| 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 |
| 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 |
