void TestValidate()
{
// Load a 2D square mesh with 1 central non-boundary node
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
BoundaryConditionsContainer<2,2,1> bcc;
// No BCs yet, so shouldn't validate
TS_ASSERT(!bcc.Validate(&mesh));
// Add some BCs
ConstBoundaryCondition<2> *bc = new ConstBoundaryCondition<2>(0.0);
bcc.AddDirichletBoundaryCondition(mesh.GetNode(0), bc);
bcc.AddDirichletBoundaryCondition(mesh.GetNode(1), bc);
bcc.AddDirichletBoundaryCondition(mesh.GetNode(3), bc);
TetrahedralMesh<2,2>::BoundaryElementIterator iter
= mesh.GetBoundaryElementIteratorEnd();
iter--;
bcc.AddNeumannBoundaryCondition(*iter, bc); // 2 to 3
iter--;
bcc.AddNeumannBoundaryCondition(*iter, bc); // 1 to 2
TS_ASSERT(bcc.Validate(&mesh));
}
void TestAnyNonZeroNeumannConditionsAndApplyNeumannToMeshBoundary()
{
// Load a 2D square mesh with 1 central non-boundary node
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
BoundaryConditionsContainer<2,2,1> bcc;
BoundaryConditionsContainer<2,2,2> bcc_2unknowns;
TS_ASSERT_EQUALS(bcc.AnyNonZeroNeumannConditions(), false);
bcc.DefineZeroNeumannOnMeshBoundary(&mesh);
TetrahedralMesh<2,2>::BoundaryElementIterator iter;
iter = mesh.GetBoundaryElementIteratorBegin();
while (iter != mesh.GetBoundaryElementIteratorEnd())
{
TS_ASSERT(bcc.HasNeumannBoundaryCondition(*iter));
double value = bcc.GetNeumannBCValue(*iter, (*iter)->GetNode(0)->GetPoint());
TS_ASSERT_DELTA(value, 0.0, 1e-8);
iter++;
}
TS_ASSERT_EQUALS(bcc.AnyNonZeroNeumannConditions(), false);
iter = mesh.GetBoundaryElementIteratorBegin();
ConstBoundaryCondition<2>* p_boundary_condition2 = new ConstBoundaryCondition<2>(-1);
bcc_2unknowns.AddNeumannBoundaryCondition(*iter, p_boundary_condition2);
TS_ASSERT_EQUALS(bcc_2unknowns.AnyNonZeroNeumannConditions(), true);
}
void TestAddNeumannBoundaryConditions()
{
// Load a 2D square mesh with 1 central non-boundary node
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
BoundaryConditionsContainer<2,2,2> bcc;
// No BCs yet, so shouldn't validate
TS_ASSERT(!bcc.Validate(&mesh));
// Add some BCs
ConstBoundaryCondition<2> *bc1 = new ConstBoundaryCondition<2>(2.0);
ConstBoundaryCondition<2> *bc2 = new ConstBoundaryCondition<2>(-3.0);
TetrahedralMesh<2,2>::BoundaryElementIterator iter = mesh.GetBoundaryElementIteratorEnd();
iter--;
bcc.AddNeumannBoundaryCondition(*iter, bc1, 0);
bcc.AddNeumannBoundaryCondition(*iter, bc2, 1);
iter--;
bcc.AddNeumannBoundaryCondition(*iter, bc1, 0);
iter--;
bcc.AddNeumannBoundaryCondition(*iter, bc2, 1);
iter = mesh.GetBoundaryElementIteratorEnd();
iter--;
TS_ASSERT_DELTA(bcc.GetNeumannBCValue(*iter, ChastePoint<2>(), 0), 2.0, 1e-9);
TS_ASSERT_DELTA(bcc.GetNeumannBCValue(*iter, ChastePoint<2>(), 1), -3.0, 1e-9);
iter--;
TS_ASSERT_DELTA(bcc.GetNeumannBCValue(*iter, ChastePoint<2>(), 0), 2.0, 1e-9);
TS_ASSERT_DELTA(bcc.GetNeumannBCValue(*iter, ChastePoint<2>(), 1), 0.0, 1e-9);
iter--;
TS_ASSERT_DELTA(bcc.GetNeumannBCValue(*iter, ChastePoint<2>(), 0), 0.0, 1e-9);
TS_ASSERT_DELTA(bcc.GetNeumannBCValue(*iter, ChastePoint<2>(), 1), -3.0, 1e-9);
}
/* Define a particular test. Note the {{{throw(Exception)}}} at the end of the
* declaration. This causes {{{Exception}}} messages to be printed out if an
* {{{Exception}}} is thrown, rather than just getting the message "terminate
* called after throwing an instance of 'Exception' " */
void TestSolvingNonlinearEllipticPde() throw(Exception)
{
/* As usual, first create a mesh. */
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_128_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
/* Next, instantiate the PDE to be solved. */
MyNonlinearPde pde;
/*
* Then we have to define the boundary conditions. First, the Dirichlet boundary
* condition, u=0 on x=0, using the boundary node iterator.
