SimPT_Sim Namespace Reference

Namespace for the core simulator. More...

Namespaces
	BoundaryType
	Namespace for Types of boundary cells.
	ClockMan
	Namespace for clock and timekeeping related classes.
	Color
	Namespace for color utilities.
	Container
	Namespace for container related classes.
	Event
	Namespace event types raised by the simulator.
	RandomEngineType
	Namespace for Types of random engines.
	Util
	Namespace for miscellaneous utilities.
	WallType
	Namespace for Types walls.

Classes
struct	AreaMoment
	Structure with functionality for calculations of the area moment of inertia. More...
class	AttributeContainer
	Manages attributes. More...
class	AttributeStore
	Store and manage attributes. More...
class	CBMBuilder
	The Copy-Based Mesh Builder directs the Mesh building process using another mesh. More...
class	Cell
	A cell contains walls and nodes. More...
class	CellAttributes
	Attributes of Cell. More...
class	CellChemistryTag
	Used in tag forwarding. More...
class	CellColorTag
	Used in tag forwarding. More...
class	CellDaughtersTag
	Used in tag forwarding. More...
class	CellDivider
	Class for handling cell division. More...
class	CellHousekeeper
	Class for handling maintenance of cell mechanics (cell housekeeping). More...
class	CellHousekeepTag
	Used in tag forwarding. More...
class	CellSplitTag
	Used in tag forwarding. More...
class	CellToCellTransportBoundaryTag
	Used in tag forwarding. More...
class	CellToCellTransportTag
	Used in tag forwarding. More...
class	ChainHull
	Compute the convex hull of a set of two-dimensional points. More...
class	ComponentFactoryBase
	Interface for ComponentFactory. More...
class	ComponentFactoryProxy
	Proxy for interaction with Component Factory of model families. More...
struct	ComponentTraits
	Primary template never gets instantiated. More...
struct	ComponentTraits< CellChemistryTag >
	Traits for CellChemistry components. More...
struct	ComponentTraits< CellColorTag >
	Traits for CellColor components. More...
struct	ComponentTraits< CellDaughtersTag >
	Traits for CellDaughters components. More...
struct	ComponentTraits< CellHousekeepTag >
	Traits for CellHousekeep components. More...
struct	ComponentTraits< CellSplitTag >
	Traits for CellSplit components. More...
struct	ComponentTraits< CellToCellTransportBoundaryTag >
	Traits for CellToCellTransportBoundaryTag components. More...
struct	ComponentTraits< CellToCellTransportTag >
	Traits for CellToCellTransport components. More...
struct	ComponentTraits< DeltaHamiltonianTag >
	Traits for DeltaHamiltonian components. More...
struct	ComponentTraits< HamiltonianTag >
	Traits for Hamiltonian components. More...
struct	ComponentTraits< MoveGeneratorTag >
	Traits for MoveGenerator components. More...
struct	ComponentTraits< TimeEvolverTag >
	Traits for TimeEvolver components. More...
struct	ComponentTraits< WallChemistryTag >
	Traits for WallChemistry components. More...
struct	CoreData
	Core data with mesh, parameters, random engine and time data. More...
class	CoupledSim
	Coupled Simulator: multiple simulators and couplers. More...
class	CouplerFactories
	A coupler factory map that is used to register names for these couplers. More...
struct	CSRMatrix
	Represents a binary matrix with n rows and m columns in a Compressed Sparse Row representation. More...
class	DeltaHamiltonianTag
	Used in tag forwarding. More...
class	DurstenfeldShuffle
	Generate a random permuted sequence of integers 0,1,..., n. More...
class	Edge
	An Edge connects two nodes and is ambidextrous. More...
class	ExchangeCoupler
	ExchangeCoupler. More...
struct	GeoData
	Plain data structure with cell geometric data (such as area). More...
class	Geom
	Provides geometric functions. More...
class	HamiltonianTag
	Used in tag forwarding. More...
class	ICoupler
	Interface for the classes coupling two parallel simulations. More...
class	MBMBuilder
	MBMBDirector directs the Mesh building process using a MeshState object. More...
class	Mesh
	Structure of cells; key data structure. More...
class	MeshCheck
	Checks mesh concistency. More...
class	MeshGeometry
	Helper functions for mesh geometry. More...
class	MeshState
	Contains the state of the whole Mesh at a given simulation step. More...
class	MeshTopology
	Helper functions for mesh topology. More...
class	MoveGeneratorTag
	Used in tag forwarding. More...
class	NeighborNodes
	Structure of neighboring nodes: two neighboring nodes from standpoint of a given cell with an ordering "first" and "second" that corresponds with the node traversal order in that cell. More...
class	Node
	Node in cell wall. More...
class	NodeAttributes
	Attributes associated with a node. More...
class	NodeInserter
	Insertion of nodes in existing edges (contributes to the cell mechanics). More...
class	NodeMover
	Cell mechanics by displacement and insertion of nodes. More...
class	OdeintFactories0Map
	Stores factory functions for odeint integrator. More...
class	OdeintFactories2Map
	Stores factory functions for odeint integrator algorithm. More...
class	OdeintFactory0
	Produces factory function for odeint integrator algorithm. More...
class	OdeintFactory2
	Produces factory function for odeint integrator algorithm. More...
class	OdeintTraits
	Contains an odeint system, a state and a solver for it. More...
class	PBMBuilder
	Class that directs ptree based mesh building process. More...
class	PtreeTissueBuilder
	Class directs ptree based tissue building process. More...
class	RandomEngine
	Creates a random generator based on a seed. More...
class	Sim
	Simulator: mesh & parameters, model & algorithms. More...
class	SimInterface
	Simulator interface. More...
class	SimState
	Contains the state of the whole Simulator at a given simulation step. More...
class	SimWrapper
	Interface exposing the simulator to Java, Python, and C++ programs. More...
struct	SimWrapperResult
	All exceptions must be dealt with internally, so each method returns an object of this type. More...
struct	SimWrapperResult< void >
	Specialization of SimWrapperResult template for type void. More...
struct	TimeData
	Time data: current simulated time, number of step in simulation history. More...
class	TimeEvolverTag
	Used in tag forwarding. More...
class	TimeSlicer
	Simulator: mesh & parameters, model & algorithms. More...
class	Tissue
	Tissue data with mesh, cell attributes, node attributes and wall attributes. More...
class	TransportEquations
	Equations for reaction and transport processes. More...
class	Wall
	A cell wall, runs between cell corner points and consists of wall elements. More...
class	WallAttributes
	Attributes associated with a wall. More...
class	WallChemistryTag
	Used in tag forwarding. More...

