| 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 |
| d2a50fd | Nick Papior | 09 October 2015, 06:52:19 UTC | bug: Fixed unit-cell creation in grids when specifying both geom and sc | 09 October 2015, 06:52:19 UTC |
| 7ea8657 | Nick Papior | 09 October 2015, 01:10:28 UTC | bug: Fixed interface to match other read_grid | 09 October 2015, 01:10:28 UTC |
| da4b84c | Nick Papior | 08 October 2015, 20:48:19 UTC | enh: appending supercell on geometry allowed - Bugfix for supercell center | 08 October 2015, 20:48:19 UTC |
| 5c26050 | Nick Papior | 08 October 2015, 20:47:30 UTC | enh: sgrid - Changed formatting of index of grid variable One can denote variable and index for an NC variable using this methodology: FILENAME:<var>,<idx> FILENAME:<idx> FILENAME:<var> where an unset index defaults to 0 and the variable is required if ambiguity rises. - Added grid_part which cuts the grid into pieces by taking the above/below parts of a full grid. sgrid --grid-part|-gp + x 10. takes the grid above the cell vector 'A' above 10. Ang These grid-part stacks and are used in sequence. - When reading in a grid from the SIESTA.nc file it will automatically be converted to eV if the attribute unit exists and is Ry. - Bugfix for __op__ for the grids The type check has to be after isinstance | 08 October 2015, 20:47:30 UTC |
| 5160f2c | Nick Papior | 07 October 2015, 00:19:30 UTC | Prepping for release | 07 October 2015, 00:19:30 UTC |
| 7763d97 | Nick Papior | 25 September 2015, 09:43:06 UTC | enh: tag.sh now requires an option for stepping | 25 September 2015, 09:43:06 UTC |
| 2a8fb74 | Nick Papior | 25 September 2015, 09:42:29 UTC | Prepping for release | 25 September 2015, 09:42:29 UTC |
| dc12c06 | Nick Papior | 22 September 2015, 10:14:05 UTC | enh: Added ability to set the bond-length specifically - Fixed test for bond-length check | 22 September 2015, 10:14:05 UTC |
| 1c4c1fe | Nick Papior | 22 September 2015, 09:57:33 UTC | bug: Fixed bond_correct radii estimation. | 22 September 2015, 09:57:33 UTC |
| 930d967 | Nick Papior | 21 September 2015, 09:33:50 UTC | enh: eigh now allows overwriting, and only calculates eig - TightBinding.eigh defaults to only returning the eigenvalues and the underlying scipy routine allows overwriting the matrices which may speed things up. | 21 September 2015, 09:33:50 UTC |
| 074598d | Nick Papior | 21 September 2015, 09:04:55 UTC | enh: Changed rotation to default to degree - Any rotation will likely be given in degrees, hence we use degrees as the default rotation angle | 21 September 2015, 09:04:55 UTC |
| 638eec6 | Nick Papior | 18 September 2015, 08:14:45 UTC | enh: Enabled estimation of super-cell in Cartesian coordinate - When the unit cell has not been supplied we guess the unit cell by estimating the cell size from the bond-length along the Cartesian directions. | 18 September 2015, 08:14:45 UTC |
| 60a3be6 | Nick Papior | 17 September 2015, 14:31:52 UTC | +wiki | 17 September 2015, 14:31:52 UTC |
| 554a4ee | Nick Papior | 17 September 2015, 15:33:18 UTC | Bugfix for wiki module, we cannot use git@ to bypass username/password | 17 September 2015, 15:33:18 UTC |
| 7c33411 | Nick Papior | 17 September 2015, 13:30:34 UTC | Update wiki commit | 17 September 2015, 13:30:34 UTC |
| 34e4257 | Nick Papior | 17 September 2015, 12:42:52 UTC | Added wiki as a submodule. | 17 September 2015, 12:42:52 UTC |
| 14deed3 | Nick Papior | 01 September 2015, 14:38:43 UTC | Prepping for release | 01 September 2015, 14:38:43 UTC |
| dfdc908 | Nick Papior | 01 September 2015, 14:38:42 UTC | enh: Changed unit handling by adding unit code - The TightBinding codes now have an intrinsic order for the energy conversion. Thus the energy conversion is made without interference. | 01 September 2015, 14:38:42 UTC |
| d4e9f3c | Nick Papior | 01 September 2015, 14:24:03 UTC | enh: Changing a supercell is now recursive - When changing the supercell of any object it recursively looks at all attributes to also set the supercell on all attributes in the current scope object. | 01 September 2015, 14:24:03 UTC |
| e244a09 | Nick Papior | 01 September 2015, 13:49:33 UTC | bug: Fixed copy of grid to retain geometry | 01 September 2015, 13:49:33 UTC |
| 8828316 | Nick Papior | 01 September 2015, 13:42:09 UTC | bug: Several bug fixes including division | 01 September 2015, 13:42:09 UTC |
| d55676e | Nick Papior | 01 September 2015, 13:36:47 UTC | bug: Several bug fixes, changed Length to Bohr - The length variable in SuperCellChild has been changed to Bohr for better consistency | 01 September 2015, 13:36:47 UTC |
| 78f37aa | Nick Papior | 01 September 2015, 13:13:56 UTC | enh: Enabled cutting grids - Taking a sub-partition of a grid is possible. Only along certain axis. - Removing certain indices of an axis. - An index function for retrieving the index Helpful to generate ranges to cut grids into smaller segments | 01 September 2015, 13:13:56 UTC |
| e9d8334 | Nick Papior | 31 August 2015, 23:28:11 UTC | Prepping for release | 31 August 2015, 23:28:11 UTC |
| cce1a77 | Nick Papior | 31 August 2015, 23:28:05 UTC | enh: Added cutting to grids - Enabled creating a grid cross-section - Enabled summing a grid along an axis - Enabled taking the average of a grid along an axis - Enabled comparisons of grids by overriding __eq__ Currently, it _ONLY_ checks for grid size. Possibly we should check for the actual cell. - Enabled __add__ of grids by overriding the method Same goes for __sub__, __div__ and __mul__ - Added is_orthogonal to the SuperCell object, this is now inherited to the SuperCellChild - Added test of is_orthogonal | 31 August 2015, 23:28:05 UTC |
| 8162d8f | Nick Papior | 31 August 2015, 11:17:43 UTC | Added PHtransSile for PHT files | 31 August 2015, 11:17:43 UTC |
| 9967c11 | Nick Papior | 29 August 2015, 10:19:01 UTC | bug: Ensured no overwriting of mutable object Atom in Geometry init | 29 August 2015, 10:19:01 UTC |
| 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 |