*/
BoundaryConditionsContainer<2,2,1> bcc;
ConstBoundaryCondition<2>* p_zero_bc = new ConstBoundaryCondition<2>(0.0);
for (TetrahedralMesh<2,2>::BoundaryNodeIterator node_iter = mesh.GetBoundaryNodeIteratorBegin();
node_iter != mesh.GetBoundaryNodeIteratorEnd();
node_iter++)
{
if (fabs((*node_iter)->GetPoint()[1]) < 1e-12)
{
bcc.AddDirichletBoundaryCondition(*node_iter, p_zero_bc);
}
}
/* And then the Neumman conditions. Neumann boundary condition are defined on
* surface elements, and for this problem, the Neumman boundary value depends
* on the position in space, so we make use of the {{{FunctionalBoundaryCondition}}}
* object, which contains a pointer to a function, and just returns the value
* of that function for the required point when the {{{GetValue}}} method is called.
*/
FunctionalBoundaryCondition<2>* p_functional_bc = new FunctionalBoundaryCondition<2>(&MyNeummanFunction);
/* Loop over surface elements. */
for (TetrahedralMesh<2,2>::BoundaryElementIterator elt_iter = mesh.GetBoundaryElementIteratorBegin();
elt_iter != mesh.GetBoundaryElementIteratorEnd();
elt_iter++)
{
/* Get the y value of any node (here, the zero-th). */
double y = (*elt_iter)->GetNodeLocation(0,1);
/* If y=1... */
if (fabs(y-1.0) < 1e-12)
{
/* ... then associate the functional boundary condition, (Dgradu).n = y,
* with the surface element... */
bcc.AddNeumannBoundaryCondition(*elt_iter, p_functional_bc);
}
else
{
/* ...else associate the zero boundary condition (i.e. zero flux) with this
* element. */
bcc.AddNeumannBoundaryCondition(*elt_iter, p_zero_bc);
}
}
/* Note that in the above loop, the zero Neumman boundary condition was applied
* to all surface elements for which y!=1, which included the Dirichlet surface
* y=0. This is OK, as Dirichlet boundary conditions are applied to the finite
* element matrix after Neumman boundary conditions, where the appropriate rows
* in the matrix are overwritten.
*
* This is the solver for solving nonlinear problems, which, as usual,
* takes in the mesh, the PDE, and the boundary conditions. */
SimpleNonlinearEllipticSolver<2,2> solver(&mesh, &pde, &bcc);
/* The solver also needs to be given an initial guess, which will be
* a PETSc vector. We can make use of a helper method to create it.
