AbstractCentreBasedCellPopulation.cpp

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#include "AbstractCentreBasedCellPopulation.hpp"
#include "RandomDirectionCentreBasedDivisionRule.hpp"
#include "RandomNumberGenerator.hpp"
#include "StepSizeException.hpp"
#include "WildTypeCellMutationState.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);
    }

    mpCentreBasedDivisionRule.reset(new RandomDirectionCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM>());
}

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>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetCellDataItemAtPdeNode(
    unsigned pdeNodeIndex,
    std::string& rVariableName,
    bool dirichletBoundaryConditionApplies,
    double dirichletBoundaryValue)
{
    CellPtr p_cell = this->GetCellUsingLocationIndex(pdeNodeIndex);
    double value = p_cell->GetCellData()->GetItem(rVariableName);

    return value;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AddCell(CellPtr pNewCell, CellPtr pParentCell)
{
    // Calculate the locations of the two daughter cells
    std::pair<c_vector<double, SPACE_DIM>, c_vector<double, SPACE_DIM> > positions = mpCentreBasedDivisionRule->CalculateCellDivisionVector(pParentCell, *this);

    c_vector<double, SPACE_DIM> parent_position = positions.first;
    c_vector<double, SPACE_DIM> daughter_position = positions.second;

    // Set the parent cell to use this location
    ChastePoint<SPACE_DIM> parent_point(parent_position);
    unsigned node_index = this->GetLocationIndexUsingCell(pParentCell);
    this->SetNode(node_index, parent_point);

    // Create a new node
    Node<SPACE_DIM>* p_new_node = new Node<SPACE_DIM>(this->GetNumNodes(), daughter_position, false); // never on boundary

    // Clear the applied force on the new node, in case velocity is ouptut on the same timestep as this cell's division
    p_new_node->ClearAppliedForce();

    // Copy any node attributes from the parent node
    if (this->GetNode(node_index)->HasNodeAttributes())
    {
        p_new_node->rGetNodeAttributes() = this->GetNode(node_index)->rGetNodeAttributes();
    }

    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>::CheckForStepSizeException(unsigned nodeIndex, c_vector<double,SPACE_DIM>& rDisplacement, double dt)
{
    double length = norm_2(rDisplacement);

    if ((length > this->mAbsoluteMovementThreshold) && (!this->IsGhostNode(nodeIndex)) && (!this->IsParticle(nodeIndex)))
    {
        std::ostringstream message;
        message << "Cells are moving by " << length;
        message << ", which is more than the AbsoluteMovementThreshold: use a smaller timestep to avoid this exception.";

        // Suggest a net time step that will give a movement smaller than the movement threshold
        double new_step = 0.95*dt*(this->mAbsoluteMovementThreshold/length);

        throw StepSizeException(new_step, message.str(), true); // terminate
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstant(unsigned nodeIndex)
{
    if (this->IsGhostNode(nodeIndex) || this->IsParticle(nodeIndex))
    {
        return this->GetDampingConstantNormal();
    }
    else
    {
        CellPtr p_cell = this->GetCellUsingLocationIndex(nodeIndex);
        if (p_cell->GetMutationState()->IsType<WildTypeCellMutationState>())
        {
            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>::AcceptCellWritersAcrossPopulation()
{
    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->rGetMesh().GetNodeIteratorBegin();
         node_iter != this->rGetMesh().GetNodeIteratorEnd();
         ++node_iter)
    {
        for (typename std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
             cell_writer_iter != this->mCellWriters.end();
             ++cell_writer_iter)
        {
            CellPtr cell_from_node = this->GetCellUsingLocationIndex(node_iter->GetIndex());
            this->AcceptCellWriter(*cell_writer_iter, cell_from_node);
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetCentreBasedDivisionRule()
{
    return mpCentreBasedDivisionRule;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetCentreBasedDivisionRule(boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > pCentreBasedDivisionRule)
{
    mpCentreBasedDivisionRule = pCentreBasedDivisionRule;
}

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

    // Add the division rule parameters
    *rParamsFile << "\t\t<CentreBasedDivisionRule>\n";
    mpCentreBasedDivisionRule->OutputCellCentreBasedDivisionRuleInfo(rParamsFile);
    *rParamsFile << "\t\t</CentreBasedDivisionRule>\n";

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDefaultTimeStep()
{
    return 1.0/120.0;
}

// 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>;