Struct CartesianCuboidVoxel2

pub struct CartesianCuboidVoxel2<const N: usize> {
    pub extracellular_concentrations: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>,
    pub extracellular_gradient: Matrix<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Const<N>, Const<1>, ArrayStorage<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, N, 1>>,
    pub diffusion_constant: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>,
    pub production_rate: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>,
    pub degradation_rate: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>,
    /* private fields */
}

Cuboid Voxel for CartesianCuboid2 in 2D

Fields

extracellular_concentrations: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>

Concentrations of the different diffusables

extracellular_gradient: Matrix<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Const<N>, Const<1>, ArrayStorage<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, N, 1>>

The gradient of diffusables at this voxel

diffusion_constant: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>

Local diffusion constant

production_rate: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>

Local production rate of diffusables

degradation_rate: Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>

Local degradation rate of diffusables

Implementations

impl<const N: usize> CartesianCuboidVoxel2<N>

pub fn get_min(&self) -> [f64; 2]

Available on crate feature cpu_os_threads only.

Get lower boundary of voxel

pub fn get_max(&self) -> [f64; 2]

Available on crate feature cpu_os_threads only.

Get upper boundary of voxel

pub fn get_middle(&self) -> [f64; 2]

Available on crate feature cpu_os_threads only.

Get middle of voxel

pub fn get_dx(&self) -> [f64; 2]

Available on crate feature cpu_os_threads only.

Get side lengths of voxel

Trait Implementations

impl<const N: usize> Clone for CartesianCuboidVoxel2<N>

fn clone(&self) -> CartesianCuboidVoxel2<N>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<const N: usize> Debug for CartesianCuboidVoxel2<N>

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

Formats the value using the given formatter.

impl<'de, const N: usize> Deserialize<'de> for CartesianCuboidVoxel2<N>

fn deserialize<__D>( __deserializer: __D, ) -> Result<CartesianCuboidVoxel2<N>, <__D as Deserializer<'de>>::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl<Cel, const N: usize> Domain<Cel, [i64; 2], CartesianCuboidVoxel2<N>> for CartesianCuboid2

where Cel: Position<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>> + Velocity<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>>,

fn apply_boundary(&self, cell: &mut Cel) -> Result<(), BoundaryError>

Applies boundary conditions to a cell in order to keep it inside the simulation. For the future, we aim to apply boundary conditions to the position of the cell rather than itself. In addition, we would like to be able to invoke events such as Remove to maximize flexibility.

fn get_voxel_index(&self, cell: &Cel) -> [i64; 2]

Provided a cell, gives the corresponding Index and thus which voxel to sort into.

fn get_all_indices(&self) -> Vec<[i64; 2]>

Get all indices that are present in the simulation. Required for initial configuration of the simulation domain.

fn get_neighbor_voxel_indices(&self, index: &[i64; 2]) -> Vec<[i64; 2]>

Retrieves the neighboring voxels of the one specified.

fn generate_contiguous_multi_voxel_regions( &self, n_regions: usize, ) -> Result<Vec<Vec<([i64; 2], CartesianCuboidVoxel2<N>)>>, CalcError>

Allows the backend to split the domain into continuous regions which contain voxels. These regions can then be used for parallelization.

impl<const N: usize> ExtracellularMechanics<[i64; 2], Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>, Matrix<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Const<N>, Const<1>, ArrayStorage<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, N, 1>>> for CartesianCuboidVoxel2<N>

fn get_extracellular_at_point( &self, pos: &Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, ) -> Result<Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>, RequestError>

Obtain the extracellular concentration at a specified point.

fn get_total_extracellular( &self, ) -> Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>

Obtain every concentration in the current voxel. This function is only relevant for the backend.

fn update_extracellular_gradient( &mut self, boundaries: &[([i64; 2], BoundaryCondition<Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>>)], ) -> Result<(), CalcError>

Update function to calculate the gradient of concentrations in this voxel.

fn get_extracellular_gradient_at_point( &self, _pos: &Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, ) -> Result<Matrix<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Const<N>, Const<1>, ArrayStorage<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, N, 1>>, RequestError>

Obtain the gradient at a certain point.

fn set_total_extracellular( &mut self, concentrations: &Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>, ) -> Result<(), CalcError>

Simple setter function to specify concentrations after backend has updated values.

fn calculate_increment( &self, total_extracellular: &Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>, point_sources: &[(Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>)], boundaries: &[([i64; 2], BoundaryCondition<Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>>)], ) -> Result<Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>, CalcError>

Calculates the time-derivative of the function that increments the concentrations.

fn boundary_condition_to_neighbor_voxel( &self, _neighbor_index: &[i64; 2], ) -> Result<BoundaryCondition<Matrix<f64, Const<N>, Const<1>, ArrayStorage<f64, N, 1>>>, IndexError>

Gets the boundary to the specified neighboring voxel.

impl<const N: usize> Serialize for CartesianCuboidVoxel2<N>

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<const N: usize> Volume for CartesianCuboidVoxel2<N>

fn get_volume(&self) -> f64

Obtain the cells current volume.

impl<const N: usize> Voxel<[i64; 2], Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>> for CartesianCuboidVoxel2<N>

fn get_index(&self) -> [i64; 2]

Gets the Index of the voxel.

fn custom_force_on_cell( &self, _pos: &Pos, _vel: &Vel, ) -> Option<Result<Force, CalcError>>

Voxels can exert custom forces on cells. In the future this function will probably be part of a different Trait.