| acos(real const &x) | colvarmodule | [inline, static] |
| analyze() | colvarmodule | |
| append_new_config(std::string const &conf) | colvarmodule | |
| asin(real const &x) | colvarmodule | [inline, static] |
| atan2(real const &x, real const &y) | colvarmodule | [inline, static] |
| atom class | colvarmodule | [friend] |
| atom_const_iter typedef | colvarmodule | |
| atom_group class | colvarmodule | [friend] |
| atom_group_by_name(std::string const &name) | colvarmodule | [static] |
| atom_iter typedef | colvarmodule | |
| atom_pos typedef | colvarmodule | |
| backup_file(char const *filename) | colvarmodule | [static] |
| bias_by_name(std::string const &name) | colvarmodule | [static] |
| biases | colvarmodule | |
| biases_active() | colvarmodule | |
| calc() | colvarmodule | |
| calc_biases() | colvarmodule | |
| calc_colvars() | colvarmodule | |
| calc_scripted_forces() | colvarmodule | |
| change_configuration(std::string const &bias_name, std::string const &conf) | colvarmodule | |
| cite_feature(std::string const &feature) | colvarmodule | |
| clear_error() | colvarmodule | [static] |
| close_traj_file() | colvarmodule | |
| colvar_by_name(std::string const &name) | colvarmodule | [static] |
| colvarmodule(colvarproxy *proxy) | colvarmodule | |
| colvarproxy class | colvarmodule | [friend] |
| colvarscript class | colvarmodule | [friend] |
| config_changed() | colvarmodule | |
| cos(real const &x) | colvarmodule | [inline, static] |
| cv_prec | colvarmodule | [static] |
| cv_traj_freq | colvarmodule | [static] |
| cv_traj_name | colvarmodule | [protected] |
| cv_traj_write_labels | colvarmodule | [protected] |
| cv_width | colvarmodule | [static] |
| debug() | colvarmodule | [inline, static] |
| debug_gradients_step_size | colvarmodule | [static] |
| decrease_depth() | colvarmodule | [static] |
| depth() | colvarmodule | [static] |
| depth_s | colvarmodule | [protected] |
| depth_v | colvarmodule | [protected] |
| dt() | colvarmodule | [static] |
| en_prec | colvarmodule | [static] |
| en_width | colvarmodule | [static] |
| end_of_step() | colvarmodule | |
| energy_difference(std::string const &bias_name, std::string const &conf) | colvarmodule | |
| error(std::string const &message, int code=COLVARS_ERROR) | colvarmodule | [static] |
| exp(real const &x) | colvarmodule | [inline, static] |
| fabs(real const &x) | colvarmodule | [inline, static] |
| feature_report(int flag=0) | colvarmodule | |
| floor(real const &x) | colvarmodule | [inline, static] |
| get_config() const | colvarmodule | |
| get_error() | colvarmodule | [inline, static] |
| get_error_bit(int code) | colvarmodule | [static] |
| getline(std::istream &is, std::string &line) | colvarmodule | [static] |
| increase_depth() | colvarmodule | [static] |
| index_file_names | colvarmodule | |
| index_group_names | colvarmodule | |
| index_groups | colvarmodule | |
| integer_power(real const &x, int const n) | colvarmodule | [inline, static] |
| it | colvarmodule | [static] |
| it_restart | colvarmodule | [static] |
| it_width | colvarmodule | [static] |
| line_marker | colvarmodule | [static] |
| load_atoms(char const *filename, atom_group &atoms, std::string const &pdb_field, double pdb_field_value=0.0) | colvarmodule | [static] |
| load_coords(char const *filename, std::vector< rvector > *pos, atom_group *atoms, std::string const &pdb_field, double pdb_field_value=0.0) | colvarmodule | [static] |
| load_coords_xyz(char const *filename, std::vector< rvector > *pos, atom_group *atoms) | colvarmodule | |
| log(std::string const &message, int min_log_level=10) | colvarmodule | [static] |
| log_default_params() | colvarmodule | [inline, static] |
| log_init_messages() | colvarmodule | [inline, static] |
| log_input_files() | colvarmodule | [inline, static] |
| log_level() | colvarmodule | [inline, static] |
| log_output_files() | colvarmodule | [inline, static] |
| log_user_params() | colvarmodule | [inline, static] |
| logn(real const &x) | colvarmodule | [inline, static] |
| main() | colvarmodule | [static] |
| num_biases() const | colvarmodule | |
| num_biases_feature(int feature_id) const | colvarmodule | |
| num_biases_type(std::string const &type) const | colvarmodule | |
| num_variables() const | colvarmodule | |
| num_variables_feature(int feature_id) const | colvarmodule | |
| open_traj_file(std::string const &file_name) | colvarmodule | |
| output_prefix() | colvarmodule | [inline, static] |
| parse | colvarmodule | [protected] |
| parse_biases(std::string const &conf) | colvarmodule | |
| parse_colvars(std::string const &conf) | colvarmodule | |
| parse_config(std::string &conf) | colvarmodule | |
