OffLatticeSimulation.cpp

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*/

#include "OffLatticeSimulation.hpp"
#include "AbstractCentreBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "T2SwapCellKiller.hpp"
#include "AbstractVertexBasedDivisionRule.hpp"
#include "Cylindrical2dMesh.hpp"
#include "Cylindrical2dVertexMesh.hpp"
#include "AbstractTwoBodyInteractionForce.hpp"
#include "CellBasedEventHandler.hpp"
#include "LogFile.hpp"
#include "Version.hpp"
#include "ExecutableSupport.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::OffLatticeSimulation(AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation,
                                                bool deleteCellPopulationInDestructor,
                                                bool initialiseCells)
    : AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>(rCellPopulation, deleteCellPopulationInDestructor, initialiseCells)
{
    if (!dynamic_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation))
    {
        EXCEPTION("OffLatticeSimulations require a subclass of AbstractOffLatticeCellPopulation.");
    }

    // Different time steps are used for cell-centre and vertex-based simulations
    if (bool(dynamic_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation)))
    {
        this->mDt = 1.0/120.0; // 30 seconds
    }
    else if (bool(dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
    {
        this->mDt = 0.002; // smaller time step required for convergence/stability

        // For VertexBasedCellPopulations we automatically add a T2SwapCellKiller. In order to inhibit T2 swaps
        // the user needs to set the threshold for T2 swaps in the mesh to 0.
        VertexBasedCellPopulation<SPACE_DIM>* p_vertex_based_cell_population = dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation);
        MAKE_PTR_ARGS(T2SwapCellKiller<SPACE_DIM>, T2_swap_cell_killer, (p_vertex_based_cell_population));
        this->AddCellKiller(T2_swap_cell_killer);
    }
    else
    {
        // All classes derived from AbstractOffLatticeCellPopulation are covered by the above (except user-derived classes),
        // i.e. if you want to use this method with your own subclass of AbstractOffLatticeCellPopulation, then simply
        // comment out the line below
        NEVER_REACHED;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::AddForce(boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > pForce)
{
    mForceCollection.push_back(pForce);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::RemoveAllForces()
{
    mForceCollection.clear();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::AddCellPopulationBoundaryCondition(boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > pBoundaryCondition)
{
    mBoundaryConditions.push_back(pBoundaryCondition);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::RemoveAllCellPopulationBoundaryConditions()
{
    mBoundaryConditions.clear();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::UpdateCellLocationsAndTopology()
{
    // Calculate forces
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::FORCE);

    // Clear all forces
    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrCellPopulation.rGetMesh().GetNodeIteratorBegin();
         node_iter != this->mrCellPopulation.rGetMesh().GetNodeIteratorEnd();
         ++node_iter)
    {
        node_iter->ClearAppliedForce();
    }

    // Now add force contributions from each AbstractForce
    for (typename std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > >::iterator iter = mForceCollection.begin();
         iter != mForceCollection.end();
         ++iter)
    {
        (*iter)->AddForceContribution(this->mrCellPopulation);
    }
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::FORCE);

    // Update node positions
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::POSITION);
    UpdateNodePositions();
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::POSITION);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::CalculateCellDivisionVector(CellPtr pParentCell)
{
    // If it is not vertex based...
    if (bool(dynamic_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))))
    {
        // Location of parent and daughter cells
        c_vector<double, SPACE_DIM> parent_coords = this->mrCellPopulation.GetLocationOfCellCentre(pParentCell);
        c_vector<double, SPACE_DIM> daughter_coords;

        // Get separation parameter
        double separation = static_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))->GetMeinekeDivisionSeparation();

        // Make a random direction vector of the required length
        c_vector<double, SPACE_DIM> random_vector;

        /*
         * Pick a random direction and move the parent cell backwards by 0.5*separation
         * in that direction and return the position of the daughter cell 0.5*separation
         * forwards in that direction.
         */
        switch (SPACE_DIM)
        {
            case 1:
            {
                double random_direction = -1.0 + 2.0*(RandomNumberGenerator::Instance()->ranf() < 0.5);

                random_vector(0) = 0.5*separation*random_direction;
                break;
            }
            case 2:
            {
                double random_angle = 2.0*M_PI*RandomNumberGenerator::Instance()->ranf();

                random_vector(0) = 0.5*separation*cos(random_angle);
                random_vector(1) = 0.5*separation*sin(random_angle);
                break;
            }
            case 3:
            {
                /*
                 * Note that to pick a random point on the surface of a sphere, it is incorrect
                 * to select spherical coordinates from uniform distributions on [0, 2*pi) and
                 * [0, pi) respectively, since points picked in this way will be 'bunched' near
                 * the poles. See #2230.
                 */
                double u = RandomNumberGenerator::Instance()->ranf();
                double v = RandomNumberGenerator::Instance()->ranf();

                double random_azimuth_angle = 2*M_PI*u;
                double random_zenith_angle = std::acos(2*v - 1);

                random_vector(0) = 0.5*separation*cos(random_azimuth_angle)*sin(random_zenith_angle);
                random_vector(1) = 0.5*separation*sin(random_azimuth_angle)*sin(random_zenith_angle);
                random_vector(2) = 0.5*separation*cos(random_zenith_angle);
                break;
            }
            default:
                // This can't happen
                NEVER_REACHED;
        }

        parent_coords = parent_coords - random_vector;
        daughter_coords = parent_coords + random_vector;

