| ▼ doc | |
| ► doxy | |
| ► headers | |
| exceptions.h | |
| input.h | |
| input_accessors.h | |
| input_types.h | |
| main_doc.hh | |
| ▼ src | |
| ► coupling | |
| balance.cc | Mass balance |
| balance.hh | |
| equation.cc | Abstract base class for equation clasess |
| equation.hh | Abstract base class for equation clasess |
| hc_explicit_sequential.cc | |
| hc_explicit_sequential.hh | |
| hm_iterative.cc | |
| hm_iterative.hh | |
| ► fem | |
| dh_cell_accessor.hh | |
| discrete_space.cc | Implementation of class which provides the finite element for every mesh cell |
| discrete_space.hh | Declaration of class which provides the finite element for every mesh cell |
| dofhandler.cc | Declaration of class which handles the ordering of degrees of freedom (dof) and mappings between local and global dofs |
| dofhandler.hh | Declaration of class which handles the ordering of degrees of freedom (dof) and mappings between local and global dofs |
| fe_p.cc | |
| fe_p.hh | Definitions of basic Lagrangean finite elements with polynomial shape functions |
| fe_rt.cc | Definitions of Raviart-Thomas finite elements |
| fe_rt.hh | Definitions of Raviart-Thomas finite elements |
| fe_system.cc | Class FESystem for compound finite elements |
| fe_system.hh | Class FESystem for compound finite elements |
| fe_values.cc | Class FEValues calculates finite element data on the actual cells such as shape function values, gradients, Jacobian of the mapping from the reference cell etc |
| fe_values.hh | Class FEValues calculates finite element data on the actual cells such as shape function values, gradients, Jacobian of the mapping from the reference cell etc |
| fe_values_views.cc | |
| fe_values_views.hh | |
| finite_element.cc | Abstract class for description of finite elements |
| finite_element.hh | Abstract class for description of finite elements |
| mapping.hh | Class Mapping calculates data related to the mapping of the reference cell to the actual cell, such as Jacobian and normal vectors |
| mapping_p1.cc | Class MappingP1 implements the affine transformation of the unit cell onto the actual cell |
| mapping_p1.hh | Class MappingP1 implements the affine transformation of the unit cell onto the actual cell |
| update_flags.hh | Enum type UpdateFlags indicates which quantities are to be recomputed on each finite element cell |
| ► fields | |
| bc_field.cc | |
| bc_field.hh | |
| bc_multi_field.cc | |
| bc_multi_field.hh | |
| equation_output.cc | |
| equation_output.hh | |
| fe_value_handler.cc | |
| fe_value_handler.hh | |
| field.cc | |
| field.hh | |
| field.impl.hh | |
| field_add_potential.hh | |
| field_add_potential.impl.hh | |
| field_algo_base.cc | |
| field_algo_base.hh | |
| field_algo_base.impl.hh | |
| field_common.cc | |
| field_common.hh | |
| field_constant.cc | |
| field_constant.hh | |
| field_elementwise.cc | |
| field_elementwise.hh | |
| field_fe.cc | |
| field_fe.hh | |
| field_flag.cc | |
| field_flag.hh | |
| field_formula.cc | |
| field_formula.hh | |
| field_instances.hh | |
| field_interpolated_p0.cc | |
| field_interpolated_p0.hh | |
| field_python.hh | |
| field_python.impl.hh | |
| field_set.cc | |
| field_set.hh | |
| field_time_function.cc | |
| field_time_function.hh | |
| field_values.cc | |
| field_values.hh | |
| generic_field.cc | |
| generic_field.hh | Fields computed from the mesh data |
| generic_field.impl.hh | |
| multi_field.cc | |
| multi_field.hh | |
| multi_field.impl.hh | |
| surface_depth.cc | |
| surface_depth.hh | |
| table_function.cc | |
| table_function.hh | |
| ► flow | |
| assembly_lmh.hh | |
| assembly_theory.hh | |
| darcy_flow_assembly.hh | |
| darcy_flow_interface.hh | |
