AbstractDynamicLinearPdeSolver.hpp

 
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#ifndef ABSTRACTDYNAMICLINEARPDESOLVER_HPP_
#define ABSTRACTDYNAMICLINEARPDESOLVER_HPP_
 
#include "Exception.hpp"
#include "TimeStepper.hpp"
#include "AbstractLinearPdeSolver.hpp"
#include "PdeSimulationTime.hpp"
#include "AbstractTimeAdaptivityController.hpp"
#include "Hdf5DataWriter.hpp"
#include "Hdf5ToVtkConverter.hpp"
#include "Hdf5ToTxtConverter.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractDynamicLinearPdeSolver : public AbstractLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>
{
    friend class TestSimpleLinearParabolicSolver;
protected:
 
    double mTstart;
 
    double mTend;
 
    bool mTimesSet;
 
    Vec mInitialCondition;
 
    bool mMatrixIsAssembled;
 
    bool mMatrixIsConstant;
 
    double mIdealTimeStep;
 
    double mLastWorkingTimeStep;
 
    AbstractTimeAdaptivityController* mpTimeAdaptivityController;
 
    bool mOutputToVtk;
 
    bool mOutputToParallelVtk;
 
    bool mOutputToTxt;
 
    std::string mOutputDirectory;
 
    std::string mFilenamePrefix;
 
    unsigned mPrintingTimestepMultiple;
 
    Hdf5DataWriter* mpHdf5Writer;
 
    std::vector<int> mVariableColumnIds;
 
    void InitialiseHdf5Writer();
 
    void WriteOneStep(double time, Vec solution);
 
public:
 
    AbstractDynamicLinearPdeSolver(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh);
 
    void SetTimes(double tStart, double tEnd);
 
    void SetTimeStep(double dt);
 
    void SetInitialCondition(Vec initialCondition);
 
    virtual Vec Solve();
 
    void SetMatrixIsNotAssembled();
 
    void SetTimeAdaptivityController(AbstractTimeAdaptivityController* pTimeAdaptivityController);
 
    void SetOutputToVtk(bool output);
 
    void SetOutputToParallelVtk(bool output);
 
    void SetOutputToTxt(bool output);
 
    void SetOutputDirectoryAndPrefix(std::string outputDirectory, std::string prefix);
 
    void SetPrintingTimestepMultiple(unsigned multiple);
};
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::InitialiseHdf5Writer()
{
    // Check that everything is set up correctly
    if ((mOutputDirectory=="") || (mFilenamePrefix==""))
    {
        EXCEPTION("Output directory or filename prefix has not been set");
    }
 
    // Create writer
    mpHdf5Writer = new Hdf5DataWriter(*(this->mpMesh)->GetDistributedVectorFactory(),
                                      mOutputDirectory,
                                      mFilenamePrefix);
 
    // Set writer to output all nodes
    mpHdf5Writer->DefineFixedDimension((this->mpMesh)->GetNumNodes());
 
    // Only used to get an estimate of the number of timesteps below
    unsigned estimated_num_printing_timesteps = 1u + (unsigned)((mTend - mTstart)/(mIdealTimeStep*mPrintingTimestepMultiple));
 
    assert(mVariableColumnIds.empty());
    for (unsigned i=0; i<PROBLEM_DIM; i++)
    {
        std::stringstream variable_name;
        variable_name << "Variable_" << i;
        mVariableColumnIds.push_back(mpHdf5Writer->DefineVariable(variable_name.str(),"undefined"));
    }
    mpHdf5Writer->DefineUnlimitedDimension("Time", "undefined", estimated_num_printing_timesteps);
 
