MeshBasedCellPopulationWithGhostNodes.cpp

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#include "MeshBasedCellPopulationWithGhostNodes.hpp"

// Cell writers
#include "CellAgesWriter.hpp"
#include "CellAncestorWriter.hpp"
#include "CellProliferativePhasesWriter.hpp"
#include "CellProliferativeTypesWriter.hpp"
#include "CellVolumesWriter.hpp"
#include "CellLocationIndexWriter.hpp"

// Cell population writers
#include "CellMutationStatesCountWriter.hpp"

template<unsigned DIM>
MeshBasedCellPopulationWithGhostNodes<DIM>::MeshBasedCellPopulationWithGhostNodes(
     MutableMesh<DIM, DIM>& rMesh,
     std::vector<CellPtr>& rCells,
     const std::vector<unsigned> locationIndices,
     bool deleteMesh,
     double ghostSpringStiffness)
             : MeshBasedCellPopulation<DIM,DIM>(rMesh, rCells, locationIndices, deleteMesh, false), // do not call the base class Validate()
               mGhostSpringStiffness(ghostSpringStiffness)
{
    if (!locationIndices.empty())
    {
        // Create a set of node indices corresponding to ghost nodes
        std::set<unsigned> node_indices;
        std::set<unsigned> location_indices;
        std::set<unsigned> ghost_node_indices;

        for (unsigned i=0; i<this->GetNumNodes(); i++)
        {
            node_indices.insert(this->GetNode(i)->GetIndex());
        }
        for (unsigned i=0; i<locationIndices.size(); i++)
        {
            location_indices.insert(locationIndices[i]);
        }

        std::set_difference(node_indices.begin(), node_indices.end(),
                            location_indices.begin(), location_indices.end(),
                            std::inserter(ghost_node_indices, ghost_node_indices.begin()));

        // This method finishes and then calls Validate()
        SetGhostNodes(ghost_node_indices);
    }
    else
    {
        this->mIsGhostNode = std::vector<bool>(this->GetNumNodes(), false);
        Validate();
    }
}

template<unsigned DIM>
MeshBasedCellPopulationWithGhostNodes<DIM>::MeshBasedCellPopulationWithGhostNodes(MutableMesh<DIM, DIM>& rMesh,
                                                                  double ghostSpringStiffness)
             : MeshBasedCellPopulation<DIM,DIM>(rMesh),
               mGhostSpringStiffness(ghostSpringStiffness)
{
}

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

template<unsigned DIM>
std::vector<bool>& MeshBasedCellPopulationWithGhostNodes<DIM>::rGetGhostNodes()
{
    return this->mIsGhostNode;
}

template<unsigned DIM>
bool MeshBasedCellPopulationWithGhostNodes<DIM>::IsGhostNode(unsigned index)
{
    return this->mIsGhostNode[index];
}

template<unsigned DIM>
std::set<unsigned> MeshBasedCellPopulationWithGhostNodes<DIM>::GetGhostNodeIndices()
{
    std::set<unsigned> ghost_node_indices;
    for (unsigned i=0; i<this->mIsGhostNode.size(); i++)
    {
        if (this->mIsGhostNode[i])
        {
            ghost_node_indices.insert(i);
        }
    }
    return ghost_node_indices;
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::SetGhostNodes(const std::set<unsigned>& rGhostNodeIndices)
{
    // Reinitialise all entries of mIsGhostNode to false
    this->mIsGhostNode = std::vector<bool>(this->mrMesh.GetNumNodes(), false);

    // Update mIsGhostNode
    for (std::set<unsigned>::iterator iter=rGhostNodeIndices.begin(); iter!=rGhostNodeIndices.end(); ++iter)
    {
        this->mIsGhostNode[*iter] = true;
    }

    Validate();
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::UpdateGhostPositions(double dt)
{
    // Initialise vector of forces on ghost nodes
    std::vector<c_vector<double, DIM> > drdt(this->GetNumNodes());
    for (unsigned i=0; i<drdt.size(); i++)
    {
        drdt[i] = zero_vector<double>(DIM);
    }

