| Chaste

This tutorial was generated from the file projects/InterfaceFocus2013/test/TestCaBasedCellPopulationUsingPdesLiteratePaper.hpp at revision r26247. Note that the code is given in full at the bottom of the page.

#include <cxxtest/TestSuite.h>

// Must be included before other cell_based headers
#include "CellBasedSimulationArchiver.hpp"

#include "CellwiseSourcePde.hpp"
#include "ConstBoundaryCondition.hpp"
#include "PetscSetupAndFinalize.hpp"
//#include "ReplicatableVector.hpp"
#include "NumericFileComparison.hpp"
//#include "FunctionalBoundaryCondition.hpp"
#include "AveragedSourcePde.hpp"

#include "PottsBasedCellPopulation.hpp"

#include "AbstractCellPopulation.hpp"
#include "PottsMeshGenerator.hpp"
#include "CellsGenerator.hpp"
#include "Owen2011OxygenBasedCellCycleModel.hpp"
#include "Owen2011OxygenBasedCellCycleModelWithoutOde.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "WildTypeCellMutationState.hpp"
#include "CancerCellMutationState.hpp"
#include "MultipleCaBasedCellPopulation.hpp"
#include "PlaneBasedCellKiller.hpp"
#include "OnLatticeSimulationInterfaceFocus.hpp"
#include "AbstractCellBasedTestSuite.hpp"
#include "SmartPointers.hpp"
#include "Owen2011MultipleCaUpdateRule.hpp"
#include "VasctumCellKiller.hpp"
#include "CellBasedPdeHandlerInterfaceFocus.hpp"

#include "Debug.hpp"

class TestMultipleCaBasedCellPopulationUsingPdesInterfaceFocus : public AbstractCellBasedTestSuite
{

private:

    double mLastStartTime;
    void setUp()
    {
        mLastStartTime = std::clock();
        AbstractCellBasedTestSuite::setUp();
    }
    void tearDown()
    {
        double time = std::clock();
        double elapsed_time = (time - mLastStartTime)/(CLOCKS_PER_SEC);
        std::cout << "Elapsed time: " << elapsed_time << std::endl;
        AbstractCellBasedTestSuite::tearDown();
    }

public:

    void TestPdesForCellGrowthWithMixedBoundaryConditions() throw (Exception)
    {
       EXIT_IF_PARALLEL;

       // Create a simple 2D PottsMesh
 	   PottsMeshGenerator<2> generator(50, 0, 0, 50, 0, 0);
       PottsMesh<2>* p_mesh = generator.GetMesh();

       // Create cells
	   std::vector<CellPtr> cells;
	   MAKE_PTR(StemCellProliferativeType, p_stem_type);
	   CellsGenerator<Owen2011OxygenBasedCellCycleModel, 2> cells_generator;
	   cells_generator.GenerateBasicRandom(cells, 1u, p_stem_type);

       // Create a cell mutation state
	   boost::shared_ptr<AbstractCellProperty> p_normal_mutation(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());

	   for (unsigned i = 0; i<cells.size(); i++)
	   {
	      cells[i]->SetMutationState(p_normal_mutation);
	      cells[i]->SetBirthTime(0.0);
	   }

	   // Specify where cells lie
	   std::vector<unsigned> location_indices;

	   for (unsigned i=1075; i<=1075; i+= 50)
	   {
		  for(unsigned j=0; j<1; j++)
		  {
			location_indices.push_back(i+j);
          }
	   }

 	   // Create cell population
	   MultipleCaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
	   cell_population.SetOutputCellIdData(true);
	   cell_population.SetOutputCellMutationStates(true);
	   cell_population.SetOutputCellProliferativeTypes(true);
	   cell_population.SetOutputCellCyclePhases(true);
	   cell_population.SetOutputCellAncestors(true);
	   cell_population.SetOutputCellAges(true);

	   cell_population.SetDataOnAllCells("oxygen", 1.0);

	   // Set up cell-based simulation
	   OnLatticeSimulationInterfaceFocus<2> simulator(cell_population);
	   std::string output_directory = "TestPdesForCellGrowthWithMixedBoundaryConditions";
	   simulator.SetOutputDirectory(output_directory);
	   simulator.SetDt(0.1);
       simulator.SetSamplingTimestepMultiple(10);
	   simulator.SetEndTime(1000.0);

