{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Setting up an OPLS force field calculation\n\n\nSuppose, we define the ethanal molecule as extended xyz file\n(``172_ext.xyz``):\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        ".. literalinclude:: ../../../examples/howtos/howto_io/172_ext.xyz\n\nThen we can read and view the structure using:\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "from ase.io.opls import OPLSStructure\nfrom ase.visualize import view\n\ns = OPLSStructure('172_ext.xyz')\nview(s)  # view with real elements\nelements = {'CT': 'Si', 'HC': 'H', 'H1': 'He'}\nview(s.colored(elements))  # view with fake elements"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Defining the force field\n\nThe definitions of the force field can be stored in an Amber like style\n(``172_defs.par``):\n\n.. literalinclude:: ../../../examples/howtos/howto_io/172_defs.par\n\nWe can write LAMMPS input using the information above:\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "from ase.io.opls import OPLSff, OPLSStructure\n\ns = OPLSStructure('172_ext.xyz')\nwith open('172_defs.par') as fd:\n    opls = OPLSff(fd)\nopls.write_lammps(s, prefix='lmp')"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "which writes the LAMMPS input files ``lmp_atoms`` defining atoms,  bonds,\netc., and ``lmp_opls`` defining the corresponding OPLS force field. A\nrudimentary ``lmp_in`` is also written.\n\n"
      ]
    }
  ],
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