AbstractNumericalMethod.cpp

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*/

#include "AbstractNumericalMethod.hpp"
#include "StepSizeException.hpp"
#include "Warnings.hpp"
#include "AbstractCentreBasedCellPopulation.hpp"
#include "NodeBasedCellPopulationWithBuskeUpdate.hpp"
#include "MeshBasedCellPopulationWithGhostNodes.hpp"
#include "CellBasedEventHandler.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::AbstractNumericalMethod()
    : mpCellPopulation(nullptr),
      mpForceCollection(nullptr),
      mUseAdaptiveTimestep(false),
      mUseUpdateNodeLocation(false),
      mGhostNodeForcesEnabled(true)
{
    // mpCellPopulation and mpForceCollection are initialized by the OffLatticeSimulation constructor
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::~AbstractNumericalMethod()
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SetCellPopulation(AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>* pPopulation)
{
    mpCellPopulation = pPopulation;

    // Set other member variables according to the type of the cell population
    if (dynamic_cast<NodeBasedCellPopulationWithBuskeUpdate<SPACE_DIM>*>(mpCellPopulation))
    {
        mUseUpdateNodeLocation = true;
        WARNING("Non-Euler steppers are not yet implemented for NodeBasedCellPopulationWithBuskeUpdate");
    }

    if (dynamic_cast<MeshBasedCellPopulationWithGhostNodes<SPACE_DIM>*>(mpCellPopulation))
    {
        mGhostNodeForcesEnabled = true;
    }
    else
    {
        mGhostNodeForcesEnabled = false;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SetForceCollection(std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > >* pForces)
{
    mpForceCollection = pForces;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SetUseAdaptiveTimestep(bool useAdaptiveTimestep)
{
    mUseAdaptiveTimestep = useAdaptiveTimestep;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::HasAdaptiveTimestep()
{
    return mUseAdaptiveTimestep;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<c_vector<double, SPACE_DIM> > AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::ComputeForcesIncludingDamping()
{
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::FORCE);

    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = mpCellPopulation->rGetMesh().GetNodeIteratorBegin();
         node_iter != mpCellPopulation->rGetMesh().GetNodeIteratorEnd(); ++node_iter)
    {
        node_iter->ClearAppliedForce();
    }

    for (typename std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > >::iterator iter = mpForceCollection->begin();
        iter != mpForceCollection->end(); ++iter)
    {
        (*iter)->AddForceContribution(*mpCellPopulation);
    }

    if (mGhostNodeForcesEnabled)
    {
        dynamic_cast<MeshBasedCellPopulationWithGhostNodes<SPACE_DIM>*>(mpCellPopulation)->ApplyGhostForces();
    }

    // Store applied forces in a vector
    std::vector<c_vector<double, SPACE_DIM> > forces_as_vector;
    forces_as_vector.reserve(mpCellPopulation->GetNumNodes());

    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = mpCellPopulation->rGetMesh().GetNodeIteratorBegin();
         node_iter != mpCellPopulation->rGetMesh().GetNodeIteratorEnd(); ++node_iter)
    {
        double damping = mpCellPopulation->GetDampingConstant(node_iter->GetIndex());
        forces_as_vector.push_back(node_iter->rGetAppliedForce()/damping);
    }

    CellBasedEventHandler::EndEvent(CellBasedEventHandler::FORCE);

    return forces_as_vector;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<c_vector<double, SPACE_DIM> > AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SaveCurrentLocations()
{
    std::vector<c_vector<double, SPACE_DIM> > current_locations;
    current_locations.reserve(mpCellPopulation->GetNumNodes());

    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = mpCellPopulation->rGetMesh().GetNodeIteratorBegin();
         node_iter != mpCellPopulation->rGetMesh().GetNodeIteratorEnd();
         ++node_iter)
    {
        current_locations.push_back(node_iter->rGetLocation());
    }

    return current_locations;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SafeNodePositionUpdate( unsigned nodeIndex, c_vector<double, SPACE_DIM> newPosition)
{
    ChastePoint<SPACE_DIM> new_point(newPosition);
    mpCellPopulation->SetNode(nodeIndex, new_point);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::DetectStepSizeExceptions(unsigned nodeIndex, c_vector<double,SPACE_DIM>& displacement, double dt)
{
    try
    {
        mpCellPopulation->CheckForStepSizeException(nodeIndex, displacement, dt);
    }
    catch (StepSizeException& e)
    {
        if (!(e.IsTerminal()) && (mUseAdaptiveTimestep==false))
        {
            /*
             * If adaptivity is turned off but the simulation can continue, just produce a warning.
             * Only the case for vertex-based cell populations, which can alter node displacement directly
             * to avoid cell rearrangement problems.
             */
            WARN_ONCE_ONLY(e.what());
        }
        else
        {
            throw e;
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SetUseUpdateNodeLocation(bool useUpdateNodeLocation)
{
    mUseUpdateNodeLocation = useUpdateNodeLocation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::GetUseUpdateNodeLocation()
{
    return mUseUpdateNodeLocation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::OutputNumericalMethodInfo(out_stream& rParamsFile)
{
    std::string numerical_method_type = GetIdentifier();

    *rParamsFile << "\t\t<" << numerical_method_type << ">\n";
    OutputNumericalMethodParameters(rParamsFile);
    *rParamsFile << "\t\t</" << numerical_method_type << ">\n";
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::OutputNumericalMethodParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<UseAdaptiveTimestep>" << mUseAdaptiveTimestep << "</UseAdaptiveTimestep> \n";
    *rParamsFile << "\t\t\t<UseUpdateNodeLocation>" << mUseUpdateNodeLocation << "</UseUpdateNodeLocation> \n";
    *rParamsFile << "\t\t\t<GhostNodeForcesEnabled>" << mGhostNodeForcesEnabled << "</GhostNodeForcesEnabled> \n";
}

// Explicit instantiation
template class AbstractNumericalMethod<1,1>;
template class AbstractNumericalMethod<1,2>;
template class AbstractNumericalMethod<2,2>;
template class AbstractNumericalMethod<1,3>;
template class AbstractNumericalMethod<2,3>;
template class AbstractNumericalMethod<3,3>;