, so I suspect it should be easy to change later on, if needed. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 October 2016, 14:55:57 UTC |
| 98f4ec6 | Nick Papior | 17 October 2016, 08:11:33 UTC | travis: the python 3.4 tests will fail for no reason Signed-off-by: Nick Papior <nickpapior@gmail.com> | 17 October 2016, 08:11:33 UTC |
| 9117a94 | Nick Papior | 14 October 2016, 18:53:15 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 October 2016, 18:53:15 UTC |
| 74d7baa | Nick Papior | 14 October 2016, 18:53:01 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 14 October 2016, 18:53:01 UTC |
| dfdd1d5 | Nick Papior | 10 October 2016, 12:40:14 UTC | bug: fixed previous commit for tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 October 2016, 12:40:14 UTC |
| 9c3dbe1 | Nick Papior | 10 October 2016, 12:22:51 UTC | enh: many features enabled for the tbtrans files, and many fixes Changed the reciprocal cell to include 2 * pi. For newcomers this seems like it is much more intuitive. Updated documentation a couple of places (we need to go through all of it and abide to: Parameters ---------- ia : `list` of `int` Atomic indices all : `bool = False` `False`, return only the first orbital ... Removed the need for opening/closing NetCDF files in the SileCDF. This was redundant as the NetCDF file is not a linear file. The SileCDF also implements a few of shorthands for retrieving values vs. variables. The sisl/io/tbtrans.py has been overhauled. Many new routines for mingling with the orbital currents. Now one may request direct unit-cell -> supercell bond/orbital currents for increased flexibility. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 10 October 2016, 12:22:51 UTC |
| ea35e7d | Nick Papior | 08 October 2016, 15:52:37 UTC | bug: changed isc parameter to None Signed-off-by: Nick Papior <nickpapior@gmail.com> | 08 October 2016, 15:52:37 UTC |
| b6faf07 | Nick Papior | 04 October 2016, 20:06:21 UTC | enh: speeded up Sk() in Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 20:06:21 UTC |
| 5b67ccc | Nick Papior | 04 October 2016, 19:58:31 UTC | bug: fixed things for the Hamiltonian object there where bugs related to passing k for eigenvalue calculations Speeded up access to overlap (moving of variable access) Changed iter_block default to above 1500 atoms Added more Hamiltonian tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 19:58:31 UTC |
| 1bf5ddd | Nick Papior | 04 October 2016, 10:51:43 UTC | test: added tests for argumentparser Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 10:51:43 UTC |
| f75ca65 | Nick Papior | 04 October 2016, 10:41:55 UTC | test: added more tests for the geometry class Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 10:41:55 UTC |
| f84e781 | Nick Papior | 04 October 2016, 10:32:26 UTC | bug: fixed interpolation of grid and index retrieval Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 10:32:26 UTC |
| 6a4178b | Nick Papior | 04 October 2016, 05:57:04 UTC | enh: changed an error in car.py to a warning Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 05:57:04 UTC |
| 6475079 | Nick Papior | 04 October 2016, 05:56:49 UTC | enh: enabled ranges with spacing 1:2:4 like normal ranges This enables very easy partitioning of the atoms if one has specific sub-lattices. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 October 2016, 05:56:49 UTC |
| cc1f167 | Nick Papior | 03 October 2016, 20:10:52 UTC | bug: fixed map function for python 3 Note that map (along many other 3.x functions) return iterables Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 20:10:52 UTC |
| 0fad4f8 | Nick Papior | 03 October 2016, 19:42:16 UTC | bug: fixes 3.x runs (second try) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 19:42:16 UTC |
| 327e2f9 | Nick Papior | 03 October 2016, 19:34:21 UTC | bug: fixes 3.x runs Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 19:34:21 UTC |
| f57c52b | Nick Papior | 03 October 2016, 19:25:48 UTC | bug: fixes for 3.x Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 19:25:48 UTC |
| 03971fd | Nick Papior | 03 October 2016, 19:16:04 UTC | bug: a lot of fixes for read/write geom These bugs where found by adding tests for the read/write routines Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 19:16:04 UTC |
| 62d5003 | Nick Papior | 03 October 2016, 09:49:28 UTC | enh: enabled cutoff for dynamical matrices Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 09:49:28 UTC |
