Functions
Overview
- add_forces_to_repatoms
- add_options
- add_thermalized_forces_to_repatoms
- add_to_container_unique
- all_reduce_cum_sum - Determines the start position of a MPI local sub array within a...
- approx
- array_from_vec
- array_from_vec
- as_kim
- as_kim
- build_adjacency_halo
- build_csr_index_map
- build_interproc_connectivity
- build_node_cell_adjacency - build adjacencies from assigned nodes and simplices
- build_node_index_key_maps
- build_periodic_connectivity - Build periodic connectivity
- build_repatoms
- build_simplex_index_key_maps
- calc_g
- calc_g_d_g
- calc_pair_potential - Find pair potential given distance and atom types
- calc_pair_potential_and_derivative - Find pair potential and its derivative given distance and atom ...
- calc_rose_embedding_energy - Rose empirical energy formula
- calc_rose_embedding_energy_and_derivative - Rose empirical energy formula and derivative
- calc_total_pair_potential
- calc_total_pair_potential_and_derivative
- can_save_lattice_vectors
- can_save_lattice_vectors - Evaluates the trait for given instance.
- cell_assign_material
- cell_density
- cell_nodes
- cell_nodes - Access the node ids belonging to a cell via @ref CellNodes.
- cell_weight - Retrieve the cell weight stored in the sampling atoms for a giv...
- clean_mesh
- clear_face_neighbours
- cluster_energy
- cluster_forces
- collect_array
- collect_cell_int_data
- collect_cell_mesh_data
- collect_cell_restart_data
- collect_entries
- collect_matrix
- collect_neighbours
- collect_nodes
- comp_embedding_func
- comp_embedding_func_and_derivative
- comp_embedding_func_with_interpolation
- comparable
- compute_concentration_forces
- compute_potential
- compute_ref_elec_density - find and store electron densities for reference configurations ...
- compute_screening
- compute_screening_and_derivatives
- count_repatoms
- create
- create
- create
- create_boundary_condition
- create_boundary_conditions
- create_external_force_applicator
- create_lattice_sites_in_bounds
- create_lattice_sites_in_bounds
- create_local_mesh
- create_local_mesh
- create_local_mesh
- create_material
- create_material_base
- create_material_base - Create a @ref MaterialBase from a @ref MaterialBase instance.
- create_material_base
- create_meam_information
- create_mesh
- create_mesh
- create_mesh
- create_plane_from_triangle
- create_solver_variables
- create_specific_material
- create_specific_material
- create_specific_material
- create_specific_material
- create_specific_material
- create_specific_material
- create_specific_material
- create_test_mesh
- d_cikj - derivative of C_ikj wrt r_ij r_jk r_ik
- deform_mesh_elements - deforms the mesh elements and computes deformation gradient
- deform_mesh_overlaps - call mesh functions to exchange displacements of overlapping me...
- deform_period_offsets
- deform_period_offsets - deform periodic offsets
- deform_sampling_atoms_and_neighbourhoods
- delta_thermal_force
- density - Access the density of a cell or node via @ref Density.
- deserialize_lattice_structure
- deserialize_lattice_structure
- deserialize_nc - Deserialize all arrays specified by @ref traits::NetCdfSchema f...
- df_cut - derivative of the cutoff function
- diag_displacement_gradient
- diff
- diff
- diff
- diff
- diff
- diff
- diff
- diff
- distribute_nodes - Share nodes between all MPI processes such that each process ha...
- distribute_vec
- distribute_vec
- distribute_vec
- distributed_bounding_box
- distributed_bounding_box - Constructs the bounding box containing a given range of points ...
- distributed_box_hull - Constructs a box containing the boxes from all MPI processes.
- do_relaxation
- dump_solver_variables_nc
- dump_solver_variables_vtk
- entropy - Access the entropy of a node via @ref Entropy.
- entropy_rate_onsager_kinetics
- evaluate_polynomial
- evaluate_polynomial - Computes the value or derivative of a polynomial given the poly...
- evaluate_polynomial_derivative
- evaluate_polynomial_derivative
- exchange_halos
- extract_site_types
- f_cut - cutoff function used in screening calculation
- find_path
- fire_parameters_from_userinput
- fmt_filename - Format a file name "{prefix}######.{ext}", where ###### is outp...
- fmt_filename - Format a file name "{prefix}######.{ext}", where ###### is outp...
