void TestBidomainWithBathCanOutputVariables() throw(Exception)
{
HeartConfig::Instance()->SetSimulationDuration(0.01); //ms
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/1D_0_to_1_10_elements_with_two_attributes");
HeartConfig::Instance()->SetOutputDirectory("BidomainBathOutputVariables");
HeartConfig::Instance()->SetOutputFilenamePrefix("BidomainLR91_1d");
HeartConfig::Instance()->SetVisualizeWithMeshalyzer();
std::vector<std::string> output_variables;
output_variables.push_back("cytosolic_calcium_concentration");
HeartConfig::Instance()->SetOutputVariables(output_variables);
std::set<unsigned> tissue_ids;
tissue_ids.insert(0); // Same as default value defined in HeartConfig
std::set<unsigned> bath_ids;
bath_ids.insert(1);
HeartConfig::Instance()->SetTissueAndBathIdentifiers(tissue_ids, bath_ids);
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 1> cell_factory;
BidomainWithBathProblem<1> bidomain_problem(&cell_factory);
bidomain_problem.Initialise();
bidomain_problem.Solve();
FileFinder calcium_results("BidomainBathOutputVariables/output/BidomainLR91_1d_cytosolic_calcium_concentration.dat",
RelativeTo::ChasteTestOutput);
TS_ASSERT_EQUALS(calcium_results.IsFile(), true);
FileFinder reference_results("heart/test/data/BidomainBathOutputVariables/BidomainLR91_1d_cytosolic_calcium_concentration.dat",
RelativeTo::ChasteSourceRoot);
NumericFileComparison comparer(calcium_results, reference_results);
TS_ASSERT_EQUALS(comparer.CompareFiles(), true);
}
void TestCheckForBathElementsNoDeadlock() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(1.0); //ms
HeartConfig::Instance()->SetOutputDirectory("bidomain_bath");
HeartConfig::Instance()->SetOutputFilenamePrefix("BidomainLR91_1d");
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 1> bidomain_cell_factory;
BidomainWithBathProblem<1> bidomain_problem( &bidomain_cell_factory );
TrianglesMeshReader<1,1> reader("mesh/test/data/1D_0_to_1_100_elements");
DistributedTetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(reader);
try
{
mesh.GetElement(0)->SetAttribute(HeartRegionCode::GetValidBathId());
}
catch(Exception&)
{
// I don't own element 0
}
bidomain_problem.SetMesh(&mesh);
// Fails because no bath
TS_ASSERT_THROWS_NOTHING(bidomain_problem.Initialise());
// Prevent an EventHandling exception in later tests
HeartEventHandler::EndEvent(HeartEventHandler::EVERYTHING);
}
void TestBathIntracellularStimulation() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(10.0); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath1d");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_1d");
c_vector<double,1> centre;
centre(0) = 0.5;
BathCellFactory<1> cell_factory(-1e6, centre); // stimulates x=0.5 node
BidomainWithBathProblem<1> bidomain_problem( &cell_factory );
TrianglesMeshReader<1,1> reader("mesh/test/data/1D_0_to_1_100_elements");
TetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(reader);
// set the x<0.25 and x>0.75 regions as the bath region
for(unsigned i=0; i<mesh.GetNumElements(); i++)
{
double x = mesh.GetElement(i)->CalculateCentroid()[0];
if( (x<0.25) || (x>0.75) )
{
mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidBathId());
}
}
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
// test V = 0 for all bath nodes
for(unsigned i=0; i<mesh.GetNumNodes(); i++)
{
if(HeartRegionCode::IsRegionBath( mesh.GetNode(i)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
}
// test symmetry of V and phi_e
for(unsigned i=0; i<=(mesh.GetNumNodes()-1)/2; i++)
{
unsigned opposite = mesh.GetNumNodes()-i-1;
TS_ASSERT_DELTA(sol_repl[2*i], sol_repl[2*opposite], 2e-3); // V
TS_ASSERT_DELTA(sol_repl[2*i+1], sol_repl[2*opposite+1], 2e-3); // phi_e
}
// a couple of hardcoded values
TS_ASSERT_DELTA(sol_repl[2*50], 3.7684, 1e-3);
TS_ASSERT_DELTA(sol_repl[2*70], 5.1777, 1e-3);
}
void Test3dBathIntracellularStimulation()
{
HeartConfig::Instance()->SetSimulationDuration(1); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath3d");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_3d");
c_vector<double,3> centre;
centre(0) = 0.05;
centre(1) = 0.05;
centre(2) = 0.05;
BathCellFactory<3> cell_factory(-2.5e7, centre); // stimulates x=0.05 node
BidomainProblem<3> bidomain_problem( &cell_factory, true );
TetrahedralMesh<3,3> mesh;
mesh.ConstructRegularSlabMesh(0.01, 0.1, 0.1, 0.1);
// Set everything outside a central sphere (radius 0.4) to be bath
for (unsigned i=0; i<mesh.GetNumElements(); i++)
{
double x = mesh.GetElement(i)->CalculateCentroid()[0];
double y = mesh.GetElement(i)->CalculateCentroid()[1];
double z = mesh.GetElement(i)->CalculateCentroid()[2];
if (sqrt((x-0.05)*(x-0.05) + (y-0.05)*(y-0.05) + (z-0.05)*(z-0.05)) > 0.04)
{
mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidBathId());
}
}
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
// test V = 0 for all bath nodes
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
if (HeartRegionCode::IsRegionBath( mesh.GetNode(i)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
}
// a hardcoded value
TS_ASSERT_DELTA(sol_repl[2*404], 39.6833, 1e-3);
}
void TestFailsIfNoBathElements() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(1.0); //ms
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/1D_0_to_1_100_elements");
HeartConfig::Instance()->SetOutputDirectory("bidomain_bath");
HeartConfig::Instance()->SetOutputFilenamePrefix("BidomainLR91_1d");
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 1> bidomain_cell_factory;
BidomainWithBathProblem<1> bidomain_problem( &bidomain_cell_factory );
// Fails because no bath
TS_ASSERT_THROWS_THIS(bidomain_problem.Initialise(), "No bath element found");
// Prevent an EventHandling exception in later tests
HeartEventHandler::EndEvent(HeartEventHandler::EVERYTHING);
}
void TestSimulation() throw(Exception)
{
HeartConfig::Instance()->SetSimulationDuration(5.0); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainTutorialWithBathAndFibres");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
/* Bath problems seem to require decreased ODE timesteps. We use the
* Backward Euler version of the Luo-Rudy model (see below) instead to
* improve code performance.
*/
HeartConfig::Instance()->SetOdeTimeStep(0.01); //ms
/* Use the {{{PlaneStimulusCellFactory}}} to define a set of Luo-Rudy cells, in this
* case with a Backward Euler solver. We pass the stimulus magnitude as 0.0
* as we don't want any stimulated cells.
*/
PlaneStimulusCellFactory<CellLuoRudy1991FromCellMLBackwardEuler,2> cell_factory(0.0);
/*
* Note that in the previous bath example, a mesh was read in and elements where then set to be
* bath elements in the test. With fibres as well, in a bath simulation, it is better to read in a
* mesh that has all the information: this mesh has bath elements defined as an extra column in the
* .ele file, and a .ortho file which defines the fibre direction for each element. Note that the
* .ortho file should include fibre information for bath elements as well, but they won't be used
* in the simulation. (The fibres read here are the same 'kinked' fibres as in the previous fibre
* tutorial).
