.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples_generated/gallery/o2pt100.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_generated_gallery_o2pt100.py>`
        to download the full example code.

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

.. _sphx_glr_examples_generated_gallery_o2pt100.py:


Dissociation of oxygen on Pt(100)
=================================

.. GENERATED FROM PYTHON SOURCE LINES 6-80



.. image-sg:: /examples_generated/gallery/images/sphx_glr_o2pt100_001.png
   :alt: o2pt100
   :srcset: /examples_generated/gallery/images/sphx_glr_o2pt100_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    PosixPath('/builds/ase/ase-deploy/examples/gallery/o2pt100.png')





|

.. code-block:: Python


    import numpy as np

    from ase.build import add_adsorbate, fcc100
    from ase.io import write

    # the metal slab
    atoms = fcc100('Pt', size=[4, 10, 3], vacuum=10)
    transmittances = [0 for a in atoms]
    bonded_atoms = []

    upper_layer_idx = [a.index for a in atoms if a.tag == 1]
    middle = atoms.positions[upper_layer_idx, :2].max(axis=0) / 2

    # the dissociating oxygen... fake some dissociation curve
    gas_dist = 1.1
    max_height = 8.0
    min_height = 1.0
    max_dist = 6

    # running index for the bonds
    index = len(atoms)

    for i, x in enumerate(np.linspace(0, 1.5, 6)):
        height = (max_height - min_height) * np.exp(-2 * x) + min_height
        d = np.exp(1.5 * x) / np.exp(1.5**2) * max_dist + gas_dist
        pos = middle + [0, d / 2]
        add_adsorbate(atoms, 'O', height=height, position=pos)
        pos = middle - [0, d / 2]
        add_adsorbate(atoms, 'O', height=height, position=pos)
        transmittances += [x / 2] * 2

        # we want bonds for the first two molecules
        if i < 2:
            bonded_atoms.append([len(atoms) - 1, len(atoms) - 2])

    textures = ['ase3' for a in atoms]

    # add some semi-transparent bath (only in x/y direction for this example)
    cell = atoms.cell

    idx = [a.index for a in atoms if a.symbol == 'Pt']

    Nbulk = len(idx)
    multiples = [0, 1, -1]
    for i in multiples:
        for j in multiples:
            if i == j == 0:
                continue
            chunk = atoms[idx]
            chunk.translate(i * cell[0] + j * cell[1])
            atoms += chunk
            transmittances += [0.8] * Nbulk
            textures += ['pale'] * Nbulk

    bbox = [-30, 10, 5, 25]

    renderer = write(
        'o2pt100.pov',
        atoms,
        rotation='90z,-75x',
        bbox=bbox,
        show_unit_cell=0,
        povray_settings=dict(
            pause=False,
            canvas_width=1024,
            bondatoms=bonded_atoms,
            camera_type='perspective',
            transmittances=transmittances,
            textures=textures,
        ),
    )

    renderer.render()


.. _sphx_glr_download_examples_generated_gallery_o2pt100.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: o2pt100.ipynb <o2pt100.ipynb>`

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

      :download:`Download Python source code: o2pt100.py <o2pt100.py>`

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

      :download:`Download zipped: o2pt100.zip <o2pt100.zip>`


.. only:: html

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

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