void EA<T>::evolve(unsigned int generations, int solution)
{
bool solution_found = false;
for (unsigned int i = 0; i < generations; i++) {
evaluate();
for (unsigned int i = 0; i < population.size(); i++) {
if (population[i]->getFitness() == solution) {
solution_found = true;
std::cout << generation << " generations. Found solution: ";
population[i]->printChromosome();
}
}
if (solution_found) {
break;
}
generation++;
evaluate();
select();
reproduce();
replace();
}
std::cout << "Solution not found..." << std::endl;
}
int main()
{
int gen = 0;
char go = 1;
srand(time(NULL));
/* 1. Choose the initial ppopulation */
initial_population();
/* 2. Evaluate the fitness of each individual in the population */
fitness();
/* 3. Repeat */
while((gen++ < MAX_GENS) && go)
{
/* printf("Find the best fittest\n");*/
/* 1. Select the best-ranking individuals to reproduce */
find_the_best_individuals();
/* Select the reproduce no, dynamicly (Ver. 2) */
reproduce();
/* 2. Breed new generation through crossover and mutation (genetic operations) and give birth to offspring */
/* 3. Evaluate the individual fitnesses of the offspring */
/* 4. Replace worst ranked part of the population with offspring */
fitness();
find_the_best_individuals();
if (population[0].fitness < OK_SNIT)
go = 0;
}
/* 4. Until <terminating condition> */
print_population();
printf("No of gen: %d\n",gen);
return 0;
}
int main(int argn, char *argv[]) {
int i;
double v;
double lambda;
parsecomamndline(argn,argv);
initialize();
populationconstraint(0);
populationconstraint(0);
if(quiet==0)print_populationdensity(0);
if(averagepopdens) {
init_averagepopdens();
}
if (quiet<2) fprintf(stdout,"%10.3lf %20.10e %.10e %.10e %.10e %.10e %.10e %.10e\n",0,0.,populationvariance,populationsize,1,xg,ucp,dv);
for(i=1;i<=maxSteps;i++) {
reproduce(i);
lambda = populationconstraint(i);
if(i%outputstep == 0) {
if (quiet<2)fprintf(stdout,"%10.3lf %20.10e %.10e %.10e %.10e %.10e %.10e %.10e\n",i*epsilon,allshifts*dx + popdens_1stmom/popdens_0thmom,populationvariance,populationsize,lambda,xg,ucp,dv);
if (quiet==0) print_populationdensity(i);
if (averagepopdens_havefile) update_averagepopdens();
if (averagepopdens_havecovarfile) update_averagecovar();
}
}
if(write_to_file)write_popdens();
if(averagepopdens_havefile)write_averagepopdens();
if(averagepopdens_havecovarfile)write_averagecovar();
cleanup();
return 0;
}
void reproduce(int *b, int *g) {
if(rand()%2)
(*b)++;
else {
(*g)++;
reproduce(b, g);
}
}
int main(int argc , char **argv)
{
int i , j , t , targetlen , parent_a , parent_b ;
int *numcorrect;
char **newpop , **oldpop , **swap;
double *normfit;
//srandom(seed);
srand((unsigned)time(NULL));
// whether to consider forcing the size to be even .
targetlen = 10;
printf("hello! \n");
newpop = malloc(sizeof(char *) * size);
oldpop = malloc(sizeof(char *) * size);
printf("hello 1-1 \n");
numcorrect = malloc(sizeof(int) * size);
normfit = malloc(sizeof(double) * size);
printf("hello2 \n");
for(i = 0 ; i < size ; i++)
{
newpop[i] = malloc(sizeof(char) * targetlen + 1);
oldpop[i] = malloc(sizeof(char) * targetlen + 1);
for(j = 0 ; j < targetlen ; j++)
{
oldpop[i][j] = random_letter_or_space();
}
newpop[i][targetlen] = 0;
oldpop[i][targetlen] = 0;
}
for(t = 0 ; t < steps ; t++)
{
compute_fitness(oldpop , numcorrect , normfit);
dump_stats(numcorrect , oldpop , t + 1 , targetlen);
for(i = 0 ; i < size ; i += 2)
{
parent_a = select_one(normfit);
parent_b = select_one(normfit);
// whether to add parent_a can not be equal to parent_b .
