:orphan:

:mod:`atsim.potentials._lammpsWriteEAM`
=======================================

.. py:module:: atsim.potentials._lammpsWriteEAM


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   atsim.potentials._lammpsWriteEAM.writeFuncFL
   atsim.potentials._lammpsWriteEAM.writeSetFL
   atsim.potentials._lammpsWriteEAM.writeSetFLFinnisSinclair


.. function:: writeFuncFL(nrho, drho, nr, dr, eampots, pairpots, out=sys.stdout, title='')

   Creates a DYNAMO ``funcfl`` formatted file suitable for use with lammps `pair_style eam <http://lammps.sandia.gov/doc/pair_eam.html>`_
   potential form. For the `pair_style eam/alloy <http://lammps.sandia.gov/doc/pair_eam.html>`_ see :func:`~atsim.potentials.writeSetFL`.

   .. seealso ::

     For a working example using this function see :ref:`eam_example_1`


   :param nrho: Number of points used to describe embedding function
   :type nrho: int

   :param drho: Step size between rho values used to describe embedding function
   :type drho: float

   :param nr:   Number of points used for the pair-potential, and density functions
   :type nr: int

   :param dr:   Step size between r values in effective charge and density functions
   :type dr: float

   :param eampots: List containing a single :class:`~atsim.potentials.EAMPotential` instance for species to be tabulated.
   :type eampots: list

   :param pairpots: List containing a single :class:`~atsim.potentials.PairPotential` instance for the X-X interaction (where X is the species represented by EAMPotential in ``eampots`` list)
   :type pairpots: list

   :param out:  Python file object to which eam table file will be written
   :type out: file object

   :param title: Title to be written as table file header
   :type title: str


.. function:: writeSetFL(nrho, drho, nr, dr, eampots, pairpots, out=sys.stdout, comments=['', '', ''], cutoff=None)

   Creates EAM potential in the DYNAMO ``setfl`` format. This format is suitable for
   use with the ``LAMMPS`` `pair_style eam/alloy <http://lammps.sandia.gov/doc/pair_eam.html>`_.

   .. seealso ::

     For a working example using this function see :ref:`eam_example_2a`


   :param nrho: Number of points used to describe embedding function
   :type nrho: int
   :param drho: Increment used when tabulating embedding function
   :type drho: float
   :param nr: Number of points used to describe density and pair potentials
   :type nr: int
   :param dr: Separation increment used when tabulating density function and pair potentials
   :type dr: float
   :param eampots: Instances of lammps.writeEAMTable.EAMPotential() which encapsulate information about each species
   :type eampots: list
   :param pairpots: Instance of potentials.Potential, these describe repulsive pair potential component of EAM potential
   :type pairpots: list
   :param out: Python file object into which EAM potential data should be written
   :type out: file object
   :param comments: List containing three strings, these form the header of the created file
   :type comments: list
   :param cutoff: Pair potential and density cutoff, if None then value of ``nr`` * ``dr`` is used.
   :type cutoff: float


.. function:: writeSetFLFinnisSinclair(nrho, drho, nr, dr, eampots, pairpots, out=sys.stdout, comments=['', '', ''], cutoff=None)

   Creates Finnis-Sinclar EAM potential in the DYNAMO ``setfl`` format. The format should be used with the
   ``LAMMPS`` `eam/fs pair_style <http://lammps.sandia.gov/doc/pair_eam.html>`_.

   The :class:`~atsim.potentials.EAMPotential` instances within the ``eampots`` list are expected to provide individual density functions
   for each species pair in the species being tabulated. See :meth:`atsim.potentials.EAMPotential.__init__` for how these are specified
   to the :class:`atsim.potentials.EAMPotential` constructor.

   .. seealso ::

     For a working example using this function see :ref:`eam_example_3a`



   :param nrho: Number of points used to describe embedding function
   :type nrho: int
   :param drho: Increment used when tabulating embedding function
   :type drho: float
   :param nr: Number of points used to describe density and pair potentials
   :type nr: int
   :param dr: Separation increment used when tabulating density function and pair potentials
   :type dr: float
   :param eampots: Instances of lammps.writeEAMTable.EAMPotential() which encapsulate information about each species
   :type eampots: list
   :param pairpots: Instance of potentials.Potential, these describe repulsive pair potential component of EAM potential
   :type pairpots: list
   :param out: Python file object into which EAM potential data should be written
   :type out: file object
   :param comments: List containing three strings, these form the header of the created file
   :type comments: list
   :param cutoff: Pair potential and density cutoff. If None then value of ``nr`` * ``dr`` is used.
   :type cutoff: float