    // Calculate forces on ghost nodes
    for (typename MutableMesh<DIM, DIM>::EdgeIterator edge_iterator = static_cast<MutableMesh<DIM, DIM>&>((this->mrMesh)).EdgesBegin();
        edge_iterator != static_cast<MutableMesh<DIM, DIM>&>((this->mrMesh)).EdgesEnd();
        ++edge_iterator)
    {
        unsigned nodeA_global_index = edge_iterator.GetNodeA()->GetIndex();
        unsigned nodeB_global_index = edge_iterator.GetNodeB()->GetIndex();

        c_vector<double, DIM> force = CalculateForceBetweenGhostNodes(nodeA_global_index, nodeB_global_index);

        double damping_constant = this->GetDampingConstantNormal();

        if (!this->mIsGhostNode[nodeA_global_index])
        {
            drdt[nodeB_global_index] -= force / damping_constant;
        }
        else
        {
            drdt[nodeA_global_index] += force / damping_constant;

            if (this->mIsGhostNode[nodeB_global_index])
            {
                drdt[nodeB_global_index] -= force / damping_constant;
            }
        }
    }

    for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
         node_iter != this->mrMesh.GetNodeIteratorEnd();
         ++node_iter)
    {
        unsigned node_index = node_iter->GetIndex();
        if (this->mIsGhostNode[node_index])
        {
            ChastePoint<DIM> new_point(node_iter->rGetLocation() + dt*drdt[node_index]);
            static_cast<MutableMesh<DIM, DIM>&>((this->mrMesh)).SetNode(node_index, new_point, false);
        }
    }
}

template<unsigned DIM>
c_vector<double, DIM> MeshBasedCellPopulationWithGhostNodes<DIM>::CalculateForceBetweenGhostNodes(const unsigned& rNodeAGlobalIndex, const unsigned& rNodeBGlobalIndex)
{
    assert(rNodeAGlobalIndex != rNodeBGlobalIndex);
    c_vector<double, DIM> unit_difference;
    c_vector<double, DIM> node_a_location = this->GetNode(rNodeAGlobalIndex)->rGetLocation();
    c_vector<double, DIM> node_b_location = this->GetNode(rNodeBGlobalIndex)->rGetLocation();

    // There is reason not to subtract one position from the other (cylindrical meshes)
    unit_difference = this->mrMesh.GetVectorFromAtoB(node_a_location, node_b_location);

    double distance_between_nodes = norm_2(unit_difference);
    unit_difference /= distance_between_nodes;

    double rest_length = 1.0;

    return mGhostSpringStiffness * unit_difference * (distance_between_nodes - rest_length);
}

template<unsigned DIM>
CellPtr MeshBasedCellPopulationWithGhostNodes<DIM>::AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell)
{
    // Add new cell to cell population
    CellPtr p_created_cell = MeshBasedCellPopulation<DIM,DIM>::AddCell(pNewCell, rCellDivisionVector, pParentCell);
    assert(p_created_cell == pNewCell);

    // Update size of mIsGhostNode if necessary
    unsigned new_node_index = this->GetLocationIndexUsingCell(p_created_cell);

    if (this->GetNumNodes() > this->mIsGhostNode.size())
    {
        this->mIsGhostNode.resize(this->GetNumNodes());
        this->mIsGhostNode[new_node_index] = false;
    }

    // Return pointer to new cell
    return p_created_cell;
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::Validate()
{
    // Get a list of all the nodes that are ghosts
    std::vector<bool> validated_node = mIsGhostNode;
    assert(mIsGhostNode.size()==this->GetNumNodes());

    // Look through all of the cells and record what node they are associated with.
    for (typename AbstractCellPopulation<DIM,DIM>::Iterator cell_iter=this->Begin(); cell_iter!=this->End(); ++cell_iter)
    {
        unsigned node_index = this->GetLocationIndexUsingCell((*cell_iter));

        // If the node attached to this cell is labelled as a ghost node, then throw an error
        if (mIsGhostNode[node_index])
        {
            EXCEPTION("Node " << node_index << " is labelled as a ghost node and has a cell attached");
        }
        validated_node[node_index] = true;
    }

    for (unsigned i=0; i<validated_node.size(); i++)
    {
        if (!validated_node[i])
        {
            EXCEPTION("Node " << i << " does not appear to be a ghost node or have a cell associated with it");
        }
    }
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::UpdateGhostNodesAfterReMesh(NodeMap& rMap)
{
    // Copy mIsGhostNode to a temporary vector
    std::vector<bool> ghost_nodes_before_remesh = mIsGhostNode;

    // Reinitialise mIsGhostNode
    mIsGhostNode.clear();
    mIsGhostNode.resize(this->GetNumNodes());

