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;
}
}
SIM* CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM>::Load(const std::string& rArchiveDirectory, const double& rTimeStamp)
{
/**
* Find the right archive (and mesh) to load. The files are contained within
* the 'archive' folder in rArchiveDirectory, with the archive itself called
* 'cell_population_sim_at_time_`rTimeStamp`.arch'. The path to this file is returned.
*
* The path to the mesh is stored in ArchiveLocationInfo for use by the
* CellPopulation de-serialization routines.
*/
std::ostringstream time_stamp;
time_stamp << rTimeStamp;
std::string archive_filename = "cell_population_sim_at_time_" + time_stamp.str() + ".arch";
std::string mesh_filename = "mesh_" + time_stamp.str();
FileFinder archive_dir(rArchiveDirectory + "/archive/", RelativeTo::ChasteTestOutput);
ArchiveLocationInfo::SetMeshPathname(archive_dir, mesh_filename);
// Create an input archive
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_filename);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
// Load the simulation
SIM* p_sim;
(*p_arch) >> p_sim;
return p_sim;
}
void TestSimpleUniformSourceParabolicPdeArchiving() throw(Exception)
{
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "SimpleUniformSourceParabolicPde.arch";
ArchiveLocationInfo::SetMeshFilename("SimpleUniformSourceParabolicPde");
{
// Create a PDE object
AbstractLinearParabolicPde<2,2>* const p_pde = new SimpleUniformSourceParabolicPde<2>(0.1);
// 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;
delete p_pde;
}
{
AbstractLinearParabolicPde<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<SimpleUniformSourceParabolicPde<2>*>(p_pde) != NULL);
SimpleUniformSourceParabolicPde<2>* p_static_cast_pde = static_cast<SimpleUniformSourceParabolicPde<2>*>(p_pde);
TS_ASSERT_EQUALS(p_static_cast_pde->GetCoefficient(),0.1);
// Avoid memory leaks
delete p_pde;
}
}
void TestArchiveDiagonalVertexBasedDivisionRule() throw(Exception)
{
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "division_rules.arch";
// Create data structures to store variables to test for equality here
{
boost::shared_ptr<AbstractVertexBasedDivisionRule<2> > p_division_rule(new DiagonalVertexBasedDivisionRule<2>());
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// Record values to test into data structures
// If necessary you can use static_cast<ConcreteClass*>(p_abstract_class)
// (if your abstract class doesn't contain the necessary variables and methods)
(*p_arch) << p_division_rule;
}
{
boost::shared_ptr<AbstractVertexBasedDivisionRule<2> > p_division_rule;
// 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 from the archive
(*p_arch) >> p_division_rule;
// Check things in the data structures with TS_ASSERTS here.
// If necessary you can use static_cast<ConcreteClass*>(p_abstract_class_2)
// (if your abstract class doesn't contain the necessary variables and methods)
// Check that we have got back the right kind of division rule.
TS_ASSERT(dynamic_cast <DiagonalVertexBasedDivisionRule<2>* > (p_division_rule.get()));
}
}
void CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM>::Save(SIM* pSim)
{
// Get the simulation time as a string
const SimulationTime* p_sim_time = SimulationTime::Instance();
assert(p_sim_time->IsStartTimeSetUp());
std::ostringstream time_stamp;
time_stamp << p_sim_time->GetTime();
// Set up folder and filename of archive
FileFinder archive_dir(pSim->GetOutputDirectory() + "/archive/", RelativeTo::ChasteTestOutput);
std::string archive_filename = "cell_population_sim_at_time_" + time_stamp.str() + ".arch";
ArchiveLocationInfo::SetMeshFilename(std::string("mesh_") + time_stamp.str());
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_filename);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// Archive the simulation (const-ness would be a pain here)
(*p_arch) & pSim;
}
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;
}
}
// NB This checks that periodicity is maintained through archiving...
void TestArchiving() throw (Exception)
{
EXIT_IF_PARALLEL; // HoneycombMeshGenerator doesn't work in parallel
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "cylindrical_nodes_only_mesh_base.arch";
ArchiveLocationInfo::SetMeshFilename("cylindrical_nodes_only_mesh");
// Create generating mesh
unsigned num_cells_across = 4;
unsigned num_cells_up = 7;
HoneycombMeshGenerator generator(num_cells_across,num_cells_up);
TetrahedralMesh<2,2>* p_generating_mesh = generator.GetMesh();
// Convert this to a Cylindrical2dNodesOnlyMesh
double periodic_width = 4.0;
Cylindrical2dNodesOnlyMesh* p_mesh = new Cylindrical2dNodesOnlyMesh(periodic_width);
p_mesh->ConstructNodesWithoutMesh(*p_generating_mesh, 1.0);
AbstractMesh<2,2>* const p_saved_mesh = p_mesh;
/*
* You need the const above to stop a BOOST_STATIC_ASSERTION failure.
* This is because the serialization library only allows you to save
* tracked objects while the compiler considers them const, to prevent
* the objects changing during the save, and so object tracking leading
* to wrong results. For example, A is saved once via pointer, then
* changed, then saved again. The second save notes that A was saved
* before, so doesn't write its data again, and the change is lost.
*/
{
// Serialize the mesh
TS_ASSERT_DELTA((static_cast<Cylindrical2dNodesOnlyMesh*>(p_saved_mesh))->GetWidth(0), periodic_width, 1e-7);
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// We have to serialize via a pointer here, or the derived class information is lost.
