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use pyo3::prelude::*;
use numpy::
{
IntoPyArray,
PyArrayDyn,
PyReadonlyArrayDyn
};
use crate::physics::BOLTZMANN_CONSTANT;
pub fn register_module(py: Python<'_>, parent_module: &PyModule) -> PyResult<()>
{
let isotensional = PyModule::new(py, "isotensional")?;
super::asymptotic::py::register_module(py, isotensional)?;
super::legendre::py::register_module(py, isotensional)?;
parent_module.add_submodule(isotensional)?;
isotensional.add_class::<LOGSQUAREDFJC>()?;
Ok(())
}
/// The log-squared link potential freely-jointed chain (log-squared-FJC) model thermodynamics in the isotensional ensemble.
#[pyclass]
#[derive(Copy, Clone)]
pub struct LOGSQUAREDFJC
{
/// The mass of each hinge in the chain in units of kg/mol.
#[pyo3(get)]
pub hinge_mass: f64,
/// The length of each link in the chain in units of nm.
#[pyo3(get)]
pub link_length: f64,
/// The number of links in the chain.
#[pyo3(get)]
pub number_of_links: u8,
/// The stiffness of each link in the chain in units of J/(molâ‹…nm^2).
#[pyo3(get)]
pub link_stiffness: f64,
/// The thermodynamic functions of the model in the isotensional ensemble approximated using an asymptotic approach.
#[pyo3(get)]
pub asymptotic: super::asymptotic::py::LOGSQUAREDFJC,
/// The thermodynamic functions of the model in the isotensional ensemble approximated using a Legendre transformation.
#[pyo3(get)]
pub legendre: super::legendre::py::LOGSQUAREDFJC
}
#[pymethods]
impl LOGSQUAREDFJC
{
#[new]
pub fn init(number_of_links: u8, link_length: f64, hinge_mass: f64, link_stiffness: f64) -> Self
{
LOGSQUAREDFJC
{
hinge_mass,
link_length,
number_of_links,
link_stiffness,
asymptotic: super::asymptotic::py::LOGSQUAREDFJC::init(number_of_links, link_length, hinge_mass, link_stiffness),
legendre: super::legendre::py::LOGSQUAREDFJC::init(number_of_links, link_length, hinge_mass, link_stiffness)
}
}
/// The expected end-to-end length as a function of the applied force and temperature,
///
/// .. math::
/// \xi(f, T) = -\frac{\partial\varphi}{\partial f}.
///
/// Args:
/// force (numpy.ndarray): The force :math:`f`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The end-to-end length :math:`\xi`.
///
pub fn end_to_end_length<'py>(&self, py: Python<'py>, force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
force.as_array().mapv(|force: f64| super::end_to_end_length(&self.number_of_links, &self.link_length, &self.link_stiffness, &force, &temperature)).into_pyarray(py)
}
/// The expected end-to-end length per link as a function of the applied force and temperature.
///
/// Args:
/// force (numpy.ndarray): The force :math:`f`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The end-to-end length per link :math:`\xi/N_b=\ell_b\gamma`.
///
pub fn end_to_end_length_per_link<'py>(&self, py: Python<'py>, force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
force.as_array().mapv(|force: f64| super::end_to_end_length_per_link(&self.link_length, &self.link_stiffness, &force, &temperature)).into_pyarray(py)
}
/// The expected nondimensional end-to-end length as a function of the applied nondimensional force.
///
/// Args:
/// nondimensional_force (numpy.ndarray): The nondimensional force :math:`\eta\equiv\beta f\ell_b`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The nondimensional end-to-end length :math:`N_b\gamma=\xi/\ell_b`.
///
pub fn nondimensional_end_to_end_length<'py>(&self, py: Python<'py>, nondimensional_force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
nondimensional_force.as_array().mapv(|nondimensional_force: f64| super::nondimensional_end_to_end_length(&self.number_of_links, &(self.link_stiffness*self.link_length.powi(2)/BOLTZMANN_CONSTANT/temperature), &nondimensional_force)).into_pyarray(py)
}
/// The expected nondimensional end-to-end length per link as a function of the applied nondimensional force, given by :footcite:t:`buche2022freely` as
///
/// .. math::
/// \gamma(\eta) = -\frac{\partial}{\partial\eta}\,\ln\left[\int \frac{\sinh(s\eta)}{s\eta}\,e^{-\beta u(s)}s^2\,ds\right].
///
/// Args:
/// nondimensional_force (numpy.ndarray): The nondimensional force :math:`\eta\equiv\beta f\ell_b`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The nondimensional end-to-end length per link :math:`\gamma\equiv \xi/N_b\ell_b`.
///
pub fn nondimensional_end_to_end_length_per_link<'py>(&self, py: Python<'py>, nondimensional_force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
nondimensional_force.as_array().mapv(|nondimensional_force: f64| super::nondimensional_end_to_end_length_per_link(&(self.link_stiffness*self.link_length.powi(2)/BOLTZMANN_CONSTANT/temperature), &nondimensional_force)).into_pyarray(py)
}
/// The Gibbs free energy as a function of the applied force and temperature,
///
/// .. math::
/// \varphi(f, T) = -kT\ln Z(f, T).
///
/// Args:
/// force (numpy.ndarray): The force :math:`f`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The Gibbs free energy :math:`\varphi`.
///
pub fn gibbs_free_energy<'py>(&self, py: Python<'py>, force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
force.as_array().mapv(|force: f64| super::gibbs_free_energy(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.link_stiffness, &force, &temperature)).into_pyarray(py)
}
/// The Gibbs free energy per link as a function of the applied force and temperature.
