SporeCloud Class Reference

#include <src/SporeCloud.h>

Inheritance diagram for SporeCloud:

[legend]Collaboration diagram for SporeCloud:

[legend]List of all members.

Detailed Description

Add a cloud of spores in the environment for the agents genetic algorithm.

We globally have these 2 options for th G.A.:

Monoparental reproduction & mutation: like bacteria division
Crossover & mutation: but the only way is to make agents meet each other.

The idea is that agents don't have yet a mating AI which alows them to reproduce by choosing their partners on self-organized criteria (like for example a pretty blue plume on the head).

Thus we're left with agents meeting each other on an explicit criterion, or chance. The first poses the problem of defining this criterion, and the second is not possible on collision only : A GA relying on collisions to reproduce would possibly end up favoring AI that collide... which we don't want.

So, a way to maximize agents interactions without relying on collision or other explicit rendez-vous points is to do like plants, fish, mushrooms... This leads to the concept of a spore cloud (thanks goes to Nawwaf Kharma for pointing this idea out).

I simulate here the spore cloud by a volumic concentration leading to probabilities of fecundation. As for the locality database, the world is divided into elementary volumes. Then when an agent wishes to get fecunded it simply gets spores from the environment:

No spore in volume => probability 0 of being fecunded
Volume saturated => probability 1 of being fecunded Actually, this probability is split proportionally to the content of the cloud. Suppose spores from individuals 1,2,3 are present in proportions 10%, 30%, 60% respectively, and the volume is 60% saturated. Then probabilities of being fecunded by individual 1,2,3 are respectively 0.06, 0.18, 0.36.

The volumic concentrations are updated by diffusion equations, using the simulator once more. Note that the integration update frequency of the cloud spore diffusion may be different than the frequency of the agents physics.

I also add a decay time after which the spores are non-functional and thus eliminated. A future extension may be to gradually reduce the spores efficiency by playing on probabilities, instead of this clear cut. Think for example of radioactive half-life time.

Note:: As a special case of thread safety, the step and addSpore method should never be called simultaneously This is guaranteed if the only access through these methods are done via simulator steps, for example.

Author:: Nicolas Brodu

Public Types

typedef SporeVolume *(* SporeVolumeFactory )(void *)

Public Member Functions

SporeCloud (double originx, double originy, double originz, double sizex, double sizey, double sizez, int divx, int divy, int divz, double baseDiffusionCoef, double lowestConcentration, SporeVolumeFactory factory=&sporeVolumeFactory, void *user=0)

double getDiffusionCoefficient ()

for info purpose

virtual void step ()

numerical integration step. Warning... condition stability applies... please use the schedule method and check the return value!

virtual bool schedule (double integrationTimeStep)

Check that the integrationTimeStep respects the stability condition and in this case, schedule the various parts of the computations by spreading them over the time step to reduce CPU peaks return true if the stability condition is OK, false otherwise.

virtual void addSpore (double x, double y, double z, Genome *genome, double concentration)

Adds an individual agent spore cloud to the global cloud for diffusion The genome will be ref'd in case the agent dies An half-life in simulator time units should be provided for the spore vitality!

virtual ConcentrationList * getConcentrationList (double x, double y, double z)

Returns a concentration list at the given location Used by agents during reproduction the concentration list for the given location. May be null.

Static Public Member Functions

static SporeVolume * sporeVolumeFactory (void *user)

Default factory creates volume objects for this class. Subclass may thus choose to create volumes of its own type. Too bad C++ doesn't allow virtual functions from constructor (I know, big debate...).

Protected Member Functions

SporeVolume * cyclicVolume (int x, int y, int z)

consider world is cyclic in XY => no boundary condition!!! Boundary condition in Z is closed world = altitude limit Please use pre-computed traversal pointers in volumes instead of this This is a utility for the constructor because I'm lazy to split all the special boundary cases! May return null pointer if this cell is unused

void intermediateStepDecay ()

computations are distributed in time

void intermediateStepXn ()

void intermediateStepXp ()

void intermediateStepYn ()

void intermediateStepYp ()

void intermediateStepZn ()

void intermediateStepZp ()

void intermediateStepPostProcess ()

Protected Attributes

SporeVolume ** volume

data structure for xyz bricks, actually a big array of spore volume list. Array is still necessary for direct access, from (x,y,z) => correct volume

SporeVolume ** volumeEnd

int vsize

SporeVolume * firstVolume

But for list traversal, it's more efficient not to visit unused cells.

SporeVolume * firstProcess

And for each step, it's even more efficient to visit only those with non-empty neighbors.

double originx

Re-used from locality DB: the origin is the super-brick corner minimum coordinates.

double originy

Re-used from locality DB: the origin is the super-brick corner minimum coordinates.

double originz

Re-used from locality DB: the origin is the super-brick corner minimum coordinates.

double sizex

Re-used from locality DB: length of the edges of the super-brick.

double sizey

Re-used from locality DB: length of the edges of the super-brick.

double sizez

Re-used from locality DB: length of the edges of the super-brick.

int divx

Re-used from locality DB: number of sub-brick divisions in each direction.

int divy

Re-used from locality DB: number of sub-brick divisions in each direction.

int divz

Re-used from locality DB: number of sub-brick divisions in each direction.

double timeStep

Used as dt for integration.

double lowestConcentration

Min concentration for a volume. Below this, consider there is no cloud.

double diffuseXN

Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?

double diffuseXP

Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?

double diffuseYN

Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?

double diffuseYP

Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?

double diffuseZN

Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?

double diffuseZP

Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?

double diffusionCoefficient

for info purpose

Classes

struct ConcentrationList

Was initially a map, but inefficient iterators => Try a sorted list Still inefficient in accessing elements & iterators (thanks oprofile) => make own structure! More...

struct Genome

struct SporeVolume

all the lists present in one volume More...