(*p_arch) << p_saved_mesh;
}
{
// De-serialize and compare
AbstractMesh<2,2>* p_loaded_mesh;
// 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 from the archive
(*p_arch) >> p_loaded_mesh;
// Compare the loaded mesh against the original
Cylindrical2dNodesOnlyMesh* p_static_cast_loaded_mesh = static_cast<Cylindrical2dNodesOnlyMesh*>(p_loaded_mesh);
Cylindrical2dNodesOnlyMesh* p_static_cast_saved_mesh = static_cast<Cylindrical2dNodesOnlyMesh*>(p_saved_mesh);
// Compare width
TS_ASSERT_DELTA(p_static_cast_loaded_mesh->GetWidth(0), periodic_width, 1e-7);
TS_ASSERT_DELTA(p_static_cast_saved_mesh->GetWidth(0), periodic_width, 1e-7);
// Compare nodes
TS_ASSERT_EQUALS(p_static_cast_saved_mesh->GetNumNodes(), p_static_cast_loaded_mesh->GetNumNodes());
TS_ASSERT_EQUALS(p_static_cast_saved_mesh->GetNumNodes(), 28u);
for (unsigned i=0; i<p_static_cast_saved_mesh->GetNumNodes(); i++)
{
Node<2>* p_node = p_static_cast_saved_mesh->GetNode(i);
Node<2>* p_node2 = p_static_cast_loaded_mesh->GetNode(i);
TS_ASSERT_EQUALS(p_node->IsDeleted(), p_node2->IsDeleted());
TS_ASSERT_EQUALS(p_node->GetIndex(), p_node2->GetIndex());
TS_ASSERT_EQUALS(p_node->IsBoundaryNode(), p_node2->IsBoundaryNode());
for (unsigned j=0; j<2; j++)
{
TS_ASSERT_DELTA(p_node->rGetLocation()[j], p_node2->rGetLocation()[j], 1e-4);
}
}
// Avoid memory leak
delete p_loaded_mesh;
}
// Avoid memory leak
delete p_mesh;
}
/**
* Tests archiving of the tissue object.
* It creates one, changes the default values of some member variables and saves.
* Then it tries to load from the archive and checks that the member variables are with the right values.
*/
void TestSaveAndLoadExtendedBidomainTissue() throw (Exception)
{
HeartConfig::Instance()->Reset();
// Archive settings
FileFinder archive_dir("extended_tissue_archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "extended_bidomain_tissue.arch";
bool cache_replication_saved = false;
double saved_printing_timestep = 2.0;
double default_printing_timestep = HeartConfig::Instance()->GetPrintingTimeStep();
c_matrix<double, 3, 3> intra_tensor_before_archiving;
c_matrix<double, 3, 3> intra_tensor_second_cell_before_archiving;
c_matrix<double, 3, 3> extra_tensor_before_archiving;
//creation and save
{
// This call is required to set the appropriate conductivity media and to make sure that HeartConfig
// knows the mesh filename despite we use our own mesh reader.
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/cube_136_elements");
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
DistributedTetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
UnStimulatedCellFactory first_cell;
StimulatedCellFactory second_cell;
ExtracellularStimulusFactory extra_factory;
first_cell.SetMesh(&mesh);
second_cell.SetMesh(&mesh);
extra_factory.SetMesh(&mesh);
ExtendedBidomainTissue<3> extended_tissue( &first_cell, &second_cell , &extra_factory);
//set a value different from default for the conductivities of the second cell
extended_tissue.SetIntracellularConductivitiesSecondCell(Create_c_vector(25.0,26.0,27.0));
//this is normally done by the problem class, but in this test we do it manually
extended_tissue.CreateIntracellularConductivityTensorSecondCell();
extended_tissue.SetCacheReplication(cache_replication_saved); // Not the default to check it is archived...
//shuffle default values to check if they get archived properly
extended_tissue.SetAmFirstCell(11.0);
extended_tissue.SetAmSecondCell(22.0);
extended_tissue.SetAmGap(33.0);
extended_tissue.SetCmFirstCell(44.0);
extended_tissue.SetCmSecondCell(55.0);
extended_tissue.SetGGap(66.0);
//again, away from default value to check for archiving
extended_tissue.SetUserSuppliedExtracellularStimulus(true);
//set some heterogeneities in Ggap
std::vector<boost::shared_ptr<AbstractChasteRegion<3> > > heterogeneity_areas;
std::vector<double> Ggap_values;
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.001, 0.001, 0.001);
boost::shared_ptr<ChasteCuboid<3> > p_cuboid_1(new ChasteCuboid<3>(cornerA, cornerB));
heterogeneity_areas.push_back(p_cuboid_1);
//within the first area
Ggap_values.push_back(143.0);
extended_tissue.SetGgapHeterogeneities(heterogeneity_areas, Ggap_values);
extended_tissue.CreateGGapConductivities();
// Some checks to make sure HeartConfig is being saved and loaded by this too.
HeartConfig::Instance()->SetPrintingTimeStep(saved_printing_timestep);
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
intra_tensor_before_archiving = extended_tissue.rGetIntracellularConductivityTensor(0);
intra_tensor_second_cell_before_archiving = extended_tissue.rGetIntracellularConductivityTensorSecondCell(0);
extra_tensor_before_archiving = extended_tissue.rGetExtracellularConductivityTensor(0);
// Save
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<3>* const p_archive_bidomain_tissue = &extended_tissue;
(*p_arch) << p_archive_bidomain_tissue;
HeartConfig::Reset();
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), default_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep);
}
//load
{
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<3>* p_abstract_tissue;
(*p_arch) >> p_abstract_tissue;
assert(p_abstract_tissue!=NULL);
//dynamic cast so we are able to test specific variables of ExtendedBidomainTissue
ExtendedBidomainTissue<3>* p_extended_tissue = dynamic_cast<ExtendedBidomainTissue<3>*>(p_abstract_tissue);
assert(p_extended_tissue != NULL);
const c_matrix<double, 3, 3>& intra_tensor_after_archiving = p_extended_tissue->rGetIntracellularConductivityTensor(0);
const c_matrix<double, 3, 3>& intra_tensor_second_cell_after_archiving = p_extended_tissue->rGetIntracellularConductivityTensorSecondCell(0);
const c_matrix<double, 3, 3>& extra_tensor_after_archiving = p_extended_tissue->rGetExtracellularConductivityTensor(0);
//check before archiving = after archiving
for(unsigned i=0; i<3; i++)
{
for(unsigned j=0; j<3; j++)
{
TS_ASSERT_DELTA(intra_tensor_before_archiving(i,j), intra_tensor_after_archiving(i,j), 1e-9);
TS_ASSERT_DELTA(intra_tensor_second_cell_before_archiving(i,j), intra_tensor_second_cell_after_archiving(i,j), 1e-9);
TS_ASSERT_DELTA(extra_tensor_before_archiving(i,j), extra_tensor_after_archiving(i,j), 1e-9);
}
}
//check that the member variable mIntracellularConductivitiesSecondCell was archived properly
TS_ASSERT_EQUALS(p_extended_tissue->GetIntracellularConductivitiesSecondCell()(0),25.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetIntracellularConductivitiesSecondCell()(1),26.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetIntracellularConductivitiesSecondCell()(2),27.0);
//check that we get the same values from the archive which are different from the default
TS_ASSERT_EQUALS(p_extended_tissue->GetAmFirstCell(), 11.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetAmSecondCell(), 22.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetAmGap(), 33.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCmFirstCell(), 44.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCmSecondCell(), 55.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetGGap(), 66.0);
// We shouldn't need to re-build the mesh, but we use it to check that the new tissue has the same mesh
// Also, when testing in parallel, we use it to get the vector factory to loop over the nodes we own.