//printf("p_a = %d , p_b = %d \n" , parent_a , parent_b);
reproduce(oldpop , newpop , parent_a , parent_b , targetlen , i);
}
swap = oldpop;
oldpop = newpop;
newpop = swap;
/*
swap = newpop;
newpop = oldpop;
oldpop = swap;
*/
}
exit(0);
}
void TestWidget::setupWidgets(void)
{
setWindowTitle(this->title);
QMenuBar *menubar = new QMenuBar(this);
QMenu *menu = new QMenu(QString("Title: ") + this->title);
QAction *action_reproduce = new QAction("Reproduce", this);
menu->addAction(action_reproduce);
menubar->addMenu(menu);
setMenuBar(menubar);
menubar->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
setCentralWidget(new QWidget(this));
centralWidget()->setLayout(new QVBoxLayout(centralWidget()));
QPushButton *button = new QPushButton("Reproduce", this);
button->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
centralWidget()->layout()->setContentsMargins(0,0,0,0);
centralWidget()->layout()->setSpacing(0);
centralWidget()->layout()->addWidget(button);
connect(action_reproduce, SIGNAL(triggered()), SLOT(reproduce()));
connect(button, SIGNAL(clicked()), SLOT(reproduce()));
}
int main() {
int couples,i,boys=0,girls=0;
printf("Enter the number of couples : ");
scanf("%d",&couples);
time_t seconds;
time(&seconds);
srand((unsigned int) seconds);
for(i=0;i<couples;i++)
reproduce(&boys, &girls);
printf("\nBoys are %d and Girls are %d (including couples)\n",boys+couples,girls+couples);
exit(0);
}
//prey.cc
void Prey::moveFrom(Coordinate from, Coordinate to) {
Cell *toCell;
--timeToReproduce;
if (to != from) {
toCell = getCellAt(to);
delete toCell;
setOffset(to);
assignCellAt(to, this);
if (timeToReproduce <= 0) {
timeToReproduce = TimeToReproduce;
assignCellAt(from, reproduce(from));
}
else
assignCellAt(from, new Cell(from));
}
}
int main(int argc, char *argv[])
{
int lc;
long seconds;
tst_parse_opts(argc, argv, options, &help);
setup();
seconds = tflag ? SAFE_STRTOL(NULL, t_opt, 1, LONG_MAX) : 15;
for (lc = 0; TEST_LOOPING(lc); lc++)
reproduce(seconds);
tst_resm(TPASS, "finished after %ld seconds", seconds);
cleanup();
tst_exit();
}
int main(int argn, char *argv[]) {
int i=1;
double v;
parsecomamndline(argn,argv);
initialize();
init_subpopulation();
populationconstraint(0);
// print_populationdensity(0);
// exit(1);
if(averagepopdens) {
init_averagepopdens();
}
if (quiet<2) fprintf(stdout,"%10.3lf %20.10e %.10e %.10e %.10e %.10e\n",i*epsilon,0.,populationvariance,populationsize,subpop_popsize,current_fixation_prob);
while(subpop_count_extinctions + subpop_count_fixations < maxSteps) {
reproduce(i);
populationconstraint(i);
if(i%outputstep == 0) {
if (quiet<2)fprintf(stdout,"%10.3lf %20.10e %.10e %.10e %.10e %.10e\n",i*epsilon,allshifts*dx + popdens_1stmom/popdens_0thmom,populationvariance,populationsize,subpop_popsize,current_fixation_prob);
if (quiet==0) print_populationdensity(i);
if (averagepopdens) update_averagepopdens();
}
if(current_fixation_prob < subpop_final_threshold) {
reset_subpopulation();
subpop_count_extinctions++;
printf("# event ( %d of %d ): extinction %lf\n",subpop_count_extinctions+subpop_count_fixations,maxSteps,i*epsilon);
i=0;
}
if(current_fixation_prob > 1-subpop_final_threshold) {
reset_subpopulation();
subpop_count_fixations++;
printf("# event ( %d of %d ): fixation %lf\n",subpop_count_extinctions+subpop_count_fixations,maxSteps,i*epsilon);
i=0;
}
i++;
}
if(write_to_file)write_popdens();
if(averagepopdens)write_averagepopdens();
cleanup();
return 0;
}
int main(int argc, char **argv)
{
int i, j, t, parent_a, parent_b;
char **swap, **newpop, **oldpop;
double *fit, *normfit;
get_options(argc, argv, options, help_string);
srandom(seed);
/* Force the size to be even. */
size += (size / 2 * 2 != size);
/* Initialize the population. */
newpop = xmalloc(sizeof(char *) * size);
oldpop = xmalloc(sizeof(char *) * size);
fit = xmalloc(sizeof(double) * size);
normfit = xmalloc(sizeof(double) * size);
for(i = 0; i < size; i++) {
newpop[i] = xmalloc(sizeof(char) * len + 1);
oldpop[i] = xmalloc(sizeof(char) * len + 1);
for(j = 0; j < len; j++)
oldpop[i][j] = random() % 2 + '0';
oldpop[i][len] = 0;
newpop[i][len] = 0;
}
/* For each time step... */
for(t = 0; t < gens; t++) {
compute_fitness(oldpop, fit, normfit);
dump_stats(t, oldpop, fit);
/* Pick two parents by fitness and mate them until the
* next generation has been made.