- force_applicator_name
- format
- format_error
- format_error
- from_json
- from_json
- from_json
- from_json
- from_json_by_variant_name
- from_json_by_variant_name
- generate_and_add_neighbourhood
- generate_basis
- generate_basis
- generate_centro_symmetry_data
- generate_centro_symmetry_data
- generate_lattice
- generate_lattice
- generate_lattice - Calls lattice generator depending on chosen method in json file.
- generate_lattice
- generate_lattice
- generate_lattice_from_method
- generate_lattice_from_method
- generate_lattice_from_method
- generate_lattice_symmetric_gb
- get_bool_env - Tries to access an environment variable and to parse its value ...
- get_closest_lattice_site
- get_concentration_averaged_t_values - calculate average t values for all atoms.
- get_concentration_averaged_t_values
- get_concentration_values
- get_density_and_derivative_of_ref_struct
- get_density_of_ref_struct - Compute electron density of a reference structure with given la...
- get_gamma_values
- get_material_density
- get_material_density
- get_name
- get_number_of_lattice_sites
- get_potential_material_name
- get_ref_shape_factors - Get shape factors assuming reference configuration. Used for re...
- get_required_neighbourhoods
- get_required_neighbourhoods_add_forces
- get_variant_name
- get_z - get number of nearest first neighbors
- get_z2_s_a_r - get number of second-nearest neighbors, screening values for th...
- ghost_mask
- ghost_mask
- have_multispecies - Return if the multispecies feature is activated and if vacancie...
- id - Access the id of a cell or node via @ref Id.
- id
- impurity_concentrations - Access the impurity concentrations of a node via @ref ImpurityC...
- impurity_concentrations - Access the impurity concentrations of a node via @ref ImpurityC...
- incident_element - get jth incident element for vertex as vid
- indexed_simplex - return indexed simplex with node Indices from id
- indices
- initial_fixed_flags
- insert_cell_without_basis - Insert a QCCellDraft into a mesh.
- insert_halo_cell - Same as @ref insert_cell, but insert to halo cells instead.
- insert_halo_node
- insert_node_from_halo - Called by qcmesh::mesh::apply_change_set
- invert_permutation
- is_fixed - Access the property of a node whether it is fixed via @IsFixed.
- is_local_node
- lattice_cache_from_config
- lattice_cache_from_config
- load_boundary_condition
- load_boundary_conditions
- load_external_force_applicator
- load_external_force_applicator
- load_external_force_applicator
- load_lattice_cache
- load_lattice_cache
- load_lattice_cache
- load_lattice_cache
- load_lattice_parameters_from_json
- load_lattice_parameters_from_json - Load from a stream.
- load_lattice_parameters_from_json - Load from a stream.
- load_lattice_parameters_from_working_dir - Load latticegenerator_parameters.json from the current working ...
- load_mesh
- load_mesh_file
- load_mesh_from_nc
- load_mesh_from_nc
- load_nc
- load_restart_file
- load_restart_mesh_from_nc
- load_userinput_from_json - Load from a stream.
- load_userinput_from_json - Load from a stream.
- load_userinput_from_json
- load_userinput_from_working_dir - Load userinput.json from the current working directory.
- local_energy
- local_k
- local_ts
- local_weight
- main
- main
- make_nc_table
- material_id - Access the material id of a cell or node via @ref MaterialId.
- mesh_insert_cell - Insert a cell from exchanged data into a mesh.
- mesh_insert_node
- mesh_point_from_index
- mpi_chunk_span - Create a @ref ChunkSpan based on the total size of a NetCdf dim...
- n_incident_elements - get number of incident elements to vertex at vid
- node_type - Access the node type of a node via @ref NodeType.
- normal - Return the normal to the line.
- ordered_keys
- ordered_keys - Extract the ordered keys of a `std::unordered_map`.
- pack_cell - Pack cell data into a datastructure suitable for an exchange wi...
- pack_node
- parse_bool - Parse a string value to a bool with a fallback value if str is ...
- parse_lattice_structure
- parse_str
- parse_str
- partition_ghost_indices
- partition_mesh
- periodic_boundary_flag - Access the property of a node whether it is at the periodic bou...
- periodic_strains
- phi_and_derivative_series_addition
- phi_series_addition - compute additional terms in series for phi (if NN2 activated)
- point_is_near_segment
- prepare_offsets
- print_matrix
- print_relaxed_cluster
- print_relaxed_info_to_files - Print post-processed quantities
- prm
- prm - Creates a CLI option (program_options value) from a struct fiel...