// this is because p_extended_tissue->pGetMesh()->GetDistributedVectorFactory() doesn't compile (discards qualifier stuff caused by use of const).
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
DistributedTetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), p_extended_tissue->pGetMesh()->GetNumNodes());//note: this is allowed because GetNumNodes has const in the signature
//check archiving of stimulus for first cell at some random times (it is unstimulated everywhere at all times)
for (unsigned i = 0; i < mesh.GetNumNodes(); i++)
{
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(i))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(0.0), 0.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(0.1), 0.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(2.5), 0.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(28.9), 0.0);
}
}
//for second cell and other stuff, we probe nodes 0 and 1.
unsigned node_0 = 0u;
unsigned node_1 = 1u;
//If the test is run in parallel, we need to work out the new indices
const std::vector<unsigned>& r_permutation = mesh.rGetNodePermutation();
if (!r_permutation.empty())
{
node_0 = r_permutation[0u];
node_1 = r_permutation[1u];
}
//second cell is stimulated in the corner (node 0) from time 0 to 1. check it gets all this after loading
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(node_0))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacSecondCell(node_0)->GetIntracellularStimulus(0.5), -105.0*1400);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacSecondCell(node_0)->GetIntracellularStimulus(2.5), 0.0);
//find local index of (the new) node_0, it should be in the heterogeneity region
unsigned ownership_range_low = mesh.GetDistributedVectorFactory()->GetLow();
unsigned local_index = node_0 - ownership_range_low;
//std::cout<<local_index<<std::endl;
TS_ASSERT_EQUALS(p_extended_tissue->rGetGapsDistributed()[local_index],143.0);//g_gap value inside heterogeneity region
}
//node 0 has extracellular stimulus (1 ms from 0.1)
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(node_0))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(0.0), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(0.5), -428000);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(1.0), -428000);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(1.15), 0);
}
//node 1 doesn't
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(node_1))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(0.0), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(0.5), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(1.0), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(1.15), 0);
//find local index of (the new) node_1, it should NOT be in the heterogeneity region
unsigned ownership_range_low = mesh.GetDistributedVectorFactory()->GetLow();
unsigned local_index = node_1 - ownership_range_low;
TS_ASSERT_EQUALS(p_extended_tissue->rGetGapsDistributed()[local_index],66.0);//standard g_gap value, outside heterogeneity region
}
//check the archiving of the flag (it would be false by default, but we set it to true before archiving)
TS_ASSERT_EQUALS(p_extended_tissue->HasTheUserSuppliedExtracellularStimulus(),true);
TS_ASSERT_EQUALS(cache_replication_saved, p_extended_tissue->GetDoCacheReplication());
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep); // Test we are testing something in case default changes
delete p_extended_tissue;
}
}
void TestArchiving() throw(Exception)
{
OutputFileHandler archive_dir_("mixed_mesh_archive"); // Clear folder
FileFinder main_archive_dir("mixed_mesh_archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "mixed_dimension_mesh.arch";
ArchiveLocationInfo::SetMeshFilename("mixed_dimension_mesh");
MixedDimensionMesh<2,2>* p_mesh = new MixedDimensionMesh<2,2>(DistributedTetrahedralMeshPartitionType::DUMB);
unsigned num_nodes;
unsigned local_num_nodes;
unsigned num_elements;
unsigned num_cable_elements;
unsigned num_local_cable_elements;
// archive
{
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements");
p_mesh->ConstructFromMeshReader(mesh_reader);
num_nodes = p_mesh->GetNumNodes();
local_num_nodes = p_mesh->GetNumLocalNodes();
num_elements = p_mesh->GetNumElements();
num_cable_elements = p_mesh->GetNumCableElements();
num_local_cable_elements = p_mesh->GetNumLocalCableElements();
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(main_archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
AbstractTetrahedralMesh<2,2>* const p_mesh_abstract = static_cast<AbstractTetrahedralMesh<2,2>* >(p_mesh);
(*p_arch) << p_mesh_abstract;
}
FileFinder ncl_file("mixed_dimension_mesh.ncl", main_archive_dir);
TS_ASSERT(ncl_file.Exists());
// restore
{
// Should archive the most abstract class you can to check boost knows what individual classes are.
// (but here AbstractMesh doesn't have the methods below).
AbstractTetrahedralMesh<2,2>* p_mesh_abstract2;
// Create an input archive
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(main_archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
// restore from the archive
(*p_arch) >> p_mesh_abstract2;
// Check we have the right number of nodes & elements
MixedDimensionMesh<2,2>* p_mesh2 = static_cast<MixedDimensionMesh<2,2>*>(p_mesh_abstract2);
TS_ASSERT_EQUALS(p_mesh2->GetNumNodes(), num_nodes);
TS_ASSERT_EQUALS(p_mesh2->GetNumLocalNodes(), local_num_nodes);
TS_ASSERT_EQUALS(p_mesh2->GetNumElements(), num_elements);
TS_ASSERT_EQUALS(p_mesh2->GetNumCableElements(), num_cable_elements);
TS_ASSERT_EQUALS(p_mesh2->GetNumLocalCableElements(), num_local_cable_elements);
// Check elements have the right nodes
for (unsigned i=0; i<num_cable_elements; i++)
{
try
{
Element<1,2>* p_element = p_mesh->GetCableElement(i);
Element<1,2>* p_element2 = p_mesh2->GetCableElement(i);
TS_ASSERT_EQUALS(p_element->GetNodeGlobalIndex(0), p_element2->GetNodeGlobalIndex(0));
}
catch(Exception& e)
{
TS_ASSERT_DIFFERS((int)e.GetShortMessage().find("does not belong to processor"),-1);
}
}
delete p_mesh2;
}
// restore from a single processor archive
{
FileFinder archive_dir("mesh/test/data/mixed_mesh_archive", RelativeTo::ChasteSourceRoot);
if ( PetscTools::IsSequential() )
{
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractTetrahedralMesh<2,2>* p_mesh_abstract3 = NULL;
(*p_arch) >> p_mesh_abstract3;
//Double check that the cables are intact
MixedDimensionMesh<2,2>* p_mesh3 = static_cast<MixedDimensionMesh<2,2>*>(p_mesh_abstract3);
Element<1,2>* p_element = p_mesh3->GetCableElement(9);
TS_ASSERT_EQUALS(p_element->GetNodeGlobalIndex(0), 64u);
TS_ASSERT_EQUALS(p_element->GetNodeGlobalIndex(1), 65u);
TS_ASSERT_DELTA(p_element->GetAttribute(), 10.5, 1e-8);
delete p_mesh_abstract3;
}
else
{
typedef ArchiveOpener<boost::archive::text_iarchive, std::ifstream> InputArchiveOpener;
if (PetscTools::GetMyRank() > 0)
{
// Should not read this archive because none exists here.
