.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/1-base.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_1-base.py>`
        to download the full example code.

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

.. _sphx_glr_examples_1-base.py:


Simple chemiscope input
=======================

This example demonstrates the basic usage of the chemiscope package, reading structures
and properties from an ASE package and preparing a chemiscope file to visualize them.
Use `chemiscope.show` in a Jupyter notebook for interactive visualization

.. GENERATED FROM PYTHON SOURCE LINES 13-18

.. code-block:: Python


    import ase.io

    import chemiscope








.. GENERATED FROM PYTHON SOURCE LINES 19-20

Load structures from an extended xyz file

.. GENERATED FROM PYTHON SOURCE LINES 21-24

.. code-block:: Python


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








.. GENERATED FROM PYTHON SOURCE LINES 25-28

A chemiscope widget can be used to visualize structures and properties.
This generates a Chemiscope object that is rendered to an interactive
widget when executed in a Jupyter notebook.

.. GENERATED FROM PYTHON SOURCE LINES 29-46

.. code-block:: Python


    chemiscope.show(
        frames=frames,
        # quickly extract properties from the ASE frames. nb: if you're doing this for
        # sharing, don't forget to also include metadata such as units and description
        properties=chemiscope.extract_properties(frames, only=["dipole_ccsd", "ccsd_pol"]),
        # it's always good to set some metadata to explain what the dataset - title is bare
        # minimum
        meta=dict(name="Dipole and polarizability"),
        # it is possible to set _all_ visualization parameters with a dictionary format.
        # this is a shortcut for the most basic ones
        settings=chemiscope.quick_settings(
            x="ccsd_pol[1]", y="ccsd_pol[2]", color="dipole_ccsd[1]"
        ),
    )




.. chemiscope:: _datasets/fig_1-base_001.json.gz
            :mode: default
        


.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">

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

.. GENERATED FROM PYTHON SOURCE LINES 47-51

For sharing with collaborators, or when one does not want to use an interactive
notebook, one can also write a JSON (or compressed JSON) file that contains all
information about structures and properties, and can be viewed at chemiscope.org
Save as a file that can be viewed at chemiscope.org

.. GENERATED FROM PYTHON SOURCE LINES 52-63

.. code-block:: Python


    chemiscope.write_input(
        "showcase.json.gz",
        frames=frames,
        properties=chemiscope.extract_properties(frames, only=["dipole_ccsd", "ccsd_pol"]),
        meta=dict(name="Dipole and polarizability"),
        settings=chemiscope.quick_settings(
            x="ccsd_pol[1]", y="ccsd_pol[2]", color="dipole_ccsd[1]"
        ),
    )








.. GENERATED FROM PYTHON SOURCE LINES 64-66

In a notebook it is also possible to load a `.json` file and create an interactive
widget from it.

.. GENERATED FROM PYTHON SOURCE LINES 67-69

.. code-block:: Python


    chemiscope.show_input("showcase.json.gz")


.. chemiscope:: _datasets/fig_1-base_002.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 0.052 seconds)


.. _sphx_glr_download_examples_1-base.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: 1-base.ipynb <1-base.ipynb>`

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

      :download:`Download Python source code: 1-base.py <1-base.py>`

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

      :download:`Download zipped: 1-base.zip <1-base.zip>`


.. only:: html

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

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