Collective Variables Module - Developer Documentation
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This is the complete list of members for colvarmodule::atom_group, 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_atom(cvm::atom const &a) | colvarmodule::atom_group | |
add_atom_id(int aid) | colvarmodule::atom_group | |
add_atom_name_residue_range(std::string const &psf_segid, std::string const &range_conf) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
add_atom_numbers(std::string const &numbers_conf) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
add_atom_numbers_range(std::string const &range_conf) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
add_atoms_of_group(atom_group const *ag) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
add_child(colvardeps *child) (defined in colvardeps) | colvardeps | |
add_index_group(std::string const &index_group_name) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
add_keyword(char const *key) | colvarparse | protected |
ag_features | colvarmodule::atom_group | static |
allowed_keywords | colvarparse | protected |
apply_colvar_force(cvm::real const &force) | colvarmodule::atom_group | |
apply_force(cvm::rvector const &force) | colvarmodule::atom_group | |
apply_translation(cvm::rvector const &t) | colvarmodule::atom_group | |
atom_group() | colvarmodule::atom_group | |
atom_group(char const *key) | colvarmodule::atom_group | |
atom_group(std::vector< cvm::atom > const &atoms_in) | colvarmodule::atom_group | |
atoms | colvarmodule::atom_group | protected |
atoms_ids | colvarmodule::atom_group | protected |
b_dummy | colvarmodule::atom_group | |
b_user_defined_fit | colvarmodule::atom_group | |
begin() (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
begin() const (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
calc_apply_roto_translation() | colvarmodule::atom_group | |
calc_center_of_geometry() | colvarmodule::atom_group | |
calc_center_of_mass() | colvarmodule::atom_group | |
calc_dipole(cvm::atom_pos const &dipole_center) | colvarmodule::atom_group | |
calc_fit_gradients() | colvarmodule::atom_group | |
calc_fit_gradients_impl() | colvarmodule::atom_group | |
calc_required_properties() | colvarmodule::atom_group | |
center_of_geometry() const | colvarmodule::atom_group | inline |
center_of_mass() const | colvarmodule::atom_group | inline |
center_of_mass_scalar_gradient() const | colvarmodule::atom_group | inline |
center_ref_pos() | colvarmodule::atom_group | |
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 | |
cog | colvarmodule::atom_group | private |
cog_orig | colvarmodule::atom_group | private |
colvardeps() (defined in colvardeps) | colvardeps | |
colvarparams() | colvarparams | protected |
colvarparse() | colvarparse | |
colvarparse(const std::string &conf) | colvarparse | |
com | colvarmodule::atom_group | private |
config_string | colvarparse | protected |
create_sorted_ids() | colvarmodule::atom_group | |
data_begin_pos | colvarparse | protected |
data_end_pos | colvarparse | protected |
decr_ref_count(int f) | colvardeps | |
delete_features() (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inlinestatic |
description (defined in colvardeps) | colvardeps | |
dip | colvarmodule::atom_group | private |
dipole() const | colvarmodule::atom_group | inline |
disable(int f) | colvardeps | |
do_feature_side_effects(int id) override | colvarmodule::atom_group | virtual |
dummy_atom_pos | colvarmodule::atom_group | protected |
enable(int f, bool dry_run=false, bool toplevel=true) | colvardeps | |
end() (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
end() const (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
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 override | colvarmodule::atom_group | inlinevirtual |
features_atomgroup enum name | colvardeps | |
features_biases enum name | colvardeps | |
features_colvar enum name | colvardeps | |
features_cvc enum name | colvardeps | |
fit_gradients | colvarmodule::atom_group | |
fitting_group | colvarmodule::atom_group | |
free_children_deps() | colvardeps | |
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_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 |
ids() const | colvarmodule::atom_group | inline |
index | colvarmodule::atom_group | protected |
init() | colvarmodule::atom_group | |
init_dependencies() override | colvarmodule::atom_group | virtual |
init_feature(int feature_id, const char *description, feature_type type) | colvardeps | |
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 |
key | colvarmodule::atom_group | |
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 |
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() override (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inlinevirtual |
name | colvarmodule::atom_group | |
noforce | colvarmodule::atom_group | |
operator[](size_t const i) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
operator[](size_t const i) const (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
overlap(const atom_group &g1, const atom_group &g2) | colvarmodule::atom_group | static |
param_exists(std::string const ¶m_name) | colvarparams | |
param_grad_map | colvarparams | protected |
param_map | colvarparams | protected |
parents | colvardeps | private |
parse(std::string const &conf) | colvarmodule::atom_group | |
parse_deprecated enum value | colvarparse | |
parse_deprecation_warning enum value | colvarparse | |
parse_echo enum value | colvarparse | |
parse_echo_default enum value | colvarparse | |
parse_fitting_options(std::string const &group_conf) (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
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 | |
positions() const | colvarmodule::atom_group | |
positions_shifted(cvm::rvector const &shift) const | colvarmodule::atom_group | |
print_atom_ids() const (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
print_properties(std::string const &colvar_name, int i, int j) | colvarmodule::atom_group | |
print_state() | colvardeps | |
provide(int feature_id, bool truefalse=true) | colvardeps | |
read_config_line(std::istream &is, std::string &line) | colvarparse | |
read_positions() | colvarmodule::atom_group | |
read_total_forces() | colvarmodule::atom_group | |
read_velocities() | colvarmodule::atom_group | |
ref_pos | colvarmodule::atom_group | |
ref_pos_cog | colvarmodule::atom_group | |
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_atom(cvm::atom_iter ai) | colvarmodule::atom_group | |
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 | |
reset_atoms_data() | colvarmodule::atom_group | inline |
restore_children_deps() | colvardeps | |
rot | colvarmodule::atom_group | |
rot_deriv | colvarmodule::atom_group | |
scalar_com_gradient | colvarmodule::atom_group | private |
set_dummy() | colvarmodule::atom_group | |
set_dummy_pos(cvm::atom_pos const &pos) | colvarmodule::atom_group | |
set_enabled(int feature_id, bool truefalse=true) | colvardeps | |
set_param(std::string const ¶m_name, void const *new_value) | colvarparams | virtual |
set_string(std::string const &conf) | colvarparse | |
set_weighted_gradient(cvm::rvector const &grad) | colvarmodule::atom_group | |
setup() | colvarmodule::atom_group | |
setup_rotation_derivative() (defined in colvarmodule::atom_group) | colvarmodule::atom_group | |
size() const (defined in colvarmodule::atom_group) | colvarmodule::atom_group | inline |
sorted_atoms_ids | colvarmodule::atom_group | protected |
sorted_atoms_ids_map | colvarmodule::atom_group | protected |
sorted_ids() const | colvarmodule::atom_group | inline |
sorted_ids_map() const | colvarmodule::atom_group | inline |
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest) | colvarparse | static |
strip_values(std::string &conf) | colvarparse | protected |
time_step_factor | colvardeps | protected |
to_lower_cppstr(std::string const &in) | colvarparse | inlinestatic |
total_charge | colvarmodule::atom_group | |
total_force() const | colvarmodule::atom_group | |
total_forces() const | colvarmodule::atom_group | |
total_mass | colvarmodule::atom_group | |
update_total_charge() | colvarmodule::atom_group | |
update_total_mass() | colvarmodule::atom_group | |
velocities() const | colvarmodule::atom_group | |
white_space | colvarparse | static |
~atom_group() override | colvarmodule::atom_group | |
~colvardeps() (defined in colvardeps) | colvardeps | virtual |
~colvarparams() | colvarparams | protectedvirtual |
~colvarparse() override | colvarparse |