https://github.com/zerothi/sisl

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Revision Author Date Message Commit Date
424ea0f Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 July 2016, 08:22:54 UTC
d60dda2 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 bug: fixed non-orthogonal S_idx in Hamiltonian Signed-off-by: Nick Papior <nickpapior@gmail.com> 30 June 2016, 09:05:03 UTC
4767983 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 doc: removed last reference to TightBinding Signed-off-by: Nick Papior <nickpapior@gmail.com> 29 June 2016, 08:51:33 UTC
1f86271 bug: fixed wrong function name Signed-off-by: Nick Papior <nickpapior@gmail.com> 29 June 2016, 08:21:13 UTC
5f8c5f9 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 13:09:10 UTC
b44d882 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 13:09:08 UTC
ac47b66 bug: 1fd4a432 was inconsistent in nnz vs. nnzpr Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 12:59:13 UTC
e2b70a4 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 12:43:14 UTC
6f40cf5 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 12:43:11 UTC
2f367b4 bug: fixed slice for hamiltonian in dH.nc Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 12:36:22 UTC
1fd4a43 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 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 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 doc: constantly updating the doi is error-prone Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 07:48:57 UTC
4be8074 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 07:33:36 UTC
520ea31 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 07:33:33 UTC
b551ea5 doc: fixed documentation to reflect orthogonal implementation Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 June 2016, 07:29:52 UTC
07fdf9e 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 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 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 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 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
cd2c2a8 api: restructured the physical quantities - Added mass retrieval of the geometry (returning an np.array) - Changed the read_tb to read_es (for electronic structure) I am twisted in selecting Hamiltonian or ElectronicStructure. Probably Hamiltonian should be ElectronicStructure and Hamiltonian should be an orthogonal special case of the ElectronicStructure - TightBinding and PhononTightBinding are deprecated classes. TightBinding is kept for backwards compatibility Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 June 2016, 09:58:30 UTC
b3067c0 maint: removed all __name__ == main Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 09:58:57 UTC
557e347 enh: added hessian read from GULP output Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 09:55:47 UTC
3e960c8 enh: added got to the GULP output file Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 08:10:55 UTC
9cc27be doc: changed bibentry to a simpler version Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 07:04:36 UTC
6ffc47c doc: added citation of sisl to README Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 07:03:39 UTC
279040b Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 06:49:07 UTC
0367a33 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 06:49:02 UTC
eaf6136 enh: changed alat to bond in honeycomb lattice Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 June 2016, 06:48:54 UTC
b7f0927 bug: fixed sgrid and setup.py scripts for io installation Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 June 2016, 15:30:06 UTC
e496ffb test: enhanced tests for fdf and generic objects Also changed POSCAR and CONTCAR to separate classes Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 June 2016, 14:51:51 UTC
fc37503 bug: removed __class__ reference in super call Using __class__ may end up in infinite recursion if the class is subclassed. Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 June 2016, 13:36:34 UTC
f7080c7 bug: removed print statements for debugging Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 June 2016, 13:28:36 UTC
266888f enh: reworked io routines All io routines have been reworked. They now have a hierachy and is more stable in the sense that each Sile is inherited through the overlying code that owns the data file type. With this methodology one can have the same file-ending and decisevely return the correct file depending on the code. Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 June 2016, 13:22:58 UTC
c3e894c enh: added warnings when using construct for 1-orbital systems In case the user accidentially have two atoms lying ontop of each other sisl will now print warnings. Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 June 2016, 12:20:54 UTC
b74dadc bug: fixed decorator usage in fdf file Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 June 2016, 12:10:57 UTC
5496c2f enh: enabled add routine for geometry (no cell change) Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 June 2016, 19:34:52 UTC
dcb8156 bug: fixed < in fdf keywords Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 June 2016, 19:32:07 UTC
df29571 enh: added decorators for opening closing files General usage of the read_x statements where wrapped with checks which may be generalised with decorators. Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 June 2016, 18:33:11 UTC
a46fda1 Changed keywords for atom key to atom, instead of A Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 June 2016, 19:44:25 UTC
93d258a enh: added read function to tightbinding class Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 June 2016, 19:32:32 UTC
5dda12a Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 May 2016, 12:59:13 UTC
2b03e98 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 May 2016, 12:58:43 UTC
eb4833c bug: fixed reading NC file and the initialization. Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 May 2016, 12:58:33 UTC
3ce0894 bug: fixed dR calculation from Geometry Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 11:35:17 UTC
