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

.. only:: html

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

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

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

.. _sphx_glr_howtos_generated_howto_io_howto_opls.py:

.. _howto_opls_setup:

Setting up an OPLS force field calculation
==========================================


Suppose, we define the ethanal molecule as extended xyz file
(``172_ext.xyz``):

.. GENERATED FROM PYTHON SOURCE LINES 12-15

.. literalinclude:: ../../../examples/howtos/howto_io/172_ext.xyz

Then we can read and view the structure using:

.. GENERATED FROM PYTHON SOURCE LINES 15-25

.. code-block:: Python


    from ase.io.opls import OPLSStructure
    from ase.visualize import view

    s = OPLSStructure('172_ext.xyz')
    view(s)  # view with real elements
    elements = {'CT': 'Si', 'HC': 'H', 'H1': 'He'}
    view(s.colored(elements))  # view with fake elements






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

 .. code-block:: none


    <Popen: returncode: None args: ['/usr/local/bin/python3.14', '-m', 'ase', 'g...>



.. GENERATED FROM PYTHON SOURCE LINES 26-35

Defining the force field
------------------------

The definitions of the force field can be stored in an Amber like style
(``172_defs.par``):

.. literalinclude:: ../../../examples/howtos/howto_io/172_defs.par

We can write LAMMPS input using the information above:

.. GENERATED FROM PYTHON SOURCE LINES 35-43

.. code-block:: Python


    from ase.io.opls import OPLSff, OPLSStructure

    s = OPLSStructure('172_ext.xyz')
    with open('172_defs.par') as fd:
        opls = OPLSff(fd)
    opls.write_lammps(s, prefix='lmp')








.. GENERATED FROM PYTHON SOURCE LINES 44-47

which writes the LAMMPS input files ``lmp_atoms`` defining atoms,  bonds,
etc., and ``lmp_opls`` defining the corresponding OPLS force field. A
rudimentary ``lmp_in`` is also written.


.. _sphx_glr_download_howtos_generated_howto_io_howto_opls.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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