| accelMD_enabled() const (defined in colvarproxy_system) | colvarproxy_system | inlinevirtual |
| add_atom_group_slot(int atom_group_id) | colvarproxy_atom_groups | protected |
| add_atom_slot(int atom_id) | colvarproxy_atoms | protected |
| add_config(std::string const &cmd, std::string const &conf) | colvarproxy | |
| add_energy(cvm::real energy) | colvarproxy_system | virtual |
| add_error_msg(std::string const &message) | colvarproxy | |
| add_volmap_slot(int volmap_id) | colvarproxy_volmaps | |
| angstrom_to_internal(cvm::real l) const | colvarproxy_system | inline |
| angstrom_value_ | colvarproxy_system | protected |
| apply_atom_force(int index, cvm::rvector const &new_force) | colvarproxy_atoms | inline |
| apply_atom_group_force(int index, cvm::rvector const &new_force) | colvarproxy_atom_groups | inline |
| apply_force_dE_dlambda(cvm::real *force) | colvarproxy_system | virtual |
| apply_volmap_force(int index, cvm::real const &new_force) | colvarproxy_volmaps | inline |
| atom_groups_charges | colvarproxy_atom_groups | protected |
| atom_groups_coms | colvarproxy_atom_groups | protected |
| atom_groups_ids | colvarproxy_atom_groups | protected |
| atom_groups_masses | colvarproxy_atom_groups | protected |
| atom_groups_max_applied_force_ | colvarproxy_atom_groups | protected |
| atom_groups_new_colvar_forces | colvarproxy_atom_groups | protected |
| atom_groups_refcount | colvarproxy_atom_groups | protected |
| atom_groups_rms_applied_force_ | colvarproxy_atom_groups | protected |
| atom_groups_total_forces | colvarproxy_atom_groups | protected |
| atoms_charges | colvarproxy_atoms | protected |
| atoms_ids | colvarproxy_atoms | protected |
| atoms_masses | colvarproxy_atoms | protected |
| atoms_max_applied_force_ | colvarproxy_atoms | protected |
| atoms_max_applied_force_id_ | colvarproxy_atoms | protected |
| atoms_new_colvar_forces | colvarproxy_atoms | protected |
| atoms_positions | colvarproxy_atoms | protected |
| atoms_refcount | colvarproxy_atoms | protected |
| atoms_rms_applied_force_ | colvarproxy_atoms | protected |
| atoms_total_forces | colvarproxy_atoms | protected |
| b_delete_requested | colvarproxy | protected |
| b_simulation_continuing | colvarproxy | protected |
| b_simulation_running | colvarproxy | protected |
| b_smp_active | colvarproxy_smp | |
| backup_file(char const *filename) | colvarproxy_io | virtual |
| backup_file(std::string const &filename) | colvarproxy_io | inline |
| boltzmann() const | colvarproxy_system | inline |
| boltzmann_ | colvarproxy_system | protected |
| boundaries_non_periodic enum value (defined in colvarproxy_system) | colvarproxy_system | protected |
| boundaries_pbc_ortho enum value (defined in colvarproxy_system) | colvarproxy_system | protected |
| boundaries_pbc_triclinic enum value (defined in colvarproxy_system) | colvarproxy_system | protected |
| Boundaries_type enum name | colvarproxy_system | protected |
| boundaries_type | colvarproxy_system | protected |
| boundaries_unsupported enum value (defined in colvarproxy_system) | colvarproxy_system | protected |
| cached_alch_lambda | colvarproxy_system | protected |
| cached_alch_lambda_changed | colvarproxy_system | protected |
| check_atom_id(int atom_number) | colvarproxy_atoms | virtual |
| check_atom_id(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) | colvarproxy_atoms | virtual |
| check_atom_name_selections_available() | colvarproxy_atoms | virtual |
| check_replicas_enabled() | colvarproxy_replicas | virtual |
| check_smp_enabled() | colvarproxy_smp | virtual |
| check_volmap_by_id(int volmap_id) | colvarproxy_volmaps | virtual |
| check_volmap_by_name(char const *volmap_name) | colvarproxy_volmaps | virtual |
| check_volmap_by_name(std::string const &volmap_name) | colvarproxy_volmaps | |