*/
for(i = 0; i < size; i += 2) {
parent_a = select_one(normfit);
parent_b = select_one(normfit);
reproduce(oldpop, newpop, parent_a, parent_b, i);
}
/* Make everything old new again. */
swap = newpop; newpop = oldpop; oldpop = swap;
}
exit(0);
}
Chromosome<T>* EA<T>::evolveThreaded(unsigned int generations, unsigned int threads)
{
Gnuplot fitnessPlot;
std::ofstream fitnessFile;
fitnessFile.open("fitness_funtion.cvs", std::ios::trunc);
fitnessFile << "Generation,Fitness value,";
for (unsigned int gen_number = 0; gen_number < population[0]->getChromosome().size(); ++gen_number)
fitnessFile << "Gen " << gen_number << ",";
fitnessFile << std::endl;
fitnessValuesMax.clear();
for (unsigned int i = 0; i < generations; i++) {
generation++;
std::cout << "Generation " << generation;
evaluateThreaded(threads);
std::cout << " evaluated." << std::endl;
select();
reproduce();
replace();
fitnessValuesMax.push_back(std::make_pair(generation, selected[0]->getFitness()));
fitnessFile << generation << "," << selected[0]->getFitness();
for (auto gen : selected[0]->getChromosome())
fitnessFile << "," << gen;
fitnessFile << std::endl;
}
evaluateThreaded(threads);
fitnessFile.close();
int best_index = 0;
double max = 0;
for (unsigned int i = 0; i < population.size(); i++) {
if (population[i]->getFitness() > max) {
max = population[i]->getFitness();
best_index = i;
}
}
//fitnessPlot << "set fitnessValuesMax [-2:2]\nset yrange [-2:2]\n";
fitnessPlot << "plot '-' with lines title 'Fitness values'\n";
fitnessPlot.send1d(fitnessValuesMax);
return population[best_index];
}
int main(void) {
unsigned i, j, s;
int minRandom;
initGraph();
/* Решение с генериране на произволни цикли */
minRandom = n*101;
for (s = 0; s < maxSteps; s++) {
for (i = 0; i < PSIZE; i++) {
randomCycle(i);
result[i] = evaluate(i);
}
for (j=0; j< PSIZE; j++) if (result[j]<minRandom) minRandom = result[j];
}
printf("Оптимално решение, намерено при генериране на произволни %ld цикъла: %d\n",
PSIZE*maxSteps, minRandom);
/* Решение с Генетичен Аглоритъм със същия брой итерации */
for (s = 0; s < maxSteps; s++) reproduce(s);
printf("Най-късите цикли, намерени от генетичния алгортиъм: \n");
for (i = 10; i > 0; i--) printf("%d, ", result[i]);
printf(" %d\n", result[0]);
return 0;
}
void next_generation( population_type &pop , fitness_type &fitness )
{
reproduce( pop , fitness );
}
int main(int argc, char** argv)
{
if(argc^7){
printf("Usage: ./osil bits seed N G Mu Chi\n");
exit(1);
}
if ((sizeof(int) < 4)|| (sizeof(long int) < 8)){
printf("Assumptions concerning bits are invalid: int has %d bits, unsigned long int has %d bits\n",
(int)(8*sizeof(int)), (int)(8*sizeof(unsigned long)));
return 1;
}
L = atol(argv[1]); // bit length
if (L > 32){
printf("Can't have more thqan 32 bits\n");
return 1;
}
int seed = atoi(argv[2]);
N = (unsigned long)atoi(argv[3]); // no. of individuals in finite population
G = (unsigned long)atol(argv[4]); // no. of generations
Mu_n = atof(argv[5]);
Chi_n = atof(argv[6]);
int i,j, n, m;
double *d1, *d2, dst1, dst2;
unsigned long *tmp_ptr;
char fname[200]; // file name
FILE *fp; // data file pointer
d1 = calloc(G, sizeof(double));
d2 = calloc(G, sizeof(double));
initrand(seed);
setup();
init(); // initializes memory for pop, M and Cr and also installs values for these
merge_sort(Pop[0], N);
// infinite population simulation
calc_px_from_finite_population(P0); // calculates haploids proportion using finite set
P1 = g_w(G, P0, P1);
display_p(P1);
// find oscillating points for infinite population
if( osc_points(P0, P1, P2, P3) ){ // if oscillation occurs
{ // compute distance between finite population to oscillating points
int a, b;
//finite population simulation
