void G1MarkSweep::mark_sweep_phase2() {
// Now all live objects are marked, compute the new object addresses.
// It is imperative that we traverse perm_gen LAST. If dead space is
// allowed a range of dead object may get overwritten by a dead int
// array. If perm_gen is not traversed last a klassOop may get
// overwritten. This is fine since it is dead, but if the class has dead
// instances we have to skip them, and in order to find their size we
// need the klassOop!
//
// It is not required that we traverse spaces in the same order in
// phase2, phase3 and phase4, but the ValidateMarkSweep live oops
// tracking expects us to do so. See comment under phase4.
G1CollectedHeap* g1h = G1CollectedHeap::heap();
Generation* pg = g1h->perm_gen();
EventMark m("2 compute new addresses");
TraceTime tm("phase 2", PrintGC && Verbose, true, gclog_or_tty);
GenMarkSweep::trace("2");
FindFirstRegionClosure cl;
g1h->heap_region_iterate(&cl);
HeapRegion *r = cl.result();
CompactibleSpace* sp = r;
if (r->isHumongous() && oop(r->bottom())->is_gc_marked()) {
sp = r->next_compaction_space();
}
G1PrepareCompactClosure blk(sp);
g1h->heap_region_iterate(&blk);
CompactPoint perm_cp(pg, NULL, NULL);
pg->prepare_for_compaction(&perm_cp);
}
void G1MarkSweep::mark_sweep_phase3() {
G1CollectedHeap* g1h = G1CollectedHeap::heap();
Generation* pg = g1h->perm_gen();
// Adjust the pointers to reflect the new locations
EventMark m("3 adjust pointers");
TraceTime tm("phase 3", PrintGC && Verbose, true, gclog_or_tty);
GenMarkSweep::trace("3");
SharedHeap* sh = SharedHeap::heap();
sh->process_strong_roots(true, // activate StrongRootsScope
true, // Collecting permanent generation.
SharedHeap::SO_AllClasses,
&GenMarkSweep::adjust_root_pointer_closure,
NULL, // do not touch code cache here
&GenMarkSweep::adjust_pointer_closure);
g1h->ref_processor()->weak_oops_do(&GenMarkSweep::adjust_root_pointer_closure);
// Now adjust pointers in remaining weak roots. (All of which should
// have been cleared if they pointed to non-surviving objects.)
g1h->g1_process_weak_roots(&GenMarkSweep::adjust_root_pointer_closure,
&GenMarkSweep::adjust_pointer_closure);
GenMarkSweep::adjust_marks();
G1AdjustPointersClosure blk;
g1h->heap_region_iterate(&blk);
pg->adjust_pointers();
}
void G1MarkSweep::mark_sweep_phase4() {
// All pointers are now adjusted, move objects accordingly
// It is imperative that we traverse perm_gen first in phase4. All
// classes must be allocated earlier than their instances, and traversing
// perm_gen first makes sure that all klassOops have moved to their new
// location before any instance does a dispatch through it's klass!
// The ValidateMarkSweep live oops tracking expects us to traverse spaces
// in the same order in phase2, phase3 and phase4. We don't quite do that
// here (perm_gen first rather than last), so we tell the validate code
// to use a higher index (saved from phase2) when verifying perm_gen.
G1CollectedHeap* g1h = G1CollectedHeap::heap();
Generation* pg = g1h->perm_gen();
EventMark m("4 compact heap");
TraceTime tm("phase 4", PrintGC && Verbose, true, gclog_or_tty);
GenMarkSweep::trace("4");
pg->compact();
G1SpaceCompactClosure blk;
g1h->heap_region_iterate(&blk);
}
void CardTableRS::clear_into_younger(Generation* gen, bool clear_perm) {
GenCollectedHeap* gch = GenCollectedHeap::heap();
// Generations younger than gen have been evacuated. We can clear
// card table entries for gen (we know that it has no pointers
// to younger gens) and for those below. The card tables for
// the youngest gen need never be cleared, and those for perm gen
// will be cleared based on the parameter clear_perm.
