//--------------------------------------------------------------------------------------------------
///
//--------------------------------------------------------------------------------------------------
void RigReservoirBuilderMock::appendNodes(const cvf::Vec3d& min, const cvf::Vec3d& max, const cvf::Vec3st& cubeDimension, std::vector<cvf::Vec3d>& nodes)
{
double dx = (max.x() - min.x()) / static_cast<double>(cubeDimension.x());
double dy = (max.y() - min.y()) / static_cast<double>(cubeDimension.y());
double dz = (max.z() - min.z()) / static_cast<double>(cubeDimension.z());
double zPos = min.z();
size_t k;
for (k = 0; k < cubeDimension.z(); k++)
{
double yPos = min.y();
size_t j;
for (j = 0; j < cubeDimension.y(); j++)
{
double xPos = min.x();
size_t i;
for (i = 0; i < cubeDimension.x(); i++)
{
cvf::Vec3d cornerA(xPos, yPos, zPos);
cvf::Vec3d cornerB(xPos + dx, yPos + dy, zPos + dz);
appendCubeNodes(cornerA, cornerB, nodes);
xPos += dx;
}
yPos += dy;
}
zPos += dz;
}
}
/**
* Tests archiving of the tissue object.
* It creates one, changes the default values of some member variables and saves.
* Then it tries to load from the archive and checks that the member variables are with the right values.
*/
void TestSaveAndLoadExtendedBidomainTissue() throw (Exception)
{
HeartConfig::Instance()->Reset();
// Archive settings
FileFinder archive_dir("extended_tissue_archive", RelativeTo::ChasteTestOutput);
std::string archive_file = "extended_bidomain_tissue.arch";
bool cache_replication_saved = false;
double saved_printing_timestep = 2.0;
double default_printing_timestep = HeartConfig::Instance()->GetPrintingTimeStep();
c_matrix<double, 3, 3> intra_tensor_before_archiving;
c_matrix<double, 3, 3> intra_tensor_second_cell_before_archiving;
c_matrix<double, 3, 3> extra_tensor_before_archiving;
//creation and save
{
// This call is required to set the appropriate conductivity media and to make sure that HeartConfig
// knows the mesh filename despite we use our own mesh reader.
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/cube_136_elements");
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
DistributedTetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
UnStimulatedCellFactory first_cell;
StimulatedCellFactory second_cell;
ExtracellularStimulusFactory extra_factory;
first_cell.SetMesh(&mesh);
second_cell.SetMesh(&mesh);
extra_factory.SetMesh(&mesh);
ExtendedBidomainTissue<3> extended_tissue( &first_cell, &second_cell , &extra_factory);
//set a value different from default for the conductivities of the second cell
extended_tissue.SetIntracellularConductivitiesSecondCell(Create_c_vector(25.0,26.0,27.0));
//this is normally done by the problem class, but in this test we do it manually
extended_tissue.CreateIntracellularConductivityTensorSecondCell();
extended_tissue.SetCacheReplication(cache_replication_saved); // Not the default to check it is archived...
//shuffle default values to check if they get archived properly
extended_tissue.SetAmFirstCell(11.0);
extended_tissue.SetAmSecondCell(22.0);
extended_tissue.SetAmGap(33.0);
extended_tissue.SetCmFirstCell(44.0);
extended_tissue.SetCmSecondCell(55.0);
extended_tissue.SetGGap(66.0);
//again, away from default value to check for archiving
extended_tissue.SetUserSuppliedExtracellularStimulus(true);
//set some heterogeneities in Ggap
std::vector<boost::shared_ptr<AbstractChasteRegion<3> > > heterogeneity_areas;
std::vector<double> Ggap_values;
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.001, 0.001, 0.001);
boost::shared_ptr<ChasteCuboid<3> > p_cuboid_1(new ChasteCuboid<3>(cornerA, cornerB));
heterogeneity_areas.push_back(p_cuboid_1);
//within the first area
Ggap_values.push_back(143.0);
extended_tissue.SetGgapHeterogeneities(heterogeneity_areas, Ggap_values);
extended_tissue.CreateGGapConductivities();
// Some checks to make sure HeartConfig is being saved and loaded by this too.