*/
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/2D_0_to_1mm_800_elements_bath_sides", cp::media_type::Orthotropic);
/* Set anistropic conductivities.
*/
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.175));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 0.7));
/* and now we define the electrodes.. */
double magnitude = -9.0e3; // uA/cm^2
double start_time = 0.0;
double duration = 2; //ms
HeartConfig::Instance()->SetElectrodeParameters(false, 0, magnitude, start_time, duration);
/* Now create the problem class, using the cell factory and passing
* in `true` as the second argument to indicate we are solving a bath
* problem, and solve.
*/
BidomainProblem<2> bidomain_problem( &cell_factory, true );
bidomain_problem.Initialise();
bidomain_problem.Solve();
}
////////////////////////////////////////////////////////////
// Compare Mono and Bidomain Simulations
////////////////////////////////////////////////////////////
void TestCompareBidomainProblemWithMonodomain3D()
{
// the bidomain equations reduce to the monodomain equations
// if sigma_e is infinite (equivalent to saying the extra_cellular
// space is grounded. sigma_e is set to be very large here:
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 1.75, 1.75));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(17500, 17500, 17500));
HeartConfig::Instance()->SetSimulationDuration(1.0); //ms
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/3D_0_to_1mm_6000_elements");
HeartConfig::Instance()->SetOutputDirectory("Monodomain3d");
HeartConfig::Instance()->SetOutputFilenamePrefix("monodomain3d");
///////////////////////////////////////////////////////////////////
// monodomain
///////////////////////////////////////////////////////////////////
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 3> cell_factory(-600.0*1000);
MonodomainProblem<3> monodomain_problem( &cell_factory );
monodomain_problem.Initialise();
monodomain_problem.Solve();
///////////////////////////////////////////////////////////////////
// bidomain
///////////////////////////////////////////////////////////////////
HeartConfig::Instance()->SetOutputDirectory("Bidomain3d");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain3d");
BidomainProblem<3> bidomain_problem( &cell_factory );
bidomain_problem.Initialise();
bidomain_problem.Solve();
///////////////////////////////////////////////////////////////////
// compare
///////////////////////////////////////////////////////////////////
DistributedVector monodomain_voltage = monodomain_problem.GetSolutionDistributedVector();
DistributedVector bidomain_solution = bidomain_problem.GetSolutionDistributedVector();
DistributedVector::Stripe bidomain_voltage(bidomain_solution,0);
DistributedVector::Stripe extracellular_potential(bidomain_solution,1);
for (DistributedVector::Iterator index = bidomain_solution.Begin();
index != bidomain_solution.End();
++index)
{
TS_ASSERT_DELTA(monodomain_voltage[index], bidomain_voltage[index], 0.5);
TS_ASSERT_DELTA(extracellular_potential[index], 0, 1.0);
}
}
void Test2dBathIntracellularStimulation() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(1.0); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath2d");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_2d");
c_vector<double,2> centre;
centre(0) = 0.05;
centre(1) = 0.05;
BathCellFactory<2> cell_factory(-5e6, centre); // stimulates x=0.05 node
BidomainWithBathProblem<2> bidomain_problem( &cell_factory );
DistributedTetrahedralMesh<2,2>* p_mesh = Load2dMeshAndSetCircularTissue<DistributedTetrahedralMesh<2,2> >(
"mesh/test/data/2D_0_to_1mm_400_elements", 0.05, 0.05, 0.04);
bidomain_problem.SetMesh(p_mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
// test V = 0 for all bath nodes
for (AbstractTetrahedralMesh<2,2>::NodeIterator iter=p_mesh->GetNodeIteratorBegin();
iter != p_mesh->GetNodeIteratorEnd(); ++iter)
{
if (HeartRegionCode::IsRegionBath( (*iter).GetRegion() )) // bath
{
unsigned index=(*iter).GetIndex();
TS_ASSERT_DELTA(sol_repl[2*index], 0.0, 1e-12);
}
}
// A couple of hardcoded values. We would normally have to look up the index in the
// permutation vector when using a DistributedTetrahedralMesh, however the call to
// Load2dMeshAndSetCircularTissue above imposes a DUMB partition, so no need.
TS_ASSERT_DELTA(sol_repl[2*50], 28.3912, 1e-3); // node 50
TS_ASSERT_DELTA(sol_repl[2*70], 28.3912, 1e-3); // node 70
delete p_mesh;
}
void TestProblemChecksUsingBathWithMultipleBathConductivities()
{
TrianglesMeshReader<2,2> reader("mesh/test/data/2D_0_to_1mm_400_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(reader);
std::set<unsigned> tissue_ids;
tissue_ids.insert(0);
std::set<unsigned> bath_ids;
bath_ids.insert(1);
bath_ids.insert(2); // non-default identifier!
HeartConfig::Instance()->SetTissueAndBathIdentifiers(tissue_ids, bath_ids);
BathCellFactory<2> cell_factory( 0.0, Create_c_vector(0.0, 0.0) );
BidomainProblem<2> bidomain_problem( &cell_factory ); // non-bath problem, despite specifying bath stuff above!
bidomain_problem.SetMesh( &mesh );
TS_ASSERT_THROWS_THIS( bidomain_problem.Initialise() , "User has set bath identifiers, but the BidomainProblem isn't expecting a bath. Did you mean to use BidomainProblem(..., true)? Or alternatively, BidomainWithBathProblem(...)?");
}
void TestLabellingNodes() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(0.01); //ms
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/1D_0_to_1_10_elements_with_two_attributes");
HeartConfig::Instance()->SetOutputDirectory("bidomain_bath");
HeartConfig::Instance()->SetOutputFilenamePrefix("BidomainLR91_1d");
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 1> bidomain_cell_factory;
BidomainWithBathProblem<1> bidomain_problem( &bidomain_cell_factory );
bidomain_problem.Initialise();
AbstractTetrahedralMesh<1,1>* p_mesh = &(bidomain_problem.rGetMesh());
// the middle 4 elements are 'heart' elements (ie region=0),
// so the middle 5 nodes should be heart nodes
char expected_node_regions[11]={ 'B', 'B', 'B',
'T', 'T', 'T', 'T', 'T',
'B','B','B'};
for (unsigned i=0; i<11; i++)
{
if (p_mesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(i))
{
if (expected_node_regions[i] == 'B')
{
TS_ASSERT(HeartRegionCode::IsRegionBath( p_mesh->GetNode(i)->GetRegion()) );
}
else
{
TS_ASSERT_EQUALS(expected_node_regions[i], 'T' );
TS_ASSERT(HeartRegionCode::IsRegionTissue( p_mesh->GetNode(i)->GetRegion()) );
}
}
}
// we need to call solve as otherwise an EventHandler exception is thrown
bidomain_problem.Solve();
}
void Test2dBathInputFluxEqualsOutputFlux() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(3.0); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath2dFluxCompare");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_2d_fluxes");
// Coverage of Hdf5ToCmguiConverter with bath
HeartConfig::Instance()->SetVisualizeWithCmgui(true);
HeartConfig::Instance()->SetOdeTimeStep(0.001); //ms
// need to create a cell factory but don't want any intra stim, so magnitude
// of stim is zero.