///
/// Args:
/// force (numpy.ndarray): The force :math:`f`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The Gibbs free energy per link :math:`\varphi/N_b`.
///
pub fn gibbs_free_energy_per_link<'py>(&self, py: Python<'py>, force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
force.as_array().mapv(|force: f64| super::gibbs_free_energy_per_link(&self.link_length, &self.hinge_mass, &self.link_stiffness, &force, &temperature)).into_pyarray(py)
}
/// The relative Gibbs free energy as a function of the applied force and temperature.
///
/// Args:
/// force (numpy.ndarray): The force :math:`f`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The relative Gibbs free energy :math:`\Delta\varphi\equiv\varphi(f,T)-\varphi(0,T)`.
///
pub fn relative_gibbs_free_energy<'py>(&self, py: Python<'py>, force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
force.as_array().mapv(|force: f64| super::relative_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.link_stiffness, &force, &temperature)).into_pyarray(py)
}
/// The relative Gibbs free energy per link as a function of the applied force and temperature.
///
/// Args:
/// force (numpy.ndarray): The force :math:`f`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The relative Gibbs free energy per link :math:`\Delta\varphi/N_b`.
///
pub fn relative_gibbs_free_energy_per_link<'py>(&self, py: Python<'py>, force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
force.as_array().mapv(|force: f64| super::relative_gibbs_free_energy_per_link(&self.link_length, &self.link_stiffness, &force, &temperature)).into_pyarray(py)
}
/// The nondimensional Gibbs free energy as a function of the applied nondimensional force and temperature.
///
/// Args:
/// nondimensional_force (numpy.ndarray): The nondimensional force :math:`\eta\equiv\beta f\ell_b`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The nondimensional Gibbs free energy :math:`\beta\varphi=N_b\varrho`.
///
pub fn nondimensional_gibbs_free_energy<'py>(&self, py: Python<'py>, nondimensional_force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
nondimensional_force.as_array().mapv(|nondimensional_force: f64| super::nondimensional_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.hinge_mass, &(self.link_stiffness*self.link_length.powi(2)/BOLTZMANN_CONSTANT/temperature), &nondimensional_force, &temperature)).into_pyarray(py)
}
/// The nondimensional Gibbs free energy per link as a function of the applied nondimensional force and temperature.
///
/// Args:
/// nondimensional_force (numpy.ndarray): The nondimensional force :math:`\eta\equiv\beta f\ell_b`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The nondimensional Gibbs free energy per link :math:`\varrho\equiv\beta\varphi/N_b`.
///
pub fn nondimensional_gibbs_free_energy_per_link<'py>(&self, py: Python<'py>, nondimensional_force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
nondimensional_force.as_array().mapv(|nondimensional_force: f64| super::nondimensional_gibbs_free_energy_per_link(&self.link_length, &self.hinge_mass, &(self.link_stiffness*self.link_length.powi(2)/BOLTZMANN_CONSTANT/temperature), &nondimensional_force, &temperature)).into_pyarray(py)
}
/// The nondimensional relative Gibbs free energy as a function of the applied nondimensional force.
///
/// Args:
/// nondimensional_force (numpy.ndarray): The nondimensional force :math:`\eta\equiv\beta f\ell_b`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The nondimensional relative Gibbs free energy :math:`\beta\Delta\varphi=N_b\Delta\varrho`.
///
pub fn nondimensional_relative_gibbs_free_energy<'py>(&self, py: Python<'py>, nondimensional_force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
nondimensional_force.as_array().mapv(|nondimensional_force: f64| super::nondimensional_relative_gibbs_free_energy(&self.number_of_links, &(self.link_stiffness*self.link_length.powi(2)/BOLTZMANN_CONSTANT/temperature), &nondimensional_force)).into_pyarray(py)
}
/// The nondimensional relative Gibbs free energy per link as a function of the applied nondimensional force, given by :footcite:t:`buche2022freely` as
///
/// .. math::
/// \Delta\varrho(\eta) = \ln\left[\int \frac{\sinh(s\eta)}{s\eta}\,e^{-\beta u(s)}s^2\,ds\right]
/// - \ln\left[\int e^{-\beta u(s)}s^2\,ds\right],
///
/// where the nondimensional link potential :math:`\beta u` is given by
///
/// .. math::
/// \beta u(\lambda) = \frac{\varepsilon}{2}\left[\ln(\lambda)\right]^2,
///
/// where :math:`\varepsilon\equiv\beta u_b=\kappa` is the nondimensional potential energy scale,
/// :math:`\kappa\equiv\beta k_b\ell_b^2` is the nondimensional link stiffness,
/// and :math:`\lambda\equiv\ell/\ell_b` is the nondimensional link stretch.
///
/// Args:
/// nondimensional_force (numpy.ndarray): The nondimensional force :math:`\eta\equiv\beta f\ell_b`.
/// temperature (float): The temperature :math:`T`.
///
/// Returns:
/// numpy.ndarray: The nondimensional relative Gibbs free energy per link :math:`\Delta\varrho\equiv\beta\Delta\varphi/N_b`.
///
pub fn nondimensional_relative_gibbs_free_energy_per_link<'py>(&self, py: Python<'py>, nondimensional_force: PyReadonlyArrayDyn<f64>, temperature: f64) -> &'py PyArrayDyn<f64>
{
nondimensional_force.as_array().mapv(|nondimensional_force: f64| super::nondimensional_relative_gibbs_free_energy_per_link(&(self.link_stiffness*self.link_length.powi(2)/BOLTZMANN_CONSTANT/temperature), &nondimensional_force)).into_pyarray(py)
}
}