Plotting atoms

This page explains how to plot a set of atoms.

import wulfric
import numpy as np

cell = np.array(
    [
        [0.000000, 4.744935, 0.000000],
        [3.553350, 0.000000, 0.000000],
        [0.000000, 0.000000, 8.760497],
    ]
)
atoms = {
    "names": ["Cr1", "Br1", "S1", "Cr2", "Br2", "S2"],
    "positions": np.array(
        [
            [0.000000, -0.500000, 0.882382],
            [0.000000, 0.000000, 0.677322],
            [-0.500000, -0.500000, 0.935321],
            [0.500000, 0.000000, 0.117618],
            [0.500000, 0.500000, 0.322678],
            [0.000000, 0.000000, 0.064679],
        ]
    ),
}


pe = wulfric.PlotlyEngine(_sphinx_gallery_fix=True)

pe.plot_atoms(cell=cell, atoms=atoms)
pe.plot_cell(cell=cell)

pe.show()

Atoms'labels are deduced based on atoms["names"].

Atom's colors are deduced based on atom's species, but can be directly passed to the function as well.

atoms = dict(positions=atoms["positions"])

pe = wulfric.PlotlyEngine(_sphinx_gallery_fix=True)

pe.plot_atoms(cell=cell, atoms=atoms)
pe.plot_cell(cell=cell)

pe.show()

/home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/0.6/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:114: RuntimeWarning: Atom species deduction failed for 'X1'. Set species to 'X'
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/0.6/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:114: RuntimeWarning: Atom species deduction failed for 'X2'. Set species to 'X'
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/0.6/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:114: RuntimeWarning: Atom species deduction failed for 'X3'. Set species to 'X'
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/0.6/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:114: RuntimeWarning: Atom species deduction failed for 'X4'. Set species to 'X'
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/0.6/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:114: RuntimeWarning: Atom species deduction failed for 'X5'. Set species to 'X'
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/0.6/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:114: RuntimeWarning: Atom species deduction failed for 'X6'. Set species to 'X'
  warnings.warn(