Module prelude

Re-exports the default simulation types and traits.

Modules

backend

Numerically solve a given simulation setup.

caracara

See cellular_raza_core::backend::cara

cartesian_cuboid_2_vertex_old

Contains deprecated cartesian cuboid implementations for an older vertex model

cartesian_cuboid_n_old

Contains deprecated cartesian cuboid implementations

cpu_os_threadscpu_os_threads

See cellular_raza_core::backend::cpu_os_threads

domain_old

Traits and types which will eventually replace the old Domain definition.

ellielli

See cellular_raza_core::backend::elli

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.

Macros

aux_storage_constructorchili

build_aux_storagechili

build_communicatorchili

communicator_generics_placeholderschili

Inserts as many blanks as generics were used to create the communicator struct by build_communicator!.

prepare_typeschili

Prepares communicator and auxiliary storage types with build_communicator! and build_aux_storage!.

run_mainchili

run_simulationchili

run_test_for_aspectschili

Run a particularly structured test multiple times for combinations of aspects

test_compatibilitychili

Checks if defined types and concepts are compatible before actually executing the simulation.

Structs

AuxStorageCyclechili

Stores intermediate information about the cell cycle.

AuxStorageInteractionchili

Helper storage for number of neighbors of Interaction trait.

AuxStorageMechanicschili

Stores intermediate information about the mechanics of a cell.

AuxStorageReactionschili

Helper storage for values regarding intracellular concentrations for the Reactions trait.

AuxStorageReactionsContactchili

Implementor of the UpdateReactionsContact trait.

BarrierSyncchili

This very simple implementation uses the [hurdles::Barrier] struct which should in theory perform faster than the std::sync::Barrier struct from the standard library.

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.

CellBoxchili

Wrapper around the user-defined CellAgent

CellIdentifierchili

Unique identifier which is given to every cell in the simulation

ChannelCommchili

Sender-Receiver Communicator based on [crossbeam_channel].

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.

DefaultHandlerchili

Handles any error which is encountered and caught (i.e. no panics) during runtime.

DivisionError

Errors related to a cell dividing process

DrawingError

Used to catch errors related to plotting

FixedStepsize

Time stepping with a fixed time length

ForceInformationchili

Return type to the requested PosInformation.

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.

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.

PosInformationchili

Send about the position of cells between threads.

ReactionsContactInformationchili

This information will be sent from one cell to another to determine their combined reactions.

ReactionsContactReturnchili

This informatino is returned after receiving ReactionsContactInformation and delivers the increment.

ReactionsExtraBorderInfochili

Carries information about the border given by the ReactionsExtra trait between subdomains.

ReactionsExtraBorderReturnchili

Return information of border value after having obtained the SubDomainReactions::BorderInfo

RequestError

Ask the wrong object for information and receive this error

RingBufferchili

A ring Buffer with constant size. Makes use of a fixed-size array internally.

RingBufferIterchili

Iterator of the RingBuffer struct.

RingBufferIterRefchili

Produced by the iter method of the RingBuffer.

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.

SendCellchili

Send cell and its AuxStorage between threads.

Settingschili

Specify settings surrounding execution and storage

SetupError

Occurs during setup of a new simulation

SimulationRunnerchili

Intermediate object which gets consumed once the simulation is run

SimulationSetupchili

Struct containing all necessary information to construct a fully working simulation and run it.

SledStorageInterface

Use the [sled] database to save results to an embedded database.

StorageAccesschili

Gathers the StorageManager for cells and voxels of the previously run simulation

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

SubDomainBoxchili

Encapsulates a subdomain with cells and other simulation aspects.

SubDomainPlainIndexchili

Identifier or subdomains

TimeError

Error related to advancing the simulation time or displaying its progress

UDGraphchili

Undirected graph

VertexDerivedInteraction

Derives an interaction potential from a point-like potential.

VertexMechanics2D

Mechanics model which represents cells as vertices with edges between them.

Voxelchili

Stores information related to a voxel of the physical simulation domain.

VoxelPlainIndexchili

Identifier for voxels used internally to get rid of user-defined ones.

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

HandlingStrategychili

Contains handling strategies for errors which can arise during the simulation process.

SimulationErrorchili

Covers all errors that can occur in this Simulation The errors are listed from very likely to be a user error from almost certainly an internal error.

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

BuildFromGraphchili

Construct a BTreeMap of the type from a graph

Communicatorchili

Handles communications between different simulation processes.

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.

DefaultFromchili

Used to construct initial (empty) AuxStorage variants.

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

ErrorHandlerchili

Handle any error which may occur as specified by SimulationError

FileBasedStorage

Abstraction and simplification of many file-based storage solutions

FromMapchili

Constructs a collection of Items from a map (graph)

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

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

SyncSubDomainschili

Responsible for syncing the simulation between different threads.

TimeStepper

Increments time of the simulation

UpdateCyclechili

Trait which describes how to store intermediate information on the cell cycle.

UpdateInteractionchili

Interface to store intermediate information about interactions.

UpdateMechanicschili

Used to store intermediate information about last positions and velocities. Can store up to N values.

UpdateReactionschili

Interface to store intermediate information about cellular reactions.

UpdateReactionsContactchili

Used to update properties of the cell related to the ReactionsContact trait.

Velocity

Methods for accessing the velocity of an agent

Xapy

Mathematical abstraction similar to the well-known axpy method.

Functions

calculate_morse_interaction

Calculates the interaction strength behind the MorsePotential and MorsePotentialF32 structs.

construct_simulation_runnerchili

Construct a new SimulationRunner from a given auxiliary storage and communicator object

local_cycle_updatechili

Advances the cycle of a cell by a small time increment dt.

local_interaction_react_to_neighborschili

Perform the Interaction::react_to_neighbors function and clear current neighbors.

local_mechanics_updatechili

We assume that cells implement the Mechanics and Interaction traits. In this last step, all ForceInformation are gathered and used to update the cells positions and velocities.

local_reactions_intracellularchili

Calculates the increment from the Reactions trait.

local_reactions_use_incrementchili

Ensures that intracellular increments have been cleared before the next update step.

local_subdomain_update_reactions_extrachili

Performs the increment operation.

local_update_contact_reactionschili

Updates the cells intracellular values from the obtained contact informations

mechanics_adams_bashforth_2chili

Two-step Adams-Bashforth method.

mechanics_adams_bashforth_3chili

Three-step Adams-Bashforth method.

mechanics_eulerchili

Classical euler solver for the Mechanics trait.

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.

reactions_contact_adams_bashforth_3rdchili

Calculates the increment introduced by the ReactionsContact aspect.

validate_mapchili

Validates a given map.

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.

Derive Macros

AuxStoragechili

CellAgent

Derive cellular concepts

Communicatorchili

Domain

FromMapchili

SubDomain