diff --git a/src/aevol_modify.cpp b/src/aevol_modify.cpp index 5637ab3271a174265e4df8ae69502abc8209cc9b..ae1fe162e9e62729678dd50e0f148180fa69d7e4 100644 --- a/src/aevol_modify.cpp +++ b/src/aevol_modify.cpp @@ -604,8 +604,7 @@ int main(int argc, char* argv[]) { exp_manager->exp_m_7_->evaluate(indiv,old_world->grid(x,y)->individual()->w_max(),selection_pressure); - local_fit_array[loc_indiv_id] = - indiv->fitness; + local_fit_array[loc_indiv_id] = indiv->fitness_; sum_local_fit += local_fit_array[loc_indiv_id]; delete indiv; diff --git a/src/libaevol/7/ExpManager_7.cpp b/src/libaevol/7/ExpManager_7.cpp index afe22560d284d170616a6e9f1202e69da0e5dedf..a08e7556a387446ba64a711d78f7e9bb39587bdd 100644 --- a/src/libaevol/7/ExpManager_7.cpp +++ b/src/libaevol/7/ExpManager_7.cpp @@ -250,7 +250,7 @@ void ExpManager_7::selection(int indiv_id) { cur_y = (y + j + grid_height_) % grid_height_; if (fitness_function == FITNESS_EXP) { - local_fit_array[count] = previous_individuals[cur_x * grid_height_ + cur_y]->fitness; + local_fit_array[count] = previous_individuals[cur_x * grid_height_ + cur_y]->fitness_; } else if (fitness_function == FITNESS_GLOBAL_SUM) { #ifdef __REGUL double composed_fitness = 0; @@ -1986,7 +1986,7 @@ void ExpManager_7::compute_fitness(Individual_7* indiv, fuzzy_factory_->give_back(delta); - indiv->fitness = exp( + indiv->fitness_ = exp( -selection_pressure * ((double)indiv->metaerror)); #endif @@ -2142,7 +2142,7 @@ void ExpManager_7::finalize_network(Individual_7* indiv, double selection_pressu indiv->metaerror / (double) (pth->nb_env_); } - indiv->fitness = exp( + indiv->fitness_ = exp( -selection_pressure * ((double) indiv->metaerror)); } @@ -2351,12 +2351,12 @@ void ExpManager_7::update_phenotype( Individual_7* indiv ) { #endif int32_t ExpManager_7::find_best_indiv_idx(Individual_7** indivs, int32_t nb_indivs) const { - double best_fitness = indivs[0]->fitness; + double best_fitness = indivs[0]->fitness_; int idx_best = 0; for (int indiv_idx = 1 ; indiv_idx < (int) nb_indivs ; ++indiv_idx) { - if (indivs[indiv_idx]->fitness > best_fitness) { + if (indivs[indiv_idx]->fitness_ > best_fitness) { idx_best = indiv_idx; - best_fitness = indivs[indiv_idx]->fitness; + best_fitness = indivs[indiv_idx]->fitness_; } } return idx_best; @@ -2538,8 +2538,7 @@ void ExpManager_7::run_a_step(double w_max, double selection_pressure) { double sum_local_fit = 0.0; for (int loc_indiv_id = 0; loc_indiv_id < nb_indivs_; loc_indiv_id++) { - local_fit_array[loc_indiv_id] = - previous_individuals[loc_indiv_id]->fitness; + local_fit_array[loc_indiv_id] = previous_individuals[loc_indiv_id]->fitness_; sum_local_fit += local_fit_array[loc_indiv_id]; } @@ -2892,11 +2891,11 @@ for (size_t index = 0; index < mutant_list_.size(); index++) { #ifndef AEVOL_NO_STATS #pragma omp single { - double best_fitness = previous_individuals[0]->fitness; + double best_fitness = previous_individuals[0]->fitness_; for (int indiv_id = 1; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) { - if (previous_individuals[indiv_id]->fitness > best_fitness) { - best_fitness = previous_individuals[indiv_id]->fitness; + if (previous_individuals[indiv_id]->fitness_ > best_fitness) { + best_fitness = previous_individuals[indiv_id]->fitness_; } diff --git a/src/libaevol/7/Individual_7.cpp b/src/libaevol/7/Individual_7.cpp index ba3f74cd3584c4f71826b9389da4b89cbd4d7e3c..72215a579399ee1136e3d6722414369dcd080faa 100644 --- a/src/libaevol/7/Individual_7.cpp +++ b/src/libaevol/7/Individual_7.cpp @@ -89,7 +89,7 @@ Individual_7::Individual_7(Individual_7* clone, metadata_ = new List_Metadata(this); #endif - fitness = clone->fitness; + fitness_ = clone->fitness_; metaerror = clone->metaerror; for (auto& strand: {Strand::LEADING, Strand::LAGGING}) { diff --git a/src/libaevol/7/Individual_7.h b/src/libaevol/7/Individual_7.h index d33edd3e02b4c7c9951d54f21d32ce5d55e8f973..9bc1aaa98c319d430a20f2b852113d1b6b84402a 100644 --- a/src/libaevol/7/Individual_7.h +++ b/src/libaevol/7/Individual_7.h @@ -90,7 +90,7 @@ class Individual_7 : public Observable { AbstractFuzzy* phenotype = nullptr; AbstractFuzzy* delta = nullptr; #endif - double fitness; + double fitness_; double metaerror; diff --git a/src/libaevol/7/Stats_7.cpp b/src/libaevol/7/Stats_7.cpp index 6b4c8b73d4301c31611a1db3bec3ed9ac48a118a..6a0c2aa73d22d2262549983b4b01bd5cf893f521 100644 --- a/src/libaevol/7/Stats_7.cpp +++ b/src/libaevol/7/Stats_7.cpp @@ -243,7 +243,7 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) { nb_clones_ = simd_individual_->nb_clones_; pop_size_ = simd_individual_->nb_indivs_; - fitness_ = indiv->fitness; + fitness_ = indiv->fitness_; metabolic_error_ = indiv->metaerror; amount_of_dna_ = indiv->dna_->length(); @@ -346,7 +346,7 @@ void Stats_7::compute_average(bool non_coding) { if (non_coding) simd_individual_->previous_individuals[indiv_id]->compute_non_coding(); - fitness_ += simd_individual_->previous_individuals[indiv_id]->fitness; + fitness_ += simd_individual_->previous_individuals[indiv_id]->fitness_; metabolic_error_ += simd_individual_->previous_individuals[indiv_id]->metaerror; amount_of_dna_ += simd_individual_->previous_individuals[indiv_id]->dna_->length(); diff --git a/src/post_treatments/aevol_post_ancestor_network_knockout_7.cpp b/src/post_treatments/aevol_post_ancestor_network_knockout_7.cpp index 0ef39b96cb81726d3ce44a8e649aa8643299146b..254c91bf3cb5b45fc85d54a92726a6412f77353e 100644 --- a/src/post_treatments/aevol_post_ancestor_network_knockout_7.cpp +++ b/src/post_treatments/aevol_post_ancestor_network_knockout_7.cpp @@ -306,7 +306,7 @@ int main(int argc, char* argv[]) { exp_manager->exp_m_7_->evaluate(indiv, w_max, selection_pressure); - printf("Initial fitness = %e\n", indiv->fitness); + printf("Initial fitness = %e\n", indiv->fitness_); printf("Initial genome size = %" PRId32 "\n", indiv->dna_->length()); double base_metaerror = 0; @@ -367,7 +367,7 @@ int main(int argc, char* argv[]) { base_metaerror += cloned->metaerror; #pragma omp atomic - base_fitness += cloned->fitness; + base_fitness += cloned->fitness_; int32_t i_edges = 0; for (Rna_7* rna : cloned->rnas()) { @@ -384,12 +384,12 @@ int main(int argc, char* argv[]) { #pragma omp atomic fabs_fitness_loss[i_edges] += - std::fabs(base_fitness - cloned->fitness); + std::fabs(base_fitness - cloned->fitness_); #pragma omp atomic fabs_fitness_loss_percent[i_edges] += - (std::fabs(base_fitness - cloned->fitness)) / - cloned->fitness; + (std::fabs(base_fitness - cloned->fitness_)) / + cloned->fitness_; affinity.enhancer_factor = saved_enhancer_factor; affinity.operator_factor = saved_operator_factor; @@ -408,7 +408,7 @@ int main(int argc, char* argv[]) { fabs_fitness_loss_percent[i] /= nb_iteration; } - indiv->fitness = base_fitness / (double)nb_iteration; + indiv->fitness_ = base_fitness / (double)nb_iteration; indiv->metaerror = base_metaerror / (double)nb_iteration; // Init protein ID: @@ -544,7 +544,7 @@ int main(int argc, char* argv[]) { delete[] pth_array; #endif if (verbose) { - printf("Initial fitness = %f\n", indiv->fitness); + printf("Initial fitness = %f\n", indiv->fitness_); printf("Initial genome size = %" PRId32 "\n", indiv->dna_->length()); } @@ -615,7 +615,7 @@ int main(int argc, char* argv[]) { if (trace_mutations) { // Store initial values before the mutation metabolic_error_before = indiv->metaerror; - fitness_before = indiv->fitness; + fitness_before = indiv->fitness_; unitlen_before = indiv->dna_->length(); } @@ -630,10 +630,9 @@ int main(int argc, char* argv[]) { double impact_on_metabolic_error = indiv->metaerror - metabolic_error_before; - double impact_on_fitness = indiv->fitness - fitness_before; + double impact_on_fitness = indiv->fitness_ - fitness_before; - double selection_coefficient = - indiv->fitness / fitness_before - 1.0; + double selection_coefficient = indiv->fitness_ / fitness_before - 1.0; mut->generic_description_string(mut_descr_string); fprintf(fixed_mutations_file, @@ -776,7 +775,7 @@ int main(int