本文整理汇总了C++中TetrahedralMesh类的典型用法代码示例。如果您正苦于以下问题:C++ TetrahedralMesh类的具体用法?C++ TetrahedralMesh怎么用?C++ TetrahedralMesh使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了TetrahedralMesh类的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: TestTranslation2DWithUblas
void TestTranslation2DWithUblas()
{
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/2D_0_to_1mm_200_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
double volume = mesh.GetVolume();
double surface_area = mesh.GetSurfaceArea();
Node<2>* p_node1 = mesh.GetNode(36);
ChastePoint<2> point1 = p_node1->GetPoint();
Node<2>* p_node2 = mesh.GetNode(23);
ChastePoint<2> point2 = p_node2->GetPoint();
c_vector<double, 2> old_location1 = point1.rGetLocation();
c_vector<double, 2> old_location2 = point2.rGetLocation();
// Set translation Vector
c_vector<double, 2> trans_vec;
trans_vec(0) = 2.0;
trans_vec(1) = 2.0;
// Translate
mesh.Translate(trans_vec);
c_vector<double, 2> new_location1 = point1.rGetLocation();
c_vector<double, 2> new_location2 = point2.rGetLocation();
// Check Volume and Surface Area are invariant
TS_ASSERT_DELTA(mesh.GetVolume(), volume, 1e-6);
TS_ASSERT_DELTA(mesh.GetSurfaceArea(), surface_area, 1e-6);
// Spot check a couple of nodes
TS_ASSERT_DELTA(inner_prod(new_location1-old_location1, trans_vec), 0, 1e-6);
TS_ASSERT_DELTA(inner_prod(new_location2-old_location2, trans_vec), 0, 1e-6);
}
示例2: TestRefreshMeshByScaling
void TestRefreshMeshByScaling()
{
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_DELTA(mesh.GetVolume(), 1.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetSurfaceArea(), 6.0, 1e-6);
// Change coordinates
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
Node<3>* p_node = mesh.GetNode(i);
ChastePoint<3> point = p_node->GetPoint();
point.SetCoordinate(0, point[0]*2.0);
point.SetCoordinate(1, point[1]*2.0);
point.SetCoordinate(2, point[2]*2.0);
p_node->SetPoint(point);
}
mesh.RefreshMesh();
TS_ASSERT_DELTA(mesh.GetVolume(), 8.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetSurfaceArea(), 24.0, 1e-6);
}
示例3: TestBathIntracellularStimulation
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);
}
示例4: TestCoverage3d
void TestCoverage3d()
{
HeartConfig::Instance()->SetSimulationDuration(0.1); //ms
HeartConfig::Instance()->SetUseStateVariableInterpolation(true);
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.005, 0.01, 0.1);
TetrahedralMesh<3,3> mesh;
mesh.ConstructRegularSlabMesh(0.02, 0.02, 0.02, 0.02);
ZeroStimulusCellFactory<CellLuoRudy1991FromCellML,3> cell_factory;
MonodomainProblem<3> monodomain_problem( &cell_factory );
monodomain_problem.SetMesh(&mesh);
monodomain_problem.Initialise();
monodomain_problem.Solve();
}
示例5: TestRemeshSingleBranch
void TestRemeshSingleBranch() throw(Exception)
{
//Load a single branch mesh file
TrianglesMeshReader<1,3> reader("mesh/test/data/1D_in_3D_0_to_1mm_10_elements");
TetrahedralMesh<1,3> mesh;
mesh.ConstructFromMeshReader(reader);
//We need to add some attributes to the mesh
for (TetrahedralMesh<1,3>::NodeIterator iter = mesh.GetNodeIteratorBegin();
iter != mesh.GetNodeIteratorEnd();
++iter)
{
iter->AddNodeAttribute(0.05);
}
//Create remesher object
AirwayRemesher remesher(mesh, 0u);
//Check intermediate elements are removed. Poiseuille resistance of the branch is
// C*0.1/((0.05^4) = C*1.6 * 10^4
MutableMesh<1,3> output_mesh_one;
remesher.Remesh(output_mesh_one, 1e5); //With this tolerance all intermediate nodes should be removed.
