AbstractNumericalMethod.cpp

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*/
 
#include "AbstractNumericalMethod.hpp"
#include "StepSizeException.hpp"
#include "Warnings.hpp"
#include "NodeBasedCellPopulationWithBuskeUpdate.hpp"
#include "ImmersedBoundaryCellPopulation.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),
      mGhostNodeForcesEnabled(true)
{
    // mpCellPopulation, mpForceCollection and mpBoundaryConditions 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;
 
    // Cell populations whose UpdateNodeLocations() is meaningful (rather than NEVER_REACHED)
    // manage their own node position updates, and must be paired with NoNumericalMethod; every
    // other population must be paired with a numerical method that does its own integration.
    bool population_requires_delegation =
        (dynamic_cast<NodeBasedCellPopulationWithBuskeUpdate<SPACE_DIM>*>(mpCellPopulation) != nullptr) ||
        (dynamic_cast<ImmersedBoundaryCellPopulation<SPACE_DIM>*>(mpCellPopulation) != nullptr);
 
    if (population_requires_delegation != this->DelegatesToPopulation())
    {
        EXCEPTION("NoNumericalMethod must be used if and only if the cell population manages its own "
                  "node position updates (currently NodeBasedCellPopulationWithBuskeUpdate and "
                  "ImmersedBoundaryCellPopulation).");
    }
 
    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>::SetBoundaryConditions(std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM, SPACE_DIM> > >* pBoundaryConditions)
{
    mpBoundaryConditions = pBoundaryConditions;
}
 
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::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::SaveCurrentNodeLocations()
{
    std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > node_locations;
 
    for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = mpCellPopulation->rGetMesh().GetNodeIteratorBegin();
            node_iter != mpCellPopulation->rGetMesh().GetNodeIteratorEnd();
            ++node_iter)
    {
        node_locations[&(*node_iter)] = (node_iter)->rGetLocation();
    }
 
    return node_locations;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::ImposeBoundaryConditions(std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> >& rOldNodeLocations)
{
    // Apply any boundary conditions
    for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator bcs_iter = mpBoundaryConditions->begin();
         bcs_iter != mpBoundaryConditions->end();
         ++bcs_iter)
    {
        (*bcs_iter)->ImposeBoundaryCondition(rOldNodeLocations);
    }
}
 
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>
bool AbstractNumericalMethod<ELEMENT_DIM,SPACE_DIM>::DelegatesToPopulation()
{
    return false;
}
 
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<DelegatesToPopulation>" << this->DelegatesToPopulation() << "</DelegatesToPopulation> \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>;