OffLatticeSimulation.cpp

/*

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*/

#include "OffLatticeSimulation.hpp"
#include "AbstractCentreBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.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),
      mOutputNodeVelocities(false)
{
    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 (dynamic_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation))
    {
        this->mDt = 1.0/120.0; // 30 seconds
    }
    else
    {
        assert (dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation));
        this->mDt = 0.002; // smaller time step required for convergence/stability
    }
}

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);

    // Initialise a vector of forces on node
    std::vector<c_vector<double, SPACE_DIM> > forces(this->mrCellPopulation.GetNumNodes(), zero_vector<double>(SPACE_DIM));

//    // First set all the forces to zero
//    for (unsigned i=0; i<forces.size(); i++)
//    {
//         forces[i].clear();
//    }
//
//    // Then resize the std::vector if the number of cells has increased or decreased
//    // (note this should be done after the above zeroing)
//    unsigned num_nodes = mrCellPopulation.GetNumNodes();
//    if (num_nodes != forces.size())
//    {
//        forces.resize(num_nodes, zero_vector<double>(DIM));
//    }

    // 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(forces, this->mrCellPopulation);
    }
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::FORCE);

    // Update node positions
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::POSITION);
    UpdateNodePositions(forces);
    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 (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:
            {
                double random_zenith_angle = M_PI*RandomNumberGenerator::Instance()->ranf(); // phi
                double random_azimuth_angle = 2*M_PI*RandomNumberGenerator::Instance()->ranf(); // theta

                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
    {
        return zero_vector<double>(SPACE_DIM);
    }
}

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 (dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&this->mrCellPopulation))
        {
           if (dynamic_cast<Cylindrical2dMesh*>(&(dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))->rGetMesh())))
           {
               *this->mpVizSetupFile << "MeshWidth\t" << this->mrCellPopulation.GetWidth(0) << "\n";
           }
        }
        else if (dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(&this->mrCellPopulation))
        {
           if (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(const std::vector< c_vector<double, SPACE_DIM> >& rNodeForces)
{
    unsigned num_nodes = this->mrCellPopulation.GetNumNodes();

    /*
     * Get the previous node positions (these may be needed when applying boundary conditions,
     * e.g. in the case of immotile cells)
     */
    std::vector<c_vector<double, SPACE_DIM> > old_node_locations;
    old_node_locations.reserve(num_nodes);
    for (unsigned node_index=0; node_index<num_nodes; node_index++)
    {
        old_node_locations[node_index] = this->mrCellPopulation.GetNode(node_index)->rGetLocation();
    }

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

    // Write node velocities to file if required
    if (mOutputNodeVelocities)
    {
        OutputFileHandler output_file_handler2(this->mSimulationOutputDirectory+"/", false);
        PetscTools::BeginRoundRobin();
        {
            if (!PetscTools::AmMaster() || SimulationTime::Instance()->GetTimeStepsElapsed()!=0)
            {
                mpNodeVelocitiesFile = output_file_handler2.OpenOutputFile("nodevelocities.dat", std::ios::app);
            }

            if (SimulationTime::Instance()->GetTimeStepsElapsed()%this->mSamplingTimestepMultiple == 0)
            {
                *mpNodeVelocitiesFile << SimulationTime::Instance()->GetTime() << "\t";

                for (unsigned node_index=0; node_index<num_nodes; node_index++)
                {
                    // We should never encounter deleted nodes due to where this method is called by Solve()
                    assert(!this->mrCellPopulation.GetNode(node_index)->IsDeleted());

                    // Check that results should be written for this node
                    bool is_real_node = true;

                    if (dynamic_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&this->mrCellPopulation))
                    {
                        if (static_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))->IsGhostNode(node_index))
                        {
                            // If this node is a ghost node then don't record its velocity
                            is_real_node = false;
                        }
                        else
                        {
                            // We should never encounter nodes associated with dead cells due to where this method is called by Solve()
                            assert(!this->mrCellPopulation.GetCellUsingLocationIndex(node_index)->IsDead());
                        }
                    }

                    // Write node data to file
                    if (is_real_node)
                    {
                        const c_vector<double,SPACE_DIM>& position = this->mrCellPopulation.GetNode(node_index)->rGetLocation();
                        double damping_constant = static_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation))->GetDampingConstant(node_index);
                        c_vector<double, SPACE_DIM> velocity = this->mDt * rNodeForces[node_index] / damping_constant;

                        *mpNodeVelocitiesFile << node_index  << " ";
                        for (unsigned i=0; i<SPACE_DIM; i++)
                        {
                            *mpNodeVelocitiesFile << position[i] << " ";
                        }
                        for (unsigned i=0; i<SPACE_DIM; i++)
                        {
                            *mpNodeVelocitiesFile << velocity[i] << " ";
                        }
                    }
                }
                *mpNodeVelocitiesFile << "\n";
            }
            mpNodeVelocitiesFile->close();
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::SetupSolve()
{
    if (mOutputNodeVelocities && PetscTools::AmMaster())
    {
        OutputFileHandler output_file_handler2(this->mSimulationOutputDirectory+"/", false);
        mpNodeVelocitiesFile = output_file_handler2.OpenOutputFile("nodevelocities.dat");
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::UpdateAtEndOfSolve()
{
    if (mOutputNodeVelocities)
    {
        mpNodeVelocitiesFile->close();
    }
}

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>
bool OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::GetOutputNodeVelocities()
{
    return mOutputNodeVelocities;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::SetOutputNodeVelocities(bool outputNodeVelocities)
{
    mOutputNodeVelocities = outputNodeVelocities;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::OutputSimulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<OutputNodeVelocities>" << mOutputNodeVelocities << "</OutputNodeVelocities>\n";

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

// Explicit instantiation

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)