Public Member Functions
	Simul ()
	constructor

virtual	~Simul ()
	destructor

void	add (Object *)
	link Object

int	add (ObjectList)
	link Objects

void	remove (Object *)
	unlink Object

void	remove (ObjectList)
	unlink Objects

void	erase (Object *)
	unlink and delete object

void	erase (ObjectList)
	unlink and delete all objects in list

void	mark (ObjectList, int)
	mark objects in list

void	erase ()
	erase simulation world (all sub-lists and variables)

real	simTime () const
	time in the simulated world

void	setTime (real t)
	set frame index

void	initialize (Glossary &)
	perform basic initialization; register callbacks More...

void	prepare (Space *spc)
	initialize the simulation engine More...

void	prepare ()
	initialize the simulation engine using the current space

bool	isReady () const
	returns true is the simulation is ready to run (or appears so)

void	relax ()
	call after a sequence of step() have been done

void	space (Space *spc)
	set current Space More...

Space *	space () const
	get current Space

Space *	firstSpace (const std::string &name)
	return first Space with this name

void	foldPosition () const
	call foldPosition() for all objects

void	step ()
	perform the Monte-Carlo part of the simulation for one time_step

void	solve ()
	calculate the mechanics of the system and move objects accordingly, for one time_step

void	calculateForces () const
	calculate Forces and Lagrange multipliers, but do not move objects

void	dump () const
	dump matrix and vector from Meca

void	setInteractions (Meca &) const
	call setInteractions(meca) for all objects More...

ObjectSet *	findSet (const std::string &kind)
	return the ObjectSet corresponding to a class

ObjectSet const *	findSet (const std::string &kind) const
	return the ObjectSet corresponding to a class

Object *	findObject (const Tag, long)
	find an object from the class-TAG and the inventory number

Object *	findObject (const std::string &, long) const
	find an object from the name of its class and the inventory number

Fiber *	findFiber (long num) const
	find a fiber from the name of the fiber

Object *	readReference (InputWrapper &, char &tag)
	read an Object reference and return the corresponding Object (`tag` is set) More...

bool	isProperty (const std::string &) const
	check if the name corresponds to a property class

Property *	findProperty (const std::string &, const std::string &) const
	get an existing property, or return zero

Property *	findProperty (const std::string &, const int index) const
	get an existing property, or return zero

SingleProp *	findSingleProp (const std::string &nm) const
	find a SingleProp

PropertyList	findProperties (const std::string &) const
	return all existing propertis of required class

Property *	newProperty (const std::string &, const std::string &, Glossary &)
	create a new property

void	writeProperties (std::ostream &, bool prune) const
	write all properties More...

void	writeProperties (std::string &file, bool prune) const
	write sim-state to a named file More...

int	readObjects (InputWrapper &)
	read sim-state from InputWrapper More...

int	readObjects (std::string const &file)
	read sim-state from a named file More...

void	writeObjects (OutputWrapper &) const
	write simulation-state to specified file

void	writeObjects (std::string const &file, bool binary, bool append) const
	write simulation-state in binary or text mode, appending to the file or not More...

void	report (std::ostream &, std::string const &str, Glossary &) const
	call one of the report function More...

void	report (std::ostream &, std::string const &what, std::string const &who, Glossary &) const
	call one of the report function More...

void	reportTime (std::ostream &) const
	print time

void	analyzeClusters () const
	analyse the network connectivity to identify isolated sub-networks More...

void	reportClusters (std::ostream &, bool) const
	print size of clusters defined by connections with Couples More...

void	reportFiber (std::ostream &) const
	print the length and the points of each fiber More...

void	reportFiberPoints (std::ostream &) const
	print the coordinates of the model-points of each fiber More...

void	reportFiberForces (std::ostream &) const
	print the coordinates and forces on the model-points of each fiber More...

void	reportFiberEnds (std::ostream &) const
	print the positions and the states of the two ends of each fiber More...

void	reportFiberLengths (std::ostream &) const
	print average length and standard deviation for each class of fiber More...

void	reportFiberLengthDistribution (std::ostream &, real delta, real max) const
	print length distribution for each class of fiber More...

void	reportFiberSegments (std::ostream &) const
	print number of kinks in each class of Fiber

void	reportFiberDynamic (std::ostream &, FiberEnd) const
	print number of fibers according to dynamic state of end More...

void	reportFiberDynamic (std::ostream &) const
	print number of fibers according to their dynamic states More...

void	reportFiberSpeckles (std::ostream &, real) const
	print coordinates of points along the length of all Fiber More...