*/
Vec initial_guess = PetscTools::CreateAndSetVec(mesh.GetNumNodes(), 0.25);
/* '''Optional:''' To use Chaste's Newton solver to solve nonlinear vector equations that are
* assembled, rather than the default PETSc nonlinear solvers, we can
* do the following: */
SimpleNewtonNonlinearSolver newton_solver;
solver.SetNonlinearSolver(&newton_solver);
/* '''Optional:''' We can also manually set tolerances, and whether to print statistics, with
* this nonlinear vector equation solver */
newton_solver.SetTolerance(1e-10);
newton_solver.SetWriteStats();
/* Now call {{{Solve}}}, passing in the initial guess */
Vec answer = solver.Solve(initial_guess);
/* Note that we could have got the solver to not use an analytical Jacobian
* and use a numerically-calculated Jacobian instead, by passing in false as a second
* parameter:
*/
//Vec answer = solver.Solve(initial_guess, false);
/* Once solved, we can check the obtained solution against the analytical
* solution. */
ReplicatableVector answer_repl(answer);
for (unsigned i=0; i<answer_repl.GetSize(); i++)
{
double y = mesh.GetNode(i)->GetPoint()[1];
double exact_u = sqrt(y*(4-y));
TS_ASSERT_DELTA(answer_repl[i], exact_u, 0.15);
}
/* Finally, we have to remember to destroy the PETSc {{{Vec}}}s. */
PetscTools::Destroy(initial_guess);
PetscTools::Destroy(answer);
}
void TestHeatEquationWithSourceWithCoupledOdeSystemIn1dWithZeroNeumann()
{
// Create mesh of domain [0,1]
TrianglesMeshReader<1,1> mesh_reader("mesh/test/data/1D_0_to_1_100_elements");
TetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Create PDE system object
HeatEquationWithSourceForCoupledOdeSystem<1> pde;
// Define zero Neumann boundary conditions
BoundaryConditionsContainer<1,1,1> bcc;
ConstBoundaryCondition<1>* p_boundary_condition = new ConstBoundaryCondition<1>(0.0);
TetrahedralMesh<1,1>::BoundaryElementIterator iter = mesh.GetBoundaryElementIteratorBegin();
bcc.AddNeumannBoundaryCondition(*iter, p_boundary_condition);
iter = mesh.GetBoundaryElementIteratorEnd();
iter--;
bcc.AddNeumannBoundaryCondition(*iter, p_boundary_condition);
// Create the correct number of ODE systems
double a = 5.0;
std::vector<AbstractOdeSystemForCoupledPdeSystem*> ode_systems;
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
ode_systems.push_back(new OdeSystemForCoupledHeatEquationWithSource(a));
}
// Create PDE system solver
LinearParabolicPdeSystemWithCoupledOdeSystemSolver<1,1,1> solver(&mesh, &pde, &bcc, ode_systems);
// Test setting end time and timestep
TS_ASSERT_THROWS_THIS(solver.SetTimes(1.0, 0.0), "Start time has to be less than end time");
TS_ASSERT_THROWS_THIS(solver.SetTimeStep(0.0), "Time step has to be greater than zero");
// Set end time and timestep
double t_end = 0.1;
solver.SetTimes(0, t_end);
solver.SetTimeStep(0.001);
// Set initial condition u(x,0) = 1 + cos(pi*x)
std::vector<double> init_cond(mesh.GetNumNodes());
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
double x = mesh.GetNode(i)->GetPoint()[0];
init_cond[i] = 1 + cos(M_PI*x);
}
Vec initial_condition = PetscTools::CreateVec(init_cond);
solver.SetInitialCondition(initial_condition);
// Solve PDE system and store result
Vec result = solver.Solve();
ReplicatableVector result_repl(result);
/*
* Test that solution is given by
*
* u(x,t) = 1 + (1 - exp(-a*t))/a + exp(-pi*pi*t)*cos(pi*x),
* v(x,t) = exp(-a*t),
*
* with t = t_end.
