void failsInParallelTestDistributedRigidBodyMethods()
{
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
DistributedTetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
c_matrix<double, 3, 3> dummy;
double jacobian_det = 0.0;
double scaled_volume = 0.0;
for (AbstractTetrahedralMesh<3, 3>::ElementIterator iter = mesh.GetElementIteratorBegin();
iter != mesh.GetElementIteratorEnd();
++iter)
{
iter->CalculateJacobian(dummy, jacobian_det);
scaled_volume += jacobian_det;
}
TS_ASSERT_DELTA(scaled_volume, 1.0*6, 1e-6);
mesh.RotateX(M_PI);
//mesh.Translate(100.0, 0.0, 0.0);
double scaled_volume_after = 0.0;
for (AbstractTetrahedralMesh<3, 3>::ElementIterator iter = mesh.GetElementIteratorBegin();
iter != mesh.GetElementIteratorEnd();
++iter)
{
iter->CalculateJacobian(dummy, jacobian_det);
scaled_volume_after += jacobian_det;
}
TS_ASSERT_DELTA(scaled_volume_after, 1.0*6, 1e-6);
}
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);
}
}
}
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 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 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
}