| parse_global_params(std::string const &conf) | colvarmodule | |
| position_distance(atom_pos const &pos1, atom_pos const &pos2) | colvarmodule | [static] |
| pow(real const &x, real const &y) | colvarmodule | [inline, static] |
| print_total_forces_errning(bool warn_total_forces) | colvarmodule | |
| proxy | colvarmodule | [static] |
| rand_gaussian(void) | colvarmodule | [static] |
| read_colvar(std::string const &name) | colvarmodule | |
| read_config_file(char const *config_file_name) | colvarmodule | |
| read_config_string(std::string const &conf) | colvarmodule | |
| read_index_file(char const *filename) | colvarmodule | |
| read_objects_state(std::istream &is) | colvarmodule | |
| read_restart(std::istream &is) | colvarmodule | |
| read_traj(char const *traj_filename, long traj_read_begin, long traj_read_end) | colvarmodule | |
| real typedef | colvarmodule | |
| register_named_atom_group(atom_group *ag) | colvarmodule | |
| request_total_force() | colvarmodule | [static] |
| reset() | colvarmodule | |
| reset_index_groups() | colvarmodule | |
| residue_id typedef | colvarmodule | |
| restart_out_freq | colvarmodule | [static] |
| restart_out_name | colvarmodule | |
| restart_version() const | colvarmodule | [inline] |
| restart_version_int | colvarmodule | [protected] |
| restart_version_number() const | colvarmodule | [inline] |
| restart_version_str | colvarmodule | [protected] |
| run_tcl_script(std::string const &filename) | colvarmodule | |
| scripted_forces() | colvarmodule | [inline, static] |
| scripting_after_biases | colvarmodule | [static] |
| set_error_bits(int code) | colvarmodule | [static] |
| setup_input() | colvarmodule | |
| setup_output() | colvarmodule | |
| sin(real const &x) | colvarmodule | [inline, static] |
| size() const | colvarmodule | |
| sqrt(real const &x) | colvarmodule | [inline, static] |
| state_file_prefix(char const *filename) | colvarmodule | [static] |
| step_absolute() | colvarmodule | [inline, static] |
| step_number typedef | colvarmodule | |
| step_relative() | colvarmodule | [inline, static] |
| time_dependent_biases() const | colvarmodule | |
| to_str(char const *s) | colvarmodule | [static] |
| to_str(std::string const &s) | colvarmodule | [static] |
| to_str(bool x) | colvarmodule | [static] |
| to_str(int const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(size_t const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(long int const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(step_number const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(real const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(rvector const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(quaternion const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(colvarvalue const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(vector1d< real > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(matrix2d< real > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< int > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< size_t > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< long int > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< real > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< rvector > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< quaternion > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< colvarvalue > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| to_str(std::vector< std::string > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
| total_bias_energy | colvarmodule | |
| unregister_named_atom_group(atom_group *ag) | colvarmodule | |
| update_colvar_forces() | colvarmodule | |
| update_engine_parameters() | colvarmodule | |
| usage_ | colvarmodule | [protected] |
| use_scripted_forces | colvarmodule | [static] |
| variables() | colvarmodule | |
| variables_active() | colvarmodule | |
| variables_active_smp() | colvarmodule | |
| variables_active_smp_items() | colvarmodule | |
| version() const | colvarmodule | [inline] |
| version_number() const | colvarmodule | [inline] |
| wrap_string(std::string const &s, size_t nchars) | colvarmodule | [static] |
| write_output_files() | colvarmodule | |
| write_restart(std::ostream &os) | colvarmodule | |
| write_restart_file(std::string const &out_name) | colvarmodule | |
| write_restart_string(std::string &output) | colvarmodule | |
| write_traj(std::ostream &os) | colvarmodule | |
| write_traj_files() | colvarmodule | |
| write_traj_label(std::ostream &os) | colvarmodule | |
| xyz_reader_use_count | colvarmodule | [protected] |
| ~colvarmodule() | colvarmodule | |