| darcy_flow_mh.cc | Setup and solve linear system of mixed-hybrid discretization of the linear porous media flow with possible preferential flow in fractures and chanels |
| darcy_flow_mh.hh | Mixed-hybrid model of linear Darcy flow, possibly unsteady |
| darcy_flow_mh_output.cc | Output class for darcy_flow_mh model |
| darcy_flow_mh_output.hh | Output class for darcy_flow_mh model |
| mh_dofhandler.cc | |
| mh_dofhandler.hh | |
| mortar_assembly.cc | |
| mortar_assembly.hh | |
| richards_lmh.cc | |
| richards_lmh.hh | |
| soil_models.cc | |
| soil_models.hh | |
| ► input | |
| ► json_spirit | |
| json_spirit.h | |
| json_spirit_error_position.h | |
| json_spirit_reader.cpp | |
| json_spirit_reader.h | |
| json_spirit_reader_template.h | |
| json_spirit_stream_reader.h | |
| json_spirit_utils.h | |
| json_spirit_value.cpp | |
| json_spirit_value.h | |
| json_spirit_writer.cpp | |
| json_spirit_writer.h | |
| json_spirit_writer_options.h | |
| json_spirit_writer_template.h | |
| accessors.cc | |
| accessors.hh | |
| accessors_forward.hh | |
| accessors_impl.hh | |
| attribute_lib.hh | |
| comment_filter.hh | |
| const_hashes.h | |
| csv_tokenizer.cc | |
| csv_tokenizer.hh | |
| factory.hh | |
| factory_impl.hh | |
| finite_state_filter.hpp | |
| flow_attribute_lib.hh | |
| input_exception.hh | |
| input_type.hh | |
| input_type_forward.hh | |
| path_base.cc | |
| path_base.hh | |
| path_json.cc | |
| path_json.hh | |
| path_yaml.cc | |
| path_yaml.hh | |
| reader_internal.cc | |
| reader_internal.hh | |
| reader_internal_base.cc | |
| reader_internal_base.hh | |
| reader_internal_csv.cc | |
| reader_internal_csv.hh | |
| reader_internal_transpose.cc | |
| reader_internal_transpose.hh | |
| reader_to_storage.cc | |
| reader_to_storage.hh | |
| storage.cc | |
| storage.hh | |
| type_abstract.cc | |
| type_abstract.hh | |
| type_base.cc | |
| type_base.hh | |
| type_generic.cc | |
| type_generic.hh | |
| type_output.cc | |
| type_output.hh | |
| type_record.cc | |
| type_record.hh | |
| type_repository.hh | |
| type_selection.cc | |
| type_selection.hh | |
| type_tuple.cc | |
| type_tuple.hh | |
| ► intersection | |
| compute_intersection.cc | |
| compute_intersection.hh | Fundamental simplicial intersections |
| inspect_elements_algorithm.cc | |
| inspect_elements_algorithm.hh | |
| intersection_aux.cc | |
| intersection_aux.hh | Internal class representing intersection object |
| intersection_local.cc | |
| intersection_local.hh | Classes with algorithms for computation of intersections of meshes |
| intersection_point_aux.cc | |
| intersection_point_aux.hh | Internal class representing intersection point |
| mixed_mesh_intersections.cc | |
| mixed_mesh_intersections.hh | |
| plucker.cc | |
| plucker.hh | Plucker coordinates class |
| ► io | |
| element_data_cache.cc | |
| element_data_cache.hh | |
| element_data_cache_base.hh | |
| msh_basereader.cc | |
| msh_basereader.hh | |
| msh_gmshreader.cc | |
| msh_gmshreader.h | |
| msh_pvdreader.cc | |
| msh_pvdreader.hh | |
| msh_vtkreader.cc | |
| msh_vtkreader.hh | |
| observe.cc | |
| observe.hh | |
| output_element.hh | Class OutputElement and its iterator OutputElementIterator on the output mesh |
| output_mesh.cc | Classes for auxiliary output mesh |
| output_mesh.hh | Classes for auxiliary output mesh |
| output_msh.cc | The functions for outputs to GMSH files |
| output_msh.hh | |
| output_time.cc | |
| output_time.hh | |
| output_time.impl.hh | |
| output_time_set.cc | |
| output_time_set.hh | |
| output_vtk.cc | The functions for outputs to VTK files |
| output_vtk.hh | |
| read_ini.cc | OPTIONS RUTINES - get program parameters, reading from options/ini file |
| read_ini.h | |
| reader_cache.cc | |
| reader_cache.hh | |
| ► la | |
| bddcml_wrapper.hpp | |
