/* The third public method overrides {{{VerifyBoundaryCondition()}}}.
* This method is called during the {{{Solve()}}} method in {{{OffLatticeSimulation}}}
* at the end of each timestep, just after {{{ImposeBoundaryCondition()}}}, and checks
* that each cell in the population now satisfies {{{MyBoundaryCondition}}}.
*/
bool VerifyBoundaryCondition()
{
bool condition_satisfied = true;
for (AbstractCellPopulation<2>::Iterator cell_iter = this->mpCellPopulation->Begin();
cell_iter != this->mpCellPopulation->End();
++cell_iter)
{
c_vector<double, 2> cell_location = this->mpCellPopulation->GetLocationOfCellCentre(*cell_iter);
double y_coordinate = cell_location(1);
if ((y_coordinate < 0.0) || (y_coordinate > 5.0))
{
condition_satisfied = false;
break;
}
}
return condition_satisfied;
}
void display_layer_update_callback(Layer *layer, GContext* ctx) {
time_t now = time(NULL);
struct tm *tick_time = localtime(&now);
graphics_context_set_fill_color(ctx, GColorWhite);
int minutes = 0;
int hour = tick_time->tm_hour;
/* convert 24 hours to 12 hours */
if (hour > 12) {
hour = hour - 12;
}
if (hour == 0) {
hour = 12;
}
int col, row, height;
for (col = 0; col < 12; col++) {
for (row = 0; row < 6; row++) {
height = col;
/* Hour mode */
if (row == 0) {
if (12 - col > hour) {
continue;
}
} else {
if (minutes++ < tick_time->tm_min) {
height = (11 - col);
} else {
continue;
}
}
graphics_fill_rect(ctx, cell_location(row, height), 0, GCornerNone);
}
}
}
void display_layer_update_callback(Layer *me, GContext* ctx) {
(void)me;
PblTm t;
get_time(&t);
unsigned short display_hour = get_display_hour(t.tm_hour);
graphics_context_set_fill_color(ctx, GColorWhite);
for (int cell_column_index = 0; cell_column_index < display_hour/10; cell_column_index++) {
graphics_fill_rect(ctx, cell_location(0, cell_column_index), 0, GCornerNone);
}
for (int cell_column_index = 0; cell_column_index < display_hour%10; cell_column_index++) {
graphics_fill_rect(ctx, cell_location(1, cell_column_index), 0, GCornerNone);
}
for (int cell_column_index = 0; cell_column_index < t.tm_min/10; cell_column_index++) {
graphics_fill_rect(ctx, cell_location(2, cell_column_index), 0, GCornerNone);
}
for (int cell_column_index = 0; cell_column_index < t.tm_min%10; cell_column_index++) {
graphics_fill_rect(ctx, cell_location(3, cell_column_index), 0, GCornerNone);
}
for (int cell_column_index = 0; cell_column_index < t.tm_sec/10; cell_column_index++) {
graphics_fill_rect(ctx, cell_location(4, cell_column_index), 0, GCornerNone);
}
for (int cell_column_index = 0; cell_column_index < t.tm_sec%10; cell_column_index++) {
graphics_fill_rect(ctx, cell_location(5, cell_column_index), 0, GCornerNone);
}
}
void TestCaBasedSquareMonolayer()
{
PottsMeshGenerator<2> generator(10, 0, 0, 10, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Scale so cells are on top of those in the above centre based tests
p_mesh->Scale(1.0,sqrt(3.0)*0.5);
// Specify where cells lie
std::vector<unsigned> location_indices;
for (unsigned i=0; i<100; i++)
{
location_indices.push_back(i);
}
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_differentiated_type);
CellsGenerator<UniformCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, location_indices.size(), p_differentiated_type);
// Make cells with x<5.0 apoptotic (so no source term)
boost::shared_ptr<AbstractCellProperty> p_apoptotic_property =
cells[0]->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<ApoptoticCellProperty>();
for (unsigned i=0; i<cells.size(); i++)
{
c_vector<double,2> cell_location;
cell_location = p_mesh->GetNode(i)->rGetLocation();
if (cell_location(0) < 5.0)
{
cells[i]->AddCellProperty(p_apoptotic_property);
}
// Set initial condition for PDE
cells[i]->GetCellData()->SetItem("variable",1.0);
}
TS_ASSERT_EQUALS(p_apoptotic_property->GetCellCount(), 50u);
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
// Set up simulation time for file output
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0, 10);
// Create PDE and boundary condition objects
MAKE_PTR_ARGS(AveragedSourceParabolicPde<2>, p_pde, (cell_population, 0.1, 1.0, -1.0));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (1.0));