- random_move
- random_move
- read_library_file
- read_library_file
- record_force
- record_force
- record_force
- redistribute - Redistribution of cells and nodes for load balancing or mesh re...
- relax_infinite
- relax_infinite
- relax_infinite
- remove_cells
- renumber_cells - hange cell keys according to global keys
- renumber_mesh_nodes
- repair_mesh - Repair a mesh by applying edge removal / face removal operation...
- repartition_cells
- repartition_cells_metis
- restart_cell_data_size
- rotate_basis
- run
- run
- run
- save_lattice_cache
- save_lattice_cache
- save_lattice_cache
- save_lattice_parameters_to_json - Save to a stream.
- save_lattice_parameters_to_json - Save to a stream.
- save_non_centrosymmetric_neighborhoods - Prints non centro-symmetric clusters if requested in the user i...
- save_userinput_to_json - Save to a stream.
- save_userinput_to_json - Save to a stream.
- serialize - Provides serialization of qcmesh::mesh::SimplexCell.
- serialize - Implement serialization for @ref netcdf_io::MeshNodalData.
- serialize - Provides serialization of qcmesh::mesh::SimplexCell.
- serialize - Provides serialization of qcmesh::mesh::SimplexCell.
- serialize
- serialize - Provides serialization of meshing::SerializedNode.
- serialize - Implement serialization for @ref qcmesh::geometry::Box.
- serialize - Provides serialization of meshing::SerializedCell.
- serialize
- serialize - Provides serialization of qcmesh::mesh::SimplexCell.
- serialize
- serialize - Provides serialization of qcmesh::mesh::SimplexCell.
- serialize
- serialize - Implement serialization for @ref netcdf_io::RestartNodalDataFin...
- serialize - Implement serialization for @ref netcdf_io::MeshCellData.
- serialize - Implement serialization for @ref netcdf_io::RestartCellData.
- serialize
- serialize
- serialize - Implement serialization for @ref netcdf_io::RestartNodalDataZer...
- serialize_lattice_structure
- set_displacement_gradient
- setup_process_boundary - Set process boundary flag for vertices connected to other proce...
- signed_distance - Distance to the line.
- signed_distance
- signed_distance
- signed_distance
- simulating_vacancies
- solve
- string_split
- string_split
- string_split
- string_split
- string_split_many
- string_split_many
- string_split_many_to_vec
- string_strip
- string_strip
- string_strip
- string_strip
- string_strip
- string_to_bool - Tries to parse a string to a bool.
- string_to_bool - Tries to parse a string to a bool.
- thermal_coordinates
- thermal_coordinates - Access the thermal coordinates of a node via @ref ThermalCoordi...
- to_json
- to_json
- to_json
- to_json
- to_string_with_zeros - An extension of std::to_string, padding the integer string with...
- total_local_impurity_concentration
- unit_vector_array
- unordered_point_array_eq
- unwrap_repatom_forces_to_petsc_vec
- unwrap_repatoms_to_petsc_vec
- update_overlapping_mesh_elements_and_nodes
- update_periodic_forces
- update_positions
- update_thermal_coordinates
- update_vectors
- update_vectors
- update_vectors
- vec_diff
- vec_to_array - Convert a std::vector <double > to a std::array <double , Size>.
- vec_to_array
- velocity_verlet_fire
- velocity_verlet_fire_infmodel
- vtk_create_array - Creates a smartpointer wrapped instance of a VTK array T, preal...
- vtk_create_array - Creates a smartpointer wrapped instance of a VTK array T, preal...
- vtk_create_grid_with_points - Creates a smartpointer wrapped vtkUnstructuredGrid, containing ...
- weight - Access the `weight` property of a cell or node via @ref Weight.
- wrap_petsc_vec_to_repatom_forces
- wrap_petsc_vec_to_repatoms - wraps the local x to repatom container locations and thermal co...
- write_mesh_2d
- write_mesh_3d
- write_mesh_file
- write_mesh_to_nc
- write_pvtk_files_2d
- write_pvtk_files_3d
- write_restart_file
- write_restart_mesh_to_nc
- write_restart_mesh_to_nc
- write_vtk_point_data_2d
- write_vtk_point_data_3d
- write_vtu_mesh_3d
- write_vtu_mesh_3d_minimal
- write_vtu_triangulation
- write_vtu_triangulation
- write_vtu_triangulation
- zbl_potential - zbl potential (blend with MEAM pair potential).
- zbl_potential_and_derivative
- zone_type_name