AbstractDynamicLinearPdeSolver.hpp

/*

Copyright (c) 2005-2016, 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 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(NULL),
      mMatrixIsAssembled(false),
      mMatrixIsConstant(false),
      mIdealTimeStep(-1.0),
      mLastWorkingTimeStep(-1),
      mpTimeAdaptivityController(NULL),
      mOutputToVtk(false),
      mOutputToParallelVtk(false),
      mOutputToTxt(false),
      mOutputDirectory(""),
      mFilenamePrefix(""),
      mPrintingTimestepMultiple(1),
      mpHdf5Writer(NULL)
{
}

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 != NULL);
    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==NULL))
    {
        EXCEPTION("SetTimeStep() has not been called");
    }
    if (mInitialCondition == NULL)
    {
        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 != NULL)
    {
        delete mpHdf5Writer;
        mpHdf5Writer = NULL;
    }

    // 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 != NULL);
    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_*/