void TestCardiacSimulationArchiveDynamic() throw(Exception)
{
#ifdef CHASTE_CAN_CHECKPOINT_DLLS
// run a monodomain simulation
{
CardiacSimulation simulation("heart/test/data/xml/save_monodomain_dynamic.xml");
}
std::string foldername = "SaveMonodomainDynamic";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "save_monodomain_dynamic", false,
foldername, "SimulationResults", true));
FileFinder file(foldername + "_checkpoints/0.2ms/" + foldername + "_0.2ms/archive.arch.0",
RelativeTo::ChasteTestOutput);
TS_ASSERT(file.Exists());
/* If you want to update the .h5 results for this test for any reason, you need to stop the following lines adding to them.
* So uncomment the assert(), run the test, and then do:
cp /tmp/chaste/testoutput/SaveMonodomainDynamic/SimulationResults.h5 heart/test/data/cardiac_simulations/save_monodomain_dynamic.h5
*/
//assert(0);
//resume the simulation
{
CardiacSimulation simulation("heart/test/data/xml/resume_monodomain_dynamic.xml");
}
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "resume_monodomain_dynamic", false,
foldername, "SimulationResults", true));
#endif // CHASTE_CAN_CHECKPOINT_DLLS
}
void TestCardiacSimulationPostprocessMonodomain() throw(Exception)
{
// run a bidomain simulation
CardiacSimulation simulation("heart/test/data/xml/postprocess_monodomain.xml");
std::string foldername = "PostprocessMonodomainNightly/";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "postprocess_monodomain_results", false,
foldername, "SimulationResults", true, 1e-9));
}
void TestCardiacSimulationBasicMonodomainShort() throw(Exception)
{
// Fox2002BackwardEuler cell model
// run a bidomain simulation
CardiacSimulation simulation("heart/test/data/xml/base_monodomain_short.xml");
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "base_monodomain_short_results", false,
"BaseMonodomainShort", "SimulationResults", true, 1e-6));
}
// requires TestCardiacSimulationArchiveMonodomain() to have been run
void TestCardiacSimulationResumeMonodomain() throw(Exception)
{
// run a monodomain simulation
HeartConfig::Instance()->SetSpaceDimension(1);
CardiacSimulation simulation("heart/test/data/xml/resume_monodomain_short.xml");
std::string foldername = "SaveMonodomainShort";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "resume_monodomain_short_results", false,
foldername, "SimulationResults", true, 1e-6));
}
void TestCardiacSimulationPostprocessMonodomain() throw(Exception)
{
// Fox2002BackwardEuler cell model
// run a bidomain simulation
CardiacSimulation simulation("heart/test/data/xml/postprocess_monodomain_short.xml");
std::string foldername = "PostprocessMonodomainShort";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "postprocess_monodomain_short_results", false,
foldername, "SimulationResults", true, 1e-6));
}
void TestMono1dSodiumBlockBySettingNamedParameter() throw(Exception)
{
CardiacSimulation simulation("heart/test/data/xml/monodomain1d_sodium_block.xml");
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "mono_1d_sodium_block", false,
"Mono1dSodiumBlock", "SimulationResults", true,
2.5e-3));
// Test exception
TS_ASSERT_THROWS_THIS(CardiacSimulation bad_param("heart/test/data/xml/bad_cell_parameter.xml"),
"No parameter named 'missing-parameter'.");
}
void TestMonoStimUsingEllipsoids() throw(Exception)
{
if (PetscTools::GetNumProcs() > 3u)
{
TS_TRACE("This test is not suitable for more than 3 processes.");
return;
}
// Fox2002BackwardEuler cell model
CardiacSimulation simulation("heart/test/data/xml/monodomain1d_stim_using_ellipsoid.xml", true);
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "monodomain1d_stim_using_ellipsoid", false,
"Mono1DStimUsingEllipsoid", "SimulationResults", true, 1e-6));
}
void TestCardiacSimulationSaveBidomain() throw(Exception)
{
// run a bidomain simulation
CardiacSimulation simulation("heart/test/data/xml/save_bidomain.xml");
std::string foldername = "SaveBidomainNightly";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "save_bidomain_results", false,
foldername, "SimulationResults", true, 1e-9));
FileFinder file(foldername + "_checkpoints/10ms/" + foldername + "_10ms/archive.arch.0",
RelativeTo::ChasteTestOutput);
TS_ASSERT(file.Exists());
}
// requires TestCardiacSimulationArchiveBidomain() to have been run
void TestCardiacSimulationResumeBidomain() throw(Exception)
{
// run a bidomain simulation
HeartConfig::Instance()->SetSpaceDimension(1);
FileFinder resume_xml("heart/test/data/xml/resume_bidomain_short.xml", RelativeTo::ChasteSourceRoot);
OutputFileHandler checkpoint_dir("SaveBidomainShort_checkpoints/0.2ms", false);
FileFinder copied_xml = checkpoint_dir.CopyFileTo(resume_xml);
CardiacSimulation simulation(copied_xml.GetAbsolutePath());
std::string foldername = "SaveBidomainShort";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "resume_bidomain_short_results", false,
foldername, "SimulationResults", true, 1e-5));
//assert(0);
}
void TestMono1dSmall() throw(Exception)
{
if (PetscTools::GetNumProcs() > 3u)
{
TS_TRACE("This test is not suitable for more than 3 processes.");
return;
}
// Fox2002BackwardEuler cell model
CardiacSimulation simulation("heart/test/data/xml/monodomain1d_small.xml", true);
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "mono_1d_small", false,
"SaveMono1D", "SimulationResults", true, 1e-6));
/* If the above fails, and you are happy the new results are correct, uncomment the following line,
* run the test, and then do
cp /tmp/$USER/testoutput/SaveMono1D/SimulationResults.h5 heart/test/data/cardiac_simulations/mono_1d_small.h5
*/
//assert(0);
CardiacSimulation simulation2("heart/test/data/xml/monodomain1d_resume.xml", true);
}
void TestCardiacSimulationArchiveMonodomain() throw(Exception)
{
// Fox2002BackwardEuler cell model
// run a bidomain simulation
CardiacSimulation simulation("heart/test/data/xml/save_monodomain_short.xml");
std::string foldername = "SaveMonodomainShort";
// compare the files, using the CompareFilesViaHdf5DataReader() method
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "save_monodomain_short_results", false,
foldername, "SimulationResults", true, 1e-6));
FileFinder file(foldername + "_checkpoints/0.2ms/" + foldername + "_0.2ms/archive.arch.0",
RelativeTo::ChasteTestOutput);
TS_ASSERT(file.Exists());
/* If you want to update the .h5 results for this test for any reason, you need to stop the following test adding to them.