TS_ASSERT_THROWS_CONTAINS(InputArchiveOpener arch_opener(archive_dir, archive_file),
"Cannot load secondary archive file:");
}
else
{
// Should not read this archive because there are two or more processes and
// this archive was written on one process.
InputArchiveOpener arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractTetrahedralMesh<2,2>* p_mesh3 = NULL;
TS_ASSERT_THROWS_THIS((*p_arch) >> p_mesh3,
"This archive was written for a different number of processors");
}
}
}
// NB This checks that periodicity is maintained through archiving...
void TestArchiving() throw (Exception)
{
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "cylindrical_mesh_base.arch";
ArchiveLocationInfo::SetMeshFilename("cylindrical_mesh");
// Set up a mesh
unsigned cells_across = 5;
unsigned cells_up = 3;
double crypt_width = 5.0;
unsigned thickness_of_ghost_layer = 0;
CylindricalHoneycombMeshGenerator generator(cells_across, cells_up, thickness_of_ghost_layer, crypt_width/cells_across);
AbstractTetrahedralMesh<2,2>* const p_mesh = generator.GetCylindricalMesh();
/*
* You need the const above to stop a BOOST_STATIC_ASSERTION failure.
* This is because the serialization library only allows you to save tracked
* objects while the compiler considers them const, to prevent the objects
* changing during the save, and so object tracking leading to wrong results.
* (e.g. A is saved once via pointer, then changed, then saved again. The second
* save notes that A was saved before, so doesn't write its data again, and the
* change is lost.)
*/
{
// Serialize the mesh
double width = p_mesh->GetWidth(0);
TS_ASSERT_DELTA(width, crypt_width, 1e-7);
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// We have to serialize via a pointer here, or the derived class information is lost.
(*p_arch) << p_mesh;
}
{
// De-serialize and compare
AbstractTetrahedralMesh<2,2>* p_mesh2;
// 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 from the archive
(*p_arch) >> p_mesh2;
// Cylindrical2dMesh now remeshes itself on load (convert from TrianglesMeshReader to normal format)
TS_ASSERT_DELTA(p_mesh2->GetWidth(0), crypt_width, 1e-7);
// Compare the loaded mesh against the original
TS_ASSERT_EQUALS(p_mesh->GetNumAllNodes(), p_mesh2->GetNumAllNodes());
TS_ASSERT_EQUALS(p_mesh->GetNumNodes(), p_mesh2->GetNumNodes());
TS_ASSERT_EQUALS(p_mesh->GetNumBoundaryNodes(), p_mesh2->GetNumBoundaryNodes());
for (unsigned i=0; i<p_mesh->GetNumAllNodes(); i++)
{
Node<2>* p_node = p_mesh->GetNode(i);
Node<2>* p_node2 = p_mesh2->GetNode(i);
TS_ASSERT_EQUALS(p_node->IsDeleted(), p_node2->IsDeleted());
TS_ASSERT_EQUALS(p_node->GetIndex(), p_node2->GetIndex());
TS_ASSERT_EQUALS(p_node->IsBoundaryNode(), p_node2->IsBoundaryNode());
for (unsigned j=0; j<2; j++)
{
TS_ASSERT_DELTA(p_node->rGetLocation()[j], p_node2->rGetLocation()[j], 1e-16);
}
}
TS_ASSERT_EQUALS(p_mesh->GetNumElements(), p_mesh2->GetNumElements());
TS_ASSERT_EQUALS(p_mesh->GetNumAllElements(), p_mesh2->GetNumAllElements());
TS_ASSERT_EQUALS(p_mesh->GetNumBoundaryElements(), p_mesh2->GetNumBoundaryElements());
TS_ASSERT_EQUALS(p_mesh->GetNumAllBoundaryElements(), p_mesh2->GetNumAllBoundaryElements());
AbstractTetrahedralMesh<2,2>::ElementIterator iter2 = p_mesh2->GetElementIteratorBegin();
for (AbstractTetrahedralMesh<2,2>::ElementIterator iter = p_mesh->GetElementIteratorBegin();
iter != p_mesh->GetElementIteratorEnd();
++iter, ++iter2)
{
TS_ASSERT_EQUALS(iter->GetNumNodes(), iter2->GetNumNodes());
for (unsigned i=0; i<iter->GetNumNodes(); i++)
{
TS_ASSERT_EQUALS(iter->GetNodeGlobalIndex(i), iter2->GetNodeGlobalIndex(i));
}
}
// We now need to free the mesh, since there is no honeycomb generator to do so.
delete p_mesh2;
}
}
void TestSaveAndLoadCardiacTissue() throw (Exception)
{
HeartConfig::Instance()->Reset();
// Archive settings
FileFinder archive_dir("monodomain_tissue_archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "monodomain_tissue.arch";
bool cache_replication_saved = false;
double saved_printing_timestep = 2.0;
double default_printing_timestep = HeartConfig::Instance()->GetPrintingTimeStep();
// Info about the first cell on this process (if any)
bool has_cell = false;
unsigned cell_v_index = (unsigned)(-1);
double cell_v = DBL_MAX;
c_matrix<double, 1, 1> tensor_before_archiving;
{
TrianglesMeshReader<1,1> mesh_reader("mesh/test/data/1D_0_to_1_10_elements");
TetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
MyCardiacCellFactory cell_factory;
cell_factory.SetMesh(&mesh);
MonodomainTissue<1> monodomain_tissue( &cell_factory );
monodomain_tissue.SetCacheReplication(cache_replication_saved); // Not the default to check it is archived...
tensor_before_archiving = monodomain_tissue.rGetIntracellularConductivityTensor(1);
// Get some info about the first cell on this process (if any)
const std::vector<AbstractCardiacCellInterface*>& r_cells = monodomain_tissue.rGetCellsDistributed();
has_cell = !r_cells.empty();
if (has_cell)
{
cell_v_index = r_cells[0]->GetVoltageIndex();
cell_v = r_cells[0]->GetVoltage();
}
// Some checks to make sure HeartConfig is being saved and loaded by this too.
