void NodeBasedCellPopulationWithParticles<DIM>::UpdateParticlePositions(double dt) { // Initialise vector of forces on particles 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 particles double damping_constant = this->GetDampingConstantNormal(); for (unsigned i=0; i<drdt.size(); i++) { drdt[i] = this->GetNode(i)->rGetAppliedForce()/damping_constant; } for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin(); node_iter != this->mrMesh.GetNodeIteratorEnd(); ++node_iter) { if (node_iter->IsParticle()) { ChastePoint<DIM> new_point(node_iter->rGetLocation() + dt*drdt[node_iter->GetIndex()]); node_iter->SetPoint(new_point); } } }
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 ForwardEulerNumericalMethod<ELEMENT_DIM,SPACE_DIM>::UpdateAllNodePositions(double dt) { if (!this->mUseUpdateNodeLocation) { // Apply forces to each cell, and save a vector of net forces F std::vector<c_vector<double, SPACE_DIM> > forces = this->ComputeForcesIncludingDamping(); unsigned index = 0; for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mpCellPopulation->rGetMesh().GetNodeIteratorBegin(); node_iter != this->mpCellPopulation->rGetMesh().GetNodeIteratorEnd(); ++node_iter, ++index) { // Get the current node location and calculate the new location according to the forward Euler method const c_vector<double, SPACE_DIM>& r_old_location = node_iter->rGetLocation(); c_vector<double, SPACE_DIM> displacement = dt * forces[index]; // In the vertex-based case, the displacement may be scaled if the cell rearrangement threshold is exceeded this->DetectStepSizeExceptions(node_iter->GetIndex(), displacement, dt); c_vector<double, SPACE_DIM> new_location = r_old_location + displacement; this->SafeNodePositionUpdate(node_iter->GetIndex(), new_location); } } else { /* * If this type of cell population does not support the new numerical methods, delegate * updating node positions to the population itself. * * This only applies to NodeBasedCellPopulationWithBuskeUpdates. */ this->mpCellPopulation->UpdateNodeLocations(dt); } }