// Solve a Purkinje problem and check that the solution for the myocardium nodes is exactly the same as
// the solution of an equivalent monodomain-only problem, that the purkinje voltage for
// purkinje nodes doesn't change (no purkinje stimulus is given), and is 0 for non-purkinje nodes.
void TestMonodomainPurkinjeSolver()
{
/* The assembly requires 1/time-step,
* here we are providing enough information without starting a whole simulation */
PdeSimulationTime::SetTime(0.0);
PdeSimulationTime::SetPdeTimeStepAndNextTime(0.01, 0.01);
HeartConfig::Instance()->SetUseAbsoluteTolerance(1e-12);
HeartConfig::Instance()->SetPurkinjeSurfaceAreaToVolumeRatio(HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio());
std::string mesh_base("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements");
TrianglesMeshReader<2,2> reader(mesh_base);
MixedDimensionMesh<2,2> mesh(DistributedTetrahedralMeshPartitionType::DUMB);
mesh.ConstructFromMeshReader(reader);
//The mixed dimension mesh specifies fibre radii, we override these for the purposes of the
//test
for (MixedDimensionMesh<2, 2>::CableElementIterator iter = mesh.GetCableElementIteratorBegin();
iter != mesh.GetCableElementIteratorEnd();
++iter)
{
(*iter)->SetAttribute(0.56419); //1/sqrt(pi), so that the fibre cross section area is 1.0
}
std::string mesh_base2("mesh/test/data/2D_0_to_1mm_200_elements");
TrianglesMeshReader<2,2> reader2(mesh_base2);
TetrahedralMesh<2,2> mesh_just_monodomain;
mesh_just_monodomain.ConstructFromMeshReader(reader2);
PurkinjeCellFactory cell_factory;
cell_factory.SetMesh(&mesh);
NonPurkinjeCellFactory cell_factory_for_just_monodomain;
cell_factory_for_just_monodomain.SetMesh(&mesh_just_monodomain);
MonodomainTissue<2> tissue( &cell_factory );
MonodomainTissue<2> tissue_for_just_monodomain( &cell_factory_for_just_monodomain );
// Create an empty BCC - zero Neumann BCs will be applied everywhere
BoundaryConditionsContainer<2,2,2> bcc;
BoundaryConditionsContainer<2,2,1> bcc_for_just_monodomain;
MonodomainPurkinjeSolver<2,2> solver(&mesh, &tissue, &bcc);
MonodomainSolver<2,2> solver_just_monodomain(&mesh_just_monodomain, &tissue_for_just_monodomain, &bcc_for_just_monodomain);
//Create an initial condition
DistributedVectorFactory* p_vector_factory = mesh.GetDistributedVectorFactory();
Vec init_cond = p_vector_factory->CreateVec(2);
Vec init_cond_just_monodomain = p_vector_factory->CreateVec(1);
// get the voltage stripes
DistributedVector ic = mesh.GetDistributedVectorFactory()->CreateDistributedVector(init_cond);
DistributedVector ic2 = mesh.GetDistributedVectorFactory()->CreateDistributedVector(init_cond_just_monodomain);
DistributedVector::Stripe volume_stripe = DistributedVector::Stripe(ic, 0);
DistributedVector::Stripe cable_stripe = DistributedVector::Stripe(ic, 1);
for (DistributedVector::Iterator index = ic.Begin();
index != ic.End();
++index)
{
volume_stripe[index] = tissue.GetCardiacCell(index.Global)->GetVoltage();
cable_stripe[index] = tissue.GetPurkinjeCell(index.Global)->GetVoltage();//doesn't matter if this is fake
// make it zero in the cable stripe for the nodes that are not in purkinje ..
}
ic.Restore();
for (DistributedVector::Iterator index = ic2.Begin();
index != ic2.End();
++index)
{
ic2[index] = tissue.GetCardiacCell(index.Global)->GetVoltage();
}
ic2.Restore();
double t_end = 1;
solver.SetTimes(0, t_end);
solver.SetTimeStep(0.01);
solver.SetInitialCondition(init_cond);
solver.SetOutputDirectoryAndPrefix("MonodomainPurkinje","results");
solver.SetOutputToTxt(true);
solver.SetPrintingTimestepMultiple(10);
Vec solution = solver.Solve();
// the following assumes Luo-Rudy!!
