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.
hide_arrows_at_atoms()	Remove all arrows from the atoms.
hide_axes()	Hide the cartesian axis.
hide_cell()	Hide the unit cell of the crystal.
show_arrows_at_atoms(arrows[, color])	Add arrows at all the atoms.
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.

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.