AbstractCentreBasedCellPopulation.cpp

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#include "AbstractCentreBasedCellPopulation.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractCentreBasedCellPopulation( AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                                                    std::vector<CellPtr>& rCells,
                                                                  const std::vector<unsigned> locationIndices)
    : AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>(rMesh, rCells, locationIndices),
      mMeinekeDivisionSeparation(0.3) // educated guess
{
    // If no location indices are specified, associate with nodes from the mesh.
    std::list<CellPtr>::iterator it = this->mCells.begin();
    typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = rMesh.GetNodeIteratorBegin();

    for (unsigned i=0; it != this->mCells.end(); ++it, ++i, ++node_iter)
    {
        unsigned index = locationIndices.empty() ? node_iter->GetIndex() : locationIndices[i]; // assume that the ordering matches
        AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::AddCellUsingLocationIndex(index,*it);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractCentreBasedCellPopulation(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh)
    : AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>(rMesh),
      mMeinekeDivisionSeparation(0.3) // educated guess

{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetLocationOfCellCentre(CellPtr pCell)
{
    return GetNodeCorrespondingToCell(pCell)->rGetLocation();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>* AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetNodeCorrespondingToCell(CellPtr pCell)
{
    unsigned index = this->GetLocationIndexUsingCell(pCell);
    return this->GetNode(index);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AddCell(CellPtr pNewCell, const c_vector<double,SPACE_DIM>& rCellDivisionVector, CellPtr pParentCell)
{
    // Create a new node
    Node<SPACE_DIM>* p_new_node = new Node<SPACE_DIM>(this->GetNumNodes(), rCellDivisionVector, false);   // never on boundary
    unsigned new_node_index = this->AddNode(p_new_node); // use copy constructor so it doesn't matter that new_node goes out of scope

    // Update cells vector
    this->mCells.push_back(pNewCell);

    // Update mappings between cells and location indices
    this->SetCellUsingLocationIndex(new_node_index, pNewCell);
    this->mCellLocationMap[pNewCell.get()] = new_node_index;

    return pNewCell;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::pair<CellPtr,CellPtr> AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::CreateCellPair(CellPtr pCell1, CellPtr pCell2)
{
    assert(pCell1);
    assert(pCell2);

    std::pair<CellPtr,CellPtr> cell_pair;

    if (pCell1->GetCellId() < pCell2->GetCellId())
    {
        cell_pair.first = pCell1;
        cell_pair.second = pCell2;
    }
    else
    {
        cell_pair.first = pCell2;
        cell_pair.second = pCell1;
    }
    return cell_pair;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsMarkedSpring(const std::pair<CellPtr,CellPtr>& rCellPair)
{
    // the pair should be ordered like this (CreateCellPair will ensure this)
    assert(rCellPair.first->GetCellId() < rCellPair.second->GetCellId());

    return mMarkedSprings.find(rCellPair) != mMarkedSprings.end();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::MarkSpring(std::pair<CellPtr,CellPtr>& rCellPair)
{
    // the pair should be ordered like this (CreateCellPair will ensure this)
    assert(rCellPair.first->GetCellId() < rCellPair.second->GetCellId());

    mMarkedSprings.insert(rCellPair);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::UnmarkSpring(std::pair<CellPtr,CellPtr>& rCellPair)
{
    // the pair should be ordered like this (CreateCellPair will ensure this)
    assert(rCellPair.first->GetCellId() < rCellPair.second->GetCellId());

    mMarkedSprings.erase(rCellPair);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsCellAssociatedWithADeletedLocation(CellPtr pCell)
{
    return GetNodeCorrespondingToCell(pCell)->IsDeleted();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::set<unsigned> AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>::GetNeighbouringLocationIndices(CellPtr pCell)
{
    unsigned node_index = this->GetLocationIndexUsingCell(pCell);
    return this->GetNeighbouringNodeIndices(node_index);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::UpdateNodeLocations(double dt)
{
    // Iterate over all nodes associated with real cells to update their positions
    for (typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        // Get index of node associated with cell
        unsigned node_index = this->GetLocationIndexUsingCell((*cell_iter));

        // Get damping constant for node
        double damping_const = this->GetDampingConstant(node_index);

        // Get displacement
        c_vector<double,SPACE_DIM> displacement=dt*this->GetNode(node_index)->rGetAppliedForce()/damping_const;

        // Throws an exception if the cell movement goes beyond mAbsoluteMovementThreshold
        if (norm_2(displacement) > this->mAbsoluteMovementThreshold)
        {
            EXCEPTION("Cells are moving by: " << norm_2(displacement) <<
                    ", which is more than the AbsoluteMovementThreshold: "
                    << this->mAbsoluteMovementThreshold <<
                    ". Use a smaller timestep to avoid this exception.");
        }

        // Get new node location
        c_vector<double, SPACE_DIM> new_node_location = this->GetNode(node_index)->rGetLocation() + displacement;

        // Create ChastePoint for new node location
        ChastePoint<SPACE_DIM> new_point(new_node_location);

        // Move the node
        this->SetNode(node_index, new_point);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstant(unsigned nodeIndex)
{
    CellPtr p_cell = this->GetCellUsingLocationIndex(nodeIndex);
    if (p_cell->GetMutationState()->IsType<WildTypeCellMutationState>() && !p_cell->HasCellProperty<CellLabel>())
    {
        return this->GetDampingConstantNormal();
    }
    else
    {
        return this->GetDampingConstantMutant();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsGhostNode(unsigned index)
{
    return false;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsParticle(unsigned index)
{
    return false;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetMeinekeDivisionSeparation()
{
    return mMeinekeDivisionSeparation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetMeinekeDivisionSeparation(double divisionSeparation)
{
    assert(divisionSeparation <= 1.0);
    assert(divisionSeparation >= 0.0);
    mMeinekeDivisionSeparation = divisionSeparation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<MeinekeDivisionSeparation>" << mMeinekeDivisionSeparation << "</MeinekeDivisionSeparation>\n";

    // Call method on direct parent class
    AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters(rParamsFile);
}

// Explicit instantiation

template class AbstractCentreBasedCellPopulation<1,1>;
template class AbstractCentreBasedCellPopulation<1,2>;
template class AbstractCentreBasedCellPopulation<2,2>;
template class AbstractCentreBasedCellPopulation<1,3>;
template class AbstractCentreBasedCellPopulation<2,3>;
template class AbstractCentreBasedCellPopulation<3,3>;