| 53dc174 | Nick Papior | 28 August 2015, 11:28:26 UTC | Prepping for release | 28 August 2015, 11:28:26 UTC |
| 8c02f5b | Nick Papior | 28 August 2015, 11:28:23 UTC | bug: warn user about non-symmetric couplings - When the TightBinding model gets finalized it will now check for symmetry in couplings. It does so simply by ensuring the non-zero elements of itself and itself plus its transpose are equal. If not a warning will be issued. - Changed tb.py and phtb.py to the full class names in lower case. Makes code tree cleaner - Added honeycomb geometry creator. - Bugfix for extension of sparsity pattern by ensuring the insertion dtype to its container. | 28 August 2015, 11:28:23 UTC |
| 8ddbc87 | Nick Papior | 28 August 2015, 07:16:27 UTC | enh: changed default angle specification to degrees - This is more in line with humans for scripts. For radians one can specify .5r | 28 August 2015, 07:16:27 UTC |
| 576c11c | Nick Papior | 26 August 2015, 07:49:18 UTC | Prepping for release | 26 August 2015, 07:49:18 UTC |
| 673b9ce | Nick Papior | 26 August 2015, 07:49:00 UTC | bug: Several bugfixes for the Grid class - Enabled reading the an FDF geometry with origo offset - Enabled geom[..] which is a shorthand for geom.xa[..] Same goes for grid with grid.grid - Ensured the grid returns the size in a numpy array - Fixed the swapaxes of the grid to ensure contiguous array. This is necessary when saving a cube. | 26 August 2015, 07:49:00 UTC |
| 61f5d99 | Nick Papior | 25 August 2015, 22:06:54 UTC | +file | 25 August 2015, 22:06:54 UTC |
| 381417c | Nick Papior | 25 August 2015, 22:03:07 UTC | enh: added generic siesta.grid.nc files for grids - Enabled reading grid.nc files from siesta. - Several bugfixes in the Grid class | 25 August 2015, 22:03:07 UTC |
| d80ecd9 | Nick Papior Andersen | 21 August 2015, 14:30:15 UTC | Prepping for release | 21 August 2015, 14:30:15 UTC |
| d143fc7 | Nick Papior Andersen | 21 August 2015, 14:30:08 UTC | enh: Added VASP CONTCAR/POSCAR reading writing - Enabled reading vasp input/output. | 21 August 2015, 14:30:08 UTC |
| e50d398 | Nick Papior Andersen | 21 August 2015, 13:22:06 UTC | enh: More functionality of Geometry and Atom - Enabled lookup of atomic radii from atoms. Currently we allow 3 different radii: 1) calculated radii 2) empirical 3) van der Waals radii all are taken from this page: https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page) - Enabled the geometry to automatically correct an atoms placement relative to another atom via the average atomic radii. This provides good estimates for the actual bond-length and starting convergence with such a bond-length is much better than a simple "approximation" - Added a test for bond_correct | 21 August 2015, 13:22:06 UTC |
| 57e612a | Nick Papior Andersen | 19 August 2015, 12:02:18 UTC | doc: added more documentation | 19 August 2015, 12:02:18 UTC |
| f834456 | Nick Papior Andersen | 19 August 2015, 12:02:01 UTC | Prepping for release | 19 August 2015, 12:02:01 UTC |
| f05455a | Nick Papior Andersen | 19 August 2015, 11:59:47 UTC | enh: More functionality of sgeom - Enabled sub(...) using sgeom -s 1-2,4-7 etc - Enabled cutting the structure sgeom --cut 4 z which corresponds to cutting the geometry 4 times, and the unit-cell direction z. | 19 August 2015, 11:59:47 UTC |
