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Collective Variables Module - Developer Documentation
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This is the complete list of members for colvar::dihedral, including all inherited members.
| _get_keyval_scalar_(std::string const &conf, char const *key, TYPE &value, TYPE const &def_value, Parse_Mode const &parse_mode) | colvarparse | protected |
| _get_keyval_scalar_novalue_(std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode) | colvarparse | protected |
| _get_keyval_scalar_novalue_(std::string const &key_str, bool &value, Parse_Mode const &parse_mode) (defined in colvarparse) | colvarparse | |
| _get_keyval_scalar_value_(std::string const &key_str, std::string const &data, TYPE &value, TYPE const &def_value) | colvarparse | protected |
| _get_keyval_scalar_value_(std::string const &key_str, std::string const &data, bool &value, bool const &) (defined in colvarparse) | colvarparse | |
| _get_keyval_vector_(std::string const &conf, char const *key, std::vector< TYPE > &values, std::vector< TYPE > const &def_values, Parse_Mode const &parse_mode) | colvarparse | protected |
| add_child(colvardeps *child) (defined in colvardeps) | colvardeps | |
| add_keyword(char const *key) | colvarparse | protected |
| allowed_keywords | colvarparse | protected |
| apply_force(colvarvalue const &cvforce) | colvar::cvc | virtual |
| atom_groups | colvar::cvc | |
| b_1site_force | colvar::dihedral | protected |
| b_try_scalable | colvar::cvc | |
| calc_fit_gradients() | colvar::cvc | |
| calc_force_invgrads() | colvar::dihedral | virtual |
| calc_gradients() | colvar::dihedral | virtual |
| calc_Jacobian_derivative() | colvar::dihedral | virtual |
| calc_value() | colvar::dihedral | virtual |
| check_ascii(std::string const &conf) | colvarparse | static |
| check_braces(std::string const &conf, size_t const start_pos) | colvarparse | static |
| check_enabled(int f, std::string const &reason) const | colvardeps | inline |
| check_keywords(std::string &conf, char const *key) | colvarparse | |
| children | colvardeps | private |
| clear() | colvarparse | |
| clear_keyword_registry() | colvarparse | |
| collect_gradients(std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients) | colvar::cvc | virtual |
| colvardeps() (defined in colvardeps) | colvardeps | |
| colvarparams() | colvarparams | protected |
| colvarparse() | colvarparse | |
| colvarparse(const std::string &conf) | colvarparse | |
| config_key | colvar::cvc | |
| config_string | colvarparse | protected |
| cvc() | colvar::cvc | |
| cvc_features | colvar::cvc | protectedstatic |
| data_begin_pos | colvarparse | protected |
| data_end_pos | colvarparse | protected |
| debug_gradients() | colvar::cvc | virtual |
| decr_ref_count(int f) | colvardeps | |
| delete_features() (defined in colvar::cvc) | colvar::cvc | inlinestatic |
| description (defined in colvardeps) | colvardeps | |
| dihedral(cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3, cvm::atom const &a4) | colvar::dihedral | |
| dihedral() (defined in colvar::dihedral) | colvar::dihedral | |
| disable(int f) | colvardeps | |
| dist2(colvarvalue const &x1, colvarvalue const &x2) const | colvar::cvc | virtual |
| dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const | colvar::cvc | virtual |
| dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const | colvar::cvc | virtual |
| do_feature_side_effects(int) | colvardeps | inlinevirtual |
| enable(int f, bool dry_run=false, bool toplevel=true) | colvardeps | |
| error_key_required(std::string const &key_str, Parse_Mode const &parse_mode) | colvarparse | protected |
| exclude_feature_self(int f, int g) | colvardeps | |
| f_ag_active enum value (defined in colvardeps) | colvardeps | |
| f_ag_atom_forces enum value (defined in colvardeps) | colvardeps | |
| f_ag_center enum value (defined in colvardeps) | colvardeps | |
| f_ag_center_origin enum value (defined in colvardeps) | colvardeps | |
| f_ag_collect_atom_ids enum value | colvardeps | |
| f_ag_explicit_gradient enum value | colvardeps | |
| f_ag_fit_gradients enum value (defined in colvardeps) | colvardeps | |
| f_ag_fitting_group enum value (defined in colvardeps) | colvardeps | |
| f_ag_ntot enum value (defined in colvardeps) | colvardeps | |
| f_ag_rotate enum value (defined in colvardeps) | colvardeps | |
| f_ag_scalable enum value (defined in colvardeps) | colvardeps | |