*/
for (unsigned i=0; i<result_repl.GetSize(); i++)
{
double x = mesh.GetNode(i)->GetPoint()[0];
double u = 1 + (1 - exp(-a*t_end))/a + exp(-M_PI*M_PI*t_end)*cos(M_PI*x);
TS_ASSERT_DELTA(result_repl[i], u, 0.1);
double u_from_v = solver.GetOdeSystemAtNode(i)->rGetPdeSolution()[0];
TS_ASSERT_DELTA(result_repl[i], u_from_v, 0.1);
double v = exp(-a*t_end);
TS_ASSERT_DELTA(ode_systems[i]->rGetStateVariables()[0], v, 0.1);
}
// Test the method GetOdeSystemAtNode()
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
TS_ASSERT(solver.GetOdeSystemAtNode(i) != NULL);
TS_ASSERT_DELTA(static_cast<OdeSystemForCoupledHeatEquationWithSource*>(solver.GetOdeSystemAtNode(i))->GetA(), 5.0, 1e-6);
}
// Tidy up
PetscTools::Destroy(initial_condition);
PetscTools::Destroy(result);
}
void TestArchiving()
{
OutputFileHandler handler("bcc_archive", false);
handler.SetArchiveDirectory();
std::string archive_filename = ArchiveLocationInfo::GetProcessUniqueFilePath("bcc.arch");
// Load a 2D square mesh with 1 central non-boundary node
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
{
BoundaryConditionsContainer<2,2,2>* p_bcc = new BoundaryConditionsContainer<2,2,2>;
// No BCs yet, so shouldn't validate
TS_ASSERT_EQUALS(p_bcc->Validate(&mesh), false);
// Add some Neumann BCs
ConstBoundaryCondition<2> *bc1 = new ConstBoundaryCondition<2>(2.0);
ConstBoundaryCondition<2> *bc2 = new ConstBoundaryCondition<2>(-3.0);
TetrahedralMesh<2,2>::BoundaryElementIterator iter = mesh.GetBoundaryElementIteratorEnd();
iter--;
p_bcc->AddNeumannBoundaryCondition(*iter, bc1, 0);
p_bcc->AddNeumannBoundaryCondition(*iter, bc2, 1);
iter--;
p_bcc->AddNeumannBoundaryCondition(*iter, bc1, 0);
iter--;
p_bcc->AddNeumannBoundaryCondition(*iter, bc2, 1);
// Add some Dirichlet BCs
ConstBoundaryCondition<2> *bc3 = new ConstBoundaryCondition<2>(2.0);
p_bcc->AddDirichletBoundaryCondition(mesh.GetNode(2), bc3);
p_bcc->AddDirichletBoundaryCondition(mesh.GetNode(3), bc3);
// Archive
std::ofstream ofs(archive_filename.c_str());
boost::archive::text_oarchive output_arch(ofs);
output_arch & p_bcc;
delete p_bcc;
}
{
std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
boost::archive::text_iarchive input_arch(ifs);
// Load container...
BoundaryConditionsContainer<2,2,2>* p_bcc;
input_arch >> p_bcc;
// ...and fill it
p_bcc->LoadFromArchive( input_arch, &mesh );
TetrahedralMesh<2,2>::BoundaryElementIterator iter = mesh.GetBoundaryElementIteratorEnd();
iter--;
TS_ASSERT_DELTA(p_bcc->GetNeumannBCValue(*iter, ChastePoint<2>(), 0), 2.0, 1e-9);
TS_ASSERT_DELTA(p_bcc->GetNeumannBCValue(*iter, ChastePoint<2>(), 1), -3.0, 1e-9);
iter--;
TS_ASSERT_DELTA(p_bcc->GetNeumannBCValue(*iter, ChastePoint<2>(), 0), 2.0, 1e-9);
TS_ASSERT_DELTA(p_bcc->GetNeumannBCValue(*iter, ChastePoint<2>(), 1), 0.0, 1e-9);
iter--;
TS_ASSERT_DELTA(p_bcc->GetNeumannBCValue(*iter, ChastePoint<2>(), 0), 0.0, 1e-9);
TS_ASSERT_DELTA(p_bcc->GetNeumannBCValue(*iter, ChastePoint<2>(), 1), -3.0, 1e-9);
TS_ASSERT_DELTA(p_bcc->GetDirichletBCValue(mesh.GetNode(2)), 2.0, 1.e-6);
TS_ASSERT_DELTA(p_bcc->GetDirichletBCValue(mesh.GetNode(3)), 2.0, 1.e-6);
delete p_bcc;
}
}
void TestSolvingEllipticPde() throw(Exception)
{
/* First we declare a mesh reader which reads mesh data files of the 'Triangle'
* format. The path given is relative to the main Chaste directory. As we are in 2d,
* the reader will look for three datafiles, [name].nodes, [name].ele and [name].edge.