c_vector<double,2> centre;
centre(0) = 0.05; // cm
centre(1) = 0.05; // cm
BathCellFactory<2> cell_factory( 0.0, centre);
BidomainWithBathProblem<2> bidomain_problem( &cell_factory );
// Coverage
TS_ASSERT(bidomain_problem.GetHasBath());
TetrahedralMesh<2,2>* p_mesh = Load2dMeshAndSetCircularTissue<TetrahedralMesh<2,2> >(
"mesh/test/data/2D_0_to_1mm_400_elements", 0.05, 0.05, 0.02);
//boundary flux for Phi_e. -10e3 is under threshold, -14e3 crashes the cell model
double boundary_flux = -11.0e3;
double start_time = 0.5;
double duration = 1.9; // of the stimulus, in ms
HeartConfig::Instance()->SetElectrodeParameters(false,0, boundary_flux, start_time, duration);
bidomain_problem.SetMesh(p_mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
bool ap_triggered = false;
/*
* We are checking the last time step. This test will only make sure that an upstroke is triggered.
* We ran longer simulation for 350 ms and a nice AP was observed.
*/
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
// test V = 0 for all bath nodes and that an AP is triggered in the tissue
if (HeartRegionCode::IsRegionBath( p_mesh->GetNode(i)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
else if (sol_repl[2*i] > 0.0)//at the last time step
{
ap_triggered = true;
}
}
TS_ASSERT_EQUALS(bidomain_problem.mpElectrodes->mAreActive, false); // should be switched off by now..
TS_ASSERT(ap_triggered);
delete p_mesh;
}
void TestBidomain3d() throw (Exception)
{
HeartEventHandler::Reset();
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 1.75, 1.75));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 7.0, 7.0));
HeartConfig::Instance()->SetSimulationDuration(4.0); //ms
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/3D_0_to_1mm_6000_elements");
HeartConfig::Instance()->SetOutputDirectory("Bidomain3d");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain3d");
// Check the linear system can be solved to a low tolerance (in particular, checks the null space
// stuff was implemented correctly
HeartConfig::Instance()->SetUseAbsoluteTolerance(1e-14);
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 3> bidomain_cell_factory(-600.0*1000);
BidomainProblem<3> bidomain_problem( &bidomain_cell_factory );
bidomain_problem.Initialise();
//bidomain_problem.SetNodeForAverageOfPhiZeroed(1330);
//bidomain_problem.SetFixedExtracellularPotentialNodes(1330);
bidomain_problem.Solve();
Vec voltage=bidomain_problem.GetSolution();
ReplicatableVector voltage_replicated;
voltage_replicated.ReplicatePetscVector(voltage);
/*
* Test the top right node against the right one in the 1D case,
* comparing voltage, and then test all the nodes on the right hand
* face of the cube against the top right one, comparing voltage.
*/
bool need_initialisation = true;
double probe_voltage=0;
need_initialisation = true;
// Test the RHF of the mesh
for (AbstractTetrahedralMesh<3,3>::NodeIterator it = bidomain_problem.rGetMesh().GetNodeIteratorBegin();
it != bidomain_problem.rGetMesh().GetNodeIteratorEnd();
++it)
{
if (it->GetPoint()[0] == 0.1)
{
// x = 0 is where the stimulus has been applied
// x = 0.1cm is the other end of the mesh and where we want to
// to test the value of the nodes
if (need_initialisation)
{
probe_voltage = voltage_replicated[2*it->GetIndex()];
need_initialisation = false;
}
else
{
// the voltage at the end face varies a little because
// of drift due to the orientation of the tets in the mesh,
// hence the tolerance of 0.2
TS_ASSERT_DELTA(voltage_replicated[2*it->GetIndex()], probe_voltage, 0.2);
}
// if a 1D simulation is run for 4ms on the 0_1mm_10elements mesh
// the result at the end node is 20.0755
TS_ASSERT_DELTA(voltage_replicated[2*it->GetIndex()], 20.0755, 1.3);
}
}
/*
* HOW_TO_TAG Cardiac/Output
* Collect and print timings to benchmark different parts of the cardiac code.
*
* N.B. You may also want to use HeartEventHandler::Reset() if you call these again.
*/
HeartEventHandler::Headings();
HeartEventHandler::Report();
}
void TestBidomainWithBathWithSvi() throw(Exception)
{
/* Make a 4x4 node mesh and set two interior elements to be bath elements */
DistributedTetrahedralMesh<2,2> mesh;
mesh.ConstructRegularSlabMesh(0.04, 0.12, 0.12);
for (AbstractTetrahedralMesh<2,2>::ElementIterator iter=mesh.GetElementIteratorBegin();
iter != mesh.GetElementIteratorEnd();
++iter)
{
unsigned element_index = iter->GetIndex();
if ( element_index==10 || element_index==17 )
{
iter->SetAttribute(HeartRegionCode::GetValidBathId());
}
else
{
iter->SetAttribute(HeartRegionCode::GetValidTissueId());
}
}
HeartConfig::Instance()->SetSimulationDuration(10.0); // ms
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.001, 0.025, 0.25);
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.17));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 0.7));
ReplicatableVector final_solution_ici;
ReplicatableVector final_solution_svi;
// ICI - ionic current interpolation (the default)
{
HeartConfig::Instance()->SetOutputDirectory("BidomainWithBathIci2d");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation(false);
BathCellFactory cell_factory;
BidomainWithBathProblem<2> 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
{
HeartConfig::Instance()->SetOutputDirectory("BidomainWithBathSvi2d");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation(true);
BathCellFactory cell_factory;
BidomainWithBathProblem<2> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
final_solution_svi.ReplicatePetscVector(bidomain_problem.GetSolution());
}
// ICI
TS_ASSERT_DELTA(final_solution_ici[15*2], 7.0918, 2e-3); // Node 15 phi_i
TS_ASSERT_DELTA(final_solution_ici[15*2+1], 0.0401, 1e-3); // Node 15 phi_e
// SVI
TS_ASSERT_DELTA(final_solution_svi[15*2], 10.6217, 2e-3); // Node 15 phi_i
TS_ASSERT_DELTA(final_solution_svi[15*2+1], -0.0180, 1e-3); // Node 15 phi_e
}
void TestWithBathAndElectrodes()
{
/* First, set the end time and output info. In this simulation
* we'll explicitly read the mesh, alter it, then pass it
* to the problem class, so we don't set the mesh file name.
*/
HeartConfig::Instance()->SetSimulationDuration(3.0); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainTutorialWithBath");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
/* Bath problems seem to require decreased ODE timesteps.
*/
HeartConfig::Instance()->SetOdeTimeStep(0.001); //ms
/* Use the {{{PlaneStimulusCellFactory}}} to define a set
* of Luo-Rudy cells. We pass the stimulus magnitude as 0.0
* as we don't want any stimulated cells.
