RigidFiber Class Reference

Detailed Description

Implements the methods of a Mecable for the FiberNaked:

1. setSpeedsFromForces() includes longitudinal incompressibility, which means keeping successive points equidistants: norm( point(p+1) - point(p) ) = segmentation()
2. addRigidity() implements bending elasticity.

Inheritance diagram for RigidFiber:

Public Member Functions
	RigidFiber ()
	Constructor.
	RigidFiber (RigidFiber const &)
	copy constructor
RigidFiber &	operator= (RigidFiber const &)
	copy assignment
virtual	~RigidFiber ()
	Destructor.
virtual unsigned	allocatePoints (unsigned nbp)
	sets the number of points in the Fiber
real	lagrange (unsigned p) const
	Lagrange multiplier for segment p.
real	tension (unsigned p) const
	longitudinal force along segment p (positive=extension, negative=compression)
real	dragCoefficient () const
	total drag-coefficient of object (force = drag * speed)
real	pointMobility () const
	mobility of one point
void	makeProjection ()
	prepare for projection
void	projectForces (const real *X, real *Y, real s, real *work) const
	apply the projection: Y <- s * P * X More...
void	makeProjectionDiff (const real *)
	prepare the correction to the projection
void	addProjectionDiff (const real *, real *) const
	add the contribution from the projection correction
real	addBrownianForces (real *rhs, real sc) const
	add displacements due to the Brownian motion to rhs[] More...
void	setSpeedsFromForces (const real *X, real *Y, real, bool) const
	calculate the speeds from the forces, including projection More...
void	addRigidity (const real *X, real *Y) const
	add the rigidity force corresponding to configuration X into vector Y More...
void	addRigidityMatUp (Matrix &, int offset) const
	add rigidity terms into the matrix
Public Member Functions inherited from FiberNaked
	FiberNaked ()
	Constructor.
	~FiberNaked ()
	Destructor.
void	setStraight (Vector const &pos, Vector const &dir)
	set position of MINUS_END and direction (length and Nb of points are not modified) More...
void	setStraight (Vector const &pos, Vector const &dir, FiberEnd ref)
	set position of 'ref' and direction of Fiber
void	setStraight (Vector const &pos, Vector const &dir, real len, FiberEnd ref)
	set position of 'ref', direction and length of Fiber
void	setShape (const real pts[], unsigned n_pts, unsigned np)
	import shape from the given array of size DIM*n_pts, and create a shape with np points More...
PointExact	exactEnd (FiberEnd) const
	exact representation of given end
PointInterpolated	interpolateEnd (FiberEnd) const
	interpolation representing a given end (CENTER is also a valid argument)
PointInterpolated	interpolateCenter () const
	interpolation representing a given end
PointInterpolated	interpolateMinusEnd () const
	interpolation representing the MINUS_END
PointInterpolated	interpolatePlusEnd () const
	interpolation representing the PLUS_END
PointInterpolated	interpolate (real ab) const
	interpolation of the site specified by its distance from the ORIGIN More...
PointInterpolated	interpolateM (real ab) const
	interpolation of the site specified from the MINUS_END More...
PointInterpolated	interpolate (real ab, FiberEnd from) const
	interpolation of a site specified by its distance from a FiberEnd
real	abscissaM () const
	signed distance from ORIGIN to MINUS_END (abscissa of MINUS_END)
real	abscissaP () const
	signed distance from ORIGIN to PLUS_END (abscissa of PLUS_END)
real	abscissaP (const real n) const
	signed distance from ORIGIN to given point or intermediate position
real	abscissa (FiberEnd end) const
	signed distance from the ORIGIN to the specified FiberEnd More...
real	abscissa (real ab, FiberEnd from) const
	converts abscissa from the specified FiberEnd, to abscissa from the ORIGIN More...
real	length () const
	the total length of the Fiber
bool	within (const real ab) const
	true if ( abscissaM() < ab < abscissaP() )
bool	withinP (const real ab) const
	true if abscissa is below abscissaP
bool	withinM (const real ab) const
	true if abscissa is above abscissaM
unsigned int	signature () const
	a random number which is used in speckle display
void	signature (unsigned int s)
	set signature
FiberEnd	whichEndDomain (real ab, real lambda) const
	calculate the domain in which ab is located (near a FiberEnd, or central) More...
Vector	pos (real ab) const
	position of a point specified by abscissa from the origin
Vector	posM (real ab) const
	position of a point specified by abscissa from the MINUS_END
Vector	pos (real ab, FiberEnd from) const
	position of a point specified by abscissa on the Fiber
Vector	posEnd (FiberEnd which) const
	position of a FiberEnd (CENTER is also a valid argument)
Vector	dirP (unsigned p) const
	normalized tangent vector to the fiber at given model point More...
Vector	dir (real ab) const
	normalized tangent vector to the fiber at given abscissa from the origin
Vector	dir (real ab, FiberEnd from) const
	normalized tangent vector to the fiber at given abscissa from given reference
Vector	dirEnd (FiberEnd which) const
	normalized tangent vector to the fiber at given end
real	projectedForceOnEnd (FiberEnd which) const
	dot-product (force/km on the end of the Fiber).(direction of Fiber growth) More...
void	segmentation (real c)
	set desired segmentation (the actual segmentation might be different)
real	segmentation () const
	the current segment length (distance between successive model-points)
real	segmentationCub () const
	returns segmentation() ^ 3
void	resegment (unsigned int nb_points)
	recalculate fiber to have nb_points model points More...
void	adjustSegmentation ()
	set the number of points to minimize abs( fnCut - fnCutWished ) More...
void	reshape ()
	re-establish the distance between successive model-points
void	getPoints (const real *x)
	set position
void	minMaxSegments (real &, real &) const
	calculate the minimum and maximum segment length More...
void	infoSegments (real &, real &) const
	calculate average and variance of the segment length More...
real	minCosinus () const
	the cosine of the maximum segment angle: indicate the errors due to curvature
unsigned	nbKinks (real threshold=0) const
	number of joints at which ( cosine(angle) < threshold ) More...
void	join (FiberNaked const *fib)
	merge two fibers by joining the PLUS_END of fib with the MINUS_END of this More...
void	growM (real dlen)
	increase/decrease length of Fiber by dlen, at the MINUS_END More...
void	addSegmentM ()
	add a segment of length segmentation() at the MINUS_END More...
void	cutM (real dlen)
	remove a piece of length dlen >= 0 at the MINUS_END More...
void	growP (real dlen)
	increase/decrease length of Fiber by dlen, at the PLUS_END More...
void	addSegmentP ()
	add a segment of length segmentation() at the MINUS_END More...
void	cutP (real dlen)
	remove a piece of length dlen >= 0 at the PLUS_END More...
void	setLength (real len, FiberEnd ref)
	adjust length without changing the position of ref
void	truncateM (unsigned int p)
	Remove all model points in [ 0, P-1 ], keep [ P, nbPoints() ].
void	truncateP (unsigned int p)
	Keep model points [ 0, p ], remove other points.
void	write (OutputWrapper &) const
	write to OutputWrapper
void	read (InputWrapper &, Simul &)
	read from InputWrapper More...
Public Member Functions inherited from PointSet
	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.
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	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 void	prepareMecable ()=0
	prepare the Mecable to solve the mechanics in Meca::solve() 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