for(i = 0; i < G; i++){ // evolve through G generations
for(j = 0; j < N; j++){ // reproduce N offsprings
a = rnd(N); b = rnd(N);
reproduce(a, b, j); // randomly two parents chosen; will be proportional to proportion
}
merge_sort(Pop[0], N);
// calculate distance to oscillating points and write to file
dst1 = dist_n(P2); // distance to 1st oscillating point
dst2 = dist_n(P3); // distance to 2nd oscillating point
d1[i] = dst1;
d2[i] = dst2;
// set new generation as parent generation for next generation
tmp_ptr = Pop[0];
Pop[0] = Pop[1];
Pop[1] = tmp_ptr;
}
}
}
deinit();
cleanup();
sprintf(fname, "b%lug%lun%lu_osc.dat", L, G, N);
if(!(fp = fopen(fname, "w"))){
printf("%s could not be opened!! Error!!\n", fname);
exit(2);
}
// write distances to file
for(n = 0; n < G; n++){
fprintf(fp, "%d ", n);
fprintf(fp, "%" PREC "lf %" PREC "lf\n", d1[n], d2[n]);
}
fclose(fp);
free(d1); free(d2);
FILE *gp = popen ("gnuplot -persistent", "w"); // open gnuplot in persistent mode
plot(gp, 0, fname, 3, "oscillation", "G", "d", 0, "" );
fflush(gp);
pclose(gp);
return 0;
}
void LayerNet::gen_init (
TrainingSet *tptr , // Training set to use
struct LearnParams *lptr // User's general learning parameters
)
{
int i, istart, individual, best_individual, generation, n_cross ;
int first_child, parent1, parent2, improved, crosspt, nchoices, *choices ;
int initpop, popsize, gens, climb, nvars, chromsize, split, ind ;
float pcross, pmutate, error, besterror, *errors, *fitness, worst ;
float fquit, favor_best, fitfac, maxerr, minerr, avgerr, overinit ;
SingularValueDecomp *sptr ;
struct GenInitParams *gptr ; // User's genetic initialization parameters
char *pool1, *pool2, *oldpop, *newpop, *popptr, *temppop, *best ;
char msg[80] ;
gptr = lptr->gp ;
popsize = gptr->pool ;
gens = gptr->gens ;
climb = gptr->climb ;
overinit = gptr->overinit ;
pcross = gptr->pcross ;
pmutate = gptr->pmutate ;
fquit = lptr->quit_err ;
favor_best = 3.1 ;
fitfac = -20.0 ;
/*
--------------------------------------------------------------------------------
Do all scratch memory allocation.
--------------------------------------------------------------------------------
*/
/*
Allocate the singular value decomposition object for REGRESS.
*/
if (nhid2 == 0) // One hidden layer
nvars = nhid1 + 1 ;
else // Two hidden layers
nvars = nhid2 + 1 ;
MEMTEXT ( "GEN_INIT: new SingularValueDecomp" ) ;
sptr = new SingularValueDecomp ( tptr->ntrain , nvars , 1 ) ;
if ((sptr == NULL) || ! sptr->ok) {
memory_message("for genetic initialization. Try ANNEAL NOREGRESS.");
neterr = 1.0 ; // Flag failure to LayerNet::learn which called us
if (sptr != NULL)
delete sptr ;
return ;
}
chromsize = nhid1 * (nin+1) ; // Length of an individual's chromosome
if (nhid2) // is the number of hidden weights
chromsize += nhid2 * (nhid1+1) ;
errors = fitness = NULL ;
choices = NULL ;
pool1 = pool2 = NULL ;
MEMTEXT ( "GEN_INIT: errors, fitness, choices, best, pool1,pool2");
if (((errors = (float*) MALLOC ( popsize * sizeof(float))) == NULL)
|| ((fitness = (float*) MALLOC ( popsize * sizeof(float))) == NULL)
|| ((best = (char*) MALLOC( chromsize )) == NULL)
|| ((choices = (int*) MALLOC ( popsize * sizeof(int))) == NULL)
|| ((pool1 = (char*) MALLOC( popsize * chromsize )) == NULL)
|| ((pool2 = (char*) MALLOC( popsize * chromsize )) == NULL)) {
if (errors != NULL)
FREE ( errors ) ;
if (fitness != NULL)
FREE ( fitness ) ;
if (choices != NULL)
FREE ( choices ) ;
if (pool1 != NULL)
FREE ( pool1 ) ;
if (pool2 != NULL)
FREE ( pool2 ) ;
delete sptr ;
memory_message("for genetic initialization. Try ANNEAL NOREGRESS." ) ;
neterr = 1.0 ; // Flag failure to LayerNet::learn which called us
return ;
}
/*
Generate initial population pool.