TS_ASSERT_EQUALS(output_mesh_one.GetNumNodes(), 2u);
TS_ASSERT_EQUALS(output_mesh_one.GetNumElements(), 1u);
TS_ASSERT_DELTA(output_mesh_one.GetElement(0)->GetAttribute(), 0.05, 1e-6);
MutableMesh<1,3> output_mesh_two;
remesher.Remesh(output_mesh_two, 0.8e4); //With this tolerance there should be one intermediate node.
TS_ASSERT_EQUALS(output_mesh_two.GetNumNodes(), 3u);
TS_ASSERT_EQUALS(output_mesh_two.GetNumElements(), 2u);
TS_ASSERT_DELTA(output_mesh_two.GetElement(0)->GetAttribute(), 0.05, 1e-6);
MutableMesh<1,3> output_mesh_three;
remesher.Remesh(output_mesh_three, 1.6e3); //With this tolerance there should be ten elements.
TS_ASSERT_EQUALS(output_mesh_three.GetNumNodes(), 11u);
TS_ASSERT_EQUALS(output_mesh_three.GetNumElements(), 10u);
TS_ASSERT_DELTA(output_mesh_three.GetElement(0)->GetAttribute(), 0.05, 1e-6);
TS_ASSERT_DELTA(output_mesh_three.GetElement(5)->GetAttribute(), 0.05, 1e-6);
//To visualise
//VtkMeshWriter<1,3> writer("TestAirwayRemesher", "1D_remeshed");
//writer.WriteFilesUsingMesh(output_mesh_three);
}
示例6: TestElementReactanceAndInertance
void TestElementReactanceAndInertance()
{
TetrahedralMesh<1,3> mesh;
TrianglesMeshReader<1,3> mesh_reader("mesh/test/data/y_branch_3d_mesh");
mesh.ConstructFromMeshReader(mesh_reader);
SimpleImpedanceProblem problem(mesh, 0u);
problem.SetRho(M_PI);
problem.SetMu(M_PI);
double l = 2.0;
double r = 2.0;
TS_ASSERT_DELTA(problem.CalculateElementResistance(r, l), 8*l/(r*r*r*r), 1e-6);
TS_ASSERT_DELTA(problem.CalculateElementInertance(r, l), l/(r*r), 1e-6);
}
示例7: TestMultipleFrequencies
void TestMultipleFrequencies() throw(Exception)
{
TetrahedralMesh<1,3> mesh;
//TrianglesMeshReader<1,3> mesh_reader("mesh/test/data/y_branch_3d_mesh");
TrianglesMeshReader<1,3> mesh_reader("lung/test/data/TestSubject002");
mesh.ConstructFromMeshReader(mesh_reader);
//Scale all radii by 0.7 to give an FRC equivalent lung
for (TetrahedralMesh<1,3>::NodeIterator node_iter = mesh.GetNodeIteratorBegin();
node_iter != mesh.GetNodeIteratorEnd();
++node_iter)
{
node_iter->rGetNodeAttributes()[0] *= 0.7;
}
std::vector<double> test_frequencies;
test_frequencies.push_back(1.0);
test_frequencies.push_back(2.0);
test_frequencies.push_back(3.0);
test_frequencies.push_back(5.0);
test_frequencies.push_back(10.0);
test_frequencies.push_back(20.0);
test_frequencies.push_back(30.0);
SimpleImpedanceProblem problem(mesh, 0u);
problem.SetMeshInMilliMetres();
problem.SetFrequencies(test_frequencies); //Set & get frequencies for coverage
std::vector<double>& freqs = problem.rGetFrequencies();
TS_ASSERT_EQUALS(freqs.size(), 7u);
problem.Solve();
std::vector<std::complex<double> > impedances = problem.rGetImpedances();
TS_ASSERT_EQUALS(impedances.size(), 7u);
//These are hard coded from previous runs, but are as expected for
//a patient with moderate to severe asthma
TS_ASSERT_DELTA(real(impedances[0])*1e-3/98, 8.45, 1e-2);
TS_ASSERT_DELTA(imag(impedances[0])*1e-3/98, -3.65, 1e-2);
TS_ASSERT_DELTA(real(impedances[6])*1e-3/98, 5.77, 1e-2);
TS_ASSERT_DELTA(imag(impedances[6])*1e-3/98, 4.12, 1e-2);
}
示例8: RunBenchMark
void RunBenchMark(double h, double dt, double endTime, bool useSvi)
{
TetrahedralMesh<3,3> mesh;
mesh.ConstructRegularSlabMesh(h, 2.0, 0.7, 0.3);
std::stringstream output_dir;
output_dir << "Benchmark" << "_h" << h << "_dt" << dt;
HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
HeartConfig::Instance()->SetOutputFilenamePrefix("results");
HeartConfig::Instance()->SetSimulationDuration(endTime); //ms
HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.005, dt, 0.1);
HeartConfig::Instance()->SetSurfaceAreaToVolumeRatio(1400); // 1400 1/cm
HeartConfig::Instance()->SetCapacitance(1); // 1uF/cm^2
HeartConfig::Instance()->SetVisualizeWithMeshalyzer(false);
// The Chaste results for the benchmark paper use STATE-VARIABLE INTERPOLATION switched on
// (see comments above)
HeartConfig::Instance()->SetUseStateVariableInterpolation(useSvi);
// Regarding the second paper described above, to run the simulations with ICI, comment out the
// above line. To run the simulation with operator splitting, or with (full) mass-lumping,
// comment out the above SVI line and uncomment one of the below. (Note: half-lumping is not
// available).
