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);
}
// 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);
}
// 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);
}
VoltageInterpolaterOntoMechanicsMesh<DIM>::VoltageInterpolaterOntoMechanicsMesh(
TetrahedralMesh<DIM,DIM>& rElectricsMesh,
QuadraticMesh<DIM>& rMechanicsMesh,
std::vector<std::string>& rVariableNames,
std::string directory,
std::string inputFileNamePrefix)
{
// Read the data from the HDF5 file
Hdf5DataReader reader(directory,inputFileNamePrefix);
unsigned num_timesteps = reader.GetUnlimitedDimensionValues().size();
// set up the elements and weights for the coarse nodes in the fine mesh
FineCoarseMeshPair<DIM> mesh_pair(rElectricsMesh, rMechanicsMesh);
mesh_pair.SetUpBoxesOnFineMesh();
mesh_pair.ComputeFineElementsAndWeightsForCoarseNodes(true);
assert(mesh_pair.rGetElementsAndWeights().size()==rMechanicsMesh.GetNumNodes());
// create and setup a writer
Hdf5DataWriter* p_writer = new Hdf5DataWriter(*rMechanicsMesh.GetDistributedVectorFactory(),
directory,
"voltage_mechanics_mesh",
false, //don't clean
false);
std::vector<int> columns_id;
for (unsigned var_index = 0; var_index < rVariableNames.size(); var_index++)
{
std::string var_name = rVariableNames[var_index];
columns_id.push_back( p_writer->DefineVariable(var_name,"mV") );
}
p_writer->DefineUnlimitedDimension("Time","msecs", num_timesteps);
p_writer->DefineFixedDimension( rMechanicsMesh.GetNumNodes() );
p_writer->EndDefineMode();
assert(columns_id.size() == rVariableNames.size());
// set up a vector to read into
DistributedVectorFactory factory(rElectricsMesh.GetNumNodes());
Vec voltage = factory.CreateVec();
std::vector<double> interpolated_voltages(rMechanicsMesh.GetNumNodes());
Vec voltage_coarse = NULL;
for(unsigned time_step=0; time_step<num_timesteps; time_step++)
{
for (unsigned var_index = 0; var_index < rVariableNames.size(); var_index++)
{
std::string var_name = rVariableNames[var_index];
// read
reader.GetVariableOverNodes(voltage, var_name, time_step);
ReplicatableVector voltage_repl(voltage);
// interpolate
for(unsigned i=0; i<mesh_pair.rGetElementsAndWeights().size(); i++)
{
double interpolated_voltage = 0;
Element<DIM,DIM>& element = *(rElectricsMesh.GetElement(mesh_pair.rGetElementsAndWeights()[i].ElementNum));
for(unsigned node_index = 0; node_index<element.GetNumNodes(); node_index++)
{
unsigned global_node_index = element.GetNodeGlobalIndex(node_index);
interpolated_voltage += voltage_repl[global_node_index]*mesh_pair.rGetElementsAndWeights()[i].Weights(node_index);
}
interpolated_voltages[i] = interpolated_voltage;
}
if(voltage_coarse!=NULL)
{
PetscTools::Destroy(voltage_coarse);
}
voltage_coarse = PetscTools::CreateVec(interpolated_voltages);
// write
p_writer->PutVector(columns_id[var_index], voltage_coarse);
}
p_writer->PutUnlimitedVariable(time_step);
p_writer->AdvanceAlongUnlimitedDimension();
}
if(voltage_coarse!=NULL)
{
PetscTools::Destroy(voltage);
PetscTools::Destroy(voltage_coarse);
}
// delete to flush
delete p_writer;
// Convert the new data to CMGUI format.
// alter the directory in HeartConfig as that is where Hdf5ToCmguiConverter decides
// where to output
std::string config_directory = HeartConfig::Instance()->GetOutputDirectory();
HeartConfig::Instance()->SetOutputDirectory(directory);
Hdf5ToCmguiConverter<DIM,DIM> converter(FileFinder(directory, RelativeTo::ChasteTestOutput),
"voltage_mechanics_mesh",
&rMechanicsMesh,
false);
HeartConfig::Instance()->SetOutputDirectory(config_directory);
}
// 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
}
}