| 9bdf9c8 | Nick Papior | 03 October 2016, 09:11:43 UTC | maint: moved np.diff to diff in sparse Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 09:11:43 UTC |
| 9325f67 | Nick Papior | 03 October 2016, 08:23:14 UTC | enh: enabled force output from data files This makes plotting forces very easy: sgeom <in-geom> --vector force <force-out> -o force.xsf Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 08:23:14 UTC |
| 5d87c77 | Nick Papior | 03 October 2016, 06:31:14 UTC | travis: fixed build matrix Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 06:31:14 UTC |
| 6ecfadb | Nick Papior | 03 October 2016, 06:29:02 UTC | test: added geom tests, fixed coverage Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 06:29:02 UTC |
| e1356af | Nick Papior | 03 October 2016, 06:22:05 UTC | test: added running the ArgumentParser in Geometry Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 06:22:05 UTC |
| cdad2ac | Nick Papior | 03 October 2016, 06:18:07 UTC | tests: added more geometry tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 06:18:07 UTC |
| 668d532 | Nick Papior | 03 October 2016, 06:13:42 UTC | bug: fixed atom Z_label for multiple queries Also added more tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 06:13:42 UTC |
| 06ab53b | Nick Papior | 03 October 2016, 05:57:58 UTC | test: updated tests of atom module Signed-off-by: Nick Papior <nickpapior@gmail.com> | 03 October 2016, 05:57:58 UTC |
| 5797419 | Nick Papior | 01 October 2016, 12:10:54 UTC | enh: removed possibility of changing the default in interface Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 October 2016, 12:10:54 UTC |
| f5883b9 | Nick Papior | 20 September 2016, 18:10:15 UTC | test: added codecoverage badge Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 September 2016, 18:10:15 UTC |
| f0eb288 | Nick Papior | 20 September 2016, 18:06:03 UTC | test: added coverage installation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 September 2016, 18:06:03 UTC |
| 4ae61c3 | Nick Papior | 20 September 2016, 17:38:48 UTC | added with-coverage for nosetests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 September 2016, 17:38:48 UTC |
| c189950 | Nick Papior | 20 September 2016, 17:30:54 UTC | test: added codecoverage Signed-off-by: Nick Papior <nickpapior@gmail.com> | 20 September 2016, 17:30:54 UTC |
| a80b56e | Nick Papior | 02 September 2016, 13:56:49 UTC | enh: updated sile naming schemes Now the default naming scheme is: <ext>Sile<Program> This should make it easier to grasp the sile names. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 September 2016, 13:56:49 UTC |
| 4ac5d51 | Nick Papior | 02 September 2016, 13:36:48 UTC | enh: updated siles Pre-changes of the siles for gulp Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 September 2016, 13:36:48 UTC |
| 6f634a1 | Nick Papior | 02 September 2016, 13:24:53 UTC | enh: speeded up close_sc a little By removing indices where the individual ranges are too far we remove the calculation of the distance for atoms which are clearly too far away. This has some overhead for small systems, but for big systems this is faster (slightly) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 September 2016, 13:24:53 UTC |
| 3d7177f | Nick Papior | 02 September 2016, 08:54:30 UTC | doc: the order of documentation for cut was wrong Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 September 2016, 08:54:30 UTC |
| 5d2f177 | Nick Papior | 31 August 2016, 15:27:14 UTC | bug: many bugfixes, added siesta out file Fixed many small bugs introduced during the past sdata addition. Changed many NotImplemented to NotImplementedError. Created default decorators which enables easy routine creation of parsers for ArgumentParser methods in classes. Pretty much done with tbtrans output netcdf file and data handling. It can do pretty advanced stuff already. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 31 August 2016, 15:27:14 UTC |
| d58b57d | Nick Papior | 25 August 2016, 08:20:04 UTC | enh: added a TabularSile and the Bands for siesta (enables plots) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 25 August 2016, 08:20:04 UTC |
| 40777bf | Nick Papior | 23 August 2016, 14:10:03 UTC | enh: added tests for the ranges functions Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 August 2016, 14:10:03 UTC |