| distribution.cc | Objects and functions for mesh partitioning |
| distribution.hh | Support classes for parallel programing |
| la_linsys_new.hh | |
| linsys.cc | Wrappers for linear systems based on MPIAIJ and MATIS format |
| linsys.hh | Wrappers for linear systems based on MPIAIJ and MATIS format |
| linsys_BDDC.cc | Solver based on Multilevel BDDC - using corresponding class of OpenFTL package |
| linsys_BDDC.hh | Solver based on Multilevel BDDC - using corresponding class of OpenFTL package |
| linsys_PETSC.cc | Solver based on the original PETSc solver using MPIAIJ matrix and succesive Schur complement construction |
| linsys_PETSC.hh | Solver based on the original PETSc solver using MPIAIJ matrix and succesive Schur complement construction |
| local_system.cc | |
| local_system.hh | |
| local_to_global_map.cc | |
| local_to_global_map.hh | |
| matrix_coo.hpp | |
| schur.cc | Assembly explicit Schur complement for the given linear system. Provides method for resolution of the full original vector of unknowns |
| schur.hh | Assembly explicit Schur complement for the given linear system. Provides method for resolution of the full original vector of unknowns |
| sparse_graph.cc | Construction and partitioning of a sparse graph |
| sparse_graph.hh | Distributed sparse graphs, partitioning |
| vector_mpi.hh | |
| ► mechanics | |
| elasticity.cc | |
| elasticity.hh | FEM for linear elasticity |
| ► mesh | |
| accessors.hh | |
| bc_mesh.cc | Mesh construction |
| bc_mesh.hh | |
| bih_node.hh | |
| bih_tree.cc | |
| bih_tree.hh | |
| boundaries.cc | Boundary conditions |
| boundaries.h | |
| bounding_box.cc | |
| bounding_box.hh | |
| duplicate_nodes.cc | Construction of mesh structure with nodes duplicated at fractures |
| duplicate_nodes.h | |
| edges.cc | |
| edges.h | |
| elements.cc | Various element oriented stuff, should be restricted to purely geometric functions |
| elements.h | |
| intersectionquadrature.cc | |
| intersectionquadrature.hh | ??? |
| long_idx.hh | |
| mesh.cc | Mesh construction |
| mesh.h | |
| mesh_types.hh | |
| neighbours.cc | Initialize neighbouring |
| neighbours.h | |
| node_accessor.hh | |
| nodes.hh | Nodes of a mesh |
| partitioning.cc | |
| partitioning.hh | |
| point.hh | |
| range_wrapper.hh | Implementation of range helper class |
| ref_element.cc | Class RefElement defines numbering of vertices, sides, calculation of normal vectors etc |
| ref_element.hh | Class RefElement defines numbering of vertices, sides, calculation of normal vectors etc |
| region.cc | |
| region.hh | |
| region_set.cc | |
| region_set.hh | |
| side_impl.hh | |
| sides.cc | Some side related functions - should be made strictly geometric |
| sides.h | |
| ► python | |
| ► benchmarks | |
| ► src | |
| ► libs | |
| json.hpp | |
| memory.cc | |
| ► quadrature | |
| intersection_quadrature.cc | |
| intersection_quadrature.hh | ??? |
| qmidpoint.hh | Midpoint rule qudrature |
| quad.c | |
| quad.h | |
| quadrature.cc | |
| quadrature.hh | Basic definitions of numerical quadrature rules |
| quadrature_lib.cc | Definitions of particular quadrature rules on simplices |
| quadrature_lib.hh | Definitions of particular quadrature rules on simplices |
| ► reaction | |
| dual_porosity.cc | |
| dual_porosity.hh | Class Dual_por_exchange implements the model of dual porosity |
| first_order_reaction.cc | |
| first_order_reaction.hh | |
| first_order_reaction_base.cc | |
| first_order_reaction_base.hh | |
| isotherm.cc | |
| isotherm.hh | Other possible transformation of coordinates: |
| linear_ode_solver.cc | |
| linear_ode_solver.hh | |
| radioactive_decay.cc | |
| radioactive_decay.hh | |
| reaction_term.cc | |
| reaction_term.hh | Class ReactionTerm is an abstract class representing reaction term in transport |