*/
PlaneStimulusCellFactory<CellLuoRudy1991FromCellMLBackwardEuler,2> cell_factory(0.0);
/*
* Now, we load up a rectangular mesh (in triangle/tetgen format), done as follows,
* using {{{TrianglesMeshReader}}}. Note that we use a distributed mesh, so the data
* is shared among processes if run in parallel.
*/
TrianglesMeshReader<2,2> reader("mesh/test/data/2D_0_to_1mm_400_elements");
DistributedTetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(reader);
/*
* In most simulations there is one valid tissue identifier and one valid bath identifier
* (for elements).
* One of these can be assigned to an element with
* * {{{mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidTissueId());}}}
* * {{{mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidBathId());}}}
*
* If we want heterogeneous conductivities outside the heart (for example for torso and blood)
* then we will need different identifiers:
*/
std::set<unsigned> tissue_ids;
static unsigned tissue_id=0;
tissue_ids.insert(tissue_id);
std::set<unsigned> bath_ids;
static unsigned bath_id1=1;
bath_ids.insert(bath_id1);
static unsigned bath_id2=2;
bath_ids.insert(bath_id2);
HeartConfig::Instance()->SetTissueAndBathIdentifiers(tissue_ids, bath_ids);
/* In bath problems, each element has an attribute which must be set
* to 0 (cardiac tissue) or 1 (bath). This can be done by having an
* extra column in the element file (see the file formats documentation,
* or for example
* mesh/test/data/1D_0_to_1_10_elements_with_two_attributes.ele,
* and note that the header in this file has 1 at the end to indicate that
* the file defines an attribute for each element). We have read in a mesh
* without this type of information set up, so we set it up manually,
* by looping over elements and setting those more than 2mm from the centre
* as bath elements (by default, the others are cardiac elements).
*/
for (AbstractTetrahedralMesh<2,2>::ElementIterator iter = mesh.GetElementIteratorBegin();
iter != mesh.GetElementIteratorEnd();
++iter)
{
double x = iter->CalculateCentroid()[0];
double y = iter->CalculateCentroid()[1];
if (sqrt((x-0.05)*(x-0.05) + (y-0.05)*(y-0.05)) > 0.02)
{
if (y<0.05)
{
//Outside circle on the bottom
iter->SetAttribute(bath_id1);
}
else
{
//Outside circle on the top
iter->SetAttribute(bath_id2);
}
}
else
{
//IDs default to 0, but we want to be safe
iter->SetAttribute(tissue_id);
}
}
/* HOW_TO_TAG Cardiac/Problem definition
* Tell Chaste that a mesh has been modified
*
* Since we have modified the mesh by setting element attributes, we need to inform Chaste of this fact.
* If we do not, problems will arise when [wiki:UserTutorials/CardiacCheckpointingAndRestarting checkpointing],
* since the code that saves the simulation state will assume that it can just reuse the original mesh files,
* and thus won't save the new element attributes.
*
* (Some mesh modifications, that use methods on the mesh class directly, will automatically record that
* the mesh has been modified. Since we're just modifying elements, this information isn't propagated at
* present.)
*/
mesh.SetMeshHasChangedSinceLoading();
/*
* The external conductivity can set two ways:
* * the default conductivity in the bath is set with {{{SetBathConductivity(double)}}}
* * heterogeneous overides can be set with {{{SetBathMultipleConductivities(std::map<unsigned, double> )}}}
*/
HeartConfig::Instance()->SetBathConductivity(7.0); //bath_id1 tags will take the default value (actually 7.0 is the default)
std::map<unsigned, double> multiple_bath_conductivities;
multiple_bath_conductivities[bath_id2] = 6.5; // mS/cm
HeartConfig::Instance()->SetBathMultipleConductivities(multiple_bath_conductivities);
/* Now we define the electrodes. First define the magnitude of the electrodes
* (ie the magnitude of the boundary extracellular stimulus), and the duration
* it lasts for. Currently, electrodes switch on at time 0 and have constant magnitude
* until they are switched off. (Note that this test has a small range of
* magnitudes that will work, perhaps because the electrodes are close to the tissue).
*/
// For default conductivities and explicit cell model -1e4 is under threshold, -1.4e4 too high - crashes the cell model
// For heterogeneous conductivities as given, -1e4 is under threshold
double magnitude = -14.0e3; // uA/cm^2
double start_time = 0.0;
double duration = 1; //ms
/* Electrodes work in two ways: the first electrode applies an input flux, and
* the opposite electrode can either be grounded or apply an equal and opposite
* flux (ie an output flux). The `false` here indicates the second electrode
* is not grounded, ie has an equal and opposite flux. The "0" indicates
* that the electrodes should be applied to the bounding surfaces in the x-direction
* (1 would be y-direction, 2 z-direction), which are X=0.0 and X=0.1 in the given mesh.
* (This explains why the full mesh ought to be rectangular/cuboid - the nodes on
* x=xmin and x=xmax ought to be form two surfaces of equal area.
*/
HeartConfig::Instance()->SetElectrodeParameters(false, 0, magnitude, start_time, duration);
/* Now create the problem class, using the cell factory and passing
* in `true` as the second argument to indicate we are solving a bath
* problem..
*/
BidomainProblem<2> bidomain_problem( &cell_factory, true );
/* ..set the mesh and electrodes.. */
bidomain_problem.SetMesh(&mesh);
/* ..and solve as before. */
bidomain_problem.Initialise();
bidomain_problem.Solve();
/* The results can be visualised as before. '''Note:''' The voltage is only
* defined at cardiac nodes (a node contained in ''any'' cardiac element), but
* for visualisation and computation a 'fake' value of ZERO is given for the
* voltage at bath nodes.
*
* Finally, we can check that an AP was induced in any of the cardiac
* cells. We use a `ReplicatableVector` as before, and make sure we
* only check the voltage at cardiac cells.
*/
Vec solution = bidomain_problem.GetSolution(); // the Vs and phi_e's, as a PetSc vector
ReplicatableVector solution_repl(solution);
bool ap_triggered = false;
for (AbstractTetrahedralMesh<2,2>::NodeIterator iter = mesh.GetNodeIteratorBegin();
iter != mesh.GetNodeIteratorEnd();
++iter)
{
if (HeartRegionCode::IsRegionTissue( iter->GetRegion() ))
{
if (solution_repl[2*iter->GetIndex()] > 0.0) // 2*i, ie the voltage for this node (would be 2*i+1 for phi_e for this node)
{
ap_triggered = true;
}
}
}
TS_ASSERT(ap_triggered);
}
void TestArchivingMeshFileWithAttributes() throw (Exception)
{
std::string archive_dir = "TestArchivingMeshFileWithAttributes";
{ // save...
HeartConfig::Instance()->SetSimulationDuration(0.01); //ms
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/1D_0_to_1_10_elements_with_three_attributes");
HeartConfig::Instance()->SetOutputDirectory(archive_dir + "Output");
HeartConfig::Instance()->SetOutputFilenamePrefix("BidomainLR91_1d");
std::set<unsigned> tissue_ids;
tissue_ids.insert(0u); // (The default)
std::set<unsigned> bath_ids;
bath_ids.insert(1u); // (The default)
bath_ids.insert(2u); // Some other type of bath
HeartConfig::Instance()->SetTissueAndBathIdentifiers(tissue_ids,bath_ids);
std::map<unsigned, double> multiple_bath_conductivities;
multiple_bath_conductivities[1] = 3.14;
multiple_bath_conductivities[2] = 2.72;
HeartConfig::Instance()->SetBathMultipleConductivities(multiple_bath_conductivities);
ZeroStimulusCellFactory<CellLuoRudy1991FromCellML, 1> bidomain_cell_factory;
BidomainWithBathProblem<1> bidomain_problem( &bidomain_cell_factory );
bidomain_problem.Initialise();
// Save using helper class
CardiacSimulationArchiver<BidomainWithBathProblem<1> >::Save(bidomain_problem, archive_dir, false);
}
HeartConfig::Instance()->Reset(); // Forget these IDs/conductivities, they should be loaded from the archive.
{ // load...
AbstractCardiacProblem<1,1,2>* p_abstract_problem = CardiacSimulationArchiver<BidomainWithBathProblem<1> >::Load(archive_dir);
// Check the identifiers have made it
std::set<unsigned> tissue_ids = HeartConfig::Instance()->rGetTissueIdentifiers();
TS_ASSERT( tissue_ids.size() == 1u );
TS_ASSERT( *(tissue_ids.begin()) == 0u );
std::set<unsigned> bath_ids = HeartConfig::Instance()->rGetBathIdentifiers();
TS_ASSERT( bath_ids.size() == 2u );
TS_ASSERT( *bath_ids.begin() == 1u );
TS_ASSERT( *(++bath_ids.begin()) == 2u );
AbstractTetrahedralMesh<1,1>* p_mesh = &(p_abstract_problem->rGetMesh());
/* Check the element ids have been loaded properly. The middle 4 elements are 'heart' elements
* (region=0). The edges are different "flavours" of bath... */
unsigned expected_element_regions[10]={ 2,1,1,0,0,0,0,1,1,2 };
for (AbstractTetrahedralMesh<1,1>::ElementIterator iter = p_mesh->GetElementIteratorBegin();
iter != p_mesh->GetElementIteratorEnd();
++iter)
{
unsigned element_index = iter->GetIndex();
unsigned element_attribute = iter->GetUnsignedAttribute();
switch ( expected_element_regions[element_index] )
{
case 0:
TS_ASSERT(HeartRegionCode::IsRegionTissue( element_attribute ));
break;
case 1:
TS_ASSERT_EQUALS( expected_element_regions[element_index], 1u);
TS_ASSERT(HeartRegionCode::IsRegionBath( element_attribute ));
TS_ASSERT_DELTA(HeartConfig::Instance()->GetBathConductivity( element_attribute ), 3.14, 1e-9);
break;
case 2:
TS_ASSERT_EQUALS( expected_element_regions[element_index], 2u);
TS_ASSERT(HeartRegionCode::IsRegionBath( element_attribute ));
TS_ASSERT_DELTA(HeartConfig::Instance()->GetBathConductivity( element_attribute ), 2.72, 1e-9);
break;
default:
NEVER_REACHED;
break;
};
}
/* ...so the middle 5 nodes should be heart nodes */
char expected_node_regions[11]={ 'B', 'B', 'B',
'T', 'T', 'T', 'T', 'T',
'B','B','B'};
for (unsigned i=0; i<10; i++)
{
if (p_mesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(i))
{
if ( expected_node_regions[i] == 'T')
{
TS_ASSERT(HeartRegionCode::IsRegionTissue( p_mesh->GetNode(i)->GetRegion() ));
}
else
{
TS_ASSERT_EQUALS( expected_node_regions[i], 'B')
TS_ASSERT(HeartRegionCode::IsRegionBath( p_mesh->GetNode(i)->GetRegion() ));
}
}
}
delete p_abstract_problem;
}
}
void TestSettingElectrodesOnResumedSimulation(void) throw(Exception)
{
std::string archive_dir = "BidomainWithElectrodesArchiving";
// Create the mesh outside the save scope, so we can compare with the loaded version.
TetrahedralMesh<2,2>* p_mesh = Load2dMeshAndSetCircularTissue<TetrahedralMesh<2,2> >(
"mesh/test/data/2D_0_to_1mm_400_elements", 0.05, 0.05, 0.02);
{ // save
HeartConfig::Instance()->SetSimulationDuration(3.0); // ms
HeartConfig::Instance()->SetOutputDirectory(archive_dir + "Output");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_2d_fluxes");
HeartConfig::Instance()->SetOdeTimeStep(0.001); // ms
// need to create a cell factory but don't want any intra stim.
ZeroStimulusCellFactory<CellTenTusscher2006EpiFromCellMLBackwardEuler, 2> cell_factory;
BidomainWithBathProblem<2> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh(p_mesh);
bidomain_problem.Initialise();
// Save using helper class
CardiacSimulationArchiver<BidomainWithBathProblem<2> >::Save(bidomain_problem, archive_dir, false);
}
{ // load
AbstractCardiacProblem<2,2,2>* p_abstract_problem = CardiacSimulationArchiver<BidomainWithBathProblem<2> >::Load(archive_dir);
// get the new mesh
AbstractTetrahedralMesh<2,2>& r_mesh = p_abstract_problem->rGetMesh();
TS_ASSERT_EQUALS(p_mesh->GetNumElements(), r_mesh.GetNumElements());
//boundary flux for Phi_e. -10e3 is under threshold, -14e3 crashes the cell model
double boundary_flux = -11.0e3;
double duration = 1.9; // of the stimulus, in ms
double start_time = 0.5; // of the stimulus, in ms
HeartConfig::Instance()->SetElectrodeParameters(false,0,boundary_flux, start_time, duration);
p_abstract_problem->SetElectrodes();
// This should only generate action potential if the electrodes were correctly saved and restored.
p_abstract_problem->Solve();
Vec sol = p_abstract_problem->GetSolution();
ReplicatableVector sol_repl(sol);
bool ap_triggered = false;
/*
* We are checking the last time step. This test will only make sure that an upstroke is triggered.
* We ran longer simulation for 350 ms and a nice AP was observed.
*/
for (unsigned i=0; i<r_mesh.GetNumNodes(); i++)
{
// test V = 0 for all bath nodes and that an AP is triggered in the tissue
if (HeartRegionCode::IsRegionBath(r_mesh.GetNode(i)->GetRegion()))
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
else if (sol_repl[2*i] > 0.0) //at the last time step
{
ap_triggered = true;
}
}
// We can get away with the following line only because this is a friend class and test.
boost::shared_ptr<Electrodes<2> > p_electrodes = static_cast<BidomainWithBathProblem<2>* >(p_abstract_problem)->mpElectrodes;
TS_ASSERT_EQUALS(p_electrodes->mAreActive, false); // should be switched off by now..
TS_ASSERT_EQUALS(ap_triggered, true);
delete p_abstract_problem;
}
delete p_mesh;
}
void Test2dBathGroundedElectrodeStimulusSwitchesOnOff() throw (Exception)
{
// Total execution time is 5 ms. Electrodes are on in [1.0, 3.0]
HeartConfig::Instance()->SetOutputDirectory("BidomainBath2dGroundedOnOff");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_2d_grounded_on_off");
HeartConfig::Instance()->SetOdeTimeStep(0.001); //ms
// need to create a cell factory but don't want any intra stim, so magnitude
// of stim is zero.
c_vector<double,2> centre;
centre(0) = 0.05; // cm
centre(1) = 0.05; // cm
BathCellFactory<2> cell_factory( 0.0, centre);
BidomainWithBathProblem<2> bidomain_problem( &cell_factory );
TetrahedralMesh<2,2>* p_mesh = Load2dMeshAndSetCircularTissue<TetrahedralMesh<2,2> >(
"mesh/test/data/2D_0_to_1mm_400_elements", 0.05, 0.05, 0.02);
//boundary flux for Phi_e. -10e3 is under threshold, -14e3 crashes the cell model
double boundary_flux = -11.0e3;
double start_time = 1.0;
double duration = 2.0; // of the stimulus, in ms
HeartConfig::Instance()->SetElectrodeParameters( true, 0, boundary_flux,start_time, duration );
bidomain_problem.SetMesh(p_mesh);
bidomain_problem.Initialise();
/*
* While t in [0.0, 1.0) electrodes are off
*/
{
HeartConfig::Instance()->SetSimulationDuration(0.5); //ms
bidomain_problem.Solve();
/// \todo: we don't need a ReplicatableVector here. Every processor can check locally
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
// test phi_e close to 0 for all bath nodes since electrodes are off
if (HeartRegionCode::IsRegionBath( p_mesh->GetNode(i)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i+1], 0.0, 0.5);
}
}
TS_ASSERT_EQUALS(bidomain_problem.mpElectrodes->mAreActive, false); // should be switched off by now..
}
/*
* At the end of the simulation AP has been triggered
*/
{
HeartConfig::Instance()->SetSimulationDuration(5.0); //ms
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
bool ap_triggered = false;
/*
* We are checking the last time step. This test will only make sure that an upstroke is triggered.
* We ran longer simulation for 350 ms and a nice AP was observed.
*/
for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
{
// test V = 0 for all bath nodes and that an AP is triggered in the tissue
if (HeartRegionCode::IsRegionBath( p_mesh->GetNode(i)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
else if (sol_repl[2*i] > 0.0)//at the last time step
{
ap_triggered = true;
}
}
// Check that grounded electrode has been successfully removed and therefore phi_e !=0.
// Nodes defining grounded electrode are 10, 21, 32, 43, 54, ... , 120
TS_ASSERT_DELTA(sol_repl[21], -80.2794, 1e-3);
TS_ASSERT_DELTA(sol_repl[43], -80.2794, 1e-3);
TS_ASSERT_DELTA(sol_repl[241], -80.2794, 1e-3);
TS_ASSERT_EQUALS(bidomain_problem.mpElectrodes->mAreActive, false); // should be switched off by now..
TS_ASSERT(ap_triggered);
}
delete p_mesh;
}
void TestConductionVelocityInCrossFibreDirection2d() throw(Exception)
{
ReplicatableVector final_solution_ici;
ReplicatableVector final_solution_svi;
HeartConfig::Instance()->SetSimulationDuration(4.0); //ms
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.005, 0.01, 0.01);
// much lower conductivity in cross-fibre direction - ICI will struggle
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.17));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 0.7));
// ICI - nodal current interpolation - the default
{
TetrahedralMesh<2,2> mesh;
mesh.ConstructRegularSlabMesh(0.02 /*h*/, 0.5, 0.3);
HeartConfig::Instance()->SetOutputDirectory("BidomainIci2d");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation(false);
BlockCellFactory<2> cell_factory;
BidomainProblem<2> 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
{
TetrahedralMesh<2,2> mesh;
mesh.ConstructRegularSlabMesh(0.02 /*h*/, 0.5, 0.3);
HeartConfig::Instance()->SetOutputDirectory("BidomainSvi2d");
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetUseStateVariableInterpolation(true);
BlockCellFactory<2> cell_factory;
BidomainProblem<2> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
final_solution_svi.ReplicatePetscVector(bidomain_problem.GetSolution());
}
// See comments in equivalent part of test/monodomain/TestMonodomainWithSvi.hpp
// For bidomain with h=0.02, SVI CV is slower in both fibre and cross-fibre
// directions
// node 20 (for h=0.02) is on the x-axis (fibre direction)
TS_ASSERT_DELTA(final_solution_ici[20*2], -64.1105, 1e-3); // Node 20 phi_i
TS_ASSERT_DELTA(final_solution_svi[20*2], -78.0936, 1e-3); // Node 20 phi_i
// node 234 (for h=0.02) is on the y-axis (cross-fibre direction)
TS_ASSERT_DELTA(final_solution_ici[234*2], -57.7239, 1e-3); // Node 234 phi_i
TS_ASSERT_DELTA(final_solution_svi[234*2], 38.9004, 1e-3); // Node 234 phi_i
}
void TestConductivityModifier() throw(Exception)
{
/*
* Generate a mesh.
*/
DistributedTetrahedralMesh<2,2> mesh;
mesh.ConstructRegularSlabMesh(0.5, 1.0, 0.5); // Mesh has 4 elements
/*
* Here we're using a trivial cell factory for simplicity, but usually you'll provide your own one.
* Set up the problem with the factory as usual.
*/
ZeroStimulusCellFactory<CellLuoRudy1991FromCellML,2> cell_factory;
BidomainProblem<2> bidomain_problem( &cell_factory );
bidomain_problem.SetMesh( &mesh );
/*
* We need to apply the modifier directly to the tissue, which comes from the problem, but is only
* accessible after `Initialise()`, so let's do that now.
*/
bidomain_problem.Initialise();
BidomainTissue<2>* p_bidomain_tissue = bidomain_problem.GetBidomainTissue();
/*
* Get the original conductivity tensor values. We haven't set them using
* `HeartConfig->SetIntra/ExtracellularConductivities` so they'll just be the defaults.
*
* The first argument below is the element ID (we just check the first element we own here). The second accesses
* the diagonal elements. We just do (0,0), as (1,1) should be the same (no fibre orientation).
* Off-diagonal elements will be 0.
*
* As we don't have many elements, when we run on more than two processors some processors
* will not own any elements. We only try to access the conductivity tensors if the process
* owns at least one element.
*
* We then check that we have the correct (default) conductivity values.
*/
double orig_intra_conductivity_0 = 0.0;
double orig_extra_conductivity_0 = 0.0;
if (mesh.GetElementIteratorBegin() != mesh.GetElementIteratorEnd())
{
unsigned first_element = mesh.GetElementIteratorBegin()->GetIndex();
orig_intra_conductivity_0 = p_bidomain_tissue->rGetIntracellularConductivityTensor(first_element)(0,0);
orig_extra_conductivity_0 = p_bidomain_tissue->rGetExtracellularConductivityTensor(first_element)(0,0);
TS_ASSERT_DELTA(orig_intra_conductivity_0, 1.75, 1e-9); // hard-coded using default
TS_ASSERT_DELTA(orig_extra_conductivity_0, 7.0, 1e-9); // hard-coded using default
}
/*
* Now we can make the modifier and apply it to the tissue using `SetConductivityModifier`.
