CardiacSimulation.hpp

/*

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*/

#ifndef CARDIACSIMULATION_HPP_
#define CARDIACSIMULATION_HPP_

#include <vector>
#include <ctime>
#include <memory>

#include "UblasIncludes.hpp"

#include "AbstractCardiacProblem.hpp"
#include "MonodomainProblem.hpp"
#include "BidomainProblem.hpp"
#include "BidomainWithBathProblem.hpp"
#include "CardiacSimulationArchiver.hpp"
#include "PetscTools.hpp"
#include "TimeStepper.hpp"
#include "Exception.hpp"

#include "HeartConfig.hpp"
#include "HeartConfigRelatedCellFactory.hpp"
#include "HeartFileFinder.hpp"

#include "TetrahedralMesh.hpp"
#include "NonCachedTetrahedralMesh.hpp"
#include "ChastePoint.hpp"
#include "ChasteCuboid.hpp"
#include "MeshalyzerMeshWriter.hpp"
#include "TrianglesMeshWriter.hpp"

#include "OrthotropicConductivityTensors.hpp"

#include "Hdf5ToMeshalyzerConverter.hpp"
#include "PostProcessingWriter.hpp"

#include "OutputDirectoryFifoQueue.hpp"
#include "ExecutableSupport.hpp"

class CardiacSimulation
{
private:
    void ReadParametersFromFile(std::string parameterFileName);

    template<class Problem, unsigned SPACE_DIM>
    void CreateAndRun()
    {
        std::auto_ptr<Problem> p_problem;

        if (HeartConfig::Instance()->IsSimulationDefined())
        {
            HeartConfigRelatedCellFactory<SPACE_DIM> cell_factory;
            p_problem.reset(new Problem(&cell_factory));

            p_problem->Initialise();
        }
        else // (HeartConfig::Instance()->IsSimulationResumed())
        {
            p_problem.reset(CardiacSimulationArchiver<Problem>::Load(HeartConfig::Instance()->GetArchivedSimulationDir()));
            // Any changes to parameters that normally only take effect at problem creation time...
            HeartConfigRelatedCellFactory<SPACE_DIM> cell_factory;
            cell_factory.SetMesh(&(p_problem->rGetMesh()));
            AbstractCardiacTissue<SPACE_DIM, SPACE_DIM>* p_tissue = p_problem->GetTissue();
            DistributedVectorFactory* p_vector_factory = p_problem->rGetMesh().GetDistributedVectorFactory();
            for (unsigned node_global_index = p_vector_factory->GetLow();
                 node_global_index < p_vector_factory->GetHigh();
                 node_global_index++)
            {
                // Overwrite any previous stimuli if new ones are defined
                cell_factory.SetCellIntracellularStimulus(p_tissue->GetCardiacCell(node_global_index), node_global_index);
                // Modify cell model parameters
                cell_factory.SetCellParameters(p_tissue->GetCardiacCell(node_global_index), node_global_index);
            }
        }

        if (HeartConfig::Instance()->GetCheckpointSimulation())
        {
            // Create the checkpoints directory and set up a fifo queue of subdirectory names
            OutputDirectoryFifoQueue directory_queue(HeartConfig::Instance()->GetOutputDirectory() + "_checkpoints/",
                                                     HeartConfig::Instance()->GetMaxCheckpointsOnDisk());

            TimeStepper checkpoint_stepper(p_problem->GetCurrentTime(), HeartConfig::Instance()->GetSimulationDuration(), HeartConfig::Instance()->GetCheckpointTimestep());
            while ( !checkpoint_stepper.IsTimeAtEnd() )
            {
                // Solve checkpoint timestep
                HeartConfig::Instance()->SetSimulationDuration(checkpoint_stepper.GetNextTime());
                p_problem->Solve();

                // Create directory that will contain archive and partial results for this checkpoint timestep.
                std::stringstream checkpoint_id;
                checkpoint_id << HeartConfig::Instance()->GetSimulationDuration() << "ms/";
                std::string checkpoint_dir_basename = directory_queue.CreateNextDir(checkpoint_id.str());

                // Archive simulation (in a subdirectory of checkpoint_dir_basename).
                std::stringstream archive_foldername;
                archive_foldername << HeartConfig::Instance()->GetOutputDirectory() << "_" << HeartConfig::Instance()->GetSimulationDuration() << "ms";
                CardiacSimulationArchiver<Problem>::Save(*(p_problem.get()), checkpoint_dir_basename + archive_foldername.str(), false);

                // Put a copy of the partial results aside (in a subdirectory of checkpoint_dir_basename).
                OutputFileHandler checkpoint_dir_basename_handler(checkpoint_dir_basename, false);
                OutputFileHandler partial_output_dir_handler(HeartConfig::Instance()->GetOutputDirectory(), false);
                if (PetscTools::AmMaster())
                {
                    ABORT_IF_NON0(system, "cp -r " + partial_output_dir_handler.GetOutputDirectoryFullPath() + " " + checkpoint_dir_basename_handler.GetOutputDirectoryFullPath());
                }

                // Create an XML file to help in resuming
                CreateResumeXmlFile(checkpoint_dir_basename, archive_foldername.str());

                // Advance time stepper
                checkpoint_stepper.AdvanceOneTimeStep();
            }
        }
        else
        {
            p_problem->Solve();
        }
        if (mSaveProblemInstance)
        {
            mSavedProblem = p_problem;
        }
    }

    void Run();

    void CreateResumeXmlFile(const std::string& rOutputDirectory, const std::string& rArchiveDirectory);

    std::string BoolToString(bool yesNo);
public:
    CardiacSimulation(std::string parameterFileName,
                      bool writeProvenanceInfo=false,
                      bool saveProblemInstance=false);

    boost::shared_ptr<AbstractUntemplatedCardiacProblem> GetSavedProblem();
private:
    bool mSaveProblemInstance;

    boost::shared_ptr<AbstractUntemplatedCardiacProblem> mSavedProblem;
};

#endif /*CARDIACSIMULATION_HPP_*/