/*
* Here we set up a test with 5 nodes, make a cell for each. We then set cell
* 0 to be associated with node 1 instead of node 0, and Validate() throws an
* exception. We then set node 0 to be a particle node, and Validate() passes.
*/
void TestValidateNodeBasedCellPopulationWithParticles() throw(Exception)
{
EXIT_IF_PARALLEL; // This test doesn't work in parallel.
// Create a simple mesh
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> generating_mesh;
generating_mesh.ConstructFromMeshReader(mesh_reader);
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes()-1);
std::vector<unsigned> cell_location_indices;
for (unsigned i=0; i<cells.size(); i++)
{
cell_location_indices.push_back(i);
}
// Fails as the cell population constructor is not given the location indices
// corresponding to real cells, so cannot work out which nodes are
// particles
std::vector<CellPtr> cells_copy(cells);
TS_ASSERT_THROWS_THIS(NodeBasedCellPopulationWithParticles<2> dodgy_cell_population(mesh, cells_copy),
"Node 4 does not appear to be a particle or has a cell associated with it");
// Passes as the cell population constructor automatically works out which
// cells are particles using the mesh and cell_location_indices
NodeBasedCellPopulationWithParticles<2> cell_population(mesh, cells, cell_location_indices);
// Here we set the particles to what they already are
std::set<unsigned> particle_indices;
particle_indices.insert(mesh.GetNumNodes()-1);
cell_population.SetParticles(particle_indices);
// So validate passes at the moment
cell_population.Validate();
// Test GetCellUsingLocationIndex()
TS_ASSERT_THROWS_NOTHING(cell_population.GetCellUsingLocationIndex(0)); // real cell
TS_ASSERT_THROWS_THIS(cell_population.GetCellUsingLocationIndex(mesh.GetNumNodes()-1u),"Location index input argument does not correspond to a Cell"); // particles
// Now we label a real cell's node as particle
particle_indices.insert(1);
// Validate detects this inconsistency
TS_ASSERT_THROWS_THIS(cell_population.SetParticles(particle_indices),"Node 1 is labelled as a particle and has a cell attached");
}
/*
* EMPTYLINE
*
* To visualize the results, open a new terminal, {{{cd}}} to the Chaste directory,
* then {{{cd}}} to {{{anim}}}. Then do: {{{java Visualize2dCentreCells /tmp/$USER/testoutput/NodeBasedMonolayer/results_from_time_0}}}.
* we need to select the 'Cells as circles` option to be able to visualize the cells, as opposed
* to just the centres.
* We may have to do: {{{javac Visualize2dCentreCells.java}}} beforehand to create the
* java executable.
*
* Alternatively, to view in Paraview, load the file {{{/tmp/$USER/testoutput/NodeBasedMonolayer/results_from_time_0/results.pvd}}}
* and add glyphs to represent cells. An option is to use 3D spherical glyphs and then make a planar cut.
* Note that, for larger simulations, you may need to unclick "Mask Points" (or similar) so as not to limit the number of glyphs
* displayed by Paraview.
*
*
*
* EMPTYLINE
*
* == Test 2 - a basic node-based simulation in 3D ==
*
* EMPTYLINE
*
* In the second test we run a simple node-based simulation in 3D. This is very similar
* to the 2D test with the dimension template (<2,2> and <2>) changed from 2 to 3 and instead of using a mesh
* generator we generate the nodes directly.
*/
void TestSpheroid()
{
/** The next line is needed because we cannot currently run node based simulations in parallel. */
EXIT_IF_PARALLEL;
/*
* First, we generate a nodes only mesh. This time we specify the nodes manually by first
* creating a vector of nodes. */
std::vector<Node<3>*> nodes;
/* We then create some nodes to add to this vector. */
nodes.push_back(new Node<3>(0u, false, 0.5, 0.0, 0.0));
nodes.push_back(new Node<3>(1u, false, -0.5, 0.0, 0.0));
nodes.push_back(new Node<3>(2u, false, 0.0, 0.5, 0.0));
nodes.push_back(new Node<3>(3u, false, 0.0, -0.5, 0.0));
/* Finally a {{{NodesOnlyMesh}}} is created and the vector of nodes is passed to
* the {{{ConstructNodesWithoutMesh}}} method. */
NodesOnlyMesh<3> mesh;
/* To run node-based simulations you need to define a cut off length (second argument in
* {{{ConstructNodesWithoutMesh}}}), which defines the connectivity of the nodes by defining
* a radius of interaction. */
mesh.ConstructNodesWithoutMesh(nodes, 1.5);
/*
* Having created a mesh, we now create a {{{std::vector}}} of {{{CellPtr}}}s.
* As before, we do this with the `CellsGenerator` helper class (this time with dimension 3).
*/
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<UniformCellCycleModel, 3> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
/* We make a {{{NodeBasedCellPopulation}}} (this time with dimension 3) as before.
*/
NodeBasedCellPopulation<3> cell_population(mesh, cells);
/* We then pass in the cell population into an {{{OffLatticeSimulation}}},
* (this time with dimension 3) and set the output directory, output multiple and end time. */
OffLatticeSimulation<3> simulator(cell_population);
simulator.SetOutputDirectory("NodeBasedSpheroid");
simulator.SetSamplingTimestepMultiple(12);
simulator.SetEndTime(10.0);
/* Again we create a force law (this time with dimension 3), and pass it to the {{{OffLatticeSimulation}}}.*/
MAKE_PTR(GeneralisedLinearSpringForce<3>, p_force);
simulator.AddForce(p_force);
/* To run the simulation, we call {{{Solve()}}}. */
simulator.Solve();
/* The next two lines are for test purposes only and are not part of this tutorial.