| check_volmaps_available() | colvarproxy_volmaps | virtual |
| clear_atom(int index) | colvarproxy_atoms | virtual |
| clear_atom_group(int index) | colvarproxy_atom_groups | virtual |
| clear_error_msgs() | colvarproxy | |
| clear_volmap(int index) | colvarproxy_volmaps | virtual |
| close_input_stream(std::string const &input_name) | colvarproxy_io | |
| close_input_streams() | colvarproxy_io | |
| close_output_stream(std::string const &output_name) | colvarproxy_io | virtual |
| close_output_streams() | colvarproxy_io | virtual |
| colvarproxy() | colvarproxy | |
| colvarproxy_atom_groups() | colvarproxy_atom_groups | |
| colvarproxy_atoms() | colvarproxy_atoms | |
| colvarproxy_io() | colvarproxy_io | |
| colvarproxy_replicas() | colvarproxy_replicas | |
| colvarproxy_script() | colvarproxy_script | |
| colvarproxy_smp() | colvarproxy_smp | |
| colvarproxy_system() | colvarproxy_system | |
| colvarproxy_tcl() | colvarproxy_tcl | |
| colvarproxy_volmaps() | colvarproxy_volmaps | |
| colvars | colvarproxy | |
| compute_max_atom_groups_applied_force() | colvarproxy_atom_groups | |
| compute_max_atoms_applied_force() | colvarproxy_atoms | |
| compute_max_volmaps_applied_force() | colvarproxy_volmaps | |
| compute_rms_atom_groups_applied_force() | colvarproxy_atom_groups | |
| compute_rms_atoms_applied_force() | colvarproxy_atoms | |
| compute_rms_volmaps_applied_force() | colvarproxy_volmaps | |
| compute_volmap(int flags, int volmap_id, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real *value, cvm::real *atom_field) | colvarproxy_volmaps | virtual |
| config_queue_ | colvarproxy | protected |
| default_restart_frequency() const | colvarproxy_io | inline |
| delete_input_stream(std::string const &input_name) | colvarproxy_io | |
| delete_requested() const | colvarproxy | inline |
| dt() const | colvarproxy_system | inline |
| end_of_step() | colvarproxy | |
| engine_name() const (defined in colvarproxy) | colvarproxy | inline |
| engine_name_ | colvarproxy | protected |
| engine_ready() const | colvarproxy | inline |
| engine_ready_ | colvarproxy | protected |
| error(std::string const &message) | colvarproxy | virtual |
| error_output | colvarproxy | protected |
| features_hash | colvarproxy | protected |
| flush_output_stream(std::string const &output_name) | colvarproxy_io | virtual |
| flush_output_streams() | colvarproxy_io | virtual |
| get_accelMD_factor() const | colvarproxy_system | inlinevirtual |
| get_alch_lambda(cvm::real *lambda) | colvarproxy_system | virtual |
| get_atom_applied_forces() const (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| get_atom_charge(int index) const | colvarproxy_atoms | inline |
| get_atom_charges() (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| get_atom_group_charge(int index) const | colvarproxy_atom_groups | inline |
| get_atom_group_com(int index) const | colvarproxy_atom_groups | inline |
| get_atom_group_id(int index) const | colvarproxy_atom_groups | inline |
| get_atom_group_ids() const (defined in colvarproxy_atom_groups) | colvarproxy_atom_groups | inline |
| get_atom_group_mass(int index) const | colvarproxy_atom_groups | inline |
| get_atom_group_total_force(int index) const | colvarproxy_atom_groups | inline |
| get_atom_group_velocity(int) | colvarproxy_atom_groups | inline |
| get_atom_id(int index) const | colvarproxy_atoms | inline |
| get_atom_ids() const (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| get_atom_mass(int index) const | colvarproxy_atoms | inline |
| get_atom_masses() const (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| get_atom_position(int index) const | colvarproxy_atoms | inline |
| get_atom_positions() const (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| get_atom_total_force(int index) const | colvarproxy_atoms | inline |
