mythos.energy.martini.m2.lj
===========================

.. py:module:: mythos.energy.martini.m2.lj

.. autoapi-nested-parse::

   Lennard-Jones potential energy function for Martini 2.



Attributes
----------

.. autoapisummary::

   mythos.energy.martini.m2.lj.LJ_SIGMA_PREFIX
   mythos.energy.martini.m2.lj.LJ_EPSILON_PREFIX


Classes
-------

.. autoapisummary::

   mythos.energy.martini.m2.lj.LJConfiguration
   mythos.energy.martini.m2.lj.LJ


Functions
---------

.. autoapisummary::

   mythos.energy.martini.m2.lj.lennard_jones
   mythos.energy.martini.m2.lj.pair_lj


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

.. py:data:: LJ_SIGMA_PREFIX
   :value: 'lj_sigma_'


.. py:data:: LJ_EPSILON_PREFIX
   :value: 'lj_epsilon_'


.. py:class:: LJConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)

   Bases: :py:obj:`mythos.energy.martini.base.MartiniEnergyConfiguration`


   "Configuration for Martini Lennard-Jones energy function.

   All parameters provided must be of the form "lj_sigma_A_B" or "lj_epsilon_A_B",
   where A and B are bead types. Pair order is ignored unless both orderings
   are provided. It is required that sigma and epsilon parameters are provided
   for any bead type pairs present in the system.

   Couplings are supported (see :class:`MartiniEnergyConfiguration` for details).


   .. py:method:: __post_init__() -> None

      Hook for additional initialization in subclasses.



.. py:function:: lennard_jones(r: float, eps: float, sigma: float) -> float

   Calculate Lennard-Jones potential given distance r, epsilon, and sigma.


.. py:function:: pair_lj(centers: mythos.utils.types.Arr_States_3, pair: mythos.utils.types.Vector2D, sigmas: mythos.utils.types.MatrixSq, epsilons: mythos.utils.types.MatrixSq, types: mythos.utils.types.Arr_N, displacement_fn: callable) -> float

   Calculate LJ energy for a given pair of particles.


.. py:class:: LJ

   Bases: :py:obj:`mythos.energy.martini.base.MartiniEnergyFunction`


   Lennard-Jones potential energy function for Martini 2.


   .. py:attribute:: params
      :type:  LJConfiguration


   .. py:method:: __post_init__(topology: None = None) -> None


   .. py:method:: compute_energy(trajectory: mythos.simulators.io.SimulatorTrajectory) -> float

      Compute the energy of the system given the nucleotide.