* Note that the first template argument here is the spatial dimension of the
* elements in the mesh ({{{ELEMENT_DIM}}}), and the second is the dimension of the nodes,
* i.e. the dimension of the space the mesh lives in ({{{SPACE_DIM}}}). Usually
* {{{ELEMENT_DIM}}} and {{{SPACE_DIM}}} will be equal. */
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_128_elements");
/* Now declare a tetrahedral mesh with the same dimensions... */
TetrahedralMesh<2,2> mesh;
/* ... and construct the mesh using the mesh reader. */
mesh.ConstructFromMeshReader(mesh_reader);
/* Next we instantiate an instance of our PDE we wish to solve. */
MyPde pde;
/* A set of boundary conditions are stored in a {{{BoundaryConditionsContainer}}}. The
* three template arguments are ELEMENT_DIM, SPACE_DIM and PROBLEM_DIM, the latter being
* the number of unknowns we are solving for. We have one unknown (ie u is a scalar, not
* a vector), so in this case {{{PROBLEM_DIM}}}=1. */
BoundaryConditionsContainer<2,2,1> bcc;
/* Defining the boundary conditions is the only particularly fiddly part of solving PDEs,
* unless they are very simple, such as u=0 on the boundary, which could be done
* as follows: */
//bcc.DefineZeroDirichletOnMeshBoundary(&mesh);
/* We want to specify u=0 on x=0 and y=0. To do this, we first create the boundary condition
* object saying what the value of the condition is at any particular point in space. Here
* we use the class `ConstBoundaryCondition`, a subclass of `AbstractBoundaryCondition` that
* yields the same constant value (0.0 here) everywhere it is used.
*
* Note that the object is allocated with `new`. The `BoundaryConditionsContainer` object deals
* with deleting its associated boundary condition objects. Note too that we could allocate a
* separate condition object for each boundary node, but using the same object where possible is
* more memory efficient.
*/
ConstBoundaryCondition<2>* p_zero_boundary_condition = new ConstBoundaryCondition<2>(0.0);
/* We then get a boundary node iterator from the mesh... */
TetrahedralMesh<2,2>::BoundaryNodeIterator iter = mesh.GetBoundaryNodeIteratorBegin();
/* ...and loop over the boundary nodes, getting the x and y values. */
while (iter < mesh.GetBoundaryNodeIteratorEnd())
{
double x = (*iter)->GetPoint()[0];
double y = (*iter)->GetPoint()[1];
/* If x=0 or y=0... */
if ((x==0) || (y==0))
{
/* ...associate the zero boundary condition created above with this boundary node
* ({{{*iter}}} being a pointer to a {{{Node<2>}}}).
*/
bcc.AddDirichletBoundaryCondition(*iter, p_zero_boundary_condition);
}
iter++;
}
/* Now we create Neumann boundary conditions for the ''surface elements'' on x=1 and y=1. Note that
* Dirichlet boundary conditions are defined on nodes, whereas Neumann boundary conditions are
* defined on surface elements. Note also that the natural boundary condition statement for this
* PDE is (D grad u).n = g(x) (where n is the outward-facing surface normal), and g(x) is a prescribed
* function, ''not'' something like du/dn=g(x). Hence the boundary condition we are specifying is
* (D grad u).n = 0.
