.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/3-trajectory.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_3-trajectory.py>`
        to download the full example code.

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

.. _sphx_glr_examples_3-trajectory.py:


Trajectory plotting
===================

This example demonstrates the visualization of trajectory data. It also includes
visualization of atomic forces.

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

.. GENERATED FROM PYTHON SOURCE LINES 14-20

.. code-block:: Python


    import ase.io
    import numpy as np

    import chemiscope








.. GENERATED FROM PYTHON SOURCE LINES 21-22

Load structures and properties

.. GENERATED FROM PYTHON SOURCE LINES 23-39

.. code-block:: Python

    frames = ase.io.read("data/trajectory.xyz", ":")

    properties = {
        # concise definition of a property, with just an array and the type
        # inferred by the size
        "index": np.arange(len(frames)),
        # an example of the verbose definition
        "energy": {
            "target": "structure",
            "values": [frame.info["energy"] for frame in frames],
            "units": "eV",
            "description": "potential energy, computed with DFTB+",
        },
    }









.. GENERATED FROM PYTHON SOURCE LINES 40-41

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

.. GENERATED FROM PYTHON SOURCE LINES 42-83

.. code-block:: Python


    chemiscope.write_input(
        "trajectory-md.json.gz",
        # dataset metadata can also be included, to provide a self-contained description
        # of the data, authors and references
        meta={
            "name": "Allyl alcohol MD trajectory.",
            "description": (
                "This dataset contains data from a DFTB+ trajectory of allyl alcohol."
            ),
            "authors": ["The chemiscope developers"],
            "references": [
                (
                    "G. Fraux, R. Cersonsky, and M. Ceriotti, "
                    '"Chemiscope: interactive structure-property explorer for materials '
                    'and molecules," JOSS 5(51), 2117 (2020).'
                )
            ],
        },
        frames=frames,
        properties=properties,
        # visualize forces as vectors
        shapes={
            "forces": chemiscope.ase_vectors_to_arrows(
                frames, "forces", scale=1, radius=0.15
            )
        },
        settings={  # these are reasonable settings for trajectory visualization
            "structure": [
                {
                    "keepOrientation": True,
                    "playbackDelay": 100,
                    "shape": "forces",  # visualize force vectors
                }
            ],
            "map": {
                "joinPoints": True,
            },
        },
    )








.. GENERATED FROM PYTHON SOURCE LINES 84-86

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 87-89

.. code-block:: Python


    chemiscope.show_input("trajectory-md.json.gz")


.. chemiscope:: _datasets/fig_3-trajectory_004.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 0.020 seconds)


.. _sphx_glr_download_examples_3-trajectory.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: 3-trajectory.ipynb <3-trajectory.ipynb>`

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

      :download:`Download Python source code: 3-trajectory.py <3-trajectory.py>`

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

      :download:`Download zipped: 3-trajectory.zip <3-trajectory.zip>`


.. only:: html

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

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