HeartConfig::Instance()->SetPrintingTimeStep(saved_printing_timestep);
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
intra_tensor_before_archiving = extended_tissue.rGetIntracellularConductivityTensor(0);
intra_tensor_second_cell_before_archiving = extended_tissue.rGetIntracellularConductivityTensorSecondCell(0);
extra_tensor_before_archiving = extended_tissue.rGetExtracellularConductivityTensor(0);
// Save
ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_dir, archive_file);
boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<3>* const p_archive_bidomain_tissue = &extended_tissue;
(*p_arch) << p_archive_bidomain_tissue;
HeartConfig::Reset();
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), default_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep);
}
//load
{
ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(archive_dir, archive_file);
boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();
AbstractCardiacTissue<3>* p_abstract_tissue;
(*p_arch) >> p_abstract_tissue;
assert(p_abstract_tissue!=NULL);
//dynamic cast so we are able to test specific variables of ExtendedBidomainTissue
ExtendedBidomainTissue<3>* p_extended_tissue = dynamic_cast<ExtendedBidomainTissue<3>*>(p_abstract_tissue);
assert(p_extended_tissue != NULL);
const c_matrix<double, 3, 3>& intra_tensor_after_archiving = p_extended_tissue->rGetIntracellularConductivityTensor(0);
const c_matrix<double, 3, 3>& intra_tensor_second_cell_after_archiving = p_extended_tissue->rGetIntracellularConductivityTensorSecondCell(0);
const c_matrix<double, 3, 3>& extra_tensor_after_archiving = p_extended_tissue->rGetExtracellularConductivityTensor(0);
//check before archiving = after archiving
for(unsigned i=0; i<3; i++)
{
for(unsigned j=0; j<3; j++)
{
TS_ASSERT_DELTA(intra_tensor_before_archiving(i,j), intra_tensor_after_archiving(i,j), 1e-9);
TS_ASSERT_DELTA(intra_tensor_second_cell_before_archiving(i,j), intra_tensor_second_cell_after_archiving(i,j), 1e-9);
TS_ASSERT_DELTA(extra_tensor_before_archiving(i,j), extra_tensor_after_archiving(i,j), 1e-9);
}
}
//check that the member variable mIntracellularConductivitiesSecondCell was archived properly
TS_ASSERT_EQUALS(p_extended_tissue->GetIntracellularConductivitiesSecondCell()(0),25.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetIntracellularConductivitiesSecondCell()(1),26.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetIntracellularConductivitiesSecondCell()(2),27.0);
//check that we get the same values from the archive which are different from the default
TS_ASSERT_EQUALS(p_extended_tissue->GetAmFirstCell(), 11.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetAmSecondCell(), 22.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetAmGap(), 33.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCmFirstCell(), 44.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCmSecondCell(), 55.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetGGap(), 66.0);
// We shouldn't need to re-build the mesh, but we use it to check that the new tissue has the same mesh
// Also, when testing in parallel, we use it to get the vector factory to loop over the nodes we own.
// this is because p_extended_tissue->pGetMesh()->GetDistributedVectorFactory() doesn't compile (discards qualifier stuff caused by use of const).
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
DistributedTetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), p_extended_tissue->pGetMesh()->GetNumNodes());//note: this is allowed because GetNumNodes has const in the signature
//check archiving of stimulus for first cell at some random times (it is unstimulated everywhere at all times)
for (unsigned i = 0; i < mesh.GetNumNodes(); i++)
{
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(i))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(0.0), 0.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(0.1), 0.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(2.5), 0.0);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacCell(i)->GetIntracellularStimulus(28.9), 0.0);
}
}
//for second cell and other stuff, we probe nodes 0 and 1.
