wulfric.PlotlyEngine.plot_atoms#

method

PlotlyEngine.plot_atoms(cell, atoms, colors=None, legend_label=None, legend_group=None, shift=(0, 0, 0), scale=1, row=1, col=1)[source]#

Plots a set of atoms.

Parameters:
cell(3, 3) array-like

Matrix of a cell, rows are interpreted as vectors.

atomsdict

Dictionary with N atoms. Expected keys:

  • "positions" : (N, 3) array-like

    Positions of the atoms in the basis of lattice vectors (cell). In other words - relative coordinates of atoms.

  • "names" : (N, ) list of str, optional See Notes

  • "species" : (N, ) list of str, optional See Notes

colorsstr or list of str, optional

Color of the atoms. Any value that is supported by Plotly. If None, then color is deduced based on atoms's species.

legend_labelstr, optional

Label of the line that is displayed in the figure.

legend_groupstr, optional

Legend's group. If None, then defaults to the random string of 10 characters.

scalefloat, default 1

Scale for the size of atoms's markers and text labels. Use scale>1 to increase the size.

rowint, default 1

Row of the subplot.

colint, default 1

Column of the subplot.

Notes

atoms["names"] is used to deduce atom's species if necessary via wulfric.crystal.get_atom_species().

atoms["species"] is used to define atom's colors if ``colors is None