Detailed Description

The FiberSet stores Fiber, and derived classes. Algorithms that specifically deal with Fibers should be contained here.

Inheritance diagram for FiberSet:

Public Member Functions
	FiberSet (Simul &s)
	creator

virtual	~FiberSet ()
	destructor

std::string	kind () const
	identifies the class

Property *	newProperty (const std::string &kind, const std::string &name, Glossary &) const
	create a new property for class `kind` with given name

Object *	newObject (const std::string &kd, const std::string &nm, Glossary &opt)
	create a new Fiber from the corresponding property More...

ObjectList	newObjects (const std::string &kd, const std::string &nm, Glossary &opt)
	create new Fibers

Object *	newObjectT (const Tag tag, int prop_index)
	construct Fiber More...

Fiber *	first () const
	first Fiber

Fiber *	last () const
	last Fiber

Fiber *	find (Number n) const
	return pointer to the Object of given inventory Number, or zero if not found

void	cutAlongPlane (Vector const &n, real a, bool(func)(Object const , void ), void )
	Cut all segments intersecting the plane defined by n.x + a = 0 More...

void	step ()
	Monte-Carlo step for every Fiber. More...

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

void	uniFiberSites (Array< FiberBinder > &, const real spread) const
	set random sites along the fibers, separated on average by `spread` More...

int	count (bool(func)(Fiber const , void ), void ) const
	number of Fiber that do not belong to an Organizer

real	totalLength () const
	total length of Fiber

real	totalLength (FiberProp const *) const
	total length of Fiber that have ( FiberProp == p )

void	infoLength (unsigned int &cnt, real &avg, real &dev, bool(func)(Fiber const , void )=0, void =0) const
	calculate: number of fibers, mean and standard-deviation of fiber length

void	infoSegments (unsigned &cnt, unsigned &joints, unsigned &kinks, real &, real &, bool(func)(Fiber const , void )=0, void =0) const
	calculate: number of fibers, number of joints and number of kinks

real	infoDirection (Vector &G, Vector &D, Vector &N, bool(func)(Fiber const , void )=0, void =0) const
	calculate: center of gravity G, average direction D, average nematic direction N More...

void	infoIntersections (int &np, int &na, Vector const &n, real a) const
	Count Fibers intersecting the plane defined by n.x + a = 0 More...

void	infoSpindle (real &ixa, real &ixs, Vector const &n, real a, real m, real da) const
	Calculate spindle indices. More...

void	infoTension (unsigned int &, real &hten, Vector const &n, real a) const
	sum Lagrange multipliers for segments that intersect the plane n.x + a = 0 More...

void	infoTension (unsigned int &, real &hten) const
	sum Lagrange multipliers for all fibers More...

void	infoRadius (unsigned int &, real &rad) const
	Calculate averaged distance from origin - for all model points.

void	infoRadius (unsigned int &, real &rad, FiberEnd) const
	Calculate averaged distance from origin - for fiber ends.

Public Member Functions inherited from ObjectSet
virtual void	freeze ()
	transfer all nodes to list ice

virtual void	thaw (bool erase)
	erase objects, or put them back in normal list

	ObjectSet (Simul &s)
	creator

virtual	~ObjectSet ()
	destructor

virtual ObjectList	newPlacedObjects (const std::string &kind, const std::string &name, Glossary &opt)
	create new objects, translate and rotate them according to specifications in opt More...

virtual void	add (Object *)
	register Object, and add it at the end of the list

void	add (ObjectList &)
	remove Object in ObjectList

virtual void	remove (Object *)
	remove Object

void	remove (ObjectList &)
	remove Object in ObjectList

virtual void	relink (Object *)
	unlink and relink object. This places it last in the list More...

void	erase (Object *)
	remove Object, and delete it

virtual void	erase ()
	delete all Objects in list and forget all serial numbers

virtual unsigned	size () const
	number of elements

virtual void	mix ()
	mix the order of elements in the doubly linked list nodes

Object *	first () const
	first Object in the list

Object *	first (const Property *) const
	return an Object which has this property More...

Object *	last () const
	last Object

Object *	find (const Number n) const
	find Object of given serial-number (see Inventoried)

Object *	findObject (long n) const
	return Object with serial-number if ( n > 0 ) or object from the end of the list if ( n <= 0 ) More...

virtual ObjectList	collect (bool(func)(Object const , void ), void ) const
	collect Object for which func(obj, val) == true

void	readObject (InputWrapper &, Tag, char pretag)
	read one Object from file More...

virtual void	write (OutputWrapper &out) const
	write all Objects to file

Additional Inherited Members
Static Public Member Functions inherited from ObjectSet
static void	translateObjects (ObjectList const &, Vector const &)
	apply translation to all Objects in ObjectList More...

static void	rotateObjects (ObjectList const &, Rotation const &)
	apply rotation to all Objects in ObjectList More...