// There's a bit of subtlety in the clear() and invalidate()
// methods that we exploit here and in invalidate_or_clear()
// below to avoid missing cards at the fringes. If clear() or
// invalidate() are changed in the future, this code should
// be revisited. 20040107.ysr
Generation* g = gen;
for(Generation* prev_gen = gch->prev_gen(g);
prev_gen != NULL;
g = prev_gen, prev_gen = gch->prev_gen(g)) {
MemRegion to_be_cleared_mr = g->prev_used_region();
clear(to_be_cleared_mr);
}
// Clear perm gen cards if asked to do so.
if (clear_perm) {
MemRegion to_be_cleared_mr = gch->perm_gen()->prev_used_region();
clear(to_be_cleared_mr);
}
}
void CardTableRS::invalidate_or_clear(Generation* gen, bool younger,
bool perm) {
GenCollectedHeap* gch = GenCollectedHeap::heap();
// For each generation gen (and younger and/or perm)
// invalidate the cards for the currently occupied part
// of that generation and clear the cards for the
// unoccupied part of the generation (if any, making use
// of that generation's prev_used_region to determine that
// region). No need to do anything for the youngest
// generation. Also see note#20040107.ysr above.
Generation* g = gen;
for(Generation* prev_gen = gch->prev_gen(g); prev_gen != NULL;
g = prev_gen, prev_gen = gch->prev_gen(g)) {
MemRegion used_mr = g->used_region();
MemRegion to_be_cleared_mr = g->prev_used_region().minus(used_mr);
if (!to_be_cleared_mr.is_empty()) {
clear(to_be_cleared_mr);
}
invalidate(used_mr);
if (!younger) break;
}
// Clear perm gen cards if asked to do so.
if (perm) {
g = gch->perm_gen();
MemRegion used_mr = g->used_region();
MemRegion to_be_cleared_mr = g->prev_used_region().minus(used_mr);
if (!to_be_cleared_mr.is_empty()) {
clear(to_be_cleared_mr);
}
invalidate(used_mr);
}
}
Generation random_generation(int size, int code_length)
{
Generation gen;
while (size--)
//Add a newprogram
gen.push_back(random_chromosome(code_length));
return gen;
}
void CardTableRS::clear_into_gen_and_younger(Generation* gen) {
GenCollectedHeap* gch = GenCollectedHeap::heap();
// Gen and all younger have been evacuated. We can clear
// remembered set entries for the next highest generation
// (we know that it has no pointers to younger gens) and
// those below.
Generation* g = gch->next_gen(gen);
while (g != NULL) {
clear(g->reserved());
g = gch->prev_gen(gen);
}
}
HeapWord* GenCollectorPolicy::expand_heap_and_allocate(size_t size,
bool is_tlab) {
GenCollectedHeap *gch = GenCollectedHeap::heap();
HeapWord* result = NULL;
for (int i = number_of_generations() - 1; i >= 0 && result == NULL; i--) {
Generation *gen = gch->get_gen(i);
if (gen->should_allocate(size, is_tlab)) {
result = gen->expand_and_allocate(size, is_tlab);
}
}
assert(result == NULL || gch->is_in_reserved(result), "result not in heap");
return result;
}
genetic::Cell genetic::gaoptimize()
{
//srand(seed);
Generation ancestor;
for(int g = 0; g < gainput.max_generation; ++g)
{
Generation nextgen;
nextgen.Generate(ancestor);
ancestor = nextgen;
}
return ancestor.Min();
}
status_t
DynamicThreadVector::_ResizeVector(unsigned minimumSize)
{
static const unsigned kInitialSize = 4;
unsigned size = std::max(minimumSize, kInitialSize);
unsigned oldSize = _Size();
if (size <= oldSize)
return B_OK;
void* newVector = realloc(*fVector, (size + 1) * sizeof(TLSBlock));
if (newVector == NULL)
return B_NO_MEMORY;
*fVector = (TLSBlock*)newVector;
memset(*fVector + oldSize + 1, 0, (size - oldSize) * sizeof(TLSBlock));
if (fGeneration == NULL) {
fGeneration = new Generation;
if (fGeneration == NULL)
return B_NO_MEMORY;
}
*(Generation**)*fVector = fGeneration;
fGeneration->SetSize(size);
return B_OK;
}
unsigned
DynamicThreadVector::_Generation() const
{
