CardiacSimulation.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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_*/