void TestSolveCellSystemsInclUpdateVoltage() throw(Exception)
{
HeartConfig::Instance()->Reset();
TetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(1.0, 1.0); // [0,1] with h=1.0, ie 2 node mesh
MyCardiacCellFactory cell_factory;
cell_factory.SetMesh(&mesh);
MonodomainTissue<1> monodomain_tissue( &cell_factory );
Vec voltage = PetscTools::CreateAndSetVec(2, -81.4354); // something that isn't resting potential
monodomain_tissue.SolveCellSystems(voltage, 0, 1, false); // solve for 1ms without updating the voltage
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(0))
{
TS_ASSERT_DELTA(monodomain_tissue.GetCardiacCell(0)->GetVoltage(), -81.4354, 1e-3);
}
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(1))
{
TS_ASSERT_DELTA(monodomain_tissue.GetCardiacCell(1)->GetVoltage(), -81.4354, 1e-3);
}
Vec voltage2 = PetscTools::CreateAndSetVec(2, -75);
monodomain_tissue.SolveCellSystems(voltage2, 1, 2, true); // solve another ms, using this new voltage, but now updating the voltage too
ReplicatableVector voltage2_repl(voltage2); // should have changed following solve
// check the new voltage in the cell is NEAR -75 (otherwise the passed in voltage wasn't used, but
// NOT EXACTLY -75, ie that the voltage was solved for.
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(0))
{
// check has been updated
TS_ASSERT_DIFFERS(monodomain_tissue.GetCardiacCell(0)->GetVoltage(), -75);
// check near -75
TS_ASSERT_DELTA(monodomain_tissue.GetCardiacCell(0)->GetVoltage(), -75, 2.0); // within 2mV
// check the passed in voltage was updated
TS_ASSERT_DELTA(voltage2_repl[0], monodomain_tissue.GetCardiacCell(0)->GetVoltage(), 1e-10);
}
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(1))
{
TS_ASSERT_DIFFERS(monodomain_tissue.GetCardiacCell(1)->GetVoltage(), -75);
TS_ASSERT_DELTA(monodomain_tissue.GetCardiacCell(1)->GetVoltage(), -75, 2.0); // within 2mV
TS_ASSERT_DELTA(voltage2_repl[1], monodomain_tissue.GetCardiacCell(1)->GetVoltage(), 1e-10);
}
PetscTools::Destroy(voltage);
PetscTools::Destroy(voltage2);
}
void TestMonodomainTissueGetCardiacCell() throw(Exception)
{
HeartConfig::Instance()->Reset();
TetrahedralMesh<1,1> mesh;
mesh.ConstructRegularSlabMesh(1.0, 1.0); // [0,1] with h=1.0, ie 2 node mesh
MyCardiacCellFactory cell_factory;
cell_factory.SetMesh(&mesh);
MonodomainTissue<1> monodomain_tissue( &cell_factory );
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(0))
{
AbstractCardiacCellInterface* cell = monodomain_tissue.GetCardiacCell(0);
TS_ASSERT_DELTA(cell->GetStimulus(0.001),-80,1e-10);
}
if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(1))
{
AbstractCardiacCellInterface* cell = monodomain_tissue.GetCardiacCell(1);
TS_ASSERT_DELTA(cell->GetStimulus(0.001),0,1e-10);
}
}
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);
}