Struct Brownian3D

pub struct Brownian3D {
    pub pos: Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>,
    pub diffusion_constant: f64,
    pub kb_temperature: f64,
}

Brownian motion of particles

Parameters & Variables

Symbol	Struct Field	Description
$D$	diffusion_constant	Damping constant of each particle.
$k_BT$	kb_temperature	Product of temperature $T$ and Boltzmann constant $k_B$.
$\vec{x}$	pos	Position of the particle.
$R(t)$	(automatically generated)	Gaussian process

Equations

We integrate the standard brownian motion stochastic differential equation. \begin{equation} \dot{\vec{x}} = -\frac{D}{k_B T}\nabla V(x) + \sqrt{2D}R(t) \end{equation} The new random vector is then also sampled by a distribution with greater width. If we choose this value larger than one, we can resolve smaller timesteps to more accurately solve the equations.

Fields

pos: Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Current position of the particle $\vec{x}$.

diffusion_constant: f64

Diffusion constant $D$.

kb_temperature: f64

The product of temperature and boltzmann constant $k_B T$.

Implementations

impl Brownian3D

pub fn new( pos: [f64; 3], diffusion_constant: f64, kb_temperature: f64, ) -> Brownian3D

Available on crate feature cpu_os_threads only.

Constructs a new Brownian3D

impl Brownian3D

pub fn set_pos(&mut self, pos: [f64; 3])

Available on crate feature cpu_os_threads only.

[pyo3] setter for pos

pub fn set_diffusion_constant(&mut self, diffusion_constant: f64)

Available on crate feature cpu_os_threads only.

[pyo3] setter for diffusion_constant

pub fn set_kb_temperature(&mut self, kb_temperature: f64)

Available on crate feature cpu_os_threads only.

[pyo3] setter for kb_temperature

pub fn get_pos(&self) -> [f64; 3]

Available on crate feature cpu_os_threads only.

[pyo3] getter for pos

pub fn get_diffusion_constant(&self) -> f64

Available on crate feature cpu_os_threads only.

[pyo3] getter for diffusion_constant

pub fn get_kb_temperature(&self) -> f64

Available on crate feature cpu_os_threads only.

[pyo3] getter for kb_temperature

Trait Implementations

impl Clone for Brownian3D

fn clone(&self) -> Brownian3D

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Brownian3D

fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Brownian3D

fn deserialize<__D>( __deserializer: __D, ) -> Result<Brownian3D, <__D as Deserializer<'de>>::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl IntoPy<Py<PyAny>> for Brownian3D

fn into_py(self, py: Python<'_>) -> Py<PyAny>

Performs the conversion.

impl Mechanics<Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>> for Brownian3D

fn get_random_contribution( &self, rng: &mut ChaCha8Rng, dt: f64, ) -> Result<(Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>), RngError>

Define a new random variable in case that the mechanics type contains a random aspect to its motion. By default this function does nothing.

fn calculate_increment( &self, force: Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, ) -> Result<(Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>), CalcError>

Calculate the time-derivative of force and velocity given all the forces that act on the cell. Simple damping effects should be included in this trait if not explicitly given by the SubDomainForce trait.

impl PartialEq for Brownian3D

fn eq(&self, other: &Brownian3D) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Position<Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>> for Brownian3D

fn pos(&self) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Gets the cells current position.

fn set_pos( &mut self, pos: &Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, )

Gets the cells current velocity.

impl PyClass for Brownian3D

type Frozen = False

Whether the pyclass is frozen.

impl PyTypeInfo for Brownian3D

const NAME: &'static str = "Brownian3D"

Class name.

const MODULE: Option<&'static str> = ::core::option::Option::None

Module name, if any.

fn type_object_raw(py: Python<'_>) -> *mut PyTypeObject

Returns the PyTypeObject instance for this type.

fn type_object_bound(py: Python<'_>) -> Bound<'_, PyType>

Returns the safe abstraction over the type object.

fn is_type_of_bound(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type or a subclass of this type.

fn is_exact_type_of_bound(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type.

impl Serialize for Brownian3D

fn serialize<__S>( &self, __serializer: __S, ) -> Result<<__S as Serializer>::Ok, <__S as Serializer>::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Velocity<Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>> for Brownian3D

fn velocity(&self) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Gets the cells current velocity.

fn set_velocity( &mut self, _velocity: &Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>, )

Sets the cells current velocity.

impl DerefToPyAny for Brownian3D

impl StructuralPartialEq for Brownian3D