Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | P | Q | R | S | T | U | V | W _ __getitem__() (smart.config.BaseConfig method) __post_init__() (smart.model.Model method) (smart.model_assembly.Compartment method) (smart.model_assembly.Parameter method) (smart.model_assembly.Reaction method) (smart.model_assembly.Species method) __setattr__() (smart.config.BaseConfig method) _get_entities() (smart.mesh._Mesh method) _init_1() (smart.model.Model method) _init_1_1_check_mesh_dimensionality() (smart.model.Model method) _init_1_2_check_namespace_conflicts() (smart.model.Model method) _init_1_3_check_parameter_dimensionality() (smart.model.Model method) _init_2() (smart.model.Model method) _init_2_1_reactions_to_symbolic_strings() (smart.model.Model method) _init_2_2_check_reaction_validity() (smart.model.Model method) _init_2_3_link_reaction_properties() (smart.model.Model method) _init_2_4_check_for_unused_parameters_species_compartments() (smart.model.Model method) _init_2_5_link_compartments_to_species() (smart.model.Model method) _init_2_6_link_species_to_compartments() (smart.model.Model method) _init_2_7_get_species_compartment_indices() (smart.model.Model method) _init_3() (smart.model.Model method) _init_3_1_define_child_meshes() (smart.model.Model method) _init_3_2_read_parent_mesh_functions_from_file() (smart.model.Model method) _init_3_3_extract_submeshes() (smart.model.Model method) _init_3_4_build_submesh_mappings() (smart.model.Model method) _init_3_7_get_integration_measures() (smart.model.Model method) _init_4() (smart.model.Model method) _init_4_0_initialize_dolfin_parameters() (smart.model.Model method) _init_4_1_get_active_compartments() (smart.model.Model method) _init_4_2_define_dolfin_function_spaces() (smart.model.Model method) _init_4_3_define_dolfin_functions() (smart.model.Model method) _init_4_4_get_species_u_v_V_dofmaps() (smart.model.Model method) _init_4_5_name_functions() (smart.model.Model method) _init_4_6_check_dolfin_function_validity() (smart.model.Model method) _init_4_7_set_initial_conditions() (smart.model.Model method) _init_5() (smart.model.Model method) _init_5_1_reactions_to_fluxes() (smart.model.Model method) _init_5_2_create_variational_forms() (smart.model.Model method) _Mesh (class in smart.mesh) _parse_custom_reaction() (smart.model_assembly.Reaction method) _read_parent_mesh_function_from_file() (smart.mesh.ParentMesh method) A adjust_dt (smart.config.SolverConfig attribute) adjust_dt() (smart.model.Model method) adjust_dt_if_pass_tfinal() (smart.model.Model method) adjust_dt_if_prescribed() (smart.model.Model method) all_meshes (smart.mesh.ParentMesh property) allow_unused_components (smart.config.FlagsConfig attribute) assemble_Fnest() (smart.solvers.smartSNESProblem method) assemble_Jnest() (smart.solvers.smartSNESProblem method) attempt_timestep_restart_on_divergence (smart.config.SolverConfig attribute) axisymm (smart.model_assembly.Reaction attribute) axisymmetric_model (smart.config.FlagsConfig attribute) B BaseConfig (class in smart.config) C cc (smart.model.Model attribute) cell_coordinates() (smart.mesh._Mesh method) cell_marker (smart.model_assembly.Compartment attribute) cells() (smart.mesh._Mesh method) check_validity() (smart.model_assembly.Compartment method) (smart.model_assembly.Parameter method) (smart.model_assembly.Reaction method) (smart.model_assembly.Species method) child_meshes (smart.mesh.ParentMesh attribute) (smart.model.Model property) child_surface_meshes (smart.mesh.ParentMesh property) child_volume_meshes (smart.mesh.ParentMesh property) ChildMesh (class in smart.mesh) Compartment (class in smart.model_assembly) compartment_name (smart.model_assembly.Species attribute) compartment_units (smart.model_assembly.Compartment attribute) compute_curvature() (in module smart.mesh_tools) concentration_units (smart.model_assembly.Species attribute) Config (class in smart.config) config (smart.model.Model attribute) constant (smart.model_assembly.ParameterType attribute) copy_u() (smart.solvers.smartSNESProblem method) create_2Dcell() (in module smart.mesh_tools) create_axisymm() (in module smart.mesh_tools) create_cubes() (in module smart.mesh_tools) create_cylinders() (in module smart.mesh_tools) create_ellipses() (in module smart.mesh_tools) create_ellipsoids() (in module smart.mesh_tools) create_spheres() (in module smart.mesh_tools) create_vtk_structures() (in module smart.visualization) cube_condition() (in module smart.mesh_tools) curvature (smart.mesh.ParentMesh attribute) D D (smart.model_assembly.Species attribute) D_quantity (smart.model_assembly.Species property) d_to_p() (smart.solvers.smartSNESProblem method) deprecated() (in module smart.deprecation) diffusion_units (smart.model_assembly.Species attribute) dimensionality (smart.mesh._Mesh attribute) (smart.model_assembly.Compartment attribute) dolfin_get_dof_indices() (smart.model.Model static method) dolfin_mesh (smart.mesh._Mesh attribute) (smart.model_assembly.Compartment property) dolfin_quantity (smart.model_assembly.Parameter property) (smart.model_assembly.Species property) dolfin_set_function_values() (smart.model.Model method) ds (smart.mesh._Mesh attribute) dx (smart.mesh._Mesh attribute) dx_uncombined (smart.mesh._Mesh attribute) E empty_sbmodel() (in module smart.model_assembly) eqn_f_str (smart.model_assembly.Reaction attribute) eqn_r_str (smart.model_assembly.Reaction attribute) eqn_str (smart.model_assembly.Reaction attribute) explicit_restriction_to_domain (smart.model_assembly.Reaction attribute) expression (smart.model_assembly.ParameterType attribute) extra_keys (smart.mesh.ParentMesh attribute) extract_submesh() (smart.mesh.ChildMesh method) F F() (smart.solvers.smartSNESProblem method) facet_coordinates() (smart.mesh._Mesh method) facet_topology() (in module smart.mesh_tools) facets() (smart.mesh._Mesh method) final_t (smart.config.SolverConfig attribute) find_surface_to_volumes_mesh_intersection() (smart.mesh.ChildMesh method) Fjk_name() (smart.solvers.smartSNESProblem method) flags (smart.config.Config attribute) FlagsConfig (class in smart.config) flux_scaling (smart.model_assembly.Reaction attribute) forward_time_step() (smart.model.Model method) from_dict() (smart.model.Model class method) (smart.model_assembly.Compartment class method) (smart.model_assembly.Parameter class method) (smart.model_assembly.Reaction class method) (smart.model_assembly.Species class method) from_expression() (smart.model_assembly.Parameter class method) from_file (smart.model_assembly.ParameterType attribute) from_file() (smart.model_assembly.Parameter class method) from_pickle() (smart.model.Model class method) G get_block_F() (smart.model.Model method) get_block_J() (smart.model.Model method) get_block_system() (smart.model.Model method) get_compartment_residual() (smart.model.Model method) get_csr_matrix() (smart.solvers.smartSNESProblem method) get_global_sizes() (smart.model.Model method) get_integration_measures() (smart.mesh._Mesh method) get_intersection_submesh() (smart.mesh.ChildMesh method) get_mesh_by_id() (smart.model.Model method) get_mesh_from_id() (smart.mesh.ParentMesh method) get_num_entities() (smart.mesh._Mesh method) get_nvolume() (smart.mesh._Mesh method) get_total_residual() (smart.model.Model method) global_settings (in module smart.config) gmsh_to_dolfin() (in module smart.mesh_tools) group (smart.model_assembly.Parameter attribute) (smart.model_assembly.Reaction attribute) (smart.model_assembly.Species attribute) H has_intersection (smart.mesh.ChildMesh attribute) has_subdomain (smart.model_assembly.Reaction attribute) has_surface (smart.mesh.ParentMesh property) I id (smart.mesh._Mesh property) implicit_curve() (in module smart.mesh_tools) init_petsc_matnest() (smart.solvers.smartSNESProblem method) init_petsc_matrix() (smart.solvers.smartSNESProblem method) init_petsc_vecnest() (smart.solvers.smartSNESProblem method) init_petsc_vector() (smart.solvers.smartSNESProblem method) initial_condition (smart.model_assembly.Species attribute) initial_condition_quantity (smart.model_assembly.Species property) initial_dt (smart.config.SolverConfig attribute) initialize() (smart.model.Model method) initialize_discrete_variational_problem_and_solver() (smart.model.Model method) intersection_dx (smart.mesh.ChildMesh attribute) intersection_map (smart.mesh.ChildMesh attribute) intersection_map_parent (smart.mesh.ChildMesh attribute) intersection_submesh (smart.mesh.ChildMesh attribute) is_surface (smart.mesh._Mesh property) is_volume (smart.mesh._Mesh property) J J() (smart.solvers.smartSNESProblem method) Jijk_name() (smart.solvers.smartSNESProblem method) json_to_ObjectContainer() (in module smart.utils) L latex_name (smart.model_assembly.Species property) lhs (smart.model_assembly.Reaction attribute) load_mesh_from_hdf5() (smart.mesh.ParentMesh method) load_mesh_from_xml() (smart.mesh.ParentMesh method) logger (in module smart.mesh) (in module smart.model) M map_cell_to_parent_entity() (smart.mesh.ChildMesh method) map_cell_to_parent_vertex() (smart.mesh.ChildMesh method) map_facet_to_parent_vertex() (smart.mesh.ChildMesh method) map_vertex_to_parent_vertex() (smart.mesh.ChildMesh method) max_dim() (smart.model.Model method) measure_units (smart.model_assembly.Compartment property) mesh_filename (smart.mesh.ParentMesh attribute) mesh_filetype (smart.mesh.ParentMesh attribute) mesh_id (smart.model_assembly.Compartment property) mesh_view (smart.mesh._Mesh property) mf (smart.mesh._Mesh attribute) mf0_to_fun() (smart.model.Model method) min_dim() (smart.model.Model