Application reference

Each source file apps/app_*.cc produces an executable with the app_ prefix removed. Debug targets append _debug. Applications read an explicit parameter-file path; when a file supports dimension dispatch, the dimension and space dimension entries select the template instantiation.

Executable	Entry point and problem	Dimensions or composition	Dependencies and input
liver_vascular	apps/app_liver_vascular.cc; surface-to-volume Domain and paired vascular growth	3D tissue with two rooted 1D-in-3D vessel trees	MPI, deal.II Gmsh API, VTK and simplex support; data/vascularization/liver.prm.in
poisson	apps/app_poisson.cc; PoissonSolver	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI; tutorials/poisson/poisson_2d.prm.in
poisson_adapter	apps/app_poisson_adapter.cc; PoissonSolver through LinearAdapter	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI; gtests/parameters/poisson_simple_2d.prm.in
elastic_static	apps/app_elastic_static.cc; ElasticStaticProblem	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI; tutorials/elastic_static/elastic_static.prm.in
elastic_static_adapter	apps/app_elastic_static_adapter.cc; ElasticStaticProblem through LinearAdapter	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI; gtests/parameters/elastic_static.prm.in
elastodynamics	apps/app_elastodynamics.cc; ElastodynamicsSolver	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI; tutorials/elastodynamics/strong_dirichlet.prm.in
elastodynamics_adapter	apps/app_elastodynamics_adapter.cc; ElastodynamicsSolver through IDAAdapter	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI and deal.II SUNDIALS; gtests/parameters/dynamic_purely_elastic.prm.in
reduced_poisson	apps/app_reduced_poisson.cc; ReducedPoisson	2/2 and 3/3 with reduced dimension 0 or 1; cross-section dimensions are checked by the application	MPI and deal.II VTK; tutorials/reduced_poisson/single_cylinder_3d.prm.in
lifted_poisson	apps/app_lifted_poisson.cc; LiftedPoisson with a modal constraint	Fixed 3D bulk plus 1D-in-3D representative	MPI; gtests/parameters/lifted_poisson.prm.in
lifted_elasticity	apps/app_lifted_elasticity.cc; LiftedElasticity with optional modal constraints	2/2 and 3/3 bulk meshes	MPI; gtests/parameters/lifted_elasticity_simplex.prm.in
coupled_poisson	apps/app_coupled_poisson.cc; 2D bulk and 1D embedded PoissonSolver with a multiplier Constraint	Fixed 2D bulk plus 1D-in-2D embedded field	MPI; tutorials/coupled_poisson/coupled_poisson.prm.in
coupled_poisson_elasticity	apps/app_coupled_poisson_elasticity.cc; 1D-in-3D PoissonSolver and 3D ElasticStaticProblem	Fixed 1D-in-3D pressure lift coupled to 3D elasticity	MPI; tutorials/coupled_poisson_elasticity/coupled_poisson_elasticity.prm.in
fiber_reinforced_elastodynamics	apps/app_fiber_reinforced_elastodynamics.cc; matrix ElastodynamicsSolver<dim,dim> and embedded line ElastodynamicsSolver<1,dim> with a multiplier constraint	2/2 and 3/3 matrix meshes with a 1D-in-dim fiber	MPI; tutorials/fiber_reinforced_elastodynamics/parameters.prm.in
fiber_reinforced_elasticity_freq	apps/app_fiber_reinforced_elasticity_freq.cc; additive harmonic reinforcement with independent or shared displacements through LinearAdapter	Root dimension selects reinforcement dimension; matrix dimension is space dimension. All 1 <= dim <= spacedim <= 3; reduced meshes lift to volumes, full-dimensional meshes use no lift	MPI; tutorials/fiber_reinforced_elasticity_freq/parameters.prm.in
metric_flow_x	apps/app_metric_flow_x.cc; MetricFlowX BloodFlowSystem<1,3> through IDAAdapter	Fixed 1D-in-3D	MPI, deal.II SUNDIALS, and MetricFlowX; gtests/parameters/metric_flow_x.prm.in
metric_flow_x_elastodynamics	apps/app_metric_flow_x_elastodynamics.cc; MetricFlowX and 3D Elastodynamics composed through weak terms and a multiplier constraint	Fixed 1D-in-3D flow and 3D wall	MPI, deal.II SUNDIALS, and MetricFlowX; tutorials/metric_flow_x_elastodynamics/two_way.prm.in
navier_stokes	apps/app_navier_stokes.cc; NavierStokesSolver	2/2, 3/3	MPI; uses IDAAdapter with deal.II SUNDIALS and the native solver path without it; tutorials/navier_stokes/transient_2d.prm.in
laplacian	apps/app_laplacian.cc; PoissonProblem	2/2, 2/3, 3/3	MPI; gtests/parameters/laplacian_simple.prm.in
elasticity	apps/app_elasticity.cc; ElasticityProblem	2/2, 2/3, 3/3	MPI; tutorials/elasticity/strong_dirichlet.prm
elasticity_freq	apps/app_elasticity_freq.cc; ElasticityFreqProblem	1/1, 1/2, 1/3, 2/2, 2/3, 3/3	MPI and Trilinos; frequency-domain amplitudes and phases
elasticity_explicit	apps/app_elasticity_explicit.cc; lumped-mass forward Euler elasticity	2/2, 2/3, 3/3	MPI and Trilinos; prms/prm_2d_euler_mms.prm
coupled_elasticity	apps/app_coupled_elasticity.cc; 3D tissue and 1D hemodynamics	3D tissue; command-line coupling controls	MPI, OpenMP, and lib1dsolver; enable with ENABLE_COUPLED_PROBLEMS
pseudocoupling1D	apps/app_pseudocoupling1D.cc; 3D tissue and 1D pseudo-coupling	3D tissue; five positional arguments	MPI, OpenMP, and lib1dsolver; enable with ENABLE_COUPLED_PROBLEMS

