_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) | 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 &) | 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) | colvardeps | |
add_keyword(char const *key) | colvarparse | [protected] |
allowed_keywords | colvarparse | [protected] |
apply_force(colvarvalue const &force) | colvar::map_total | [virtual] |
atom_groups | colvar::cvc | |
atom_weights | colvar::map_total | [protected] |
atoms | colvar::map_total | [protected] |
b_try_scalable | colvar::cvc | |
calc_fit_gradients() | colvar::cvc | |
calc_force_invgrads() | colvar::cvc | [virtual] |
calc_gradients() | colvar::map_total | [virtual] |
calc_Jacobian_derivative() | colvar::cvc | [virtual] |
calc_value() | colvar::map_total | [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 | |
clear() | colvarparse | |
clear_keyword_registry() | colvarparse | |
collect_gradients(std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients) | colvar::cvc | [virtual] |
colvardeps() | colvardeps | |
colvarparams() | colvarparams | [protected] |
colvarparse() | colvarparse | |
colvarparse(const std::string &conf) | colvarparse | |
config_key | colvar::cvc | |
config_string | colvarparse | [protected] |
cvc(std::string const &conf) | colvar::cvc | |
cvc() | colvar::cvc | |
cvc_features | colvar::cvc | [static] |
data_begin_pos | colvarparse | [protected] |
data_end_pos | colvarparse | [protected] |
debug_gradients() | colvar::cvc | [virtual] |
decr_ref_count(int f) | colvardeps | |
delete_features() | colvar::cvc | [inline, static] |
description | colvardeps | |
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 | [inline, virtual] |
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 | colvardeps | |
f_ag_atom_forces enum value | colvardeps | |
f_ag_center enum value | colvardeps | |
f_ag_center_origin enum value | colvardeps | |
f_ag_collect_atom_ids enum value | colvardeps | |
f_ag_explicit_gradient enum value | colvardeps | |
f_ag_fit_gradients enum value | colvardeps | |
f_ag_fitting_group enum value | colvardeps | |
f_ag_ntot enum value | colvardeps | |
f_ag_rotate enum value | colvardeps | |
f_ag_scalable enum value | colvardeps | |
f_ag_scalable_com enum value | 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 | colvardeps | |
f_cv_Jacobian enum value | colvardeps | |
f_cv_Langevin enum value | colvardeps | |
f_cv_linear enum value | 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_get_total_force enum value | colvardeps | |
f_cvb_history_dependent enum value | colvardeps | |
f_cvb_ntot enum value | 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_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 | colvardeps | [protected] |
f_type_not_set enum value | colvardeps | [protected] |
f_type_static enum value | colvardeps | [protected] |
f_type_user enum value | colvardeps | [protected] |
feature_states | colvardeps | [protected] |
feature_type enum name | colvardeps | [protected] |
features() const | colvar::cvc | [inline, virtual] |
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 | 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=(int) 0, Parse_Mode const parse_mode=parse_normal) | colvarparse | |
get_keyval(std::string const &conf, char const *key, size_t &value, size_t const &def_value=(size_t) 0, Parse_Mode const parse_mode=parse_normal) | colvarparse | |
get_keyval(std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal) | 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) | 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) | colvarparse | |
get_keyval(std::string const &conf, char const *key, cvm::real &value, cvm::real const &def_value=(cvm::real) 0.0, Parse_Mode const parse_mode=parse_normal) | 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) | 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) | 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) | colvarparse | |
get_keyval(std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal) | colvarparse | |
get_keyval(std::string const &conf, char const *key, std::vector< int > &values, std::vector< int > const &def_values=std::vector< int >(0,(int) 0), Parse_Mode const parse_mode=parse_normal) | 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,(size_t) 0), Parse_Mode const parse_mode=parse_normal) | colvarparse | |
get_keyval(std::string const &conf, char const *key, std::vector< long > &values, std::vector< long > const &def_values=std::vector< long >(0,(long) 0), Parse_Mode const parse_mode=parse_normal) | 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) | 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,(cvm::real) 0.0), Parse_Mode const parse_mode=parse_normal) | 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) | 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) | 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) | 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] |
init(std::string const &conf) | colvar::map_total | [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 | [virtual] |
is_available(int f=f_cv_active) const | colvardeps | [inline] |
is_dynamic(int id) | colvardeps | [inline] |
is_enabled(int f=f_cv_active) const | colvardeps | [inline] |
is_not_set(int id) | colvardeps | [inline] |
is_static(int id) | colvardeps | [inline] |
is_user(int id) | 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=NULL, size_t *save_pos=NULL) | colvarparse | |
key_not_set enum value | colvarparse | [protected] |
key_set_default enum value | colvarparse | [protected] |
key_set_mode enum name | colvarparse | [protected] |
key_set_modes | colvarparse | [protected] |
key_set_user enum value | colvarparse | [protected] |
keyword_delimiters_left | colvarparse | [protected] |
keyword_delimiters_right | colvarparse | [protected] |
lower_boundary | colvar::cvc | [protected] |
map_total() | colvar::map_total | |
map_total(std::string const &conf) | colvar::map_total | |
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() | colvar::cvc | [inline, virtual] |
name | colvar::cvc | |
param_exists(std::string const ¶m_name) | colvarparams | |
param_grad_map | colvarparams | [protected] |
param_map | colvarparams | [protected] |
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 | |
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 | |
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) | 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 | |
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 | [inline, static] |
total_force() const | colvar::cvc | [inline] |
upper_boundary | colvar::cvc | [protected] |
value() const | colvar::cvc | [inline] |
volmap_id | colvar::map_total | [protected] |
volmap_index | colvar::map_total | [protected] |
volmap_name | colvar::map_total | [protected] |
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() | colvardeps | [virtual] |
~colvarparams() | colvarparams | [protected, virtual] |
~colvarparse() | colvarparse | [virtual] |
~cvc() | colvar::cvc | [virtual] |
~map_total() | colvar::map_total | [inline, virtual] |