cellular_raza_core/backend/chili/mod.rs
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//! 🌶️ A modular, reusable, general-purpose backend
//!
//! # Usage
//!
//! In the following example, we provide an extremely short basic usage of the [run_simulation]
//! macro.
//! It performs the numerical integration of a well-defined problem.
//! We assume that the `MyAgent` struct and `MyDomain` have already been defined and implement the
//! [Mechanics](cellular_raza_concepts::Mechanics) concept.
//! More details about how to use pre-existing building blocks or derive their functionality is
//! provided by the
//! [cellular_raza_building_blocks](https://cellular-raza.com/docs/cellular_raza_building_blocks)
//! crate.
//! We will then solve our system for the
//! [`Mechanics`](https://cellular-raza.com/internals/concepts/cell/mechanics) aspect.
//!
//! ```
//! # use cellular_raza_core::backend::chili::*;
//! # use cellular_raza_core::{storage::*, time::*};
//! # use cellular_raza_concepts::*;
//! # use rand_chacha::ChaCha8Rng;
//! # use serde::{Deserialize, Serialize};
//! # use std::collections::{BTreeMap, BTreeSet};
//! # // Define agents and domain
//! # #[derive(Clone, Debug, Deserialize, Serialize)]
//! # struct MyAgent {
//! # pos: f64,
//! # vel: f64
//! # }
//! # impl Position<f64> for MyAgent {
//! # fn pos(&self) -> f64 {
//! # self.pos
//! # }
//! # fn set_pos(&mut self, pos: &f64) {
//! # self.pos = *pos
//! # }
//! # }
//! # impl Velocity<f64> for MyAgent {
//! # fn velocity(&self) -> f64 {
//! # self.vel
//! # }
//! # fn set_velocity(&mut self, vel: &f64) {
//! # self.vel = *vel
//! # }
//! # }
//! # impl Mechanics<f64, f64, f64> for MyAgent {
//! # fn get_random_contribution(
//! # &self,
//! # _rng: &mut ChaCha8Rng,
//! # _dt: f64,
//! # ) -> Result<(f64, f64), RngError> {
//! # Ok((0.0, 0.0))
//! # }
//! # fn calculate_increment(&self, force: f64) -> Result<(f64, f64), CalcError> {
//! # Ok((self.vel, force))
//! # }
//! # }
//! # #[derive(Clone, Debug, Deserialize, Serialize)]
//! # struct MyDomain {};
//! # impl<Ci> Domain<MyAgent, MyDomain, Ci> for MyDomain
//! # where
//! # Ci: IntoIterator<Item = MyAgent>
//! # {
//! # type VoxelIndex = usize;
//! # type SubDomainIndex = usize;
//! # fn decompose(
//! # self,
//! # _: core::num::NonZeroUsize,
//! # cells: Ci,
//! # ) -> Result<
//! # DecomposedDomain<Self::SubDomainIndex, MyDomain, MyAgent>,
//! # cellular_raza_concepts::DecomposeError,
//! # > {
//! # Ok(DecomposedDomain {
//! # n_subdomains: 1.try_into().unwrap(),
//! # index_subdomain_cells: vec![(1, MyDomain {}, cells.into_iter().collect())],
//! # neighbor_map: BTreeMap::from([(1, BTreeSet::new())]),
//! # rng_seed: 1,
//! # })
//! # }
//! # }
//! # impl SubDomain for MyDomain {
//! # type VoxelIndex = usize;
//! # fn get_neighbor_voxel_indices(&self, _: &Self::VoxelIndex) -> Vec<Self::VoxelIndex> {
//! # Vec::new()
//! # }
//! # fn get_all_indices(&self) -> Vec<Self::VoxelIndex> {
//! # vec![1]
//! # }
//! # }
//! # impl SortCells<MyAgent> for MyDomain {
//! # type VoxelIndex = usize;
//! # fn get_voxel_index_of(
//! # &self,
//! # _: &MyAgent,
//! # ) -> Result<Self::VoxelIndex, cellular_raza_concepts::BoundaryError> {
//! # Ok(1)
//! # }
//! # }
//! # impl SubDomainMechanics<f64, f64> for MyDomain {
//! # fn apply_boundary(
//! # &self,
//! # _: &mut f64,
//! # _: &mut f64,
//! # ) -> Result<(), cellular_raza_concepts::BoundaryError> {
//! # Ok(())
//! # }
//! # }
//! # let t0 = 0.0;
//! # let dt = 0.1;
//! # let tmax = 20.0;
//! # let save_interval = 2.0;
//! # let initial_vel = 0.1;
//! # let n_threads = 1.try_into().unwrap();
//! // Initialize agents, domain, solving time and how to store results
//! let agents = (0..10).map(|n| MyAgent {
//! /* Define the agent's properties */
//! # pos: n as f64,
//! # vel: initial_vel,
//! });
//! let domain = MyDomain {/* Define the domain*/};
//! let time = FixedStepsize::from_partial_save_interval(t0, dt, tmax, save_interval)?;
//! let storage = StorageBuilder::new().priority([StorageOption::Memory]);
//!
