.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/4-colors.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_4-colors.py>`
        to download the full example code.

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

.. _sphx_glr_examples_4-colors.py:


Atom property coloring
======================

This example demonstrates how to color atoms based on scalar properties.

Note that the same parameters can be used with `chemiscope.show` to visualize an
interactive widget in a Jupyter notebook.

.. GENERATED FROM PYTHON SOURCE LINES 13-19

.. code-block:: Python


    import ase.io
    import numpy as np

    import chemiscope








.. GENERATED FROM PYTHON SOURCE LINES 20-21

Load a dataset of structures containing polarizability and dipole data

.. GENERATED FROM PYTHON SOURCE LINES 22-25

.. code-block:: Python


    frames = ase.io.read("data/alpha-mu.xyz", ":")








.. GENERATED FROM PYTHON SOURCE LINES 26-27

Compute some scalar quantities to display as atom coloring

.. GENERATED FROM PYTHON SOURCE LINES 28-54

.. code-block:: Python


    polarizability = []
    alpha_eigenvalues = []
    anisotropy = []

    for frame in frames:
        # center molecule in the box
        frame.positions += frame.cell.diagonal() * 0.5
        for axx, ayy, azz, axy, axz, ayz in zip(
            frame.arrays["axx"],
            frame.arrays["ayy"],
            frame.arrays["azz"],
            frame.arrays["axy"],
            frame.arrays["axz"],
            frame.arrays["ayz"],
        ):
            polarizability.append((axx + ayy + azz) / 3)

            # one possible measure of anisotropy...
            eigenvalues = np.linalg.eigvalsh(
                [[axx, axy, axz], [axy, ayy, ayz], [axz, ayz, azz]]
            )
            alpha_eigenvalues.append(eigenvalues)

            anisotropy.append(eigenvalues[2] - eigenvalues[0])








.. GENERATED FROM PYTHON SOURCE LINES 55-56

Create a visualization and save it as a file that can be viewed at chemiscope.org

.. GENERATED FROM PYTHON SOURCE LINES 57-87

.. code-block:: Python


    chemiscope.write_input(
        "colors-example.json.gz",
        frames=frames,
        # properties can also be extracted from the ASE.Atoms frames
        properties={
            "polarizability": np.vstack(polarizability),
            "anisotropy": np.vstack(anisotropy),
            "alpha_eigenvalues": np.vstack(alpha_eigenvalues),
        },
        # it is also possible to define the default visualization settings
        settings={
            "map": {
                "x": {"property": "alpha_eigenvalues[1]"},
                "y": {"property": "alpha_eigenvalues[2]"},
                "z": {"property": "alpha_eigenvalues[3]"},
                "color": {"property": "anisotropy"},
            },
            "structure": [
                {
                    "color": {"property": "anisotropy"},
                }
            ],
        },
        # the properties we want to visualise are atomic properties - in order to view them
        # in map panel we must indicate the list of environments (all atoms in this case)
        environments=chemiscope.all_atomic_environments(frames),
    )









.. GENERATED FROM PYTHON SOURCE LINES 88-90

The file can also be viewed in a notebook. Use `chemiscope.show` above to bypass the
creation of a JSON file and directly create a viewer.

.. GENERATED FROM PYTHON SOURCE LINES 91-93

.. code-block:: Python


    chemiscope.show_input("colors-example.json.gz")


.. chemiscope:: _datasets/fig_4-colors_005.json.gz
            :mode: default
        


.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">

    </div>
    <br />
    <br />


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

   **Total running time of the script:** (0 minutes 0.008 seconds)


.. _sphx_glr_download_examples_4-colors.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: 4-colors.ipynb <4-colors.ipynb>`

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

      :download:`Download Python source code: 4-colors.py <4-colors.py>`

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

      :download:`Download zipped: 4-colors.zip <4-colors.zip>`


.. only:: html

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

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