We also preserve the best weights across all generations,
as this is what we will ultimately return to the user.
Its mean square error is besterror.
*/
besterror = 1.e30 ; // For saving best (across all individuals and gens)
maxerr = avgerr = 0.0 ; // For progress display only
best_individual = 0 ; // Safety only
initpop = popsize * overinit ; // Overinitialization of initial population
progress_message ( "\nGenerating initial population" ) ;
for (ind=0 ; ind<initpop ; ind++) { // Try overinitialization times
if (ind<popsize) // If still in pop size limit
individual = ind ; // just use next avail space
else { // Else we search entire pop
worst = -1. ; // for the worst member
for (i=0 ; i<popsize ; i++) { // which we will then replace
if (errors[i] > worst) {
worst = errors[i] ;
individual = i ;
}
}
avgerr -= worst ; // Exclude discards from average
}
popptr = pool1 + individual * chromsize ; // Build init pop in pool1
rand_ind ( popptr , chromsize ) ; // Randomly generate individual
decode ( popptr , nin , nhid1 , nhid2 , // Convert genotype (chromosome)
hid1_coefs , hid2_coefs ); // to phenotype (weights)
error = regress ( tptr , sptr ) ; // Evaluate network error
errors[individual] = error ; // and keep all errors
if (error < besterror) { // Keep track of best
besterror = error ; // as it is returned to user
best_individual = individual ; // This is its index in pool1
}
if (error > maxerr) // Max and average error are
maxerr = error ; // for progress display only
avgerr += error ;
if (error <= fquit)
break ;
progress_message ( "." ) ;
}
sprintf (msg , "\nInitial pop: Min err=%7.4lf Max=%7.4lf Avg=%7.4lf",
100. * besterror, 100. * maxerr, 100.0 * avgerr / (float) popsize);
progress_message ( msg ) ;
/*
The initial population has been built in pool1.
Copy its best member to 'best' in case it never gets beat (unlikely
but possible!).
Also, we will need best if the climb option is true.
*/
popptr = pool1 + best_individual * chromsize ; // Point to best
memcpy ( best , popptr , chromsize ) ; // and save it
/*
This is the main generation loop. There are two areas for population pool
storage: pool1 and pool2. At any given time, oldpop will be set to one of
them, and newpop to the other. This avoids a lot of copying.
*/
oldpop = pool1 ; // This is the initial population
newpop = pool2 ; // The next generation is created here
for (generation=0 ; generation<gens ; generation++) {
if (error <= fquit) // We may have satisfied this in init pop
break ; // So we test at start of generation loop
error_to_fitness ( popsize , favor_best , fitfac , errors , fitness ) ;
fitness_to_choices ( popsize , fitness , choices ) ;
nchoices = popsize ; // Will count down as choices array emptied
n_cross = pcross * popsize ; // Number crossing over
first_child = 1 ; // Generating first of parent's 2 children?
improved = 0 ; // Flags if we beat best
if (climb) { // If we are to hill climb
memcpy ( newpop , best , chromsize ) ; // start with best
errors[0] = besterror ; // Record its error
istart = 1 ; // and start children past it
}
else
istart = 0 ;
/*
Generate the children
*/
maxerr = avgerr = 0.0 ; // For progress display only
minerr = 1.0 ; // Ditto
for (individual=istart ; individual<popsize ; individual++) {
popptr = newpop + individual * chromsize ; // Will put this child here
if (first_child) // If this is the first of 2 children, pick parents
pick_parents ( &nchoices , choices , &parent1 , &parent2 ) ;
if (n_cross-- > 0) // Do crossovers first
reproduce ( oldpop + parent1 * chromsize , oldpop + parent2 * chromsize ,
first_child , chromsize , popptr , &crosspt , &split ) ;
else if (first_child) // No more crossovers, so just copy parent
memcpy ( popptr , oldpop + parent1 * chromsize , chromsize ) ;
else
memcpy ( popptr , oldpop + parent2 * chromsize , chromsize );
if (pmutate > 0.0)
mutate ( popptr , chromsize , pmutate ) ;
decode ( popptr , nin , nhid1 , nhid2 , hid1_coefs , hid2_coefs ) ;
error = regress ( tptr , sptr ) ; // Evaluate child's error
errors[individual] = error ; // and keep each
if (error < besterror) { // Keep track of best
besterror = error ; // It will be returned to user
best_individual = individual ; // This is its index in newpop
improved = 1 ; // Flag so we copy it later
}
if (error > maxerr) // Min, max and average error
maxerr = error ; // for progress display only
if (error < minerr)
minerr = error ;
avgerr += error ;
if (error <= fquit)
break ;
first_child = ! first_child ;
} // For all genes in population
/*
We finished generating all children. If we improved (one of these
children beat the best so far) then copy that child to the best.
