Crate cellular_raza_concepts

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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§

  • 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
  • Id
    Specifies how to retrieve a unique identifier of an object.
  • Interaction
    Trait describing force-interactions between cellular agents.
  • 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.
  • Reactions
    Describes purely intracellular reactions of a cellagent.
  • ReactionsContact
    TODO add description
  • ReactionsExtra
    TODO add description
  • 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§