Struct SubDomainBox

pub struct SubDomainBox<I, S, C, A, Com, Sy = BarrierSync>
where
    S: SubDomain,
{ /* private fields */ }

Available on crate feature chili only.

Encapsulates a subdomain with cells and other simulation aspects.

Implementations

impl<I, S, C, A, Com, Sy> SubDomainBox<I, S, C, A, Com, Sy>

where S: SubDomain,

pub fn sync(&mut self) -> Result<(), SimulationError>

where Sy: SyncSubDomains,

Available on crate feature cpu_os_threads only.

Allows to sync between threads. In the most simplest case of BarrierSync syncing is done by a global barrier.

pub fn store_error( &mut self, maybe_error: Result<(), SimulationError>, ) -> Result<bool, SimulationError>

where Sy: SyncSubDomains,

Available on crate feature cpu_os_threads only.

Stores an error which has occurred and notifies other running threads to wind down.

pub fn insert_cells( &mut self, new_cells: &mut Vec<(C, Option<A>)>, init_aux_storage: impl Fn(&C) -> A, ) -> Result<(), BoundaryError>

where <S as SubDomain>::VoxelIndex: Eq + Hash + Ord, S: SortCells<C, VoxelIndex = <S as SubDomain>::VoxelIndex>,

Available on crate feature cpu_os_threads only.

Allows insertion of cells into the subdomain.

pub fn run_local_cell_funcs<Func, F>( &mut self, func: Func, next_time_point: &NextTimePoint<F>, ) -> Result<(), SimulationError>

where Func: Fn(&mut C, &mut A, F, &mut ChaCha8Rng) -> Result<(), SimulationError>, F: Copy,

Available on crate feature cpu_os_threads only.

Update all purely local functions

Used to iterate over all cells in the current subdomain and running local functions which need no communication with other subdomains

pub fn run_local_subdomain_funcs<Func, F>( &mut self, func: Func, next_time_point: &NextTimePoint<F>, ) -> Result<(), SimulationError>

where Func: Fn(&mut S, F) -> Result<(), SimulationError>, F: Copy,

Available on crate feature cpu_os_threads only.

TODO

pub fn save_subdomains<F>( &self, storage_manager: &mut StorageManager<SubDomainPlainIndex, S>, next_time_point: &NextTimePoint<F>, ) -> Result<(), StorageError>

where F: Debug, S: Clone + Serialize,

Available on crate feature cpu_os_threads only.

Save all subdomains with the given storage manager.

pub fn save_cells<F>( &self, storage_manager: &mut StorageManager<CellIdentifier, (CellBox<C>, A)>, next_time_point: &NextTimePoint<F>, ) -> Result<(), StorageError>

where F: Debug, A: Clone + Serialize, C: Clone + Serialize, CellBox<C>: Id<Identifier = CellIdentifier>,

Available on crate feature cpu_os_threads only.

Stores all cells of the subdomain via the given storage_manager

impl<I, S, C, A, Com, Sy> SubDomainBox<I, S, C, A, Com, Sy>

where S: SubDomain,

pub fn update_cell_cycle_4<F, Func>( &mut self, default_from: &Func, ) -> Result<(), SimulationError>

where F: Debug, C: Cycle<C, F>, A: UpdateCycle, Func: Fn(&C) -> A,

Available on crate feature cpu_os_threads only.

Separate function to update the cell cycle

Instead of running one big update function for all local rules, we have to treat this cell cycle differently since new cells could be generated and thus have consequences for other update steps as well.

impl<I, S, C, A, Com, Sy> SubDomainBox<I, S, C, A, Com, Sy>

where S: SubDomain,

pub fn update_mechanics_interaction_step_1<Pos, Vel, For, Float, Inf, const N: usize>( &mut self, ) -> Result<(), SimulationError>

where Pos: Clone, Vel: Clone, Inf: Clone, C: Position<Pos> + Velocity<Vel> + Mechanics<Pos, Vel, For, Float> + Interaction<Pos, Vel, For, Inf>, A: UpdateMechanics<Pos, Vel, For, N> + UpdateInteraction, For: Xapy<Float> + AddAssign, Float: Float + AddAssign, <S as SubDomain>::VoxelIndex: Ord, S: SubDomainMechanics<Pos, Vel>, Com: Communicator<SubDomainPlainIndex, PosInformation<Pos, Vel, Inf>>,

Available on crate feature cpu_os_threads only.