//HeartConfig::Instance()->SetUseMassLumping(true); // what is described as full-lumping in this paper
//HeartConfig::Instance()->SetUseReactionDiffusionOperatorSplitting(true);
double long_conductance = 0.17 * 0.62/(0.17+0.62) * 10; // harmonic mean of 0.17, 0.62 S/m converted to mS/cm
double trans_conductance = 0.019 * 0.24/(0.019+0.24) * 10; // harmonic mean of 0.019,0.24 S/m converted to mS/cm
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(long_conductance, trans_conductance, trans_conductance));
BenchmarkCellFactory cell_factory;
MonodomainProblem<3> problem( &cell_factory );
problem.SetMesh(&mesh);
problem.Initialise();
problem.SetWriteInfo();
problem.Solve();
}
示例9: TestAcinarImpedance
void TestAcinarImpedance() throw(Exception)
{
TetrahedralMesh<1,3> mesh;
TrianglesMeshReader<1,3> mesh_reader("mesh/test/data/y_branch_3d_mesh");
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_THROWS_CONTAINS(SimpleImpedanceProblem(mesh, 1u), "Outlet node is not a boundary node");
SimpleImpedanceProblem problem(mesh, 0u);
problem.rGetMesh(); //for coverage
unsigned node_index = 3; //Arbitrary terminal node
problem.SetElastance(2*M_PI/2.0);
TS_ASSERT_DELTA(real(problem.CalculateAcinusImpedance(mesh.GetNode(node_index), 0.0)), 0.0, 1e-6);
TS_ASSERT_DELTA(real(problem.CalculateAcinusImpedance(mesh.GetNode(node_index), 1.0)), 0.0, 1e-6);
TS_ASSERT_DELTA(imag(problem.CalculateAcinusImpedance(mesh.GetNode(node_index), 1.0)), -1.0, 1e-6);
}
示例10: TestGetSingleRadiusVector
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);
}
示例11: TestSimpleLinearParabolicSolver3DZeroDirich
/**
* Simple Parabolic PDE u' = del squared u
*
* With u = 0 on the boundaries of the unit cube. Subject to the initial
* condition u(0,x,y,z)=sin( PI x)sin( PI y)sin( PI z).
*/
void TestSimpleLinearParabolicSolver3DZeroDirich()
{
// read mesh on [0,1]x[0,1]x[0,1]
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 - zero dirichlet everywhere on boundary
BoundaryConditionsContainer<3,3,1> bcc;
bcc.DefineZeroDirichletOnMeshBoundary(&mesh);
// Solver
SimpleLinearParabolicSolver<3,3> solver(&mesh,&pde,&bcc);
/*
* Choose initial condition sin(x*pi)*sin(y*pi)*sin(z*pi) as
* this is an eigenfunction of the heat equation.
