FiniteElementSolver.cpp

/*

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#include <math.h>
#include "SimpleLinearEllipticSolver.hpp"
#include "SimpleNonlinearEllipticSolver.hpp"
#include "SimpleNewtonNonlinearSolver.hpp"
#include "FiniteElementSolver.hpp"

template<unsigned DIM>
FiniteElementSolver<DIM>::FiniteElementSolver()
    : AbstractUnstructuredGridDiscreteContinuumSolver<DIM>(),
      mUseNewton(false),
      mUseLinearSolveForGuess(false),
      mGuess()
{

}

template<unsigned DIM>
FiniteElementSolver<DIM>::~FiniteElementSolver()
{

}

template <unsigned DIM>
boost::shared_ptr<FiniteElementSolver<DIM> > FiniteElementSolver<DIM>::Create()
{
    MAKE_PTR(FiniteElementSolver<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
void FiniteElementSolver<DIM>::Update()
{
    if(this->mpPde)
    {
        this->mpPde->UpdateDiscreteSourceStrengths();
    }
    else
    {
        this->mpNonLinearPde->UpdateDiscreteSourceStrengths();
    }
}

template<unsigned DIM>
void FiniteElementSolver<DIM>::SetGuess(const std::vector<double>& guess)
{
    mGuess = guess;
}

template<unsigned DIM>
void FiniteElementSolver<DIM>::SetUseSimpleNetonSolver(bool useNewton)
{
    mUseNewton = useNewton;
}

template<unsigned DIM>
void FiniteElementSolver<DIM>::SetUseLinearSolveForGuess(bool useLinearSolve)
{
    mUseLinearSolveForGuess = useLinearSolve;
}

template<unsigned DIM>
void FiniteElementSolver<DIM>::Solve()
{
    if(!this->IsSetupForSolve)
    {
        this->Setup();
    }

    // Set up the boundary conditions in the Chaste format
    boost::shared_ptr<BoundaryConditionsContainer<DIM, DIM, 1> > p_bcc =
            boost::shared_ptr<BoundaryConditionsContainer<DIM, DIM, 1> >(new BoundaryConditionsContainer<DIM, DIM, 1> );

    for(unsigned idx=0; idx<this->mBoundaryConditions.size(); idx++)
    {
        this->mBoundaryConditions[idx]->SetMesh(this->mpMesh);
        this->mBoundaryConditions[idx]->UpdateBoundaryConditionContainer(p_bcc);
    }

    // Do the solve
    // Check the type of pde
    if(this->mpPde and !this->mpNonLinearPde)
    {
        this->mpPde->SetUseRegularGrid(false);
        this->mpPde->SetMesh(this->mpMesh);
        this->mpPde->UpdateDiscreteSourceStrengths();

        SimpleLinearEllipticSolver<DIM, DIM> static_solver(this->mpMesh.get(), this->mpPde.get(), p_bcc.get());
        ReplicatableVector solution_repl(static_solver.Solve());

        this->mSolution = std::vector<double>(solution_repl.GetSize());
        this->mConcentrations = std::vector<units::quantity<unit::concentration> >(solution_repl.GetSize());
        for(unsigned idx = 0; idx < solution_repl.GetSize(); idx++)
        {
            this->mSolution[idx] = solution_repl[idx];
            this->mConcentrations[idx] = solution_repl[idx]*this->mReferenceConcentration;
        }
        this->UpdateSolution(this->mSolution);
    }
    else if(this->mpNonLinearPde)
    {
        this->mpNonLinearPde->SetUseRegularGrid(false);
        this->mpNonLinearPde->SetMesh(this->mpMesh);
        this->mpNonLinearPde->UpdateDiscreteSourceStrengths();

        if (this->mpPde)
        {
            this->mpPde->SetUseRegularGrid(false);
            this->mpPde->SetMesh(this->mpMesh);
            this->mpPde->UpdateDiscreteSourceStrengths();

            SimpleLinearEllipticSolver<DIM, DIM> static_solver(this->mpMesh.get(), this->mpPde.get(), p_bcc.get());
            ReplicatableVector static_solution_repl(static_solver.Solve());

            std::vector<double> solution = std::vector<double>(static_solution_repl.GetSize());
            for(unsigned idx = 0; idx < static_solution_repl.GetSize(); idx++)
            {
                solution[idx]= static_solution_repl[idx];
                // Dont want negative solutions going into the initial guess
                if(solution[idx]<0.0)
                {
                    solution[idx] = 0.0;
                }
            }

            Vec initial_guess = PetscTools::CreateVec(this->mpMesh->GetNumNodes());
            for(unsigned idx=0; idx<solution.size();idx++)
            {
                PetscVecTools::SetElement(initial_guess, idx, solution[idx]);
            }
            PetscVecTools::Finalise(initial_guess);

            SimpleNonlinearEllipticSolver<DIM, DIM> solver(this->mpMesh.get(), this->mpNonLinearPde.get(), p_bcc.get());
            SimpleNewtonNonlinearSolver newton_solver;
            if(mUseNewton)
            {
                solver.SetNonlinearSolver(&newton_solver);
                newton_solver.SetTolerance(1e-5);
                newton_solver.SetWriteStats();
            }

            ReplicatableVector solution_repl(solver.Solve(initial_guess));
            this->mSolution = std::vector<double>(solution_repl.GetSize());
            this->mConcentrations = std::vector<units::quantity<unit::concentration> >(solution_repl.GetSize());
            for(unsigned idx = 0; idx < solution_repl.GetSize(); idx++)
            {
                this->mSolution[idx] = solution_repl[idx];
                this->mConcentrations[idx] = solution_repl[idx]*this->mReferenceConcentration;
            }
            this->UpdateSolution(this->mSolution);
            PetscTools::Destroy(initial_guess);
        }
        else
        {
            Vec initial_guess = PetscTools::CreateAndSetVec(this->mpMesh->GetNumNodes(), this->mBoundaryConditions[0]->GetValue()/this->mReferenceConcentration);
            SimpleNonlinearEllipticSolver<DIM, DIM> solver(this->mpMesh.get(), this->mpNonLinearPde.get(), p_bcc.get());
            SimpleNewtonNonlinearSolver newton_solver;
            if(mUseNewton)
            {
                solver.SetNonlinearSolver(&newton_solver);
                newton_solver.SetTolerance(1e-5);
                newton_solver.SetWriteStats();
            }

            ReplicatableVector solution_repl(solver.Solve(initial_guess));
            this->mSolution = std::vector<double>(solution_repl.GetSize());
            this->mConcentrations = std::vector<units::quantity<unit::concentration> >(solution_repl.GetSize());
            for(unsigned idx = 0; idx < solution_repl.GetSize(); idx++)
            {
                this->mSolution[idx] = solution_repl[idx];
                this->mConcentrations[idx] = solution_repl[idx]*this->mReferenceConcentration;
            }
            this->UpdateSolution(this->mSolution);
            PetscTools::Destroy(initial_guess);
        }
    }
    else
    {
        EXCEPTION("PDE Type could not be identified, did you set a PDE?");
    }

    if(this->mWriteSolution)
    {
        this->Write();
    }
}

// Explicit instantiation
template class FiniteElementSolver<2> ;
template class FiniteElementSolver<3> ;