    // Update mIsGhostNode using the node map
    for (unsigned old_index=0; old_index<rMap.GetSize(); old_index++)
    {
        if (!rMap.IsDeleted(old_index))
        {
            unsigned new_index = rMap.GetNewIndex(old_index);
            mIsGhostNode[new_index] = ghost_nodes_before_remesh[old_index];
        }
    }
}

template<unsigned DIM>
std::set<unsigned> MeshBasedCellPopulationWithGhostNodes<DIM>::GetNeighbouringLocationIndices(CellPtr pCell)
{
    unsigned node_index = this->GetLocationIndexUsingCell(pCell);
    std::set<unsigned> neighbour_indices = this->GetNeighbouringNodeIndices(node_index);

    // Remove ghost nodes from the neighbour indices
    for (std::set<unsigned>::iterator iter = neighbour_indices.begin();
         iter != neighbour_indices.end();)
    {
        if (this->IsGhostNode(*iter))
        {
            neighbour_indices.erase(iter++);
        }
        else
        {
            ++iter;
        }
    }

    return neighbour_indices;
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::UpdateNodeLocations(double dt)
{
    // First update ghost positions first because they do not affect the real cells
    UpdateGhostPositions(dt);

    // Then call the base class method
    AbstractCentreBasedCellPopulation<DIM,DIM>::UpdateNodeLocations(dt);
}


template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::OpenWritersFiles(OutputFileHandler& rOutputFileHandler)
{
    if (this->mOutputResultsForChasteVisualizer)
    {
        if (!this-> template HasWriter<CellLocationIndexWriter>())
        {
            this-> template AddCellWriter<CellLocationIndexWriter>();
        }
    }

    MeshBasedCellPopulation<DIM, DIM>::OpenWritersFiles(rOutputFileHandler);
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
    if (this->mpVoronoiTessellation != NULL)
    {
        unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
        std::stringstream time;
        time << num_timesteps;

        // Create mesh writer for VTK output
        VertexMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results", false);

        // Iterate over any cell writers that are present
        unsigned num_vtk_cells = this->mpVoronoiTessellation->GetNumElements();
        for (typename std::vector<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
             cell_writer_iter != this->mCellWriters.end();
             ++cell_writer_iter)
        {
            // Create vector to store VTK cell data
            std::vector<double> vtk_cell_data(num_vtk_cells);

            // Loop over elements of mpVoronoiTessellation
            for (typename VertexMesh<DIM, DIM>::VertexElementIterator elem_iter = this->mpVoronoiTessellation->GetElementIteratorBegin();
                 elem_iter != this->mpVoronoiTessellation->GetElementIteratorEnd();
                 ++elem_iter)
            {
                // Get the indices of this element and the corresponding node in mrMesh
                unsigned elem_index = elem_iter->GetIndex();
                unsigned node_index = this->mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);

                // If this node corresponds to a ghost node, set any "cell" data to be -1.0
                if (this->IsGhostNode(node_index))
                {
                    // Populate the vector of VTK cell data
                    vtk_cell_data[elem_index] = -1.0;
                }
                else
                {
                    // Get the cell corresponding to this node
                    CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);

                    // Populate the vector of VTK cell data
                    vtk_cell_data[elem_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
                }
            }

            mesh_writer.AddCellData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
        }

        // Next, record which nodes are ghost nodes
        // Note that the cell writer hierarchy can not be used to do this as ghost nodes don't have corresponding cells.
        std::vector<double> ghosts(num_vtk_cells);
        for (typename VertexMesh<DIM, DIM>::VertexElementIterator elem_iter = this->mpVoronoiTessellation->GetElementIteratorBegin();
             elem_iter != this->mpVoronoiTessellation->GetElementIteratorEnd();
             ++elem_iter)
        {
            unsigned elem_index = elem_iter->GetIndex();
            unsigned node_index = this->mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
            ghosts[elem_index]  = (double) (this->IsGhostNode(node_index));
        }
        mesh_writer.AddCellData("Non-ghosts", ghosts);


        mesh_writer.WriteVtkUsingMesh(*(this->mpVoronoiTessellation), time.str());
        *(this->mpVtkMetaFile) << "        <DataSet timestep=\"";
        *(this->mpVtkMetaFile) << num_timesteps;
        *(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
        *(this->mpVtkMetaFile) << num_timesteps;
        *(this->mpVtkMetaFile) << ".vtu\"/>\n";
    }
#endif //CHASTE_VTK
}

template<unsigned DIM>
void MeshBasedCellPopulationWithGhostNodes<DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<GhostSpringStiffness>" << mGhostSpringStiffness << "</GhostSpringStiffness>\n";

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

// Explicit instantiation
template class MeshBasedCellPopulationWithGhostNodes<1>;
template class MeshBasedCellPopulationWithGhostNodes<2>;
template class MeshBasedCellPopulationWithGhostNodes<3>;

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