| f_ag_scalable_com enum value (defined in colvardeps) | colvardeps | |
| f_cv_active enum value | colvardeps | |
| f_cv_awake enum value | colvardeps | |
| f_cv_collect_atom_ids enum value | colvardeps | |
| f_cv_collect_gradient enum value | colvardeps | |
| f_cv_corrfunc enum value | colvardeps | |
| f_cv_custom_function enum value | colvardeps | |
| f_cv_extended_Lagrangian enum value | colvardeps | |
| f_cv_external enum value | colvardeps | |
| f_cv_fdiff_velocity enum value | colvardeps | |
| f_cv_gradient enum value | colvardeps | |
| f_cv_grid enum value | colvardeps | |
| f_cv_hard_lower_boundary enum value | colvardeps | |
| f_cv_hard_upper_boundary enum value | colvardeps | |
| f_cv_hide_Jacobian enum value | colvardeps | |
| f_cv_homogeneous enum value (defined in colvardeps) | colvardeps | |
| f_cv_Jacobian enum value | colvardeps | |
| f_cv_Langevin enum value | colvardeps | |
| f_cv_linear enum value (defined in colvardeps) | colvardeps | |
| f_cv_lower_boundary enum value | colvardeps | |
| f_cv_multiple_ts enum value | colvardeps | |
| f_cv_ntot enum value | colvardeps | |
| f_cv_output_applied_force enum value | colvardeps | |
| f_cv_output_energy enum value | colvardeps | |
| f_cv_output_total_force enum value | colvardeps | |
| f_cv_output_value enum value | colvardeps | |
| f_cv_output_velocity enum value | colvardeps | |
| f_cv_periodic enum value | colvardeps | |
| f_cv_reflecting_lower_boundary enum value | colvardeps | |
| f_cv_reflecting_upper_boundary enum value | colvardeps | |
| f_cv_runave enum value | colvardeps | |
| f_cv_scalar enum value | colvardeps | |
| f_cv_scripted enum value | colvardeps | |
| f_cv_single_cvc enum value | colvardeps | |
| f_cv_subtract_applied_force enum value | colvardeps | |
| f_cv_total_force enum value | colvardeps | |
| f_cv_total_force_calc enum value | colvardeps | |
| f_cv_upper_boundary enum value | colvardeps | |
| f_cvb_active enum value | colvardeps | |
| f_cvb_apply_force enum value | colvardeps | |
| f_cvb_awake enum value | colvardeps | |
| f_cvb_bypass_ext_lagrangian enum value | colvardeps | |
| f_cvb_calc_pmf enum value | colvardeps | |
| f_cvb_calc_ti_samples enum value | colvardeps | |
| f_cvb_extended enum value | colvardeps | |
| f_cvb_get_total_force enum value | colvardeps | |
| f_cvb_history_dependent enum value | colvardeps | |
| f_cvb_ntot enum value (defined in colvardeps) | colvardeps | |
| f_cvb_output_acc_work enum value | colvardeps | |
| f_cvb_scalar_variables enum value | colvardeps | |
| f_cvb_scale_biasing_force enum value | colvardeps | |
| f_cvb_step_zero_data enum value | colvardeps | |
| f_cvb_time_dependent enum value | colvardeps | |
| f_cvb_write_ti_pmf enum value | colvardeps | |
| f_cvb_write_ti_samples enum value | colvardeps | |
| f_cvc_active enum value | colvardeps | |
| f_cvc_collect_atom_ids enum value | colvardeps | |
| f_cvc_com_based enum value | colvardeps | |
| f_cvc_debug_gradient enum value | colvardeps | |
| f_cvc_explicit_atom_groups enum value | colvardeps | |
| f_cvc_explicit_gradient enum value | colvardeps | |
| f_cvc_gradient enum value | colvardeps | |
| f_cvc_inv_gradient enum value | colvardeps | |
| f_cvc_Jacobian enum value | colvardeps | |
| f_cvc_lower_boundary enum value | colvardeps | |
| f_cvc_ntot enum value | colvardeps | |
| f_cvc_one_site_total_force enum value | colvardeps | |
| f_cvc_pbc_minimum_image enum value | colvardeps | |
| f_cvc_periodic enum value | colvardeps | |
| f_cvc_scalable enum value | colvardeps | |
| f_cvc_scalable_com enum value | colvardeps | |
| f_cvc_scalar enum value | colvardeps | |
| f_cvc_upper_boundary enum value | colvardeps | |
| f_cvc_width enum value | colvardeps | |
| f_type_dynamic enum value (defined in colvardeps) | colvardeps | protected |
| f_type_not_set enum value (defined in colvardeps) | colvardeps | protected |
| f_type_static enum value (defined in colvardeps) | colvardeps | protected |
| f_type_user enum value (defined in colvardeps) | colvardeps | protected |
| feature_states | colvardeps | protected |
| feature_type enum name | colvardeps | protected |
| features() const | colvar::cvc | inlinevirtual |
| features_atomgroup enum name | colvardeps | |
| features_biases enum name | colvardeps | |
| features_colvar enum name | colvardeps | |
| features_cvc enum name | colvardeps | |
| free_children_deps() | colvardeps | |
| ft | colvar::cvc | protected |
| function_type() const | colvar::cvc | |
| function_types | colvar::cvc | protected |