MetricFlowX executables are excluded from the build unless both MetricFlowX and deal.II SUNDIALS are available. The two lib1dsolver executables are built from their source files, but their functional code is enabled only when ENABLE_COUPLED_PROBLEMS is on and the library passes the dependency and RTTI link check. All other executables are part of the normal application target set. The running applications guide explains the parameter-file command format.

When Coral is installed, equivalent graph examples are installed under share/immersx/coral/examples. See the Coral backend guide for plugin selection, graph execution, and conditional coupled workflows.

Every mesh must contain a single physical reference-cell type. Select either triangles/tetrahedra or quadrilaterals/hexahedra for each mesh; mixed meshes are rejected. Simplex applications use the fully distributed backend and refine before distribution. The simplex examples below use one solve cycle; legacy convergence tables and post-distribution adaptive refinement remain available for hypercube meshes. See weak-term integration supports for reference-cell selection in Fields, weak terms, and constraints.

For elasticity_freq, select fullydistributed under Immersed Problem/Grid generation/Triangulation type when importing triangles or tetrahedra. FE degree selects FE_SimplexP on these meshes. Keep one refinement cycle; initial refinement happens before distribution. The generated gtests/parameters/elasticity_freq_simplex.prm provides a tetrahedral example with a nonzero affine displacement at a nonzero frequency.

For elasticity, import triangles or tetrahedra with fullydistributed under Immersed Problem/Grid generation. FE degree selects the corresponding simplex displacement element. Strong and weak Dirichlet conditions use the same reference-cell mapping as assembly and output. Use one refinement cycle; initial refinement is performed before distribution. Parsed convergence tables are available on hypercube meshes. The generated gtests/parameters/elasticity_simplex.prm is a forced quadratic example.

elasticity_explicit also accepts uniform simplex meshes with Immersed Problem/Grid generation/Triangulation type = fullydistributed. Set FE degree = 1: higher-degree simplex elements have zero or negative row-sum nodal masses and are rejected. The existing restriction against hanging nodes also applies. The generated gtests/parameters/elasticity_explicit_simplex.prm advances a freely translating body with nonzero forcing.

For laplacian, select fullydistributed under Immersed Problem/Domain/Triangulation type when importing simplex meshes. The assembled solver selects simplex elements from FE degree. Set the number of refinement cycles to one and use Domain/Initial refinement for refinement before distribution. Parsed convergence tables and the experimental compile-time matrix-free path require hypercube meshes. The generated gtests/parameters/laplacian_simplex.prm solves a forced quadratic problem.

For navier_stokes, import uniform triangle or tetrahedron meshes using Navier-Stokes/Domain/Triangulation type = fullydistributed. The velocity and pressure degrees select simplex Taylor-Hood elements; the pressure degree must remain smaller than the velocity degree. The native solver and IDA application path use the same reference-cell mapping and quadrature. gtests/parameters/navier_stokes_simplex.prm maintains a nonzero Poiseuille velocity with constant body force on a tetrahedral mesh.