a55cbc0 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 11:26:23 UTC
f15a401 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 11:25:59 UTC
8af21b5 bug: build-system Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 11:21:38 UTC
691db79 bug: fixed installation of sisl Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 11:06:02 UTC
515c564 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 10:38:08 UTC
5512acb Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 10:37:47 UTC
579bcc7 bug: fixed possible read of write_version Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 09:59:41 UTC
bfa9f89 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 08:59:45 UTC
9152424 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 08:59:18 UTC
c51ad8a fixed tag.sh Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 08:59:09 UTC
98b280d bug: fixed travis Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 07:55:44 UTC
20bd617 API: changed project name to sisl Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 07:43:05 UTC
3247707 enh: created wheel installation Signed-off-by: Nick Papior <nickpapior@gmail.com> 10 May 2016, 07:39:00 UTC
df5ae0f Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 21:59:33 UTC
f55f276 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 21:59:32 UTC
fc61120 enh: enabled wheel distribution build Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 21:59:10 UTC
6730921 doc: POTCAR also contain species information Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 21:42:46 UTC
3b1f5c8 pep8: used autopep8 -a -a Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 13:33:26 UTC
497e7e8 enh: added bond-currents (reduced orbital currents) This requires a passing of the orbital_current data and thus requires an initial call to orbital_current. Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 13:27:55 UTC
ae653a3 bug: fixed bond-currents and DOS Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 10:00:17 UTC
4dbfd5c bug: default NCSile to access = 1 This meant some restructuring of the getattr function Signed-off-by: Nick Papior <nickpapior@gmail.com> 09 May 2016, 09:41:13 UTC
96fab7a enh: added alot of variable reads to tbtrans This will accommodate interaction with data models in a more stringent way. Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 May 2016, 20:32:45 UTC
7917b1c enh: changed default access of NetCDF files to access=1 Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 May 2016, 20:32:15 UTC
0b03978 enh: added len(Atom) to return # of orbitals Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 May 2016, 20:31:52 UTC
781dc39 doc: changed README.md Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 May 2016, 20:06:36 UTC
093bc74 enh: added read for SuperCell Changed README.md documentation of reading a geometry so that they interact through the Geometry object. Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 May 2016, 08:55:40 UTC
42f1bd5 bug: Fixed dR read and POSCAR file reads The dR value was not updated if changing the atoms. This attribute is now a property. The POSCAR reading had a bug, now it reads it correctly. Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 May 2016, 15:06:06 UTC
535e59d enh: Added documentation of Ef for write_tb Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 May 2016, 08:53:21 UTC
9512038 enh: Speed up functions slightly by reducing numpy lookup Made direct function references for common used functions in heavy duty routines. This should only have a minor effect. Signed-off-by: Nick Papior <nickpapior@gmail.com> 01 May 2016, 18:46:35 UTC
fb99ffe bug: fixed reading variables from netcdf tbtrans Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 March 2016, 10:27:25 UTC
0eb994d enh: added swap interface for swapping atomic indices Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 March 2016, 16:59:41 UTC
b75efd9 enh: pretty-print of geometry for many species Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 March 2016, 10:18:01 UTC
0a48ace bug: removed sys from read_geom Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 March 2016, 10:15:27 UTC
53c991d bug: fixed wrong index usage in species index Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 March 2016, 10:14:59 UTC
d188023 Small bug-fixes for FDF reading - Still a bug regarding the case of species Signed-off-by: Nick Papior <nickpapior@gmail.com> 02 March 2016, 10:08:09 UTC
6c51ec9 Fixed case checking for reading/writing fdf Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 February 2016, 22:11:49 UTC
9646ab8 Fixed sgeom -R flags, and corrected 56d4cf28 Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 February 2016, 22:04:09 UTC
56d4cf2 Fixed fdf block reading without endblock with signature Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 February 2016, 21:57:07 UTC
8fec8c5 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 February 2016, 01:14:44 UTC
c7899b2 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 February 2016, 01:14:34 UTC
13513ad 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 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 February 2016, 01:04:29 UTC
a4186c5 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 February 2016, 01:04:14 UTC
1a0cfbe 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 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 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 enh: enabled geom import statements Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 January 2016, 08:08:45 UTC
3b2fff4 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 January 2016, 17:54:18 UTC
e1392f8 Prepping for release Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 January 2016, 17:54:09 UTC
8bfe94d enh: removed reading which does not always work. Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 January 2016, 17:40:58 UTC
1d78287 enh: script change for sgeom Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 January 2016, 17:36:57 UTC
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