unsigned node_0 = 0u;
unsigned node_1 = 1u;
//If the test is run in parallel, we need to work out the new indices
const std::vector<unsigned>& r_permutation = mesh.rGetNodePermutation();
if (!r_permutation.empty())
{
node_0 = r_permutation[0u];
node_1 = r_permutation[1u];
}
//second cell is stimulated in the corner (node 0) from time 0 to 1. check it gets all this after loading
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(node_0))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacSecondCell(node_0)->GetIntracellularStimulus(0.5), -105.0*1400);
TS_ASSERT_EQUALS(p_extended_tissue->GetCardiacSecondCell(node_0)->GetIntracellularStimulus(2.5), 0.0);
//find local index of (the new) node_0, it should be in the heterogeneity region
unsigned ownership_range_low = mesh.GetDistributedVectorFactory()->GetLow();
unsigned local_index = node_0 - ownership_range_low;
//std::cout<<local_index<<std::endl;
TS_ASSERT_EQUALS(p_extended_tissue->rGetGapsDistributed()[local_index],143.0);//g_gap value inside heterogeneity region
}
//node 0 has extracellular stimulus (1 ms from 0.1)
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(node_0))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(0.0), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(0.5), -428000);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(1.0), -428000);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_0)->GetStimulus(1.15), 0);
}
//node 1 doesn't
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(node_1))
{
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(0.0), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(0.5), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(1.0), 0);
TS_ASSERT_EQUALS(p_extended_tissue->GetExtracellularStimulus(node_1)->GetStimulus(1.15), 0);
//find local index of (the new) node_1, it should NOT be in the heterogeneity region
unsigned ownership_range_low = mesh.GetDistributedVectorFactory()->GetLow();
unsigned local_index = node_1 - ownership_range_low;
TS_ASSERT_EQUALS(p_extended_tissue->rGetGapsDistributed()[local_index],66.0);//standard g_gap value, outside heterogeneity region
}
//check the archiving of the flag (it would be false by default, but we set it to true before archiving)
TS_ASSERT_EQUALS(p_extended_tissue->HasTheUserSuppliedExtracellularStimulus(),true);
TS_ASSERT_EQUALS(cache_replication_saved, p_extended_tissue->GetDoCacheReplication());
TS_ASSERT_DELTA(HeartConfig::Instance()->GetPrintingTimeStep(), saved_printing_timestep, 1e-9);
TS_ASSERT_DIFFERS(saved_printing_timestep, default_printing_timestep); // Test we are testing something in case default changes
delete p_extended_tissue;
}
}
void TestExtendedTissueHeterogeneousGgap3D() throw (Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
std::vector<boost::shared_ptr<AbstractChasteRegion<3> > > heterogeneity_areas;
std::vector<double> Ggap_values;
//first cuboid include node 0
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.001, 0.001, 0.001);
boost::shared_ptr<ChasteCuboid<3> > p_cuboid_1(new ChasteCuboid<3>(cornerA, cornerB));
heterogeneity_areas.push_back(p_cuboid_1);
//second cuboid include node 6
ChastePoint<3> cornerC(0.199, 0.199, 0.199);
ChastePoint<3> cornerD(0.25, 0.25, 0.25);
boost::shared_ptr<ChasteCuboid<3> > p_cuboid_2(new ChasteCuboid<3>(cornerC, cornerD));
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_areas.push_back(p_cuboid_2);
//within the first area
Ggap_values.push_back(143.0);
//within the second area
Ggap_values.push_back(9143.0);
//elsewhere
double isotropic_ggap=586.0;
StimulatedCellFactory stimulated_cell_factory;
UnStimulatedCellFactory unstimulated_cell_factory;
ExtracellularStimulusFactory extracellular_stimulus_factory;
stimulated_cell_factory.SetMesh(&mesh);
unstimulated_cell_factory.SetMesh(&mesh);
extracellular_stimulus_factory.SetMesh(&mesh);
ExtendedBidomainTissue<3> extended_bidomain_tissue( &stimulated_cell_factory, &unstimulated_cell_factory, &extracellular_stimulus_factory);
extended_bidomain_tissue.SetGGap(isotropic_ggap);//this is what the problem class does first
extended_bidomain_tissue.SetGgapHeterogeneities(heterogeneity_areas, Ggap_values);
extended_bidomain_tissue.CreateGGapConductivities();
unsigned probe_node_1 = 0u;
unsigned probe_node_2 = 6u;
unsigned probe_node_3 = 5u;
const std::vector<unsigned>& r_permutation = mesh.rGetNodePermutation();
if (!r_permutation.empty())
{
probe_node_1 = r_permutation[0u];//within first cuboid
probe_node_2 = r_permutation[6u];//within second cuboid
probe_node_3 = r_permutation[5u];//elsewhere
}
Vec vector = mesh.GetDistributedVectorFactory()->CreateVec();
DistributedVector dist_solution = mesh.GetDistributedVectorFactory()->CreateDistributedVector(vector);
for (DistributedVector::Iterator index = dist_solution.Begin();
index != dist_solution.End();
++index)
{
extended_bidomain_tissue.UpdateAdditionalCaches(index.Global, index.Local, 2.0);
}
extended_bidomain_tissue.ReplicateAdditionalCaches();
//Ggap
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetGgapCacheReplicated()[probe_node_1],143.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetGgapCacheReplicated()[probe_node_2],9143.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetGgapCacheReplicated()[probe_node_3],586.0);//elsewhere
PetscTools::Destroy(vector);
}
void TestExtendedTissueHeterogeneousConductivities2D() throw (Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//HeartConfig setup needs to be in 3D anyway (hardcoded in HeartConfig).