Public Attributes inherited from ObjectSet
Inventory	inventory
	holds pointers to the Objects in a array of Numbers

NodeList	nodes
	holds pointers to the Objects in a doubly linked list

Simul &	simul
	the Simul containing this ObjectSet

Protected Member Functions inherited from ObjectSet
void	forget (NodeList &)
	remove all nodes in the list from the inventory

virtual void	link (Object *)
	link the object last in the list More...

Static Protected Member Functions inherited from ObjectSet
static ObjectList	collect (const NodeList &, bool(func)(Object const , void ), void )
	collect Object from NodeList for which func(obj, val) == true

static void	write (const NodeList &, OutputWrapper &)
	write Object in NodeList to file More...

static Vector	placeObjects (ObjectList const &, Glossary &opt, const Space *)
	place all Objects in ObjectList using the same combinations of translation/rotation More...

Protected Attributes inherited from ObjectSet
NodeList	ice
	a list used to store the objects temporarily while a state is imported

Member Function Documentation

void cutAlongPlane	(	Vector const &	n,
		real	a,
		bool()(Object const , void *)	func,
		void *
	)

Cut all Fibers along the plane defined by n.x + a = 0. function argument func can be specified to specify which fibers can be cut. If ( func != 0 ), a fiber fib will be cut only if

func(fib, arg) == true

real infoDirection	(	Vector &	G,
		Vector &	D,
		Vector &	N,
		bool()(Fiber const , void *)	func = `0`,
		void *	arg = `0`
	)		const

Each Fiber segment is weigthed by its length.

Returns: G = average center of gravity; D = average direction; N = average nematic direction

To calculate the Nematic direction, we average the square of the imaginary number representing the direction vector.

This works in 2D by producing a nematic tensor, but in 3D this is only correct if the average direction is roughly already aligned with the X-axis.

Todo:: better nematic tensor calculation in 3D.

void infoIntersections	(	int &	np,
		int &	na,
		Vector const &	n,
		real	a
	)		const

Counts the number of fiber intersecting the plane defined by n.x + a = 0 in two categories, depending on the direction with which they cross the plane:

np = number of parallel segments ( the scalar product dir.n is strictly positive )
na = number of anti-parallel segments ( dir.n < 0 )

void infoSpindle	(	real &	ixa,
		real &	ixp,
		Vector const &	n,
		real	a,
		real	m,
		real	dm
	)		const

Calculate two indices characterizing the organization of the fibers along the axis n.

ixa = average { ( o - i ) }
ixp = average { ( r - l ) }

where:

o = number of fiber pointing outward (away from the mid-plane),
i = number of fiber pointing inward (toward the mid-plane),
r = number of fiber pointing right (in direction of n),
l = number of fiber pointing left.

The indices are averaged over planar sections taken every dm units of space, and the values for each planar section are weighted by the number of fibers. The central symmetry plane is defined by n.x+a=0, and the edges correspond to n.x+a=+/-m.

The results characterize broadly the type of fiber organization:

ixa = 1, ixp = 0: aster,
ixa = -1, ixp = 0: anti-aster,
ixa = 0, ixp = 1: parallel overlap,
ixa = 0, ixp = 0: anti-parallel overlap (50/50).

void infoTension	(	unsigned int &	cnt,
		real &	ten,
		Vector const &	n,
		real	a
	)		const

Sum tension of all the segments that intersect the plane defined by n.x + a = 0 The tension dipole along the segment is obtained from the Lagrange multiplier associated with the length of each segment. The magnitude of the dipole is multiplied by the cosine of the angle between the segment and the plane normal.

Returns: cnt = number of segments intersecting the plane; ten = sum of tension

void infoTension	(	unsigned int &	cnt,
		real &	ten
	)		const

Sum tension of all the segments

Returns: cnt = number of segments intersecting the plane; ten = sum of tension

Object * newObject	(	const std::string &	kd,
		const std::string &	nm,
		Glossary &	opt
	)

virtual

The initialization options depends on the type of fiber: Fiber, DynamicFiber, ClassicFiber, Tubule.

Implements ObjectSet.

Object * newObjectT	(	const Tag	tag,
		int	idx
	)

virtual

The fiber is not initialized, since this is used for file input

Implements ObjectSet.

void step ( )

Calculate the free monomer concentration. Calls step() once for every Fiber.

void uniFiberSites	(	Array< FiberBinder > &	res,
		const real	spread
	)		const

Set a list of Locations on the fibers, chosen randomly with uniform sampling. The number of site over a stretch of length len should be len/spread .

Condition: ( spread > 0 )

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation