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 TestReadMeshes(void) throw(Exception)
{
{
READER_2D reader("mesh/test/data/square_4_elements_gmsh.msh");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 5u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 4u);
TS_ASSERT_EQUALS(mesh.GetNumBoundaryElements(), 4u);
}
{
READER_3D reader("mesh/test/data/simple_cube_gmsh.msh");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 14u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 24u);
TS_ASSERT_EQUALS(mesh.GetNumBoundaryElements(), 24u);
}
{
READER_2D reader("mesh/test/data/quad_square_4_elements_gmsh.msh",2,2);
QuadraticMesh<2> mesh;
mesh.ConstructFromMeshReader(reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 13u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 4u);
TS_ASSERT_EQUALS(mesh.GetNumBoundaryElements(), 4u);
}
{
READER_3D reader("mesh/test/data/quad_cube_gmsh.msh",2,2);
QuadraticMesh<3> mesh;
mesh.ConstructFromMeshReader(reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 63u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 24u);
TS_ASSERT_EQUALS(mesh.GetNumBoundaryElements(), 24u);
}
}
void TestDistancesToFaceDumb()
{
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_21_nodes_side/Cube21"); // 5x5x5mm cube (internode distance = 0.25mm)
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 9261u); // 21x21x21 nodes
TS_ASSERT_EQUALS(mesh.GetNumElements(), 48000u);
TS_ASSERT_EQUALS(mesh.GetNumBoundaryElements(), 4800u);
DistributedTetrahedralMesh<3,3> parallel_mesh(DistributedTetrahedralMeshPartitionType::DUMB); // No reordering
parallel_mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(parallel_mesh.GetNumNodes(), 9261u); // 21x21x21 nodes
TS_ASSERT_EQUALS(parallel_mesh.GetNumElements(), 48000u);
TS_ASSERT_EQUALS(parallel_mesh.GetNumBoundaryElements(), 4800u);
std::vector<unsigned> map_left;
for (unsigned index=0; index<mesh.GetNumNodes(); index++)
{
// Get the nodes at the left face of the cube
if (mesh.GetNode(index)->rGetLocation()[0] + 0.25 < 1e-6)
{
map_left.push_back(index);
}
}
TS_ASSERT_EQUALS(map_left.size(), 21u*21u);
DistanceMapCalculator<3,3> distance_calculator(mesh);
std::vector<double> distances;
distance_calculator.ComputeDistanceMap(map_left, distances);
DistanceMapCalculator<3,3> parallel_distance_calculator(parallel_mesh);
std::vector<double> parallel_distances;
parallel_distance_calculator.ComputeDistanceMap(map_left, parallel_distances);
TS_ASSERT_EQUALS(distance_calculator.mRoundCounter, 1u);
TS_ASSERT_DELTA(parallel_distance_calculator.mRoundCounter, 2u, 1u);// 1 2 or 3
for (unsigned index=0; index<distances.size(); index++)
{
// The distance should be equal to the x-coordinate of the point (minus the offset of the left face of the cube)
c_vector<double, 3> node = mesh.GetNode(index)->rGetLocation();
TS_ASSERT_DELTA(distances[index], node[0]+0.25,1e-11);
TS_ASSERT_DELTA(parallel_distances[index], node[0]+0.25,1e-11);
}
}
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 TestGetSingleRadiusVector(void) throw(Exception)
{
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/simple_cube");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetNumElements(),12u);
PapillaryFibreCalculator calculator(mesh);
// Call GetRadiusVectors on an element
unsigned element_index = 0;
c_vector<double, 3> radius_vector = calculator.GetRadiusVectorForOneElement(element_index);
// Check they are right
TS_ASSERT_DELTA(radius_vector[0], -0.275, 1e-9);
TS_ASSERT_DELTA(radius_vector[1], -0.025, 1e-9);
TS_ASSERT_DELTA(radius_vector[2], -0.275, 1e-9);
}
void TestRemeshFullTree() throw(Exception)
{
TrianglesMeshReader<1,3> reader("lung/test/data/TestSubject002");
TetrahedralMesh<1,3> mesh;
mesh.ConstructFromMeshReader(reader);
AirwayPropertiesCalculator calculator(mesh, 0);
TS_ASSERT_EQUALS( mesh.GetNumNodes(), 136625u);
TS_ASSERT_EQUALS( mesh.GetNumElements(), 136624u);
//Create remesher object
AirwayRemesher remesher(mesh, 0u);
MutableMesh<1,3> output_mesh_one;
remesher.Remesh(output_mesh_one, calculator.GetBranches()[0]->GetPoiseuilleResistance()*1e7); //Key the tolerance relative to the trachea
TS_ASSERT_EQUALS( output_mesh_one.GetNumNodes(), 168045u);
TS_ASSERT_EQUALS( output_mesh_one.GetNumElements(), 168044u);
// //To visualise
//
// VtkMeshWriter<1,3> writer("TestAirwayRemesher", "Novartis002_remeshed");
// std::vector<double> radii(output_mesh_one.GetNumElements());
//
// for(TetrahedralMesh<1,3>::ElementIterator iter = output_mesh_one.GetElementIteratorBegin();
// iter != output_mesh_one.GetElementIteratorEnd();
// ++iter)
// {