*/
TS_ASSERT_EQUALS(cell_population.GetNumRealCells(), 8u);
TS_ASSERT_DELTA(SimulationTime::Instance()->GetTime(), 10.0, 1e-10);
/* To avoid memory leaks, we conclude by deleting any pointers that we created in the test.*/
for (unsigned i=0; i<nodes.size(); i++)
{
delete nodes[i];
}
}
void TestConstruct2dParallelPopulation() throw (Exception)
{
NodesOnlyMesh<2> mesh;
mesh.SetMaximumInteractionDistance(0.5);
std::vector<CellPtr> cells;
ParallelCellsGenerator<StochasticDurationGenerationBasedCellCycleModel, 2> generator;
c_vector<double, 4> bounding_box = generator.GetArchiveBoundingBox("cell_based/test/data/TestParallelConstruction/Population2d.dat");
TS_ASSERT_DELTA(bounding_box[0], 0.0, 1e-4);
TS_ASSERT_DELTA(bounding_box[1], 1.0, 1e-4);
TS_ASSERT_DELTA(bounding_box[2], 0.0, 1e-4);
TS_ASSERT_DELTA(bounding_box[3], 1.0, 1e-4);
generator.GenerateParallelCells("cell_based/test/data/TestParallelConstruction/Population2d.dat", cells, mesh, CellPropertyRegistry::Instance()->Get<TransitCellProliferativeType>());
unsigned num_nodes = mesh.GetNumNodes();
unsigned total_nodes;
MPI_Allreduce(&num_nodes, &total_nodes, 1, MPI_UNSIGNED, MPI_SUM, PetscTools::GetWorld());
TS_ASSERT_EQUALS(total_nodes, 4u);
unsigned num_cells = cells.size();
unsigned total_cells;
MPI_Allreduce(&num_cells, &total_cells, 1, MPI_UNSIGNED, MPI_SUM, PetscTools::GetWorld());
TS_ASSERT_EQUALS(total_cells, 4u);
for (unsigned i=0; i<cells.size(); i++)
{
TS_ASSERT(cells[i]->GetCellProliferativeType()->IsType<TransitCellProliferativeType>());
}
}
void TestConstruct1dParallelPopulation() throw (Exception)
{
NodesOnlyMesh<1> mesh;
mesh.SetMaximumInteractionDistance(0.5);
std::vector<CellPtr> cells;
ParallelCellsGenerator<FixedDurationGenerationBasedCellCycleModel, 1> generator;
c_vector<double, 2> bounding_box = generator.GetArchiveBoundingBox("cell_based/test/data/TestParallelConstruction/Population1d.dat");
TS_ASSERT_DELTA(bounding_box[0], 0.0, 1e-4);
TS_ASSERT_DELTA(bounding_box[1], 1.0, 1e-4);
// Check an assertion which tests whether the space dimensions of the mesh and archive file are consistent.
TS_ASSERT_THROWS_THIS(generator.GetArchiveBoundingBox("cell_based/test/data/TestParallelConstruction/Population2d.dat"), "Space dimension of ParallelCellsGenerator and archive file do not match");
generator.GenerateParallelCells("cell_based/test/data/TestParallelConstruction/Population1d.dat", cells, mesh, CellPropertyRegistry::Instance()->Get<DifferentiatedCellProliferativeType>());
unsigned num_nodes = mesh.GetNumNodes();
unsigned total_nodes;
MPI_Allreduce(&num_nodes, &total_nodes, 1, MPI_UNSIGNED, MPI_SUM, PetscTools::GetWorld());
TS_ASSERT_EQUALS(total_nodes, 2u);
unsigned num_cells = cells.size();
unsigned total_cells;
MPI_Allreduce(&num_cells, &total_cells, 1, MPI_UNSIGNED, MPI_SUM, PetscTools::GetWorld());
TS_ASSERT_EQUALS(total_cells, 2u);
for (unsigned i=0; i<cells.size(); i++)
{
TS_ASSERT(cells[i]->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>());
}
}
void TestConstructor() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a cell population
HoneycombMeshGenerator generator(2, 2, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
// Test that member variables are initialised correctly
TS_ASSERT_EQUALS(pde_handler.GetCellPopulation(), &cell_population);
TS_ASSERT_EQUALS(pde_handler.GetWriteAverageRadialPdeSolution(), false);
TS_ASSERT_EQUALS(pde_handler.GetWriteDailyAverageRadialPdeSolution(), false);
TS_ASSERT_EQUALS(pde_handler.GetImposeBcsOnCoarseBoundary(), true);
TS_ASSERT_EQUALS(pde_handler.GetNumRadialIntervals(), UNSIGNED_UNSET);
TS_ASSERT(pde_handler.GetCoarsePdeMesh() == NULL);
}
void TestVolumeDependentAveragedSourcePdeArchiving() throw(Exception)
{
EXIT_IF_PARALLEL;
// Set up simulation time
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0, 1);
// Set up cell population
HoneycombMeshGenerator generator(5, 5, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "VolumeDependentAveragedSourcePde.arch";
ArchiveLocationInfo::SetMeshFilename("VolumeDependentAveragedSourcePde");
{
// Create a PDE object
AbstractLinearEllipticPde<2,2>* const p_pde = new VolumeDependentAveragedSourcePde<2>(cell_population, 0.05);
// Create output archive and archive PDE object
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
(*p_arch) << p_pde;
// Avoid memory leak
delete p_pde;
}
{
AbstractLinearEllipticPde<2,2>* p_pde;
// Create an input archive and restore PDE object from archive
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
(*p_arch) >> p_pde;
// Test that the PDE and its member variables were archived correctly
TS_ASSERT(dynamic_cast<VolumeDependentAveragedSourcePde<2>*>(p_pde) != NULL);
VolumeDependentAveragedSourcePde<2>* p_static_cast_pde = static_cast<VolumeDependentAveragedSourcePde<2>*>(p_pde);
TS_ASSERT_DELTA(p_static_cast_pde->GetCoefficient(), 0.05, 1e-6);
TS_ASSERT_EQUALS(p_static_cast_pde->mrCellPopulation.GetNumRealCells(), 25u);
TS_ASSERT(p_static_cast_pde->mpStaticCastCellPopulation != NULL);
TS_ASSERT_EQUALS(p_static_cast_pde->mpStaticCastCellPopulation->GetNumRealCells(), 25u);
// Avoid memory leaks
delete &(p_static_cast_pde->mrCellPopulation);
delete p_pde;
}
}
void TestStandardResultForArchivingTestsBelow() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenereator does not work in parallel.
// Create a simple mesh
int num_cells_depth = 5;
int num_cells_width = 5;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 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);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithNodeBasedCellPopulationStandardResult");
simulator.SetEndTime(2.5);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Create some boundary conditions and pass them to the simulation
c_vector<double,2> normal = zero_vector<double>(2);
normal(1) =-1.0;
MAKE_PTR_ARGS(PlaneBoundaryCondition<2>, p_bc, (&node_based_cell_population, zero_vector<double>(2), normal)); // y>0
simulator.AddCellPopulationBoundaryCondition(p_bc);
// Solve
simulator.Solve();
// Check some results
mNode3x = 3.0454;
mNode3y = 0.0000;
mNode4x = 4.0468;
mNode4y = 0.0101;
std::vector<double> node_3_location = simulator.GetNodeLocation(3);
TS_ASSERT_DELTA(node_3_location[0], mNode3x, 1e-4);
TS_ASSERT_DELTA(node_3_location[1], mNode3y, 1e-4);
std::vector<double> node_4_location = simulator.GetNodeLocation(4);
TS_ASSERT_DELTA(node_4_location[0], mNode4x, 1e-4);
TS_ASSERT_DELTA(node_4_location[1], mNode4y, 1e-4);
}
void TestUpdateCellProcessLocation() throw (Exception)
{
if (PetscTools::GetNumProcs() > 1)
{
if (PetscTools::AmMaster())
{
// Move node to the next location.