| 99282ca | Nick Papior Andersen | 18 August 2015, 22:46:15 UTC | Prepping for release | 18 August 2015, 22:46:15 UTC |
| 7f03247 | Nick Papior Andersen | 18 August 2015, 22:46:13 UTC | enh: lots of enhancements, sgeom, geometries - Enabled piping in sgeom script Piping is done intrinsically for the sgeom script by allowing a specific keyword for out files - Changed -o to -O for translating to origin in sgeom - Added uc translation which moves all atoms into the unit-cell. This can either be achieved using the sgeom -uc translate option which is a mere translation. Or sgeom -uc mod which takes the modular offset to get its equivalent coordinate in the UC - If no out-file is specified the geometry will be printed on the stdout - Bugfix in close_sc function. - Enabled reciprocal cell return for the SuperCell and its children It is returned in the rcell[0,:] common format as cell, hence rcell[0,:] is the first reciprocal cell vector, unlike the scipy.linalg.inv()[:,0] - Added test of reciprocal cell | 18 August 2015, 22:46:13 UTC |
| ed855d6 | Nick Papior Andersen | 18 August 2015, 14:07:05 UTC | bug: use set_supercell, no influence currently | 18 August 2015, 14:07:05 UTC |
| 8e019b6 | Nick Papior Andersen | 18 August 2015, 14:06:01 UTC | Prepping for release | 18 August 2015, 14:06:01 UTC |
| a236e88 | Nick Papior Andersen | 18 August 2015, 14:05:58 UTC | enh: Enabled returning a specific cut segment - By passing an extra integer one can return the corresponding segment from the cut. This can be usefull if one wants to retrieve a specific part of the geometry. | 18 August 2015, 14:05:58 UTC |
| 2a45dfb | Nick Papior Andersen | 18 August 2015, 13:48:44 UTC | bug: Fixed spell-error bug - Added test for said bug | 18 August 2015, 13:48:44 UTC |
| c9b3754 | Nick Papior Andersen | 16 August 2015, 21:50:22 UTC | Prepping for release | 16 August 2015, 21:50:22 UTC |
| edab924 | Nick Papior Andersen | 16 August 2015, 21:50:19 UTC | enh: added write to grid - Enabled writing a cube file using the Grid object - Moved the Length parameter to the SuperCellChild object This Length parameter should be changed to some standard unit-parent container. | 16 August 2015, 21:50:19 UTC |
| 9715282 | Nick Papior Andersen | 16 August 2015, 12:44:58 UTC | doc: Added documentation and tests | 16 August 2015, 12:44:58 UTC |
| baad778 | Nick Papior Andersen | 14 August 2015, 09:52:24 UTC | enh: Added cube file - Added the cube file format - Added tests of the get_sile function - Added geom to the grid (not necessary) | 14 August 2015, 09:52:24 UTC |
| a2993b5 | Nick Papior Andersen | 13 August 2015, 21:35:28 UTC | Prepping for release | 13 August 2015, 21:35:28 UTC |
| 111ac74 | Nick Papior Andersen | 13 August 2015, 21:24:07 UTC | enh: Separated read_geom to read_geom and read_sc - Sometimes read_sc is all you want. This is now accomplished in several of the siles TODO add the write_sc as a separate routine - Added dtype when creating a Grid object - Allowed reading a Grid from the SIESTA.nc files TODO add tests | 13 August 2015, 21:24:07 UTC |
