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]); } } };