if (fGeneration != NULL)
return fGeneration->Counter();
return unsigned(-1);
}
TLSBlock&
DynamicThreadVector::operator[](unsigned dso)
{
unsigned generation = TLSBlockTemplates::Get().GetGeneration(-1);
if (_Generation() < generation) {
for (unsigned i = 0; i < _Size(); i++) {
TLSBlock& block = (*fVector)[i + 1];
unsigned dsoGeneration
= TLSBlockTemplates::Get().GetGeneration(dso);
if (_Generation() < dsoGeneration && dsoGeneration <= generation)
block.Destroy();
}
fGeneration->SetCounter(generation);
}
if (_Size() <= dso) {
status_t result = _ResizeVector(dso + 1);
if (result != B_OK)
return fNullBlock;
}
TLSBlock& block = (*fVector)[dso + 1];
if (block.IsInvalid()) {
status_t result = block.Initialize(dso);
if (result != B_OK)
return fNullBlock;
};
return block;
}
ScoredGeneration score_generation(const Generation &generation,
std::function<unsigned int(Code)> fitness_fct)
{
ScoredGeneration scored_generation;
for (int i = 0; i < generation.size(); i++)
{
auto fitness = fitness_fct(generation[i]);
scored_generation.push_back(std::make_pair(fitness, generation[i]));
}
return scored_generation;
}
void CardTableRS::verify() {
// At present, we only know how to verify the card table RS for
// generational heaps.
VerifyCTGenClosure blk(this);
CollectedHeap* ch = Universe::heap();
// We will do the perm-gen portion of the card table, too.
Generation* pg = SharedHeap::heap()->perm_gen();
HeapWord* pg_boundary = pg->reserved().start();
if (ch->kind() == CollectedHeap::GenCollectedHeap) {
GenCollectedHeap::heap()->generation_iterate(&blk, false);
_ct_bs->verify();
// If the old gen collections also collect perm, then we are only
// interested in perm-to-young pointers, not perm-to-old pointers.
GenCollectedHeap* gch = GenCollectedHeap::heap();
CollectorPolicy* cp = gch->collector_policy();
if (cp->is_mark_sweep_policy() || cp->is_concurrent_mark_sweep_policy()) {
pg_boundary = gch->get_gen(1)->reserved().start();
}
}
VerifyCTSpaceClosure perm_space_blk(this, pg_boundary);
SharedHeap::heap()->perm_gen()->space_iterate(&perm_space_blk, true);
}
HeapWord* GenCollectorPolicy::expand_heap_and_allocate(size_t size,
bool is_tlab) {
GenCollectedHeap *gch = GenCollectedHeap::heap();
HeapWord* result = NULL;
Generation *old = gch->old_gen();
if (old->should_allocate(size, is_tlab)) {
result = old->expand_and_allocate(size, is_tlab);
}
if (result == NULL) {
Generation *young = gch->young_gen();
if (young->should_allocate(size, is_tlab)) {
result = young->expand_and_allocate(size, is_tlab);
}
}
assert(result == NULL || gch->is_in_reserved(result), "result not in heap");
return result;
}
virtual void object_iterate(ObjectClosure* cl) {
Generation* g = as_gen();
assert(g != NULL, "as_gen() NULL");
g->object_iterate(cl);
}
// Performance Counter support
virtual void update_counters() {
Generation* g = as_gen();
assert(g != NULL, "as_gen() NULL");
g->update_counters();
}
HeapWord* GenCollectorPolicy::mem_allocate_work(size_t size,
bool is_tlab,
bool* gc_overhead_limit_was_exceeded) {
GenCollectedHeap *gch = GenCollectedHeap::heap();
debug_only(gch->check_for_valid_allocation_state());
assert(gch->no_gc_in_progress(), "Allocation during gc not allowed");
// In general gc_overhead_limit_was_exceeded should be false so
// set it so here and reset it to true only if the gc time
// limit is being exceeded as checked below.
*gc_overhead_limit_was_exceeded = false;
HeapWord* result = NULL;
// Loop until the allocation is satisfied, or unsatisfied after GC.
for (uint try_count = 1, gclocker_stalled_count = 0; /* return or throw */; try_count += 1) {
HandleMark hm; // Discard any handles allocated in each iteration.
// First allocation attempt is lock-free.