| 58d2bab | Nick Papior Andersen | 13 August 2015, 11:05:04 UTC | enh: SuperCell creation made possible by only cell - Added possibility of creating the supercell by passing a unit-cell, instead of a supercell object. It makes the creation of geometries more flexible. | 13 August 2015, 11:05:04 UTC |
| 02d2ff0 | Nick Papior Andersen | 12 August 2015, 15:03:31 UTC | Prepping for release | 12 August 2015, 15:03:31 UTC |
| e15bc94 | Nick Papior Andersen | 12 August 2015, 15:00:38 UTC | Prepping for release | 12 August 2015, 15:00:38 UTC |
| f4f63d9 | Nick Papior Andersen | 12 August 2015, 14:59:58 UTC | Prepping for release | 12 August 2015, 14:59:58 UTC |
| 3bec578 | Nick Papior Andersen | 12 August 2015, 14:59:55 UTC | bug: added missing import warnings | 12 August 2015, 14:59:55 UTC |
| ab04fb1 | Nick Papior Andersen | 12 August 2015, 13:46:20 UTC | Prepping for release | 12 August 2015, 13:46:20 UTC |
| 1dcdeec | Nick Papior Andersen | 12 August 2015, 13:45:55 UTC | enh: Removed graphene_square for square as keyword | 12 August 2015, 13:45:55 UTC |
| 336877e | Nick Papior Andersen | 12 August 2015, 13:42:04 UTC | Prepping for release | 12 August 2015, 13:42:04 UTC |
| e78a710 | Nick Papior Andersen | 12 August 2015, 13:41:04 UTC | enh: Enabled writing of file directly, hcp added - Added the hcp structure - Added python version basestring if one needs to check for isinstance(var,str) - Added simple cubic lattice - Enabled FCC, BCC, HPC as square unit-cells Simply add flag square=True in the fcc call - Enabled importing the sile objects in the Geometry and TightBinding classes, this enables direct writing of files without the need for the obscure write(get_sile(...,'w')) - Enabled SuperCell to accept the cell keyword as a list of 6 elements which then corresponds to the a, b, c, alpha, beta, gamma parameters for a cell. - Created a Base class for the Sile object. In that way we can more easily detect Sile or NCSile objects. - Bugfix for the geom default package which was left out. | 12 August 2015, 13:41:04 UTC |
| 8bbff9e | Nick Papior Andersen | 10 August 2015, 15:00:26 UTC | bug: clarification of routine name | 10 August 2015, 15:00:26 UTC |
| cf3303a | Nick Papior Andersen | 10 August 2015, 11:03:36 UTC | Prepping for release | 10 August 2015, 11:03:36 UTC |
| 9a80d10 | Nick Papior Andersen | 10 August 2015, 11:02:40 UTC | enh: added set_nsc to SuperCellChild | 10 August 2015, 11:02:40 UTC |
| 064d774 | Nick Papior Andersen | 10 August 2015, 10:59:14 UTC | bug: fixed a lot of bugs - Changed gulp output file name, gout - Fixed GULPSile to regular Sile, it was NCSile - A lot of references to isc_off, and sc_idx has been removed to the correct names sc_off and sc_index. - Fixed cut routine for the TightBinding class | 10 August 2015, 10:59:14 UTC |
| b3ef399 | Nick Papior Andersen | 07 August 2015, 08:52:26 UTC | Prepping for release | 07 August 2015, 08:52:26 UTC |
| dda7ea2 | Nick Papior Andersen | 07 August 2015, 08:49:11 UTC | test: added more tests - Fixed bug which meant bcc and fcc where not available - Changed import for the basic structures, such as bcc, fcc, graphene, etc | 07 August 2015, 08:49:11 UTC |
| 7de78e8 | Nick Papior Andersen | 06 August 2015, 13:13:05 UTC | bug+enh: added b/fcc, typo in tb - A typo in the tight-binding module prohibited the setup of the tight-binding model. - Allowed creation of bcc and fcc crystal structures | 06 August 2015, 13:13:05 UTC |