Protected Member Functions
void	storeDifferences ()
	calculate the average difference of successive model-point in rfDiff[] More...
Protected Member Functions inherited from FiberNaked
virtual void	updateRange ()=0
	callback for function that elongates or shorten the Fiber

Protected Attributes
real	rfMobility
	mobility of the points More...
real	rfRigidity
	rigidity scaling factor used in addRigidity()
Protected Attributes inherited from PointSet
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 Member Functions inherited from PointSet
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...
Static Public Attributes inherited from Object
static const Tag	TAG = 'v'
	Object::TAG = 'v' represents the 'void' pointer.

Member Function Documentation

real addBrownianForces ( real *  rhs, real  sc  ) const

virtual

The argument should be: sc = kT / dt;

Reimplemented from Mecable.

void addRigidity ( const real *  X, real *  Y  ) const

virtual

calculate the second-differential of points, scale by the rigidity term, and add to vector Y

Reimplemented from Mecable.

void projectForces	(	const real *	X,
		real *	Y,
		real	s,
		real *	work
	)		const

work should be of size nbSegments() at least

void setSpeedsFromForces ( const real *  X, real *  Y, real  sc, bool  rhs  ) const

virtual

If ( rhs != 0 ), then the local array rfLag[] is used, thus saving the Lagrange multiplier associated with the constraints for later use.

Implements Mecable.

void storeDifferences ( )

protected

Calculate the normalized difference between successive model point of the fiber:

for ( int n = 0; n < DIM*lastPoint(); ++n )
    rfDiff[n] = ( psPos[n+DIM] - psPos[n] ) / segmentation();

Member Data Documentation

real rfMobility

protected

The entire Fiber's mobility is rfMobility/nbPoints()