Collective Variables Module - Developer Documentation
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colvarmodule::atom_group Member List

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)colvarparseprotected
_get_keyval_scalar_novalue_(std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode)colvarparseprotected
_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)colvarparseprotected
_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)colvarparseprotected
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, bool silent=false) (defined in colvarmodule::atom_group)colvarmodule::atom_group
add_keyword(char const *key)colvarparseprotected
ag_featurescolvarmodule::atom_groupstatic
allowed_keywordscolvarparseprotected
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
atomscolvarmodule::atom_groupprotected
atoms_idscolvarmodule::atom_groupprotected
b_dummycolvarmodule::atom_group
b_user_defined_fitcolvarmodule::atom_group
begin() (defined in colvarmodule::atom_group)colvarmodule::atom_groupinline
begin() const (defined in colvarmodule::atom_group)colvarmodule::atom_groupinline
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_forces(main_force_accessor_T accessor_main, fitting_force_accessor_T accessor_fitting) constcolvarmodule::atom_group
calc_fit_forces_impl(main_force_accessor_T accessor_main, fitting_force_accessor_T accessor_fitting) constcolvarmodule::atom_group
calc_fit_gradients()colvarmodule::atom_group
calc_required_properties()colvarmodule::atom_group
center_of_geometry() constcolvarmodule::atom_groupinline
center_of_mass() constcolvarmodule::atom_groupinline
center_of_mass_scalar_gradient() constcolvarmodule::atom_groupinline
center_ref_pos()colvarmodule::atom_group
check_ascii(std::string const &conf)colvarparsestatic
check_braces(std::string const &conf, size_t const start_pos)colvarparsestatic
check_enabled(int f, std::string const &reason) constcolvardepsinline
check_keywords(std::string &conf, char const *key)colvarparse
childrencolvardepsprivate
clear()colvarparse
clear_keyword_registry()colvarparse
cogcolvarmodule::atom_groupprivate
cog_origcolvarmodule::atom_groupprivate
colvardeps() (defined in colvardeps)colvardeps
colvarparams()colvarparamsprotected
colvarparse()colvarparse
colvarparse(const std::string &conf)colvarparse
comcolvarmodule::atom_groupprivate
config_stringcolvarparseprotected
create_sorted_ids()colvarmodule::atom_group
data_begin_poscolvarparseprotected
data_end_poscolvarparseprotected
decr_ref_count(int f)colvardeps
delete_features() (defined in colvarmodule::atom_group)colvarmodule::atom_groupinlinestatic
description (defined in colvardeps)colvardeps
dipcolvarmodule::atom_groupprivate
dipole() constcolvarmodule::atom_groupinline
disable(int f)colvardeps
do_feature_side_effects(int id) overridecolvarmodule::atom_groupvirtual
dummy_atom_poscolvarmodule::atom_groupprotected
enable(int f, bool dry_run=false, bool toplevel=true)colvardeps
end() (defined in colvarmodule::atom_group)colvarmodule::atom_groupinline
end() const (defined in colvarmodule::atom_group)colvarmodule::atom_groupinline
error_key_required(std::string const &key_str, Parse_Mode const &parse_mode)colvarparseprotected
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 valuecolvardeps
f_ag_explicit_gradient enum valuecolvardeps
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 valuecolvardeps
f_cv_awake enum valuecolvardeps
f_cv_collect_atom_ids enum valuecolvardeps
f_cv_collect_gradient enum valuecolvardeps
f_cv_corrfunc enum valuecolvardeps
f_cv_custom_function enum valuecolvardeps
f_cv_extended_Lagrangian enum valuecolvardeps
f_cv_external enum valuecolvardeps
f_cv_fdiff_velocity enum valuecolvardeps
f_cv_gradient enum valuecolvardeps
f_cv_grid enum valuecolvardeps
f_cv_hard_lower_boundary enum valuecolvardeps
f_cv_hard_upper_boundary enum valuecolvardeps
f_cv_hide_Jacobian enum valuecolvardeps
f_cv_homogeneous enum value (defined in colvardeps)colvardeps
f_cv_Jacobian enum valuecolvardeps
f_cv_Langevin enum valuecolvardeps