method) Model (class in smart.model) module smart smart.common smart.config smart.deprecation smart.mesh smart.mesh_tools smart.model smart.model_assembly smart.solvers smart.units smart.utils smart.visualization monolithic_solve() (smart.model.Model method) mpi_am_i_root (smart.model.Model property) N name (smart.mesh._Mesh attribute) (smart.model.Model attribute) (smart.model_assembly.Compartment attribute) (smart.model_assembly.Parameter attribute) (smart.model_assembly.Reaction attribute) (smart.model_assembly.Species attribute) notes (smart.model_assembly.Parameter attribute) num_active_compartments (smart.model.Model property) num_cells (smart.model_assembly.Compartment property) num_cells() (smart.mesh._Mesh method) num_dofs (smart.model_assembly.Compartment property) num_dofs_local (smart.model_assembly.Compartment property) num_facets (smart.model_assembly.Compartment property) num_facets() (smart.mesh._Mesh method) num_vertices (smart.model_assembly.Compartment property) num_vertices() (smart.mesh._Mesh method) nvolume (smart.model_assembly.Compartment property) nvolume() (smart.mesh._Mesh method) P param_map (smart.model_assembly.Reaction attribute) Parameter (class in smart.model_assembly) ParameterType (class in smart.model_assembly) parent_mesh (smart.mesh._Mesh attribute) (smart.mesh.ParentMesh attribute) (smart.model.Model attribute) ParentMesh (class in smart.mesh) pause() (smart.common.Stopwatch method) pc (smart.model.Model attribute) plot() (in module smart.visualization) print_Jijk_info() (smart.solvers.smartSNESProblem method) print_last_stop() (smart.common.Stopwatch method) print_meshes() (smart.model.Model method) print_val (smart.model_assembly.Parameter property) print_verbose_info (smart.config.FlagsConfig attribute) Q quantity (smart.model_assembly.Parameter property) quantity_to_unit() (in module smart.units) R rc (smart.model.Model attribute) Reaction (class in smart.model_assembly) reaction_database (smart.config.Config property) reaction_to_fluxes() (smart.model_assembly.Reaction method) reaction_type (smart.model_assembly.Reaction attribute) read_parent_mesh_functions_from_file() (smart.mesh.ParentMesh method) reset_timestep() (smart.model.Model method) reset_timestep_for_negative_solution (smart.config.SolverConfig attribute) restrict_to_subdomain() (smart.model_assembly.Reaction method) (smart.model_assembly.Species method) rhs (smart.model_assembly.Reaction attribute) rounded_decimal() (smart.model.Model method) S sbmodel_from_locals() (in module smart.model_assembly) sc (smart.model.Model attribute) set_dt() (smart.model.Model method) set_form_scaling() (smart.model.Model method) set_parent_mesh() (smart.mesh.ChildMesh method) set_time() (smart.model.Model method) set_timing() (smart.common.Stopwatch method) smart module smart.common module smart.config module smart.deprecation module smart.mesh module smart.mesh_tools module smart.model module smart.model_assembly module smart.solvers module smart.units module smart.utils module smart.visualization module smart_expressions() (in module smart.common) smartSNESProblem (class in smart.solvers) snes_preassemble_linear_system (smart.config.SolverConfig attribute) sol (smart.model_assembly.Species property) solver (smart.config.Config attribute) SolverConfig (class in smart.config) Species (class in smart.model_assembly) species_map (smart.model_assembly.Reaction attribute) specify_nonadjacency() (smart.model_assembly.Compartment method) start() (smart.common.Stopwatch method) stop() (smart.common.Stopwatch method) Stopwatch (class in smart.common) sub() (in module smart.common) subfacets() (smart.mesh._Mesh method) sym (smart.model_assembly.Species property) sym_expr (smart.model_assembly.Parameter attribute) T time_precision (smart.config.SolverConfig attribute) time_str() (smart.common.Stopwatch method) to_dict() (smart.model.Model method) (smart.model_assembly.Compartment method) (smart.model_assembly.Parameter method) (smart.model_assembly.Reaction method) (smart.model_assembly.Species method) to_pickle() (smart.model.Model method) topology (smart.model_assembly.Reaction attribute) track_value (smart.model_assembly.Reaction attribute) U unit (in module smart.units) (smart.model_assembly.Parameter attribute) unit_to_quantity() (in module smart.units) update() (smart.config.BaseConfig method) update_solution() (smart.model.Model method) update_time_dependent_parameters() (smart.model.Model method) use_partition (smart.mesh.ParentMesh attribute) use_preintegration (smart.model_assembly.Parameter attribute) use_snes (smart.config.SolverConfig attribute) V value (smart.model_assembly.Parameter attribute) vertices() (smart.mesh._Mesh method) vscalar() (smart.model_assembly.Species method) W write_mesh() (in module smart.mesh_tools)