*/
SimpleConductivityModifier modifier;
p_bidomain_tissue->SetConductivityModifier( &modifier );
/*
* To confirm that the conductivities have changed, let's iterate over all elements owned by this process
* and check their conductivity against what we expect.
*/
for (AbstractTetrahedralMesh<2,2>::ElementIterator elt_iter=mesh.GetElementIteratorBegin();
elt_iter!=mesh.GetElementIteratorEnd();
++elt_iter)
{
unsigned index = elt_iter->GetIndex();
if (index == 0u)
{
TS_ASSERT_DELTA(p_bidomain_tissue->rGetIntracellularConductivityTensor(0)(0,0), 3.14, 1e-9);
TS_ASSERT_DELTA(p_bidomain_tissue->rGetExtracellularConductivityTensor(0)(0,0), 3.14, 1e-9);
TS_ASSERT_DELTA(p_bidomain_tissue->rGetIntracellularConductivityTensor(0)(1,1), 0.707, 1e-9);
TS_ASSERT_DELTA(p_bidomain_tissue->rGetExtracellularConductivityTensor(0)(1,1), 0.707, 1e-9);
}
else
{
TS_ASSERT_DELTA(p_bidomain_tissue->rGetIntracellularConductivityTensor(index)(0,0), 1.0*index*orig_intra_conductivity_0, 1e-9);
TS_ASSERT_DELTA(p_bidomain_tissue->rGetExtracellularConductivityTensor(index)(0,0), 1.5*index*orig_extra_conductivity_0, 1e-9);
}
}
}
// see #1061
void Test2dBathExtracellularStimulusOneEdgeGroundedOnOppositeEdge()
{
HeartConfig::Instance()->SetSimulationDuration(40); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath2dExtraStimGrounded");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_2d");
HeartConfig::Instance()->SetOdeTimeStep(0.005); //ms
// need to create a cell factory but don't want any intra stim, so magnitude
// of stim is zero.
c_vector<double,2> centre;
centre(0) = 0.05;
centre(1) = 0.05;
BathCellFactory<2> cell_factory( 0.0, centre);
BidomainProblem<2> bidomain_problem( &cell_factory, true );
TrianglesMeshReader<2,2> reader("mesh/test/data/2D_0_to_1mm_400_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(reader);
// Set everything outside a central circle (radius 0.4) to be bath
for (unsigned i=0; i<mesh.GetNumElements(); i++)
{
double x = mesh.GetElement(i)->CalculateCentroid()[0];
double y = mesh.GetElement(i)->CalculateCentroid()[1];
if (sqrt((x-0.05)*(x-0.05) + (y-0.05)*(y-0.05)) > 0.02)
{
mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidBathId());
}
}
bidomain_problem.SetMesh(&mesh);
//boundary flux for Phi_e
//-4e3 is enough to trigger an action potential, -3e3 is below threshold, -5e3 crashes the cell model.
double boundary_flux = -9e3;
double duration = 2.5; //ms
HeartConfig::Instance()->SetElectrodeParameters(true,0,boundary_flux, 0.0, duration);
bidomain_problem.Initialise();
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
bool ap_triggered = false;
/*
* We are checking the last time step. This test will only make sure that an upstroke is triggered.
* We ran longer simulation for 350 ms and a nice AP was observed.
*/
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
// test V = 0 for all bath nodes
if (mesh.GetNode(i)->GetRegion()==1) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
else if (sol_repl[2*i] > 0.0)
{
ap_triggered = true;
}
}
TS_ASSERT(ap_triggered);
}
// In this test we have no cardiac tissue, so that the equations are just sigma * phi_e''=0
// throughout the domain (with a Neumann boundary condition on x=1 and a dirichlet boundary
// condition (ie grounding) on x=0), so the exact solution can be calculated and compared
// against.
void Test1dProblemOnlyBathGroundedOneSide() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(0.5); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBathOnlyBath");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath");
c_vector<double,1> centre;
centre(0) = 0.5;
BathCellFactory<1> cell_factory(-1e6, centre);
TrianglesMeshReader<1,1> reader("mesh/test/data/1D_0_to_1_10_elements");
TetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(reader);
for(unsigned i=0; i<mesh.GetNumElements(); i++)
{
mesh.GetElement(i)->SetAttribute(HeartRegionCode::GetValidBathId());
}
// create boundary conditions container
double boundary_val = 1.0;
boost::shared_ptr<BoundaryConditionsContainer<1,1,2> > p_bcc(new BoundaryConditionsContainer<1,1,2>);
ConstBoundaryCondition<1>* p_bc_stim = new ConstBoundaryCondition<1>(boundary_val);
ConstBoundaryCondition<1>* p_zero_stim = new ConstBoundaryCondition<1>(0.0);
// loop over boundary elements and set (sigma\gradphi).n = 1.0 on RHS edge
for(TetrahedralMesh<1,1>::BoundaryElementIterator iter
= mesh.GetBoundaryElementIteratorBegin();
iter != mesh.GetBoundaryElementIteratorEnd();
iter++)
{
if (((*iter)->GetNodeLocation(0))[0]==1.0)
{
/// \todo: I think you need to provide a boundary condition for unknown#1 if you are gonig to provide one for unknown#2?
p_bcc->AddNeumannBoundaryCondition(*iter, p_zero_stim, 0);
p_bcc->AddNeumannBoundaryCondition(*iter, p_bc_stim, 1);
}
}
BidomainWithBathProblem<1> bidomain_problem( &cell_factory );
bidomain_problem.SetBoundaryConditionsContainer(p_bcc);
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
// fix phi=0 on LHS edge
std::vector<unsigned> fixed_nodes;
fixed_nodes.push_back(0);
bidomain_problem.SetFixedExtracellularPotentialNodes(fixed_nodes);
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
// test phi = x*boundary_val/sigma (solution of phi''=0, phi(0)=0, sigma*phi'(1)=boundary_val
for(unsigned i=0; i<mesh.GetNumNodes(); i++)
{
double bath_cond = HeartConfig::Instance()->GetBathConductivity();
double x = mesh.GetNode(i)->rGetLocation()[0];
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12); // V
TS_ASSERT_DELTA(sol_repl[2*i+1], x*boundary_val/bath_cond, 1e-4); // phi_e
}
}
// see #1061
void Test3dBathExtracellularStimulusOneEdgeGroundedOnOppositeEdge()
{
HeartConfig::Instance()->SetSimulationDuration(6); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath3dExtraStimGrounded");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_3d");
HeartConfig::Instance()->SetOdeTimeStep(0.005); //ms
// need to create a cell factory but don't want any intra stim, so magnitude
// of stim is zero.