void	reportFiberStates (std::ostream &) const
	print dynamic states of Fiber

void	reportFiberTension (std::ostream &, Glossary &opt) const
	print Fiber tensions along certain planes defined in `opt` More...

void	reportOrganizer (std::ostream &) const
	print Aster positions More...

void	reportBeadSingles (std::ostream &) const
	print Bead positions More...

void	reportBeadPosition (std::ostream &) const
	print Bead positions More...

void	reportSolid (std::ostream &) const
	print Solid positions More...

void	reportCouple (std::ostream &) const
	print state of Couples More...

void	reportCouplePosition (std::ostream &) const
	print position of Couples More...

void	reportCouplePosition (std::ostream &, std::string const &) const
	print position of Couples of a certain kind More...

void	reportSingle (std::ostream &) const
	print state of Singles More...

void	reportSinglePosition (std::ostream &) const
	print position of Singles More...

void	reportSingleForce (std::ostream &) const
	print position of Singles More...

void	reportSinglePosition (std::ostream &, std::string const &) const
	print position of Singles of a certain kind More...

void	reportSphere (std::ostream &) const
	print state of Couples More...

void	reportSpace (std::ostream &) const
	print something about Spaces More...

void	reportCustom (std::ostream &) const
	print something More...

void	custom0 ()
	custom function

void	custom1 ()
	custom function

void	custom2 ()
	custom function

void	custom3 ()
	custom function

void	custom4 ()
	custom function

void	custom5 ()
	custom function

void	custom6 ()
	custom function

void	custom7 ()
	custom function

void	custom8 ()
	custom function

void	custom9 ()
	custom function

Public Attributes
SimulProp *	prop
	Global cytosim parameters.

PropertyList	properties
	holds all Property, except the SimulProp

SpaceSet	spaces
	list of Space

FieldSet	fields
	list of Field

FiberSet	fibers
	list of Fiber

SphereSet	spheres
	list of Sphere

BeadSet	beads
	list of Bead

SolidSet	solids
	list of Solid

SingleSet	singles
	list of Single

CoupleSet	couples
	list of Couple

OrganizerSet	organizers
	list of organizers

Member Function Documentation

void analyzeClusters ( ) const

Set Fiber::fleck to indicated Fibers that are connected by Couple.

The clusters are defined by the Couple that are bridging Fibers: Two fibers are in the same cluster if there is a Couple connecting them, of if they can be indirectly connected in this way via other Fibers.

This analysis can be useful to identify mechanically isolated sub-networks in the simulation. The result can be visualized in play with the option fiber:coloring=4, and it can also be printed with the tool report fiber:cluster

void initialize ( Glossary & glos )

This will initialize the simulation by registering callbacks. You should still call Simul::prepare() before calling step()

void prepare ( Space * spc )

Will pepare the simulation engine to make it ready to make a step():

set FiberGrid used for attachment of Hands,
set StericGrid
call complete() for all registered Property

The simulated objects should not be changed.

int readObjects ( InputWrapper & in )

Before reading, all objects are transfered to a secondary list called 'ice'. Every object encountered in the file is updated, and then transferred back to the normal list.

When the read is complete, the objects that are still on 'ice' are deleted. In this way the new state reflects exactly the system that was read from file.

Returns

0 = success
1 = EOF

int readObjects ( std::string const & file )

Create an InputWrapper and calls readObjects(in)

Object * readReference	(	InputWrapper &	in,
		char &	tag
	)

We do not allow property()->index() of an Object to change during import from a file. However, there is no structural reason that prevent this in the code. If necessary, it should be possible to remove this limitation.

The Object is not modified

void report	(	std::ostream &	out,
		std::string const &	str,
		Glossary &	opt
	)		const

void report	(	std::ostream &	out,
		std::string const &	what,
		std::string const &	who,
		Glossary &	opt
	)		const

WHAT	output
`organizer`	Position of the center of asters and other organizers
`bead`	Position of beads
`couple`	Number and state of couples
`fiber`	Length and position of the ends of fibers
`single`	Number and state of singles
`solid`	Position of center and first point of solids
`sphere`	Position of center and first point of spheres
`time`	Time
`parameters`	All object properties

