jax_dna.energy.potentials
=========================

.. py:module:: jax_dna.energy.potentials

.. autoapi-nested-parse::

   This module contains the potential energy functions used in the oxDNA DNA1 model.



Functions
---------

.. autoapisummary::

   jax_dna.energy.potentials.v_fene
   jax_dna.energy.potentials.v_morse
   jax_dna.energy.potentials.v_harmonic
   jax_dna.energy.potentials.v_lj
   jax_dna.energy.potentials.v_mod
   jax_dna.energy.potentials.v_smooth


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

.. py:function:: v_fene(r: jax_dna.utils.types.ARR_OR_SCALAR, eps: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar, delt: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   FENE spring (used to connect backbones).

   This is based on equation 2.1 from the oxDNA paper.


.. py:function:: v_morse(r: jax_dna.utils.types.ARR_OR_SCALAR, eps: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   Morse potential (used for stacking and H-bonding).

   This is based on equation 2.2 from the oxDNA paper.


.. py:function:: v_harmonic(r: jax_dna.utils.types.ARR_OR_SCALAR, k: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   Harmonic potential (used for cross-stacking and coaxial stacking).

   This is based on equation 2.3 from the oxDNA paper.


.. py:function:: v_lj(r: jax_dna.utils.types.ARR_OR_SCALAR, eps: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   Lennard - Jones potential (used for soft repulsion).

   This is based on equation 2.4 from the oxDNA paper.


.. py:function:: v_mod(theta: jax_dna.utils.types.ARR_OR_SCALAR, a: jax_dna.utils.types.Scalar, theta0: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   Quadratic terms (used for modulation).

   This is based on equation 2.5 from the oxDNA paper.


.. py:function:: v_smooth(x: jax_dna.utils.types.ARR_OR_SCALAR, b: jax_dna.utils.types.Scalar, x_c: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   Quadratic smoothing terms for truncation.

   This is based on equation 2.6 from the oxDNA paper.