*
* '''Important note for 1D:''' This means that if we were solving 2u,,xx,,=f(x) in 1D, and
* wanted to specify du/dx=1 on the LHS boundary, the Neumann boundary value we have to specify is
* -2, as n=-1 (outward facing normal) so (D gradu).n = -2 when du/dx=1.
*
* To define Neumann bcs, we reuse the zero boundary condition object defined above, but apply it
* at surface elements. We loop over these using another iterator provided by the mesh class.
*/
TetrahedralMesh<2,2>::BoundaryElementIterator surf_iter
= mesh.GetBoundaryElementIteratorBegin();
while (surf_iter != mesh.GetBoundaryElementIteratorEnd())
{
/* Get the x and y values of any node (here, the 0th) in the element. */
unsigned node_index = (*surf_iter)->GetNodeGlobalIndex(0);
double x = mesh.GetNode(node_index)->GetPoint()[0];
double y = mesh.GetNode(node_index)->GetPoint()[1];
/* If x=1 or y=1... */
if ( (fabs(x-1.0) < 1e-6) || (fabs(y-1.0) < 1e-6) )
{
/* ...associate the boundary condition with the surface element. */
bcc.AddNeumannBoundaryCondition(*surf_iter, p_zero_boundary_condition);
}
/* Finally increment the iterator. */
surf_iter++;
}
/* Next we define the solver of the PDE.
* To solve an {{{AbstractLinearEllipticPde}}} (which is the type of PDE {{{MyPde}}} is),
* we use a {{{SimpleLinearEllipticSolver}}}. The solver, again templated over
* {{{ELEMENT_DIM}}} and {{{SPACE_DIM}}}, needs to be given (pointers to) the mesh,
* pde and boundary conditions.
*/
SimpleLinearEllipticSolver<2,2> solver(&mesh, &pde, &bcc);
/* To solve, just call {{{Solve()}}}. A PETSc vector is returned. */
Vec result = solver.Solve();
/* It is a pain to access the individual components of a PETSc vector, even when running only on
* one process. A helper class called {{{ReplicatableVector}}} has been created. Create
* an instance of one of these, using the PETSc {{{Vec}}} as the data. The ''i''th
* component of {{{result}}} can now be obtained by simply doing {{{result_repl[i]}}}.
*/
ReplicatableVector result_repl(result);
/* Let us write out the solution to a file. To do this, create an
* {{{OutputFileHandler}}}, passing in the directory we want files written to.
* This is relative to the directory defined by the CHASTE_TEST_OUTPUT environment
* variable - usually `/tmp/$USER/testoutput`. Note by default the output directory
* passed in is emptied by this command. To avoid this, {{{false}}} can be passed in as a second
* parameter.
*/
OutputFileHandler output_file_handler("TestSolvingLinearPdeTutorial");
/* Create an {{{out_stream}}}, which is a stream to a particular file. An {{{out_stream}}}
* is a smart pointer to a `std::ofstream`. */
out_stream p_file = output_file_handler.OpenOutputFile("linear_solution.txt");
/* Loop over the entries of the solution. */
for (unsigned i=0; i<result_repl.GetSize(); i++)
{
/* Get the x and y-values of the node corresponding to this entry. The method
* {{{GetNode}}} on the mesh class returns a pointer to a {{{Node}}}. */
double x = mesh.GetNode(i)->rGetLocation()[0];
double y = mesh.GetNode(i)->rGetLocation()[1];
/* Get the computed solution at this node from the {{{ReplicatableVector}}}. */
double u = result_repl[i];
/* Finally, write x, y and u to the output file. The solution could then be
* visualised in (eg) matlab, using the commands:
* {{{sol=load('linear_solution.txt'); plot3(sol(:,1),sol(:,2),sol(:,3),'.');}}}*/
(*p_file) << x << " " << y << " " << u << "\n";
}
/* All PETSc {{{Vec}}}s should be destroyed when they are no longer needed, or you will have a memory leak. */
PetscTools::Destroy(result);
}
// 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
}
}
// test 2D problem - takes a long time to run.
