PlaneBoundaryCondition.cpp

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#include "PlaneBoundaryCondition.hpp"
#include "AbstractCentreBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "RandomNumberGenerator.hpp"

template<unsigned DIM>
PlaneBoundaryCondition<DIM>::PlaneBoundaryCondition(AbstractCellPopulation<DIM>* pCellPopulation,
                                                    c_vector<double, DIM> point,
                                                    c_vector<double, DIM> normal)
        : AbstractCellPopulationBoundaryCondition<DIM>(pCellPopulation),
          mPointOnPlane(point),
          mUseJiggledNodesOnPlane(false)
{
    assert(norm_2(normal) > 0.0);
    mNormalToPlane = normal/norm_2(normal);
}

template<unsigned DIM>
const c_vector<double, DIM>& PlaneBoundaryCondition<DIM>::rGetPointOnPlane() const
{
    return mPointOnPlane;
}

template<unsigned DIM>
const c_vector<double, DIM>& PlaneBoundaryCondition<DIM>::rGetNormalToPlane() const
{
    return mNormalToPlane;
}


template<unsigned DIM>
void PlaneBoundaryCondition<DIM>::SetUseJiggledNodesOnPlane(bool useJiggledNodesOnPlane)
{
    mUseJiggledNodesOnPlane = useJiggledNodesOnPlane;
}

template<unsigned DIM>
bool PlaneBoundaryCondition<DIM>::GetUseJiggledNodesOnPlane()
{
    return mUseJiggledNodesOnPlane;
}

template<unsigned DIM>
void PlaneBoundaryCondition<DIM>::ImposeBoundaryCondition(const std::map<Node<DIM>*, c_vector<double, DIM> >& rOldLocations)
{
    if (dynamic_cast<AbstractOffLatticeCellPopulation<DIM>*>(this->mpCellPopulation)==NULL)
    {
        EXCEPTION("PlaneBoundaryCondition requires a subclass of AbstractOffLatticeCellPopulation.");
    }

    assert((dynamic_cast<AbstractCentreBasedCellPopulation<DIM>*>(this->mpCellPopulation))
            || (dynamic_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation)) );

    // THis is a magic number.
    double max_jiggle = 1e-4;

    if (DIM != 1)
    {
        if (dynamic_cast<AbstractCentreBasedCellPopulation<DIM>*>(this->mpCellPopulation))
        {
            for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
                 cell_iter != this->mpCellPopulation->End();
                 ++cell_iter)
            {
                unsigned node_index = this->mpCellPopulation->GetLocationIndexUsingCell(*cell_iter);
                Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);

                c_vector<double, DIM> node_location = p_node->rGetLocation();

                double signed_distance = inner_prod(node_location - mPointOnPlane, mNormalToPlane);
                if (signed_distance > 0.0)
                {
                    // For the closest point on the plane we travel from node_location the signed_distance in the direction of -mNormalToPlane
                    c_vector<double, DIM> nearest_point;
                    if (mUseJiggledNodesOnPlane)
                    {
                        nearest_point = node_location - (signed_distance+max_jiggle*RandomNumberGenerator::Instance()->ranf())*mNormalToPlane;
                    }
                    else
                    {
                        nearest_point = node_location - signed_distance*mNormalToPlane;
                    }
                    p_node->rGetModifiableLocation() = nearest_point;
                }
            }
        }
        else
        {
            assert(dynamic_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation));

            VertexBasedCellPopulation<DIM>* pStaticCastCellPopulation = static_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation);

            // Iterate over all nodes and update their positions according to the boundary conditions
            unsigned num_nodes = pStaticCastCellPopulation->GetNumNodes();
            for (unsigned node_index=0; node_index<num_nodes; node_index++)
            {
                Node<DIM>* p_node = pStaticCastCellPopulation->GetNode(node_index);
                c_vector<double, DIM> node_location = p_node->rGetLocation();

                double signed_distance = inner_prod(node_location - mPointOnPlane, mNormalToPlane);
                if (signed_distance > 0.0)
                {
                    // For the closest point on the plane we travel from node_location the signed_distance in the direction of -mNormalToPlane
                    c_vector<double, DIM> nearest_point;
                    if (mUseJiggledNodesOnPlane)
                    {
                        nearest_point = node_location - (signed_distance+max_jiggle*RandomNumberGenerator::Instance()->ranf())*mNormalToPlane;
                    }
                    else
                    {
                        nearest_point = node_location - signed_distance*mNormalToPlane;
                    }
                    p_node->rGetModifiableLocation() = nearest_point;
                }
            }
        }
    }
    else
    {
        // DIM == 1
        NEVER_REACHED;
        //PlaneBoundaryCondition::ImposeBoundaryCondition is not implemented in 1D
    }
}

template<unsigned DIM>
bool PlaneBoundaryCondition<DIM>::VerifyBoundaryCondition()
{
    bool condition_satisfied = true;

    if (DIM == 1)
    {
        EXCEPTION("PlaneBoundaryCondition is not implemented in 1D");
    }
    else
    {
        for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
             cell_iter != this->mpCellPopulation->End();
             ++cell_iter)
        {
            c_vector<double, DIM> cell_location = this->mpCellPopulation->GetLocationOfCellCentre(*cell_iter);

            if (inner_prod(cell_location - mPointOnPlane, mNormalToPlane) > 0.0)
            {
                condition_satisfied = false;
                break;
            }
        }
    }

    return condition_satisfied;
}

template<unsigned DIM>
void PlaneBoundaryCondition<DIM>::OutputCellPopulationBoundaryConditionParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<PointOnPlane>";
    for (unsigned index=0; index != DIM-1U; index++) // Note: inequality avoids testing index < 0U when DIM=1
    {
        *rParamsFile << mPointOnPlane[index] << ",";
    }
    *rParamsFile << mPointOnPlane[DIM-1] << "</PointOnPlane>\n";

    *rParamsFile << "\t\t\t<NormalToPlane>";
    for (unsigned index=0; index != DIM-1U; index++) // Note: inequality avoids testing index < 0U when DIM=1
    {
        *rParamsFile << mNormalToPlane[index] << ",";
    }
    *rParamsFile << mNormalToPlane[DIM-1] << "</NormalToPlane>\n";
    *rParamsFile << "\t\t\t<UseJiggledNodesOnPlane>" << mUseJiggledNodesOnPlane << "</UseJiggledNodesOnPlane>\n";

    // Call method on direct parent class
    AbstractCellPopulationBoundaryCondition<DIM>::OutputCellPopulationBoundaryConditionParameters(rParamsFile);
}

// Explicit instantiation

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

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