| get_atom_lists() | colvar::cvc | virtual |
| get_config() const | colvarparse | inline |
| get_key_string_multi_value(std::string const &conf, char const *key, std::vector< std::string > &data) | colvarparse | protected |
| get_key_string_value(std::string const &conf, char const *key, std::string &data) | colvarparse | protected |
| get_keyval(std::string const &conf, char const *key, int &value, int const &def_value=0, Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, size_t &value, size_t const &def_value=0, Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, cvm::step_number &value, cvm::step_number const &def_value=0, Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::string &value, std::string const &def_value=std::string(""), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, cvm::real &value, cvm::real const &def_value=0.0, Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, cvm::rvector &value, cvm::rvector const &def_value=cvm::rvector(), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, cvm::quaternion &value, cvm::quaternion const &def_value=cvm::quaternion(), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, colvarvalue &value, colvarvalue const &def_value=colvarvalue(colvarvalue::type_notset), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< int > &values, std::vector< int > const &def_values=std::vector< int >(0, 0), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< size_t > &values, std::vector< size_t > const &def_values=std::vector< size_t >(0, 0), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< long > &values, std::vector< long > const &def_values=std::vector< long >(0, 0), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< std::string > &values, std::vector< std::string > const &def_values=std::vector< std::string >(0, std::string("")), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< cvm::real > &values, std::vector< cvm::real > const &def_values=std::vector< cvm::real >(0, 0.0), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< cvm::rvector > &values, std::vector< cvm::rvector > const &def_values=std::vector< cvm::rvector >(0, cvm::rvector()), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< cvm::quaternion > &values, std::vector< cvm::quaternion > const &def_values=std::vector< cvm::quaternion >(0, cvm::quaternion()), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval(std::string const &conf, char const *key, std::vector< colvarvalue > &values, std::vector< colvarvalue > const &def_values=std::vector< colvarvalue >(0, colvarvalue(colvarvalue::type_notset)), Parse_Mode const parse_mode=parse_normal) (defined in colvarparse) | colvarparse | |
| get_keyval_feature(colvarparse *cvp, std::string const &conf, char const *key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal) | colvardeps | protected |
| get_param(std::string const ¶m_name) | colvarparams | virtual |
| get_param_grad(std::string const ¶m_name) | colvar::cvc | virtual |
| get_param_grad_names() | colvarparams | virtual |
| get_param_grad_ptr(std::string const ¶m_name) | colvarparams | virtual |
| get_param_names() | colvarparams | virtual |
| get_param_ptr(std::string const ¶m_name) | colvarparams | virtual |
| get_time_step_factor() const | colvardeps | inline |
| getline_nocomments(std::istream &is, std::string &s) | colvarparse | static |
| group1 | colvar::dihedral | protected |
| group2 | colvar::dihedral | protected |
| group3 | colvar::dihedral | protected |
| group4 | colvar::dihedral | protected |
| init(std::string const &conf) | colvar::dihedral | virtual |
| init_as_angle() | colvar::cvc | protected |
| init_as_distance() | colvar::cvc | protected |
| init_as_periodic_angle() | colvar::cvc | protected |
| init_dependencies() | colvar::cvc | virtual |
| init_feature(int feature_id, const char *description, feature_type type) | colvardeps | |
| init_scalar_boundaries(cvm::real lb, cvm::real ub) | colvar::cvc | protected |
| init_total_force_params(std::string const &conf) | colvar::cvc | protectedvirtual |
| is_available(int f=f_cv_active) const (defined in colvardeps) | colvardeps | inline |
| is_dynamic(int id) (defined in colvardeps) | colvardeps | inline |
| is_enabled(int f=f_cv_active) const (defined in colvardeps) | colvardeps | inline |
| is_not_set(int id) (defined in colvardeps) | colvardeps | inline |
| is_static(int id) (defined in colvardeps) | colvardeps | inline |
| is_user(int id) (defined in colvardeps) | colvardeps | inline |