HeartConfig::Instance()->SetPrintingTimeStep(saved_printing_timestep);
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
// Save
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<1>* const p_archive_monodomain_tissue = &monodomain_tissue;
(*p_arch) << p_archive_monodomain_tissue;
HeartConfig::Reset();
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), default_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep);
}
{
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<1>* p_monodomain_tissue;
(*p_arch) >> p_monodomain_tissue;
// Test rGetIntracellularConductivityTensor
const c_matrix<double, 1, 1>& tensor_after_archiving = p_monodomain_tissue->rGetIntracellularConductivityTensor(1);
TS_ASSERT_DELTA(tensor_before_archiving(0,0), tensor_after_archiving(0,0), 1e-9);
TS_ASSERT_EQUALS(cache_replication_saved, p_monodomain_tissue->GetDoCacheReplication());
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep); // Test we are testing something in case default changes
// Test cardiac cells have also been archived
const std::vector<AbstractCardiacCellInterface*>& r_cells = p_monodomain_tissue->rGetCellsDistributed();
TS_ASSERT_EQUALS(has_cell, !r_cells.empty());
if (has_cell)
{
TS_ASSERT_EQUALS(cell_v_index, r_cells[0]->GetVoltageIndex());
TS_ASSERT_EQUALS(cell_v, r_cells[0]->GetVoltage());
}
delete p_monodomain_tissue;
}
}
void TestSaveAndLoadCardiacPDE()
{
HeartConfig::Instance()->Reset();
// Archive settings
FileFinder archive_dir("tissue_archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "bidomain_tissue.arch";
bool cache_replication_saved = false;
double saved_printing_timestep = 2.0;
double default_printing_timestep = HeartConfig::Instance()->GetPrintingTimeStep();
std::vector<cp::media_type> media_types;
media_types.push_back(cp::media_type::Orthotropic);
media_types.push_back(cp::media_type::Axisymmetric);
media_types.push_back(cp::media_type::NoFibreOrientation);
for (std::vector<cp::media_type>::iterator it = media_types.begin();
it != media_types.end();
++it)
{
c_matrix<double, 3, 3> intra_tensor_before_archiving;
c_matrix<double, 3, 3> extra_tensor_before_archiving;
{
// This call is required to set the appropriate conductivity media and to make sure that HeartConfig
// knows the mesh filename despite we use our own mesh reader.
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/3D_Single_tetrahedron_element", *it);
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/3D_Single_tetrahedron_element");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
MyCardiacCellFactory<3> cell_factory;
cell_factory.SetMesh(&mesh);
BidomainTissue<3> bidomain_tissue( &cell_factory );
bidomain_tissue.SetCacheReplication(cache_replication_saved); // Not the default to check it is archived...
// Some checks to make sure HeartConfig is being saved and loaded by this too.
HeartConfig::Instance()->SetPrintingTimeStep(saved_printing_timestep);
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
intra_tensor_before_archiving = bidomain_tissue.rGetIntracellularConductivityTensor(0);
extra_tensor_before_archiving = bidomain_tissue.rGetExtracellularConductivityTensor(0);
// Save
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<3>* const p_archive_bidomain_tissue = &bidomain_tissue;
(*p_arch) << p_archive_bidomain_tissue;
HeartConfig::Reset();
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), default_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep);
}
{
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<3>* p_bidomain_tissue;
(*p_arch) >> p_bidomain_tissue;
assert(p_bidomain_tissue!=NULL);
const c_matrix<double, 3, 3>& intra_tensor_after_archiving = p_bidomain_tissue->rGetIntracellularConductivityTensor(0);
const c_matrix<double, 3, 3>& extra_tensor_after_archiving = dynamic_cast<BidomainTissue<3>*>(p_bidomain_tissue)->rGetExtracellularConductivityTensor(0); //Naughty Gary using dynamic cast, but only for testing...
for(unsigned i=0; i<3; i++)
{
for(unsigned j=0; j<3; j++)
{
TS_ASSERT_DELTA(intra_tensor_before_archiving(i,j), intra_tensor_after_archiving(i,j), 1e-9);
TS_ASSERT_DELTA(extra_tensor_before_archiving(i,j), extra_tensor_after_archiving(i,j), 1e-9);
}
}
TS_ASSERT_EQUALS(cache_replication_saved, p_bidomain_tissue->GetDoCacheReplication());
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep); // Test we are testing something in case default changes
delete p_bidomain_tissue;
}
}
}
void TestArchiving() throw(Exception)
{
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "potts_cell_population_2d.arch";
// The following line is required because the loading of a cell population
// is usually called by the method CellBasedSimulation::Load()
ArchiveLocationInfo::SetMeshFilename("potts_mesh_2d");
// Create mesh
PottsMeshReader<2> mesh_reader("cell_based/test/data/TestPottsMeshWriter/potts_mesh_2d");
PottsMesh<2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Archive cell population
{
// Need to set up time
unsigned num_steps = 10;
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(1.0, num_steps+1);
// Create a Potts-based cell population object
std::vector<CellPtr> cells;
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasic(cells, mesh.GetNumElements());
// Create cell population
AbstractCellPopulation<2>* const p_cell_population = new PottsBasedCellPopulation<2>(mesh, cells);
// Cells have been given birth times of 0, -1, -2, -3, -4.
