FieldBase< VAL > Class Template Reference

Detailed Description

template<typename VAL>
class FieldBase< VAL >

The field is build on a Grid with square cells, because diffusion/reaction are then easier to implement. The Grid does not necessarily match the edges of the Space exactly, but instead extends outside, such as to cover the Space::inside entirely.

Each cell holds the amount of molecules. The local concentration can be obtained by dividing by the cell volume:

concentration = FieldGrid::cell(position) / FieldGrid::cellVolume();

Inheritance diagram for FieldBase< VAL >:

Public Types
typedef Grid< DIM, VAL, unsigned int >	FieldGrid
	the type of Grid from which the Field is derived
Public Types inherited from Grid< DIM, VAL, unsigned int >
typedef VAL	cell_type
	The type of cells (=CELL)
typedef unsigned int	index_type
	the type for indices (=INDEX)

Public Member Functions
	FieldBase (FieldProp const *p)
	constructor
	~FieldBase ()
	destructor
void	setField ()
	initialize with squares of size 'step'
bool	hasField () const
	true if field was set
real	cellWidth () const
	size of cell
void	setConcentration (real conc)
	set all cells to value = volume * conc
real	sumValues ()
	total value
void	step (FiberSet &, real)
	simulation step
void	prepare ()
	initialize diffusion matrix (only for FieldScalar)
Tag	tag () const
	return unique character identifying the class
const Property *	property () const
	return index of 'prop' in corresponding PropertyList
void	write (OutputWrapper &out) const
	write Field to file using VAL::write() More...
void	read_data (InputWrapper &in, Simul &)
	read Field from file using VAL::read()
void	read (InputWrapper &in, Simul &sim)
	read Field and checks that the Grid::step has not changed
template<>
void	prepare ()
template<>
void	step (FiberSet &, real time_step)
template<>
void	prepare ()
template<>
void	step (FiberSet &, real)
Public Member Functions inherited from Grid< DIM, VAL, unsigned int >
	Grid ()
	constructor
void	destroy ()
	Free memory.
virtual	~Grid ()
	Destructor.
bool	periodic ()
	true if boundary conditions are periodic
void	periodic (const bool p)
	change boundary conditions
void	setDimensions (const real infs[ORD], real sups[ORD], const int nbcells[ORD])
	set the sizes of the real space dimensions
bool	hasDimensions ()
	true if setDimensions() was called
unsigned int	nbCells () const
	total number of cells in the map
unsigned int	nbCells (int d) const
	number of cells in dimensionality d
unsigned int	dim () const
unsigned int	dim (int d) const
const real *	inf () const
	position of the inferior (left/bottom/etc) edge
real	inf (int d) const
const real *	sup () const
	position of the superior (right/top/etc) edge
real	sup (int d) const
const real *	delta () const
	the widths of a cell
real	delta (int d) const
const real *	cellWidth () const
real	cellWidth (int d) const
real	position (int d, real c) const
real	cellVolume () const
	the volume of a cell
real	diagonalLength () const
	the length of the diagonal of a cell = sqrt( sum(cWidth[d]^2) )
real	minimumWidth (unsigned int min_size) const
	the smallest cell width, along dimensions that have more than min_size cells
bool	inside (const int coord[ORD]) const
	checks if coordinates are inside the box
bool	inside (const real w[ORD]) const
	checks if point is inside the box
void	bringInside (int coord[ORD]) const
	periodic image
void	setCoordinatesFromIndex (int coord[ORD], unsigned intindx) const
	conversion from index to coordinates
void	setCoordinatesFromPosition (int coord[ORD], const real w[ORD], const real offset=0) const
	conversion from Position to coordinates (offset should be in [0,1])
void	setPositionFromIndex (real w[ORD], unsigned intindx, real offset=0) const
	conversion from Index to Position (offset should be in [0,1])
void	setPositionFromCoordinates (real w[ORD], const int coord[ORD], real offset=0) const
	conversion from Coordinates to Position (offset should be in [0,1])
unsigned int	indexFromCoordinates (const int coord[ORD]) const
	conversion from coordinates to index
unsigned int	index (const real w[ORD], const real offset=0) const
	returns the index of the cell whose center is closest to the point w[]
void	createCells ()
	allocate the array of cells
bool	hasCells () const
	returns true if cells have been allocated
void	deleteCells ()
	deallocate array of cells
void	clear ()
	call function clear() for all cells
VAL *	cell_addr ()
	address of the cell array ( equivalent to &cell(0) )
VAL &	cell (const unsigned intindx) const
	return cell at index 'indx'
VAL &	cell (const real w[ORD]) const
	reference to CELL whose center is closest to w[]
VAL &	cell (const int c[ORD]) const
	reference to CELL of coordinates c[]
VAL &	operator[] (const unsigned intindx) const
