AbstractVariableSizeTwoBodyInteractionForce.cpp

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#include "AbstractVariableSizeTwoBodyInteractionForce.hpp"
 
#include "AbstractCentreBasedCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "NodeBasedCellPopulation.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::AbstractVariableSizeTwoBodyInteractionForce()
    : AbstractTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>(),
      mSpringStiffness(15.0),
      mDivisionRestingSpringLength(0.5),
      mSpringGrowthDuration(1.0)
{
    if constexpr (SPACE_DIM == 1)
    {
        mSpringStiffness = 30.0;
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::~AbstractVariableSizeTwoBodyInteractionForce()
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::VariableSpringConstantMultiplicationFactor(
    unsigned nodeAGlobalIndex,
    unsigned nodeBGlobalIndex,
    AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation,
    bool isCloserThanRestLength)
{
    return 1.0;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::CalculateForceBetweenNodes(
    unsigned nodeAGlobalIndex,
    unsigned nodeBGlobalIndex,
    AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation)
{
    // We should only ever calculate the force between two distinct nodes
    assert(nodeAGlobalIndex != nodeBGlobalIndex);
 
    Node<SPACE_DIM>* p_node_a = rCellPopulation.GetNode(nodeAGlobalIndex);
    Node<SPACE_DIM>* p_node_b = rCellPopulation.GetNode(nodeBGlobalIndex);
 
    // Get the node locations
    const c_vector<double, SPACE_DIM>& r_node_a_location = p_node_a->rGetLocation();
    const c_vector<double, SPACE_DIM>& r_node_b_location = p_node_b->rGetLocation();
 
    // Get the node radii for a NodeBasedCellPopulation
    double node_a_radius = 0.0;
    double node_b_radius = 0.0;
 
    if (bool(dynamic_cast<NodeBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
    {
        node_a_radius = p_node_a->GetRadius();
        node_b_radius = p_node_b->GetRadius();
    }
 
    // Get the unit vector parallel to the line joining the two nodes
    c_vector<double, SPACE_DIM> unit_difference;
    /*
     * We use the mesh method GetVectorFromAtoB() to compute the direction of the
     * unit vector along the line joining the two nodes, rather than simply subtract
     * their positions, because this method can be overloaded (e.g. to enforce a
     * periodic boundary in Cylindrical2dMesh).
     */
    unit_difference = rCellPopulation.rGetMesh().GetVectorFromAtoB(r_node_a_location, r_node_b_location);
 
    // Calculate the distance between the two nodes
    double distance_between_nodes = norm_2(unit_difference);
    assert(distance_between_nodes > 0);
    assert(!std::isnan(distance_between_nodes));
 
    unit_difference /= distance_between_nodes;
 
    /*
     * If mUseCutOffLength has been set, then there is zero force between
     * two nodes located a distance apart greater than mMechanicsCutOffLength in AbstractTwoBodyInteractionForce.
     */
    if (this->mUseCutOffLength)
    {
        if (distance_between_nodes >= this->GetCutOffLength())
        {
            return zero_vector<double>(SPACE_DIM); // c_vector<double,SPACE_DIM>() is not guaranteed to be fresh memory
        }
    }
 
    /*
     * Calculate the rest length of the spring connecting the two nodes with a default
     * value of 1.0.
     */
    double rest_length_final = 1.0;
 
    if (bool(dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation)))
    {
        rest_length_final = static_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation)->GetRestLength(nodeAGlobalIndex, nodeBGlobalIndex);
    }
    else if (bool(dynamic_cast<NodeBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
    {
        assert(node_a_radius > 0 && node_b_radius > 0);
        rest_length_final = node_a_radius + node_b_radius;
    }
 
    double rest_length = rest_length_final;
 
    CellPtr p_cell_A = rCellPopulation.GetCellUsingLocationIndex(nodeAGlobalIndex);
    CellPtr p_cell_B = rCellPopulation.GetCellUsingLocationIndex(nodeBGlobalIndex);
 
    double ageA = p_cell_A->GetAge();
    double ageB = p_cell_B->GetAge();
 
    assert(!std::isnan(ageA));
    assert(!std::isnan(ageB));
 
