void TestConductionVelocityConvergesFasterWithSvi1d()
{
double h[3] = {0.001,0.01,0.02};
unsigned probe_node_index[3] = {300, 30, 15};
unsigned number_of_nodes[3] = {1001, 101, 51};
std::vector<double> conduction_vel_ici(3);
std::vector<double> conduction_vel_svi(3);
ReplicatableVector final_voltage_ici;
ReplicatableVector final_voltage_svi;
//HeartConfig::Instance()->SetUseRelativeTolerance(1e-8);
HeartConfig::Instance()->SetSimulationDuration(4.0); //ms
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.01, 0.01, 0.01);
for (unsigned i=0; i<3; i++)
{
// ICI - ionic current interpolation - the default
{
DistributedTetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(h[i], 1.0);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), number_of_nodes[i]);
//Double check (for later) that the indexing is as expected
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal( probe_node_index[i] ))
{
TS_ASSERT_DELTA(mesh.GetNode( probe_node_index[i] )->rGetLocation()[0], 0.3, 1e-8);
}
std::stringstream output_dir;
output_dir << "MonodomainIci_" << h[i];
HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
// need to have this for i=1,2 cases!!
HeartConfig::Instance()->SetUseStateVariableInterpolation(false);
BlockCellFactory<1> cell_factory;
MonodomainProblem<1> monodomain_problem( &cell_factory );
monodomain_problem.SetMesh(&mesh);
monodomain_problem.Initialise();
monodomain_problem.Solve();
final_voltage_ici.ReplicatePetscVector(monodomain_problem.GetSolution());
//// see #1633
//// end time needs to be increased for these (say, to 7ms)
// Hdf5DataReader simulation_data(OutputFileHandler::GetChasteTestOutputDirectory() + output_dir.str(),
// "results", false);
// PropagationPropertiesCalculator ppc(&simulation_data);
// unsigned node_at_0_04 = (unsigned)round(0.04/h[i]);
// unsigned node_at_0_40 = (unsigned)round(0.40/h[i]);
// assert(fabs(mesh.GetNode(node_at_0_04)->rGetLocation()[0]-0.04)<1e-6);
// assert(fabs(mesh.GetNode(node_at_0_40)->rGetLocation()[0]-0.40)<1e-6);
// conduction_vel_ici[i] = ppc.CalculateConductionVelocity(node_at_0_04,node_at_0_40,0.36);
// std::cout << "conduction_vel_ici = " << conduction_vel_ici[i] << "\n";
}
// SVI - state variable interpolation
{
DistributedTetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(h[i], 1.0);
//Double check (for later) that the indexing is as expected
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal( probe_node_index[i] ))
{
TS_ASSERT_DELTA(mesh.GetNode( probe_node_index[i] )->rGetLocation()[0], 0.3, 1e-8);
}
std::stringstream output_dir;
output_dir << "MonodomainSvi_" << h[i];
HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation();
BlockCellFactory<1> cell_factory;
MonodomainProblem<1> monodomain_problem( &cell_factory );
monodomain_problem.SetMesh(&mesh);
monodomain_problem.Initialise();
monodomain_problem.Solve();
final_voltage_svi.ReplicatePetscVector(monodomain_problem.GetSolution());
// Hdf5DataReader simulation_data(OutputFileHandler::GetChasteTestOutputDirectory() + output_dir.str(),
// "results", false);
// PropagationPropertiesCalculator ppc(&simulation_data);
// unsigned node_at_0_04 = (unsigned)round(0.04/h[i]);
// unsigned node_at_0_40 = (unsigned)round(0.40/h[i]);
// assert(fabs(mesh.GetNode(node_at_0_04)->rGetLocation()[0]-0.04)<1e-6);
// assert(fabs(mesh.GetNode(node_at_0_40)->rGetLocation()[0]-0.40)<1e-6);
// conduction_vel_svi[i] = ppc.CalculateConductionVelocity(node_at_0_04,node_at_0_40,0.36);
// std::cout << "conduction_vel_svi = " << conduction_vel_svi[i] << "\n";
}
if (i==0) // finest mesh
{
for (unsigned j=0; j<final_voltage_ici.GetSize(); j++)
{
// visually checked they agree at this mesh resolution, and chosen tolerance from results
TS_ASSERT_DELTA(final_voltage_ici[j], final_voltage_svi[j], 0.3);
if (final_voltage_ici[j]>-80)
{
// shouldn't be exactly equal, as long as away from resting potential
TS_ASSERT_DIFFERS(final_voltage_ici[j], final_voltage_svi[j]);
}
}
double ici_voltage_at_0_03_finest_mesh = final_voltage_ici[ probe_node_index[i] ];
double svi_voltage_at_0_03_finest_mesh = final_voltage_svi[ probe_node_index[i] ];
TS_ASSERT_DELTA(svi_voltage_at_0_03_finest_mesh, 11.0067, 2e-4); //hardcoded value from fine svi
TS_ASSERT_DELTA(ici_voltage_at_0_03_finest_mesh, 11.0067, 1.2e-1); //hardcoded value from fine svi
}
else if (i==1)
{
