NodeBasedCellPopulationWithParticles<DIM>::NodeBasedCellPopulationWithParticles(NodesOnlyMesh<DIM>& rMesh,
std::vector<CellPtr>& rCells,
const std::vector<unsigned> locationIndices,
bool deleteMesh)
: NodeBasedCellPopulation<DIM>(rMesh, rCells, locationIndices, deleteMesh, false)
{
EXCEPT_IF_NOT(PetscTools::IsSequential());
if (!locationIndices.empty())
{
// Create a set of node indices corresponding to particles
std::set<unsigned> node_indices;
std::set<unsigned> location_indices;
std::set<unsigned> particle_indices;
for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = rMesh.GetNodeIteratorBegin();
node_iter != rMesh.GetNodeIteratorEnd();
++node_iter)
{
node_indices.insert(node_iter->GetIndex());
}
for (unsigned i=0; i<locationIndices.size(); i++)
{
location_indices.insert(locationIndices[i]);
}
std::set_difference(node_indices.begin(), node_indices.end(),
location_indices.begin(), location_indices.end(),
std::inserter(particle_indices, particle_indices.begin()));
// This method finishes and then calls Validate()
SetParticles(particle_indices);
}
else
{
for (typename NodesOnlyMesh<DIM>::NodeIterator node_iter = rMesh.GetNodeIteratorBegin();
node_iter != rMesh.GetNodeIteratorEnd();
++node_iter)
{
(*node_iter).SetIsParticle(false);
}
NodeBasedCellPopulationWithParticles::Validate();
}
}
void TestUpdateCellLocationsAndTopologyWithNoForce()
{
// Creates nodes and mesh
std::vector<Node<2>*> nodes;
nodes.push_back(new Node<2>(0, false, 0.0, 0.0));
nodes.push_back(new Node<2>(0, false, 0.0, 0.3));
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(nodes, 1.5);
// Create cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes());
// Create a node based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
node_based_cell_population.SetAbsoluteMovementThreshold(1e-6);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetEndTime(0.1);
simulator.SetOutputDirectory("TestOffLatticeSimulationUpdateCellLocationsAndTopologyWithNoForce");
simulator.SetupSolve();
simulator.UpdateCellLocationsAndTopology();
if (PetscTools::AmMaster())
{
for (AbstractMesh<2,2>::NodeIterator node_iter = mesh.GetNodeIteratorBegin();
node_iter != mesh.GetNodeIteratorEnd();
++node_iter)
{
for (unsigned d=0; d<2; d++)
{
TS_ASSERT_DELTA(node_iter->rGetAppliedForce()[d], 0.0, 1e-15);
}
}
}
// Avoid memory leak
delete nodes[0];
delete nodes[1];
}
void TestVertexCryptBoundaryForceForceWithNonVertexCellPopulation() throw (Exception)
{
// Create a NodeBasedCellPopulation
std::vector<Node<2>*> nodes;
unsigned num_nodes = 10;
for (unsigned i=0; i<num_nodes; i++)
{
double x = (double)(i);
double y = (double)(i);
nodes.push_back(new Node<2>(i, true, x, y));
}
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(nodes, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> non_vertex_cell_population(mesh, cells);
for (AbstractMesh<2,2>::NodeIterator node_iter = mesh.GetNodeIteratorBegin();
node_iter != mesh.GetNodeIteratorEnd();
++node_iter)
{
node_iter->ClearAppliedForce();
}
// Test that VertexCryptBoundaryForce throws the correct exception
VertexCryptBoundaryForce<2> force(100);
TS_ASSERT_THROWS_THIS(force.AddForceContribution(non_vertex_cell_population),
"VertexCryptBoundaryForce is to be used with VertexBasedCellPopulations only");
// Avoid memory leak
for (unsigned i=0; i<nodes.size(); i++)
{
delete nodes[i];
}
}
void TestRemoveDeadCellsAndReMeshWithParticles()
{
EXIT_IF_PARALLEL; // This test doesn't work in parallel.
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(10.0, 1);
// Create a simple mesh
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_128_elements");
TetrahedralMesh<2,2> generating_mesh;
generating_mesh.ConstructFromMeshReader(mesh_reader);
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(generating_mesh, 1.2);
// Create vector of cell location indices
std::vector<unsigned> cell_location_indices;
for (unsigned i=10; i<mesh.GetNumNodes(); i++)
{
if (i != 80)
{
cell_location_indices.push_back(i);
}
}
// Set up cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, cell_location_indices.size());
cells[27]->StartApoptosis();
// Create a cell population, with some random particles
NodeBasedCellPopulationWithParticles<2> cell_population_with_particles(mesh, cells, cell_location_indices);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 81u);
// Num real cells should be num_nodes (81) - num_particles (11) = 70
TS_ASSERT_EQUALS(cell_population_with_particles.GetNumRealCells(), 70u);
p_simulation_time->IncrementTimeOneStep();
unsigned num_removed_with_particles = cell_population_with_particles.RemoveDeadCells();
TS_ASSERT_EQUALS(num_removed_with_particles, 1u);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 80u);
TS_ASSERT_DIFFERS(cell_population_with_particles.rGetCells().size(), cells.size()); // CellPopulation now copies cells
// Num real cells should be num_nodes (81) - num_particle (11) - 1 deleted node = 69
TS_ASSERT_EQUALS(cell_population_with_particles.GetNumRealCells(), 69u);
cell_population_with_particles.Update();
// For coverage
NodeMap map(mesh.GetNumAllNodes());
map.ResetToIdentity();
cell_population_with_particles.UpdateParticlesAfterReMesh(map);
// Num real cells should be new_num_nodes (80) - num_particles (11)
TS_ASSERT_EQUALS(cell_population_with_particles.GetNumRealCells(), 69u);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), mesh.GetNumAllNodes());
// Nodes 0-9 should not been renumbered so are still particles.
// the particle at node 80 is now at 79 as node 27 was deleted..
for (AbstractMesh<2,2>::NodeIterator node_iter = mesh.GetNodeIteratorBegin();
node_iter != mesh.GetNodeIteratorEnd();
++node_iter)
{
unsigned index = node_iter->GetIndex();
// True (ie should be a particle) if i<10 or i==79, else false
TS_ASSERT_EQUALS(cell_population_with_particles.IsParticle(index), ((index<10)||(index==80)));
}
// Finally, check the cells node indices have updated
// We expect the cell node indices to be {10,11,...,79}
std::set<unsigned> expected_node_indices;
for (unsigned i=0; i<cell_population_with_particles.GetNumRealCells(); i++)
{
if (i!=27)
{
expected_node_indices.insert(i+10);
}
}
expected_node_indices.insert(79);
// Get actual cell node indices
std::set<unsigned> node_indices_with_particles;
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population_with_particles.Begin();
cell_iter != cell_population_with_particles.End();
++cell_iter)
{
// Record node index corresponding to cell
unsigned node_index_with_particles = cell_population_with_particles.GetLocationIndexUsingCell(*cell_iter);
node_indices_with_particles.insert(node_index_with_particles);
}
TS_ASSERT_EQUALS(node_indices_with_particles, expected_node_indices);
}