c_vector<double, 3> new_location = zero_vector<double>(3);
new_location[2] = 1.6;
ChastePoint<3> point(new_location);
mpNodesOnlyMesh->GetNode(0)->SetPoint(point);
}
if (PetscTools::GetMyRank() == 1)
{
// Move node to the next location.
c_vector<double, 3> new_location = zero_vector<double>(3);
new_location[2] = 0.5;
ChastePoint<3> point(new_location);
mpNodesOnlyMesh->GetNode(1)->SetPoint(point);
}
#if BOOST_VERSION < 103700
TS_ASSERT_THROWS_THIS(mpNodeBasedCellPopulation->SendCellsToNeighbourProcesses(),
"Parallel cell-based Chaste requires Boost >= 1.37");
#else
mpNodeBasedCellPopulation->UpdateCellProcessLocation();
if (PetscTools::AmMaster())
{
TS_ASSERT_EQUALS(mpNodesOnlyMesh->GetNumNodes(), 1u);
TS_ASSERT_EQUALS(mpNodeBasedCellPopulation->GetNumRealCells(), 1u);
}
if (PetscTools::GetMyRank() == 1)
{
TS_ASSERT_EQUALS(mpNodesOnlyMesh->GetNumNodes(), 1u);
TS_ASSERT_EQUALS(mpNodeBasedCellPopulation->GetNumRealCells(), 1u);
AbstractMesh<3,3>::NodeIterator node_iter = mpNodesOnlyMesh->GetNodeIteratorBegin();
TS_ASSERT_DELTA(node_iter->rGetLocation()[2], 1.6, 1e-4);
}
#endif
}
}
// Testing Save()
void TestSave() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenereator does not work in parallel
// Create a simple mesh
unsigned num_cells_depth = 5;
unsigned num_cells_width = 5;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 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);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithNodeBasedCellPopulationSaveAndLoad");
simulator.SetEndTime(0.1);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Create some boundary conditions and pass them to the simulation
c_vector<double,2> normal = zero_vector<double>(2);
normal(1) =-1.0;
MAKE_PTR_ARGS(PlaneBoundaryCondition<2>, p_bc, (&node_based_cell_population, zero_vector<double>(2), normal)); // y>0
simulator.AddCellPopulationBoundaryCondition(p_bc);
/*
* For more thorough testing of serialization, we 'turn on' adaptivity.
* Note that this has no effect on the numerical results, since the
* conditions under which the time step would be adapted are not invoked
* in this example.
*/
boost::shared_ptr<AbstractNumericalMethod<2,2> > p_method(new ForwardEulerNumericalMethod<2,2>());
p_method->SetUseAdaptiveTimestep(true);
simulator.SetNumericalMethod(p_method);
// Solve
simulator.Solve();
// Save the results
CellBasedSimulationArchiver<2, OffLatticeSimulation<2> >::Save(&simulator);
}
/**
* Create a simulation of a NodeBasedCellPopulation with a NodeBasedCellPopulationMechanicsSystem.
* Test that no exceptions are thrown, and write the results to file.
*/
void TestSimpleMonolayer() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenereator does not work in parallel.
// Create a simple mesh
unsigned num_cells_depth = 5;
unsigned num_cells_width = 5;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 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);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithNodeBasedCellPopulation");
// No need to go for long, don't want any birth or regular grid will be disrupted.
simulator.SetEndTime(0.5);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
simulator.Solve();
// Check that nothing's gone badly wrong by testing that nodes aren't too close together
double min_distance_between_cells = 1.0;
for (unsigned i=0; i<simulator.rGetCellPopulation().GetNumNodes(); i++)
{
for (unsigned j=i+1; j<simulator.rGetCellPopulation().GetNumNodes(); j++)
{
double distance = norm_2(simulator.rGetCellPopulation().GetNode(i)->rGetLocation()-simulator.rGetCellPopulation().GetNode(j)->rGetLocation());
if (distance < min_distance_between_cells)
{
min_distance_between_cells = distance;
}
}
}
TS_ASSERT(min_distance_between_cells > 0.999);
}
/**
* Create a simulation of a NodeBasedCellPopulation with a BuskeCompressionForce system.
* Test that no exceptions are thrown, and write the results to file.
*/
void TestSimpleMonolayerWithBuskeCompressionForce() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesn't work in parallel
// Create a simple mesh
unsigned num_cells_depth = 5;
unsigned num_cells_width = 5;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
// Create a node-based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithBuskeCompressionForce");
simulator.SetEndTime(5.0);
// Create a force law and pass it to the simulation
MAKE_PTR(BuskeCompressionForce<2>, buske_compression_force);
buske_compression_force->SetCompressionEnergyParameter(0.01);
simulator.AddForce(buske_compression_force);
simulator.Solve();
// Check that nothing's gone badly wrong by testing that nodes aren't too close together
double min_distance_between_cells = 1.0;
for (unsigned i=0; i<simulator.rGetCellPopulation().GetNumNodes(); i++)
{
for (unsigned j=i+1; j<simulator.rGetCellPopulation().GetNumNodes(); j++)
{
double distance = norm_2(simulator.rGetCellPopulation().GetNode(i)->rGetLocation()-simulator.rGetCellPopulation().GetNode(j)->rGetLocation());
if (distance < min_distance_between_cells)
{
min_distance_between_cells = distance;
}
}
}
TS_ASSERT(min_distance_between_cells > 1e-3);
}
void TestVolumeDependentAveragedSourcePdeMethods() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a cell population
HoneycombMeshGenerator generator(5, 5, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE object
VolumeDependentAveragedSourcePde<2> pde(cell_population, 0.05);
// Test that the member variables have been initialised correctly
TS_ASSERT(pde.mpStaticCastCellPopulation != NULL);
// For simplicity we create a very large coarse mesh, so we know that all cells are contained in one element
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_2_elements");
TetrahedralMesh<2,2> coarse_mesh;
coarse_mesh.ConstructFromMeshReader(mesh_reader);
coarse_mesh.Scale(10.0, 10.0);
// Test SetupSourceTerms() when no map between cells and coarse mesh elements is supplied
pde.SetupSourceTerms(coarse_mesh);
TS_ASSERT_EQUALS(pde.mCellDensityOnCoarseElements.size(), 2u);
// The first element has area 0.5*10*10 = 50 and there are 5*5 = 25 cells, so the cell density is 25/50 = 0.5
// The radius of each node is 0.5 and the density is normalized with cell area (1/4.0) in `VolumeDependentAveragedSourcePde`.