std::vector<ChasteCuboid<3> > heterogeneity_area;
std::vector< c_vector<double,3> > intra_conductivities;
std::vector< c_vector<double,3> > extra_conductivities;
//first cuboid includes element 0
ChastePoint<3> cornerA(-1, -1,-1);
ChastePoint<3> cornerB(0.48, 2.0, 0.48);
ChasteCuboid<3> cuboid_1(cornerA, cornerB);
heterogeneity_area.push_back(cuboid_1);
//second cuboid includes element 2
ChastePoint<3> cornerC(0.52, -1, 0.52);
ChastePoint<3> cornerD(2, 2, 2);
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_area.push_back(cuboid_2);
//within the first area
intra_conductivities.push_back( Create_c_vector(1.0, 2.0, 3.0) );
extra_conductivities.push_back( Create_c_vector(51.0, 52.0, 53.0) );
//within the second area
intra_conductivities.push_back( Create_c_vector(11.0, 22.0, 33.0) );
extra_conductivities.push_back( Create_c_vector(151.0, 152.0, 153.0) );
HeartConfig::Instance()->SetConductivityHeterogeneities(heterogeneity_area, intra_conductivities, extra_conductivities);
//elsewhere
double isotropic_intra_conductivity=15.0;
double isotropic_extra_conductivity=65.0;
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(isotropic_extra_conductivity, isotropic_extra_conductivity, isotropic_extra_conductivity));
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 2> cell_factory_1;
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 2> cell_factory_2;
StimulusFactory2D extracellular_stimulus_factory;
cell_factory_1.SetMesh(&mesh);
cell_factory_2.SetMesh(&mesh);
extracellular_stimulus_factory.SetMesh(&mesh);
//2D tissue
ExtendedBidomainTissue<2> extended_bidomain_tissue( &cell_factory_1, &cell_factory_2, &extracellular_stimulus_factory);
// Do conductivity modifier here too (for coverage)
SimpleConductivityModifier conductivity_modifier;
extended_bidomain_tissue.SetConductivityModifier( &conductivity_modifier );
extended_bidomain_tissue.SetIntracellularConductivitiesSecondCell(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity));
extended_bidomain_tissue.CreateIntracellularConductivityTensorSecondCell();
//first cell
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(1u)(0,0),30.0);//within no cuboid (modified from 15 to 30!)
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(2u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(3u)(0,0),15.0);//within no cuboid
//second cell, should be the same as first cell
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(1u)(0,0),30.0);//within no cuboid (modified from 15 to 30!)
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(2u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(3u)(0,0),15.0);//within no cuboid
//sigma_e
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(0u)(0,0),51.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(1u)(0,0),130.0);//within no cuboid (modified from 65 to 130!)
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(2u)(1,1),152.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(3u)(0,0),65.0);//within no cuboid
}
/**This test checks heterogeneous conductivities*/
void TestExtendedTissueHeterogeneous3D() throw (Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
std::vector<ChasteCuboid<3> > heterogeneity_area;
std::vector< c_vector<double,3> > intra_conductivities;
std::vector< c_vector<double,3> > extra_conductivities;
//first cuboid include element 0
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.1, 0.2, 0.2);
ChasteCuboid<3> cuboid_1(cornerA, cornerB);
heterogeneity_area.push_back(cuboid_1);
//second cuboid include element 4
ChastePoint<3> cornerC(0.11, 0.0, 0);
ChastePoint<3> cornerD(0.2, 0.11, 0.2);
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_area.push_back(cuboid_2);
//within the first area
intra_conductivities.push_back( Create_c_vector(1.0, 2.0, 3.0) );
extra_conductivities.push_back( Create_c_vector(51.0, 52.0, 53.0) );
//within the second area
intra_conductivities.push_back( Create_c_vector(11.0, 22.0, 33.0) );
extra_conductivities.push_back( Create_c_vector(151.0, 152.0, 153.0) );
HeartConfig::Instance()->SetConductivityHeterogeneities(heterogeneity_area, intra_conductivities, extra_conductivities);
//elsewhere
double isotropic_intra_conductivity=15.0;
double isotropic_extra_conductivity=65.0;
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(isotropic_extra_conductivity, isotropic_extra_conductivity, isotropic_extra_conductivity));
StimulatedCellFactory stimulated_cell_factory;
UnStimulatedCellFactory unstimulated_cell_factory;
ExtracellularStimulusFactory extracellular_stimulus_factory;
stimulated_cell_factory.SetMesh(&mesh);
unstimulated_cell_factory.SetMesh(&mesh);
extracellular_stimulus_factory.SetMesh(&mesh);