Swap oldpop and newpop for the next generation.
*/
if (improved) {
popptr = newpop + best_individual * chromsize ; // Point to best
memcpy ( best , popptr , chromsize ) ; // and save it
}
temppop = oldpop ; // Switch old and new pops for next generation
oldpop = newpop ;
newpop = temppop ;
sprintf(msg, "\nGeneration %3d: Min err=%7.4lf Max=%7.4lf Avg=%7.4lf",
generation+1, 100. * minerr, 100. * maxerr,
100.0 * avgerr / (float) popsize ) ;
progress_message ( msg ) ;
}
/*
We are all done.
*/
decode ( best , nin , nhid1 , nhid2 , hid1_coefs , hid2_coefs ) ;
besterror = regress ( tptr , sptr ) ; // Evaluate network error
MEMTEXT ( "GEN_INIT: errors, fitness, choices, best, pool1,pool2");
FREE ( errors ) ;
FREE ( fitness ) ;
FREE ( choices ) ;
FREE ( best ) ;
FREE ( pool1 ) ;
FREE ( pool2 ) ;
MEMTEXT ( "GEN_INIT: delete sptr" ) ;
delete sptr ;
}
double genetic (
double (*func)( int n , double *x ) , // Function to be minimized
int ngens , // Number of complete generations
int popsize , // Number of individuals in population
int climb , // Do we hill climb via elitism?
double stddev , // Standard deviation for initial population
double pcross , // Probability of crossover (.6-.9 typical)
double pmutate , // Probability of mutation (.0001 to .001 typical)
double favor_best ,// Factor for favoring best over average (2-3 is good)
double fitfac , // Factor for converting fval to raw fitness (-20 good)
double fquit , // Quit if function reduced to this amount
int nvars , // Number of variables in x
double *x , // Set to starting estimate when called; returns best
double *best, // Work vector nvars long
int *choices , // Work vector popsize long
double *fvals , // Work vector popsize long
double *fitness , // Work vector popsize long
double *pool1, // Work vector nvars * popsize long
double *pool2 ) // Work vector nvars * popsize long
{
int istart, individual, best_individual, generation, n_cross ;
int first_child, parent1, parent2, improved, crosspt, nchoices ;
double fval, bestfval, *oldpop, *newpop, *popptr, *temppop ;
/*
Generate initial population pool.
We also preserve the best point across all generations, as this is what
we will ultimately return to the user. Its objective function value is
bestfval.
*/
bestfval = 1.e30 ; // For saving best (across all individuals)
best_individual = 0 ; // Safety only
for (individual=0 ; individual<popsize ; individual++) {
popptr = pool1 + individual * nvars ; // Build population in pool1
shake ( nvars , x , popptr , stddev ) ; // Randomly perturb about init x
fval = (*func) ( nvars , popptr ) ; // Evaluate function there
fvals[individual] = fval ; // and keep function value of each
if (fval < bestfval) { // Keep track of best
bestfval = fval ; // as it will be returned to user
best_individual = individual ; // This is its index in pool1
}
if (fval <= fquit)
break ;
}
/*
The initial population has been built in pool1.
Copy its best member to 'best' in case it never gets beat (unlikely
but possible!).
*/
popptr = pool1 + best_individual * nvars ; // Point to best
memcpy ( best , popptr , nvars * sizeof(double) ) ; // and save it
/*
This is the main generation loop. There are two areas for population pool
storage: pool1 and pool2. At any given time, oldpop will be set to one of
them, and newpop to the other. This avoids a lot of copying.
*/
oldpop = pool1 ; // This is the initial population
newpop = pool2 ; // The next generation is created here
for (generation=0 ; generation<ngens ; generation++) {
if (fval <= fquit) // We may have satisfied this in initial population
break ; // So we test at start of generation loop
fval_to_fitness ( popsize , favor_best , fitfac , fvals , fitness ) ;
fitness_to_choices ( popsize , fitness , choices ) ;
nchoices = popsize ; // Will count down as choices array emptied
n_cross = pcross * popsize ; // Number crossing over
first_child = 1 ; // Generating first of parent's 2 children?