TS_ASSERT_DELTA(pde.mCellDensityOnCoarseElements[0], 0.5/4.0, 1e-6);
// The first element doesn't contain any cells, so the cell density is zero
TS_ASSERT_DELTA(pde.mCellDensityOnCoarseElements[1], 0.0, 1e-6);
// Now test SetupSourceTerms() when a map between cells and coarse mesh elements is supplied
std::map<CellPtr, unsigned> cell_pde_element_map;
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
cell_pde_element_map[*cell_iter] = 0;
}
pde.SetupSourceTerms(coarse_mesh, &cell_pde_element_map);
TS_ASSERT_DELTA(pde.mCellDensityOnCoarseElements[0], 0.5/4.0, 1e-6);
TS_ASSERT_DELTA(pde.mCellDensityOnCoarseElements[1], 0.0, 1e-6);
}
void TestInitialiseCellPdeElementMapAndFindCoarseElementContainingCell() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a cell population
HoneycombMeshGenerator generator(4, 4, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
TS_ASSERT_EQUALS(pde_handler.mCellPdeElementMap.size(), 0u);
// Test that InitialiseCellPdeElementMap() throws an exception if mpCoarsePdeMesh is not set up
TS_ASSERT_THROWS_THIS(pde_handler.InitialiseCellPdeElementMap(),
"InitialiseCellPdeElementMap() should only be called if mpCoarsePdeMesh is set up.");
// Set up PDE and pass to handler
AveragedSourcePde<2> pde(cell_population, -0.1);
ConstBoundaryCondition<2> bc(1.0);
PdeAndBoundaryConditions<2> pde_and_bc(&pde, &bc, false);
pde_handler.AddPdeAndBc(&pde_and_bc);
// Use a coarse PDE mesh
ChastePoint<2> lower(0.0, 0.0);
ChastePoint<2> upper(9.0, 9.0);
ChasteCuboid<2> cuboid(lower, upper);
pde_handler.UseCoarsePdeMesh(3.0, cuboid, true);
// Test that mCellPdeElementMap is initialised correctly
pde_handler.InitialiseCellPdeElementMap();
TS_ASSERT_EQUALS(pde_handler.mCellPdeElementMap.size(), cell_population.GetNumRealCells());
for (AbstractCellPopulation<2>::Iterator cell_iter = cell_population.Begin();
cell_iter != cell_population.End();
++cell_iter)
{
unsigned containing_element_index = pde_handler.mCellPdeElementMap[*cell_iter];
TS_ASSERT_LESS_THAN(containing_element_index, pde_handler.GetCoarsePdeMesh()->GetNumElements());
TS_ASSERT_EQUALS(containing_element_index, pde_handler.FindCoarseElementContainingCell(*cell_iter));
}
}
/*
* To visualize the results, open a new terminal, {{{cd}}} to the Chaste directory,
* then {{{cd}}} to {{{anim}}}. Then do: {{{java Visualize2dVertexCells /tmp/$USER/testoutput/CellBasedDemo1/results_from_time_0}}}.
* We may have to do: {{{javac Visualize2dVertexCells.java}}} beforehand to create the
* java executable.
*
* EMPTYLINE
*
* The {{{make_a_movie}}} script can be used to generate a video based on the results of your simulation.
* To do this, first visualize the results using {{{Visualize2dVertexCells}}} as described above. Click
* on the box marked "Output" and play through the whole simulation to generate a sequence of {{{.png}}}
* images, one for each time step. Next, still in the {{{anim}}} folder, do: {{{./make_a_movie}}}.
* This reads in the {{{.png}}} files and creates a video file called {{{simulation.mpeg}}}.
*
* EMPTYLINE
*
* Results can also be visualized using Paraview. See the UserTutorials/VisualizingWithParaview tutorial for more information.
*
* EMPTYLINE
*
* == Test 2 - basic node-based simulation ==
*
* We next show how to modify the previous test to implement a 'node-based' simulation,
* in which cells are represented by overlapping spheres (actually circles, since we're
* in 2D).
*/
void TestNodeBasedMonolayer() throw (Exception)
{
/* We now need to create a {{{NodesOnlyMesh}}} we do this by first creating a {{{MutableMesh}}}
* and passing this to a helper method {{{ConstructNodesWithoutMesh}}} along with a interaction cut off length
* that defines the connectivity in the mesh.
*/
HoneycombMeshGenerator generator(2, 2); //**Changed**//
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh(); //**Changed**//
NodesOnlyMesh<2> mesh; //**Changed**//
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5); //**Changed**//
/* We create the cells as before, only this time we need one cell per node.*/
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<StochasticDurationCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type); //**Changed**//
/* This time we create a {{{NodeBasedCellPopulation}}} as we are using a {{{NodesOnlyMesh}}}.*/
NodeBasedCellPopulation<2> cell_population(mesh, cells);//**Changed**//
/* We create an {{{OffLatticeSimulation}}} object as before, all we change is the output directory
* and output results more often as a larger default timestep is used for these simulations. */
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("CellBasedDemo2"); //**Changed**//
simulator.SetSamplingTimestepMultiple(12); //**Changed**//
simulator.SetEndTime(20.0);
/* We use a different {{{Force}}} which is suitable for node based simulations.
*/
MAKE_PTR(RepulsionForce<2>, p_force); //**Changed**//
simulator.AddForce(p_force);
/* In all types of simulation you may specify how cells are removed from the simulation by specifying
* a {{{CellKiller}}}. You create these in the same was as the {{{Force}}} and pass them to the {{{CellBasedSimulation}}}.
* Note that here the constructor for {{{RandomCellKiller}}} requires some arguments to be passed to it, therefore we use the
* {{{MAKE_PTR_ARGS}}} macro.
*/
MAKE_PTR_ARGS(RandomCellKiller<2>, p_cell_killer, (&cell_population, 0.01)); //**Changed**//
simulator.AddCellKiller(p_cell_killer);
/* Again we call the {{{Solve}}} method on the simulation to run the simulation.*/
simulator.Solve();
/* The next two lines are for test purposes only and are not part of this tutorial.
* Again, we are checking that we reached the end time of the simulation
* with the correct number of cells.