Generation *young = gch->young_gen();
assert(young->supports_inline_contig_alloc(),
"Otherwise, must do alloc within heap lock");
if (young->should_allocate(size, is_tlab)) {
result = young->par_allocate(size, is_tlab);
if (result != NULL) {
assert(gch->is_in_reserved(result), "result not in heap");
return result;
}
}
uint gc_count_before; // Read inside the Heap_lock locked region.
{
MutexLocker ml(Heap_lock);
log_trace(gc, alloc)("GenCollectorPolicy::mem_allocate_work: attempting locked slow path allocation");
// Note that only large objects get a shot at being
// allocated in later generations.
bool first_only = ! should_try_older_generation_allocation(size);
result = gch->attempt_allocation(size, is_tlab, first_only);
if (result != NULL) {
assert(gch->is_in_reserved(result), "result not in heap");
return result;
}
if (GCLocker::is_active_and_needs_gc()) {
if (is_tlab) {
return NULL; // Caller will retry allocating individual object.
}
if (!gch->is_maximal_no_gc()) {
// Try and expand heap to satisfy request.
result = expand_heap_and_allocate(size, is_tlab);
// Result could be null if we are out of space.
if (result != NULL) {
return result;
}
}
if (gclocker_stalled_count > GCLockerRetryAllocationCount) {
return NULL; // We didn't get to do a GC and we didn't get any memory.
}
// If this thread is not in a jni critical section, we stall
// the requestor until the critical section has cleared and
// GC allowed. When the critical section clears, a GC is
// initiated by the last thread exiting the critical section; so
// we retry the allocation sequence from the beginning of the loop,
// rather than causing more, now probably unnecessary, GC attempts.
JavaThread* jthr = JavaThread::current();
if (!jthr->in_critical()) {
MutexUnlocker mul(Heap_lock);
// Wait for JNI critical section to be exited
GCLocker::stall_until_clear();
gclocker_stalled_count += 1;
continue;
} else {
if (CheckJNICalls) {
fatal("Possible deadlock due to allocating while"
" in jni critical section");
}
return NULL;
}
}
// Read the gc count while the heap lock is held.
gc_count_before = gch->total_collections();
}
VM_GenCollectForAllocation op(size, is_tlab, gc_count_before);
VMThread::execute(&op);
if (op.prologue_succeeded()) {
result = op.result();
if (op.gc_locked()) {
assert(result == NULL, "must be NULL if gc_locked() is true");
continue; // Retry and/or stall as necessary.
}
// Allocation has failed and a collection
// has been done. If the gc time limit was exceeded the
// this time, return NULL so that an out-of-memory
// will be thrown. Clear gc_overhead_limit_exceeded
// so that the overhead exceeded does not persist.
const bool limit_exceeded = size_policy()->gc_overhead_limit_exceeded();
const bool softrefs_clear = all_soft_refs_clear();
if (limit_exceeded && softrefs_clear) {
*gc_overhead_limit_was_exceeded = true;
size_policy()->set_gc_overhead_limit_exceeded(false);
if (op.result() != NULL) {
CollectedHeap::fill_with_object(op.result(), size);
}
return NULL;
}
assert(result == NULL || gch->is_in_reserved(result),
"result not in heap");
return result;
}
// Give a warning if we seem to be looping forever.
if ((QueuedAllocationWarningCount > 0) &&
(try_count % QueuedAllocationWarningCount == 0)) {
log_warning(gc, ergo)("GenCollectorPolicy::mem_allocate_work retries %d times,"
" size=" SIZE_FORMAT " %s", try_count, size, is_tlab ? "(TLAB)" : "");
}
}
}
HeapWord* TwoGenerationCollectorPolicy::satisfy_failed_allocation(size_t size,
bool is_large_noref,
bool is_tlab,
bool* notify_ref_lock) {
GenCollectedHeap *gch = GenCollectedHeap::heap();
GCCauseSetter x(gch, GCCause::_allocation_failure);
HeapWord* result = NULL;
// The gc_prologues have not executed yet. The value
// for incremental_collection_will_fail() is the remanent
// of the last collection.
if (!gch->incremental_collection_will_fail()) {
// Do an incremental collection.
gch->do_collection(false /* full */,
false /* clear_all_soft_refs */,
size /* size */,
is_large_noref /* is_large_noref */,
is_tlab /* is_tlab */,
number_of_generations() - 1 /* max_level */,
notify_ref_lock /* notify_ref_lock */);
} else {
// The incremental_collection_will_fail flag is set if the
// next incremental collection will not succeed (e.g., the
// DefNewGeneration didn't think it had space to promote all
// its objects). However, that last incremental collection
// continued, allowing all older generations to collect (and
// perhaps change the state of the flag).