// loop over them to run to time 0.0;
for (AbstractCellPopulation<2>::Iterator cell_iter = p_cell_population->Begin();
cell_iter != p_cell_population->End();
++cell_iter)
{
cell_iter->ReadyToDivide();
}
// Create an update rule and pass to the population
MAKE_PTR(VolumeConstraintPottsUpdateRule<2>, p_volume_constraint_update_rule);
static_cast<PottsBasedCellPopulation<2>*>(p_cell_population)->AddUpdateRule(p_volume_constraint_update_rule);
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// Set member variables in order to test that they are archived correctly
static_cast<PottsBasedCellPopulation<2>*>(p_cell_population)->SetTemperature(0.25);
static_cast<PottsBasedCellPopulation<2>*>(p_cell_population)->SetNumSweepsPerTimestep(3);
static_cast<PottsBasedCellPopulation<2>*>(p_cell_population)->SetUpdateNodesInRandomOrder(false);
static_cast<PottsBasedCellPopulation<2>*>(p_cell_population)->SetIterateRandomlyOverUpdateRuleCollection(true);
// Archive the cell population
(*p_arch) << static_cast<const SimulationTime&>(*p_simulation_time);
(*p_arch) << p_cell_population;
// Tidy up
SimulationTime::Destroy();
delete p_cell_population;
}
// Restore cell population
{
// Need to set up time
unsigned num_steps = 10;
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetStartTime(0.0);
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(1.0, num_steps+1);
p_simulation_time->IncrementTimeOneStep();
AbstractCellPopulation<2>* p_cell_population;
// 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 the cell population
(*p_arch) >> *p_simulation_time;
(*p_arch) >> p_cell_population;
// Test that the member variables have been archived correctly
PottsBasedCellPopulation<2>* p_static_population = static_cast<PottsBasedCellPopulation<2>*>(p_cell_population);
TS_ASSERT_DELTA(p_static_population->GetTemperature(), 0.25, 1e-6);
TS_ASSERT_EQUALS(p_static_population->GetNumSweepsPerTimestep(), 3u);
TS_ASSERT_EQUALS(p_static_population->GetUpdateNodesInRandomOrder(), false);
TS_ASSERT_EQUALS(p_static_population->GetIterateRandomlyOverUpdateRuleCollection(), true);
// Test that the update rule has been archived correctly
std::vector<boost::shared_ptr<AbstractPottsUpdateRule<2> > > update_rule_collection = p_static_population->rGetUpdateRuleCollection();
TS_ASSERT_EQUALS(update_rule_collection.size(), 1u);
TS_ASSERT_EQUALS((*update_rule_collection[0]).GetIdentifier(), "VolumeConstraintPottsUpdateRule-2");
// Tidy up
delete p_cell_population;
}
}
void TestMonodomainTissueUsingPurkinjeCellFactory() throw(Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<2,2> reader("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements");
MixedDimensionMesh<2,2> mixed_mesh;
mixed_mesh.ConstructFromMeshReader(reader);
PurkinjeCellFactory cell_factory;
cell_factory.SetMesh(&mixed_mesh);
MonodomainTissue<2> tissue( &cell_factory );
TS_ASSERT(tissue.HasPurkinje());
TS_ASSERT_EQUALS(tissue.rGetPurkinjeCellsDistributed().size(), tissue.rGetCellsDistributed().size());
TS_ASSERT_EQUALS(tissue.rGetPurkinjeIionicCacheReplicated().GetSize(),
tissue.rGetIionicCacheReplicated().GetSize());
for (AbstractTetrahedralMesh<2,2>::NodeIterator current_node = mixed_mesh.GetNodeIteratorBegin();
current_node != mixed_mesh.GetNodeIteratorEnd();
++current_node)
{
unsigned global_index = current_node->GetIndex();
AbstractCardiacCellInterface* p_purkinje_cell = tissue.GetPurkinjeCell(global_index);
double y = current_node->rGetLocation()[1];
// cable nodes are on y=0.05 (we don't test by index because indices may be permuted in parallel).
if( fabs(y-0.05) < 1e-8 )
{
TS_ASSERT(dynamic_cast<CellDiFrancescoNoble1985FromCellML*>(p_purkinje_cell) != NULL);
}
else
{
TS_ASSERT(dynamic_cast<FakeBathCell*>(p_purkinje_cell) != NULL);
}
TS_ASSERT_EQUALS(tissue.rGetPurkinjeCellsDistributed()[global_index-mixed_mesh.GetDistributedVectorFactory()->GetLow()],
p_purkinje_cell);
}
// Test archiving too
FileFinder archive_dir("monodomain_tissue_purkinje_archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "monodomain_tissue_purkinje.arch";
{
// Save to archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// Make sure at least one Purkinje cell has a non-initial-condition state variable to compare
if (mixed_mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(0u))
{
tissue.GetPurkinjeCell(0u)->SetVoltage(1234.5);
}
AbstractCardiacTissue<2>* const p_archive_tissue = &tissue;
(*p_arch) << p_archive_tissue;
}
{
// Load from archive and compare
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<2>* p_tissue;
(*p_arch) >> p_tissue;
TS_ASSERT(p_tissue->HasPurkinje());
TS_ASSERT_EQUALS(p_tissue->rGetPurkinjeCellsDistributed().size(), tissue.rGetPurkinjeCellsDistributed().size());
TS_ASSERT_EQUALS(p_tissue->rGetPurkinjeIionicCacheReplicated().GetSize(), tissue.rGetPurkinjeIionicCacheReplicated().GetSize());
for (AbstractTetrahedralMesh<2,2>::NodeIterator current_node = p_tissue->mpMesh->GetNodeIteratorBegin();
current_node != p_tissue->mpMesh->GetNodeIteratorEnd();
++current_node)
{
unsigned global_index = current_node->GetIndex();
AbstractCardiacCellInterface* p_purkinje_cell = p_tissue->GetPurkinjeCell(global_index);
double y = current_node->rGetLocation()[1];
// cable nodes are on y=0.05 (we don't test by index because indices may be permuted in parallel).
if( fabs(y-0.05) < 1e-8 )
{
TS_ASSERT(dynamic_cast<CellDiFrancescoNoble1985FromCellML*>(p_purkinje_cell) != NULL);
}
else
{
TS_ASSERT(dynamic_cast<FakeBathCell*>(p_purkinje_cell) != NULL);
}
TS_ASSERT_EQUALS(p_purkinje_cell->GetVoltage(),
tissue.GetPurkinjeCell(global_index)->GetVoltage());
TS_ASSERT_EQUALS(p_tissue->rGetPurkinjeCellsDistributed()[global_index-p_tissue->mpMesh->GetDistributedVectorFactory()->GetLow()],
p_purkinje_cell);
}
delete p_tissue;
}
const std::string migration_archive_dir("TestMonodomainTissue/purkinje_migration_archive");
{
// Save via MonodomainProblem so we can migrate
// Note: from Chaste release 3.1 onward we no longer support Boost 1.33.