// radii[iter->GetIndex()] = iter->GetAttribute();
// }
//
// writer.AddCellData("radii", radii);
// writer.WriteFilesUsingMesh(output_mesh_one);
//
// TrianglesMeshWriter<1,3> writer2("TestAirwayRemesher", "Novartis002_remeshed", false);
// writer2.WriteFilesUsingMesh(output_mesh_one);
}
void TestDistancesToCorner() throw (Exception)
{
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_21_nodes_side/Cube21"); // 5x5x5mm cube (internode distance = 0.25mm)
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
unsigned num_nodes=9261u;
TS_ASSERT_EQUALS(mesh.GetNumNodes(), num_nodes); // 21x21x21 nodes
TS_ASSERT_EQUALS(mesh.GetNumElements(), 48000u);
TS_ASSERT_EQUALS(mesh.GetNumBoundaryElements(), 4800u);
DistributedTetrahedralMesh<3,3> parallel_mesh(DistributedTetrahedralMeshPartitionType::DUMB); // No reordering;
parallel_mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(parallel_mesh.GetNumNodes(), num_nodes); // 21x21x21 nodes
TS_ASSERT_EQUALS(parallel_mesh.GetNumElements(), 48000u);
TS_ASSERT_EQUALS(parallel_mesh.GetNumBoundaryElements(), 4800u);
unsigned far_index=9260u;
c_vector<double,3> far_corner=mesh.GetNode(far_index)->rGetLocation();
TS_ASSERT_DELTA( far_corner[0], 0.25, 1e-11);
TS_ASSERT_DELTA( far_corner[1], 0.25, 1e-11);
TS_ASSERT_DELTA( far_corner[2], 0.25, 1e-11);
try
{
c_vector<double,3> parallel_far_corner=parallel_mesh.GetNode(far_index)->rGetLocation();
TS_ASSERT_DELTA( parallel_far_corner[0], 0.25, 1e-11);
TS_ASSERT_DELTA( parallel_far_corner[1], 0.25, 1e-11);
TS_ASSERT_DELTA( parallel_far_corner[2], 0.25, 1e-11);
}
catch (Exception&)
{
}
std::vector<unsigned> map_far_corner;
map_far_corner.push_back(far_index);
DistanceMapCalculator<3,3> distance_calculator(mesh);
std::vector<double> distances;
distance_calculator.ComputeDistanceMap(map_far_corner, distances);
DistanceMapCalculator<3,3> parallel_distance_calculator(parallel_mesh);
std::vector<double> parallel_distances;
parallel_distance_calculator.ComputeDistanceMap(map_far_corner, parallel_distances);
TS_ASSERT_EQUALS(distance_calculator.mRoundCounter, 1u);
//Nodes in mesh are order such that a dumb partitioning will give a sequential handover from proc0 to proc1...
TS_ASSERT_EQUALS(parallel_distance_calculator.mRoundCounter, PetscTools::GetNumProcs());
//Note unsigned division is okay here
TS_ASSERT_DELTA(parallel_distance_calculator.mPopCounter, num_nodes/PetscTools::GetNumProcs(), 1u);
TS_ASSERT_DELTA(distance_calculator.mPopCounter, num_nodes, 1u);
for (unsigned index=0; index<distances.size(); index++)
{
c_vector<double, 3> node = mesh.GetNode(index)->rGetLocation();
//Straightline distance
double euclidean_distance = norm_2(far_corner - node);
// x + y + z distance
double manhattan_distance = norm_1(far_corner - node);
//If they differ, then allow the in-mesh distance to be in between
double error_bound = (manhattan_distance - euclidean_distance)/2.0;
//If they don't differ, then we expect the in-mesh distance to be similar
if (error_bound < 1e-15)
{
error_bound = 1e-15;
}
TS_ASSERT_LESS_THAN_EQUALS(distances[index], manhattan_distance+DBL_EPSILON);
TS_ASSERT_LESS_THAN_EQUALS(euclidean_distance, distances[index]+DBL_EPSILON);
TS_ASSERT_DELTA(distances[index], euclidean_distance, error_bound);
TS_ASSERT_DELTA(distances[index], parallel_distances[index], 1e-15);
}
// Test some point-to-point distances
RandomNumberGenerator::Instance()->Reseed(1);
unsigned trials=25;
unsigned pops=0;
unsigned sequential_pops=0;
for (unsigned i=0; i<trials; i++)
{
unsigned index=RandomNumberGenerator::Instance()->randMod(parallel_distances.size());
TS_ASSERT_DELTA(parallel_distance_calculator.SingleDistance(9260u, index), parallel_distances[index], 1e-15);
TS_ASSERT_DELTA(distance_calculator.SingleDistance(9260u, index), parallel_distances[index], 1e-15);
pops += parallel_distance_calculator.mPopCounter;
sequential_pops += distance_calculator.mPopCounter;
TS_ASSERT_LESS_THAN_EQUALS(parallel_distance_calculator.mRoundCounter, PetscTools::GetNumProcs()+2);
}
// Without A*: TS_ASSERT_DELTA(sequential_pops/(double)trials, num_nodes/2, 300);
TS_ASSERT_LESS_THAN(sequential_pops/(double)trials, num_nodes/20.0);
if (PetscTools::IsSequential())
{
//Early termination
TS_ASSERT_EQUALS(pops, sequential_pops);
}
else
{
//Early termination on remote processes is not yet possible
//This may lead to multiple updates from remote
//A* Leads to even more updates on average
// Without A*: TS_ASSERT_DELTA(pops/(double)trials, num_nodes/PetscTools::GetNumProcs(), 700.0);
TS_ASSERT_LESS_THAN(pops/(double)trials, num_nodes/10.0 );
}
//Reverse - to check that cached information is flushed.
