C++ DistributedTetrahedralMesh::GetNode方法代码示例

    void TestSimpleSimulation() throw(Exception)
    {
        /*Simulation parameters*/
        HeartConfig::Instance()->SetSimulationDuration(0.7); //ms (falls over after this)
        HeartConfig::Instance()->SetUseAbsoluteTolerance(1e-6);
        //HeartConfig::Instance()->SetOdeTimeStep(0.01);

        const double width = 0.1;
        const double height = 0.1;
        const double depth = 0.1;

        const unsigned num_elem_x = 8;
        const double space_step = width/num_elem_x;

        /* Make the mesh*/
        DistributedTetrahedralMesh<3,3> mesh;
        mesh.ConstructRegularSlabMesh(space_step, width, height, depth);

        /*Create a cell factory of the type we defined above. */
        GeneralPlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 3> cell_factory(num_elem_x, width);

        /* monodomain problem class using (a pointer to) the cell factory */
        BidomainProblem<3> problem( &cell_factory );
        problem.SetMesh(&mesh);

        /*
        * HOW_TO_TAG Cardiac/Problem definition
        * Set discrete '''cuboid''' areas to have heterogeneous (intra- and/or extra-cellular) conductivity tensors.
        */
        std::vector<ChasteCuboid<3> > input_areas;
        std::vector< c_vector<double,3> > intra_conductivities;
        std::vector< c_vector<double,3> > extra_conductivities;
        ChastePoint<3> corner_a(width/2, 0, 0);
        ChastePoint<3> corner_b(width, height, depth);

        input_areas.push_back(ChasteCuboid<3> (corner_a, corner_b));
        //within the cuboid
        intra_conductivities.push_back( Create_c_vector(0.1, 0.1, 0.1) );
        extra_conductivities.push_back( Create_c_vector(0.0, 0.0, 0.0) );
        //This test should *fail* if you comment out the following line
        //(which blocks conductivity on the RHS of the slab).
        HeartConfig::Instance()->SetConductivityHeterogeneities(input_areas, intra_conductivities, extra_conductivities);

        //elsewhere
        HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.2, 1.2, 1.2));
        HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(1.2, 1.2, 1.2));

        /* set  parameters*/
        // HeartConfig::Instance()->SetSurfaceAreaToVolumeRatio(1.0);
        // HeartConfig::Instance()->SetCapacitance(1.0);

         /* Output Directory and prefix (for the hdf5 file), relative to CHASTE_TEST_OUTPUT*/
        HeartConfig::Instance()->SetOutputDirectory("slab_results_het_halfcond");
        HeartConfig::Instance()->SetOutputFilenamePrefix("Slab_small");

        /* Initialise the problem*/
        problem.Initialise();

        /* Solve the PDE monodomain equaion*/
        problem.Solve();

        ReplicatableVector voltage_replicated(problem.GetSolution());
        TS_ASSERT_EQUALS(mesh.GetNumNodes() * 2, voltage_replicated.GetSize());
        unsigned lo, hi;
        lo = mesh.GetDistributedVectorFactory()->GetLow();
        hi = mesh.GetDistributedVectorFactory()->GetHigh();

        for (unsigned i=lo; i<hi; i++)
        {
            double x = mesh.GetNode(i)->rGetLocation()[0];
            if (x<width/2)
            {
                 //Left side is stimulated
                 TS_ASSERT_LESS_THAN(-71.0,voltage_replicated[2 * i]);
            }
            else if (x>width/2)
            {
                //Right side is blocked
                TS_ASSERT_LESS_THAN(voltage_replicated[2 * i],-82.0);
            }
        }
    }

    void TestConductionVelocityConvergesFasterWithSvi1d()
    {
        double h[3] = {0.001,0.01,0.02};
        unsigned probe_node_index[3] = {300, 30, 15};
        unsigned number_of_nodes[3] = {1001, 101, 51};
        std::vector<double> conduction_vel_ici(3);
        std::vector<double> conduction_vel_svi(3);

        ReplicatableVector final_voltage_ici;
        ReplicatableVector final_voltage_svi;

        //HeartConfig::Instance()->SetUseRelativeTolerance(1e-8);
        HeartConfig::Instance()->SetSimulationDuration(4.0); //ms
        HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.01, 0.01, 0.01);

        for (unsigned i=0; i<3; i++)
        {
            // ICI - ionic current interpolation - the default
            {
                DistributedTetrahedralMesh<1,1> mesh;
                mesh.ConstructRegularSlabMesh(h[i], 1.0);
                TS_ASSERT_EQUALS(mesh.GetNumNodes(), number_of_nodes[i]);