argc, char* argv[]) { base_metaerror += cloned->metaerror; //#pragma omp atomic - base_fitness += cloned->fitness; + base_fitness += cloned->fitness_; int32_t i_edges = 0; for (Rna_7* rna : cloned->rnas()) { @@ -825,12 +824,12 @@ int main(int argc, char* argv[]) { #pragma omp atomic fabs_fitness_loss[i_edges] += - std::fabs(base_fitness - cloned->fitness); + std::fabs(base_fitness - cloned->fitness_); #pragma omp atomic fabs_fitness_loss_percent[i_edges] += - (std::fabs(base_fitness - cloned->fitness)) / - cloned->fitness; + (std::fabs(base_fitness - cloned->fitness_)) / + cloned->fitness_; affinity.enhancer_factor = saved_enhancer_factor; @@ -850,7 +849,7 @@ int main(int argc, char* argv[]) { fabs_fitness_loss_percent[i] /= nb_iteration; } - cloned_generation->fitness = base_fitness / (double)nb_iteration; + cloned_generation->fitness_ = base_fitness / (double)nb_iteration; cloned_generation->metaerror = base_metaerror / (double)nb_iteration; diff --git a/src/post_treatments/aevol_post_ancestor_stats_7.cpp b/src/post_treatments/aevol_post_ancestor_stats_7.cpp index 46b35b5b008d5c3d13507a1e908754e0830b8e05..642d4c41d3d4a1e8a72aa32e9788def7b2397fab 100644 --- a/src/post_treatments/aevol_post_ancestor_stats_7.cpp +++ b/src/post_treatments/aevol_post_ancestor_stats_7.cpp @@ -231,7 +231,7 @@ int main(int argc, char* argv[]) { exp_manager->exp_m_7_->evaluate(indiv,w_max,selection_pressure,phenotypic_target_handler_); - printf("Initial fitness = %e\n", indiv->fitness); + printf("Initial fitness = %e\n", indiv->fitness_); printf("Initial genome size = %" PRId32 "\n", indiv->dna_->length()); double base_metaerror = 0; @@ -260,18 +260,18 @@ int main(int argc, char* argv[]) { base_metaerror += cloned->metaerror; #pragma omp atomic - base_fitness += cloned->fitness; + base_fitness += cloned->fitness_; #pragma omp critical fitmeta << t0 << ",RANDOM," << i << "," << cloned->metaerror << "," - << cloned->fitness << std::endl; + << cloned->fitness_ << std::endl; //printf("Iteration RANDOM at %d : %d/%d : %lf %e\n", t, i, nb_iteration, // cloned->dist_to_target_by_feature(METABOLISM), cloned->fitness()); delete cloned; } - indiv->fitness = base_fitness / (double) nb_iteration; + indiv->fitness_ = base_fitness / (double) nb_iteration; indiv->metaerror = base_metaerror / (double) nb_iteration; exp_manager->exp_m_7_->write_stat(stats_anc,indiv,AeTime::time(),true); @@ -311,7 +311,7 @@ int main(int argc, char* argv[]) { delete [] pth_array_0; #endif if (verbose) { - printf("Initial fitness = %f\n", indiv->fitness); + printf("Initial fitness = %f\n", indiv->fitness_); printf("Initial genome size = %" PRId32 "\n", indiv->dna_->length()); } @@ -381,7 +381,7 @@ int main(int argc, char* argv[]) { if (trace_mutations) { // Store initial values before the mutation metabolic_error_before = indiv->metaerror; - fitness_before = indiv->fitness; + fitness_before = indiv->fitness_; unitlen_before = indiv->dna_->length(); } @@ -397,9 +397,9 @@ int main(int argc, char* argv[]) { indiv->metaerror - metabolic_error_before; - double impact_on_fitness = indiv->fitness - fitness_before; + double impact_on_fitness = indiv->fitness_ - fitness_before; - double selection_coefficient = indiv->fitness / fitness_before - 1.0; + double selection_coefficient = indiv->fitness_ / fitness_before - 1.0; mut->generic_description_string(mut_descr_string); fprintf(fixed_mutations_file, @@ -502,7 +502,7 @@ int main(int argc, char* argv[]) { base_metaerror += cloned->metaerror; //#pragma omp atomic - base_fitness += cloned->fitness; + base_fitness += cloned->fitness_; //#pragma omp critical // fitmeta << current_generation << ",RANDOM," << i << "," << cloned->metaerror << "," @@ -513,7 +513,7 @@ int main(int argc, char* argv[]) { delete cloned; } - cloned_generation->fitness = base_fitness / (double) nb_iteration; + cloned_generation->fitness_ = base_fitness / (double) nb_iteration; cloned_generation->metaerror = base_metaerror / (double) nb_iteration; #pragma omp critical