| Jacobian_derivative() const | colvar::cvc | inline |
| jd | colvar::cvc | protected |
| key_already_set(std::string const &key_str) | colvarparse | protected |
| key_lookup(std::string const &conf, char const *key, std::string *data=nullptr, size_t *save_pos=nullptr) | colvarparse | |
| key_not_set enum value (defined in colvarparse) | colvarparse | protected |
| key_set_default enum value (defined in colvarparse) | colvarparse | protected |
| key_set_mode enum name | colvarparse | protected |
| key_set_modes | colvarparse | protected |
| key_set_user enum value (defined in colvarparse) | colvarparse | protected |
| keyword_delimiters_left | colvarparse | protected |
| keyword_delimiters_right | colvarparse | protected |
| lower_boundary | colvar::cvc | protected |
| mark_key_set_default(std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode) | colvarparse | protected |
| mark_key_set_user(std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode) | colvarparse | protected |
| modify_features() (defined in colvar::cvc) | colvar::cvc | inlinevirtual |
| name | colvar::cvc | |
| param_exists(std::string const ¶m_name) | colvarparams | |
| param_grad_map | colvarparams | protected |
| param_map | colvarparams | protected |
| parents | colvardeps | private |
| parse_deprecated enum value | colvarparse | |
| parse_deprecation_warning enum value | colvarparse | |
| parse_echo enum value | colvarparse | |
| parse_echo_default enum value | colvarparse | |
| parse_group(std::string const &conf, char const *group_key, bool optional=false) | colvar::cvc | protected |
| Parse_Mode enum name | colvarparse | |
| parse_normal enum value | colvarparse | |
| parse_null enum value | colvarparse | |
| parse_override enum value | colvarparse | |
| parse_required enum value | colvarparse | |
| parse_restart enum value | colvarparse | |
| parse_silent enum value | colvarparse | |
| period | colvar::cvc | |
| print_state() | colvardeps | |
| provide(int feature_id, bool truefalse=true) | colvardeps | |
| r12 | colvar::dihedral | protected |
| r23 (defined in colvar::dihedral) | colvar::dihedral | protected |
| r34 (defined in colvar::dihedral) | colvar::dihedral | protected |
| read_config_line(std::istream &is, std::string &line) | colvarparse | |
| read_data() | colvar::cvc | virtual |
| register_atom_group(cvm::atom_group *ag) | colvar::cvc | |
| register_param(std::string const ¶m_name, void *param_ptr) | colvarparams | protected |
| register_param_grad(std::string const ¶m_name, colvarvalue *param_grad_ptr) | colvarparams | protected |
| remove_all_children() | colvardeps | |
| remove_child(colvardeps *child) (defined in colvardeps) | colvardeps | |
| require_feature_alt(int f, int g, int h) | colvardeps | |
| require_feature_alt(int f, int g, int h, int i) | colvardeps | |
| require_feature_alt(int f, int g, int h, int i, int j) | colvardeps | |
| require_feature_children(int f, int g) | colvardeps | |
| require_feature_self(int f, int g) | colvardeps | |
| restore_children_deps() | colvardeps | |
| set_enabled(int feature_id, bool truefalse=true) | colvardeps | |
| set_function_type(std::string const &type) | colvar::cvc | protected |
| set_param(std::string const ¶m_name, void const *new_value) | colvar::cvc | virtual |
| set_string(std::string const &conf) | colvarparse | |
| set_value(colvarvalue const &new_value) | colvar::cvc | inline |
| setup() | colvar::cvc | |
| split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest) | colvarparse | static |
| strip_values(std::string &conf) | colvarparse | protected |
| sup_coeff | colvar::cvc | |
| sup_np | colvar::cvc | |
| time_step_factor | colvardeps | protected |
| to_lower_cppstr(std::string const &in) | colvarparse | inlinestatic |
| total_force() const | colvar::cvc | inline |
| update_description() | colvar::cvc | protected |
| upper_boundary | colvar::cvc | protected |
| value() const | colvar::cvc | inline |
| white_space | colvarparse | static |
| width | colvar::cvc | protected |
| wrap(colvarvalue &x_unwrapped) const | colvar::cvc | virtual |
| wrap_center | colvar::cvc | |
| x | colvar::cvc | protected |
| x_old | colvar::cvc | protected |
| ~colvardeps() (defined in colvardeps) | colvardeps | virtual |
| ~colvarparams() | colvarparams | protectedvirtual |
| ~colvarparse() override | colvarparse | |
| ~cvc() | colvar::cvc | virtual |
| ~dihedral() (defined in colvar::dihedral) | colvar::dihedral | inlinevirtual |
1.9.5