        // Set the parent to use this location
        ChastePoint<SPACE_DIM> parent_coords_point(parent_coords);
        unsigned node_index = this->mrCellPopulation.GetLocationIndexUsingCell(pParentCell);
        this->mrCellPopulation.SetNode(node_index, parent_coords_point);

        return daughter_coords;
    }
    else if (bool(dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&(this->mrCellPopulation))))
    {
        VertexBasedCellPopulation<SPACE_DIM>* p_vertex_population = dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&(this->mrCellPopulation));
        boost::shared_ptr<AbstractVertexBasedDivisionRule<SPACE_DIM> > p_division_rule = p_vertex_population->GetVertexBasedDivisionRule();

        return p_division_rule->CalculateCellDivisionVector(pParentCell, *p_vertex_population);
    }
    else
    {
        // All classes derived from AbstractOffLatticeCellPopulation are covered by the above (except user-derived classes),
        // i.e. if you want to use this class with your own subclass of AbstractOffLatticeCellPopulation, then simply
        // comment out the line below
        NEVER_REACHED;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::WriteVisualizerSetupFile()
{
    if (PetscTools::AmMaster())
    {
        for (unsigned i=0; i<this->mForceCollection.size(); i++)
        {
            // This may cause compilation problems, probably due to AbstractTwoBodyInteractionForce not having two template parameters

            boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > p_force = this->mForceCollection[i];
            if (boost::dynamic_pointer_cast<AbstractTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM> >(p_force))
            {
                double cutoff = (boost::static_pointer_cast<AbstractTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM> >(p_force))->GetCutOffLength();
                *(this->mpVizSetupFile) << "Cutoff\t" << cutoff << "\n";
            }
        }

        // This is a quick and dirty check to see if the mesh is periodic
        if (bool(dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&this->mrCellPopulation)))
        {
           if (bool(dynamic_cast<Cylindrical2dMesh*>(&(dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))->rGetMesh()))))
           {
               *this->mpVizSetupFile << "MeshWidth\t" << this->mrCellPopulation.GetWidth(0) << "\n";
           }
        }
        else if (bool(dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&this->mrCellPopulation)))
        {
           if (bool(dynamic_cast<Cylindrical2dVertexMesh*>(&(dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&(this->mrCellPopulation))->rGetMesh()))))
           {
               *this->mpVizSetupFile << "MeshWidth\t" << this->mrCellPopulation.GetWidth(0) << "\n";
           }
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::UpdateNodePositions()
{
    /*
     * Get the previous node positions (these may be needed when applying boundary conditions,
     * e.g. in the case of immotile cells)
     */
    std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > old_node_locations;
    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrCellPopulation.rGetMesh().GetNodeIteratorBegin();
         node_iter != this->mrCellPopulation.rGetMesh().GetNodeIteratorEnd();
         ++node_iter)
    {
        old_node_locations[&(*node_iter)] = (node_iter)->rGetLocation();
    }

    // Update node locations
    static_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))->UpdateNodeLocations(this->mDt);

    // Apply any boundary conditions
    for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator bcs_iter = mBoundaryConditions.begin();
         bcs_iter != mBoundaryConditions.end();
         ++bcs_iter)
    {
        (*bcs_iter)->ImposeBoundaryCondition(old_node_locations);
    }

    // Verify that each boundary condition is now satisfied
    for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator bcs_iter = mBoundaryConditions.begin();
         bcs_iter != mBoundaryConditions.end();
         ++bcs_iter)
    {
        if (!((*bcs_iter)->VerifyBoundaryCondition()))
        {
            EXCEPTION("The cell population boundary conditions are incompatible.");
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::SetupSolve()
{
    // Clear all forces
    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrCellPopulation.rGetMesh().GetNodeIteratorBegin();
         node_iter != this->mrCellPopulation.rGetMesh().GetNodeIteratorEnd();
         ++node_iter)
    {
        node_iter->ClearAppliedForce();
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::OutputAdditionalSimulationSetup(out_stream& rParamsFile)
{
    // Loop over forces
    *rParamsFile << "\n\t<Forces>\n";
    for (typename std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > >::iterator iter = mForceCollection.begin();
         iter != mForceCollection.end();
         ++iter)
    {
        // Output force details
        (*iter)->OutputForceInfo(rParamsFile);
    }
    *rParamsFile << "\t</Forces>\n";

    // Loop over cell population boundary conditions
    *rParamsFile << "\n\t<CellPopulationBoundaryConditions>\n";
    for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator iter = mBoundaryConditions.begin();
         iter != mBoundaryConditions.end();
         ++iter)
    {
        // Output cell Boundary condition details
        (*iter)->OutputCellPopulationBoundaryConditionInfo(rParamsFile);
    }
    *rParamsFile << "\t</CellPopulationBoundaryConditions>\n";
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::OutputSimulationParameters(out_stream& rParamsFile)
{
    // Call method on direct parent class
    AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::OutputSimulationParameters(rParamsFile);
}

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

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(OffLatticeSimulation)