pyxtal.viz module
This module handles visualization. Mostly powered by py3Dmol
- pyxtal.viz.display_atomic(struc, size=(600, 300), scale=0.25, radius=0.1, supercell=(1, 1, 1), show_wp=False)[source]
display the molecular crystals generated from pyxtal. If the animation is False, only dump the structure to cif and let py3Dmol display it. If animation is on, show the generation of molecules in the crystal as an animation.
- Parameters:
size – (width, height) in tuple
scale – the size of sphere
radius – the size of stick
supercell – replicate the crystal (valid only when animation is False)
show_wp – whether or not highlight the unique wyckoff site
- Returns:
py3Dmol object
- pyxtal.viz.display_cluster(molecules, cell, Ps, cmap='YlGn', s_opacity=0.5, size=(400, 300), style='sphere')[source]
- pyxtal.viz.display_crystals(strucs, size=(600, 300), supercell=(1, 1, 1), labels=None)[source]
display the molecular crystals generated from pyxtal. two modes of animations are supported: slider or movie
- Parameters:
size – (width, height) in tuple
supercell – replicate the crystal (valid only when animation is False)
labels – labels for each structures
- Returns:
py3Dmol object
- pyxtal.viz.display_mol_crystals(strucs, size=(600, 300), supercell=(1, 1, 1), axis=None, animation='slider', interval=2000)[source]
display the molecular crystals generated from pyxtal. two modes of animations are supported: slider or movie
- Parameters:
size – (width, height) in tuple
supercell – replicate the crystal (valid only when animation is False)
animation – slider or movie
- Returns:
py3Dmol object
- pyxtal.viz.display_molecular(struc, size=(600, 300), supercell=(1, 1, 1), axis=None, animation=False, interval=2000)[source]
display the molecular crystals generated from pyxtal. If the animation is False, only dump the structure to cif and let py3Dmol display it. If animation is on, show the generation of molecules in the crystal as an animation.
- Parameters:
size – (width, height) in tuple
supercell – replicate the crystal (valid only when animation is False)
axis – 3-vector to reprent the rotational axis
animation – whether or not display the animation
- Returns:
py3Dmol object
- pyxtal.viz.display_molecular_site(site, id=None, size=(400, 300), axis=True, ax_id=range(0, 3), box=False)[source]
display the Wyckoff site in the molecular crystals generated from pyxtal.
- Parameters:
site – pyxtal.wyckoff_site.mol_site object
id – list of molecules to display. If None, display all molecules in this site
size – (width, height) in tuple
axis – boolean, whether or not display the rotational axis
axis_label – whether or not display the unitcell axis labels
- Returns:
py3Dmol object
- pyxtal.viz.display_molecule(molecule, center, cell, size=(400, 300))[source]
display the molecules in Pymatgen object.
- Parameters:
mol – pymatgen molecule
center – molecular
size – (width, height) in tuple
- Returns:
py3Dmol object
- pyxtal.viz.display_molecules(molecules, size=(400, 300), animation=False, center=False)[source]
display the molecules in Pymatgen object.
- Parameters:
molecules – a list of pymatgen molecules
size – (width, height) in tuple
animation – whether or not display animation
center – highlight center or not
- Returns:
py3Dmol object