    /*
     * If the cells are both newly divided, then the rest length of the spring
     * connecting them grows linearly with time, until 1 hour after division.
     */
    if (ageA < mSpringGrowthDuration && ageB < mSpringGrowthDuration)
    {
        AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>* p_static_cast_cell_population = static_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation);
 
        std::pair<CellPtr,CellPtr> cell_pair = p_static_cast_cell_population->CreateCellPair(p_cell_A, p_cell_B);
 
        if (p_static_cast_cell_population->IsMarkedSpring(cell_pair))
        {
            // Spring rest length increases from a small value to the normal rest length over 1 hour
            double lambda = mDivisionRestingSpringLength;
            rest_length = lambda + (rest_length_final - lambda) * ageA/mSpringGrowthDuration;
        }
        if (ageA + SimulationTime::Instance()->GetTimeStep() >= mSpringGrowthDuration)
        {
            // This spring is about to go out of scope
            p_static_cast_cell_population->UnmarkSpring(cell_pair);
        }
    }
 
    /*
     * For apoptosis, progressively reduce the radius of the cell.
     */
    double a_rest_length = rest_length*0.5;
    double b_rest_length = a_rest_length;
 
    if (bool(dynamic_cast<NodeBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
    {
        assert(node_a_radius > 0 && node_b_radius > 0);
        a_rest_length = (node_a_radius/(node_a_radius+node_b_radius))*rest_length;
        b_rest_length = (node_b_radius/(node_a_radius+node_b_radius))*rest_length;
    }
 
    /*
     * If either of the cells has begun apoptosis, then the length of the spring
     * connecting them decreases linearly with time.
     */
    if (p_cell_A->HasApoptosisBegun())
    {
        double time_until_death_a = p_cell_A->GetTimeUntilDeath();
        a_rest_length = a_rest_length * time_until_death_a / p_cell_A->GetApoptosisTime();
    }
    if (p_cell_B->HasApoptosisBegun())
    {
        double time_until_death_b = p_cell_B->GetTimeUntilDeath();
        b_rest_length = b_rest_length * time_until_death_b / p_cell_B->GetApoptosisTime();
    }
 
    rest_length = a_rest_length + b_rest_length;
 
    double overlap = distance_between_nodes - rest_length;
    bool is_closer_than_rest_length = (overlap <= 0);
    double multiplication_factor = VariableSpringConstantMultiplicationFactor(nodeAGlobalIndex,
                                                                              nodeBGlobalIndex,
                                                                              rCellPopulation,
                                                                              is_closer_than_rest_length);
 
    // TODO issue 1017 This should be rest_length not rest_length_final, keeping it the same for now to maintain backwards compatibility with existing force laws, but we should eventually change it and update the force laws accordingly.
    return CalculateLinkInteraction(overlap, rest_length_final, unit_difference, multiplication_factor);
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::GetSpringStiffness()
{
    return mSpringStiffness;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::GetDivisionRestingSpringLength()
{
    return mDivisionRestingSpringLength;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::GetSpringGrowthDuration()
{
    return mSpringGrowthDuration;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::SetSpringStiffness(double springStiffness)
{
    assert(springStiffness > 0.0);
    mSpringStiffness = springStiffness;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::SetDivisionRestingSpringLength(double divisionRestingSpringLength)
{
    assert(divisionRestingSpringLength <= 1.0);
    assert(divisionRestingSpringLength >= 0.0);
 
    mDivisionRestingSpringLength = divisionRestingSpringLength;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::SetSpringGrowthDuration(double springGrowthDuration)
{
    assert(springGrowthDuration >= 0.0);
 
    mSpringGrowthDuration = springGrowthDuration;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractVariableSizeTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::OutputForceParameters(out_stream& rParamsFile)
{
    AbstractTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>::OutputForceParameters(rParamsFile);
}
 
// Explicit instantiation
template class AbstractVariableSizeTwoBodyInteractionForce<1,1>;
template class AbstractVariableSizeTwoBodyInteractionForce<1,2>;
template class AbstractVariableSizeTwoBodyInteractionForce<2,2>;
template class AbstractVariableSizeTwoBodyInteractionForce<1,3>;
template class AbstractVariableSizeTwoBodyInteractionForce<2,3>;
template class AbstractVariableSizeTwoBodyInteractionForce<3,3>;