| ee96308 | Nick Papior | 23 August 2016, 14:09:15 UTC | enh: updated fdf-files return quantities with units Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 August 2016, 14:09:15 UTC |
| ec57662 | Nick Papior | 23 August 2016, 14:07:53 UTC | doc: Added XSF notation in the list of files Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 August 2016, 14:07:53 UTC |
| be317ef | Nick Papior | 23 August 2016, 14:07:39 UTC | enh: changed sgrid to use the ArgumentParser method All arguments to sgrid are now grabbed by the Grid.ArgumentParser method. Updated misc routines for ranges. They are now more versatile and produce more consistent results. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 23 August 2016, 14:07:39 UTC |
| 3971243 | Nick Papior | 22 August 2016, 10:11:00 UTC | enh: fixed name specifications on the commandline Now sdata test.fdf --fdf meshcutoff{eV} will print the meshcutoff in eV, no matter the definition in the fdf file. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 August 2016, 10:11:00 UTC |
| 03d27bd | Nick Papior | 22 August 2016, 09:49:19 UTC | test: added xsf tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 August 2016, 09:49:19 UTC |
| 3366ef2 | Nick Papior | 22 August 2016, 09:38:09 UTC | enh: added XSF file format for reading/writing single geometry The XSF (XCrySDen) file format is now supported. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 August 2016, 09:38:09 UTC |
| 70a8042 | Nick Papior | 22 August 2016, 09:17:20 UTC | bug: fixed no arguments to sgeom/sdata - sgeom/sdata Defaulted the argument to --help - Added a units library This should constitute the units used throughout Each program should have their own sub-package which enables an easy extraction of units from different unit-tables. This also shows a limitation in the package directories. Perhaps there should be a sisl.program.* directory with associated sisl.program.siesta.io sisl.program.siesta.units sisl.program.vasp.io sisl.program.vasp.units for a better tree-structure. - Added --info flag for geometries for simplistic information about the geometry. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 22 August 2016, 09:17:20 UTC |
| 70a2f27 | Nick Papior | 19 August 2016, 15:12:57 UTC | enh: added sdata as an initial code Due to the previous enhancement we can collect all command line options into a single command line utility. This is named sdata It creates the command line arguments dependent on the file it is passed. As such it is exactly the same as sgeom for files which only has geometry information (xyz, XV, etc.) Siles which does not have implemented an ArgumentParser will issue a warning about missing implementation. This is on purpose and any change in the corresponding Sile's will result in immediate benefit in the sdata command. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 August 2016, 15:12:57 UTC |
| ce598f1 | Nick Papior | 19 August 2016, 12:32:26 UTC | enh: moved arguments to specific class handlers Moved arguments to be handled by the parenting class that enables the constructs. For instance the entire sgeom script was focused on the Geometry class. Instead of forcing the options and handling in the script (sgeom), we may change the actions to perform the required actions dependent on the input sequence. The constructs are very basic: 1. Each class creates arguments with appropriate actions. 2. Any top-level script or other class may inherit these arguments to create even more complicated constructs and control the arguments without ever complicating the script itself. 3. Outside applications may also "steal" arguments to control the sequence appropriately. This is apparent by looking at the updated sgeom script. Now it is only 20 or so lines of code, _everything_ is handled in the Geometry class. These changes opted for improving and creating consistent interfaces for common algorithms. See e.g. the new directory utils Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 August 2016, 12:32:26 UTC |
| 116c2c6 | Nick Papior | 05 August 2016, 14:19:38 UTC | enh: changed base NCSile to SileCDF for easier recognition. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 August 2016, 14:19:38 UTC |
| 5da3bdd | Nick Papior | 05 August 2016, 07:28:58 UTC | api: changed atoms name for Geometry to atom All places have been updated and the tests go through. This change is consistent with the single-atom-picture Signed-off-by: Nick Papior <nickpapior@gmail.com> | 05 August 2016, 07:28:58 UTC |
