jax_dna.energy.dna1.base_smoothing_functions
============================================

.. py:module:: jax_dna.energy.dna1.base_smoothing_functions

.. autoapi-nested-parse::

   Smoothing functions for the base functions in DNA1 model.

   functional forms from oxDNA paper
   https://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719/files/mdcac62bc9133143fc05070ed20048c50
   # Section 2.4.1



Functions
---------

.. autoapisummary::

   jax_dna.energy.dna1.base_smoothing_functions._solve_f1_b
   jax_dna.energy.dna1.base_smoothing_functions._solve_f1_xc_star
   jax_dna.energy.dna1.base_smoothing_functions.get_f1_smoothing_params
   jax_dna.energy.dna1.base_smoothing_functions._solve_f2_b
   jax_dna.energy.dna1.base_smoothing_functions._solve_f2_xc_star
   jax_dna.energy.dna1.base_smoothing_functions.get_f2_smoothing_params
   jax_dna.energy.dna1.base_smoothing_functions._solve_f3_b
   jax_dna.energy.dna1.base_smoothing_functions._solve_f3_xc
   jax_dna.energy.dna1.base_smoothing_functions.get_f3_smoothing_params
   jax_dna.energy.dna1.base_smoothing_functions._solve_f4_b
   jax_dna.energy.dna1.base_smoothing_functions._solve_f4_xc
   jax_dna.energy.dna1.base_smoothing_functions.get_f4_smoothing_params
   jax_dna.energy.dna1.base_smoothing_functions._solve_f5_b
   jax_dna.energy.dna1.base_smoothing_functions._solve_f5_xc
   jax_dna.energy.dna1.base_smoothing_functions.get_f5_smoothing_params


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

.. py:function:: _solve_f1_b(x: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter b in the f1 smoothing function.


.. py:function:: _solve_f1_xc_star(x: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter xc_star in the f1 smoothing function.


.. py:function:: get_f1_smoothing_params(x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar, x_low: jax_dna.utils.types.Scalar, x_high: jax_dna.utils.types.Scalar) -> tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

   Get the smoothing parameters for the f1 smoothing function.


.. py:function:: _solve_f2_b(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter b in the f2 smoothing function.


.. py:function:: _solve_f2_xc_star(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter xc_star in the f2 smoothing function.


.. py:function:: get_f2_smoothing_params(x0: jax_dna.utils.types.Scalar, xc: jax_dna.utils.types.Scalar, x_low: jax_dna.utils.types.Scalar, x_high: jax_dna.utils.types.Scalar) -> tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

   Get the smoothing parameters for the f2 smoothing function.


.. py:function:: _solve_f3_b(x: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter b in the f3 smoothing function.


.. py:function:: _solve_f3_xc(x: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter xc in the f3 smoothing function.


.. py:function:: get_f3_smoothing_params(r_star: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) -> tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

   Get the smoothing parameters for the f3 smoothing function.


.. py:function:: _solve_f4_b(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter b in the f4 smoothing function.


.. py:function:: _solve_f4_xc(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter xc in the f4 smoothing function.


.. py:function:: get_f4_smoothing_params(a: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, delta_x_star: jax_dna.utils.types.Scalar) -> tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

   Get the smoothing parameters for the f4 smoothing function.


.. py:function:: _solve_f5_b(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter b in the f5 smoothing function.


.. py:function:: _solve_f5_xc(x: jax_dna.utils.types.Scalar, x0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Solve for the smoothing parameter xc in the f5 smoothing function.


.. py:function:: get_f5_smoothing_params(a: jax_dna.utils.types.Scalar, x_star: jax_dna.utils.types.Scalar) -> tuple[jax_dna.utils.types.Scalar, jax_dna.utils.types.Scalar]

   Get the smoothing parameters for the f5 smoothing function.