| get_atom_total_forces() const (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| get_atom_velocity(int) | colvarproxy_atoms | inline |
| get_current_work_dir() const | colvarproxy_io | |
| get_d2E_dlambda2(cvm::real *d2E_dlambda2) | colvarproxy_system | virtual |
| get_dE_dlambda(cvm::real *dE_dlambda) | colvarproxy_system | virtual |
| get_error_msgs() | colvarproxy | |
| get_frame(long int &) | colvarproxy_io | virtual |
| get_molid(int &molid) | colvarproxy_system | virtual |
| get_num_active_atom_groups() const | colvarproxy_atom_groups | |
| get_num_active_atoms() const | colvarproxy_atoms | |
| get_tcl_interp() | colvarproxy_tcl | inline |
| get_version_from_string(char const *version_string) | colvarproxy | |
| get_volmap_id(int index) const | colvarproxy_volmaps | inline |
| get_volmap_id_from_name(char const *volmap_name) | colvarproxy_volmaps | virtual |
| get_volmap_value(int index) const | colvarproxy_volmaps | inline |
| have_scripts | colvarproxy_script | |
| increase_refcount(int index) | colvarproxy_atoms | inline |
| indirect_lambda_biasing_force | colvarproxy_system | |
| init_atom(int atom_number) | colvarproxy_atoms | virtual |
| init_atom(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) | colvarproxy_atoms | virtual |
| init_atom_group(std::vector< int > const &atoms_ids) | colvarproxy_atom_groups | virtual |
| init_tcl_pointers() | colvarproxy_tcl | virtual |
| init_volmap_by_id(int volmap_id) | colvarproxy_volmaps | virtual |
| init_volmap_by_name(char const *volmap_name) | colvarproxy_volmaps | virtual |
| init_volmap_by_name(std::string const &volmap_name) | colvarproxy_volmaps | |
| input_prefix() const | colvarproxy_io | inline |
| input_prefix_str | colvarproxy_io | protected |
| input_stream(std::string const &input_name, std::string const description="file/channel", bool error_on_fail=true) | colvarproxy_io | |
| input_stream_error_ | colvarproxy_io | protected |
| input_stream_exists(std::string const &input_name) | colvarproxy_io | |
| input_stream_from_string(std::string const &input_name, std::string const &content, std::string const description="string") | colvarproxy_io | |
| input_streams_ | colvarproxy_io | protected |
| internal_to_angstrom(cvm::real l) const | colvarproxy_system | inline |
| io_available() override | colvarproxy | virtual |
| join_paths(std::string const &path1, std::string const &path2) const | colvarproxy_io | |
| kcal_mol_value_ | colvarproxy_system | protected |
| list_input_stream_names() const | colvarproxy_io | |
| load_atoms_pdb(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double pdb_field_value) | colvarproxy | virtual |
| load_coords_pdb(char const *filename, std::vector< cvm::atom_pos > &pos, std::vector< int > const &sorted_ids, std::string const &pdb_field, double pdb_field_value) | colvarproxy | virtual |
| log(std::string const &message) | colvarproxy | virtual |
| max_atom_groups_applied_force() const | colvarproxy_atom_groups | inline |
| max_atoms_applied_force() const | colvarproxy_atoms | inline |
| max_atoms_applied_force_id() const | colvarproxy_atoms | inline |
| modified_atom_list() const | colvarproxy_atoms | inline |
| modified_atom_list_ | colvarproxy_atoms | protected |
| modify_atom_applied_forces() (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| modify_atom_charges() (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| modify_atom_group_applied_forces() (defined in colvarproxy_atom_groups) | colvarproxy_atom_groups | inline |
| modify_atom_group_charges() (defined in colvarproxy_atom_groups) | colvarproxy_atom_groups | inline |
| modify_atom_group_masses() (defined in colvarproxy_atom_groups) | colvarproxy_atom_groups | inline |