c_vector<double,3> centre;
centre(0) = 0.1;
centre(1) = 0.1;
centre(2) = 0.1;
BathCellFactory<3> cell_factory( 0.0, centre);
BidomainProblem<3> bidomain_problem( &cell_factory, true );
TrianglesMeshReader<3,3> reader("mesh/test/data/cube_2mm_1016_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(reader);
// Set everything outside a central sphere (radius 0.4) to be bath
for (unsigned i=0; i<mesh.GetNumElements(); i++)
{
double x = mesh.GetElement(i)->CalculateCentroid()[0];
double y = mesh.GetElement(i)->CalculateCentroid()[1];
double z = mesh.GetElement(i)->CalculateCentroid()[2];
if (sqrt((x-0.1)*(x-0.1) + (y-0.1)*(y-0.1) + (z-0.1)*(z-0.1)) > 0.03)
{
mesh.GetElement(i)->SetAttribute(1);
}
}
bidomain_problem.SetMesh(&mesh);
//boundary flux for Phi_e
double boundary_flux = -4e3;
double duration = 2.5; //ms
HeartConfig::Instance()->SetElectrodeParameters(true,0,boundary_flux, 0.0, duration);
bidomain_problem.Initialise();
bidomain_problem.Solve();
Vec sol = bidomain_problem.GetSolution();
ReplicatableVector sol_repl(sol);
bool ap_triggered = false;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
// test V = 0 for all bath nodes
if (HeartRegionCode::IsRegionBath( mesh.GetNode(i)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(sol_repl[2*i], 0.0, 1e-12);
}
else if (sol_repl[2*i] > 0.0)
{
ap_triggered = true;
}
}
TS_ASSERT(ap_triggered);
}
void Test2dBathMultipleBathConductivities() throw (Exception)
{
HeartConfig::Instance()->SetSimulationDuration(2.0); //ms
HeartConfig::Instance()->SetOutputDirectory("BidomainBath2dMultipleBathConductivities");
HeartConfig::Instance()->SetOutputFilenamePrefix("bidomain_bath_2d");
HeartConfig::Instance()->SetOdeTimeStep(0.001); //ms ???
std::set<unsigned> tissue_ids;
tissue_ids.insert(0); // Same as default value defined in HeartConfig
std::set<unsigned> bath_ids;
bath_ids.insert(2);
bath_ids.insert(3);
bath_ids.insert(4);
HeartConfig::Instance()->SetTissueAndBathIdentifiers(tissue_ids, bath_ids);
// need to create a cell factory but don't want any intra stim, so magnitude
// of stim is zero.
c_vector<double,2> centre;
centre(0) = 0.05; // cm
centre(1) = 0.05; // cm
BathCellFactory<2> cell_factory( 0.0, centre);
BidomainWithBathProblem<2> bidomain_problem( &cell_factory );
DistributedTetrahedralMesh<2,2> mesh;
mesh.ConstructRegularSlabMesh(0.05, 0.9, 0.9);
// set the x<0.25 and x>0.75 regions as the bath region
for (AbstractTetrahedralMesh<2,2>::ElementIterator iter = mesh.GetElementIteratorBegin();
iter != mesh.GetElementIteratorEnd();
++iter)
{
double x = iter->CalculateCentroid()[0];
double y = iter->CalculateCentroid()[1];
if( (x>0.3) && (x<0.6) && (y>0.3) && (y<0.6) )
{
iter->SetAttribute(0);
}
else
{
if (y<0.2)
{
iter->SetAttribute(2);
}
else if (y<0.7)
{
iter->SetAttribute(3);
}
else if (y<0.9)
{
iter->SetAttribute(4);
}
}
}
std::map<unsigned, double> multiple_bath_conductivities;
multiple_bath_conductivities[2] = 7.0;
multiple_bath_conductivities[3] = 1.0;
multiple_bath_conductivities[4] = 0.001;
HeartConfig::Instance()->SetBathMultipleConductivities(multiple_bath_conductivities);
double boundary_flux = -3.0e3;
double start_time = 0.0;
double duration = 1.0; // of the stimulus, in ms
HeartConfig::Instance()->SetElectrodeParameters(false, 0, boundary_flux, start_time, duration);
bidomain_problem.SetMesh(&mesh);
bidomain_problem.Initialise();
bidomain_problem.Solve();
DistributedVector distributed_solution = bidomain_problem.GetSolutionDistributedVector();
DistributedVector::Stripe voltage(distributed_solution, 0);
/*
* We are checking the last time step. This test will only make sure that an AP is triggered.
*/
bool ap_triggered = false;
for (DistributedVector::Iterator index = distributed_solution.Begin();
index!= distributed_solution.End();
++index)
{
// test V = 0 for all bath nodes and that an AP is triggered in the tissue
if (HeartRegionCode::IsRegionBath( mesh.GetNode(index.Global)->GetRegion() )) // bath
{
TS_ASSERT_DELTA(voltage[index], 0.0, 1e-12);
}
else if (voltage[index] > 0.0)//at the last time step
{
ap_triggered = true;
}
}
TS_ASSERT(PetscTools::ReplicateBool(ap_triggered));
}
void TestBidomain3d() throw (Exception)
{
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 1.75, 1.75));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 7.0, 7.0));
HeartConfig::Instance()->SetSimulationDuration(150.0); //ms
//Note that we can only call the old permute nodes funcutionality on the sequential mesh object
//HeartConfig::Instance()->SetMeshFileName("mesh/test/data/3D_0_to_.5mm_1889_elements_irregular");
BidomainFaceStimulusCellFactory bidomain_cell_factory;
BidomainProblem<3> bidomain_problem( &bidomain_cell_factory );
TetrahedralMesh<3,3> mesh;
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/3D_0_to_.5mm_1889_elements_irregular");
mesh.ConstructFromMeshReader(mesh_reader);
bidomain_problem.SetMesh(&mesh);
bidomain_problem.PrintOutput(false);
HeartConfig::Instance()->SetKSPSolver("symmlq");
HeartConfig::Instance()->SetKSPPreconditioner("bjacobi");
PetscOptionsSetValue("-log_summary", "");
bidomain_problem.Initialise();
//Mesh isn't actually loaded until initialise method is called
RandomNumberGenerator::Instance();
bidomain_problem.rGetMesh().PermuteNodes();
RandomNumberGenerator::Destroy();
bidomain_problem.Solve();
Vec voltage=bidomain_problem.GetSolution();
ReplicatableVector voltage_replicated;
voltage_replicated.ReplicatePetscVector(voltage);
/*
* Test the top right node against the right one in the 1D case,
* comparing voltage, and then test all the nodes on the right hand
* face of the cube against the top right one, comparing voltage.
*/
bool need_initialisation = true;
double probe_voltage=-9999.;
need_initialisation = true;
// Test the RHF of the mesh
for (unsigned i = 0; i < bidomain_problem.rGetMesh().GetNumNodes(); i++)
{
if (bidomain_problem.rGetMesh().GetNode(i)->GetPoint()[0] == 0.05)
{
// x = 0 is where the stimulus has been applied
// x = 0.05cm is the other end of the mesh and where we want to
// to test the value of the nodes
if (need_initialisation)
{
probe_voltage = voltage_replicated[2*i];
need_initialisation = false;
}
else
{
// the voltage at the end face varies a little because
// of drift due to the orientation of the tets in the mesh,
// hence the tolerance of 0.02
TS_ASSERT_DELTA(voltage_replicated[2*i], probe_voltage, 0.02);
}
// Check against hard coded value
// For 50 ms test TS_ASSERT_DELTA(voltage_replicated[2*i], 7.3, 0.2);
// For 150 ms test
TS_ASSERT_DELTA(voltage_replicated[2*i], -1.735, 0.1);
}
}
}
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);
}
}
}