void TestPottsBasedWithCoarseMeshTwoEquations() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a simple 2D PottsMesh
PottsMeshGenerator<2> generator(6, 2, 2, 6, 2, 2);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, p_mesh->GetNumElements(), p_diff_type);
// Create cell population
PottsBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set up cell-based simulation
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestPottsBasedCellPopulationWithTwoPdes");
simulator.SetEndTime(0.1);
// Set up PDE and pass to simulation via handler (zero uptake to check analytic solution)
AveragedSourcePde<2> pde_1(cell_population, 0.0);
ConstBoundaryCondition<2> bc_1(1.0);
PdeAndBoundaryConditions<2> pde_and_bc_1(&pde_1, &bc_1, false);
pde_and_bc_1.SetDependentVariableName("quantity 1");
AveragedSourcePde<2> pde_2(cell_population, 0.0);
ConstBoundaryCondition<2> bc_2(1.0);
PdeAndBoundaryConditions<2> pde_and_bc_2(&pde_2, &bc_2, false);
pde_and_bc_2.SetDependentVariableName("quantity 2");
CellBasedPdeHandler<2> pde_handler(&cell_population);
pde_handler.AddPdeAndBc(&pde_and_bc_1);
pde_handler.AddPdeAndBc(&pde_and_bc_2);
ChastePoint<2> lower(0.0, 0.0);
ChastePoint<2> upper(50.0, 50.0);
ChasteCuboid<2> cuboid(lower, upper);
pde_handler.UseCoarsePdeMesh(10.0, cuboid, true);
pde_handler.SetImposeBcsOnCoarseBoundary(true);
simulator.SetCellBasedPdeHandler(&pde_handler);
// Create update rules and pass to the simulation
MAKE_PTR(VolumeConstraintPottsUpdateRule<2>, p_volume_constraint_update_rule);
simulator.AddPottsUpdateRule(p_volume_constraint_update_rule);
MAKE_PTR(AdhesionPottsUpdateRule<2>, p_adhesion_update_rule);
simulator.AddPottsUpdateRule(p_adhesion_update_rule);
// Solve the system
simulator.Solve();
// Test solution is constant
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
double analytic_solution = 1.0;
// Test that PDE solver is working correctly on both pdes
TS_ASSERT_DELTA(cell_iter->GetCellData()->GetItem("quantity 1"), analytic_solution, 1e-2);
TS_ASSERT_DELTA(cell_iter->GetCellData()->GetItem("quantity 2"), analytic_solution, 1e-2);
}
#ifdef CHASTE_VTK
//First file exists
FileFinder vtk_file("TestPottsBasedCellPopulationWithTwoPdes/results_from_time_0/pde_results_1.vtu", RelativeTo::ChasteTestOutput);
TS_ASSERT(vtk_file.Exists());
// Check that the second VTK file for the solution has the dependent quantities
OutputFileHandler handler("TestPottsBasedCellPopulationWithTwoPdes", false);
VtkMeshReader<3,3> vtk_reader(handler.GetOutputDirectoryFullPath()+"results_from_time_0/pde_results_2.vtu");
std::vector<double> data1;
//There is no Oxygen
TS_ASSERT_THROWS_CONTAINS(vtk_reader.GetPointData("Oxygen", data1), "No point data");
TS_ASSERT(data1.empty());
vtk_reader.GetPointData("quantity 1", data1);
TS_ASSERT_EQUALS(data1.size(), 6u*6u);
std::vector<double> data2;
vtk_reader.GetPointData("quantity 2", data2);
TS_ASSERT_EQUALS(data1.size(), data2.size());
#endif //CHASTE_VTK
}
void TestPottsSpheroidCellSorting() throw (Exception)
{
EXIT_IF_PARALLEL; // Potts simulations don't work in parallel because they depend on NodesOnlyMesh for writing.