| 9975725 | Nick Papior Andersen | 05 August 2015, 21:37:31 UTC | doc: updated documentation | 05 August 2015, 21:37:31 UTC |
| 736a82b | Nick Papior Andersen | 05 August 2015, 21:33:11 UTC | Prepping for release | 05 August 2015, 21:33:11 UTC |
| 96097ef | Nick Papior Andersen | 05 August 2015, 21:15:10 UTC | bug: nested fdf and LatticeParameters - Added possibility to read the LatticeParameters from fdf files. - the directory variable did not correctly save the current directory. We assert it is at least ./ if no directory can be found from the file (i.e. t.fdf has directory(t.fdf)=='') | 05 August 2015, 21:15:10 UTC |
| cb551f3 | Nick Papior Andersen | 05 August 2015, 20:33:52 UTC | enh: initial commit for streamlining the implementation Added grid to do grid-based operations. This should constitute an easier transition for grid based calculations from siesta calculations. | 05 August 2015, 20:33:52 UTC |
| 8960b5b | Nick Papior Andersen | 21 July 2015, 00:18:14 UTC | bug: we should have used the exp(-ikr) notation | 21 July 2015, 00:18:14 UTC |
| 0f56b38 | Nick Papior Andersen | 15 July 2015, 10:48:04 UTC | Prepping for release | 15 July 2015, 10:48:04 UTC |
| 6f50638 | Nick Papior Andersen | 15 July 2015, 10:48:02 UTC | doc: fix in doc | 15 July 2015, 10:48:02 UTC |
| 2905318 | Nick Papior Andersen | 15 July 2015, 10:47:06 UTC | enh: Added several new routines on Geometry - Add rotate_miller which enables rotating a Miller direction onto another direction - Enabled rotate to accept a degree quantity - Added swapaxes which swaps the cell, xyz axes. This enables one to swap two directions easily. - Added reverse routine which reverses the order of atoms in the geometry - added insert which inserts a geometry right before an atom, this routine does not alter the cell. - center, revert takes an optional list of atoms to operate on | 15 July 2015, 10:47:06 UTC |
| 0b6302a | Nick Papior Andersen | 14 July 2015, 14:11:01 UTC | Prepping for release | 14 July 2015, 14:11:01 UTC |
| 9e162a9 | Nick Papior Andersen | 14 July 2015, 13:39:33 UTC | bug: fixed capatilization of sgeom | 14 July 2015, 13:39:33 UTC |
| 155a7b5 | Nick Papior Andersen | 14 July 2015, 10:17:42 UTC | Prepping for release | 14 July 2015, 10:17:42 UTC |
| d454f94 | Nick Papior Andersen | 14 July 2015, 10:50:09 UTC | bug: bugfix for dR calculation | 14 July 2015, 10:50:09 UTC |
| 62a65c8 | Nick Papior Andersen | 14 July 2015, 10:35:27 UTC | bug: fixed fdf with specific directories | 14 July 2015, 10:35:27 UTC |
| 370bf10 | Nick Papior Andersen | 14 July 2015, 08:43:41 UTC | Prepping for release | 14 July 2015, 08:43:41 UTC |
| 7faa8bd | Nick Papior Andersen | 14 July 2015, 08:37:21 UTC | enh: Added tbtrans file object | 14 July 2015, 08:37:21 UTC |
| a6d1de9 | Nick Papior Andersen | 13 July 2015, 12:07:30 UTC | Streamlined list perception of atoms | 13 July 2015, 12:07:30 UTC |
| cb237e2 | Nick Papior Andersen | 13 July 2015, 09:37:15 UTC | Prepping for release | 13 July 2015, 09:37:15 UTC |
| 2b4122e | Nick Papior Andersen | 13 July 2015, 09:37:08 UTC | enh: Mirroring can be done around atoms, and will not infer mirroring subset | 13 July 2015, 09:37:08 UTC |
