├── .gitignore ├── .travis.yml ├── CMakeLists.txt ├── Doxyfile.in ├── Doxygen └── bibliography.bib ├── LICENSE ├── README.md ├── cmake ├── config │ ├── pidomusConfig.cmake.in │ └── pidomusConfigVersion.cmake.in └── pidomus_invoke_autopilot.cmake ├── docker └── Dockerfile ├── examples ├── CMakeLists.txt └── heat-equation │ ├── CMakeLists.txt │ ├── heat.cc │ ├── heat.prm │ └── heat_interface.h ├── include ├── base_interface.h ├── copy_data.h ├── interfaces │ ├── ALE_navier_stokes.h │ ├── cahn-hilliard.h │ ├── compressible_neo_hookean.h │ ├── compressible_neo_hookean_nitsche.h │ ├── eikonal_equation.h │ ├── eikonal_equation_two_steps.h │ ├── hydrogels_one_field.h │ ├── hydrogels_three_fields.h │ ├── hydrogels_two_fields_transient.h │ ├── navier_stokes.h │ ├── neo_hookean_two_fields.h │ ├── neo_hookean_two_fields_nitsche.h │ ├── poisson_problem.h │ ├── poisson_problem_nitsche.h │ ├── poisson_problem_signals.h │ ├── scalar_reaction_diffusion_convection.h │ ├── scalar_reaction_diffusion_convection_stabilized.h │ ├── stokes.h │ ├── template.h │ └── turbulence_k_omega.h ├── lac │ ├── lac_initializer.h │ └── lac_type.h ├── old_interfaces │ ├── conservative.h │ ├── conservative │ │ ├── compressible_neo_hookean.h │ │ ├── compressible_neo_hookean_direct.h │ │ ├── free_swelling_three_fields.h │ │ ├── heat_equation.h │ │ └── neo_hookean_two_fields.h │ ├── non_conservative.h │ └── old_interface.h ├── pde_system_interface.h ├── pidomus.h ├── pidomus_lambdas.h ├── pidomus_macros.h ├── pidomus_signals.h ├── simulator_access.h └── tria_helper.h ├── main ├── fluid-dynamics.cc ├── hydrogels.cc ├── scalar_reaction_diffusion_convection.cc └── turbulence.cc ├── scripts ├── analytical_stokes │ ├── analytical_stokes_3d.py │ ├── io_tools.py │ └── nabla.py ├── astyle.rc ├── build_documentation.sh ├── check_indentation.sh ├── check_test ├── dr.sh ├── indent ├── run_travis_commands.sh └── setup_astyle.sh ├── source ├── base_interface.cc ├── pidomus.cc ├── pidomus_assemble.cc ├── pidomus_boundary_conditions_and_forcing_terms.cc ├── pidomus_eigen.cc ├── pidomus_helper_functions.cc ├── pidomus_lambdas.cc ├── pidomus_mesh_refinement.cc ├── pidomus_parameters.cc ├── simulator_access.cc └── tria_helper.cc ├── tests ├── CMakeLists.txt ├── arpack_01.cc ├── arpack_01.with_arpack=on.with_zz=on.output ├── cahn-hilliard_01.cc ├── cahn-hilliard_01.output ├── compressible_neo_hookean_01.cc ├── compressible_neo_hookean_01.output ├── compressible_neo_hookean_02.cc ├── compressible_neo_hookean_02.output ├── compressible_neo_hookean_03.cc ├── compressible_neo_hookean_03.output ├── compressible_neo_hookean_04.cc ├── compressible_neo_hookean_04.output ├── compressible_neo_hookean_05.cc ├── compressible_neo_hookean_05.output ├── eikonal_equation_01.cc ├── eikonal_equation_01.output ├── eikonal_equation_02.cc ├── eikonal_equation_02.output ├── eikonal_equation_03.cc ├── eikonal_equation_03.output ├── eikonal_equation_04.cc ├── eikonal_equation_04.output ├── hydrogels_one_field_01.cc ├── hydrogels_one_field_01.output ├── hydrogels_one_field_02.cc ├── hydrogels_one_field_02.output ├── hydrogels_three_fields_01.cc ├── hydrogels_three_fields_01.output ├── hydrogels_three_fields_02.cc ├── hydrogels_three_fields_02.output ├── hydrogels_three_fields_03.cc ├── hydrogels_three_fields_03.with_zz=on.output ├── hydrogels_two_fields_transient_01.cc ├── hydrogels_two_fields_transient_01.output ├── incompressible_neo_hookean_two_fields_01.cc ├── incompressible_neo_hookean_two_fields_01.output ├── incompressible_neo_hookean_two_fields_02.cc ├── incompressible_neo_hookean_two_fields_02.with_zz=on.output ├── incompressible_neo_hookean_two_fields_03.cc ├── incompressible_neo_hookean_two_fields_03.output ├── navier_stokes_00.cc ├── navier_stokes_00.output ├── navier_stokes_01.cc ├── navier_stokes_01.output ├── navier_stokes_02.cc ├── navier_stokes_02.output ├── navier_stokes_03.cc ├── navier_stokes_03.output ├── navier_stokes_04.cc ├── navier_stokes_04.output ├── navier_stokes_05.cc ├── navier_stokes_05.output ├── parameters │ ├── arpack_01.prm │ ├── cahn_hilliard_01.prm │ ├── compressible_neo_hookean_01.prm │ ├── compressible_neo_hookean_02.prm │ ├── compressible_neo_hookean_03.prm │ ├── compressible_neo_hookean_04.prm │ ├── compressible_neo_hookean_05.prm │ ├── eikonal_equation_01.prm │ ├── eikonal_equation_02.prm │ ├── eikonal_equation_03.prm │ ├── eikonal_equation_04.prm │ ├── hydrogels_one_field_01.prm │ ├── hydrogels_one_field_02.prm │ ├── hydrogels_three_fields_01.prm │ ├── hydrogels_three_fields_02.prm │ ├── hydrogels_three_fields_03.prm │ ├── hydrogels_two_fields_transient_01.prm │ ├── incompressible_neo_hookean_two_fields_01.prm │ ├── incompressible_neo_hookean_two_fields_02.prm │ ├── incompressible_neo_hookean_two_fields_03.prm │ ├── k_omega_00.prm │ ├── navier_stokes_00.prm │ ├── navier_stokes_01.prm │ ├── navier_stokes_02.prm │ ├── navier_stokes_03.prm │ ├── navier_stokes_04.prm │ ├── navier_stokes_05.prm │ ├── parpack_01.prm │ ├── poisson_nitsche_01.prm │ ├── poisson_problem_01.prm │ ├── poisson_problem_02.prm │ ├── poisson_problem_03.prm │ ├── stokes_00.prm │ ├── stokes_01.prm │ ├── stokes_02.prm │ ├── stokes_03.prm │ ├── stokes_04.prm │ └── stokes_05.prm ├── parpack_01.cc ├── parpack_01.with_parpack=on.with_mpi=on.mpirun=4.output ├── poisson_01.cc ├── poisson_01.output ├── poisson_02.cc ├── poisson_02.output ├── poisson_03.cc ├── poisson_03.output ├── poisson_nitsche_01.cc ├── poisson_nitsche_01.output ├── set_constrained_to_zero.cc ├── set_constrained_to_zero.with_mpi=on.mpirun=2.output ├── signals_01.cc ├── signals_01.output ├── stokes_00.cc ├── stokes_00.output ├── stokes_01.cc ├── stokes_01.output ├── stokes_02.cc ├── stokes_02.output ├── stokes_03.cc ├── stokes_03.output ├── stokes_04.cc ├── stokes_04.output ├── stokes_05.cc ├── stokes_05.output ├── tests.h └── tests_to_check │ ├── ale_navier_stokes_00.cc │ ├── ale_navier_stokes_00.output │ ├── ale_navier_stokes_01.cc │ ├── ale_navier_stokes_01.output │ ├── ale_navier_stokes_02.cc │ ├── ale_navier_stokes_02.output │ ├── compressible_neo_hookean_01.cc │ ├── compressible_neo_hookean_01.output │ ├── compressible_neo_hookean_02.cc │ ├── compressible_neo_hookean_02.output │ ├── compressible_neo_hookean_03.cc │ ├── compressible_neo_hookean_03.output │ ├── design_01.cc │ ├── design_01.output │ ├── free_swelling_three_fields_01.cc │ ├── free_swelling_three_fields_01.output │ ├── free_swelling_three_fields_02.cc │ ├── free_swelling_three_fields_02.output │ ├── free_swelling_three_fields_03.cc │ ├── free_swelling_three_fields_03.output │ ├── free_swelling_three_fields_04.cc │ ├── free_swelling_three_fields_04.output │ ├── heat_equation_01.cc │ ├── heat_equation_01.output │ ├── heat_equation_02.cc │ ├── heat_equation_02.output │ ├── heat_equation_03.cc │ ├── heat_equation_03.output │ ├── heat_equation_04.cc │ ├── heat_equation_04.output │ ├── heat_equation_05.cc │ ├── heat_equation_05.output │ ├── heat_equation_06.cc │ ├── heat_equation_06.output │ ├── heat_equation_07.cc │ ├── heat_equation_07.output │ ├── heat_equation_08.cc │ ├── heat_equation_08.output │ ├── heat_equation_09.cc │ ├── heat_equation_09.output │ ├── heat_equation_10.cc │ ├── heat_equation_10.output │ ├── heat_equation_11.cc │ ├── heat_equation_11.output │ ├── incompressible_neo_hookean_two_fields.cc │ ├── incompressible_neo_hookean_two_fields.output │ ├── linear_operator_00.cc │ ├── linear_operator_01.cc │ ├── linear_operator_01.output │ ├── linear_operator_01.with_mpi=on,mpirun=2.output │ ├── navier_stokes_01.cc │ ├── navier_stokes_01.output │ ├── navier_stokes_02.cc │ ├── navier_stokes_02.output │ ├── ode_argument_trilinos_01.cc │ ├── ode_argument_trilinos_01.with_mpi=on.mpirun=2.output │ ├── old_prm │ ├── ale_navier_stokes_00.prm │ ├── ale_navier_stokes_00_old.prm │ ├── ale_navier_stokes_01.prm │ ├── ale_navier_stokes_02.prm │ ├── compressible_neo_hookean.prm │ ├── compressible_neo_hookean_01.prm │ ├── compressible_neo_hookean_02.prm │ ├── compressible_neo_hookean_03.prm │ ├── free_swelling_01.prm │ ├── free_swelling_02.prm │ ├── free_swelling_03.prm │ ├── free_swelling_04.prm │ ├── heat_equation_01.prm │ ├── heat_equation_02.prm │ ├── heat_equation_03.prm │ ├── heat_equation_04.prm │ ├── heat_equation_05.prm │ ├── heat_equation_06.prm │ ├── heat_equation_07.prm │ ├── heat_equation_08.prm │ ├── heat_equation_09.prm │ ├── heat_equation_10.prm │ ├── heat_equation_11.prm │ ├── incompressible_neo_hookean_two_fields.prm │ ├── n_fields_problem_01.prm │ ├── navier_stokes_01.prm │ ├── navier_stokes_02.prm │ ├── ode_argument_trilinos.prm │ ├── output.gnuplot │ ├── poiseuille.prm │ ├── stokes_01.prm │ ├── stokes_forcing_01.prm │ ├── stokes_forcing_02.prm │ └── stokes_unit_force_x.prm │ ├── params.prm │ ├── pidomus_01.cc │ ├── pidomus_01.output │ ├── poiseuille.cc │ ├── poiseuille.output │ ├── stokes_forcing_01.cc │ ├── stokes_forcing_01.output │ ├── stokes_forcing_02.cc │ ├── stokes_forcing_02.output │ ├── stokes_unit_x_force.cc │ ├── stokes_unit_x_force.output │ ├── utilities_07.cc │ └── utilities_07.output └── utilities ├── grids ├── 2D │ ├── rectangle_with_circular_hole.inp │ └── rectangle_with_circular_hole.ucd ├── 3D │ ├── hyper_rectangle_with_cylinder_hole.msh │ └── hyper_rectangle_with_cylinder_hole.ucd ├── rectangle_with_two_circular_holes.ucd └── rectangle_with_two_circular_holes.ucd_old └── prm ├── hydrogels ├── constrained-swelling-one-field.prm ├── constrained-swelling-three-fields.prm ├── free-swelling-one-field.prm ├── free-swelling-three-fields.prm ├── wrinkling-one-field.prm └── wrinkling-three-fields.prm ├── navier_stokes ├── ALE_test.prm ├── default.prm ├── flow_past_a_cylinder_2D_00.prm ├── flow_past_a_cylinder_2D_01.prm ├── flow_past_a_cylinder_3D.prm ├── flow_past_two_cylinders.prm ├── lid_cavity_2D.prm └── lid_cavity_3D.prm └── turbulence └── k_omega_2D.prm /.gitignore: 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