*/
TS_ASSERT_EQUALS(cell_population.GetNumRealCells(), 7u);
TS_ASSERT_DELTA(SimulationTime::Instance()->GetTime(), 20.0, 1e-10);
}
void TestUseCoarsePdeMeshNotCentredOnPopulation() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a cell population
HoneycombMeshGenerator generator(4, 4, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
// Test that UseCoarsePdeMesh() throws an exception if no PDEs are specified
ChastePoint<2> lower(0.0, 0.0);
ChastePoint<2> upper(9.0, 9.0);
ChasteCuboid<2> cuboid(lower, upper);
// Set up PDE and pass to handler
AveragedSourcePde<2> pde(cell_population, -0.1);
ConstBoundaryCondition<2> bc(1.0);
PdeAndBoundaryConditions<2> pde_and_bc(&pde, &bc, false);
pde_handler.AddPdeAndBc(&pde_and_bc);
// Test UseCoarsePdeMesh() again
pde_handler.UseCoarsePdeMesh(3.0, cuboid);
// Check that the centre of the mesh co-incides with centre of the cuboid.
c_vector<double,2> centre_of_coarse_mesh = zero_vector<double>(2);
for (unsigned i=0; i<pde_handler.GetCoarsePdeMesh()->GetNumNodes(); i++)
{
centre_of_coarse_mesh += pde_handler.GetCoarsePdeMesh()->GetNode(i)->rGetLocation();
}
centre_of_coarse_mesh /= pde_handler.GetCoarsePdeMesh()->GetNumNodes();
c_vector<double,2> centre_of_cuboid = 0.5*(lower.rGetLocation() + upper.rGetLocation());
TS_ASSERT_DELTA(norm_2(centre_of_cuboid - centre_of_coarse_mesh), 0.0, 1e-4);
}
// Testing Save
void TestSave() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenereator does not work in parallel
// Create a simple mesh
int num_cells_depth = 5;
int num_cells_width = 5;
HoneycombMeshGenerator generator(num_cells_width, num_cells_depth, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 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);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithNodeBasedCellPopulationSaveAndLoad");
simulator.SetEndTime(0.1);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Create some boundary conditions and pass them to the simulation
c_vector<double,2> normal = zero_vector<double>(2);
normal(1) =-1.0;
MAKE_PTR_ARGS(PlaneBoundaryCondition<2>, p_bc, (&node_based_cell_population, zero_vector<double>(2), normal)); // y>0
simulator.AddCellPopulationBoundaryCondition(p_bc);
// Solve
simulator.Solve();
// Save the results
CellBasedSimulationArchiver<2, OffLatticeSimulation<2> >::Save(&simulator);
}
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];
}
/**
* Test that two nodes relax to the equilibrium distance.
*/
void TestBuskeRelaxationForces() throw (Exception)
{
EXIT_IF_PARALLEL;
// Create a simple mesh with two nodes
HoneycombMeshGenerator generator(2, 1, 0, 0.9);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator_buske;
cells_generator_buske.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_diff_type);
// Create a node-based cell population
NodeBasedCellPopulation<2> node_based_cell_population_buske(mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population_buske);
simulator.SetOutputDirectory("TestBuskeRelaxation");
simulator.SetEndTime(1.0);
// Create all three Buske force laws and pass to the simulation
MAKE_PTR(BuskeCompressionForce<2>, p_buske_compression_force);
MAKE_PTR(BuskeElasticForce<2>, p_buske_elastic_force);
MAKE_PTR(BuskeAdhesiveForce<2>, p_buske_adhesive_force);
simulator.AddForce(p_buske_compression_force);
simulator.AddForce(p_buske_elastic_force);
simulator.AddForce(p_buske_adhesive_force);
// Solve
simulator.Solve();
// The nodes should be about 0.85 apart as this is the minimum of the sum of the energies.
TS_ASSERT_DELTA(simulator.rGetCellPopulation().GetNode(0)->rGetLocation()[0], 0.0155, 1e-4);
TS_ASSERT_DELTA(simulator.rGetCellPopulation().GetNode(1)->rGetLocation()[0], 0.8844, 1e-4);
}
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 TestCellBasedPdeHandlerOutputParameters() throw(Exception)
{
EXIT_IF_PARALLEL;
std::string output_directory = "TestCellBasedPdeHandlerOutputParameters";
OutputFileHandler output_file_handler(output_directory, false);
// Create a cell population
HoneycombMeshGenerator generator(2, 2, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
// Test output methods
TS_ASSERT_EQUALS(pde_handler.GetIdentifier(), "CellBasedPdeHandler-2");
out_stream pde_handler_parameter_file = output_file_handler.OpenOutputFile("CellBasedPdeHandler.parameters");
pde_handler.OutputParameters(pde_handler_parameter_file);
pde_handler_parameter_file->close();
{
// Compare the generated file in test output with a reference copy in the source code.
FileFinder generated = output_file_handler.FindFile("CellBasedPdeHandler.parameters");
FileFinder reference("cell_based/test/data/TestCellBasedPdeHandler/CellBasedPdeHandler.parameters",
RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated, reference);
TS_ASSERT(comparer.CompareFiles());
}
}
/**
* Create a simulation of a NodeBasedCellPopulation to test movement threshold.
*/
void TestMovementThreshold() throw (Exception)
{
EXIT_IF_PARALLEL; // This test doesn't work in parallel because only one process will throw.
// 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("TestOffLatticeSimulationWithNodeBasedCellPopulationThreshold");
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Solve
TS_ASSERT_THROWS_CONTAINS(simulator.Solve(),
"which is more than the AbsoluteMovementThreshold:");
// Avoid memory leak
delete nodes[0];
delete nodes[1];
}
void TestOnLatticeSimulationExceptions()
{
EXIT_IF_PARALLEL;
// Create a simple tetrahedral mesh
HoneycombMeshGenerator generator(3, 3, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 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);
TS_ASSERT_THROWS_THIS(OnLatticeSimulation<2> simulator(node_based_cell_population),
"OnLatticeSimulations require a subclass of AbstractOnLatticeCellPopulation.");
}
/*
* === Using the modifier in a cell-based simulation ===
*
* We conclude with a brief test demonstrating how {{{CellHeightTrackingModifier}}} can be used
* in a cell-based simulation.
*/
void TestOffLatticeSimulationWithCellHeightTrackingModifier()
{
/*
* In this case, we choose to create a small {{{NodeBasedCellPopulation}}} comprising 25 cells.
* We choose a cut-off for mechanical interactions between cells of 1.5 units and add a
* simple {{{ReplusionForce}}} to the simulation. We use a {{{UniformCellCycleModel}}}
* to implement some random proliferation in the simulation.
*/
HoneycombMeshGenerator generator(2, 2, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<UniformCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
NodeBasedCellPopulation<2> cell_population(mesh, cells);
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithCellHeightTrackingModifier");
simulator.SetSamplingTimestepMultiple(12);
simulator.SetEndTime(20.0);
MAKE_PTR(RepulsionForce<2>, p_force);
simulator.AddForce(p_force);
/*
* Finally, we add a {{{CellHeightTrackingModifier}}} to the simulation.
*/
MAKE_PTR(CellHeightTrackingModifier, p_modifier);
simulator.AddSimulationModifier(p_modifier);
/* To run the simulation, we call {{{Solve()}}}. */
simulator.Solve();
}
/**
* Create a simulation of a NodeBasedCellPopulation with all Buske forces.