//
// If we reach here, we know that an incremental collection of
// all generations left us in the state where incremental collections
// will fail, so we just try allocating the requested space.
// If the allocation fails everywhere, force a full collection.
// We're probably very close to being out of memory, so forcing many
// collections now probably won't help.
if (PrintGC && Verbose) {
gclog_or_tty->print_cr("TwoGenerationCollectorPolicy::satisfy_failed_allocation:"
" attempting allocation anywhere before full collection");
}
result = gch->attempt_allocation(size,
is_large_noref,
is_tlab,
false /* first_only */);
if (result != NULL) {
assert(gch->is_in(result), "result not in heap");
return result;
}
// Allocation request hasn't yet been met; try a full collection.
gch->do_collection(true /* full */,
false /* clear_all_soft_refs */,
size /* size */,
is_large_noref /* is_large_noref */,
is_tlab /* is_tlab */,
number_of_generations() - 1 /* max_level */,
notify_ref_lock /* notify_ref_lock */);
}
result = gch->attempt_allocation(size, is_large_noref, is_tlab, false /*first_only*/);
if (result != NULL) {
assert(gch->is_in(result), "result not in heap");
return result;
}
// OK, collection failed, try expansion.
for (int i = number_of_generations() - 1 ; i>= 0; i--) {
Generation *gen = gch->get_gen(i);
if (gen->should_allocate(size, is_large_noref, is_tlab)) {
result = gen->expand_and_allocate(size, is_large_noref, is_tlab);
if (result != NULL) {
assert(gch->is_in(result), "result not in heap");
return result;
}
}
}
// If we reach this point, we're really out of memory. Try every trick
// we can to reclaim memory. Force collection of soft references. Force
// a complete compaction of the heap. Any additional methods for finding
// free memory should be here, especially if they are expensive. If this
// attempt fails, an OOM exception will be thrown.
{
IntFlagSetting flag_change(MarkSweepAlwaysCompactCount, 1); // Make sure the heap is fully compacted
gch->do_collection(true /* full */,
true /* clear_all_soft_refs */,
size /* size */,
is_large_noref /* is_large_noref */,
is_tlab /* is_tlab */,
number_of_generations() - 1 /* max_level */,
notify_ref_lock /* notify_ref_lock */);
}
result = gch->attempt_allocation(size, is_large_noref, is_tlab, false /* first_only */);
if (result != NULL) {
assert(gch->is_in(result), "result not in heap");
return result;
}
// What else? We might try synchronous finalization later. If the total
// space available is large enough for the allocation, then a more
// complete compaction phase than we've tried so far might be
// appropriate.
