Module cpu_os_threads

Available on crate feature cpu_os_threads only.

Expand description

See cellular_raza_core::backend::cpu_os_threads

Note that this backend is NOT compatible with the cellular_raza_core::backend::chili. In order to use this backend, import it with

use cellular_raza::prelude::cpu_os_threads::*;

Modules§

backend: Numerically solve a given simulation setup.
cartesian_cuboid_2_vertex_old: Contains deprecated cartesian cuboid implementations for an older vertex model
cartesian_cuboid_n_old: Contains deprecated cartesian cuboid implementations
domain_old: Traits and types which will eventually replace the old Domain definition.
pool_bacteria: Objects and definitions surrounding the bacterial pool model
rayon: Rayon is a data-parallelism library that makes it easy to convert sequential computations into parallel.
reactions_old: Contains traits and types which specify cellular reactions specific to the cpu_os_threads backend.
storage: Interface and methods to store and load simulation aspects.
time: Controls how the simulation time is advanced
tracing: A scoped, structured logging and diagnostics system.

Structs§

AuxiliaryCellPropertyStorage: Contains auxiliary information to update cellular properties
BatchSaveFormat: Define how batches of elements and identifiers are saved when being serialized.
BoundLennardJones: Lennard-Jones interaction potential with numerical upper and lower limit.
BoundLennardJonesF32: Identical to BoundLennardJones but for f32 type.
BoundaryError: Can occur during boundary calculation
Brownian1D: Brownian motion of particles
Brownian1DF32: Brownian motion of particles
Brownian2D: Brownian motion of particles
Brownian2DF32: Brownian motion of particles
Brownian3D: Brownian motion of particles
Brownian3DF32: Brownian motion of particles
CalcError: General Calculation Error
CartesianCuboid: A generic Domain with a cuboid layout.
CartesianCuboid1New: Cartesian cuboid in 1D with float type f64
CartesianCuboid1NewF32: Cartesian cuboid in 1D with float type f32
CartesianCuboid2New: Cartesian cuboid in 2D with float type f64
CartesianCuboid2NewF32: Cartesian cuboid in 2D with float type f32
CartesianCuboid3New: Cartesian cuboid in 3D with float type f64
CartesianCuboid3NewF32: Cartesian cuboid in 3D with float type f32
CartesianCuboidRods: Cells are represented by rods
CartesianSubDomain: Subdomain corresponding to the CartesianCuboid struct.
CartesianSubDomain1: Subdomain of CartesianCuboid1New
CartesianSubDomain2: Subdomain of CartesianCuboid2New
CartesianSubDomain3: Subdomain of CartesianCuboid3New
CartesianSubDomain1F32: Subdomain of CartesianCuboid1NewF32
CartesianSubDomain2F32: Subdomain of CartesianCuboid2NewF32
CartesianSubDomain3F32: Subdomain of CartesianCuboid3NewF32
CartesianSubDomainRods: The corresponding SubDomain of the CartesianCuboidRods domain.
CartesianVoxel1: Voxel of the CartesianSubDomain1
CartesianVoxel2: Voxel of the CartesianSubDomain2
CartesianVoxel3: Voxel of the CartesianSubDomain3
CartesianVoxel1F32: Voxel of the CartesianSubDomain1F32
CartesianVoxel2F32: Voxel of the CartesianSubDomain2F32
CartesianVoxel3F32: Voxel of the CartesianSubDomain3F32
CellAgentBox: A container struct containing meta-information of a given Cell Some variables such as id are not required and not desired to be initialized by the user. This CellAgentBox acts as a container around the cell to hold these variables.
CombinedSaveFormat: Define how elements and identifiers are saved when being serialized together.
CommunicationError: Error which occurs during sending, receiving or transmitting information between threads
ControllerError: Occurs when incorrectly applying a controller effect
DeathError: Errors occurring during the final death step of a cell
DecomposedDomain: Generated by the decompose method. The backend will know how to deal with this type and crate a working simulation from it.
DivisionError: Errors related to a cell dividing process
DomainBox: Wrapper around the user-defined simulation Domain
DrawingError: Used to catch errors related to plotting
FixedStepsize: Time stepping with a fixed time length
IndexError: Can occur internally when information is not present at expected place
JsonStorageInterface: Save elements as json files with serde_json.
Langevin1D: Langevin dynamics
Langevin1DF32: Langevin dynamics
Langevin2D: Langevin dynamics
Langevin2DF32: Langevin dynamics
Langevin3D: Langevin dynamics
Langevin3DF32: Langevin dynamics
MemoryStorageInterface: Use the [sled] database to save results to an embedded database.
MiePotential: Generalizeation of the BoundLennardJones potential.
MiePotentialF32: Generalizeation of the BoundLennardJones potential.
ModularCell: Superseded by the CellAgent derive macro.
MorsePotential: Famous Morse potential for diatomic molecules.
MorsePotentialF32: Famous Morse potential for diatomic molecules.
MultiVoxelContainer: Subdomain which consists of multiple Voxels
NewtonDamped1D: Newtonian dynamics governed by mass and damping.
NewtonDamped1DF32: Newtonian dynamics governed by mass and damping.
NewtonDamped2D: Newtonian dynamics governed by mass and damping.
NewtonDamped2DF32: Newtonian dynamics governed by mass and damping.
NewtonDamped3D: Newtonian dynamics governed by mass and damping.
NewtonDamped3DF32: Newtonian dynamics governed by mass and damping.
NextTimePoint: Represents the next time point which is returned by the TimeStepper::advance method.
NoCellularReactions: Do not model intracellular reactions at all.
NoCycle: No cycle of the cell.
NoExtracellularGradientSensing: Type which allows to simply not model gradients.
NoInteraction: No interaction of the cell with any other.
PlottingConfig: Contains settings for plotting results.
RequestError: Ask the wrong object for information and receive this error
RngError: Can occur when generating distributions or drawing samples from them.
RodInteraction: Automatically derives a Interaction suitable for rods from a point-wise interaction.
RodMechanics: A mechanical model for Bacterial Rods
RonStorageInterface: Save elements as ron files with ron.
SetupError: Occurs during setup of a new simulation
SimulationConfig: Contains non-volatile configurations such as display settings etc.
SimulationMetaParams: Store meta parameters for simulation
SimulationResult: Returned after finishing a full simulation
SimulationSetup: Complete Set of parameters controlling execution flow of simulation
SimulationSupervisor: Supervisor controlling simulation execution
SledStorageInterface: Use the [sled] database to save results to an embedded database.
StorageBuilder: Used to construct a StorageManager
StorageManager: This manager handles if multiple storage options have been specified It can load resources from one storage aspect and will
Strategies: Contains methods to modify voxels when initializing the simulation domain.
TimeError: Error related to advancing the simulation time or displaying its progress
TimeSetup: Contains information about the discretization of time and when to save results.
VertexDerivedInteraction: Derives an interaction potential from a point-like potential.
VertexMechanics2D: Mechanics model which represents cells as vertices with edges between them.
VoxelBox: Wrapper for a Voxel struct that includes more information and cells.