Update cells position and velocity

We assume that cells implement the Mechanics and Interaction traits. Then, threads will exchange information in the PosInformation format to calculate the forces acting on the cells.

pub fn calculate_custom_domain_force<Pos, Vel, For, const N: usize>( &mut self, ) -> Result<(), SimulationError>

where Pos: Clone, Vel: Clone, C: Position<Pos> + Velocity<Vel>, A: UpdateMechanics<Pos, Vel, For, N>, S: SubDomainForce<Pos, Vel, For>,

Available on crate feature cpu_os_threads only.

Calculates the custom force of the domain on the cells.

pub fn update_mechanics_interaction_step_2<Pos, Vel, For, Float, Inf, const N: usize>( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where For: Xapy<Float> + Clone + AddAssign, A: UpdateMechanics<Pos, Vel, For, N> + UpdateInteraction, Float: Float, Pos: Clone, Vel: Clone, C: Position<Pos> + Velocity<Vel> + Mechanics<Pos, Vel, For, Float> + Interaction<Pos, Vel, For, Inf>, Com: Communicator<SubDomainPlainIndex, PosInformation<Pos, Vel, Inf>> + Communicator<SubDomainPlainIndex, ForceInformation<For>>,

Available on crate feature cpu_os_threads only.

Update cells position and velocity

We assume that cells implement the Mechanics and Interaction traits. Then, threads will use the previously exchanged PosInformation to calculate forces and send back information about the acting force in the ForceInformation format. In addition, this method also applies the inverse force to local cells.

pub fn update_mechanics_interaction_step_3<Pos, Vel, For, const N: usize>( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where A: UpdateMechanics<Pos, Vel, For, N>, Com: Communicator<SubDomainPlainIndex, ForceInformation<For>>,

Available on crate feature cpu_os_threads only.

Receive all calculated forces and include them for later update steps.

pub fn apply_boundary<Pos, Vel>(&mut self) -> Result<(), BoundaryError>

where C: Position<Pos> + Velocity<Vel>, S: SubDomainMechanics<Pos, Vel>,

Available on crate feature cpu_os_threads only.

Applies boundary conditions to cells. For the future, we hope to be using previous and current position of cells rather than the cell itself.

pub fn sort_cells_in_voxels_step_1(&mut self) -> Result<(), SimulationError>

where Com: Communicator<SubDomainPlainIndex, SendCell<CellBox<C>, A>>, S: SortCells<C, VoxelIndex = <S as SubDomain>::VoxelIndex>, <S as SubDomain>::VoxelIndex: Eq + Hash + Ord,

Available on crate feature cpu_os_threads only.

Sort new cells into respective voxels

This step determines if a cell is still in its correct location after its position has changed. This can be due to the SubDomainBox::update_mechanics_interaction_step_3 method or due to other effects such as cell-division by the cellular_raza_concepts::Cycle trait.

If the cell is not in the correct voxel, we either directly insert this cell into the voxel or send it to the other SubDomainBox to take care of this.

pub fn sort_cells_in_voxels_step_2( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where Com: Communicator<SubDomainPlainIndex, SendCell<CellBox<C>, A>>, <S as SubDomain>::VoxelIndex: Eq + Hash + Ord, S: SortCells<C, VoxelIndex = <S as SubDomain>::VoxelIndex>,

Available on crate feature cpu_os_threads only.

