Detailed Description

A Mecable is an Object made of points that can can be simulated in Meca.

Mecable defines an interface that is implemented in Bead and PointSet. Mecable is also a Buddy, and can thus be part of an Organizer.

Inheritance diagram for Mecable:

Public Member Functions
	Mecable ()
	The constructor resets the pointers.

virtual	~Mecable ()
	Destructor de-allocates memory.

virtual unsigned	nbPoints () const =0
	Number of points.

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.

virtual void	write (OutputWrapper &) const =0
	write Object data to file

virtual void	read (InputWrapper &, Simul &)=0
	read Object from file, within the Simul

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 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

Additional Inherited Members
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.

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

virtual void addProjectionDiff	(	const real *	X,
		real *	Y
	)		const

inlinevirtual

This is enabled by a keyword PROJECTION_DIFF in meca.cc

Reimplemented in RigidFiber.

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

inlinevirtual

Rigidity can be any force acting internally to the objects for example, the bending rigidity of Fibers. This version is used to calculate the Matrix * Vector in Meca.

Reimplemented in RigidFiber.

virtual void addRigidityMatUp	(	Matrix &	mB,
		int	offset
	)		const

inlinevirtual

The function should add terms to the upper part of matrix mB, at indices starting from offset. It should fill at maximum the upper part of the diagonal block corresponding to indices [offset - offset+DIM*nbPoints()]. This version is used to build the preconditionner in Meca. It should be consistent with addRigidity(): add the same terms.

Reimplemented in RigidFiber.

virtual void makeProjectionDiff ( const real * forces )

inlinevirtual

This is enabled by a keyword PROJECTION_DIFF in meca.cc

Reimplemented in RigidFiber.

Matrix::index_type matIndex ( ) const

inline

X1 is stored at DIM*matIndex(), Y1 at DIM*matIndex()+1, Z1 at DIM*matIndex()+2 then X2, Y2, Z2...

virtual void prepareMecable ( )

pure virtual

This is called in Meca, before the system is solved, and it should prepare all the variables necessary for:

addRigidity() -> set rigidity coefficients
setSpeedsFromForces() -> call setDragCoefficient(),
set matrix/variables necessary for constrained dynamics

Implemented in Bead, Solid, Sphere, and Fiber.

virtual void setSpeedsFromForces	(	const real *	X,
		real *	Y,
		real	sc = `1.0`,
		bool	rhs = `false`
	)		const

pure virtual

The function should perform Y <- sc * mobility * X.

X and Y are vectors of size DIM*nbPoints().
sc is a provided scalar, and mobility is known by the object.
if rhs==true, the call was made with X containing the true force in the system.

Implemented in Sphere, Bead, RigidFiber, and Solid.

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation