PointSet Class Reference

Detailed Description

This implements the interface defined by Mecable, and defines an Object with a variable number of points.

Inheritance diagram for PointSet:

Public Member Functions
	PointSet ()
	Constructor.
	PointSet (const PointSet &)
	Copy constructor.
PointSet &	operator= (const PointSet &)
	Assignement operator.
virtual	~PointSet ()
	Destructor.
virtual unsigned int	allocatePoints (unsigned int nbp)
	allocate memory to store 'nbp' points More...
virtual void	deallocatePoints ()
	free memory allocated by allocatePoints()
unsigned int	nbPoints () const
	Number of points.
unsigned int	lastPoint () const
	Index of the last point = nbPoints - 1.
unsigned int	nbSegments () const
	Number of segments = nbPoints - 1.
unsigned int	lastSegment () const
	Index of the last segment = nbPoints - 2.
Vector	posP (const unsigned p) const
	Position of point 'p' of the object.
real const *	addr () const
	Address of point p.
real const *	addrPoint (const unsigned p) const
	Address of point p.
void	setPoint (unsigned p, Vector const &w)
	Set position of point p to w.
void	nbPoints (const unsigned n)
	Set the number of points in the array.
unsigned int	addPoint (Vector const &w)
	Add a point, returning the array index that was used.
void	removePoint (unsigned int p)
	Remove a point from the array psPos, returns number of points remaining.
virtual void	truncateM (unsigned int p)
	Remove all points with indices [ 0, p-1 ], keep [ p, nbPoints() ]. More...
virtual void	truncateP (unsigned int p)
	Keep points [ 0, p ], remove other points. More...
void	clearPoints ()
	Remove all points.
void	resetPoints ()
	Set all coordinates to zero (nicer for debug/testing)
void	addNoise (real amount)
	Add random noise uniformly to all coordinate (used for testing purposes)
virtual void	putPoints (real *) const
	copy current coordinates to argument
virtual void	getPoints (const real *)
	replace current coordinates by provided ones
virtual void	getForces (const real *ptr)
	replace current forces by the ones provided
Vector	netForceP (const unsigned p) const
	Force on point p calculate by Brownian dynamics.
void	movePoint (const unsigned int p, Vector const &w)
	Shift point at index p by vector w.
Vector	diffPoints (const unsigned p) const
	Difference of two points = Q - P = vector PQ.
Vector	diffPoints (const unsigned int p, const unsigned int q) const
	Difference of two points = Q - P = vector PQ.
Vector	interpolatePoints (const unsigned int p, const unsigned int q, const real a) const
	Calculate intermediate position = P + a ( Q - P )
void	calculateMomentum (real[], bool divide=false)
	calculate first momentum of point coordinates More...
void	calculateMomentum (real[], real[], bool divide=false)
	calculate first and second momentum of point coordinates More...
virtual Vector	position () const
	Position of center of gravity. More...
virtual bool	translatable () const
	true if object accepts translations
virtual void	translate (Vector const &)
	Translate object (moves all the points by w)
virtual bool	rotatable () const
	true if object accepts translations
virtual void	rotate (Rotation const &)
	Rotate object by given rotation.
virtual void	foldPosition (const Modulo *)
	Modulo around the first point.
virtual void	foldPositionG (const Modulo *)
	Call modulo around the center of gravity.
void	write (OutputWrapper &) const
	Write to file.
void	read (InputWrapper &, Simul &)
	Read from file.
Public Member Functions inherited from Mecable
	Mecable ()
	The constructor resets the pointers.
virtual	~Mecable ()
	Destructor de-allocates memory.
virtual Vector	posP (unsigned int P) const =0
	return position of point P
virtual void	putPoints (real[]) const =0
	copy current coordinates to provided array
virtual void	getPoints (const real[])=0
	replace current coordinates of points by values from the provided array
virtual Vector	netForceP (unsigned int p) const =0
	return Force on point p calculated at previous step by Brownian dynamics
virtual void	getForces (const real[])=0
	replace current forces by the ones provided
void	matIndex (Matrix::index_type index)
	Store the index where coordinates are located in Meca.
Matrix::index_type	matIndex () const
	Index in mB of the first point. the index in the vectors is DIM*matIndex() More...
bool	useBlock () const
	Tell Meca to use preconditionning on this object or not.
void	useBlock (bool b)
	change preconditionning flag
real *	allocateBlock (unsigned)
	Allocate a block of the requested size.
real *	block () const
	return allocated block
virtual void	setDragCoefficient ()=0
	Calculate the mobility coefficient.
virtual real	dragCoefficient () const =0
	The total drag coefficient of object ( force = drag * speed )
virtual void	prepareMecable ()=0
	prepare the Mecable to solve the mechanics in Meca::solve() More...
virtual real	addBrownianForces (real *rhs, real sc) const
	Add Brownian noise terms to a force vector (sc = kT / dt)
virtual void	addRigidity (const real *X, real *Y) const
	Add rigidity terms Y <- Y + Rigidity * X. More...
virtual void	addRigidityMatUp (Matrix &mB, int offset) const
	Add rigidity matrix elements (which should be symmetric) to provided matrix. More...
virtual void	setSpeedsFromForces (const real *X, real *Y, real sc=1.0, bool rhs=false) const =0
	Calculate speeds from given forces. More...
virtual void	makeProjectionDiff (const real *forces)
	set the terms obtained from the linearization of the Projection operator, from the given forces More...
virtual void	addProjectionDiff (const real *X, real *Y) const
	add terms from projection correction terms: Y <- Y + P' * X; More...
virtual void	setInteractions (Meca &) const
	add the interactions (for example due to confinements)
Public Member Functions inherited from Object
	Object ()
	constructor
virtual Tag	tag () const =0
	an ASCII character identifying the ObjectSet corresponding to this object
virtual const Property *	property () const =0
	Property associated with the Object.
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 void	setPosition (Vector const &)
	move object to specified position More...
virtual void	rotateP (Rotation const &)
	rotate the object around its current position More...
Public Member Functions inherited from Buddy
virtual	~Buddy ()
	upon destruction, goodbye is called for all buddies
void	hello (Buddy *b)
	will make this and b mutual buddies
virtual void	goodbye (Buddy *)
	this is called everytime a known buddy is destroyed
Buddy *	buddy (unsigned int ix) const
	return buddy at index ix
void	buddy (Buddy *b, unsigned int ix)
	replace the buddy that may have been at index ix