* Test that no exceptions are thrown.
*/
void TestAllBuskeForces() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesn't work in parallel
// Create a simple mesh
HoneycombMeshGenerator generator(5, 5, 0);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a NodesOnlyMesh
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(TransitCellProliferativeType, p_transit_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
// Create a node-based cell population
NodeBasedCellPopulation<2> node_based_cell_population(mesh, cells);
// Set up cell-based simulation
OffLatticeSimulation<2> simulator(node_based_cell_population);
simulator.SetOutputDirectory("TestAllBuskeForces");
simulator.SetEndTime(5.0);
// Create a force law and pass it to the simulation
MAKE_PTR(BuskeCompressionForce<2>, p_buske_compression_force);
MAKE_PTR(BuskeElasticForce<2>, p_buske_elastic_force);
MAKE_PTR(BuskeAdhesiveForce<2>, p_buske_adhesive_force);
p_buske_compression_force->SetCompressionEnergyParameter(0.01);
simulator.AddForce(p_buske_compression_force);
simulator.AddForce(p_buske_elastic_force);
simulator.AddForce(p_buske_adhesive_force);
simulator.Solve();
}
void setUp()
{
AbstractCellBasedTestSuite::setUp();
std::vector<Node<3>* > nodes;
for (unsigned i=0; i<PetscTools::GetNumProcs(); i++)
{
nodes.push_back(new Node<3>(0, false, 0.0, 0.0, 0.5+(double)i));
}
mpNodesOnlyMesh = new NodesOnlyMesh<3>;
mpNodesOnlyMesh->ConstructNodesWithoutMesh(nodes, 1.0);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 3> cells_generator;
cells_generator.GenerateBasic(cells, mpNodesOnlyMesh->GetNumNodes());
mpNodeBasedCellPopulation = new NodeBasedCellPopulation<3>(*mpNodesOnlyMesh, cells);
for (unsigned i=0; i<nodes.size(); i++)
{
delete nodes[i];
}
}
/*
* === Using the cell property in a cell-based simulation ===
*
* We conclude with a brief test demonstrating how {{{MotileCellProperty}}} can be used
* in a cell-based simulation.
*/
void TestOffLatticeSimulationWithMotileCellProperty() throw(Exception)
{
/* Note that HoneycombMeshGenerator, used in this test, is not
* yet implemented in parallel. */
/* We use the {{{HoneycombMeshGenerator}}} to create a honeycomb mesh covering a
* circular domain of given radius, and use this to generate a {{{NodesOnlyMesh}}}
* as follows. */
HoneycombMeshGenerator generator(10, 10);
MutableMesh<2,2>* p_generating_mesh = generator.GetCircularMesh(5);
NodesOnlyMesh<2> mesh;
/* We construct the mesh using the generating mesh and a cut-off 1.5 which defines the
* connectivity in the mesh.
*/
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
/* We now create a shared pointer to our new property, as follows. */
MAKE_PTR(MotileCellProperty, p_motile);
/*
* Also create a shared pointer to a cell label so we can visualize the
* different cell types. Note that this is also a {{{CellProperty}}}.
*/
MAKE_PTR(CellLabel, p_label);
/* Next, we create some cells. We don't use a Generator as we want to give some cells the new cell property, therefore
* we create the cells in a loop, as follows.*/
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
std::vector<CellPtr> cells;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
/* For each node we create a cell with our cell-cycle model and the wild-type cell mutation state.
* We then add the property {{{MotileCellProperty}}} to a random selection of the cells, as follows. */
FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
CellPropertyCollection collection;
if (RandomNumberGenerator::Instance()->ranf() < 0.2)
{
collection.AddProperty(p_motile);
collection.AddProperty(p_label);
}
CellPtr p_cell(new Cell(p_state, p_model, false, collection));
p_cell->SetCellProliferativeType(p_diff_type);
/* Now, we define a random birth time, chosen from [-T,0], where
* T = t,,1,, + t,,2,,, where t,,1,, is a parameter representing the G,,1,, duration
* of a stem cell, and t,,2,, is the basic S+G,,2,,+M phases duration.
*/
double birth_time = - RandomNumberGenerator::Instance()->ranf() *
(p_model->GetStemCellG1Duration()
+ p_model->GetSG2MDuration());
/* Finally, we set the birth time and push the cell back into the vector of cells. */
p_cell->SetBirthTime(birth_time);
cells.push_back(p_cell);
}
/* Now that we have defined the mesh and cells, we can define the cell population. The constructor
* takes in the mesh and the cells vector. */
NodeBasedCellPopulation<2> cell_population(mesh, cells);
/* In order to visualize labelled cells we need to use the following command.*/
cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>();
/* We then pass in the cell population into an {{{OffLatticeSimulation}}},
* and set the output directory, output multiple, and end time. */
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("TestOffLatticeSimulationWithMotileCellProperty");
simulator.SetSamplingTimestepMultiple(12);
simulator.SetEndTime(10.0);
/* We create a force law and pass it to the {{{OffLatticeSimulation}}}. */
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
/* Now create a {{{MotlieForce}}} and pass it to the {{{OffLatticeSimulation}}}. */
MAKE_PTR(MyMotiveForce, p_motive_force);
simulator.AddForce(p_motive_force);
/* To run the simulation, we call {{{Solve()}}}. */
simulator.Solve();
}
void TestWritingToFile() throw(Exception)
{
EXIT_IF_PARALLEL;
std::string output_directory = "TestCellBasedPdeHandlerWritingToFile";
// Create a cell population
HoneycombMeshGenerator generator(4, 4, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
TS_ASSERT_EQUALS(cells.size(), mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