  	   // Set up PDE and pass to simulation via handler
	   OxygenPde<2> pde_1(cell_population, 0.1);
	   ConstBoundaryCondition<2> bc_1(0.0);
	   PdeAndBoundaryConditions<2> pde_and_bc_1(&pde_1, &bc_1, true);
	   pde_and_bc_1.SetDependentVariableName("oxygen");
	   CellBasedPdeHandlerInterfaceFocus<2> pde_handler(&cell_population);
       pde_handler.AddPdeAndBc(&pde_and_bc_1);

	   ChastePoint<2> lower(-0.5, -0.5);
	   ChastePoint<2> upper(49.5, 49.5);
	   ChasteCuboid<2> cuboid(lower, upper);

	   pde_handler.UseCoarsePdeMesh(1.0, cuboid);
	   pde_handler.SetImposeBcsOnCoarseBoundary(true);

       simulator.SetCellBasedPdeHandler(&pde_handler);

       // Create cell killer
       MAKE_PTR_ARGS(VasctumCellKiller<2>, cell_killer,(&cell_population));

       simulator.AddCellKiller(cell_killer);

       // Run simulation
       PRINT_VARIABLE("Before solve");
 	   simulator.Solve();
    }

    void NOTestPdesForCellGrowthWithDirichletBoundaryConditions() throw (Exception)
    {
	   EXIT_IF_PARALLEL;

       // Create a simple 2D PottsMesh
	   PottsMeshGenerator<2> generator(50, 0, 0, 50, 0, 0);
	   PottsMesh<2>* p_mesh = generator.GetMesh();

       // Create cells
	   std::vector<CellPtr> cells;
	   MAKE_PTR(StemCellProliferativeType, p_stem_type);
	   CellsGenerator<Owen2011OxygenBasedCellCycleModel, 2> cells_generator;
	   cells_generator.GenerateBasicRandom(cells, 1u, p_stem_type);

	   // Create a cell mutation state
  	   boost::shared_ptr<AbstractCellProperty> p_normal_mutation(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());

       for (unsigned i = 0; i<cells.size(); i++)
       {
          cells[i]->SetMutationState(p_normal_mutation);
		  cells[i]->SetBirthTime(0.0);
	   }

       // Specify where cells lie
	   std::vector<unsigned> location_indices;

       for (unsigned i=1075; i<=1075; i=i+50)
       {
		  for(unsigned j=0; j<1; j++)
		  {
		     location_indices.push_back(i+j);
		  }
       }

  	   // Create cell population
       MultipleCaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
       cell_population.SetOutputCellIdData(true);
       cell_population.SetOutputCellMutationStates(true);
       cell_population.SetOutputCellProliferativeTypes(true);
       cell_population.SetOutputCellCyclePhases(true);
       cell_population.SetOutputCellAncestors(true);
       cell_population.SetOutputCellAges(true);

       cell_population.SetDataOnAllCells("oxygen", 1.0);

  	   // Set up cell-based simulation
	   OnLatticeSimulationInterfaceFocus<2> simulator(cell_population);
	   std::string output_directory = "TestPdesForCellGrowthWithDirichletBoundaryConditions";
	   simulator.SetOutputDirectory(output_directory);
	   simulator.SetDt(0.1);
	   simulator.SetSamplingTimestepMultiple(10);
	   simulator.SetEndTime(1000.0);

  	   // Set up PDE and pass to simulation via handler
	   OxygenPde<2> pde_1(cell_population, 0.1);
	   ConstBoundaryCondition<2> bc_1(30.0);
	   PdeAndBoundaryConditions<2> pde_and_bc_1(&pde_1, &bc_1, false);
	   pde_and_bc_1.SetDependentVariableName("oxygen");

  	   CellBasedPdeHandlerInterfaceFocus<2> pde_handler(&cell_population);
	   pde_handler.AddPdeAndBc(&pde_and_bc_1);
	   ChastePoint<2> lower(-0.5, -0.5);
	   ChastePoint<2> upper(49.5, 49.5);
	   ChasteCuboid<2> cuboid(lower, upper);
	   //pde_handler.UseCoarsePdeMesh(1.0, cuboid);
	   pde_handler.SetImposeBcsOnCoarseBoundary(true);

  	   simulator.SetCellBasedPdeHandler(&pde_handler);

 	   // Create cell killer
	   MAKE_PTR_ARGS(VasctumCellKiller<2>, cell_killer,(&cell_population));

	   simulator.AddCellKiller(cell_killer);

       // Run simulation
	   simulator.Solve();
    }
};

