Source code for matador.utils.viz_utils

# coding: utf-8
# Distributed under the terms of the MIT License.

""" This submodule contains a dirty wrapper of ase-gui for quick
visualisation, and nglview wrapper for JupyterNotebook visualisation,
and some colour definitions scraped from VESTA configs.


from matador.utils.ase_utils import doc2ase

[docs]def viz(doc): """ Quick and dirty ase-gui visualisation from matador doc. """ from ase.visualize import view view(doc2ase(doc)) return
[docs]def get_element_colours(): """ Read element colours from VESTA file. The colours file can be specified in the matadorrc. If unspecified, the default ../config/vesta_elements.ini will be used. """ import os from matador.config import load_custom_settings, SETTINGS # check if element_colours has been given as an absolute path if SETTINGS: colours_fname = SETTINGS.get('plotting', {}).get('element_colours') else: colours_fname = load_custom_settings().get('plotting', {}).get('element_colours') if colours_fname is None: colours_fname = '/'.join(os.path.realpath(__file__).split('/')[:-1]) + '/../config/vesta_elements.ini' elif not os.path.isfile(colours_fname): print('Could not find {}, please specify an absolute path. Falling back to default...'.format(colours_fname)) # otherwise fallback to ../config/vesta_elements.ini colours_fname = '/'.join(os.path.realpath(__file__).split('/')[:-1]) + '/../config/vesta_elements.ini' with open(colours_fname, 'r') as f: flines = f.readlines() element_colours = dict() for line in flines: line = line.split() elem = line[1] colour = list(map(float, line[-3:])) element_colours[elem] = colour return element_colours
[docs]def nb_viz(doc, repeat=1, bonds=None): """ Return an ipywidget for nglview visualisation in a Jupyter notebook or otherwise. Parameters: doc (matador.crystal.Crystal / dict): matador document to show. Keyword arguments: repeat (int): number of periodic images to include. bonds (str): custom bond selection. """ import nglview atoms = doc2ase(doc) atoms = atoms.repeat((repeat, repeat, repeat)) view = nglview.show_ase(atoms) view.add_unitcell() view.remove_ball_and_stick() view.add_spacefill(radius_type='vdw', scale=0.3) if bonds is None: for elements in set(doc['atom_types']): view.add_ball_and_stick(selection='#{}'.format(elements.upper())) else: if not isinstance(bonds, list): bonds = [bonds] for bond in bonds: view.add_ball_and_stick(selection='#{}'.format(bond.upper())) view.parameters = {'clipDist': 0} = 'orthographic' view.background = '#FFFFFF' return view