.. _file_formats:

File Formats
============

.. _xyz_file_format:

``.xyz`` files
--------------

``atomaccess`` expects the XMOL standard for ``.xyz`` files, and will exit with an error message if this standard is not followed.

A ``.xyz`` file should be formatted as follows

.. code-block::
   :caption: ``.xyz`` file format supported by ``atom_access``

    NUMBER OF ATOMS AS INTEGER
    COMMENT LINE (CAN BE EMPTY)
    ATOMLABEL1 XCOORD YCOORD ZCOORD
    ATOMLABEL2 XCOORD YCOORD ZCOORD
    ATOMLABEL3 XCOORD YCOORD ZCOORD
    ...

Where the atom label consists only of letters, and all coordinates are in Angstrom.


For example, here is the contents of a valid ``.xyz`` file for benzene

.. code-block::
   :caption: ``benzene.xyz``

    12
    Benzene
    H      1.2194     -0.1652      2.1600
    C      0.6825     -0.0924      1.2087
    C     -0.7075     -0.0352      1.1973
    H     -1.2644     -0.0630      2.1393
    C     -1.3898      0.0572     -0.0114
    H     -2.4836      0.1021     -0.0204
    C     -0.6824      0.0925     -1.2088
    H     -1.2194      0.1652     -2.1599
    C      0.7075      0.0352     -1.1973
    H      1.2641      0.0628     -2.1395
    C      1.3899     -0.0572      0.0114
    H      2.4836     -0.1022      0.0205