return NULL;
}
Generation::Generation(Generation ancestors, bool debug)
{
for (int s = 0; s < GENERATION_SIZE; s++) {
this->solutions[s] = Solution(ancestors.solutions[s], ancestors.getSolution());
}
}
void GeneticAlgorithm::run_optimization(std::vector<exp_signal> const& signals_exp,
Spin const& spinA, Spin const& spinB,
std::vector<int> const& param_numbers,
std::vector<int> const& param_modes,
std::vector<bound> const& param_bounds,
genetic_parameters const& genetic_param,
output_parameters const& output_param) const
{
// Initialize the calculator of PELDOR signals
PeldorCalculator* peldor_calc = new PeldorCalculator(genetic_param.num_avg);
peldor_calc->calculate_spinA_excitation(signals_exp, spinA);
// Calculate the spectrum of the spin system
if (output_param.record_spectrum) {
std::cout << " Recording the spectrum... ";
peldor_calc->save_spectrum(signals_exp, spinA, spinB, output_param);
std::cout << "Done!" << std::endl;
}
// Start optimization
int n = 1;
std::cout << " Optimization step " << n << "/" << genetic_param.num_generations_max << std::endl;
// Create a first generation
Generation* generation = new Generation(genetic_param);
generation->create_initial_generation(param_bounds, genetic_param);
// Score first generation
generation->score_chromosomes(*peldor_calc, signals_exp, spinA, spinB, param_numbers, param_modes, genetic_param);
generation->sort_chromosomes();
std::vector<double> best_fitness; best_fitness.reserve(genetic_param.num_generations_max);
best_fitness.push_back(generation->chromosomes[0].fitness);
// Proceed with next generations
for (int n = 2; n <= genetic_param.num_generations_max; ++n) { // loop over generations
std::cout << " Optimization step " << n << "/" << genetic_param.num_generations_max << std::endl;
// Create next generation
generation->produce_offspring(genetic_param, param_bounds);
// Score the generation
generation->score_chromosomes(*peldor_calc, signals_exp, spinA, spinB, param_numbers, param_modes, genetic_param);
generation->sort_chromosomes();
best_fitness.push_back(generation->chromosomes[0].fitness);
}
// Save the fitness of the best chromosome
if (output_param.record_score) {
std::cout << " Recording the fitness vs the number of optimization steps... ";
record_score(best_fitness, genetic_param, output_param);
std::cout << "Done!" << std::endl;
}
// Save the calculated fit to the PELDOR signals for the best chromosome
if (output_param.record_fit) {
std::cout << " Recording the fit to the PELDOR signals... ";
record_fit(*peldor_calc, generation->chromosomes[0], signals_exp, spinA, spinB, param_numbers, param_modes, output_param);
std::cout << "Done!" << std::endl;
}
// Save the genes of the best chromosome
if (output_param.record_parameters) {
std::cout << " Recording the best values of fitting parameters... ";
record_parameters(generation->chromosomes[0], param_numbers, param_modes, output_param);
std::cout << "Done!" << std::endl;
}
// Record the calculated for-factors for the PELDOR signals
if (output_param.record_form_factor) {
std::cout << " Recording the form-factors of PELDOR signals... ";
record_form_factor(*peldor_calc, generation->chromosomes[0], signals_exp, spinA, spinB,
param_numbers, param_modes, output_param);
std::cout << "Done!" << std::endl;
}
// Record the symmetry-related sets of fitting parameters
if (output_param.record_symmetric_solutions) {
std::cout << " Recording the symmetry-related sets of fitting parameters... ";
record_symmetric_parameters(*peldor_calc, generation->chromosomes[0], signals_exp, spinA, spinB,
param_numbers, param_modes, param_bounds, genetic_param, output_param);
std::cout << "Done!" << std::endl;
}
// Record the error plots
if (output_param.record_error_plot) {
std::cout << " Recording the error plot... ";
record_error_plot(*peldor_calc, generation->chromosomes[0], signals_exp, spinA, spinB,
param_numbers, param_modes, param_bounds, genetic_param, output_param);
std::cout << "Done!" << std::endl;
}
// Clean up
delete peldor_calc;
delete generation;
}
size_t used_in_bytes() {
return _gen->used();
}
virtual void oop_iterate(OopClosure* cl) {
Generation* g = as_gen();
assert(g != NULL, "as_gen() NULL");
g->oop_iterate(cl);
}
int main(int argc, char* argv[]) {
if (argc < 5) {
std::cout << argv[0] << " <numberOfGenerations> <sizeOfPopulation> <numberOfAtoms> <percentageMutation>" << std::endl;
