AbstractDynamicAssemblerMixin.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 _ABSTRACTDYNAMICASSEMBLERMIXIN_HPP_
#define _ABSTRACTDYNAMICASSEMBLERMIXIN_HPP_

#include <vector>
#include <petscvec.h>

#include "AbstractAssembler.hpp"
#include "TimeStepper.hpp"
#include "PdeSimulationTime.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractDynamicAssemblerMixin : virtual public AbstractAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>
{
protected:

    double mTstart;

    double mTend;

    double mDt;

    double mDtInverse;

    bool mTimesSet;

    Vec mInitialCondition;

    bool mMatrixIsAssembled;

    bool mMatrixIsConstant;

    bool mUseMatrixBasedRhsAssembly;

    Mat* mpMatrixForMatrixBasedRhsAssembly;

    Vec mVectorForMatrixBasedRhsAssembly;

    void DoMatrixBasedRhsAssembly(Vec currentSolution, double time);

public:

    AbstractDynamicAssemblerMixin();

    void SetTimes(double tStart, double tEnd, double dt);

    void SetInitialCondition(Vec initialCondition);

    void SetMatrixIsConstant(bool matrixIsConstant=true);

    void SetMatrixIsNotAssembled();

    Vec Solve(Vec currentSolutionOrGuess=NULL, double currentTime=0.0);

    virtual void ConstructVectorForMatrixBasedRhsAssembly(Vec currentSolution);

};


// Implementation


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::DoMatrixBasedRhsAssembly(Vec currentSolution, double time)
{
    assert(mpMatrixForMatrixBasedRhsAssembly!=NULL);

    // as bypassing AssembleSystem, need to make sure we call
    // Prepare and Finalize
    this->PrepareForAssembleSystem(currentSolution, time);

    HeartEventHandler::BeginEvent(HeartEventHandler::ASSEMBLE_RHS);

    (*(this->GetLinearSystem()))->ZeroRhsVector();

    // construct z
    ConstructVectorForMatrixBasedRhsAssembly(currentSolution);

    // b = Bz
    MatMult(*mpMatrixForMatrixBasedRhsAssembly, mVectorForMatrixBasedRhsAssembly, (*(this->GetLinearSystem()))->rGetRhsVector());

    // apply boundary conditions
    this->ApplyNeummanBoundaryConditions();
    (*(this->GetLinearSystem()))->AssembleRhsVector();

    this->ApplyDirichletConditions(currentSolution, false);

    // as bypassing AssembleSystem, need to make sure we call
    // Prepare and Finalise
    this->FinaliseAssembleSystem(currentSolution, time);
    (*(this->GetLinearSystem()))->AssembleRhsVector();

    HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractDynamicAssemblerMixin()
    : mTimesSet(false),
      mInitialCondition(NULL),
      mMatrixIsAssembled(false),
      mMatrixIsConstant(false),
      mUseMatrixBasedRhsAssembly(false),
      mpMatrixForMatrixBasedRhsAssembly(NULL)
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetTimes(double tStart, double tEnd, double dt)
{
    mTstart = tStart;
    mTend   = tEnd;

    if (mTstart >= mTend)
    {
        EXCEPTION("Starting time has to less than ending time");
    }

    mDt     = dt;

    if (mDt <= 0)
    {
        EXCEPTION("Time step has to be greater than zero");
    }

    mDtInverse = 1/dt;
    mTimesSet = true;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicAssemblerMixin<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 AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetMatrixIsConstant(bool matrixIsConstant)
{
    mMatrixIsConstant = matrixIsConstant;
    this->SetMatrixIsConst(mMatrixIsConstant);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetMatrixIsNotAssembled()
{
    mMatrixIsAssembled = false;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::Solve(Vec currentSolutionOrGuess, double currentTime)
{
    assert(mTimesSet);
    assert(mInitialCondition != NULL);

    this->PrepareForSolve();
    this->InitialiseForSolve(mInitialCondition);

    TimeStepper stepper(mTstart, mTend, mDt, mMatrixIsConstant);

    Vec current_solution = mInitialCondition;
    Vec next_solution;

    while ( !stepper.IsTimeAtEnd() )
    {
        mDt = stepper.GetNextTimeStep();
        mDtInverse = 1.0/mDt;

        PdeSimulationTime::SetTime(stepper.GetTime());

        // NOTE: even if mUseMatrixBasedRhsAssembly==true,
        // the RHS is assembled without using matrix-based assembly
        // in the first timestep (when the LHS matrix is set up) - no
        // easy way around this
        if (!mUseMatrixBasedRhsAssembly || !mMatrixIsAssembled)
        {
            // matrix is constant case: only assembler matrix the first time
            // matrix is not constant case: always assemble
            bool assemble_matrix = (!mMatrixIsConstant || !mMatrixIsAssembled);

            next_solution = this->StaticSolve(current_solution, stepper.GetTime(), assemble_matrix);
        }
        else
        {
            DoMatrixBasedRhsAssembly(current_solution, stepper.GetTime());
            next_solution = (*(this->GetLinearSystem()))->Solve(current_solution);
        }

        if (mMatrixIsConstant)
        {
            mMatrixIsAssembled = true;
        }

        stepper.AdvanceOneTimeStep();

        // Avoid memory leaks
        if (current_solution != mInitialCondition)
        {
            HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
            VecDestroy(current_solution);
            HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
        }
        current_solution = next_solution;
    }
    return current_solution;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractDynamicAssemblerMixin<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::ConstructVectorForMatrixBasedRhsAssembly(Vec currentSolution)
{
    #define COVERAGE_IGNORE
    EXCEPTION("mUseMatrixBasedRhsAssembly=true but ConstructVectorForMatrixBasedRhsAssembly() has not been overloaded");
    #undef COVERAGE_IGNORE
}

#endif //_ABSTRACTDYNAMICASSEMBLERMIXIN_HPP_