	operator access to a cell by index
VAL &	operator() (const real w[ORD]) const
	operator access to a cell by position
VAL &	operator() (const int c[ORD]) const
	short-hand access to a cell by co-oordinates
void	create1D (real min, real max, int nbcells)
	create a 1D-map
VAL &	cell1D (const int x) const
	access to cell for ORD==1
VAL &	cell2D (const int x, const int y) const
	access to cell for ORD==2
VAL &	cell3D (const int x, const int y, const int z) const
	access to cell for ORD==3
void	createSquareRegions (const real radius)
	create regions which contains cells at a distance 'range' or less More...
void	createRoundRegions (const real radius)
	create regions which contains cells at a distance 'range' or less More...
void	createSideRegions (const int radius)
	regions that only contain cells of greater index. More...
bool	hasRegions () const
	true is createRegions() or createRoundRegions() was called
int	getRegion (int *&offsets, const unsigned intindx) const
	set region array 'offsets' for cell index More...
void	deleteRegions ()
	free memory occupied by the regions
VAL	interpolate (const real w[ORD]) const
	return linear interpolation of values stored at the center of each cell
VAL	interpolate2D (const real w[ORD]) const
	return linear interpolation of values stored at the center of each cell, but only if ORD==2
VAL	interpolate3D (const real w[ORD]) const
	return linear interpolation of values stored at the center of each cell, but only if ORD==3
void	setValues (const VALval)
	set all cells to zero, if CELL supports this operation
void	scaleValues (const VALval)
	set all cells to zero, if CELL supports this operation
VAL	sumValues () const
	sum of all values, if CELL supports the addition
VAL	maxValue () const
	maximum value over all cells
VAL	minValue () const
	minimum value over all cells
bool	hasNegativeValue () const
	true if any( cells[] < 0 )
VAL	sumValuesInRegion (const unsigned intindx) const
	the sum of the values in the region around cell referred by 'indx'
VAL	avgValueInRegion (const unsigned intindx) const
	the sum of the values in the region around cell referred by 'indx'
VAL	maxValueInRegion (const unsigned intindx) const
	the maximum of the values in the region around cell referred by 'indx'
void	printValues (FILE *file, const real offset) const
	write values to a file, with the position for each cell (file can be stdout)
void	printValuesWithRange (FILE *file) const
	write values to a file, with the range for each cell (file can be stdout)
Public Member Functions inherited from Object
	Object ()
	constructor
std::string	reference () const
	concatenation of [ tag(), property()->index(), number() ] in plain ascii More...
void	writeReference (OutputWrapper &) const
	write a reference that identifies the Object uniquely More...
void	writeReference (OutputWrapper &, Tag tag) const
	write a reference, but using the provided Tag More...
int	mark () const
	birth mark value
void	mark (int m)
	set birth mark
int	fleck () const
	fleck value (not stored in trajectory files)
void	fleck (int f) const
	set fleck (the value is not stored in trajectory files)
Object *	next () const
	extends Node::next(), with a cast to preserve type
Object *	prev () const
	extends Node::prev(), with a cast to preserve type
Public Member Functions inherited from Node
	Node ()
	constructor set as unlinked
virtual	~Node ()
	destructor More...
bool	linked () const
	true if Node is linked
Node *	next () const
	the next Node in the list, or zero if this is last
Node *	prev () const
	the previous Node in the list, or zero if this is first
NodeList *	list () const
	the list where the object is linked, or zero
ObjectSet *	objset () const
	return associated ObjectSet
Public Member Functions inherited from Inventoried
	Inventoried ()
	initialize (name=0)
	~Inventoried ()
	destructor
void	number (Number n)
	change the serial number
Number	number () const
	serial number : a integer identifier, unique within each class
Public Member Functions inherited from Movable
	Movable ()
	constructor
virtual	~Movable ()
	destructor
virtual Vector	position () const
	return the position in space of the object
virtual void	setPosition (Vector const &)
	move object to specified position More...
virtual bool	translatable () const
	true if object accepts translations (default=false)
virtual void	translate (Vector const &)
	move the object ( position += given vector ) More...
virtual bool	rotatable () const
	true if object accepts rotations (default=false)
virtual void	rotate (Rotation const &)
	rotate the object around the origin of coordinates More...
virtual void	rotateP (Rotation const &)
	rotate the object around its current position More...
virtual void	foldPosition (Modulo const *)
	perform modulo for periodic boundary conditions More...

