CardiacSimulation.hpp

/*
 
Copyright (c) 2005-2024, University of Oxford.
All rights reserved.
 
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.
 
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#ifndef CARDIACSIMULATION_HPP_
#define CARDIACSIMULATION_HPP_
 
#include <vector>
#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 "PostProcessingWriter.hpp"
 
#include "OutputDirectoryFifoQueue.hpp"
#include "ExecutableSupport.hpp"
 
class CardiacSimulation
{
private:
    void ReadParametersFromFile(std::string parameterFileName);
 
    template<class Problem, unsigned SPACE_DIM>
    void CreateAndRun()
    {
        boost::shared_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).
                char time_stamp[60]; // Write out without scientific notation in time - ticket 2861
 
                // Here we cope with times of up to 16 significant figures, which should be OK without floating-point crazy decimal places like 1.000000000000000000000000000000000001
                std::sprintf(time_stamp,"%0.16g",HeartConfig::Instance()->GetSimulationDuration());
 
                std::stringstream archive_foldername;
                archive_foldername << HeartConfig::Instance()->GetOutputDirectory() << "_" << time_stamp << "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);
 
                TRY_IF_MASTER(
                        partial_output_dir_handler.FindFile("").CopyTo(checkpoint_dir_basename_handler.FindFile(""));
                );
 
                // 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_*/