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Create and visualize vacancy site on surface
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Build a Au (111) surface.

>>> from ase.build import fcc111
>>> from batoms import Batoms
>>> atoms = fcc111("Au", size = (5, 5, 4), vacuum=0)
>>> au111 = Batoms(label = "au111", from_ase = atoms)
>>> au111.cell[2, 2] += 10

Select gold atoms, press ``Tab`` key to switch to ``Edit`` mode. Choose the index of atom for the vacancy.

.. image:: /images/vacancy-edit.png
   :width: 20cm


Set the vacancy atom to a ghost species ``X``.

>>> au111.replace([87], "X")

Then increase the size and set a different color for ``X`` species, and make it a little transparent.

>>> au111['X'].scale = 1.2
>>> au111['X'].color = [0.8, 0.0, 0.8, 0.2]

Save structure to file, and renering the image:

>>> au111.write("POSCAR")
>>> au111.get_image([1, -0.4, 0.4], output = "au111-vacancy.png")


.. image:: /images/vacancy-au111.png
   :width: 8cm


.. note::

    We use ``X`` only for visualization. The ghost species ``X`` will not save to file, thus we make a real vacancy for the surface in the saved file.
    
    Others ways to create a real vacancy is deleting the atom: 

    You can:

    >>> del au111[[87]]

    Or in the ``Edit`` mode, selet the atom, press ``X`` key and delete ``vertices``.

.. note::

    Use ``Cycles`` render engine to get a better image.
    
    >>> au111.render.lights["Default"].energy = 25
    >>> au111.render.engine = "cycles"
    >>> au111.get_image([1, -0.4, 0.4], output = "au111-vacancy-cycles.png")

    .. image:: /images/vacancy-au111-cycles.png
        :width: 12cm