CellBasedPdeHandlerOnCuboid.cpp

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*/

#include "CellBasedPdeHandlerOnCuboid.hpp"
#include "ConstBoundaryCondition.hpp"

template<unsigned DIM>
CellBasedPdeHandlerOnCuboid<DIM>::CellBasedPdeHandlerOnCuboid(AbstractCellPopulation<DIM>* pCellPopulation,
                                              bool deleteMemberPointersInDestructor)
    : CellBasedPdeHandler<DIM>(pCellPopulation, deleteMemberPointersInDestructor)
{
}

template<unsigned DIM>
CellBasedPdeHandlerOnCuboid<DIM>::~CellBasedPdeHandlerOnCuboid()
{
    // Delete all boundary conditions
    for (unsigned i=0; i<mConstBoundaryConditions.size(); i++)
    {
        delete mConstBoundaryConditions[i];
    }
}

template<unsigned DIM>
std::auto_ptr<BoundaryConditionsContainer<DIM,DIM,1> > CellBasedPdeHandlerOnCuboid<DIM>::ConstructBoundaryConditionsContainer(
        PdeAndBoundaryConditions<DIM>* pPdeAndBc,
        TetrahedralMesh<DIM,DIM>* pMesh)
{
    // Not using the inputs as there's only one BC
    assert(DIM==2);

    std::auto_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,1>(false));

    // Use these two vectors to define what's happening on the top right bottom and left boundaries

    // Specify which sides are Neumann boundaries
    c_vector<bool,4> are_neumann_boundaries;
    are_neumann_boundaries[0] = false; // Top
    are_neumann_boundaries[1] = true;  // Right
    are_neumann_boundaries[2] = false; // Bottom
    are_neumann_boundaries[3] = true;  // Left

    // Specify the value of the boundary condition on each boundary
    c_vector<double,4> boundary_condition_values;
    boundary_condition_values[0] = 1.0; // Top
    boundary_condition_values[1] = 1.0; // Right
    boundary_condition_values[2] = 1.0; // Bottom
    boundary_condition_values[3] = 1.0; // Left

    // Delete all previous boundary conditions
    for (unsigned i=0; i<mConstBoundaryConditions.size(); i++)
    {
        delete mConstBoundaryConditions[i];
    }
    mConstBoundaryConditions.clear();

    mConstBoundaryConditions.push_back(new ConstBoundaryCondition<DIM>(boundary_condition_values[0]));
    mConstBoundaryConditions.push_back(new ConstBoundaryCondition<DIM>(boundary_condition_values[1]));
    mConstBoundaryConditions.push_back(new ConstBoundaryCondition<DIM>(boundary_condition_values[2]));
    mConstBoundaryConditions.push_back(new ConstBoundaryCondition<DIM>(boundary_condition_values[3]));

    ChasteCuboid<DIM> cuboid = pMesh->CalculateBoundingBox();

    double left = cuboid.rGetLowerCorner()[0];
    double bottom = cuboid.rGetLowerCorner()[1];
    double right = cuboid.rGetUpperCorner()[0];
    double top = cuboid.rGetUpperCorner()[1];
    double fudge_factor = 1e-6;

    // Apply Neumann boundary conditions
    for (typename TetrahedralMesh<DIM,DIM>::BoundaryElementIterator elem_iter = pMesh->GetBoundaryElementIteratorBegin();
         elem_iter != pMesh->GetBoundaryElementIteratorEnd();
         ++elem_iter)
    {
        double x_1 = (*elem_iter)->GetNodeLocation(0)[0];
//        double y_1 = (*elem_iter)->GetNodeLocation(0)[1];
        double x_2 = (*elem_iter)->GetNodeLocation(1)[0];
//        double y_2 = (*elem_iter)->GetNodeLocation(1)[1];

        assert(!are_neumann_boundaries[0]);
//        if (are_neumann_boundaries[0]) // Top is Neumann boundary
//        {
//            if ( (y_1  > (top-fudge_factor) ) &&  (y_2 > (top-fudge_factor) ))
//            {
//                p_bcc->AddNeumannBoundaryCondition(*elem_iter, mConstBoundaryConditions[0]);
//            }
//        }
        if (are_neumann_boundaries[1]) // Right is Neumann boundary
        {
            if ( (x_1  > (right-fudge_factor) ) &&  (x_2 > (right-fudge_factor) ))
            {
                p_bcc->AddNeumannBoundaryCondition(*elem_iter, mConstBoundaryConditions[1]);
            }
        }
        assert(!are_neumann_boundaries[2]);
//        if (are_neumann_boundaries[2]) // Bottom is Neumann boundary
//        {
//            if ( (y_1  < (bottom+fudge_factor) ) &&  (y_2 < (bottom+fudge_factor) ))
//            {
//                p_bcc->AddNeumannBoundaryCondition(*elem_iter, mConstBoundaryConditions[2]);
//            }
//        }
        if (are_neumann_boundaries[3]) // Left is Neumann Boundary
        {
            if ( (x_1  > (left+fudge_factor) ) &&  (x_2 < (left+fudge_factor) ))
            {
                p_bcc->AddNeumannBoundaryCondition(*elem_iter, mConstBoundaryConditions[3]);
            }
        }
    }


    // Apply dirichlet Boundaries
    for (typename TetrahedralMesh<DIM,DIM>::BoundaryNodeIterator node_iter = pMesh->GetBoundaryNodeIteratorBegin();
         node_iter != pMesh->GetBoundaryNodeIteratorEnd();
         ++node_iter)
    {
//        double x = (*node_iter)->GetPoint()[0];
        double y = (*node_iter)->GetPoint()[1];

        if (!are_neumann_boundaries[0]) // Top is Dirichlet boundary
        {
            if (y > top-fudge_factor)
            {
                p_bcc->AddDirichletBoundaryCondition(*node_iter, mConstBoundaryConditions[0]);
            }
        }
        assert(are_neumann_boundaries[1]);
//        if (!are_neumann_boundaries[1]) // Right is Dirichlet boundary
//        {
//            if (x > right-fudge_factor)
//            {
//                p_bcc->AddDirichletBoundaryCondition(*node_iter, mConstBoundaryConditions[1]);
//            }
//        }
        if (!are_neumann_boundaries[2]) // Bottom is Dirichlet boundary
        {
            if (y < bottom+fudge_factor)
            {
                p_bcc->AddDirichletBoundaryCondition(*node_iter, mConstBoundaryConditions[2]);
            }
        }
        assert(are_neumann_boundaries[3]);
//        if (!are_neumann_boundaries[3]) // Left is Dirichlet boundary
//        {
//            if (x < left+fudge_factor)
//            {
//                p_bcc->AddDirichletBoundaryCondition(*node_iter, mConstBoundaryConditions[3]);
//            }
//        }
    }

    return p_bcc;
}

template<unsigned DIM>
void CellBasedPdeHandlerOnCuboid<DIM>::OutputParameters(out_stream& rParamsFile)
{
    CellBasedPdeHandler<DIM>::OutputParameters(rParamsFile);
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CellBasedPdeHandlerOnCuboid)


// Explicit instantiation

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