Member Function Documentation

bool SporeCloud::schedule ( double integrationTimeStep ) [virtual]

Check that the integrationTimeStep respects the stability condition and in this case, schedule the various parts of the computations by spreading them over the time step to reduce CPU peaks return true if the stability condition is OK, false otherwise.
Now schedule intermediate steps to distribute computations in time In fact: final step + post process + next decay still no match for an intermediate step according to oprofile => schedule all these in only one delta compared to intermediate steps.
Now computations are distributed in time, let the fun begins!

void SporeCloud::step ( ) [virtual]

numerical integration step. Warning... condition stability applies... please use the schedule method and check the return value!
Original all-in-one code below. Now split into several parts to distribute the computations in time thanks to the simulator Step does the final update TODO: restore all-in-one mode for batch mode, where peaks don't matter => could this improve perfs by de-allocating lists only once per update?
Reimplemented in DrawableSporeCloud.

The documentation for this class was generated from the following files:

SporeCloud.h
SporeCloud.cpp

Generated on Mon Mar 28 11:27:58 2005 for Crogai by

1.4.1


Public Types
typedef SporeVolume (	SporeVolumeFactory )(void *)
Public Member Functions
	SporeCloud (double originx, double originy, double originz, double sizex, double sizey, double sizez, int divx, int divy, int divz, double baseDiffusionCoef, double lowestConcentration, SporeVolumeFactory factory=&sporeVolumeFactory, void *user=0)
double	getDiffusionCoefficient ()
	for info purpose
virtual void	step ()
	numerical integration step. Warning... condition stability applies... please use the schedule method and check the return value!
virtual bool	schedule (double integrationTimeStep)
	Check that the integrationTimeStep respects the stability condition and in this case, schedule the various parts of the computations by spreading them over the time step to reduce CPU peaks return true if the stability condition is OK, false otherwise.
virtual void	addSpore (double x, double y, double z, Genome *genome, double concentration)
	Adds an individual agent spore cloud to the global cloud for diffusion The genome will be ref'd in case the agent dies An half-life in simulator time units should be provided for the spore vitality!
virtual ConcentrationList *	getConcentrationList (double x, double y, double z)
	Returns a concentration list at the given location Used by agents during reproduction the concentration list for the given location. May be null.
Static Public Member Functions
static SporeVolume *	sporeVolumeFactory (void *user)
	Default factory creates volume objects for this class. Subclass may thus choose to create volumes of its own type. Too bad C++ doesn't allow virtual functions from constructor (I know, big debate...).
Protected Member Functions
SporeVolume *	cyclicVolume (int x, int y, int z)
	consider world is cyclic in XY => no boundary condition!!! Boundary condition in Z is closed world = altitude limit Please use pre-computed traversal pointers in volumes instead of this This is a utility for the constructor because I'm lazy to split all the special boundary cases! May return null pointer if this cell is unused
void	intermediateStepDecay ()
	computations are distributed in time
void	intermediateStepXn ()
void	intermediateStepXp ()
void	intermediateStepYn ()
void	intermediateStepYp ()
void	intermediateStepZn ()
void	intermediateStepZp ()
void	intermediateStepPostProcess ()
Protected Attributes
SporeVolume **	volume
	data structure for xyz bricks, actually a big array of spore volume list. Array is still necessary for direct access, from (x,y,z) => correct volume
SporeVolume **	volumeEnd
int	vsize
SporeVolume *	firstVolume
	But for list traversal, it's more efficient not to visit unused cells.
SporeVolume *	firstProcess
	And for each step, it's even more efficient to visit only those with non-empty neighbors.
double	originx
	Re-used from locality DB: the origin is the super-brick corner minimum coordinates.
double	originy
	Re-used from locality DB: the origin is the super-brick corner minimum coordinates.
double	originz
	Re-used from locality DB: the origin is the super-brick corner minimum coordinates.
double	sizex
	Re-used from locality DB: length of the edges of the super-brick.
double	sizey
	Re-used from locality DB: length of the edges of the super-brick.
double	sizez
	Re-used from locality DB: length of the edges of the super-brick.
int	divx
	Re-used from locality DB: number of sub-brick divisions in each direction.
int	divy
	Re-used from locality DB: number of sub-brick divisions in each direction.
int	divz
	Re-used from locality DB: number of sub-brick divisions in each direction.
double	timeStep
	Used as dt for integration.
double	lowestConcentration
	Min concentration for a volume. Below this, consider there is no cloud.
double	diffuseXN
	Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?
double	diffuseXP
	Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?
double	diffuseYN
	Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?
double	diffuseYP
	Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?
double	diffuseZN
	Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?
double	diffuseZP
	Diffusion coefficients constants, precomputed with grid size & time step Plan for anisotropic diffusion if gravity taken into account & maybe global wind?
double	diffusionCoefficient
	for info purpose
Classes
struct	ConcentrationList
	Was initially a map, but inefficient iterators => Try a sorted list Still inefficient in accessing elements & iterators (thanks oprofile) => make own structure! More...
struct	Genome
struct	SporeVolume
	all the lists present in one volume More...