// solution is incorrect to specified tolerance.
void xTestSimpleLinearParabolicSolver2DNeumannWithSmallTimeStepAndFineMesh()
{
// Create mesh from mesh reader
FemlabMeshReader<2,2> mesh_reader("mesh/test/data/",
"femlab_fine_square_nodes.dat",
"femlab_fine_square_elements.dat",
"femlab_fine_square_edges.dat");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Instantiate PDE object
HeatEquation<2> pde;
// Boundary conditions - zero dirichlet on boundary;
BoundaryConditionsContainer<2,2,1> bcc;
TetrahedralMesh<2,2>::BoundaryNodeIterator iter = mesh.GetBoundaryNodeIteratorBegin();
while (iter != mesh.GetBoundaryNodeIteratorEnd())
{
double x = (*iter)->GetPoint()[0];
double y = (*iter)->GetPoint()[1];
ConstBoundaryCondition<2>* p_dirichlet_boundary_condition =
new ConstBoundaryCondition<2>(x);
if (fabs(y) < 0.01)
{
bcc.AddDirichletBoundaryCondition(*iter, p_dirichlet_boundary_condition);
}
if (fabs(y - 1.0) < 0.01)
{
bcc.AddDirichletBoundaryCondition(*iter, p_dirichlet_boundary_condition);
}
if (fabs(x) < 0.01)
{
bcc.AddDirichletBoundaryCondition(*iter, p_dirichlet_boundary_condition);
}
iter++;
}
TetrahedralMesh<2,2>::BoundaryElementIterator surf_iter = mesh.GetBoundaryElementIteratorBegin();
ConstBoundaryCondition<2>* p_neumann_boundary_condition =
new ConstBoundaryCondition<2>(1.0);
while (surf_iter != mesh.GetBoundaryElementIteratorEnd())
{
int node = (*surf_iter)->GetNodeGlobalIndex(0);
double x = mesh.GetNode(node)->GetPoint()[0];
if (fabs(x - 1.0) < 0.01)
{
bcc.AddNeumannBoundaryCondition(*surf_iter, p_neumann_boundary_condition);
}
surf_iter++;
}
// Solver
SimpleLinearParabolicSolver<2,2> solver(&mesh,&pde,&bcc);
// Initial condition u(0,x,y) = sin(0.5*M_PI*x)*sin(M_PI*y)+x
std::vector<double> init_cond(mesh.GetNumNodes());
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
double x = mesh.GetNode(i)->GetPoint()[0];
double y = mesh.GetNode(i)->GetPoint()[1];
init_cond[i] = sin(0.5*M_PI*x)*sin(M_PI*y)+x;
}
Vec initial_condition = PetscTools::CreateVec(init_cond);
double t_end = 0.1;
solver.SetTimes(0, t_end);
solver.SetTimeStep(0.001);
solver.SetInitialCondition(initial_condition);
Vec result = solver.Solve();
ReplicatableVector result_repl(result);
// Check solution is u = e^{-5/4*M_PI*M_PI*t} sin(0.5*M_PI*x)*sin(M_PI*y)+x, t=0.1
for (unsigned i=0; i<result_repl.GetSize(); i++)
{
double x = mesh.GetNode(i)->GetPoint()[0];
double y = mesh.GetNode(i)->GetPoint()[1];
double u = exp((-5/4)*M_PI*M_PI*t_end) * sin(0.5*M_PI*x) * sin(M_PI*y) + x;
TS_ASSERT_DELTA(result_repl[i], u, 0.001);
}
PetscTools::Destroy(result);
PetscTools::Destroy(initial_condition);
}
/**
* Simple Parabolic PDE u' = del squared u
*
* With u = x on 5 boundaries of the unit cube, and
* u_n = 1 on the x face of the cube.
