framework/biocro_simulation.h at main · biocro/framework · GitHub

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#ifndef BIOCRO_SIMULATION_H
#define BIOCRO_SIMULATION_H

#include <memory>            // for unique_ptr, shared_ptr
#include "state_map.h"       // for state_map, state_vector_map
#include "module_creator.h"  // for mc_vector
#include "dynamical_system.h"
#include "ode_solver.h"
#include "ode_solver_library/ode_solver_factory.h"

// Class that represents a BioCro simulation
class biocro_simulation
{
   public:
    biocro_simulation(
        // parameters passed to dynamical_system constructor
        state_map const& initial_values,
        state_map const& parameters,
        state_vector_map const& drivers,
        mc_vector const& direct_mcs,
        mc_vector const& differential_mcs,
        // parameters passed to ode_solver_factory::create
        std::string ode_solver_name,
        double output_step_size,
        double adaptive_rel_error_tol,
        double adaptive_abs_error_tol,
        int adaptive_max_steps)
    {
        // Create the system
        sys = std::shared_ptr<dynamical_system>(
            new dynamical_system(initial_values, parameters,
                                 drivers, direct_mcs,
                                 differential_mcs));

        // Create the ode_solver that will be used to solve the system
        system_solver =
            std::unique_ptr<ode_solver>(
                ode_solver_factory::create(
                    ode_solver_name,
                    output_step_size,
                    adaptive_rel_error_tol,
                    adaptive_abs_error_tol,
                    adaptive_max_steps));
    }

    state_vector_map run_simulation()
    {
        return system_solver->integrate(sys);
    }

    std::string generate_report() const
    {
        std::string report;
        report += "\nSystem startup information:\n" +
                  sys->generate_startup_report() +
                  "\nODE solver description:\n" +
                  system_solver->generate_info_report() +
                  "\n\nThe ODE solver reports the following:\n" +
                  system_solver->generate_integrate_report() +
                  "\nThe dynamical system reports the following:\n" +
                  sys->generate_usage_report() +
                  "\n\n";
        return report;
    }

   private:
    std::shared_ptr<dynamical_system> sys;
    std::unique_ptr<ode_solver> system_solver;
};

#endif