CellBasedPdeSolver.cpp

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*/

#include "CellBasedPdeSolver.hpp"
#include "TetrahedralMesh.hpp"
#include "SimpleLinearEllipticSolver.hpp"

template<unsigned DIM>
CellBasedPdeSolver<DIM>::CellBasedPdeSolver(TetrahedralMesh<DIM,DIM>* pMesh,
                              AbstractLinearEllipticPde<DIM,DIM>* pPde,
                              BoundaryConditionsContainer<DIM,DIM,1>* pBoundaryConditions)
     : SimpleLinearEllipticSolver<DIM, DIM>(pMesh, pPde, pBoundaryConditions)
{
}

template<unsigned DIM>
CellBasedPdeSolver<DIM>::~CellBasedPdeSolver()
{
}

template<unsigned DIM>
c_vector<double, 1*(DIM+1)> CellBasedPdeSolver<DIM>::ComputeVectorTerm(
        c_vector<double, DIM+1>& rPhi,
        c_matrix<double, DIM, DIM+1>& rGradPhi,
        ChastePoint<DIM>& rX,
        c_vector<double, 1>& rU,
        c_matrix<double, 1, DIM>& rGradU /* not used */,
        Element<DIM, DIM>* pElement)
{
    return mConstantInUSourceTerm * rPhi;
}

template<unsigned DIM>
c_matrix<double, 1*(DIM+1), 1*(DIM+1)> CellBasedPdeSolver<DIM>::ComputeMatrixTerm(
        c_vector<double, DIM+1>& rPhi,
        c_matrix<double, DIM, DIM+1>& rGradPhi,
        ChastePoint<DIM>& rX,
        c_vector<double, 1>& rU,
        c_matrix<double, 1, DIM>& rGradU,
        Element<DIM, DIM>* pElement)
{
    c_matrix<double, DIM, DIM> pde_diffusion_term = this->mpEllipticPde->ComputeDiffusionTerm(rX);

    // This if statement just saves computing phi*phi^T if it is to be multiplied by zero
    if (mLinearInUCoeffInSourceTerm != 0)
    {
        return   prod( trans(rGradPhi), c_matrix<double, DIM, DIM+1>(prod(pde_diffusion_term, rGradPhi)) )
               - mLinearInUCoeffInSourceTerm * outer_prod(rPhi,rPhi);
    }
    else
    {
        return   prod( trans(rGradPhi), c_matrix<double, DIM, DIM+1>(prod(pde_diffusion_term, rGradPhi)) );
    }
}

template<unsigned DIM>
void CellBasedPdeSolver<DIM>::ResetInterpolatedQuantities()
{
    mConstantInUSourceTerm = 0;
    mLinearInUCoeffInSourceTerm = 0;
}

template<unsigned DIM>
void CellBasedPdeSolver<DIM>::IncrementInterpolatedQuantities(double phiI, const Node<DIM>* pNode)
{
    mConstantInUSourceTerm += phiI * this->mpEllipticPde->ComputeConstantInUSourceTermAtNode(*pNode);
    mLinearInUCoeffInSourceTerm += phiI * this->mpEllipticPde->ComputeLinearInUCoeffInSourceTermAtNode(*pNode);
}

template<unsigned DIM>
void CellBasedPdeSolver<DIM>::InitialiseForSolve(Vec initialSolution)
{
    // Linear system created here
    SimpleLinearEllipticSolver<DIM,DIM>::InitialiseForSolve(initialSolution);

    this->mpLinearSystem->SetMatrixIsSymmetric(true);
}

// Explicit instantiation

template class CellBasedPdeSolver<1>;
template class CellBasedPdeSolver<2>;
template class CellBasedPdeSolver<3>;