void VertexCryptBoundaryForce<DIM>::AddForceContribution(AbstractCellPopulation<DIM>& rCellPopulation)
{
// Helper variable that is a static cast of the cell population
VertexBasedCellPopulation<DIM>* p_cell_population = static_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation);
// Throw an exception message if not using a VertexBasedCellPopulation
if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation) == nullptr)
{
EXCEPTION("VertexCryptBoundaryForce is to be used with VertexBasedCellPopulations only");
}
// Iterate over nodes
for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = p_cell_population->rGetMesh().GetNodeIteratorBegin();
node_iter != p_cell_population->rGetMesh().GetNodeIteratorEnd();
++node_iter)
{
double y = node_iter->rGetLocation()[1]; // y-coordinate of node
// If the node lies below the line y=0, then add the boundary force contribution to the node forces
if (y < 0.0)
{
c_vector<double, DIM> boundary_force = zero_vector<double>(DIM);
boundary_force[1] = mForceStrength*SmallPow(y, 2);
node_iter->AddAppliedForceContribution(boundary_force);
}
}
}
void TCellDiffusionForce<DIM>::AddForceContribution(AbstractCellPopulation<DIM>& rCellPopulation)
{
double dt = SimulationTime::Instance()->GetTimeStep();
// Iterate over the nodes
for (typename AbstractMesh<DIM, DIM>::NodeIterator node_iter = rCellPopulation.rGetMesh().GetNodeIteratorBegin();
node_iter != rCellPopulation.rGetMesh().GetNodeIteratorEnd();
++node_iter)
{
// Get the radius of this node
unsigned node_index = node_iter->GetIndex();
double node_radius = node_iter->GetRadius();
// Get cell associated with this index
CellPtr p_cell = rCellPopulation.GetCellUsingLocationIndex(node_index);
// Reject if no radius has been set
if (node_radius == 0.0)
{
EXCEPTION("SetRadius() must be called on each Node before calling TCellDiffusionForce::AddForceContribution() to avoid a division by zero error");
}
// If the selected cell is a Unlabelled Differentiated T Cell, apply diffusion force contribution.
if ( (p_cell->GetMutationState()->IsType<TCellMutationState>()) && (p_cell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
&& !(p_cell->HasCellProperty<CellLabel>()) )
{
double nu = dynamic_cast<AbstractOffLatticeCellPopulation<DIM>*>(&rCellPopulation)->GetDampingConstant(node_index);
/* Compute the diffusion coefficient D as D = k*T/(6*pi*eta*r), where
*
* k = Boltzmann's constant,
* T = absolute temperature,
* eta = dynamic viscosity,
* r = cell radius. */
double diffusion_const_scaling = GetDiffusionScalingConstant();
double diffusion_constant = diffusion_const_scaling/node_radius;
c_vector<double, DIM> force_contribution;
for (unsigned i=0; i<DIM; i++)
{
/* The force on this cell is scaled with the timestep such that when it is
* used in the discretised equation of motion for the cell, we obtain the
* correct formula
*
* x_new = x_old + sqrt(2*D*dt)*W
*
* where W is a standard normal random variable. */
double xi = RandomNumberGenerator::Instance()->StandardNormalRandomDeviate();
force_contribution[i] = mStrengthParameter * ((nu*sqrt(2.0*diffusion_constant*dt)/dt)*xi);
}
node_iter->AddAppliedForceContribution(force_contribution);
}
}
}
void MeshBasedCellPopulationWithGhostNodes<DIM>::ApplyGhostForces(){
// Initialise vector of forces on ghost nodes
std::vector<c_vector<double, DIM> > drdt(this->GetNumNodes());
for (unsigned i=0; i<drdt.size(); i++)
{
drdt[i] = zero_vector<double>(DIM);
}
// Calculate forces on ghost nodes
for (typename MutableMesh<DIM, DIM>::EdgeIterator edge_iterator = static_cast<MutableMesh<DIM, DIM>&>((this->mrMesh)).EdgesBegin();
edge_iterator != static_cast<MutableMesh<DIM, DIM>&>((this->mrMesh)).EdgesEnd();
++edge_iterator)
{
unsigned nodeA_global_index = edge_iterator.GetNodeA()->GetIndex();
unsigned nodeB_global_index = edge_iterator.GetNodeB()->GetIndex();
c_vector<double, DIM> force = CalculateForceBetweenGhostNodes(nodeA_global_index, nodeB_global_index);
if (!this->mIsGhostNode[nodeA_global_index])
{
drdt[nodeB_global_index] -= force;
}
else
{
drdt[nodeA_global_index] += force;
if (this->mIsGhostNode[nodeB_global_index])
{
drdt[nodeB_global_index] -= force;
}
}
}
for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
node_iter != this->mrMesh.GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
if (this->mIsGhostNode[node_index])
{
node_iter->ClearAppliedForce();
node_iter->AddAppliedForceContribution(drdt[node_index]);
}
}
};