for (unsigned i=0; i<3; i++)
{
unsigned index=RandomNumberGenerator::Instance()->randMod(parallel_distances.size());
TS_ASSERT_DELTA(parallel_distance_calculator.SingleDistance(index, 9260u), parallel_distances[index], 1e-15);
}
}
void TestGetRadiusVectorsAndConstructStructureTensors(void) throw(Exception)
{
// Test in three parts to use the results of one test in the next...
//
//
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/simple_cube");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetNumElements(),12u);
PapillaryFibreCalculator calculator(mesh);
// Call GetRadiusVectors on an element
calculator.GetRadiusVectors();
std::vector< c_vector<double,3> >& radius_vectors = calculator.mRadiusVectors;
// Check they are right
TS_ASSERT_DELTA(radius_vectors[0][0], -0.275, 1e-9);
TS_ASSERT_DELTA(radius_vectors[0][1], -0.025, 1e-9);
TS_ASSERT_DELTA(radius_vectors[0][2], -0.275, 1e-9);
TS_ASSERT_DELTA(radius_vectors[5][0], 0.475, 1e-9);
TS_ASSERT_DELTA(radius_vectors[5][1], 0.225, 1e-9);
TS_ASSERT_DELTA(radius_vectors[5][2], 0.475, 1e-9);
TS_ASSERT_EQUALS(radius_vectors.size(), mesh.GetNumElements());
///////////////////////////////////////////////////////////
// Test ConstructStructureTensors()
///////////////////////////////////////////////////////////
calculator.ConstructStructureTensors();
std::vector< c_matrix<double,3,3> >& tensor_i = calculator.mStructureTensors;
// Worked out by hand...
TS_ASSERT_DELTA(tensor_i[0](0,0),7.5625e-02,1e-9);
TS_ASSERT_DELTA(tensor_i[0](0,1),6.8750e-03,1e-9);
TS_ASSERT_DELTA(tensor_i[0](0,2),7.5625e-02,1e-9);
TS_ASSERT_DELTA(tensor_i[0](1,0),6.8750e-03,1e-9);
TS_ASSERT_DELTA(tensor_i[0](1,1),6.2500e-04,1e-9);
TS_ASSERT_DELTA(tensor_i[0](1,2),6.8750e-03,1e-9);
TS_ASSERT_DELTA(tensor_i[0](2,0),7.5625e-02,1e-9);
TS_ASSERT_DELTA(tensor_i[0](2,1),6.8750e-03,1e-9);
TS_ASSERT_DELTA(tensor_i[0](2,2),7.5625e-02,1e-9);
TS_ASSERT_DELTA(tensor_i[5](0,0),0.225625,1e-9);
TS_ASSERT_DELTA(tensor_i[5](0,1),0.106875,1e-9);
TS_ASSERT_DELTA(tensor_i[5](0,2),0.225625,1e-9);
TS_ASSERT_DELTA(tensor_i[5](1,0),0.106875,1e-9);
TS_ASSERT_DELTA(tensor_i[5](1,1),0.050625,1e-9);
TS_ASSERT_DELTA(tensor_i[5](1,2),0.106875,1e-9);
TS_ASSERT_DELTA(tensor_i[5](2,0),0.225625,1e-9);
TS_ASSERT_DELTA(tensor_i[5](2,1),0.106875,1e-9);
TS_ASSERT_DELTA(tensor_i[5](2,2),0.225625,1e-9);
//////////////////////////////////////////////////////////////
// Test SmoothStructureTensor()
//////////////////////////////////////////////////////////////
calculator.SmoothStructureTensors();
std::vector< c_matrix<double,3,3> >& tensor_smooth = calculator.mSmoothedStructureTensors;
// hard-coded (as difficult to test)
TS_ASSERT_DELTA(tensor_smooth[0](0,0), 0.075625, 1e-5);
}
// 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);
}
// 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
}
}