// Create a simple 3D PottsMesh
unsigned domain_size = 10;
unsigned element_number = 4;
unsigned element_size = 2;
PottsMeshGenerator<3> generator(domain_size, element_number, element_size, domain_size, element_number, element_size, domain_size, element_number, element_size);
PottsMesh<3>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 3> cells_generator;
cells_generator.GenerateBasicRandom(cells, p_mesh->GetNumElements(), p_diff_type);
// Randomly label some cells
boost::shared_ptr<AbstractCellProperty> p_label(CellPropertyRegistry::Instance()->Get<CellLabel>());
RandomlyLabelCells(cells, p_label, 0.5);
// Create cell population
PottsBasedCellPopulation<3> cell_population(*p_mesh, cells);
cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>(); // So outputs the labelled cells
// Set up cell-based simulation
OnLatticeSimulation<3> simulator(cell_population);
simulator.SetOutputDirectory("TestPotts3DCellSorting");
simulator.SetDt(0.1);
simulator.SetEndTime(1.0);
// Create update rules and pass to the simulation
MAKE_PTR(VolumeConstraintPottsUpdateRule<3>, p_volume_constraint_update_rule);
p_volume_constraint_update_rule->SetMatureCellTargetVolume(element_size*element_size*element_size);
p_volume_constraint_update_rule->SetDeformationEnergyParameter(0.2);
simulator.AddPottsUpdateRule(p_volume_constraint_update_rule);
MAKE_PTR(DifferentialAdhesionPottsUpdateRule<3>, p_differential_adhesion_update_rule);
p_differential_adhesion_update_rule->SetLabelledCellLabelledCellAdhesionEnergyParameter(0.16);
p_differential_adhesion_update_rule->SetLabelledCellCellAdhesionEnergyParameter(0.11);
p_differential_adhesion_update_rule->SetCellCellAdhesionEnergyParameter(0.02);
p_differential_adhesion_update_rule->SetLabelledCellBoundaryAdhesionEnergyParameter(0.16);
p_differential_adhesion_update_rule->SetCellBoundaryAdhesionEnergyParameter(0.16);
simulator.AddPottsUpdateRule(p_differential_adhesion_update_rule);
// Run simulation
simulator.Solve();
// Check that the same number of cells
TS_ASSERT_EQUALS(simulator.rGetCellPopulation().GetNumRealCells(), 64u);
// Test no births or deaths
TS_ASSERT_EQUALS(simulator.GetNumBirths(), 0u);
TS_ASSERT_EQUALS(simulator.GetNumDeaths(), 0u);
#ifdef CHASTE_VTK
// Test that VTK writer has produced some files
OutputFileHandler handler("TestPotts3DCellSorting", false);
std::string results_dir = handler.GetOutputDirectoryFullPath();
// Initial condition file
FileFinder vtk_file(results_dir + "results_from_time_0/results_0.vtu", RelativeTo::Absolute);
TS_ASSERT(vtk_file.Exists());
// Final file
FileFinder vtk_file2(results_dir + "results_from_time_0/results_10.vtu", RelativeTo::Absolute);
TS_ASSERT(vtk_file2.Exists());
// Check that the second VTK file for Potts specific data (element IDs)
VtkMeshReader<3,3> vtk_reader(results_dir + "results_from_time_0/results_10.vtu");
std::vector<double> cell_types;
vtk_reader.GetPointData("Cell types", cell_types);
TS_ASSERT_EQUALS(cell_types.size(), 1000u);
// The cell types are between -1 and 5. Check the maximum
TS_ASSERT_DELTA(*max_element(cell_types.begin(), cell_types.end()), 5.0, 1e-12);
std::vector<double> cell_ids;
vtk_reader.GetPointData("Cell IDs", cell_ids);
// Prior to release 3.2 this was called "Element index".
// It is changed to cell_id as this is preferable for VTK output.
TS_ASSERT_EQUALS(cell_ids.size(), 1000u);
TS_ASSERT_DELTA(*max_element(cell_ids.begin(), cell_ids.end()), 63.0, 1e-12);
#endif //CHASTE_VTK
}