| sorption.cc | |
| sorption.hh | This file contains classes representing sorption model. Sorption model can be computed both in case the dual porosity is considered or not |
| sorption_base.cc | |
| sorption_base.hh | Class SorptionBase is abstract class representing model of sorption in transport |
| ► semchem | |
| che_read.cc | |
| che_semchem.cc | |
| che_semchem.h | |
| semchem_interface.cc | |
| semchem_interface.hh | |
| ► system | |
| ► fmt | |
| format.cc | |
| format.h | |
| ostream.cc | |
| ostream.h | |
| posix.cc | |
| posix.h | |
| printf.h | |
| string.h | |
| ► mpiuni | |
| mpi.c | |
| mpi.h | |
| application_base.cc | |
| application_base.hh | |
| armadillo_tools.cc | |
| armadillo_tools.hh | |
| armor.hh | |
| asserts.cc | Definitions of ASSERTS |
| asserts.hh | Definitions of ASSERTS |
| exc_common.hh | |
| exceptions.cc | |
| exceptions.hh | |
| file_path.cc | |
| file_path.hh | |
| flag_array.hh | |
| global_defs.h | Global macros to enhance readability and debugging, general constants |
| lazy_dependecy.hh | |
| logger.cc | |
| logger.hh | |
| logger_options.cc | |
| logger_options.hh | |
| math_fce.cc | Auxiliary math functions |
| math_fce.h | |
| python_loader.cc | |
| python_loader.hh | |
| simple_allocator.hh | |
| stack_trace.cc | |
| stack_trace.hh | |
| sys_profiler.cc | Profiler |
| sys_profiler.hh | |
| sys_vector.hh | Vector classes to support both Iterator, index and Id access and creating co-located vectors |
| system.cc | Various system-wide functions |
| system.hh | |
| time_point.cc | |
| time_point.hh | |
| tokenizer.cc | |
| tokenizer.hh | |
| xio.cc | I/O functions with filename storing, able to track current line in opened file. All standard stdio functions working with files (not stdin, stdout, stderr) should be replaced by their equivalents from XIO library |
| xio.h | I/O functions with filename storing, able to track current line in opened file. All standard stdio functions working with files (not stdin, stdout, stderr) should be replaced by their equivalents from XIO library |
| ► tools | |
| adaptivesimpson.cc | |
| adaptivesimpson.hh | |
| bidirectional_map.hh | Implementation of bidirectional map |
| functors.hh | |
| functors_impl.hh | |
| general_iterator.hh | Template Iter serves as general template for internal iterators |
| interpolant.cc | |
| interpolant.hh | |
| interpolant_impl.hh | |
| time_governor.cc | Basic time management class |
| time_governor.hh | Basic time management class |
| time_marks.cc | |
| time_marks.hh | |
| unit_converter.cc | |
| unit_converter.hh | |
| unit_converter_template.hh | |
| unit_si.cc | |
| unit_si.hh | |
| ► transport | |
| advection_diffusion_model.hh | Discontinuous Galerkin method for equation of transport with dispersion |
| advection_process_base.hh | |
| concentration_model.cc | Discontinuous Galerkin method for equation of transport with dispersion |
| concentration_model.hh | Discontinuous Galerkin method for equation of transport with dispersion |
| heat_model.cc | Discontinuous Galerkin method for equation of transport with dispersion |
| heat_model.hh | Discontinuous Galerkin method for equation of transport with dispersion |
| substance.cc | Classes for storing substance data |
| substance.hh | Classes for storing substance data |
| transport.cc | Transport |
| transport.h | |
| transport_dg.cc | Discontinuous Galerkin method for equation of transport with dispersion |
| transport_dg.hh | Discontinuous Galerkin method for equation of transport with dispersion |
| transport_operator_splitting.cc | |
| transport_operator_splitting.hh | |
| doxy_dummy_defs.hh | |
| main.cc | This file should contain only creation of Application object |
| main.h | |