cell_population.SetDataOnAllCells("variable", 1.0);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
TS_ASSERT_THROWS_THIS(pde_handler.OpenResultsFiles(output_directory),
"Trying to solve a PDE on a cell population that doesn't have a mesh. Try calling UseCoarsePdeMesh().");
// Use a coarse PDE mesh since we are using a node-based cell population
AveragedSourcePde<2> pde(cell_population, -0.1);
ConstBoundaryCondition<2> bc(1.0);
PdeAndBoundaryConditions<2> pde_and_bc(&pde, &bc, false);
pde_and_bc.SetDependentVariableName("variable");
pde_handler.AddPdeAndBc(&pde_and_bc);
ChastePoint<2> lower(0.0, 0.0);
ChastePoint<2> upper(9.0, 9.0);
ChasteCuboid<2> cuboid(lower, upper);
pde_handler.UseCoarsePdeMesh(3.0, cuboid, true);
// For coverage, call SetWriteAverageRadialPdeSolution() prior to output
pde_handler.SetWriteAverageRadialPdeSolution("variable", 5, true);
// Test that output files are opened correctly
pde_handler.OpenResultsFiles(output_directory);
FileFinder file_finder(output_directory + "/results.vizcoarsepdesolution", RelativeTo::ChasteTestOutput);
TS_ASSERT(file_finder.Exists());
TS_ASSERT(file_finder.IsFile());
FileFinder file_finder2(output_directory + "/radial_dist.dat", RelativeTo::ChasteTestOutput);
TS_ASSERT(file_finder2.Exists());
TS_ASSERT(file_finder2.IsFile());
TS_ASSERT_THROWS_NOTHING(pde_handler.CloseResultsFiles());
// For coverage, also test that output files are opened correctly when not using a coarse PDE mesh
HoneycombMeshGenerator generator2(5, 5, 0);
MutableMesh<2,2>* p_mesh2 = generator2.GetMesh();
std::vector<CellPtr> cells2;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator2;
cells_generator2.GenerateBasic(cells2, p_mesh2->GetNumNodes());
MeshBasedCellPopulation<2> cell_population2(*p_mesh2, cells2);
cell_population2.SetDataOnAllCells("another variable", 1.0);
CellBasedPdeHandler<2> pde_handler2(&cell_population2);
pde_handler2.OpenResultsFiles(output_directory);
FileFinder file_finder3(output_directory + "/results.vizpdesolution", RelativeTo::ChasteTestOutput);
TS_ASSERT(file_finder3.Exists());
TS_ASSERT(file_finder3.IsFile());
pde_handler2.CloseResultsFiles();
}
void TestUseCoarsePdeMesh() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a cell population
HoneycombMeshGenerator generator(4, 4, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
// Test that UseCoarsePdeMesh() throws an exception if no PDEs are specified
ChastePoint<2> lower(0.0, 0.0);
ChastePoint<2> upper(9.0, 9.0);
ChasteCuboid<2> cuboid(lower, upper);
TS_ASSERT_THROWS_THIS(pde_handler.UseCoarsePdeMesh(3.0, cuboid, true),
"mPdeAndBcCollection should be populated prior to calling UseCoarsePdeMesh().");
// Set up PDE and pass to handler
AveragedSourcePde<2> pde(cell_population, -0.1);
ConstBoundaryCondition<2> bc(1.0);
PdeAndBoundaryConditions<2> pde_and_bc(&pde, &bc, false);
pde_handler.AddPdeAndBc(&pde_and_bc);
// Test UseCoarsePdeMesh() again
pde_handler.UseCoarsePdeMesh(3.0, cuboid, true);
// Test that the coarse mesh has the correct number of nodes and elements
TetrahedralMesh<2,2>* p_coarse_mesh = pde_handler.GetCoarsePdeMesh();
TS_ASSERT_EQUALS(p_coarse_mesh->GetNumNodes(), 16u);
TS_ASSERT_EQUALS(p_coarse_mesh->GetNumElements(), 18u);
// Find centre of cell population
c_vector<double,2> centre_of_cell_population = cell_population.GetCentroidOfCellPopulation();
// Find centre of coarse PDE mesh
c_vector<double,2> centre_of_coarse_pde_mesh = zero_vector<double>(2);
for (unsigned i=0; i<p_coarse_mesh->GetNumNodes(); i++)
{
centre_of_coarse_pde_mesh += p_coarse_mesh->GetNode(i)->rGetLocation();
}
centre_of_coarse_pde_mesh /= p_coarse_mesh->GetNumNodes();
// Test that the two centres match
c_vector<double,2> centre_difference = centre_of_cell_population - centre_of_coarse_pde_mesh;
TS_ASSERT_DELTA(norm_2(centre_difference), 0.0, 1e-4);
// Test that UseCoarsePdeMesh() throws an exception if the wrong type of PDE is specified
SimpleUniformSourcePde<2> pde2(-0.1);
ConstBoundaryCondition<2> bc2(1.0);
PdeAndBoundaryConditions<2> pde_and_bc2(&pde2, &bc2, false);
pde_and_bc2.SetDependentVariableName("second variable");
pde_handler.AddPdeAndBc(&pde_and_bc2);
TS_ASSERT_THROWS_THIS(pde_handler.UseCoarsePdeMesh(3.0, cuboid, true),
"UseCoarsePdeMesh() should only be called if averaged-source PDEs are specified.");
// Now test the 1D case
std::vector<Node<1>*> nodes_1d;
nodes_1d.push_back(new Node<1>(0, true, 0.0));
NodesOnlyMesh<1> mesh_1d;
mesh_1d.ConstructNodesWithoutMesh(nodes_1d, 1.5);
std::vector<CellPtr> cells_1d;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 1> cells_generator_1d;
cells_generator_1d.GenerateBasic(cells_1d, mesh_1d.GetNumNodes());
NodeBasedCellPopulation<1> cell_population_1d(mesh_1d, cells_1d);
CellBasedPdeHandler<1> pde_handler_1d(&cell_population_1d);
AveragedSourcePde<1> pde_1d(cell_population_1d, -0.1);
ConstBoundaryCondition<1> bc_1d(1.0);
PdeAndBoundaryConditions<1> pde_and_bc_1d(&pde_1d, &bc_1d, false);
pde_handler_1d.AddPdeAndBc(&pde_and_bc_1d);
ChastePoint<1> lower1(0.0);
ChastePoint<1> upper1(9.0);
ChasteCuboid<1> cuboid1(lower1, upper1);
pde_handler_1d.UseCoarsePdeMesh(3.0, cuboid1, true);
// Test that the coarse mesh has the correct number of nodes and elements
TetrahedralMesh<1,1>* p_coarse_mesh_1d = pde_handler_1d.GetCoarsePdeMesh();
TS_ASSERT_EQUALS(p_coarse_mesh_1d->GetNumNodes(), 4u);
TS_ASSERT_EQUALS(p_coarse_mesh_1d->GetNumElements(), 3u);
// Now test the 3D case
std::vector<Node<3>*> nodes_3d;
nodes_3d.push_back(new Node<3>(0, true, 0.0));
NodesOnlyMesh<3> mesh_3d;
mesh_3d.ConstructNodesWithoutMesh(nodes_3d, 1.5);