Static Public Member Functions
static Vector	diffPoints (const real *src, const unsigned p)
	Difference of two points = P+1 - P.
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
real *	psPos
	psPos[] of size DIM*psAllocated contains DIM*psSize point-coordinates
real const *	psFor
	psFor[] of size DIM*psAllocated contains DIM*psSize force-coordinates
Vector	psCenter
	Center of gravity calculed in calculatePosition()
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()

Additional Inherited Members
Static Public Attributes inherited from Object
static const Tag	TAG = 'v'
	Object::TAG = 'v' represents the 'void' pointer.

Member Function Documentation

unsigned int allocatePoints ( unsigned int  nbp )

virtual

allocate(size) ensures that the set can hold size points it returns the size if new memory was allocated

Reimplemented in Fiber, and Solid.

void calculateMomentum	(	real	cc[],
		bool	divide = false
	)

Calculate cc[DIM] = sum( psPos )

void calculateMomentum	(	real	cc[],
		real	pp[],
		bool	divide = false
	)

Calculate cc[DIM] = sum( psPos ) and pp[DIM] = sum( psPos * psPos );

Vector position ( ) const

virtual

Calculate the center of gravity of all points

Reimplemented from Movable.

Reimplemented in Sphere.

void truncateM ( unsigned int  p )

virtual

shifts ending-part of the array to indices starting at 0.

Reimplemented in FiberNaked.

void truncateP ( unsigned int  p )

virtual

erase higher indices of array

Reimplemented in FiberNaked.