f_cv_linear enum value (defined in colvardeps)colvardeps
f_cv_lower_boundary enum valuecolvardeps
f_cv_multiple_ts enum valuecolvardeps
f_cv_ntot enum valuecolvardeps
f_cv_output_applied_force enum valuecolvardeps
f_cv_output_energy enum valuecolvardeps
f_cv_output_total_force enum valuecolvardeps
f_cv_output_value enum valuecolvardeps
f_cv_output_velocity enum valuecolvardeps
f_cv_periodic enum valuecolvardeps
f_cv_reflecting_lower_boundary enum valuecolvardeps
f_cv_reflecting_upper_boundary enum valuecolvardeps
f_cv_runave enum valuecolvardeps
f_cv_scalar enum valuecolvardeps
f_cv_scripted enum valuecolvardeps
f_cv_single_cvc enum valuecolvardeps
f_cv_subtract_applied_force enum valuecolvardeps
f_cv_total_force enum valuecolvardeps
f_cv_total_force_calc enum valuecolvardeps
f_cv_upper_boundary enum valuecolvardeps
f_cvb_active enum valuecolvardeps
f_cvb_apply_force enum valuecolvardeps
f_cvb_awake enum valuecolvardeps
f_cvb_bypass_ext_lagrangian enum valuecolvardeps
f_cvb_calc_pmf enum valuecolvardeps
f_cvb_calc_ti_samples enum valuecolvardeps
f_cvb_extended enum valuecolvardeps
f_cvb_get_total_force enum valuecolvardeps
f_cvb_history_dependent enum valuecolvardeps
f_cvb_ntot enum value (defined in colvardeps)colvardeps
f_cvb_output_acc_work enum valuecolvardeps
f_cvb_scalar_variables enum valuecolvardeps
f_cvb_scale_biasing_force enum valuecolvardeps
f_cvb_step_zero_data enum valuecolvardeps
f_cvb_time_dependent enum valuecolvardeps
f_cvb_write_ti_pmf enum valuecolvardeps
f_cvb_write_ti_samples enum valuecolvardeps
f_cvc_active enum valuecolvardeps
f_cvc_collect_atom_ids enum valuecolvardeps
f_cvc_com_based enum valuecolvardeps
f_cvc_debug_gradient enum valuecolvardeps
f_cvc_explicit_atom_groups enum valuecolvardeps
f_cvc_explicit_gradient enum valuecolvardeps
f_cvc_gradient enum valuecolvardeps
f_cvc_inv_gradient enum valuecolvardeps
f_cvc_Jacobian enum valuecolvardeps
f_cvc_lower_boundary enum valuecolvardeps
f_cvc_ntot enum valuecolvardeps
f_cvc_one_site_total_force enum valuecolvardeps
f_cvc_pbc_minimum_image enum valuecolvardeps
f_cvc_periodic enum valuecolvardeps
f_cvc_scalable enum valuecolvardeps
f_cvc_scalable_com enum valuecolvardeps
f_cvc_scalar enum valuecolvardeps
f_cvc_upper_boundary enum valuecolvardeps
f_cvc_width enum valuecolvardeps
f_type_dynamic enum value (defined in colvardeps)colvardepsprotected
f_type_not_set enum value (defined in colvardeps)colvardepsprotected
f_type_static enum value (defined in colvardeps)colvardepsprotected
f_type_user enum value (defined in colvardeps)colvardepsprotected
feature_statescolvardepsprotected
feature_type enum namecolvardepsprotected
features() const overridecolvarmodule::atom_groupinlinevirtual
features_atomgroup enum namecolvardeps
features_biases enum namecolvardeps
features_colvar enum namecolvardeps
features_cvc enum namecolvardeps
fit_gradientscolvarmodule::atom_group
fitting_groupcolvarmodule::atom_group
free_children_deps()colvardeps
get_config() constcolvarparseinline
get_group_force_object() (defined in colvarmodule::atom_group)colvarmodule::atom_group
get_key_string_multi_value(std::string const &conf, char const *key, std::vector< std::string > &data)colvarparseprotected
get_key_string_value(std::string const &conf, char const *key, std::string &data)colvarparseprotected
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)colvardepsprotected
get_param(std::string const &param_name)colvarparamsvirtual
get_param_grad_names()colvarparamsvirtual
get_param_grad_ptr(std::string const &param_name)colvarparamsvirtual
get_param_names()colvarparamsvirtual
get_param_ptr(std::string const &param_name)colvarparamsvirtual
get_time_step_factor() constcolvardepsinline
getline_nocomments(std::istream &is, std::string &s)colvarparsestatic
group_forcescolvarmodule::atom_groupprotected
ids() constcolvarmodule::atom_groupinline
indexcolvarmodule::atom_groupprotected
init()colvarmodule::atom_group
init_dependencies() overridecolvarmodule::atom_groupvirtual
init_feature(int feature_id, const char *description, feature_type type)colvardeps