Enums§

CycleEvent: Contains all events which can arise during the cell cycle and need to be communciated to the simulation engine (see also Cycle).
DecomposeError: Error during decomposition of a SimulationDomain into multiple subdomains
ImageType: Image type used for saving results to a file.
SimulationError: Covers all errors that can occur in this Simulation
StorageError: Error related to storing and reading elements
StorageMode: The mode in which to generate paths and store results.
StorageOption: Define how to store results of the simulation.
TimeEvent: A TimeEvent describes that a certain action is to be executed after the next iteration step.

Traits§

Agent: Encapsulates all concepts that can be specified for a Agent
CreatePlottingRoot: Creates a new plotting root which can then be drawn upon.
Cycle: This trait represents all cycles of a cell and works in tandem with the CycleEvent enum.
Domain: Provides an abstraction of the physical total simulation domain.
DomainCreateSubDomains: Generate SubDomains from an existing Domain
DomainRngSeed: Manage the current rng seed of a Domain
FileBasedStorage: Abstraction and simplification of many file-based storage solutions
ForceBound: Represents a force which can act between two cells.
Id: Specifies how to retrieve a unique identifier of an object.
Interaction: Trait describing force-interactions between cellular agents.
InteractionInformation: Trait implementations needed for the information generic parameter of Interaction.
Intracellular: Setter and Getter for intracellular values of a cellagent.
Mechanics: Describes the position of a cell-agent and allows to calculate increments and set/get information of the agent.
PlotSelf: Allows elements of the simulation such as cells and voxels to draw themselves onto a plotting root. Typically, voxels will draw first and cells afterwards.
Position: Methods for accessing the position of an agent.
PositionBound: Represents the current position of a cell-agent.
Reactions: Describes purely intracellular reactions of a cellagent.
ReactionsContact: Reactions between cells which are in direct contact
ReactionsExtra: This trait models extracellular reactions which interact with agents.
SortCells: Assign an VoxelIndex to a given cell.
StorageInterface: Provide methods to initialize, store and load single and multiple elements at iterations.
StorageInterfaceLoad: Handles loading of elements
StorageInterfaceOpen: Open or create a new instance of the Storage controller.
StorageInterfaceStore: Handles storing of elements
SubDomain: Subdomains are produced by decomposing a Domain into multiple physical regions.
SubDomainForce: Apply a force on a cell depending on its position and velocity.
SubDomainMechanics: Apply boundary conditions to a cells position and velocity.
SubDomainReactions: Describes extracellular reactions and fluid dynamics
TimeStepper: Increments time of the simulation
Velocity: Methods for accessing the velocity of an agent
VelocityBound: Represents the velocity of a cell.
Xapy: Mathematical abstraction similar to the well-known axpy method.

Functions§

calculate_morse_interaction: Calculates the interaction strength behind the MorsePotential and MorsePotentialF32 structs.
nearest_point_from_point_to_line: Calculate the point on a line which is closest to an external given point.
nearest_point_from_point_to_multiple_lines: Generalizes the nearest_point_from_point_to_line function for a collection of line segments.
ray_intersects_line_segment: Implements the ray-casting algorithm to check if a ray intersects with a given line segment.
wiener_process: Generate a vector corresponding to a wiener process.

Type Aliases§

CellularIdentifier: This is a unique identifier which is deterministic even in multi-threading situations. Its components are
Nothing: Type alias used when not wanting to simulate any cellular reactions for example.
PlainIndex: This is a purely implementational detail and should not be of any concern to the end user.

Derive Macros§

CellAgent: Derive cellular concepts
Domain
SubDomain

Module cpu_os_threadsCopy item path