.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "user-guide/usage/visualization/plot_5_atoms.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_user-guide_usage_visualization_plot_5_atoms.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_user-guide_usage_visualization_plot_5_atoms.py:


**************
Plotting atoms
**************

This page explains how to plot a set of atoms.

.. GENERATED FROM PYTHON SOURCE LINES 29-62

.. code-block:: Python


    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()






.. raw:: html

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                       {"template":{"data":{"scatter":[{"type":"scatter"}]}},"scene":{"domain":{"x":[0.0,1.0],"y":[0.0,1.0]},"xaxis":{"range":[-1.86550875,4.477220999999999]},"yaxis":{"range":[-2.4910908750000003,5.9786181]},"zaxis":{"range":[0.0,11.038226220000002]},"aspectratio":{"x":0.5746149447913741,"y":0.7673070660260484,"z":1},"aspectmode":"manual"},"legend":{"yanchor":"bottom","y":1.0,"xanchor":"center","x":0.5}},                        {"responsive": true}                    )                };            </script>        </div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 63-67

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.

.. GENERATED FROM PYTHON SOURCE LINES 67-78

.. code-block:: Python



    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()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/latest/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:112: RuntimeWarning: Atom species deduction failed for 'X1'. Set species to 'X'
      warnings.warn(
    /home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/latest/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:112: RuntimeWarning: Atom species deduction failed for 'X2'. Set species to 'X'
      warnings.warn(
    /home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/latest/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:112: RuntimeWarning: Atom species deduction failed for 'X3'. Set species to 'X'
      warnings.warn(
    /home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/latest/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:112: RuntimeWarning: Atom species deduction failed for 'X4'. Set species to 'X'
      warnings.warn(
    /home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/latest/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:112: RuntimeWarning: Atom species deduction failed for 'X5'. Set species to 'X'
      warnings.warn(
    /home/docs/checkouts/readthedocs.org/user_builds/wulfric/envs/latest/lib/python3.11/site-packages/wulfric/crystal/_atoms.py:112: RuntimeWarning: Atom species deduction failed for 'X6'. Set species to 'X'
      warnings.warn(


.. raw:: html

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.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.083 seconds)


.. _sphx_glr_download_user-guide_usage_visualization_plot_5_atoms.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_5_atoms.ipynb <plot_5_atoms.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_5_atoms.py <plot_5_atoms.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_5_atoms.zip <plot_5_atoms.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_