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:synopsis: File input-output module
File input and output
=====================
The :mod:`ase.io` module has two basic functions: :func:`read` and
:func:`write`. The two methods are described here:
.. autofunction:: read
.. autofunction:: write
The :func:`read` function is only designed to retrieve the atomic configuration
from a file, but for the CUBE format you can import the function:
.. function:: read_cube_data
which will return a ``(data, atoms)`` tuple::
from ase.io.cube import read_cube_data
data, atoms = read_cube_data('abc.cube')
Examples
========
::
from ase.lattice.surface import *
adsorbate = Atoms('CO')
adsorbate[1].z = 1.1
a = 3.61
slab = fcc111('Cu', (2, 2, 3), a=a, vacuum=7.0)
add_adsorbate(slab, adsorbate, 1.8, 'ontop')
Write PNG image::
write('slab.png', slab * (3, 3, 1), rotation='10z,-80x')
.. image:: io1.png
Write POVRAY file::
write('slab.pov', slab * (3, 3, 1), rotation='10z,-80x')
This will write both a ``slab.pov`` and a ``slab.ini`` file. Convert
to PNG with the command ``povray slab.ini`` or use the
``run_povray=True`` option:
.. image:: io2.png
Here is an example using ``bbox``::
d = a / 2**0.5
write('slab.pov', slab * (2, 2, 1),
bbox=(d, 0, 3 * d, d * 3**0.5))
.. image:: io3.png
Note that the XYZ-format does not contain information about the unic cell:
>>> write('slab.xyz', slab)
>>> a = read('slab.xyz')
>>> a.get_cell()
array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
>>> a.get_pbc()
array([False, False, False], dtype=bool)
Use ASE's native format for writing all information:
>>> write('slab.traj', slab)
>>> b = read('slab.traj')
>>> b.get_cell()
array([[ 5.10531096e+00, -4.11836034e-16, 1.99569088e-16],
[ 2.55265548e+00, 4.42132899e+00, 7.11236625e-17],
[ 8.11559027e+00, 4.68553823e+00, 1.32527034e+01]])
>>> b.get_pbc()
array([ True, True, True], dtype=bool)
A script showing all of the povray parameters, and generating the image below,
can be found here: :download:`save_pov.py`
.. image:: NaCl_C6H6.png
An other example showing how to change colors and textures in pov can
be found here: :download:`../tutorials/saving_graphics.py`.
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