    // End the define mode of the writer
    mpHdf5Writer->EndDefineMode();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractDynamicLinearPdeSolver(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
    : AbstractLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>(pMesh),
      mTimesSet(false),
      mInitialCondition(nullptr),
      mMatrixIsAssembled(false),
      mMatrixIsConstant(false),
      mIdealTimeStep(-1.0),
      mLastWorkingTimeStep(-1),
      mpTimeAdaptivityController(nullptr),
      mOutputToVtk(false),
      mOutputToParallelVtk(false),
      mOutputToTxt(false),
      mOutputDirectory(""),
      mFilenamePrefix(""),
      mPrintingTimestepMultiple(1),
      mpHdf5Writer(nullptr)
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetTimes(double tStart, double tEnd)
{
    mTstart = tStart;
    mTend = tEnd;
 
    if (mTstart >= mTend)
    {
        EXCEPTION("Start time has to be less than end time");
    }
 
    mTimesSet = true;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetTimeStep(double dt)
{
    if (dt <= 0)
    {
        EXCEPTION("Time step has to be greater than zero");
    }
 
    mIdealTimeStep = dt;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetInitialCondition(Vec initialCondition)
{
    assert(initialCondition != nullptr);
    mInitialCondition = initialCondition;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::WriteOneStep(double time, Vec solution)
{
    mpHdf5Writer->PutUnlimitedVariable(time);
    if (PROBLEM_DIM == 1)
    {
        mpHdf5Writer->PutVector(mVariableColumnIds[0], solution);
    }
    else
    {
        mpHdf5Writer->PutStripedVector(mVariableColumnIds, solution);
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::Solve()
{
    // Begin by checking that everything has been set up correctly
    if (!mTimesSet)
    {
        EXCEPTION("SetTimes() has not been called");
    }
    if ((mIdealTimeStep <= 0.0) && (mpTimeAdaptivityController==nullptr))
    {
        EXCEPTION("SetTimeStep() has not been called");
    }
    if (mInitialCondition == nullptr)
    {
        EXCEPTION("SetInitialCondition() has not been called");
    }
 
    // If required, initialise HDF5 writer and output initial condition to HDF5 file
    bool print_output = (mOutputToVtk || mOutputToParallelVtk || mOutputToTxt);
    if (print_output)
    {
        InitialiseHdf5Writer();
        WriteOneStep(mTstart, mInitialCondition);
        mpHdf5Writer->AdvanceAlongUnlimitedDimension();
    }
 
    this->InitialiseForSolve(mInitialCondition);
 
    if (mIdealTimeStep < 0) // hasn't been set, so a controller must have been given
    {
        mIdealTimeStep = mpTimeAdaptivityController->GetNextTimeStep(mTstart, mInitialCondition);
    }
 
    /*
     * Note: we use the mIdealTimeStep here (the original timestep that was passed in, or
     * the last timestep suggested by the controller), rather than the last timestep used
     * (mLastWorkingTimeStep), because the timestep will be very slightly altered by the
     * stepper in the final timestep of the last printing-timestep-loop, and these floating
     * point errors can add up and eventually cause exceptions being thrown.
     */
    TimeStepper stepper(mTstart, mTend, mIdealTimeStep, mMatrixIsConstant);
 
    Vec solution = mInitialCondition;
    Vec next_solution;
 
    while (!stepper.IsTimeAtEnd())
    {
        bool timestep_changed = false;
 
        PdeSimulationTime::SetTime(stepper.GetTime());
 
        // Determine timestep to use
        double new_dt;
        if (mpTimeAdaptivityController)
        {
            // Get the timestep the controller wants to use and store it as the ideal timestep
            mIdealTimeStep = mpTimeAdaptivityController->GetNextTimeStep(stepper.GetTime(), solution);
 
            // Tell the stepper to use this timestep from now on...
            stepper.ResetTimeStep(mIdealTimeStep);
 
            // ..but now get the timestep from the stepper, as the stepper might need
            // to trim the timestep if it would take us over the end time
            new_dt = stepper.GetNextTimeStep();
            // Changes in timestep bigger than 0.001% will trigger matrix re-computation
            timestep_changed = (fabs(new_dt/mLastWorkingTimeStep - 1.0) > 1e-5);
        }
        else
        {
            new_dt = stepper.GetNextTimeStep();
 
            //new_dt should be roughly the same size as mIdealTimeStep - we should never need to take a tiny step
 
            if (mMatrixIsConstant && fabs(new_dt/mIdealTimeStep - 1.0) > 1e-5)
            {
                // Here we allow for changes of up to 0.001%
                // Note that the TimeStepper guarantees that changes in dt are no bigger than DBL_EPSILON*current_time
                NEVER_REACHED;
            }
        }
 