For reduced_poisson, select fullydistributed under Reduced Poisson/Grid generation/Triangulation type and import a uniform simplex mesh. FE degree selects simplex bulk elements. Set one refinement cycle; initial refinement and local co-refinement take place before partitioning. The generated reduced_poisson_simplex_line_3d.prm and reduced_poisson_simplex_point_3d.prm under gtests/parameters provide quadratic checks with a Schur solver and nonzero Dirichlet data.

For lifted_poisson, select a fully distributed background and set Background space/Finite element = FE_SimplexP<3>(2) for quadratic tetrahedra. The representative line retains its one-dimensional element. Error diagnostics use the bulk mapping and reference-cell quadrature. The generated gtests/parameters/lifted_poisson_simplex.prm checks a nonzero quadratic solution and a zero multiplier.

lifted_elasticity selects vector simplex elements when Displacement space/Finite element is auto and its fully distributed Domain contains triangles or tetrahedra. Set FE degree normally. Strong and weak Dirichlet terms use the same mapping. The legacy convergence table is omitted for simplex meshes; numerical tests check the displacement and residual directly.

coupled_poisson accepts a fully distributed triangular Poisson/Domain. Its embedded line and multiplier remain one-dimensional. The generated coupled_poisson_simplex.prm uses quadratic physical fields with nonzero boundary data; the continuity multiplier is zero for its exact solution.

coupled_poisson_elasticity accepts tetrahedra in Elastic static/Domain. The pressure line and its lifted surface use the existing coupling parameters. The generated coupled_poisson_elasticity_simplex.prm places the axial line inside a tetrahedral cube; tests check the exact line pressure and balance its traction against the elastic stiffness action.

For fiber_reinforced_elastodynamics, import triangles or tetrahedra into the fully distributed Matrix Elastodynamics/Domain. The line fiber and velocity multiplier retain their one-dimensional elements. The generated fiber_reinforced_simplex_2d.prm and fiber_reinforced_simplex_3d.prm exercise forced rigid translation; tests check both fixed steps and IDA against their respective displacement and velocity solutions.

fiber_reinforced_elasticity_freq accepts simplex matrices and reinforcement meshes, including triangular sheets in 3D and full-dimensional triangles or tetrahedra. Automatic multiplier elements follow the reinforcement reference cell. Both independent and shared formulations use the physical volume measure. The generated fiber_harmonic_simplex_22.prm, _23.prm, and _33.prm check a complex forced translation with damping.

The standalone metric_flow_x mesh consists of line segments. These are the one-dimensional simplex reference cell, so its existing vessel mesh and finite-element settings already apply. Its integration test checks the cell family and advances a nonzero inflow through IDA. Triangle and tetrahedron selection belongs to the solid Domain in metric_flow_x_elastodynamics.

For metric_flow_x_elastodynamics, select fullydistributed and a tetrahedral mesh under Elastodynamics/Domain. Keep enough unconstrained solid DoFs for the vessel-wall multiplier. The generated gtests/parameters/metric_flow_x_rcr_simplex_coupled.prm uses quadratic solid elements around two vessels with RCR outlets. CTest runs both default and immersed vessel ownership and checks accepted times and all three output collections in serial and MPI.

The tissue component used by coupled_elasticity and pseudocoupling1D is available without lib1dsolver. Select a fully distributed tetrahedral mesh under Immersed Problem/Grid generation and refine before distribution. VesselElasticityProblem::run_timestep0() prepares it; update displacement data and call run_timestep() for each tissue solve. Pointwise data use the overload taking one sample count per vessel. Gather inclusion pressures on all ranks before calling split_pressure_over_inclusions on rank zero. That interpolation performs no MPI operations.

The generated gtests/parameters/coupled_elasticity_simplex.prm exercises this interface. The external 1D drivers still require a complete library compatible with the compiler and dependencies. Linux OpenMP test builds compile their full driver bodies independently of the library link check.

For pseudocoupling1D, vesselwise displacement data use the flat-vector overload of update_inclusions_data. The generated gtests/parameters/pseudocoupling_simplex.prm checks two successive tissue solves with changed data and their displacement, multiplier, and pressure response in serial and MPI.