WHAT:WHO	output
`fiber:lengths`	Average length and standard deviation of fibers
`fiber:dynamics`	Number of fiber classified by PLUS_END Dynamic state
`fiber:points`	coordinates of model points of all fibers
`fiber:speckles`	coordinates of points randomly distributed along all fibers
`fiber:segments`	information about lengths of segments, number of kinks
`fiber:ends`	Positions and dynamic states of all fiber ends
`fiber:forces`	Position of model points and Forces acting on model points
`fiber:tensions`	Internal stress along fibers
`fiber:clusters`	Clusters made of fibers connected by Couples
`bead:all`	Position of beads
`bead:singles`	Number of Beads with no single attached, 1 single attached etc.
`single:all`	Position and force of singles
`single:NAME`	Position of singles of class NAME
`couple:all`	Position of couples
`couple:NAME`	Position of couples of class NAME

void reportBeadPosition ( std::ostream & out ) const

Export position of Beads

void reportBeadSingles ( std::ostream & out ) const

Export number of beads classified as a function of the number of grafted Single that are attached to Fibers

void reportClusters	(	std::ostream &	out,
		bool	details
	)		const

Export size of clusters found by Simul::analyzeClusters()

void reportCouple ( std::ostream & out ) const

Export state of Couples

void reportCouplePosition ( std::ostream & out ) const

Export position of Couples

void reportCouplePosition	(	std::ostream &	out,
		std::string const &	who
	)		const

Export position of Couples of a certain kind

void reportCustom ( std::ostream & out ) const

Export end-to-end distance of Fiber

void reportFiber ( std::ostream & out ) const

Export length, position and directions at center of fibers

void reportFiberDynamic	(	std::ostream &	out,
		FiberEnd	end
	)		const

Export number of fiber, classified according to dynamic state of one end

void reportFiberDynamic ( std::ostream & out ) const

Export number of fiber, classified according to dynamic state of one end

void reportFiberEnds ( std::ostream & out ) const

Export dynamic state, positions and directions of fiber ends

void reportFiberForces ( std::ostream & out ) const

Export Fiber-number, position of model points

void reportFiberLengthDistribution	(	std::ostream &	out,
		real	delta,
		real	max
	)		const

Export average length and standard-deviation for each class of fiber

void reportFiberLengths ( std::ostream & out ) const

Export average length and standard-deviation for each class of fiber

void reportFiberPoints ( std::ostream & out ) const

Export Fiber-number, position of model points

void reportFiberSpeckles	(	std::ostream &	out,
		real	spread
	)		const

Export positions of points taken randomly along all fibers, but that remain static with respect to the lattice of each fiber, during the life-time of this fiber.

This is meant to simulate the speckle microscopy that is obtained in microcscopy with a low amount of fluorescent-monomers.

The distance between the speckles follows an exponential distribution with an average defined by the parameter spread.

void reportFiberTension	(	std::ostream &	out,
		Glossary &	opt
	)		const

Sum of the internal tensions from fiber segments that intersect a plane specified in opt. The plane is defined by n.x + a = 0

plane = NORMAL, SCALAR

void reportOrganizer ( std::ostream & out ) const

Export position of Asters and other organizers

void reportSingle ( std::ostream & out ) const

Export state of Single

void reportSingleForce ( std::ostream & out ) const

Export position of Singles

void reportSinglePosition ( std::ostream & out ) const

Export position of Singles

void reportSinglePosition	(	std::ostream &	out,
		std::string const &	who
	)		const

Export position of Singles

void reportSolid ( std::ostream & out ) const

Export position of Solids

void reportSpace ( std::ostream & out ) const

Export something about Space

void reportSphere ( std::ostream & out ) const

Export position of Sphere

void setInteractions ( Meca & meca ) const

This will:

Register all Mecables in the Meca: Fiber Solid Bead and Sphere
call setInteractions() for all objects in the system,
call setStericInteractions() if prop->steric is true.

void space ( Space * spc )

set current Space to spc. (zero is a valid argument).

This also set the space of all objects to spc.

void writeObjects	(	std::string const &	file,
		bool	binary,
		bool	append
	)		const

This appends the current state to a trajectory file. Normally, this is objects.cmo in the current directory.

If the file does not exist, it is created de novo.

void writeProperties	(	std::ostream &	os,
		bool	prune
	)		const

The order of the output is important, since some properties depend on others (eg. SingleProp and CoupleProp use HandProp). Luckily, there is no circular dependency in Cytosim at the moment.

Thus we simply follow the order in which properties were defined, and which is the order in which properties appear in the PropertyList.

void writeProperties	(	std::string &	file,
		bool	prune
	)		const

At the first call, this will write all properties to file, and save a copy of what was written to a string properties_saved.

The next time this is called, the properties will be compared to the string, and the file will be rewritten only if there is a difference.

Public Member Functions

Public Attributes

Member Function Documentation