* So uncomment the assert(), run the test, and then do:
cp /tmp/chaste/testoutput/SaveMonodomainShort/SimulationResults.h5 heart/test/data/cardiac_simulations/save_monodomain_short_results.h5
*/
//assert(0);
}
FileFinder from_directory2(source_directory + folder_2, RelativeTo::ChasteSourceRoot);
TRY_IF_MASTER(
to_directory1.Remove();
to_directory2.Remove();
TS_ASSERT_EQUALS(to_directory1.Exists(), false);
TS_ASSERT_EQUALS(to_directory2.Exists(), false);
from_directory1.CopyTo(to_directory1);
from_directory2.CopyTo(to_directory2);
);
// Resume
CardiacSimulation simulation("heart/test/data/xml/resume_migration.xml");
// Compare results
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/cardiac_simulations", "resume_bidomain_short_results", false,
"SaveBidomainShort", "SimulationResults", true, 1e-5));
}
void runSimulation(const std::string& rParametersFileName)
{
CardiacSimulation simulation(rParametersFileName);
}
void checkParameter(AbstractCardiacCellInterface* pCell, unsigned globalIndex)
{
// Check one of the parameters has been set in the central region
TS_ASSERT_EQUALS(pCell->GetNumberOfParameters(), 3u);
double expected_value;
if (globalIndex <= 4 || globalIndex >= 16)
{
expected_value = 23.0;
/**
* This test is aimed at comparing the extended bidomain implementation in Chaste with
* the original Finite Difference code developed by Martin Buist.
*
* All the parameters are chosen to replicate the same conditions as in his code.
*/
void TestExtendedProblemVsMartincCode() throw (Exception)
{
SetupParameters();
TetrahedralMesh<1,1> mesh;
unsigned number_of_elements = 100;//this is nGrid in Martin's code
double length = 10.0;//100mm as in Martin's code
mesh.ConstructRegularSlabMesh(length/number_of_elements, length);
TS_ASSERT_EQUALS(mesh.GetNumAllNodes(), number_of_elements + 1);
double Am_icc = 1000.0;
double Am_smc = 1000.0;
double Am_gap = 1.0;
double Cm_icc = 1.0;
double Cm_smc = 1.0;
double G_gap = 20.0;//mS/cm^2
HeartConfig::Instance()->SetSimulationDuration(1000.0); //ms.
ICC_Cell_factory icc_factory;
SMC_Cell_factory smc_factory;
std::string dir = "ICCandSMC";
std::string filename = "extended1d";
HeartConfig::Instance()->SetOutputDirectory(dir);
HeartConfig::Instance()->SetOutputFilenamePrefix(filename);
ExtendedBidomainProblem<1> extended_problem( &icc_factory , &smc_factory);
extended_problem.SetMesh(&mesh);
extended_problem.SetExtendedBidomainParameters(Am_icc,Am_smc, Am_gap, Cm_icc, Cm_smc, G_gap);
extended_problem.SetIntracellularConductivitiesForSecondCell(Create_c_vector(1.0));
std::vector<unsigned> outputnodes;
outputnodes.push_back(50u);
HeartConfig::Instance()->SetRequestedNodalTimeTraces(outputnodes);
extended_problem.Initialise();
extended_problem.Solve();
HeartEventHandler::Headings();
HeartEventHandler::Report();
/**
* Compare with valid data.
* As Martin's code is an FD code, results will never match exactly.
* The comparison below is done against a 'valid' h5 file.
*
* The h5 file (1DValid.h5) is a Chaste (old phi_i formulation) file with is valid because, when extrapolating results from it, they look very similar
* (except for a few points at the end of the upstroke) to the results taken
* directly from Martin's code.
* A plot of Chaste results versus Martin's result (at node 50) is stored
* in the file 1DChasteVsMartin.eps for reference.
*
* A second plot comparing the old formulation (with phi_i) to the new formulation with V_m is contained in
*.1DChasteNewFormulation.png
*
*/
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/extendedbidomain", "1DValid", false,
dir, filename, true,
0.2));
/*
* Here we compare the new formulation (V_m1, V_m2, phi_e)
* with the previous formulation (phi_i1, phi_i2, phi_e) running with GMRES and an absolute KSP tolerance of 1e-8.
*/
TS_ASSERT( CompareFilesViaHdf5DataReader("heart/test/data/extendedbidomain", "extended1d_previous_chaste_formulation_abs_tol_1e-8", false,
dir, filename, true,
1e-2));
}