return EXIT_FAILURE;
}
std::fstream out;
out.open("../results/ga-out", std::ios::out);
assert(out.is_open());
int maxDistance = 1000;
int numberOfGenerations = std::stoi(argv[1]);
int sizeOfPopulation = std::stoi(argv[2]);
int numberOfAtoms = std::stoi(argv[3]);
int percentage = std::stoi(argv[4]);
Randomize* randomize = new Randomize();
Evolution* evolution = new Evolution();
out << "genetico" << std::endl;
out << numberOfAtoms << std::endl;
// generate random generation
Generation* pGen = randomize->randomGeneration(maxDistance, sizeOfPopulation, numberOfAtoms);
Molecule** pMol = pGen->molecules();
// calculate potential
for (int i = 0; i < sizeOfPopulation; i++) {
Molecule* m = pMol[i];
m->setPotential(evolution->lennardJones(m));
}
// ordering molecules
QuickSort<Molecule>::sort(pMol, 0, sizeOfPopulation - 1);
Atom** pAtom = pMol[0]->atoms();
for (int i = 0; i < pMol[0]->numberOfAtoms(); i++) {
out << "Au" << "\t" << pAtom[i]->_x << "\t" << pAtom[i]->_y << "\t" << pAtom[i]->_z << std::endl;
}
// calculates next generations
Molecule* idv1 = NULL;
Molecule* idv2 = NULL;
Generation* nGen = NULL;
Molecule** nMol = NULL;
int generationID = 1;
while (numberOfGenerations > 0) {
// create new generation
nGen = new Generation(generationID);
for (int i = 0; i < sizeOfPopulation; i++) {
// select individuals
idv1 = pMol[randomize->randomInt(sizeOfPopulation)];
idv2 = pMol[randomize->randomInt(sizeOfPopulation)];
// create new individual
nGen->addMolecule(*evolution->reprodution(idv1, idv2, maxDistance, percentage));
}
delete pGen;
pGen = nGen;
pMol = pGen->molecules();
// calculate potential
for (int i = 0; i < sizeOfPopulation; i++) {
Molecule* m = pMol[i];
m->setPotential(evolution->lennardJones(m));
}
// ordering molecules
QuickSort<Molecule>::sort(pMol, 0, sizeOfPopulation - 1);
pAtom = pMol[0]->atoms();
for (int j = 0; j < pMol[0]->numberOfAtoms(); j++) {
out << "Au" << "\t" << pAtom[j]->_x << "\t" << pAtom[j]->_y << "\t" << pAtom[j]->_z << std::endl;
}
// increment
generationID++;
numberOfGenerations--;
}
out.close();
delete pGen;
// delete nGen;
delete randomize;
delete evolution;
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]) {
Generation moms;
Generation dads;
Generation x;
Individual *mom;
Individual *dad;
Individual *child;
UniformRNG r(0.0,1.0);
int i;
init();
// Create 10 males and 10 females, and give them each 2 mutations.
// Then create a child and put it in generation x:
for (i=0; i<gsize; i++) {
dad = new Individual;
dad->set_sex(MALE);
dad->genes->add_mutations(2);
cout << dad->get_id() << ": " << *dad;
dads.insert(dad);
mom = new Individual;
mom->set_sex(FEMALE);
mom->genes->add_mutations(2);
moms.insert(mom);
cout << mom->get_id() << ": " << *mom;
child = new Individual;
child->set_sex((++r < 0.5) ? MALE : FEMALE);
child->genes->combine(dad->genes,mom->genes);
x.insert(child);
cout << child->get_id() << ": " << *child;
cout << endl;
}
// Test the remove function and error detection in the Generation class.
// Print the first three, remove the second, and print again:
cout << "First three individuals in x: \n ";
for (i=0; i<3; i++)
cout << x[i]->get_id() << " ";
cout << endl;
child = x.remove(1);
cout << "individual removed: " << child->get_id() << endl;
cout << "First three individuals remaining in x: \n ";
for (i=0; i<3; i++)
cout << x[i]->get_id() << " ";
cout << endl << endl;
// Same test, but now remove the first one (special case):
cout << "First three individuals in x: \n ";
for (i=0; i<3; i++)
cout << x[i]->get_id() << " ";
cout << endl;
child = x.remove(0);
cout << "individual removed: " << child->get_id() << endl;
cout << "First three individuals remaining in x: \n ";
for (i=0; i<3; i++)
cout << x[i]->get_id() << " ";
cout << endl << endl;
// There are now gsize-2 individuals in x. Whittle it down to 2:
for (i = 0; i < gsize-4; i++)
child = x.remove(0);
// Print the remaining two individuals:
cout << "last two individuals in x: " << x[0]->get_id() << " and " << x[1]->get_id() << endl;
// These should cause an error message:
child = x[2];
child = x.remove(2);
// Test removing the last item:
child = x.remove(1);
cout << child->get_id() << endl;
child = x.remove(0);
cout << child->get_id() << endl;
// Gen X should now be empty:
cout << "Gen X size = " << x.size() << endl;
}