Typedefs
using	CellChemistryComponent = std::function< void(Cell *, double *)>
	CellChemistry component interface.
using	CellColorComponent = std::function< std::array< double, 3 >(Cell *)>
	CellColor component interface.
using	CellDaughtersComponent = std::function< void(Cell *, Cell *)>
	CellDaughters component interface.
using	CellHousekeepComponent = std::function< void(Cell *)>
	CellHousekeep component interface.
using	CellSplitComponent = std::function< std::tuple< bool, bool, std::array< double, 3 >>(Cell *)>
	CellSplit component interface.
using	CellToCellTransportBoundaryComponent = std::function< void(Wall *w, double *dchem_c1, double *dchem_c2)>
	CellToCellTransport boundary condition component interface.
using	CellToCellTransportComponent = std::function< void(Wall *, double *, double *)>
	CellToCellTransport component interface.
using	CellType = unsigned int
	We have a CellType, but for now it is is just an unsigned int.
using	DeltaHamiltonianComponent = std::function< double(const NeighborNodes &, Node *, std::array< double, 3 >)>
	DeltaHamiltonian component interface.
using	HamiltonianComponent = std::function< double(Cell *)>
	Hamiltonian component interface.
using	MoveGeneratorComponent = std::function< std::array< double, 3 >()>
	MoveGenerator component interface.
using	SimTimingTraits = ClockMan::ClockTraits< ClockMan::ClockCLib, std::chrono::milliseconds >
using	TimeEvolverComponent = std::function< std::tuple< SimTimingTraits::CumulativeTimings, bool >(double, SimPhase)>
	Time Evolver component interface.
using	WallChemistryComponent = std::function< void(Wall *, double *, double *)>
	Wall chemistry component interface.