        // Save the timestep as the last one use, and also put it in PdeSimulationTime
        // so everyone can see it
        mLastWorkingTimeStep = new_dt;
        PdeSimulationTime::SetPdeTimeStepAndNextTime(new_dt, stepper.GetNextTime());
 
        // Solve
        try
        {
            // (This runs the cell ODE models in heart simulations)
            this->PrepareForSetupLinearSystem(solution);
        }
        catch(Exception& e)
        {
            // We only need to clean up memory if we are NOT on the first PDE time step,
            // as someone else cleans up the mInitialCondition vector in higher classes.
            if (solution != mInitialCondition)
            {
                HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
                PetscTools::Destroy(solution);
                HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
            }
            throw e;
        }
 
        bool compute_matrix = (!mMatrixIsConstant || !mMatrixIsAssembled || timestep_changed);
 
        this->SetupLinearSystem(solution, compute_matrix);
 
        this->FinaliseLinearSystem(solution);
 
        if (compute_matrix)
        {
            this->mpLinearSystem->ResetKspSolver();
        }
 
        next_solution = this->mpLinearSystem->Solve(solution);
 
        if (mMatrixIsConstant)
        {
            mMatrixIsAssembled = true;
        }
 
        this->FollowingSolveLinearSystem(next_solution);
 
        stepper.AdvanceOneTimeStep();
 
        // Avoid memory leaks
        if (solution != mInitialCondition)
        {
            HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
            PetscTools::Destroy(solution);
            HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
        }
        solution = next_solution;
 
        // If required, output next solution to HDF5 file
        if (print_output && (stepper.GetTotalTimeStepsTaken()%mPrintingTimestepMultiple == 0) )
        {
            WriteOneStep(stepper.GetTime(), solution);
            mpHdf5Writer->AdvanceAlongUnlimitedDimension();
        }
    }
 
    // Avoid memory leaks
    if (mpHdf5Writer != nullptr)
    {
        delete mpHdf5Writer;
        mpHdf5Writer = nullptr;
    }
 
    // Convert HDF5 output to other formats as required
 
    if (mOutputToVtk)
    {
        Hdf5ToVtkConverter<ELEMENT_DIM,SPACE_DIM> converter(FileFinder(mOutputDirectory, RelativeTo::ChasteTestOutput),
                                                            mFilenamePrefix, this->mpMesh, false, false);
    }
    if (mOutputToParallelVtk)
    {
        Hdf5ToVtkConverter<ELEMENT_DIM,SPACE_DIM> converter(FileFinder(mOutputDirectory, RelativeTo::ChasteTestOutput),
                                                            mFilenamePrefix, this->mpMesh, true, false);
    }
    if (mOutputToTxt)
    {
        Hdf5ToTxtConverter<ELEMENT_DIM,SPACE_DIM> converter(FileFinder(mOutputDirectory, RelativeTo::ChasteTestOutput),
                                                            mFilenamePrefix, this->mpMesh);
    }
 
    return solution;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetMatrixIsNotAssembled()
{
    mMatrixIsAssembled = false;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetTimeAdaptivityController(AbstractTimeAdaptivityController* pTimeAdaptivityController)
{
    assert(pTimeAdaptivityController != nullptr);
    assert(mpTimeAdaptivityController == NULL);
    mpTimeAdaptivityController = pTimeAdaptivityController;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetOutputToVtk(bool output)
{
    mOutputToVtk = output;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetOutputToParallelVtk(bool output)
{
    mOutputToParallelVtk = output;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetOutputToTxt(bool output)
{
    mOutputToTxt = output;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetOutputDirectoryAndPrefix(std::string outputDirectory, std::string prefix)
{
    mOutputDirectory = outputDirectory;
    mFilenamePrefix = prefix;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetPrintingTimestepMultiple(unsigned multiple)
{
    mPrintingTimestepMultiple = multiple;
}
 
#endif /*ABSTRACTDYNAMICLINEARPDESOLVER_HPP_*/