//! // Group them together
//! let settings = Settings {
//! n_threads,
//! time,
//! storage,
//! show_progressbar: false,
//! };
//!
//! // This will perform the numerical simulation
//! let storage_access = run_simulation!(
//! agents: agents,
//! domain: domain,
//! settings: settings,
//! aspects: [Mechanics],
//! core_path: cellular_raza_core,
//! )?;
//!
//! // Use calculated results
//! let history = storage_access.cells.load_all_elements()?;
//! for (iteration, cells) in history {
//! // ...
//! # assert!(iteration > 0);
//! # assert_eq!(cells.len(), 10);
//! # for (_, (cbox, _)) in cells {
//! # let calculated = cbox.get_id().1 as f64 + iteration as f64 * 0.1 * initial_vel;
//! # let cr = cbox.cell.pos;
//! # assert!((calculated - cr).abs() < 1e-5);
//! # }
//! }
//! # Ok::<(), SimulationError>(())
//! ```
//!
//! This example cannot contain all the functionality which the [chili](self) backend provides.
//! We encourage the user to look at the
//! [cellular-raza.com/guides](https://cellular-raza.com/guides) and
//! [cellular-raza.com/showcase](https://cellular-raza.com/showcase) sections to get started.
//!
//! # Internals
//! The [chili](self) backend uses procedural macros to generate code which
//! results in a fully working simulation.
//! The methods, functions and objects used in this way are formualted with generics.
//! This enables us to write general-purpose solvers for a wide range of problems.
//! The most important macro is the [run_simulation] macro which can be solely used to run
//! simulations.
//! This macro itself can be broken down into smaller pieces.
//! - [prepare_types] Defines types used in simulation
//! - [build_aux_storage] AuxStorage struct used to store intermediate
//! values for update steps of aspects
//! - [build_communicator] Type which handles communication between
//! threads
//! - [test_compatibility] Test compatibility of all types involved
//! - [run_main] Defines main loop and performs the simulation
//!
//! These macros take a subset of keyword arguments of the [run_simulation] macro.
//! The arguments are documented under the [run_simulation] macro.
//!
//! # Main Loop
//! The [run_main] macro constructs the main loop of the simulation.
//! It inserts functions depending on the given simulation aspects.
//! They can be grouped into 6 steps
//! Below, we show a list of all these functions and their corresponding aspects.
//!
//! #### Step 1 - Send Information
//!
//! In this step, each sub
//!
//! <style>
//! div table {
//! width: 100%;
//! }
//! table th:first-of-type {
//! width: 20%;
//! }
//! table th:nth-of-type(2) {
//! width: 35%;
//! }
//! table th:nth-of-type(3) {
//! width: 45%;
//! }
//! </style>
//!
//! | Aspects | Function | Purpose |
//! | --- | --- | --- |
#\
| Send [PosInformation](PosInformation) between threads to get back \
[ForceInformation](ForceInformation) |"]
#\
| Uses the [SubDomainForce](cellular_raza_concepts::SubDomainForce) trait to add \
custom external force. |"]
#![doc = "\
| `ReactionsContact`\
| [update_contact_reactions_step_1]\
(SubDomainBox::update_contact_reactions_step_1) \
| Sends [ReactionsContactInformation](ReactionsContactInformation) between threads. |"]
# \
| Sends [ReactionsExtraBorderInfo](ReactionsExtraBorderInfo) between threads. |"]
# | Wait for threads to have finished until proceeding. |"]
//!
//! #### Step 2 - Calculate and Return
//! | Aspects | Function | Purpose |
//! | --- | --- | --- |
# \
| Calculate forces and return [ForceInformation](ForceInformation) to the original \
sender. |"]
# \
| Calculates the combined increment and returns \
[ReactionsContactReturn](ReactionsContactReturn) |"]
# \
| Returns [ReactionsExtraBorderReturn](ReactionsExtraBorderReturn) |"]
//!
//! #### Step 3 - Receive and Apply
//! | Aspects | Function | Purpose |
//! | --- | --- | --- |
# \
| Receives the [ForceInformation](ForceInformation) and adds within the \
`aux_storage`. |"]
# \
| Receives the [ReactionsContactReturn](ReactionsContactReturn) and adds within the `aux_storage`. |"]
# \
| Receives the [ReactionsExtraBorderReturn](ReactionsExtraBorderReturn). |"]
//!
//! #### Pure Local Functions - Perform Update
//! | Aspects | Function | Purpose |
//! | --- | --- | --- |
# \
| Performs numerical integration of the position and velocity. |"]
# \
| Performs changes due to neighbor counting. |"]
# \
| Advances the cycle of the cell. This may introduce a\
[CycleEvent](cellular_raza_concepts::CycleEvent) |"]
# \
| Calculates increment from purely intracellular reactions. |"]
# \
| Performs the update of the contact reactions. |"]
# \
| Performs the update of the extracellular reactions. |"]
# \
| Calculates increment from purely intracellular reactions. |"]
//!
