This tutorial was generated from the file projects/Harvey2015/test/TestValidateSimulationLiteratePaper.hpp at revision r23521. Note that the code is given in full at the bottom of the page.

Validate a 256 cell simulation in parallel and serial (Figure 3)

This class was used to generate the results in Figure 3. A script CompareParallelResults.py is provided to aid comparison of the output results of the simulation.

Note: before compiling this code you need to alter the precision of the output. You can do so by adding single line setprecision(..) to NodeLocationWriter in the main code base


Index: cell_based/src/population/writers/population_writers/NodeLocationWriter.cpp
===================================================================
--- cell_based/src/population/writers/population_writers/NodeLocationWriter.cpp (revision 21854)
+++ cell_based/src/population/writers/population_writers/NodeLocationWriter.cpp (working copy)
@@ -50,6 +50,7 @@
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void NodeLocationWriter<ELEMENT_DIM, SPACE_DIM>::VisitAnyPopulation(AbstractCellPopulation<SPACE_DIM, SPACE_DIM>* pCellPopulation)
{
+    *this->mpOutStream << setprecision(20);
for (typename AbstractMesh<SPACE_DIM, SPACE_DIM>::NodeIterator node_iter = pCellPopulation->rGetMesh().GetNodeIteratorBegin();
node_iter != pCellPopulation->rGetMesh().GetNodeIteratorEnd();
++node_iter)

Use

This test suite is designed to be run twice. Each run will take roughly a minute (depending on your machine configuration).


## in serial
scons build=GccOptNative projects/Harvey2015/test/TestValidateSimulationLiteratePaper.hpp
## In parallel
scons build=GccOptNative_2 projects/Harvey2015/test/TestValidateSimulationLiteratePaper.hpp

After this the positional output may be checked to machine output precision:


## May need to see this to $CHASTE_TEST_OUTPUT
export OUTPUT=/tmp/$USER/testoutput
./projects/Harvey2015/test/CompareParallelResults.py 2 $OUTPUT/ValidateSimulation3Rand1/results_from_time_0/results.viznodes $OUTPUT/ValidateSimulation3Rand2/results_from_time_0/results.viznodes

Code overview

The first thing to do is to include the necessary header files.

Include header files

// The testing framework
#include <cxxtest/TestSuite.h>
#include "AbstractCellBasedTestSuite.hpp"

// Cell-based Chaste include files
#include "NodeBasedCellPopulation.hpp"
#include "CellBasedEventHandler.hpp"
#include "ParallelCellsGenerator.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "OffLatticeSimulation.hpp"
#include "SmartPointers.hpp"

// Needed for parallel code
#include "PetscSetupAndFinalize.hpp"

/**
 *
 * == The test suite ==
 */
class TestValidateSimulation : public AbstractCellBasedTestSuite
{
public:

    void Test2dSimulation() throw (Exception)
    {
        NodesOnlyMesh<2> mesh;
        mesh.SetCalculateNodeNeighbours(false);
        mesh.SetMaximumInteractionDistance(1.6);

        std::vector<CellPtr> cells;

Here we call a parallel helper method which reads the cell locations from a file on disk.

The proliferative type ensures that the cells are not growing.

        ParallelCellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> generator;

        generator.GenerateParallelCells("projects/Harvey2015/test/data/2DCellsCircle.dat",
                                        cells,
                                        mesh,
                                        CellPropertyRegistry::Instance()->Get<DifferentiatedCellProliferativeType>());

        // 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);

Output from this simulation is to be found relative to CHASTE_TEST_OUTPUT which by default is /tmp/$USER/testoutput The folder is suffixed by the number of processes involved in this calculation.

        std::ostringstream procs;
        procs << PetscTools::GetNumProcs();
        std::string output_directory = "ValidateSimulation3Rand" + procs.str();
        simulator.SetOutputDirectory(output_directory);

        // Create a force law and pass it to the simulation
        MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
        p_force->SetCutOffLength(1.5);

        simulator.AddForce(p_force);

        simulator.SetDt(1.0/240.0);
        simulator.SetSamplingTimestepMultiple(240);
        simulator.SetEndTime(100.0);
        simulator.Solve();

Report on the time taken to run the simulation

        CellBasedEventHandler::Headings();
        CellBasedEventHandler::Report();
    }
};

Code

The full code is given below

File name TestValidateSimulationLiteratePaper.hpp

// The testing framework
#include <cxxtest/TestSuite.h>
#include "AbstractCellBasedTestSuite.hpp"

// Cell-based Chaste include files
#include "NodeBasedCellPopulation.hpp"
#include "CellBasedEventHandler.hpp"
#include "ParallelCellsGenerator.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "OffLatticeSimulation.hpp"
#include "SmartPointers.hpp"

// Needed for parallel code
#include "PetscSetupAndFinalize.hpp"

/**
 *
 * == The test suite ==
 */
class TestValidateSimulation : public AbstractCellBasedTestSuite
{
public:

    void Test2dSimulation() throw (Exception)
    {
        NodesOnlyMesh<2> mesh;
        mesh.SetCalculateNodeNeighbours(false);
        mesh.SetMaximumInteractionDistance(1.6);

        std::vector<CellPtr> cells;

        ParallelCellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> generator;

        generator.GenerateParallelCells("projects/Harvey2015/test/data/2DCellsCircle.dat",
                                        cells,
                                        mesh,
                                        CellPropertyRegistry::Instance()->Get<DifferentiatedCellProliferativeType>());

        // 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);

        std::ostringstream procs;
        procs << PetscTools::GetNumProcs();
        std::string output_directory = "ValidateSimulation3Rand" + procs.str();
        simulator.SetOutputDirectory(output_directory);

        // Create a force law and pass it to the simulation
        MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
        p_force->SetCutOffLength(1.5);

        simulator.AddForce(p_force);

        simulator.SetDt(1.0/240.0);
        simulator.SetSamplingTimestepMultiple(240);
        simulator.SetEndTime(100.0);
        simulator.Solve();

        CellBasedEventHandler::Headings();
        CellBasedEventHandler::Report();
    }
};
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