Class representing a grid for molecule diffusion. More...

#include <DiffusionGrid.hpp>

Public Member Functions
	DiffusionGrid ()=default
	Default constructor. More...

	DiffusionGrid (double dx, double accuracy)
	Constructor with grid parameters. More...

double	getDx () const
	Gets the grid cell size. More...

void	setDx (double _dx)
	Sets the grid cell size. More...

void	setAccuracy (double a)
	Sets the diffusion accuracy. More...

MecaCell::Vec	getIndexFromPosition (const MecaCell::Vec &v) const
	Gets the grid index from a position. More...

double	getMolecule (MecaCell::Vec v, int m)
	Gets the quantity of a molecule at a position. More...

size_t	size () const
	Gets the size of the grid. More...

unordered_map< MecaCell::Vec, GridCell > &	getGrid ()
	Gets the grid. More...

double	getCellSize () const
	Gets the grid cell size. More...

vector< Molecule >	getMolecules () const
	Gets the molecules in the grid. More...

void	addMolecule (int n, Molecule m)
	Adds a molecule to the grid. More...

template<typename world_t >
void	updateBoundary (world_t *w)
	Updates the grid boundaries and consumptions. More...

template<typename world_t >
void	computeMolecules (world_t *w)
	Updates the quantities of molecules in the grid. More...

double	getMoleculeRealPos (const MecaCell::Vec &v, int mol)
	Gets the quantity of a molecule at a real position. More...

Public Attributes
unordered_map< int, int >	moleculesDict

Private Member Functions
double	deriv2nd (double xm1, double x, double xp1)
	Calculates the second derivative. More...

void	nextStep (int i)
	Initializes the next step for a molecule. More...

void	allCellEmpty ()
	Empties all cells. More...

void	cleanCellOutBoundary ()
	Cleans cells that are out of boundaries. More...

bool	isOutBoundary (const MecaCell::Vec &v)
	Checks if a position is out of boundaries. More...

double	getDt (double D) const
	Gets the diffusion time step. More...

double	computeStep (int i)
	Updates the quantity of a molecule for each cell and returns the total amount of this molecule. More...

Private Attributes
double	dx = 5.

double	accuracy = 0.1

unordered_map< MecaCell::Vec, GridCell >	grid

vector< Molecule >	molecules

MecaCell::Vec	minBoundary

MecaCell::Vec	maxBoundary

Detailed Description

Class representing a grid for molecule diffusion.

Definition at line 80 of file DiffusionGrid.hpp.

Constructor & Destructor Documentation

◆ DiffusionGrid() [1/2]

Diffusion::DiffusionGrid::DiffusionGrid ( )

default

Default constructor.

◆ DiffusionGrid() [2/2]

Diffusion::DiffusionGrid::DiffusionGrid	(	double	dx,
		double	accuracy
	)

inline

Constructor with grid parameters.

Parameters

dx	Grid cell size
accuracy	Diffusion accuracy

Definition at line 191 of file DiffusionGrid.hpp.

Member Function Documentation

◆ addMolecule()

void Diffusion::DiffusionGrid::addMolecule	(	int	n,
		Molecule	m
	)

inline

Adds a molecule to the grid.

Parameters

n	Molecule index
m	Molecule to be added

Definition at line 263 of file DiffusionGrid.hpp.

◆ allCellEmpty()

void Diffusion::DiffusionGrid::allCellEmpty ( )

inlineprivate

Empties all cells.

Definition at line 113 of file DiffusionGrid.hpp.

◆ cleanCellOutBoundary()

void Diffusion::DiffusionGrid::cleanCellOutBoundary ( )

inlineprivate

Cleans cells that are out of boundaries.

Definition at line 124 of file DiffusionGrid.hpp.

◆ computeMolecules()

template<typename world_t >

void Diffusion::DiffusionGrid::computeMolecules ( world_t * w )

inline

Updates the quantities of molecules in the grid.

Template Parameters

world_t Type of the world

Parameters

w	Pointer to the world

Definition at line 324 of file DiffusionGrid.hpp.

◆ computeStep()

double Diffusion::DiffusionGrid::computeStep ( int i )

inlineprivate

Updates the quantity of a molecule for each cell and returns the total amount of this molecule.

Parameters

i	Molecule index

Returns: Total quantity of the molecule

Definition at line 153 of file DiffusionGrid.hpp.

◆ deriv2nd()

double Diffusion::DiffusionGrid::deriv2nd	(	double	xm1,
		double	x,
		double	xp1
	)

inlineprivate

Calculates the second derivative.

Parameters

xm1	Value at x-1
x	Value at x
xp1	Value at x+1

Returns: Approximate second derivative at x

Definition at line 98 of file DiffusionGrid.hpp.

◆ getCellSize()

double Diffusion::DiffusionGrid::getCellSize ( ) const

inline

Gets the grid cell size.

Returns: Grid cell size

Definition at line 250 of file DiffusionGrid.hpp.

◆ getDt()

double Diffusion::DiffusionGrid::getDt ( double D ) const

inlineprivate

Gets the diffusion time step.

Parameters

D	Diffusion constant of the molecule

Returns: Diffusion time step

Definition at line 146 of file DiffusionGrid.hpp.

◆ getDx()

double Diffusion::DiffusionGrid::getDx ( ) const

inline

Gets the grid cell size.