Code

The full code is given below

File name `TestCaBasedCellPopulationUsingPdesLiteratePaper.hpp`

#include <cxxtest/TestSuite.h>

// Must be included before other cell_based headers
#include "CellBasedSimulationArchiver.hpp"

#include "CellwiseSourcePde.hpp"
#include "ConstBoundaryCondition.hpp"
#include "PetscSetupAndFinalize.hpp"
//#include "ReplicatableVector.hpp"
#include "NumericFileComparison.hpp"
//#include "FunctionalBoundaryCondition.hpp"
#include "AveragedSourcePde.hpp"

#include "PottsBasedCellPopulation.hpp"

#include "AbstractCellPopulation.hpp"
#include "PottsMeshGenerator.hpp"
#include "CellsGenerator.hpp"
#include "Owen2011OxygenBasedCellCycleModel.hpp"
#include "Owen2011OxygenBasedCellCycleModelWithoutOde.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "WildTypeCellMutationState.hpp"
#include "CancerCellMutationState.hpp"
#include "MultipleCaBasedCellPopulation.hpp"
#include "PlaneBasedCellKiller.hpp"
#include "OnLatticeSimulationInterfaceFocus.hpp"
#include "AbstractCellBasedTestSuite.hpp"
#include "SmartPointers.hpp"
#include "Owen2011MultipleCaUpdateRule.hpp"
#include "VasctumCellKiller.hpp"
#include "CellBasedPdeHandlerInterfaceFocus.hpp"

#include "Debug.hpp"

class TestMultipleCaBasedCellPopulationUsingPdesInterfaceFocus : public AbstractCellBasedTestSuite
{

private:

    double mLastStartTime;
    void setUp()
    {
        mLastStartTime = std::clock();
        AbstractCellBasedTestSuite::setUp();
    }
    void tearDown()
    {
        double time = std::clock();
        double elapsed_time = (time - mLastStartTime)/(CLOCKS_PER_SEC);
        std::cout << "Elapsed time: " << elapsed_time << std::endl;
        AbstractCellBasedTestSuite::tearDown();
    }

public:

    void TestPdesForCellGrowthWithMixedBoundaryConditions() throw (Exception)
    {
       EXIT_IF_PARALLEL;

       // Create a simple 2D PottsMesh
 	   PottsMeshGenerator<2> generator(50, 0, 0, 50, 0, 0);
       PottsMesh<2>* p_mesh = generator.GetMesh();

       // Create cells
	   std::vector<CellPtr> cells;
	   MAKE_PTR(StemCellProliferativeType, p_stem_type);
	   CellsGenerator<Owen2011OxygenBasedCellCycleModel, 2> cells_generator;
	   cells_generator.GenerateBasicRandom(cells, 1u, p_stem_type);

       // Create a cell mutation state
	   boost::shared_ptr<AbstractCellProperty> p_normal_mutation(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());

	   for (unsigned i = 0; i<cells.size(); i++)
	   {
	      cells[i]->SetMutationState(p_normal_mutation);
	      cells[i]->SetBirthTime(0.0);
	   }

	   // Specify where cells lie
	   std::vector<unsigned> location_indices;

	   for (unsigned i=1075; i<=1075; i+= 50)
	   {
		  for(unsigned j=0; j<1; j++)
		  {
			location_indices.push_back(i+j);
          }
	   }

 	   // Create cell population
	   MultipleCaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
	   cell_population.SetOutputCellIdData(true);
	   cell_population.SetOutputCellMutationStates(true);
	   cell_population.SetOutputCellProliferativeTypes(true);
	   cell_population.SetOutputCellCyclePhases(true);
	   cell_population.SetOutputCellAncestors(true);
	   cell_population.SetOutputCellAges(true);

	   cell_population.SetDataOnAllCells("oxygen", 1.0);

	   // Set up cell-based simulation
	   OnLatticeSimulationInterfaceFocus<2> simulator(cell_population);
	   std::string output_directory = "TestPdesForCellGrowthWithMixedBoundaryConditions";
	   simulator.SetOutputDirectory(output_directory);
	   simulator.SetDt(0.1);
       simulator.SetSamplingTimestepMultiple(10);
	   simulator.SetEndTime(1000.0);

  	   // Set up PDE and pass to simulation via handler
	   OxygenPde<2> pde_1(cell_population, 0.1);
	   ConstBoundaryCondition<2> bc_1(0.0);
	   PdeAndBoundaryConditions<2> pde_and_bc_1(&pde_1, &bc_1, true);
	   pde_and_bc_1.SetDependentVariableName("oxygen");
	   CellBasedPdeHandlerInterfaceFocus<2> pde_handler(&cell_population);
       pde_handler.AddPdeAndBc(&pde_and_bc_1);