*/
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];
double z = mesh.GetNode(i)->GetPoint()[2];
init_cond[i] = sin(x*M_PI)*sin(y*M_PI)*sin(z*M_PI);
}
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^{-3*t*pi*pi} sin(x*pi)*sin(y*pi)*sin(z*pi), 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 z = mesh.GetNode(i)->GetPoint()[2];
double u = exp(-3*t_end*M_PI*M_PI)*sin(x*M_PI)*sin(y*M_PI)*sin(z*M_PI);
TS_ASSERT_DELTA(result_repl[i], u, 0.1);
}
PetscTools::Destroy(initial_condition);
PetscTools::Destroy(result);
}
示例12: TestProblemChecksUsingBathWithMultipleBathConductivities
void TestProblemChecksUsingBathWithMultipleBathConductivities()
{
TrianglesMeshReader<2,2> reader("mesh/test/data/2D_0_to_1mm_400_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(reader);
std::set<unsigned> tissue_ids;
tissue_ids.insert(0);
std::set<unsigned> bath_ids;
bath_ids.insert(1);
bath_ids.insert(2); // non-default identifier!
HeartConfig::Instance()->SetTissueAndBathIdentifiers(tissue_ids, bath_ids);
BathCellFactory<2> cell_factory( 0.0, Create_c_vector(0.0, 0.0) );
BidomainProblem<2> bidomain_problem( &cell_factory ); // non-bath problem, despite specifying bath stuff above!
bidomain_problem.SetMesh( &mesh );
TS_ASSERT_THROWS_THIS( bidomain_problem.Initialise() , "User has set bath identifiers, but the BidomainProblem isn't expecting a bath. Did you mean to use BidomainProblem(..., true)? Or alternatively, BidomainWithBathProblem(...)?");
}
示例13: EXCEPTION
std::vector<unsigned> NonlinearElasticityTools<DIM>::GetNodesByComponentValue(TetrahedralMesh<DIM,DIM>& rMesh,
unsigned component,
double value)
{
std::vector<unsigned> fixed_nodes;
double tol = 1e-8;
for (unsigned i=0; i<rMesh.GetNumNodes(); i++)
{
if ( fabs(rMesh.GetNode(i)->rGetLocation()[component] - value)<1e-8)
{
fixed_nodes.push_back(i);
}
}
if (fixed_nodes.size() == 0)
{
EXCEPTION("Could not find any nodes on requested surface (note: tolerance = "<<tol<<")");
}
return fixed_nodes;
}
示例14: TestDefineZeroDirichletOnMeshBoundary
void TestDefineZeroDirichletOnMeshBoundary()
{
// 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;
bcc.DefineZeroDirichletOnMeshBoundary(&mesh);
// Check boundary nodes have the right condition
for (int i=0; i<4; i++)
{
double value = bcc.GetDirichletBCValue(mesh.GetNode(i));
TS_ASSERT_DELTA(value, 0.0, 1e-12);
}
// Check non-boundary node has no condition
TS_ASSERT(!bcc.HasDirichletBoundaryCondition(mesh.GetNode(4)));
}
示例15: TestMeshalyzerConversionLotsOfVariables
// This test covers the case when the hdf5 file contains more than 3 variables
void TestMeshalyzerConversionLotsOfVariables() throw(Exception)
{
std::string output_dir = "TestHdf5Converters_TestMeshalyzerConversionLotsOfVariables";
/*
* Firstly, copy the .h5 file to CHASTE_TEST_OUTPUT/TestHdf5ToMeshalyzerConverter,
* as that is where the reader reads from.
*/
CopyToTestOutputDirectory("heart/test/data/many_variables/many_variables.h5", output_dir);
TrianglesMeshReader<1,1> mesh_reader("heart/test/data/many_variables/1D_65_elements");
TetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Convert
Hdf5ToMeshalyzerConverter<1,1> converter(FileFinder(output_dir, RelativeTo::ChasteTestOutput),
"many_variables", &mesh, true);
std::vector<std::string> variable_names;
variable_names.push_back("V");
variable_names.push_back("I_ks");
variable_names.push_back("I_kr");
variable_names.push_back("I_Ca_tot");
variable_names.push_back("I_tot");
variable_names.push_back("I_Na_tot");
std::string test_output_directory = OutputFileHandler::GetChasteTestOutputDirectory();
for (unsigned i=0; i<variable_names.size(); i++)
{
// Compare the results files
FileComparison(test_output_directory + "/" + output_dir + "/output/many_variables_"
+ variable_names[i] + ".dat",
"heart/test/data/many_variables/many_variables_"
+ variable_names[i] + ".dat").CompareFiles();
}
// Compare the time information file
FileComparison(test_output_directory + output_dir + "/output/many_variables_times.info",
"heart/test/data/many_variables/many_variables_times.info").CompareFiles();
}