improved = 0 ; // Flags if we beat best
if (climb) { // If we are to hill climb
memcpy ( newpop , best , nvars * sizeof(double) ) ; // start with best
fvals[0] = bestfval ; // Record its error
istart = 1 ; // and start children past it
}
else
istart = 0 ;
/*
Generate the children
*/
for (individual=istart ; individual<popsize ; individual++) {
popptr = newpop + individual * nvars ; // Will put this child here
if (first_child) // If this is the first of 2 children, pick parents
pick_parents ( &nchoices , choices , &parent1 , &parent2 ) ;
if (n_cross-- > 0) // Do crossovers first
reproduce ( oldpop + parent1 * nvars , oldpop + parent2 * nvars ,
first_child , nvars , popptr , &crosspt ) ;
else if (first_child) // No more crossovers, so just copy parent
memcpy( popptr , oldpop + parent1 * nvars , nvars * sizeof(double));
else
memcpy( popptr , oldpop + parent2 * nvars , nvars * sizeof(double));
if (pmutate > 0.0)
mutate ( popptr , nvars , stddev , pmutate ) ;
fval = (*func) ( nvars , popptr ) ; // Evaluate function for this child
fvals[individual] = fval ; // and keep function value of each
if (fval < bestfval) { // Keep track of best
bestfval = fval ; // It will be returned to user
best_individual = individual ; // This is its index in newpop
improved = 1 ; // Flag so we copy it later
}
if (fval <= fquit)
break ;
first_child = ! first_child ;
} // For all genes in population
/*
We finished generating all children. If we improved (one of these
children beat the best so far) then copy that child to the best.
Swap oldpop and newpop for the next generation.
*/
if (improved) {
popptr = newpop + best_individual * nvars ; // Point to best
memcpy ( best , popptr , nvars * sizeof(double) ) ; // and save it
}
temppop = oldpop ; // Switch old and new pops for next generation
oldpop = newpop ;
newpop = temppop ;
}
/*
We are all done. Copy the best to x, as that is how we return it.
*/
memcpy ( x , best , nvars * sizeof(double) ) ; // Return best
return bestfval ;
}
int main(int argc, char **argv)
{
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc (T);
gsl_rng_set(r, time(NULL));
Graph *g = new Graph();
g->addVertex(Vertex(1, "v1", 0, 0, 0, 1.0, 1.0, 1.0));
g->addVertex(Vertex(2, "v2", 0, 0, 0, 1.0, 0.2, 0.2));
g->addVertex(Vertex(3, "v3", 0, 0, 0, 0.2, 1.0, 0.2));
g->addVertex(Vertex(4, "v4", 0, 0, 0, 0.2, 0.2, 1.0));
g->addEdge(1, 2);
g->addEdge(1, 3);
g->addEdge(3, 4);
ptr population(new std::vector<Graph>(4, *g));
/*
std::cout << "Population" << std::endl;
printgraph(population);
ptr reproduced = reproduce(population);
std::cout << "Reproduced" << std::endl;
printgraph(reproduced);
ptr offsprings = genetic(reproduced);
std::cout << "Offsprings" << std::endl;
printgraph(offsprings);
population = succession(population, offsprings);
std::cout << "After one iteration" << std::endl;
printgraph(population);
*/
int iterationcount = 0;
double bestv = best(population);
double bestvold = bestv * 2;
std::cout << "best " << bestv << "; bestvold " << bestvold << std::endl;
while (fabs(bestvold - bestv)/bestvold > 0.00000001)
{
++iterationcount;
ptr offsprings = genetic(reproduce(population));
population = succession(population, offsprings);
bestvold = bestv;
bestv = best(population);
}
std::cout << "Possible result found after " << iterationcount << "iterations: " << std::endl;
printgraph(population);
const Graph *bestgraph = bestg(population);
for (Graph::vertices_const_iterator i = bestgraph->vertices.begin(); i != bestgraph->vertices.end(); ++i)
{
const Vertex &v = i->second;
std::cout << "\"" << v.name << "\"";
std::cout << "\t@" << v.x << " " << v.y << " " << v.z;
std::cout << "\tcolor" << v.r << " " << v.g << " " << v.b;
std::cout << "\tfrozen light size 1.0" << std::endl;
}
gsl_rng_free (r);
return 0;
}
int main()
{
// initialise
const unsigned int kGridSize = 25;
const unsigned int kPopulationMax = 30;
const unsigned int kFoodMax = 50;
const unsigned int kReproduceEnergy = 120;
const unsigned int kCellStartEnergy = 100;
const unsigned int kMaxFoodEnergy = 100;
