AbstractOffLatticeCellPopulation.cpp

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*/
 
#include "AbstractOffLatticeCellPopulation.hpp"
#include "StepSizeException.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractOffLatticeCellPopulation( AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                                                    std::vector<CellPtr>& rCells,
                                                                    const std::vector<unsigned> locationIndices)
    : AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>(rMesh, rCells, locationIndices),
      mDampingConstantNormal(1.0),
      mDampingConstantMutant(1.0),
      mAbsoluteMovementThreshold(2.0)
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractOffLatticeCellPopulation(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh)
    : AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>(rMesh)
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::CheckForStepSizeException(unsigned nodeIndex, c_vector<double,SPACE_DIM>& rDisplacement, double dt)
{
    double length = norm_2(rDisplacement);
 
    if (length > this->mAbsoluteMovementThreshold)
    {
        std::ostringstream message;
        message << "Cells are moving by " << length;
        message << ", which is more than the AbsoluteMovementThreshold: use a smaller timestep to avoid this exception.";
 
        /* Divide dt by the smallest power of 2 such that the node moves less than the threshold
         * Note that this is the optimal power of 2 to divide by for the Forward Euler Method.
         * For higher order methods, the optimal divisor may be different, but this is an upper bound that works for all methods.
         */
        double divisor = 1.0;
        while (length / divisor >= this->mAbsoluteMovementThreshold)
        {
            divisor *= 2.0;
        }
        double new_step = dt / divisor;
 
        throw StepSizeException(new_step, message.str(), true); // terminate
    }
}
 
// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::UpdateNodeLocations(double dt)
{
  // This method is deprecated by the NumericalMethod class hierarchy; the only population that calls this method is the NodeBasedCellPopulationWithBuskeUpdate.
  NEVER_REACHED;
}
// LCOV_EXCL_STOP
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetDampingConstantNormal(double dampingConstantNormal)
{
    assert(dampingConstantNormal > 0.0);
    mDampingConstantNormal = dampingConstantNormal;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetDampingConstantMutant(double dampingConstantMutant)
{
    assert(dampingConstantMutant > 0.0);
    mDampingConstantMutant = dampingConstantMutant;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetAbsoluteMovementThreshold(double absoluteMovementThreshold)
{
    mAbsoluteMovementThreshold = absoluteMovementThreshold;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstantNormal()
{
    return mDampingConstantNormal;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstantMutant()
{
    return mDampingConstantMutant;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetAbsoluteMovementThreshold()
{
    return mAbsoluteMovementThreshold;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
const std::vector<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::rGetNodePairs() const
{
    return mNodePairs;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::rGetModifiableNodePairs()
{
    return mNodePairs;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<DampingConstantNormal>" << mDampingConstantNormal << "</DampingConstantNormal>\n";
    *rParamsFile << "\t\t<DampingConstantMutant>" << mDampingConstantMutant << "</DampingConstantMutant>\n";
 
    // Call method on direct parent class
    AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters(rParamsFile);
}
 
// Explicit instantiation
template class AbstractOffLatticeCellPopulation<1,1>;
template class AbstractOffLatticeCellPopulation<1,2>;
template class AbstractOffLatticeCellPopulation<2,2>;
template class AbstractOffLatticeCellPopulation<1,3>;
template class AbstractOffLatticeCellPopulation<2,3>;
template class AbstractOffLatticeCellPopulation<3,3>;