double ici_voltage_at_0_03_middle_mesh = final_voltage_ici[ probe_node_index[i] ];
double svi_voltage_at_0_03_middle_mesh = final_voltage_svi[ probe_node_index[i] ];
// ICI conduction velocity > SVI conduction velocity
// and both should be greater than CV on finesh mesh
TS_ASSERT_DELTA(ici_voltage_at_0_03_middle_mesh, 19.8924, 1e-3);
TS_ASSERT_DELTA(svi_voltage_at_0_03_middle_mesh, 14.9579, 1e-3);
}
else
{
double ici_voltage_at_0_03_coarse_mesh = final_voltage_ici[ probe_node_index[i] ];
double svi_voltage_at_0_03_coarse_mesh = final_voltage_svi[ probe_node_index[i] ];
// ICI conduction velocity even greater than SVI conduction
// velocity
TS_ASSERT_DELTA(ici_voltage_at_0_03_coarse_mesh, 24.4938, 1e-3);
TS_ASSERT_DELTA(svi_voltage_at_0_03_coarse_mesh, 17.3131, 1e-3);
}
}
}
void TestConductionVelocityConvergesFasterWithSvi1d() throw(Exception)
{
double h[3] = {0.001,0.01,0.02};
std::vector<double> conduction_vel_nci(3);
std::vector<double> conduction_vel_svi(3);
ReplicatableVector final_solution_ici;
ReplicatableVector final_solution_svi;
ReplicatableVector final_solution_svit;
HeartConfig::Instance()->SetSimulationDuration(4.0); //ms
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.01, 0.01, 0.01);
for(unsigned i=0; i<3; i++)
{
// ICI - ionic current interpolation - the default
{
TetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(h[i], 1.0);
std::stringstream output_dir;
output_dir << "BidomainIci_" << h[i];
HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
// need to have this for i=1,2 cases!!
HeartConfig::Instance()->SetUseStateVariableInterpolation(false);
BlockCellFactory<1> cell_factory;
BidomainProblem<1> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
final_solution_ici.ReplicatePetscVector(bidomain_problem.GetSolution());
}
// SVI - state variable interpolation
{
DistributedTetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(h[i], 1.0);
std::stringstream output_dir;
output_dir << "BidomainSvi_" << h[i];
HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation();
BlockCellFactory<1> cell_factory;
BidomainProblem<1> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
final_solution_svi.ReplicatePetscVector(bidomain_problem.GetSolution());
}
// SVIT - state variable interpolation on straight (not distributed) tetrahedral mesh
{
TetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(h[i], 1.0);
std::stringstream output_dir;
output_dir << "BidomainSviTet_" << h[i];
HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation();
BlockCellFactory<1> cell_factory;
BidomainProblem<1> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
final_solution_svit.ReplicatePetscVector(bidomain_problem.GetSolution());
}
double voltage_at_0_03_finest_mesh;
if(i==0) // finest mesh
{
for(unsigned j=0; j<final_solution_ici.GetSize(); j++)
{
// visually checked they agree at this mesh resolution, and chosen tolerance from results
TS_ASSERT_DELTA(final_solution_ici[j], final_solution_svi[j], 0.35);
TS_ASSERT_DELTA(final_solution_svit[j], final_solution_svi[j], 1e-8);
if(j%2==0 /* just look at voltage */ && final_solution_ici[j]>-80)
{
// shouldn't be exactly equal, as long as away from resting potential
TS_ASSERT_DIFFERS(final_solution_ici[j], final_solution_svi[j]);
}
}
voltage_at_0_03_finest_mesh = final_solution_ici[600];
TS_ASSERT_DELTA(voltage_at_0_03_finest_mesh, -65.2218, 1e-2); //hardcoded value
}
else if(i==1)
{
double nci_voltage_at_0_03_middle_mesh = final_solution_ici[60];
double svi_voltage_at_0_03_middle_mesh = final_solution_svi[60];
double svit_voltage_at_0_03_middle_mesh = final_solution_svit[60];
// ICI conduction velocity > SVI conduction velocity
// and both should be greater than CV on finesh mesh
TS_ASSERT_DELTA(nci_voltage_at_0_03_middle_mesh, -44.3111, 1e-3);
TS_ASSERT_DELTA(svi_voltage_at_0_03_middle_mesh, -60.7765, 1e-3);
TS_ASSERT_DELTA(svit_voltage_at_0_03_middle_mesh, -60.7765, 1e-3);
}
else
{
double nci_voltage_at_0_03_coarse_mesh = final_solution_ici[30];
double svi_voltage_at_0_03_coarse_mesh = final_solution_svi[30];
double svit_voltage_at_0_03_coarse_mesh = final_solution_svit[30];
// ICI conduction velocity even greater than SVI conduction
// velocity
TS_ASSERT_DELTA(nci_voltage_at_0_03_coarse_mesh, -6.5622, 1e-3);
TS_ASSERT_DELTA(svi_voltage_at_0_03_coarse_mesh, -51.8848, 1e-3);
TS_ASSERT_DELTA(svit_voltage_at_0_03_coarse_mesh, -51.8848, 1e-3);
}
}
}