| 236ee46 | Nick Papior | 04 August 2016, 17:46:15 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 August 2016, 17:46:15 UTC |
| 12e03ed | Nick Papior | 04 August 2016, 17:46:02 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 August 2016, 17:46:02 UTC |
| 0545b31 | Nick Papior | 04 August 2016, 11:26:23 UTC | doc: added PayPal button Signed-off-by: Nick Papior <nickpapior@gmail.com> | 04 August 2016, 11:26:23 UTC |
| 39833af | Nick Papior | 01 August 2016, 07:14:22 UTC | enh: renamed atoms to atom in Geometry. This makes it non-plural which I think is more conforment to experience. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 August 2016, 07:14:22 UTC |
| fc670a7 | Nick Papior | 01 August 2016, 06:26:49 UTC | enh: added *args and **kwargs for read in SuperCell Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 August 2016, 06:26:49 UTC |
| 208e967 | Nick Papior | 19 July 2016, 12:47:17 UTC | doc: updated readme to reflect Wannier90 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 19 July 2016, 12:47:17 UTC |
| 8c2539a | Nick Papior | 15 July 2016, 09:11:40 UTC | test: added test of W90SeedSile Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2016, 09:11:40 UTC |
| 7b0e63b | Nick Papior | 15 July 2016, 09:09:53 UTC | enh: set cutoff to 0.00001 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2016, 09:09:53 UTC |
| a47bcf4 | Nick Papior | 15 July 2016, 09:08:24 UTC | enh: enabled wannier90 reading of the Hamiltonian - Added seedname for wannier reading. It will automatically defer to _centres.xyz and _hr.dat files which contain the MLWF centres and the Hamiltonian, respectively. - A couple of bugs was solved. - TODO there is still a bug in the extend method which I should really address. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 15 July 2016, 09:08:24 UTC |
| 26dcce5 | Nick Papior | 02 July 2016, 17:23:03 UTC | build: updated build to me up-to-date with dependencies Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 July 2016, 17:23:03 UTC |
| 147ce06 | Nick Papior | 02 July 2016, 11:10:26 UTC | build: update requirements of numpy to 1.7 Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 July 2016, 11:10:26 UTC |
| ca9c62a | Nick Papior | 02 July 2016, 11:00:53 UTC | bug: fixed tag.sh for pypi upload Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 July 2016, 11:00:53 UTC |
| b110dbe | Nick Papior | 02 July 2016, 10:42:12 UTC | enh: updated upload to pypi to twine. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 July 2016, 10:42:12 UTC |
| acca9a4 | Nick Papior | 02 July 2016, 10:32:18 UTC | test: added test for querying sile with sub-class Signed-off-by: Nick Papior <nickpapior@gmail.com> | 02 July 2016, 10:32:18 UTC |
| 08334e0 | Nick Papior | 01 July 2016, 20:17:09 UTC | bug: several bugs occured when adding more tests - changing shapes cannot be done on a per-item level. They are now cast to lists and then used. - Added dtype property of Hamiltonian - Fixed empty for SparseCSR The ncol was erroneously overwritting by an integer - Added several new tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 July 2016, 20:17:09 UTC |
| 72fec2a | Nick Papior | 01 July 2016, 08:22:59 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 July 2016, 08:22:59 UTC |
| 424ea0f | Nick Papior | 01 July 2016, 08:22:54 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 July 2016, 08:22:54 UTC |
| d60dda2 | Nick Papior | 01 July 2016, 08:16:14 UTC | bug: several bugs occured when adding more tests - changing shapes cannot be done on a per-item level. They are now cast to lists and then used. - Added dtype property of Hamiltonian - Fixed empty for SparseCSR The ncol was erroneously overwritting by an integer - Added several new tests Signed-off-by: Nick Papior <nickpapior@gmail.com> | 01 July 2016, 08:16:14 UTC |
| 58a4008 | Nick Papior | 30 June 2016, 09:05:03 UTC | bug: fixed non-orthogonal S_idx in Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 June 2016, 09:05:03 UTC |
| 4767983 | Nick Papior | 30 June 2016, 06:30:19 UTC | enh: added more tests and fixed some minor bugs Signed-off-by: Nick Papior <nickpapior@gmail.com> | 30 June 2016, 06:30:19 UTC |
| 665a4d0 | Nick Papior | 29 June 2016, 08:51:33 UTC | doc: removed last reference to TightBinding Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 June 2016, 08:51:33 UTC |