| modify_atom_group_positions() (defined in colvarproxy_atom_groups) | colvarproxy_atom_groups | inline |
| modify_atom_group_total_forces() (defined in colvarproxy_atom_groups) | colvarproxy_atom_groups | inline |
| modify_atom_masses() (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| modify_atom_positions() (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| modify_atom_total_forces() (defined in colvarproxy_atoms) | colvarproxy_atoms | inline |
| num_replicas() | colvarproxy_replicas | virtual |
| omp_lock_state | colvarproxy_smp | protected |
| output_prefix() const | colvarproxy_io | inline |
| output_prefix_str | colvarproxy_io | protected |
| output_stream(std::string const &output_name, std::string const description) | colvarproxy_io | virtual |
| output_stream_error_ | colvarproxy_io | protected |
| output_stream_exists(std::string const &output_name) | colvarproxy_io | virtual |
| output_streams_ | colvarproxy_io | protected |
| parse_module_config() | colvarproxy | virtual |
| position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const | colvarproxy_system | virtual |
| post_run() | colvarproxy | |
| print_input_atomic_data() | colvarproxy | |
| print_output_atomic_data() | colvarproxy | |
| rand_gaussian(void) | colvarproxy_system | virtual |
| reciprocal_cell_x | colvarproxy_system | protected |
| reciprocal_cell_y (defined in colvarproxy_system) | colvarproxy_system | protected |
| reciprocal_cell_z (defined in colvarproxy_system) | colvarproxy_system | protected |
| remove_file(char const *filename) | colvarproxy_io | virtual |
| remove_file(std::string const &filename) | colvarproxy_io | inline |
| rename_file(char const *filename, char const *newfilename) | colvarproxy_io | virtual |
| rename_file(std::string const &filename, std::string const &newfilename) | colvarproxy_io | inline |
| replica_comm_barrier() | colvarproxy_replicas | virtual |
| replica_comm_recv(char *msg_data, int buf_len, int src_rep) | colvarproxy_replicas | virtual |
| replica_comm_send(char *msg_data, int msg_len, int dest_rep) | colvarproxy_replicas | virtual |
| replica_index() | colvarproxy_replicas | virtual |
| replicas_mpi_comm | colvarproxy_replicas | protected |
| replicas_mpi_num | colvarproxy_replicas | protected |
| replicas_mpi_rank | colvarproxy_replicas | protected |
| request_deletion() | colvarproxy | virtual |
| request_total_force(bool yesno) | colvarproxy_system | virtual |
| reset() | colvarproxy | virtual |
| reset_modified_atom_list() | colvarproxy_atoms | inline |
| reset_pbc_lattice() | colvarproxy_system | |
| restart_frequency_engine | colvarproxy_io | protected |
| restart_output_prefix() const | colvarproxy_io | inline |
| restart_output_prefix_str | colvarproxy_io | protected |
| rms_atom_groups_applied_force() const | colvarproxy_atom_groups | inline |
| rms_atoms_applied_force() const | colvarproxy_atoms | inline |
| run_colvar_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value) (defined in colvarproxy_script) | colvarproxy_script | virtual |
| run_colvar_gradient_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient) (defined in colvarproxy_script) | colvarproxy_script | virtual |
| run_force_callback() | colvarproxy_script | virtual |
| scalable_group_coms() | colvarproxy_atom_groups | virtual |
| script | colvarproxy_script | |
| send_alch_lambda() | colvarproxy_system | virtual |
| set_alch_lambda(cvm::real lambda) | colvarproxy_system | |
| set_default_restart_frequency(int freq) | colvarproxy_io | virtual |
| set_frame(long int) | colvarproxy_io | virtual |
| set_input_prefix(std::string const &prefix) | colvarproxy_io | virtual |
| set_integration_timestep(cvm::real dt) | colvarproxy_system | virtual |
| set_output_prefix(std::string const &prefix) | colvarproxy_io | virtual |