| af28e68 | Nick Papior Andersen | 13 July 2015, 08:58:23 UTC | enh: added mirror function | 13 July 2015, 08:58:23 UTC |
| ebd233c | Nick Papior Andersen | 13 July 2015, 07:35:52 UTC | changed casing for get_Sile/add_Sile to lowercase More stringent API | 13 July 2015, 07:35:52 UTC |
| a859e83 | Nick Papior Andersen | 13 July 2015, 08:35:22 UTC | Change sgeom to not have subparsers | 13 July 2015, 08:35:22 UTC |
| 4b91211 | Nick Papior Andersen | 10 July 2015, 10:05:27 UTC | bug: xyz requires an extra newline for molden | 10 July 2015, 10:05:27 UTC |
| 98bba1c | Nick Papior Andersen | 10 July 2015, 07:39:33 UTC | Prepping for release | 10 July 2015, 07:39:33 UTC |
| 39220e4 | Nick Papior Andersen | 10 July 2015, 07:36:28 UTC | enh: added sgeom script Enabled tree reading of geometries in fdf files Enabled center-of mass, position, cell calculations | 10 July 2015, 07:36:28 UTC |
| 7ad0dc2 | Nick Papior Andersen | 09 July 2015, 07:53:36 UTC | Prepping for release | 09 July 2015, 07:53:36 UTC |
| 6299874 | Nick Papior Andersen | 09 July 2015, 07:53:26 UTC | enh: Added several new routines on Geometry - Add rotate_miller which enables rotating a Miller direction onto another direction - Enabled rotate to accept a degree quantity - Added swapaxes which swaps the cell, xyz axes. This enables one to swap two directions easily. - Added reverse routine which reverses the order of atoms in the geometry - added insert which inserts a geometry right before an atom, this routine does not alter the cell. - center, revert takes an optional list of atoms to operate on | 09 July 2015, 07:53:26 UTC |
| ecabbc7 | Nick Papior Andersen | 08 July 2015, 23:59:19 UTC | enh: added Geometry.center, returns mean of xyz | 08 July 2015, 23:59:19 UTC |
| 8478dea | Nick Papior Andersen | 07 July 2015, 23:00:24 UTC | Prepping for release | 07 July 2015, 23:00:24 UTC |
| 084ffdc | Nick Papior Andersen | 07 July 2015, 22:58:23 UTC | enh: API change rotate returns a new object This makes it much more useful in in-line expressions. Few corrections of comments | 07 July 2015, 22:58:23 UTC |
| 830baea | Nick Papior Andersen | 07 July 2015, 08:07:40 UTC | doc: more docs | 07 July 2015, 08:07:40 UTC |
| 71a22c7 | Nick Papior Andersen | 06 July 2015, 07:40:22 UTC | enh: enabled sc2uc to accomodate a keyword for uniq=True|False | 06 July 2015, 07:40:22 UTC |
| f954975 | Nick Papior Andersen | 06 July 2015, 07:39:47 UTC | doc: updated readme | 06 July 2015, 07:39:47 UTC |
| c1ab655 | Nick Papior Andersen | 03 July 2015, 11:14:08 UTC | Prepping for release | 03 July 2015, 11:14:08 UTC |
| aadc22f | Nick Papior Andersen | 03 July 2015, 11:13:17 UTC | enh: enabled import sids and no further Every module which are commonly used are accessed directly via the sids module import. It is no longer necessary to do explicit import of the sub-modules. | 03 July 2015, 11:13:17 UTC |
| 52aaffa | Nick Papior Andersen | 02 July 2015, 15:09:25 UTC | Prepping for release | 02 July 2015, 15:09:25 UTC |
| e09e8b5 | Nick Papior Andersen | 02 July 2015, 15:09:21 UTC | enh: changed tag.sh file | 02 July 2015, 15:09:21 UTC |
| abb0296 | Nick Papior Andersen | 02 July 2015, 13:34:55 UTC | bug: fixed finalization before writing a tb | 02 July 2015, 13:34:55 UTC |
