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;
}