| set_replicas_mpi_communicator(replicas_mpi_comm_t comm) | colvarproxy_replicas | virtual |
| set_restart_output_prefix(std::string const &prefix) | colvarproxy_io | virtual |
| set_target_temperature(cvm::real T) | colvarproxy_system | virtual |
| set_tcl_interp(Tcl_Interp *interp) | colvarproxy_tcl | inline |
| set_unit_system(std::string const &units, bool check_only) | colvarproxy_system | virtual |
| setup() | colvarproxy | virtual |
| simulation_continuing() const | colvarproxy | inline |
| simulation_running() const | colvarproxy | inline |
| smp_biases_loop() | colvarproxy_smp | virtual |
| smp_biases_script_loop() | colvarproxy_smp | virtual |
| smp_colvars_loop() | colvarproxy_smp | virtual |
| smp_lock() | colvarproxy_smp | virtual |
| smp_num_threads() | colvarproxy_smp | virtual |
| smp_thread_id() | colvarproxy_smp | virtual |
| smp_trylock() | colvarproxy_smp | virtual |
| smp_unlock() | colvarproxy_smp | virtual |
| target_temperature() const | colvarproxy_system | inline |
| target_temperature_ | colvarproxy_system | protected |
| tcl_available() | colvarproxy_tcl | inline |
| tcl_get_str(void *obj) | colvarproxy_tcl | |
| tcl_interp_ | colvarproxy_tcl | protected |
| tcl_run_colvar_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value) | colvarproxy_tcl | |
| tcl_run_colvar_gradient_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient) | colvarproxy_tcl | |
| tcl_run_file(std::string const &fileName) (defined in colvarproxy_tcl) | colvarproxy_tcl | |
| tcl_run_force_callback() | colvarproxy_tcl | |
| tcl_run_script(std::string const &script) (defined in colvarproxy_tcl) | colvarproxy_tcl | |
| timestep_ | colvarproxy_system | protected |
| total_force_requested | colvarproxy_system | protected |
| total_forces_enabled() const | colvarproxy_system | virtual |
| total_forces_same_step() const | colvarproxy_system | virtual |
| unit_cell_x | colvarproxy_system | protected |
| unit_cell_y (defined in colvarproxy_system) | colvarproxy_system | protected |
| unit_cell_z (defined in colvarproxy_system) | colvarproxy_system | protected |
| units | colvarproxy_system | |
| update_input() | colvarproxy | virtual |
| update_output() | colvarproxy | virtual |
| update_pbc_lattice() | colvarproxy_system | |
| updated_charges() const | colvarproxy_atoms | inline |
| updated_charges_ (defined in colvarproxy_atoms) | colvarproxy_atoms | protected |
| updated_masses() const | colvarproxy_atoms | inline |
| updated_masses_ | colvarproxy_atoms | protected |
| version_int | colvarproxy | protected |
| version_number() const | colvarproxy | inline |
| volmap_flag_gradients enum value (defined in colvarproxy_volmaps) | colvarproxy_volmaps | |
| volmap_flag_null enum value (defined in colvarproxy_volmaps) | colvarproxy_volmaps | |
| volmap_flag_use_atom_field enum value (defined in colvarproxy_volmaps) | colvarproxy_volmaps | |
| volmaps_ids | colvarproxy_volmaps | protected |
| volmaps_max_applied_force_ | colvarproxy_volmaps | protected |
| volmaps_new_colvar_forces | colvarproxy_volmaps | protected |
| volmaps_refcount | colvarproxy_volmaps | protected |
| volmaps_rms_applied_force_ | colvarproxy_volmaps | protected |
| volmaps_values | colvarproxy_volmaps | protected |
| ~colvarproxy() override | colvarproxy | |
| ~colvarproxy_atom_groups() | colvarproxy_atom_groups | virtual |
| ~colvarproxy_atoms() | colvarproxy_atoms | virtual |
| ~colvarproxy_io() | colvarproxy_io | virtual |
| ~colvarproxy_replicas() | colvarproxy_replicas | virtual |
| ~colvarproxy_script() | colvarproxy_script | virtual |
| ~colvarproxy_smp() | colvarproxy_smp | virtual |
| ~colvarproxy_system() | colvarproxy_system | virtual |
| ~colvarproxy_tcl() | colvarproxy_tcl | virtual |
| ~colvarproxy_volmaps() | colvarproxy_volmaps | virtual |