Sort new cells into respective voxels

After having sent cells to the new SubDomainBox in the SubDomainBox::sort_cells_in_voxels_step_1 method, we receive these new cells and insert them into their respective voxels.

impl<I, S, C, A, Com, Sy> SubDomainBox<I, S, C, A, Com, Sy>

where S: SubDomain,

pub fn update_reactions_extra_step_1<Pos, Ri, Re, Float>( &mut self, ) -> Result<(), SimulationError>

where C: ReactionsExtra<Ri, Re>, S: SubDomainReactions<Pos, Re, Float>, Com: Communicator<SubDomainPlainIndex, ReactionsExtraBorderInfo<<S as SubDomainReactions<Pos, Re, Float>>::BorderInfo>>,

Available on crate feature cpu_os_threads only.

Send ReactionsExtraBorderInfo to neighboring subdomains

pub fn update_reactions_extra_step_2<Pos, Ri, Re, Float>( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where C: ReactionsExtra<Ri, Re>, S: SubDomainReactions<Pos, Re, Float>, Com: Communicator<SubDomainPlainIndex, ReactionsExtraBorderReturn<<S as SubDomainReactions<Pos, Re, Float>>::NeighborValue>> + Communicator<SubDomainPlainIndex, ReactionsExtraBorderInfo<<S as SubDomainReactions<Pos, Re, Float>>::BorderInfo>>,

Available on crate feature cpu_os_threads only.

Receive ReactionsExtraBorderInfo of neighboring subdomains and return ReactionsExtraBorderReturn

pub fn update_reactions_extra_step_3<Pos, Ri, Re, Float>( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where C: ReactionsExtra<Ri, Re> + Intracellular<Ri> + Position<Pos>, A: UpdateReactions<Ri>, S: SubDomainReactions<Pos, Re, Float>, Com: Communicator<SubDomainPlainIndex, ReactionsExtraBorderReturn<<S as SubDomainReactions<Pos, Re, Float>>::NeighborValue>>,

Available on crate feature cpu_os_threads only.

Receive ReactionsExtraBorderReturn and update values.

impl<I, S, C, A, Com, Sy> SubDomainBox<I, S, C, A, Com, Sy>

where S: SubDomain,

pub fn update_contact_reactions_step_1<Ri, Pos, RInf, Float, const N: usize>( &mut self, ) -> Result<(), SimulationError>

where Pos: Clone, C: ReactionsContact<Ri, Pos, Float, RInf> + Intracellular<Ri> + Position<Pos>, A: UpdateReactions<Ri> + UpdateReactionsContact<Ri, N>, Ri: Xapy<Float> + Clone, RInf: Clone, Float: Float, Com: Communicator<SubDomainPlainIndex, ReactionsContactInformation<Pos, Ri, RInf>>,

Available on crate feature cpu_os_threads only.

Send ReactionsContactInformation to neighboring subdomains.

pub fn update_contact_reactions_step_2<Ri, Pos, RInf, Float, const N: usize>( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where C: ReactionsContact<Ri, Pos, Float, RInf> + Position<Pos> + Intracellular<Ri>, A: UpdateReactions<Ri> + UpdateReactionsContact<Ri, N>, Ri: Xapy<Float>, Float: Float, Pos: Clone, Com: Communicator<SubDomainPlainIndex, ReactionsContactInformation<Pos, Ri, RInf>> + Communicator<SubDomainPlainIndex, ReactionsContactReturn<Ri>>,

Available on crate feature cpu_os_threads only.

Receive ReactionsContactInformation, perform calculations of increments of ReactionsContact and return ReactionsContactReturn

pub fn update_contact_reactions_step_3<Ri>( &mut self, determinism: bool, ) -> Result<(), SimulationError>

where A: UpdateReactions<Ri>, Com: Communicator<SubDomainPlainIndex, ReactionsContactReturn<Ri>>,

Available on crate feature cpu_os_threads only.

Receive all calculated increments and include them for later update steps.