| 1f86271 | Nick Papior | 29 June 2016, 08:21:13 UTC | bug: fixed wrong function name Signed-off-by: Nick Papior <nickpapior@gmail.com> | 29 June 2016, 08:21:13 UTC |
| 5f8c5f9 | Nick Papior | 28 June 2016, 13:09:10 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 13:09:10 UTC |
| b44d882 | Nick Papior | 28 June 2016, 13:09:08 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 13:09:08 UTC |
| ac47b66 | Nick Papior | 28 June 2016, 12:59:13 UTC | bug: 1fd4a432 was inconsistent in nnz vs. nnzpr Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 12:59:13 UTC |
| e2b70a4 | Nick Papior | 28 June 2016, 12:43:14 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 12:43:14 UTC |
| 6f40cf5 | Nick Papior | 28 June 2016, 12:43:11 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 12:43:11 UTC |
| 2f367b4 | Nick Papior | 28 June 2016, 12:36:22 UTC | bug: fixed slice for hamiltonian in dH.nc Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 12:36:22 UTC |
| 1fd4a43 | Nick Papior | 28 June 2016, 09:36:21 UTC | bug: dtype for Hamiltonian, # of nnz elements using copy - the dtype wasn't correctly used when creating the sparse matrix. - number of sparse elements is now easier to grasp, if nnz is supplied this will take precedence of the nnzpr variable. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 09:36:21 UTC |
| 68570d5 | Nick Papior | 28 June 2016, 09:16:50 UTC | bug: forced the SparseCSR.empty(False) to make un-finalized Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 09:16:50 UTC |
| e6b7b8d | Nick Papior | 28 June 2016, 09:01:03 UTC | bug: fixed erroneous warning in SparseCSR.finalize - The check should be performed after the finalization to not check possible empty values. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 09:01:03 UTC |
| 558cfad | Nick Papior | 28 June 2016, 07:48:57 UTC | doc: constantly updating the doi is error-prone Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 07:48:57 UTC |
| 4be8074 | Nick Papior | 28 June 2016, 07:33:36 UTC | Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 07:33:36 UTC |
| 520ea31 | Nick Papior | 28 June 2016, 07:33:33 UTC | Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 07:33:33 UTC |
| b551ea5 | Nick Papior | 28 June 2016, 07:29:52 UTC | doc: fixed documentation to reflect orthogonal implementation Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 07:29:52 UTC |
| 07fdf9e | Nick Papior | 28 June 2016, 07:25:23 UTC | bug: fixed errors in HEAD^1 - The Hamiltonian is by default orthogonal This meant a few changes across the tests. - Added a test with a non-orthogonal case. - Forgot to add the dtype of the Hamiltonian to reference the _data._D.dtype. - Bug in tuple index assignment (we just convert to list) Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 07:25:23 UTC |
| 9beee2b | Nick Papior | 28 June 2016, 07:03:11 UTC | enh: enabled orthogonal Hamiltonian - Enabled orthogonal Hamiltonian which then does not store the overlap matrix. This also makes eigsh easier as it can intrinsically test whether the electronic structure is comprised of orthogonal basis functions. This may be queried by Hamiltonian.orthogonal. - Added a copy routine for the SparseCSR matrix. It allows an exact copy of the data object. The user may decide to copy some of the dimensions or all, if required. - Added more tests which uncovered a few programming mistakes in the Atom and Geometry class. - Removed all references to __main__ in the codes. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 28 June 2016, 07:03:11 UTC |
| c8869e8 | Nick Papior | 27 June 2016, 14:07:37 UTC | enh: added nanotube for the geometry creation - Changed ASE to fromASE in the geometry class. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 June 2016, 14:07:37 UTC |
| 3b658da | Nick Papior | 27 June 2016, 13:38:34 UTC | enh: enabled dH.nc file for tbtrans dH functionality - Added a simple test for the dH functionality - Enabled empty'ing the sparse data such that the sparsity data may be retained. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 June 2016, 13:38:34 UTC |
| 6ac7366 | Nick Papior | 27 June 2016, 10:13:49 UTC | enh: updated warning when having overlying atoms - The overlying atoms are now printed alltogether to limit the noise of the warning system. Signed-off-by: Nick Papior <nickpapior@gmail.com> | 27 June 2016, 10:13:49 UTC |