Returns: Grid cell size

Definition at line 197 of file DiffusionGrid.hpp.

◆ getGrid()

unordered_map< MecaCell::Vec, GridCell > & Diffusion::DiffusionGrid::getGrid ( )

inline

Gets the grid.

Returns: Grid

Definition at line 244 of file DiffusionGrid.hpp.

◆ getIndexFromPosition()

MecaCell::Vec Diffusion::DiffusionGrid::getIndexFromPosition ( const MecaCell::Vec & v ) const

inline

Gets the grid index from a position.

Parameters

v	Position vector

Returns: Grid index of the position

Definition at line 216 of file DiffusionGrid.hpp.

◆ getMolecule()

double Diffusion::DiffusionGrid::getMolecule	(	MecaCell::Vec	v,
		int	m
	)

inline

Gets the quantity of a molecule at a position.

Parameters

v	Position vector
m	Molecule index

Returns: Quantity of the molecule at the position

Definition at line 227 of file DiffusionGrid.hpp.

◆ getMoleculeRealPos()

double Diffusion::DiffusionGrid::getMoleculeRealPos	(	const MecaCell::Vec &	v,
		int	mol
	)

inline

Gets the quantity of a molecule at a real position.

Parameters

v	Position vector
mol	Molecule index

Returns: Quantity of the molecule at the position

Definition at line 347 of file DiffusionGrid.hpp.

◆ getMolecules()

vector< Molecule > Diffusion::DiffusionGrid::getMolecules ( ) const

inline

Gets the molecules in the grid.

Returns: Molecules

Definition at line 256 of file DiffusionGrid.hpp.

◆ isOutBoundary()

bool Diffusion::DiffusionGrid::isOutBoundary ( const MecaCell::Vec & v )

inlineprivate

Checks if a position is out of boundaries.

Parameters

v	Position vector

Returns: True if the position is out of boundaries, false otherwise

Definition at line 137 of file DiffusionGrid.hpp.

◆ nextStep()

void Diffusion::DiffusionGrid::nextStep ( int i )

inlineprivate

Initializes the next step for a molecule.

Parameters

i	Molecule index

Definition at line 104 of file DiffusionGrid.hpp.

◆ setAccuracy()

void Diffusion::DiffusionGrid::setAccuracy ( double a )

inline

Sets the diffusion accuracy.

Parameters

a	Diffusion accuracy

Definition at line 209 of file DiffusionGrid.hpp.

◆ setDx()

void Diffusion::DiffusionGrid::setDx ( double _dx )

inline

Sets the grid cell size.

Parameters

_dx	Grid cell size

Definition at line 203 of file DiffusionGrid.hpp.

◆ size()

size_t Diffusion::DiffusionGrid::size ( ) const

inline

Gets the size of the grid.

Returns: Size of the grid

Definition at line 238 of file DiffusionGrid.hpp.

◆ updateBoundary()

template<typename world_t >

void Diffusion::DiffusionGrid::updateBoundary ( world_t * w )

inline

Updates the grid boundaries and consumptions.

Template Parameters

world_t Type of the world

Parameters

w	Pointer to the world

Definition at line 274 of file DiffusionGrid.hpp.

Member Data Documentation

◆ accuracy

double Diffusion::DiffusionGrid::accuracy = 0.1

private

Precision of the diffusion

Definition at line 83 of file DiffusionGrid.hpp.

◆ dx

double Diffusion::DiffusionGrid::dx = 5.

private

Cell size

Definition at line 82 of file DiffusionGrid.hpp.

◆ grid

unordered_map<MecaCell::Vec, GridCell> Diffusion::DiffusionGrid::grid

private

Grid cells hashmap

Definition at line 84 of file DiffusionGrid.hpp.

◆ maxBoundary

MecaCell::Vec Diffusion::DiffusionGrid::maxBoundary

private

Definition at line 89 of file DiffusionGrid.hpp.

◆ minBoundary

MecaCell::Vec Diffusion::DiffusionGrid::minBoundary

private

Definition at line 88 of file DiffusionGrid.hpp.

◆ molecules

vector<Molecule> Diffusion::DiffusionGrid::molecules

private

Existing molecules in the simulation

Definition at line 85 of file DiffusionGrid.hpp.

◆ moleculesDict

unordered_map<int,int> Diffusion::DiffusionGrid::moleculesDict

Dictionary mapping molecule indices

Definition at line 179 of file DiffusionGrid.hpp.

The documentation for this class was generated from the following file:

modules/cellModules/Diffusion/DiffusionGrid.hpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DiffusionGrid() [1/2]

◆ DiffusionGrid() [2/2]

Member Function Documentation

◆ addMolecule()

◆ allCellEmpty()

◆ cleanCellOutBoundary()

◆ computeMolecules()

◆ computeStep()

◆ deriv2nd()

◆ getCellSize()

◆ getDt()

◆ getDx()

◆ getGrid()

◆ getIndexFromPosition()

◆ getMolecule()

◆ getMoleculeRealPos()

◆ getMolecules()

◆ isOutBoundary()

◆ nextStep()

◆ setAccuracy()

◆ setDx()

◆ size()

◆ updateBoundary()

Member Data Documentation

◆ accuracy

◆ dx

◆ grid

◆ maxBoundary

◆ minBoundary

◆ molecules

◆ moleculesDict