//! #### Step 4 - Treat Cell Positions
//! | Aspects | Function | Purpose |
//! | --- | --- | --- |
# \
| Apply a boundary condition. |"]
# \
| Performs cell-division and other cycle events. |"]
# \
| Checks if cells need to be sent to different subdomain and sends them. |"]
//!
//! #### Step 5 - Include new Cells
//! | Aspects | Function | Purpose |
//! | --- | --- | --- |
# \
| Include newly received cells into correct subdomains. |"]
//!
//! # Return Type
//! After the simulation is done, we return a [StorageAccess] struct to interoperate with stored
//! results.
use serde::{Deserialize, Serialize};
/// Identifier for voxels used internally to get rid of user-defined ones.
#[cfg_attr(feature = "pyo3", pyo3::pyclass)]
#[derive(Clone, Copy, Debug, Deserialize, Hash, PartialEq, Eq, Ord, PartialOrd, Serialize)]
pub struct VoxelPlainIndex(pub usize);
/// This is mainly used by the simulation_flow::cocmmunicator for testing purposes
#[allow(unused)]
#[doc(hidden)]
impl VoxelPlainIndex {
pub fn new(value: usize) -> Self {
Self(value)
}
}
/// Identifier or subdomains
#[derive(Clone, Copy, Debug, Deserialize, Hash, PartialEq, Eq, Ord, PartialOrd, Serialize)]
#[cfg_attr(feature = "pyo3", pyo3::pyclass)]
pub struct SubDomainPlainIndex(usize);
/// Unique identifier which is given to every cell in the simulation
///
/// The identifier is comprised of the [VoxelPlainIndex] in which the cell was first spawned.
/// This can be due to initial setup or due to other methods such as division in a cell cycle.
/// The second parameter is a counter which is unique for each voxel.
/// This ensures that each cell obtains a unique identifier over the course of the simulation.
#[cfg_attr(feature = "pyo3", pyo3::pyclass)]
#[derive(Clone, Copy, Debug, Deserialize, Hash, PartialEq, Eq, Ord, PartialOrd, Serialize)]
pub struct CellIdentifier(pub VoxelPlainIndex, pub u64);
#[cfg(feature = "pyo3")]
#[pyo3::pymethods]
impl CellIdentifier {
/// Constructs a new CellIdentifier
#[new]
pub fn new(voxel_plain_index: VoxelPlainIndex, counter: u64) -> Self {
Self(voxel_plain_index, counter)
}
/// Returns an identical clone of the identifier
pub fn __deepcopy__(&self, _memo: pyo3::Bound<pyo3::types::PyDict>) -> Self {
self.clone()
}
/// Returns an identical clone of the identifier
pub fn copy(&self) -> Self {
self.clone()
}
/// Returns an identical clone of the identifier
pub fn __copy__(&self) -> Self {
self.clone()
}
/// Formats the CellIdentifier
pub fn __repr__(&self) -> String {
format!("{:?}", self)
}
/// Performs the `==` operation.
pub fn __eq__(&self, other: &Self) -> bool {
self.eq(other)
}
/// Calculates a hash value of type `u64`
pub fn __hash__(&self) -> u64 {
use core::hash::{Hash, Hasher};
let mut hasher = std::collections::hash_map::DefaultHasher::new();
self.hash(&mut hasher);
hasher.finish()
}
/// Performs the `<` operation
pub fn __lt__(&self, other: &Self) -> bool {
self.lt(other)
}
/// Implementes the `__getitem__` method. Since the [CellIdentifier] is built like a list this
/// only works for the entires 0 and 1 and will yield an error otherwise
pub fn __getitem__<'py>(
&self,
py: pyo3::Python<'py>,
key: usize,
) -> pyo3::PyResult<pyo3::Bound<'py, pyo3::PyAny>> {
use pyo3::IntoPyObject;
if key == 0 {
Ok(self.0.into_pyobject(py)?.into_any())
} else if key == 1 {
Ok(self.1.into_pyobject(py)?.into_any())
} else {
Err(pyo3::exceptions::PyValueError::new_err(
"CellIdentifier can only be indexed at 0 and 1",
))
}
}
}
/// Contains structs to store aspects of the simulation and macros to construct them.
mod aux_storage;
#[doc(hidden)]
pub mod compatibility_tests;
mod datastructures;
mod errors;
mod proc_macro;
mod result;
mod setup;
mod simulation_flow;
mod solvers;
mod update_cycle;
mod update_mechanics;
mod update_reactions;
pub use aux_storage::*;
pub use datastructures::*;
pub use errors::*;
pub use proc_macro::*;
pub use result::*;
pub use setup::*;
pub use simulation_flow::*;
pub use solvers::*;
pub use update_cycle::*;
pub use update_mechanics::*;
pub use update_reactions::*;