is_available(int f=f_cv_active) const (defined in colvardeps)colvardepsinline
is_dynamic(int id) (defined in colvardeps)colvardepsinline
is_enabled(int f=f_cv_active) const (defined in colvardeps)colvardepsinline
is_not_set(int id) (defined in colvardeps)colvardepsinline
is_static(int id) (defined in colvardeps)colvardepsinline
is_user(int id) (defined in colvardeps)colvardepsinline
keycolvarmodule::atom_group
key_already_set(std::string const &key_str)colvarparseprotected
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)colvarparseprotected
key_set_default enum value (defined in colvarparse)colvarparseprotected
key_set_mode enum namecolvarparseprotected
key_set_modescolvarparseprotected
key_set_user enum value (defined in colvarparse)colvarparseprotected
keyword_delimiters_leftcolvarparseprotected
keyword_delimiters_rightcolvarparseprotected
mark_key_set_default(std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode)colvarparseprotected
mark_key_set_user(std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode)colvarparseprotected
modify_features() override (defined in colvarmodule::atom_group)colvarmodule::atom_groupinlinevirtual
namecolvarmodule::atom_group
noforcecolvarmodule::atom_group
operator[](size_t const i) (defined in colvarmodule::atom_group)colvarmodule::atom_groupinline
operator[](size_t const i) const (defined in colvarmodule::atom_group)colvarmodule::atom_groupinline
overlap(const atom_group &g1, const atom_group &g2)colvarmodule::atom_groupstatic
param_exists(std::string const &param_name)colvarparams
param_grad_mapcolvarparamsprotected
param_mapcolvarparamsprotected
parentscolvardepsprivate
parse(std::string const &conf)colvarmodule::atom_group
parse_deprecated enum valuecolvarparse
parse_deprecation_warning enum valuecolvarparse
parse_echo enum valuecolvarparse
parse_echo_default enum valuecolvarparse
parse_fitting_options(std::string const &group_conf) (defined in colvarmodule::atom_group)colvarmodule::atom_group
Parse_Mode enum namecolvarparse
parse_normal enum valuecolvarparse
parse_null enum valuecolvarparse
parse_override enum valuecolvarparse
parse_required enum valuecolvarparse
parse_restart enum valuecolvarparse
parse_silent enum valuecolvarparse
pos_unrotatedcolvarmodule::atom_groupprivate
positions() constcolvarmodule::atom_group
positions_shifted(cvm::rvector const &shift) constcolvarmodule::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_poscolvarmodule::atom_group
ref_pos_cogcolvarmodule::atom_group
register_param(std::string const &param_name, void *param_ptr)colvarparamsprotected
register_param_grad(std::string const &param_name, colvarvalue *param_grad_ptr)colvarparamsprotected
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_groupinline
restore_children_deps()colvardeps
rotcolvarmodule::atom_group
rot_derivcolvarmodule::atom_group
scalar_com_gradientcolvarmodule::atom_groupprivate
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 &param_name, void const *new_value)colvarparamsvirtual
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_groupinline
sorted_atoms_idscolvarmodule::atom_groupprotected
sorted_atoms_ids_mapcolvarmodule::atom_groupprotected
sorted_ids() constcolvarmodule::atom_groupinline
sorted_ids_map() constcolvarmodule::atom_groupinline
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest)colvarparsestatic
strip_values(std::string &conf)colvarparseprotected
time_step_factorcolvardepsprotected
to_lower_cppstr(std::string const &in)colvarparseinlinestatic
total_chargecolvarmodule::atom_group
total_force() constcolvarmodule::atom_group
total_forces() constcolvarmodule::atom_group
total_masscolvarmodule::atom_group
update_total_charge()colvarmodule::atom_group
update_total_mass()colvarmodule::atom_group
velocities() constcolvarmodule::atom_group
white_spacecolvarparsestatic
~atom_group() overridecolvarmodule::atom_group
~colvardeps() (defined in colvardeps)colvardepsvirtual
~colvarparams()colvarparamsprotectedvirtual
~colvarparse() overridecolvarparse