Viewer3d¶
- class py4vasp.data.Viewer3d(viewer)¶
Bases:
object
Collection of data and elements to be displayed in a structure viewer.
- Parameters
viewer (nglview.NGLWidget) – The raw viewer used to display the structure. Currently we are only supporting the nglview package.
Methods Summary
from_structure
(structure[, supercell])Generate a new Viewer3d from a structure.
from_trajectory
(trajectory)Generate a new Viewer3d from a trajectory.
Remove all arrows from the atoms.
Hide the cartesian axis.
Hide the unit cell of the crystal.
show_arrows_at_atoms
(arrows[, color])Add arrows at all the atoms.
Show the cartesian axis in the corner of the figure.
Show the unit cell of the crystal.
show_isosurface
(volume_data, **kwargs)Add an isosurface to the structure.
Methods Documentation
- classmethod from_structure(structure, supercell=None)¶
Generate a new Viewer3d from a structure.
- Parameters
structure (data.Structure) – Defines the structure of the Vasp calculation.
supercell (int or np.ndarray) – If present the cell is extended by the specified factor along each axis.
- classmethod from_trajectory(trajectory)¶
Generate a new Viewer3d from a trajectory.
- Parameters
trajectory (data.Structure) – Defines the trajectory of the Vasp MD run.
supercell (int or np.ndarray) – If present the cell is extended by the specified factor along each axis.
- hide_arrows_at_atoms()¶
Remove all arrows from the atoms.
Notes
If two different kind of atoms have been added to the system, there is currently no option to distinguish between them.
- hide_axes()¶
Hide the cartesian axis.
- hide_cell()¶
Hide the unit cell of the crystal.
- show_arrows_at_atoms(arrows, color=[0.1, 0.1, 0.8])¶
Add arrows at all the atoms.
- Parameters
arrows (np.ndarray) – An array containing the direction of an arrow for every atom in the unit cell. This arrow will be drawn in the figure.
color (np.ndarray) – rgb values of the arrow, defaulting to blue.
Notes
If you are working on a supercell, the code will automatically extend the size of the array to show arrows in the supercell, too.
- show_axes()¶
Show the cartesian axis in the corner of the figure.
- show_cell()¶
Show the unit cell of the crystal.
- show_isosurface(volume_data, **kwargs)¶
Add an isosurface to the structure.
- Parameters
volume_data (np.ndarray) – The raw data represented on a 3d grid. Make sure the grid aligns with the FFT grid used in the Vasp calculation.
kwargs – Additional parameters passed on to the visualizer. Most relevant is the isolevel changing the position at which the isosurface is drawn.