Vec init_cond_for_just_monodomain = PetscTools::CreateAndSetVec(mesh.GetNumNodes(), -83.853);
solver_just_monodomain.SetTimes(0, t_end);
solver_just_monodomain.SetTimeStep(0.01);
solver_just_monodomain.SetInitialCondition(init_cond_for_just_monodomain);
Vec solution_just_monodomain = solver_just_monodomain.Solve();
// Test that certain blocks of the matrix and rhs vector in the monodomain-purkinje solve
// match the matrix and vector for a normal monodomain solve
Vec& r_purk_rhs = solver.GetLinearSystem()->rGetRhsVector();
Vec& r_mono_rhs = solver_just_monodomain.GetLinearSystem()->rGetRhsVector();
Mat& r_purk_mat = solver.GetLinearSystem()->rGetLhsMatrix();
Mat& r_mono_mat = solver_just_monodomain.GetLinearSystem()->rGetLhsMatrix();
TS_ASSERT_EQUALS(PetscVecTools::GetSize(r_purk_rhs), 2*PetscVecTools::GetSize(r_mono_rhs));
assert(PetscVecTools::GetSize(r_mono_rhs)==mesh.GetNumNodes());
int lo, hi;
VecGetOwnershipRange(r_mono_rhs, &lo, &hi);
// We don't explicitly test the values of the rhs, as this is also tested by comparing the solutions.
// As the system matrices are different, the results won't be identical (but will be close) for the same linear solver tolerance.
// for(int i=lo; i<hi; i++)
// {
// TS_ASSERT_DELTA(PetscVecTools::GetElement(r_purk_rhs, 2*i), PetscVecTools::GetElement(r_mono_rhs, i), 1e-8);
// }
for(int i=lo; i<hi; i++)
{
for(unsigned j=0; j<mesh.GetNumNodes(); j++)
{
// 'top-left' block
TS_ASSERT_DELTA(PetscMatTools::GetElement(r_purk_mat, 2*i,2*j), PetscMatTools::GetElement(r_mono_mat, i,j), 1e-8);
// 'off-diagonal' blocks
TS_ASSERT_DELTA(PetscMatTools::GetElement(r_purk_mat, 2*i,2*j+1), 0.0, 1e-8);
TS_ASSERT_DELTA(PetscMatTools::GetElement(r_purk_mat, 2*i+1,2*j), 0.0, 1e-8);
}
}
ReplicatableVector soln_repl(solution);
ReplicatableVector soln_mono_repl(solution_just_monodomain);
for(unsigned i=0; i<mesh.GetNumNodes(); i++)
{
if(55<=i && i<=65) // purkinje nodes for this mesh
{
//The Purkinje domain is a 1D line embedded within the tissue.
//It is stimulated in the same way as the tissue domain, therefore
//the propagation velocity should be the same (within numerical error).
TS_ASSERT_DELTA(soln_repl[2*i+1], soln_repl[2*i], 1e-1);
}
else
{
TS_ASSERT_DELTA(soln_repl[2*i+1], 0.0, 1e-4)
}
TS_ASSERT_DELTA(soln_repl[2*i], soln_mono_repl[i], 1e-5);
}
HeartConfig::Instance()->SetUseStateVariableInterpolation(true);
TS_ASSERT_THROWS_THIS(MonodomainPurkinjeSolver2d bad_solver(&mesh, &tissue, &bcc),"State-variable interpolation is not yet supported with Purkinje");
HeartConfig::Instance()->SetUseStateVariableInterpolation(false);
PetscTools::Destroy(solution);
PetscTools::Destroy(init_cond);
PetscTools::Destroy(init_cond_for_just_monodomain);
PetscTools::Destroy(solution_just_monodomain);
PetscTools::Destroy(init_cond_just_monodomain);
}
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);
}