Dish petri(kGridSize);
unsigned int total_population = 15;
unsigned int total_food = 30;
std::vector<Cell> population;
for (unsigned int i = 0; i < total_population; i++) {
population.push_back(Cell(kGridSize, kCellStartEnergy));
}
std::list<Food> supply;
for (unsigned int i = 0; i < total_food; i++) {
supply.push_back(Food(kGridSize, kMaxFoodEnergy));
}
bool exit = false;
unsigned int w = 1;
while (w < 50) {
/*
// Process step
*/
for (auto cell = population.begin(); cell != population.end(); ++cell) {
if (cell->alive() == true) {
// move
cell->move(kGridSize);
for (auto food = supply.begin(); food != supply.end(); ++food) {
if (cell->location() == food->location()) {
total_food = supply.size();
cell->consume_food(*food);
food = supply.erase(food);
}
}
for (auto target = population.begin(); target != population.end(); ++target) {
switch (can_consume_cell(*cell, *target))
{
case false:
continue;
case true:
target = population.erase(target);
break;
default:
break;
}
}
// reproduce
if ((total_population < kPopulationMax) && (cell->reproduce())) {
population.push_back(Cell(kGridSize, cell->energy() / 2));
cell->set_energy(cell->energy() / 2);
total_population = population.size();
}
// death
if (cell->energy() <= 0) {
cell->set_alive(false);
}
}
}
if (total_food < kFoodMax) {
supply.push_back(Food(kGridSize, kMaxFoodEnergy));
total_food = supply.size();
}
/*
// Input step
*/
// poll user input
/*
// Display step
*/
// display grid
// TODO: Optimise this horrible loop
for (unsigned int i = 0; i < kGridSize; i++) {
for (unsigned int j = 0; j < kGridSize; j++) {
bool occupied = false;
position display_location;
display_location.x = i;
display_location.y = j;
for (Cell cell : population) {
if (cell.location() == display_location) {
if (cell.alive() == true) {
std::cout << cell.energy();
}
else {
std::cout << "-";
}
occupied = true;
}
}
for (Food food : supply) {
if (food.location() == display_location) {
std::cout << ".";
occupied = true;
}
}
if (occupied == false) {
std::cout << " ";
}
else {
occupied = false;
}
}
std::cout << "\n";
}
for (unsigned int i = 0; i < kGridSize; i++) {
std::cout << "=";
}
std::cout << "\n" << total_population;
std::cout.flush();
Sleep(1500);
w++;
}
population.clear();
supply.clear();
return 0;
}
void run(struct block * b){
if(!b->die && (b->energy <= 0 || b->nutrients <= 0 || b->pos > INSTRUCTIONS - 1)){
die(b);
return;
}
energymean += b->energy;
if(!b->die){
switch(b->program[b->pos]){
case 0:
if(b->lastRep > 0) break;
b->pos = (b->pos + 1) % INSTRUCTIONS;
reproduce(b);
break;
case 1:
getEnegy(b);
break;
case 2:
getNutrients(b);
break;
case 3:
break;
b->pos = (b->pos + 1) % INSTRUCTIONS;
switch(b->program[b->pos]){
case 0:
move(b, 1, 0);
b->energy -= 5;
break;
case 1:
move(b, 1, 0);
b->energy -= 5;
break;
case 2:
b->energy -= 5;
break;
case 3:
move(b, -1, 0);
b->energy -= 5;
break;
case 4:
move(b, -1, 0);
b->energy -= 5;
break;
case 5:
move(b, -1, -1);
b->energy -= 2;
break;
case 6:
move(b, 0, -1);
b->energy += 1;
break;
case 7:
move(b, 1, -1);
b->energy -= 2;
break;
}
if(b->y > Y_SIZE - 1) kill(b);
break;
case 4:
atack(b);
break;
case 5: //Logic Operations
b->pos = (b->pos + 1) % INSTRUCTIONS;
switch(b->program[b->pos]){
case 0:
++b->ptr;
if(b->ptr >= INSTRUCTIONS) die(b);
break;
case 1:
--b->ptr;
if(b->ptr < 0) die(b);
break;
case 2:
++b->memory[b->ptr];
break;
case 3:
--b->memory[b->ptr];
if(b->memory[b->ptr] < 0) die(b);
break;
case 4:
if(b->loops >= 19) break;
b->loops_adr[b->loops].progPos = b->pos + 1;
b->loops_adr[b->loops++].memAdr = b->ptr;
break;
case 5:
if(b->loops > 0 && b->memory[b->loops_adr[b->loops - 1].memAdr]){
b->pos = b->loops_adr[b->loops - 1].progPos;
}else if(b->loops > 0){
--b->loops;
}else{
die(b);
}
break;
}
break;
case 6:
die(b);
break;
}
}else{
switch(b->program[b->pos]){
case 1:
getEnegy(b);
break;
case 2:
getNutrients(b);
break;
}
}
if(b->energy < 10){
kill(b);
}
b->pos = (b->pos + 1) % INSTRUCTIONS;
++b->age;
--b->lastRep;
b->energy -= b->age / 800.0;
b->nutrients -= b->age / 800.0;
}