// The earliest version of Boost supported in 1.34
// Run the test with b=_hostconfig,boost=1-34_5 to save
/*
scons b=_hostconfig,boost=1-34_5 ts=heart/test/monodomain/TestMonodomainTissue.hpp
*
*/
MonodomainProblem<2> monodomain_problem( &cell_factory );
monodomain_problem.SetMesh(&mixed_mesh);
monodomain_problem.Initialise();
TS_ASSERT(monodomain_problem.GetMonodomainTissue()->HasPurkinje());
CardiacSimulationArchiver<MonodomainProblem<2> >::Save(monodomain_problem, migration_archive_dir);
}
TS_ASSERT_EQUALS(tissue.rGetPurkinjeIionicCacheReplicated().GetSize(), 121u);
}
void TestArchiving() throw (Exception)
{
// Set archiving location
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "mvmwr.arch";
ArchiveLocationInfo::SetMeshFilename("mvmwr");
// Create mesh
MutableVertexMesh<2,2>* p_mesh = ConstructFiveCellRosette();
// Set member variables
p_mesh->SetProtorosetteFormationProbability(0.123);
p_mesh->SetProtorosetteResolutionProbabilityPerTimestep(0.234);
p_mesh->SetRosetteResolutionProbabilityPerTimestep(0.345);
AbstractMesh<2,2>* const p_abstract_mesh = p_mesh;
/*
* You need the const above to stop a BOOST_STATIC_ASSERTION failure.
* This is because the serialization library only allows you to save tracked
* objects while the compiler considers them const, to prevent the objects
* changing during the save, and so object tracking leading to wrong results.
*
* E.g. A is saved once via pointer, then changed, then saved again. The second
* save notes that A was saved before, so doesn't write its data again, and the
* change is lost.
*/
// Create an output archive
{
TS_ASSERT_EQUALS((static_cast<MutableVertexMesh<2,2>*>(p_abstract_mesh))->GetNumNodes(), 11u);
TS_ASSERT_EQUALS((static_cast<MutableVertexMesh<2,2>*>(p_abstract_mesh))->GetNumElements(), 5u);
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// We have to serialize via a pointer here, or the derived class information is lost
(*p_arch) << p_abstract_mesh;
}
{
// De-serialize and compare
AbstractMesh<2,2>* p_abstract_mesh_2;
// 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 from the archive
(*p_arch) >> p_abstract_mesh_2;
MutableVertexMesh<2,2>* p_mesh_original = static_cast<MutableVertexMesh<2,2>*>(p_abstract_mesh);
MutableVertexMesh<2,2>* p_mesh_loaded = static_cast<MutableVertexMesh<2,2>*>(p_abstract_mesh_2);
// Test member variables were archived correctly
TS_ASSERT_DELTA(p_mesh_original->GetProtorosetteFormationProbability(), 0.123, 1e-10);
TS_ASSERT_DELTA(p_mesh_loaded->GetProtorosetteFormationProbability(), 0.123, 1e-10);
TS_ASSERT_DELTA(p_mesh_original->GetProtorosetteResolutionProbabilityPerTimestep(), 0.234, 1e-10);
TS_ASSERT_DELTA(p_mesh_loaded->GetProtorosetteResolutionProbabilityPerTimestep(), 0.234, 1e-10);
TS_ASSERT_DELTA(p_mesh_original->GetRosetteResolutionProbabilityPerTimestep(), 0.345, 1e-10);
TS_ASSERT_DELTA(p_mesh_loaded->GetRosetteResolutionProbabilityPerTimestep(), 0.345, 1e-10);
// Compare the loaded mesh against the original
TS_ASSERT_EQUALS(p_mesh_original->GetNumNodes(), 11u);
TS_ASSERT_EQUALS(p_mesh_original->GetNumNodes(), p_mesh_loaded->GetNumNodes());
TS_ASSERT_EQUALS(p_mesh_original->GetNumElements(), 5u);
TS_ASSERT_EQUALS(p_mesh_original->GetNumElements(), p_mesh_loaded->GetNumElements());
for (unsigned node_idx = 0 ; node_idx < p_mesh_original->GetNumNodes() ; node_idx++)
{
Node<2>* p_node = p_mesh_original->GetNode(node_idx);
Node<2>* p_node2 = p_mesh_loaded->GetNode(node_idx);
TS_ASSERT_EQUALS(p_node->IsDeleted(), p_node2->IsDeleted());
TS_ASSERT_EQUALS(p_node->GetIndex(), p_node2->GetIndex());
TS_ASSERT_EQUALS(p_node->IsBoundaryNode(), p_node2->IsBoundaryNode());
TS_ASSERT_DELTA(p_node->rGetLocation()[0], p_node2->rGetLocation()[0], 1e-10);
TS_ASSERT_DELTA(p_node->rGetLocation()[1], p_node2->rGetLocation()[1], 1e-10);
}
for (unsigned elem_idx = 0 ; elem_idx < p_mesh_original->GetNumElements() ; elem_idx++)
{
TS_ASSERT_EQUALS(p_mesh_original->GetElement(elem_idx)->GetNumNodes(),
p_mesh_loaded->GetElement(elem_idx)->GetNumNodes());
for (unsigned local_index=0; local_index<p_mesh_original->GetElement(elem_idx)->GetNumNodes(); local_index++)
{
TS_ASSERT_EQUALS(p_mesh_original->GetElement(elem_idx)->GetNodeGlobalIndex(local_index),
p_mesh_loaded->GetElement(elem_idx)->GetNodeGlobalIndex(local_index));
}
}
// Tidy up
delete p_mesh_original;
delete p_mesh_loaded;
}
}
void TestArchiving() throw (Exception)
{
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "cylindrical_vertex_mesh_base.arch";
ArchiveLocationInfo::SetMeshFilename("cylindrical_vertex_mesh");
// Create mesh
unsigned num_cells_across = 4;
unsigned num_cells_up = 7;
CylindricalHoneycombVertexMeshGenerator generator(num_cells_across, num_cells_up);
AbstractMesh<2,2>* const p_saved_mesh = generator.GetCylindricalMesh();
double crypt_width = num_cells_across;
/*
* You need the const above to stop a BOOST_STATIC_ASSERTION failure.