// Create a ChasteCuboid on which to base the finite element mesh used to solve the PDE
ChastePoint<2> lower(-5.0, -5.0);
ChastePoint<2> upper(15.0, 15.0);
MAKE_PTR_ARGS(ChasteCuboid<2>, p_cuboid, (lower, upper));
// Create a PDE modifier and set the name of the dependent variable in the PDE
MAKE_PTR_ARGS(ParabolicBoxDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, false, p_cuboid));
p_pde_modifier->SetDependentVariableName("variable");
// For coverage, output the solution gradient
p_pde_modifier->SetOutputGradient(true);
p_pde_modifier->SetupSolve(cell_population,"TestAveragedParabolicPdeWithNodeOnSquare");
// Run for 10 time steps
for (unsigned i=0; i<10; i++)
{
SimulationTime::Instance()->IncrementTimeOneStep();
p_pde_modifier->UpdateAtEndOfTimeStep(cell_population);
p_pde_modifier->UpdateAtEndOfOutputTimeStep(cell_population);
}
// Test the solution at some fixed points to compare with other cell populations
CellPtr p_cell_0 = cell_population.GetCellUsingLocationIndex(0);
TS_ASSERT_DELTA(cell_population.GetLocationOfCellCentre(p_cell_0)[0], 0, 1e-4);
TS_ASSERT_DELTA(cell_population.GetLocationOfCellCentre(p_cell_0)[1], 0.0, 1e-4);
TS_ASSERT_DELTA( p_cell_0->GetCellData()->GetItem("variable"), 0.8513, 2e-2); // Low tolerance as mesh is slightly larger than for off-lattice models
// Checking it doesn't change for this cell population
TS_ASSERT_DELTA(p_cell_0->GetCellData()->GetItem("variable"), 0.8343, 1e-4);
}
void TestNodeBasedSquareMonolayer()
{
HoneycombMeshGenerator generator(10,10,0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
NodesOnlyMesh<2>* p_mesh = new NodesOnlyMesh<2>;
p_mesh->ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_differentiated_type);
CellsGenerator<UniformCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, p_mesh->GetNumNodes(), p_differentiated_type);
// Make cells with x<5.0 apoptotic (so no source term)
boost::shared_ptr<AbstractCellProperty> p_apoptotic_property =
cells[0]->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<ApoptoticCellProperty>();
for (unsigned i=0; i<cells.size(); i++)
{
c_vector<double,2> cell_location;
cell_location = p_mesh->GetNode(i)->rGetLocation();
if (cell_location(0) < 5.0)
{
cells[i]->AddCellProperty(p_apoptotic_property);
}
// Set initial condition for PDE
cells[i]->GetCellData()->SetItem("variable",1.0);
}
TS_ASSERT_EQUALS(p_apoptotic_property->GetCellCount(), 50u);
NodeBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set up simulation time for file output
SimulationTime::Instance()->SetEndTimeAndNumberOfTimeSteps(1.0, 10);
// Create PDE and boundary condition objects
MAKE_PTR_ARGS(AveragedSourceParabolicPde<2>, p_pde, (cell_population, 0.1, 1.0, -1.0));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (1.0));
// Create a ChasteCuboid on which to base the finite element mesh used to solve the PDE
ChastePoint<2> lower(-5.0, -5.0);
ChastePoint<2> upper(15.0, 15.0);
MAKE_PTR_ARGS(ChasteCuboid<2>, p_cuboid, (lower, upper));
// Create a PDE modifier and set the name of the dependent variable in the PDE
MAKE_PTR_ARGS(ParabolicBoxDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, false, p_cuboid));
p_pde_modifier->SetDependentVariableName("variable");
// For coverage, output the solution gradient
p_pde_modifier->SetOutputGradient(true);
p_pde_modifier->SetupSolve(cell_population,"TestAveragedParabolicPdeWithNodeOnSquare");
// Run for 10 time steps
for (unsigned i=0; i<10; i++)
{
SimulationTime::Instance()->IncrementTimeOneStep();
p_pde_modifier->UpdateAtEndOfTimeStep(cell_population);
p_pde_modifier->UpdateAtEndOfOutputTimeStep(cell_population);
}
// Test the solution at some fixed points to compare with other cell populations
CellPtr p_cell_0 = cell_population.GetCellUsingLocationIndex(0);
TS_ASSERT_DELTA(cell_population.GetLocationOfCellCentre(p_cell_0)[0], 0, 1e-4);
TS_ASSERT_DELTA(cell_population.GetLocationOfCellCentre(p_cell_0)[1], 0.0, 1e-4);
TS_ASSERT_DELTA( p_cell_0->GetCellData()->GetItem("variable"), 0.8513, 1e-4);
// Clear memory
delete p_mesh;
}