Public Attributes
FieldProp const *	prop
	property

Static Public Attributes
static const Tag	TAG = 'i'
	a unique character identifying the class
Static Public Attributes inherited from Object
static const Tag	TAG = 'v'
	Object::TAG = 'v' represents the 'void' pointer.

Additional Inherited Members
Static Public Member Functions inherited from Grid< DIM, VAL, unsigned int >
static int	ffloor (real x)
	a fast floor function
Static Public Member Functions inherited from Object
static std::string	strReference (char, int, Number, int)
	build a string reference by concatenating (tag, property_index, number, mark) More...
static void	readReference (InputWrapper &, int &, Number &, int &, char pretag)
	read a reference (property_index, number, mark) from input More...
static void	writeNullReference (OutputWrapper &)
	write a reference that does not refer to any Object
Static Public Member Functions inherited from Movable
static Vector	readPrimitive (std::istream &, const Space *)
	read a position specified with primitives, such as 'circle 5', etc. More...
static Vector	readPosition (std::istream &, const Space *)
	read a position in space More...
static Vector	readDirection (std::istream &, const Vector &, const Space *)
	read an orientation, and return a normalized vector More...
static Rotation	readRotation (std::istream &, const Vector &, const Space *)
	read a rotation specified in is, at position pos More...
Protected Attributes inherited from Grid< DIM, VAL, unsigned int >
VAL *	gCell
	The array of pointers to cells.
unsigned int	nCells
	The number of cells in the map; size of cells[].
unsigned int	gDim [ORD]
	The number of cells in each dimension of the real space.
real	gInf [ORD]
	The position of the inferior edge (min) in each dimension.
real	gSup [ORD]
	The position of the superior edge (max) in each dimension.
real	cWidth [ORD]
	cWidth[d] = ( gSup[d] - inf[d] ) / gDim[d]
real	cDelta [ORD]
	cDelta[d] = 1.0 / cWidth[d]
real	cVolume
	The volume occupied by one cell.
Protected Attributes inherited from Node
Node *	nNext
	the next Node in the list
Node *	nPrev
	the previous Node in the list
Protected Attributes inherited from Inventoried
Number	nNumber
	object identifier, unique within the class defined by tag()

Member Function Documentation

void step	(	FiberSet &	,
		real	time_step
	)

Todo:

implement Crank-Nicholson for diffusion

void write ( OutputWrapper &  out ) const

inlinevirtual

Some of this should be moved to Grid

Implements Object.