ExtendedBidomainTissue<3> extended_bidomain_tissue( &stimulated_cell_factory, &unstimulated_cell_factory, &extracellular_stimulus_factory);
extended_bidomain_tissue.SetIntracellularConductivitiesSecondCell(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
extended_bidomain_tissue.CreateIntracellularConductivityTensorSecondCell();
//first cell
// TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(0u)(0,0),1.0);//within first cuboid
//Line above commented due to curious problem with IntelProduction interprocedural optimisation
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(4u)(0,0),11.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(4u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(8u)(0,0),15.0);//elsewhere, e.g. element 8
//second cell, should be the same as first cell
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(4u)(0,0),11.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(4u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(8u)(0,0),15.0);//elsewhere, e.g. element 8
//sigma_e
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(0u)(0,0),51.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(4u)(0,0),151.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(4u)(1,1),152.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(8u)(0,0),65.0);//elsewhere, e.g. element 8
}
void TestBidomainTissueWithHeterogeneousConductivitiesDistributed() throw (Exception)
{
HeartConfig::Instance()->Reset();
// This call is required to set the appropriate conductivity media and to make sure that
// HeartConfig knows the mesh filename despite we use our own mesh reader.
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/cube_2mm_12_elements", cp::media_type::NoFibreOrientation);
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
// METIS_LIBRARY partition ensures that we have never own all the elements (even when there are as few as 2 processes)
// DUMB and PARMETIS_LIBRARY may allow single process to see all the elements because it's a very small mesh
DistributedTetrahedralMesh<3,3> mesh(DistributedTetrahedralMeshPartitionType::METIS_LIBRARY);
mesh.ConstructFromMeshReader(mesh_reader);
// Check that if we're in parallel no single process owns every element (to ensure that the conductivities
// really are distributed).
if (PetscTools::IsParallel())
{
TS_ASSERT_DIFFERS( mesh.GetNumElements(), mesh.GetNumLocalElements() );
}
std::vector<ChasteCuboid<3> > heterogeneity_area;
std::vector< c_vector<double,3> > intra_conductivities;
std::vector< c_vector<double,3> > extra_conductivities;
//first cuboid include element 0
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.1, 0.2, 0.2);
ChasteCuboid<3> cuboid_1(cornerA, cornerB);
heterogeneity_area.push_back(cuboid_1);
//second cuboid include element 4
ChastePoint<3> cornerC(0.11, 0.0, 0);
ChastePoint<3> cornerD(0.2, 0.11, 0.2);
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_area.push_back(cuboid_2);
//within the first area
intra_conductivities.push_back( Create_c_vector(1.0, 2.0, 3.0) );
extra_conductivities.push_back( Create_c_vector(51.0, 52.0, 53.0) );
//within the second area
intra_conductivities.push_back( Create_c_vector(11.0, 22.0, 33.0) );
extra_conductivities.push_back( Create_c_vector(151.0, 152.0, 153.0) );
HeartConfig::Instance()->SetConductivityHeterogeneities(heterogeneity_area, intra_conductivities, extra_conductivities);
//elsewhere
double isotropic_intra_conductivity=15.0;
double isotropic_extra_conductivity=65.0;
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(isotropic_extra_conductivity, isotropic_extra_conductivity, isotropic_extra_conductivity));
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML,3> cell_factory_for_het;
cell_factory_for_het.SetMesh(&mesh);
//CreateIntracellularConductivityTensor called in the constructor
BidomainTissue<3> bidomain_tissue( &cell_factory_for_het );
if (mesh.CalculateDesignatedOwnershipOfElement(0u))
{
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(0u)(0,0),51.0);//within first cuboid
}
if (mesh.CalculateDesignatedOwnershipOfElement(4u))
{
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(4u)(0,0),11.0);//within second cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(4u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(4u)(0,0),151.0);//within second cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(4u)(1,1),152.0);//within second cuboid
}
if (mesh.CalculateDesignatedOwnershipOfElement(8u))
{
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(8u)(0,0),15.0);//elsewhere, e.g. element 8
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(8u)(0,0),65.0);//elsewhere, e.g. element 8
}
}
