Detailed Description

The Bead is the simplest Mecable. It represents a spherical object using:

a position vector,
a radius.

The orientational degrees of freedom are neglected. Translation follows Stokes's law. A Single can be attached in the center of the bead.

For more elaborate models, see Sphere and Solid.

Inheritance diagram for Bead:

Public Member Functions
	Bead (BeadProp const *, Vector pos, real rad)
	create following specifications

virtual	~Bead ()
	destructor

Vector	position () const
	return the position in space of the object

bool	translatable () const
	true if object accepts translations (default=false)

void	translate (Vector const &w)
	move the object position ( position += given vector )

void	setPosition (Vector const &w)
	set the object position ( position = given vector )

void	foldPosition (const Modulo *)
	modulo the position (periodic boundary conditions)

real	radius () const
	the radius of the Bead

real	radiusSqr () const
	the volume of the bead

void	resize (real R)
	set the radius of the Bead

real	volume () const
	the volume of the bead

unsigned int	nbPoints () const
	can only have one point

Vector	posP (unsigned n) const
	return position of point

void	putPoints (real *x) const
	copy coordinates to given array

void	getPoints (const real *x)
	set position

Vector	netForceP (unsigned n) const
	return Force on point x calculated at previous step by Brownian dynamics

void	getForces (const real *x)
	replace current forces by the ones provided

void	setDragCoefficient ()
	sets the mobility More...

real	dragCoefficient () const
	the total drag-coefficient of object (force = drag * speed)

void	prepareMecable ()
	sets the mobility (called at every step) More...

void	setSpeedsFromForces (const real X, real Y, real, bool) const
	calculates the speed of points in Y, for the forces given in X More...

real	addBrownianForces (real *rhs, real sc) const
	add contribution of Brownian forces

void	setInteractions (Meca &) const
	add the interactions due to confinement

void	step ()
	monte-carlo step

Bead *	next () const
	a static_cast<> of Node::next()

Bead *	prev () const
	a static_cast<> of Node::prev()

Tag	tag () const
	return unique character identifying the class

const Property *	property () const
	return Object Property

void	read (InputWrapper &, Simul &)
	read from file

void	write (OutputWrapper &) const
	write to 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	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	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...

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 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...

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

Public Attributes
BeadProp const *	prop
	Property.

Static Public Attributes
static const Tag	TAG = 'b'
	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 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 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 prepareMecable ( )

inlinevirtual

setDragCoefficient() is called when the Bead is created, or when it is resized, and nothing needs to be done here.

Implements Mecable.

void setDragCoefficient ( )

virtual

Bead follow Stokes' law.

Translation:

muT = 6*M_PI*viscosity*soRadius[pp];

muT * dx/dt = force

Rotation:

muR = 8*M_PI*viscosity*cub(soRadius[pp])

muR * d(angle)/dt = momentum-of-forces

Implements Mecable.

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

virtual

The projection is trivial

Implements Mecable.

Detailed Description

Public Member Functions

Public Attributes

Static Public Attributes

Additional Inherited Members

Member Function Documentation