std::vector<CellPtr> cells_3d;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 3> cells_generator_3d;
cells_generator_3d.GenerateBasic(cells_3d, mesh_3d.GetNumNodes());
NodeBasedCellPopulation<3> cell_population_3d(mesh_3d, cells_3d);
CellBasedPdeHandler<3> pde_handler_3d(&cell_population_3d);
AveragedSourcePde<3> pde_3d(cell_population_3d, -0.1);
ConstBoundaryCondition<3> bc_3d(1.0);
PdeAndBoundaryConditions<3> pde_and_bc_3d(&pde_3d, &bc_3d, false);
pde_handler_3d.AddPdeAndBc(&pde_and_bc_3d);
ChastePoint<3> lower3(0.0, 0.0, 0.0);
ChastePoint<3> upper3(9.0, 9.0, 9.0);
ChasteCuboid<3> cuboid3(lower3, upper3);
pde_handler_3d.UseCoarsePdeMesh(3.0, cuboid3, true);
// Test that the coarse mesh has the correct number of nodes and elements
TetrahedralMesh<3,3>* p_coarse_mesh_3d = pde_handler_3d.GetCoarsePdeMesh();
TS_ASSERT_EQUALS(p_coarse_mesh_3d->GetNumNodes(), 64u);
TS_ASSERT_EQUALS(p_coarse_mesh_3d->GetNumElements(), 162u);
// Avoid memory leak
for (unsigned i=0; i<nodes_1d.size(); i++)
{
delete nodes_1d[i];
delete nodes_3d[i];
}
}
void TestArchivingOfPdeHandlerOnCuboid() throw(Exception)
{
EXIT_IF_PARALLEL;
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "CellBasedPdeHandlerOnCuboid.arch";
ArchiveLocationInfo::SetMeshFilename("pde_handler_mesh");
{
// Create a cell population
HoneycombMeshGenerator generator(2, 2, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandlerOnCuboid<2>* const p_pde_handler = new CellBasedPdeHandlerOnCuboid<2>(&cell_population);
// Set member variables for testing
p_pde_handler->SetWriteAverageRadialPdeSolution("averaged quantity", 5, true);
p_pde_handler->SetImposeBcsOnCoarseBoundary(false);
// Set up PDE and pass to handler
AveragedSourcePde<2> pde(cell_population, -0.1);
ConstBoundaryCondition<2> bc(1.0);
PdeAndBoundaryConditions<2> pde_and_bc(&pde, &bc, false);
pde_and_bc.SetDependentVariableName("averaged quantity");
p_pde_handler->AddPdeAndBc(&pde_and_bc);
// Test UseCoarsePdeMesh() again
ChastePoint<2> lower(0.0, 0.0);
ChastePoint<2> upper(9.0, 9.0);
ChasteCuboid<2> cuboid(lower, upper);
p_pde_handler->UseCoarsePdeMesh(3.0, cuboid, true);
// Create an output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// Archive object
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(1.0, 11);
(*p_arch) << static_cast<const SimulationTime&>(*p_simulation_time);
(*p_arch) << p_pde_handler;
// Tidy up
SimulationTime::Destroy();
delete p_pde_handler;
}
{
CellBasedPdeHandlerOnCuboid<2>* p_pde_handler;
// Create an input archive
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
// Restore object from the archive
SimulationTime* p_simulation_time = SimulationTime::Instance();
(*p_arch) >> *p_simulation_time;
(*p_arch) >> p_pde_handler;
// Test that the member variables were archived correctly
TS_ASSERT_EQUALS(p_pde_handler->mpCellPopulation->GetNumRealCells(), 4u);
TS_ASSERT_EQUALS(p_pde_handler->GetWriteAverageRadialPdeSolution(), true);
TS_ASSERT_EQUALS(p_pde_handler->GetWriteDailyAverageRadialPdeSolution(), true);
TS_ASSERT_EQUALS(p_pde_handler->GetImposeBcsOnCoarseBoundary(), false);
TS_ASSERT_EQUALS(p_pde_handler->GetNumRadialIntervals(), 5u);
TS_ASSERT_EQUALS(p_pde_handler->mAverageRadialSolutionVariableName, "averaged quantity");
///\todo we currently do not archive mpCoarsePdeMesh - consider doing this (#1891)
TS_ASSERT(p_pde_handler->GetCoarsePdeMesh() == NULL);
TS_ASSERT_EQUALS(p_pde_handler->mPdeAndBcCollection.size(), 1u);
TS_ASSERT_EQUALS(p_pde_handler->mPdeAndBcCollection[0]->IsNeumannBoundaryCondition(), false);
// Tidy up
delete p_pde_handler->mpCellPopulation;
delete p_pde_handler;
}
}
void TestSetMethods() throw(Exception)
{
EXIT_IF_PARALLEL;
// Create a cell population
HoneycombMeshGenerator generator(2, 2, 0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2> mesh;
mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumNodes());
NodeBasedCellPopulation<2> cell_population(mesh, cells);
// Create a PDE handler object using this cell population
CellBasedPdeHandler<2> pde_handler(&cell_population);
// Test set and get methods
pde_handler.SetWriteAverageRadialPdeSolution("averaged quantity");
TS_ASSERT_EQUALS(pde_handler.GetWriteAverageRadialPdeSolution(), true);
TS_ASSERT_EQUALS(pde_handler.GetWriteDailyAverageRadialPdeSolution(), false);
TS_ASSERT_EQUALS(pde_handler.GetNumRadialIntervals(), 10u);
pde_handler.SetWriteAverageRadialPdeSolution("averaged quantity", 5, true);
TS_ASSERT_EQUALS(pde_handler.GetWriteAverageRadialPdeSolution(), true);
TS_ASSERT_EQUALS(pde_handler.GetWriteDailyAverageRadialPdeSolution(), true);
TS_ASSERT_EQUALS(pde_handler.GetNumRadialIntervals(), 5u);
pde_handler.SetImposeBcsOnCoarseBoundary(false);
TS_ASSERT_EQUALS(pde_handler.GetImposeBcsOnCoarseBoundary(), false);
// Test AddPdeAndBc()
SimpleUniformSourcePde<2> pde(-0.1);
ConstBoundaryCondition<2> bc(1.0);
PdeAndBoundaryConditions<2> pde_and_bc(&pde, &bc, false);
pde_and_bc.SetDependentVariableName("averaged quantity");
unsigned num_nodes = mesh.GetNumNodes();
std::vector<double> data(num_nodes);
for (unsigned i=0; i<num_nodes; i++)
{
data[i] = i + 0.45;
}
Vec vector = PetscTools::CreateVec(data);
pde_and_bc.SetSolution(vector);
pde_handler.AddPdeAndBc(&pde_and_bc);
TS_ASSERT_EQUALS(pde_handler.mPdeAndBcCollection[0]->IsNeumannBoundaryCondition(), false);
TS_ASSERT_EQUALS(pde_handler.mPdeAndBcCollection[0]->HasAveragedSourcePde(), false);
ReplicatableVector solution(pde_handler.GetPdeSolution());
TS_ASSERT_EQUALS(solution.GetSize(), num_nodes);
for (unsigned i=0; i<num_nodes; i++)
{
TS_ASSERT_DELTA(solution[i], i + 0.45, 1e-4);
}
}