Enumerations
enum	BoundaryType { None, NoFlux, SourceSink, SAM }
	Enumerates cell boundary types.
enum	SimPhase {   NONE, _1, _2, _3,   _4, COUPLING }
enum	SimWrapperStatus { SUCCESS, FAILURE }
	Shows whether a time step was a success or not.

Functions
template<>
std::map< std::string, std::vector< std::string > > &	AttributeContainer::Attributes< std::string > ()
template<>
const std::map< std::string, std::vector< std::string > > &	AttributeContainer::Attributes< std::string > () const
template<>
AttributeStore::MapType< std::string > &	AttributeStore::IndexMap< std::string > ()
template<>
const AttributeStore::MapType< std::string > &	AttributeStore::IndexMap< std::string > () const
GeoData	ModifyForMove (const GeoData &old_geo, const std::array< double, 3 > &nb1_p, const std::array< double, 3 > &nb2_p, const std::array< double, 3 > &now_p, const std::array< double, 3 > &mov_p)
AreaMoment	operator+ (const AreaMoment &i1, const AreaMoment &i2)
GeoData	operator+ (const GeoData &i1, const GeoData &i2)
AreaMoment	operator- (const AreaMoment &i1, const AreaMoment &i2)
GeoData	operator- (const GeoData &i1, const GeoData &i2)
bool	operator< (ChainHull::Point const &p1, ChainHull::Point const &p2)
	Required to sort points (e.g. More...
std::ostream &	operator<< (std::ostream &os, BoundaryType b)
ostream &	operator<< (std::ostream &os, const NeighborNodes &n)
	Insert Neighbor into output stream.
ostream &	operator<< (ostream &os, Node const &n)
std::ostream &	operator<< (std::ostream &os, const AreaMoment &i)
std::ostream &	operator<< (std::ostream &os, const Edge &e)
ostream &	operator<< (ostream &os, CellAttributes const &c)
ostream &	operator<< (std::ostream &os, const AttributeStore &a)
	Insertion of text representation in ostream.
std::ostream &	operator<< (std::ostream &os, const Node &n)
std::ostream &	operator<< (std::ostream &os, const GeoData &c)
std::ostream &	operator<< (std::ostream &os, Cell const &v)
ostream &	operator<< (ostream &os, const Wall &w)
ostream &	operator<< (ostream &os, const Cell &c)
std::istream &	operator>> (std::istream &is, BoundaryType &b)
template<typename T >
void	para_seed (std::vector< T > &rngs, const unsigned long seed)
	Seed a vector of random number generators and splits in 'n' parallel streams using the leapfrog scheme, where 'n' is the size of the vector 'rngs'. More...
template<typename T >
void	para_seed (std::vector< T > &rngs, const std::string &state)
	Seed a vector of random number generators and splits in 'n' parallel streams using the leapfrog scheme, where 'n' is the size of the vector 'rngs'. More...
template<typename R >
R	ReduceCellWalls (Cell *cell, std::function< R(Cell *, Cell *, Wall *)> f)
	Traverse walls of cell and apply functor.

Detailed Description

Namespace for the core simulator.

Function Documentation

bool SimPT_Sim::operator<	(	ChainHull::Point const &	p1,
		ChainHull::Point const &	p2
	)

Required to sort points (e.g.

Qt's qSort()).

Definition at line 72 of file ChainHull.cpp.

template<typename T >

void SimPT_Sim::para_seed	(	std::vector< T > &	rngs,
		const unsigned long	seed
	)

Seed a vector of random number generators and splits in 'n' parallel streams using the leapfrog scheme, where 'n' is the size of the vector 'rngs'.

This function is used as a quick utility routine in RandomEngine::SetState and might be replaced in the future with a C++14 polymorphic lambda.

Definition at line 115 of file RandomEngine.cpp.

template<typename T >

void SimPT_Sim::para_seed	(	std::vector< T > &	rngs,
		const std::string &	state
	)

Seed a vector of random number generators and splits in 'n' parallel streams using the leapfrog scheme, where 'n' is the size of the vector 'rngs'.

This function is used as a quick utility routine in RandomEngine::SetState and might be replaced in the future with a C++14 polymorphic lambda.

Definition at line 152 of file RandomEngine.cpp.