*
* Subject to the initial condition
* u(0,x,y,z)=sin( PI x)sin( PI y)sin( PI z) + x
*/
void TestSimpleLinearParabolicSolver3DNeumannOnCoarseMesh()
{
// Create mesh from mesh reader
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Instantiate PDE object
HeatEquation<3> pde;
// Boundary conditions
BoundaryConditionsContainer<3,3,1> bcc;
TetrahedralMesh<3,3>::BoundaryNodeIterator iter = mesh.GetBoundaryNodeIteratorBegin();
while (iter != mesh.GetBoundaryNodeIteratorEnd())
{
double x = (*iter)->GetPoint()[0];
double y = (*iter)->GetPoint()[1];
double z = (*iter)->GetPoint()[2];
if ((fabs(y) < 0.01) || (fabs(y - 1.0) < 0.01) ||
(fabs(x) < 0.01) ||
(fabs(z) < 0.01) || (fabs(z - 1.0) < 0.01) )
{
ConstBoundaryCondition<3>* p_dirichlet_boundary_condition =
new ConstBoundaryCondition<3>(x);
bcc.AddDirichletBoundaryCondition(*iter, p_dirichlet_boundary_condition);
}
iter++;
}
TetrahedralMesh<3,3>::BoundaryElementIterator surf_iter = mesh.GetBoundaryElementIteratorBegin();
ConstBoundaryCondition<3>* p_neumann_boundary_condition =
new ConstBoundaryCondition<3>(1.0);
while (surf_iter != mesh.GetBoundaryElementIteratorEnd())
{
int node = (*surf_iter)->GetNodeGlobalIndex(0);
double x = mesh.GetNode(node)->GetPoint()[0];
if (fabs(x - 1.0) < 0.01)
{
bcc.AddNeumannBoundaryCondition(*surf_iter, p_neumann_boundary_condition);
}
surf_iter++;
}
// Solver
SimpleLinearParabolicSolver<3,3> solver(&mesh,&pde,&bcc);
// Initial condition u(0,x,y) = sin(0.5*PI*x)*sin(PI*y)+x
Vec initial_condition = PetscTools::CreateVec(mesh.GetNumNodes());
double* p_initial_condition;
VecGetArray(initial_condition, &p_initial_condition);
int lo, hi;
VecGetOwnershipRange(initial_condition, &lo, &hi);
for (int global_index = lo; global_index < hi; global_index++)
{
int local_index = global_index - lo;
double x = mesh.GetNode(global_index)->GetPoint()[0];
double y = mesh.GetNode(global_index)->GetPoint()[1];
double z = mesh.GetNode(global_index)->GetPoint()[2];
p_initial_condition[local_index] = sin(0.5*M_PI*x)*sin(M_PI*y)*sin(M_PI*z)+x;
}
VecRestoreArray(initial_condition, &p_initial_condition);
solver.SetTimes(0, 0.1);
solver.SetTimeStep(0.01);
solver.SetInitialCondition(initial_condition);
Vec result = solver.Solve();
// Check result
double* p_result;
VecGetArray(result, &p_result);
// Solution should be u = e^{-5/2*PI*PI*t} sin(0.5*PI*x)*sin(PI*y)*sin(PI*z)+x, t=0.1
for (int global_index = lo; global_index < hi; global_index++)
{
int local_index = global_index - lo;
double x = mesh.GetNode(global_index)->GetPoint()[0];
double y = mesh.GetNode(global_index)->GetPoint()[1];
double z = mesh.GetNode(global_index)->GetPoint()[2];
double u = exp((-5/2)*M_PI*M_PI*0.1) * sin(0.5*M_PI*x) * sin(M_PI*y)* sin(M_PI*z) + x;
TS_ASSERT_DELTA(p_result[local_index], u, u*0.15);
}
VecRestoreArray(result, &p_result);
PetscTools::Destroy(initial_condition);
PetscTools::Destroy(result);
}