Crate cellular_raza_concepts

Expand description

This crate encapsulates concepts which govern an agent-based model specified by cellular_raza. To learn more about the math and philosophy behind these concepts please refer to cellular-raza.com.

Modules§

domain_old: Traits and types which will eventually replace the old Domain definition.
reactions_old: Contains traits and types which specify cellular reactions specific to the cpu_os_threads backend.

Structs§

BoundaryError: Can occur during boundary calculation
CalcError: General Calculation Error
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.
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
DrawingError: Used to catch errors related to plotting
IndexError: Can occur internally when information is not present at expected place
RequestError: Ask the wrong object for information and receive this error
RngError: Can occur when generating distributions or drawing samples from them.
SetupError: Occurs during setup of a new simulation
TimeError: Error related to advancing the simulation time or displaying its progress

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

Traits§

CreatePlottingRootplotters: 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
Id: Specifies how to retrieve a unique identifier of an object.
Interaction: Trait describing force-interactions between cellular agents.
InteractionInformation: Exposes information which is used to calculate interactions between cells and the domain.
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.
PlotSelfplotters: 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.
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.
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
Velocity: Methods for accessing the velocity of an agent
Xapy: Mathematical abstraction similar to the well-known axpy method.

Type Aliases§

CellularIdentifier: This is a unique identifier which is deterministic even in multi-threading situations. Its components are

Derive Macros§

CellAgent: Derive cellular concepts
Domain: Derives aspects related to the simulation Domain
SubDomain: This trait derives the different aspects of a SubDomain.