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