	   ChastePoint<2> lower(-0.5, -0.5);
	   ChastePoint<2> upper(49.5, 49.5);
	   ChasteCuboid<2> cuboid(lower, upper);

	   pde_handler.UseCoarsePdeMesh(1.0, cuboid);
	   pde_handler.SetImposeBcsOnCoarseBoundary(true);

       simulator.SetCellBasedPdeHandler(&pde_handler);

       // Create cell killer
       MAKE_PTR_ARGS(VasctumCellKiller<2>, cell_killer,(&cell_population));

       simulator.AddCellKiller(cell_killer);

       // Run simulation
       PRINT_VARIABLE("Before solve");
 	   simulator.Solve();
    }

    void NOTestPdesForCellGrowthWithDirichletBoundaryConditions() throw (Exception)
    {
	   EXIT_IF_PARALLEL;

       // Create a simple 2D PottsMesh
	   PottsMeshGenerator<2> generator(50, 0, 0, 50, 0, 0);
	   PottsMesh<2>* p_mesh = generator.GetMesh();

       // Create cells
	   std::vector<CellPtr> cells;
	   MAKE_PTR(StemCellProliferativeType, p_stem_type);
	   CellsGenerator<Owen2011OxygenBasedCellCycleModel, 2> cells_generator;
	   cells_generator.GenerateBasicRandom(cells, 1u, p_stem_type);

	   // Create a cell mutation state
  	   boost::shared_ptr<AbstractCellProperty> p_normal_mutation(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());

       for (unsigned i = 0; i<cells.size(); i++)
       {
          cells[i]->SetMutationState(p_normal_mutation);
		  cells[i]->SetBirthTime(0.0);
	   }

       // Specify where cells lie
	   std::vector<unsigned> location_indices;

       for (unsigned i=1075; i<=1075; i=i+50)
       {
		  for(unsigned j=0; j<1; j++)
		  {
		     location_indices.push_back(i+j);
		  }
       }

  	   // Create cell population
       MultipleCaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
       cell_population.SetOutputCellIdData(true);
       cell_population.SetOutputCellMutationStates(true);
       cell_population.SetOutputCellProliferativeTypes(true);
       cell_population.SetOutputCellCyclePhases(true);
       cell_population.SetOutputCellAncestors(true);
       cell_population.SetOutputCellAges(true);

       cell_population.SetDataOnAllCells("oxygen", 1.0);

  	   // Set up cell-based simulation
	   OnLatticeSimulationInterfaceFocus<2> simulator(cell_population);
	   std::string output_directory = "TestPdesForCellGrowthWithDirichletBoundaryConditions";
	   simulator.SetOutputDirectory(output_directory);
	   simulator.SetDt(0.1);
	   simulator.SetSamplingTimestepMultiple(10);
	   simulator.SetEndTime(1000.0);

  	   // Set up PDE and pass to simulation via handler
	   OxygenPde<2> pde_1(cell_population, 0.1);
	   ConstBoundaryCondition<2> bc_1(30.0);
	   PdeAndBoundaryConditions<2> pde_and_bc_1(&pde_1, &bc_1, false);
	   pde_and_bc_1.SetDependentVariableName("oxygen");

  	   CellBasedPdeHandlerInterfaceFocus<2> pde_handler(&cell_population);
	   pde_handler.AddPdeAndBc(&pde_and_bc_1);
	   ChastePoint<2> lower(-0.5, -0.5);
	   ChastePoint<2> upper(49.5, 49.5);
	   ChasteCuboid<2> cuboid(lower, upper);
	   //pde_handler.UseCoarsePdeMesh(1.0, cuboid);
	   pde_handler.SetImposeBcsOnCoarseBoundary(true);

  	   simulator.SetCellBasedPdeHandler(&pde_handler);

 	   // Create cell killer
	   MAKE_PTR_ARGS(VasctumCellKiller<2>, cell_killer,(&cell_population));

	   simulator.AddCellKiller(cell_killer);

       // Run simulation
	   simulator.Solve();
    }
};

Code#

File name TestCaBasedCellPopulationUsingPdesLiteratePaper.hpp#

Code

File name `TestCaBasedCellPopulationUsingPdesLiteratePaper.hpp`