                //Double check (for later) that the indexing is as expected
                if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal( probe_node_index[i] ))
                {
                    TS_ASSERT_DELTA(mesh.GetNode( probe_node_index[i] )->rGetLocation()[0], 0.3, 1e-8);
                }
                std::stringstream output_dir;
                output_dir << "MonodomainIci_" << h[i];
                HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
                HeartConfig::Instance()->SetOutputFilenamePrefix("results");

                // need to have this for i=1,2 cases!!
                HeartConfig::Instance()->SetUseStateVariableInterpolation(false);

                BlockCellFactory<1> cell_factory;
                MonodomainProblem<1> monodomain_problem( &cell_factory );
                monodomain_problem.SetMesh(&mesh);
                monodomain_problem.Initialise();

                monodomain_problem.Solve();

                final_voltage_ici.ReplicatePetscVector(monodomain_problem.GetSolution());

//// see #1633
//// end time needs to be increased for these (say, to 7ms)
//                Hdf5DataReader simulation_data(OutputFileHandler::GetChasteTestOutputDirectory() + output_dir.str(),
//                                               "results", false);
//                PropagationPropertiesCalculator ppc(&simulation_data);
//                unsigned node_at_0_04 = (unsigned)round(0.04/h[i]);
//                unsigned node_at_0_40 = (unsigned)round(0.40/h[i]);
//                assert(fabs(mesh.GetNode(node_at_0_04)->rGetLocation()[0]-0.04)<1e-6);
//                assert(fabs(mesh.GetNode(node_at_0_40)->rGetLocation()[0]-0.40)<1e-6);
//                conduction_vel_ici[i] = ppc.CalculateConductionVelocity(node_at_0_04,node_at_0_40,0.36);
//                std::cout << "conduction_vel_ici = " << conduction_vel_ici[i] << "\n";
            }

            // SVI - state variable interpolation
            {
                DistributedTetrahedralMesh<1,1> mesh;
                mesh.ConstructRegularSlabMesh(h[i], 1.0);

                //Double check (for later) that the indexing is as expected
                if (mesh.GetDistributedVectorFactory()->IsGlobalIndexLocal( probe_node_index[i] ))
                {
                    TS_ASSERT_DELTA(mesh.GetNode( probe_node_index[i] )->rGetLocation()[0], 0.3, 1e-8);
                }
                std::stringstream output_dir;
                output_dir << "MonodomainSvi_" << h[i];
                HeartConfig::Instance()->SetOutputDirectory(output_dir.str());
                HeartConfig::Instance()->SetOutputFilenamePrefix("results");

                HeartConfig::Instance()->SetUseStateVariableInterpolation();

                BlockCellFactory<1> cell_factory;
                MonodomainProblem<1> monodomain_problem( &cell_factory );
                monodomain_problem.SetMesh(&mesh);
                monodomain_problem.Initialise();

                monodomain_problem.Solve();

                final_voltage_svi.ReplicatePetscVector(monodomain_problem.GetSolution());

//                Hdf5DataReader simulation_data(OutputFileHandler::GetChasteTestOutputDirectory() + output_dir.str(),
//                                               "results", false);
//                PropagationPropertiesCalculator ppc(&simulation_data);
//                unsigned node_at_0_04 = (unsigned)round(0.04/h[i]);
//                unsigned node_at_0_40 = (unsigned)round(0.40/h[i]);
//                assert(fabs(mesh.GetNode(node_at_0_04)->rGetLocation()[0]-0.04)<1e-6);
//                assert(fabs(mesh.GetNode(node_at_0_40)->rGetLocation()[0]-0.40)<1e-6);
//                conduction_vel_svi[i] = ppc.CalculateConductionVelocity(node_at_0_04,node_at_0_40,0.36);
//                std::cout << "conduction_vel_svi = " << conduction_vel_svi[i] << "\n";
            }

            if (i==0) // finest mesh
            {
                for (unsigned j=0; j<final_voltage_ici.GetSize(); j++)
                {
                    // visually checked they agree at this mesh resolution, and chosen tolerance from results
//.........这里部分代码省略.........

    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));
//.........这里部分代码省略.........