| d26fe8b | Nick Papior Andersen | 02 July 2015, 11:26:35 UTC | Stored n_s when using set_supercell, added axyzsc for coords of supercell indices | 02 July 2015, 11:26:35 UTC |
| 5e79809 | Nick Papior Andersen | 02 July 2015, 10:35:57 UTC | Added tag.sh script | 02 July 2015, 10:36:19 UTC |
| 7b9289a | Nick Papior Andersen | 02 July 2015, 10:35:12 UTC | Prepping for release | 02 July 2015, 10:35:12 UTC |
| b49a1ba | Nick Papior Andersen | 02 July 2015, 10:34:30 UTC | enh: translate function to geometry, returns copy | 02 July 2015, 10:34:30 UTC |
| 40f54c1 | Nick Papior Andersen | 02 July 2015, 08:49:59 UTC | enh: added square graphene unit-cell Creating default structures requires the passing of the atom structure | 02 July 2015, 08:49:59 UTC |
| 990c234 | Nick Papior Andersen | 02 July 2015, 00:25:53 UTC | bug: fix for import of used class | 02 July 2015, 00:25:53 UTC |
| 0216b07 | Nick Papior Andersen | 02 July 2015, 00:11:10 UTC | bug: setup installation | 02 July 2015, 00:11:10 UTC |
| 0d911e6 | Nick Papior Andersen | 01 July 2015, 22:34:33 UTC | test: added test directory | 01 July 2015, 22:34:33 UTC |
| da81965 | Nick Papior Andersen | 01 July 2015, 22:32:08 UTC | test: added new IO tests | 01 July 2015, 22:32:08 UTC |
| db2a153 | Nick Papior Andersen | 01 July 2015, 15:04:29 UTC | travis: removal of 2.6 tests, conda does not like it | 01 July 2015, 15:04:29 UTC |
| 9b0a010 | Nick Papior Andersen | 01 July 2015, 14:51:18 UTC | bugfixes for python3 support | 01 July 2015, 14:51:18 UTC |
| 6bf6c90 | Nick Papior Andersen | 01 July 2015, 14:04:39 UTC | +travis | 01 July 2015, 14:04:39 UTC |
| e4cf644 | Nick Papior Andersen | 01 July 2015, 13:57:00 UTC | +travis | 01 July 2015, 13:57:00 UTC |
| c9b4bae | Nick Papior Andersen | 01 July 2015, 13:40:42 UTC | +travis | 01 July 2015, 13:40:42 UTC |
| dfad4b2 | Nick Papior Andersen | 01 July 2015, 13:35:37 UTC | +travis | 01 July 2015, 13:35:37 UTC |
| 97263b9 | Nick Papior Andersen | 01 July 2015, 13:32:54 UTC | test: added geom.rotate test | 01 July 2015, 13:32:54 UTC |
| 73c9e98 | Nick Papior Andersen | 01 July 2015, 13:26:57 UTC | travis: added travis test and a first nosetests | 01 July 2015, 13:26:57 UTC |
| 6182388 | Nick Papior Andersen | 01 July 2015, 12:28:36 UTC | enh: added XV file format for reading and writing | 01 July 2015, 12:28:36 UTC |
| 3688c49 | Nick Papior Andersen | 01 July 2015, 12:08:58 UTC | Added __all__ to all python files | 01 July 2015, 12:08:58 UTC |
| f926dce | Nick Papior Andersen | 01 July 2015, 12:04:21 UTC | enh: Added writing of tight-binding models Added write-out of tight-binding models Added Phonon tight-binding model with the newton corrections Smaller bug-fixes around | 01 July 2015, 12:04:21 UTC |
| 707a02f | Nick Papior Andersen | 01 July 2015, 08:04:26 UTC | enh: added GULP and TB files Added two new file reads, GULP output and TB files Streamlined a few calls for the remaining IO objects | 01 July 2015, 08:04:26 UTC |
| ca5921f | Nick Papior Andersen | 01 July 2015, 06:41:19 UTC | enh: Allowed automatic expansion of the sparsity pattern Instead of forcing the user to restart creating the TB model we expand the sparsity pattern by 10 elements on each request of an element non-existing. | 01 July 2015, 06:41:19 UTC |