* This is because the serialization library only allows you to save
* tracked objects while the compiler considers them const, to prevent
* the objects changing during the save, and so object tracking leading
* to wrong results. For example, A is saved once via pointer, then
* changed, then saved again. The second save notes that A was saved
* before, so doesn't write its data again, and the change is lost.
*/
{
// Serialize the mesh
TS_ASSERT_DELTA((static_cast<Cylindrical2dVertexMesh*>(p_saved_mesh))->GetWidth(0), crypt_width, 1e-7);
// Create output archive
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
// We have to serialize via a pointer here, or the derived class information is lost.
(*p_arch) << p_saved_mesh;
}
{
// De-serialize and compare
AbstractMesh<2,2>* p_loaded_mesh;
// 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 from the archive
(*p_arch) >> p_loaded_mesh;
// Compare the loaded mesh against the original
Cylindrical2dVertexMesh* p_mesh2 = static_cast<Cylindrical2dVertexMesh*>(p_loaded_mesh);
Cylindrical2dVertexMesh* p_mesh = static_cast<Cylindrical2dVertexMesh*>(p_saved_mesh);
// Compare width
TS_ASSERT_DELTA(p_mesh2->GetWidth(0), crypt_width, 1e-7);
TS_ASSERT_DELTA(p_mesh->GetWidth(0), crypt_width, 1e-7);
// Compare nodes
TS_ASSERT_EQUALS(p_mesh->GetNumNodes(), p_mesh2->GetNumNodes());
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
Node<2>* p_node = p_mesh->GetNode(i);
Node<2>* p_node2 = p_mesh2->GetNode(i);
TS_ASSERT_EQUALS(p_node->IsDeleted(), p_node2->IsDeleted());
TS_ASSERT_EQUALS(p_node->GetIndex(), p_node2->GetIndex());
TS_ASSERT_EQUALS(p_node->IsBoundaryNode(), p_node2->IsBoundaryNode());
for (unsigned j=0; j<2; j++)
{
TS_ASSERT_DELTA(p_node->rGetLocation()[j], p_node2->rGetLocation()[j], 1e-4);
}
}
// Compare elements
TS_ASSERT_EQUALS(p_mesh->GetNumElements(), p_mesh2->GetNumElements());
TS_ASSERT_EQUALS(p_mesh->GetNumAllElements(), p_mesh2->GetNumAllElements());
for (unsigned i=0; i<p_mesh->GetNumElements(); i++)
{
VertexElement<2,2>* p_elt = p_mesh->GetElement(i);
VertexElement<2,2>* p_elt2 = p_mesh2->GetElement(i);
TS_ASSERT_EQUALS(p_elt->GetNumNodes(), p_elt2->GetNumNodes());
for (unsigned j=0; j<p_elt->GetNumNodes(); j++)
{
TS_ASSERT_EQUALS(p_elt->GetNodeGlobalIndex(j), p_elt2->GetNodeGlobalIndex(j));
}
}
// Tidy up
delete p_mesh2;
}
}
void TestArchivingCellPopulation() throw (Exception)
{
EXIT_IF_PARALLEL; // This test doesn't work in parallel.
FileFinder archive_dir("archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "node_based_cell_population_with_particles.arch";
ArchiveLocationInfo::SetMeshFilename("node_based_cell_population_with_particles_mesh");
{
// Need to set up time
unsigned num_steps = 10;
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(1.0, num_steps+1);
// 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());
// Create a cell population
NodeBasedCellPopulationWithParticles<2>* const p_cell_population = new NodeBasedCellPopulationWithParticles<2>(mesh, cells);
// Cells have been given birth times of 0, -1, -2, -3, -4.
// loop over them to run to time 0.0;
for (AbstractCellPopulation<2>::Iterator cell_iter = p_cell_population->Begin();
cell_iter != p_cell_population->End();
++cell_iter)
{
cell_iter->ReadyToDivide();
}
// 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();
// Write the cell population to the archive
(*p_arch) << static_cast<const SimulationTime&>(*p_simulation_time);
(*p_arch) << p_cell_population;
// Avoid memory leak
SimulationTime::Destroy();
delete p_cell_population;
}
{
// Need to set up time
unsigned num_steps = 10;
SimulationTime* p_simulation_time = SimulationTime::Instance();
p_simulation_time->SetStartTime(0.0);
p_simulation_time->SetEndTimeAndNumberOfTimeSteps(1.0, num_steps+1);
p_simulation_time->IncrementTimeOneStep();
NodeBasedCellPopulationWithParticles<2>* p_cell_population;
// Restore the cell population
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_simulation_time;
(*p_arch) >> p_cell_population;
// Cells have been given birth times of 0, -1, -2, -3, -4.
// this checks that individual cells and their models are archived.
unsigned counter = 0;
for (AbstractCellPopulation<2>::Iterator cell_iter = p_cell_population->Begin();
cell_iter != p_cell_population->End();
++cell_iter)
{
TS_ASSERT_DELTA(cell_iter->GetAge(), (double)(counter), 1e-7);
counter++;
}
// Check the simulation time has been restored (through the cell)
TS_ASSERT_EQUALS(p_simulation_time->GetTime(), 0.0);
// Check the cell population has been restored
TS_ASSERT_EQUALS(p_cell_population->rGetCells().size(), 5u);
TS_ASSERT_DELTA(p_cell_population->GetMechanicsCutOffLength(), 1.5, 1e-6);
// Check number of nodes
TS_ASSERT_EQUALS(p_cell_population->GetNumNodes(), 5u);
// Check some node positions
TS_ASSERT_EQUALS(p_cell_population->GetNode(3)->GetIndex(), 3u);
TS_ASSERT_EQUALS(p_cell_population->GetNode(4)->GetIndex(), 4u);
TS_ASSERT_DELTA(p_cell_population->GetNode(3)->rGetLocation()[0], 0.0, 1e-9);
TS_ASSERT_DELTA(p_cell_population->GetNode(3)->rGetLocation()[1], 1.0, 1e-9);
TS_ASSERT_DELTA(p_cell_population->GetNode(4)->rGetLocation()[0], 0.5, 1e-9);
TS_ASSERT_DELTA(p_cell_population->GetNode(4)->rGetLocation()[1], 0.5, 1e-9);
// Check the member variables have been restored
TS_ASSERT_DELTA(p_cell_population->GetMechanicsCutOffLength(), 1.5, 1e-9);
// Tidy up
delete p_cell_population;
}
}
