Collective Variables Module - Developer Documentation
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colvar::cvc Member List

This is the complete list of members for colvar::cvc, 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_child(colvardeps *child) (defined in colvardeps)colvardeps
add_keyword(char const *key)colvarparseprotected
allowed_keywordscolvarparseprotected
apply_force(colvarvalue const &cvforce)=0colvar::cvcpure virtual
atom_groupscolvar::cvc
b_try_scalablecolvar::cvc
calc_fit_gradients()colvar::cvc
calc_force_invgrads()colvar::cvcvirtual
calc_gradients()colvar::cvcinlinevirtual
calc_Jacobian_derivative()colvar::cvcvirtual
calc_value()=0colvar::cvcpure virtual
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
collect_gradients(std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)colvar::cvcvirtual
colvardeps() (defined in colvardeps)colvardeps
colvarparams()colvarparamsprotected
colvarparse()colvarparse
colvarparse(const std::string &conf)colvarparse
config_keycolvar::cvc
config_stringcolvarparseprotected
cvc(std::string const &conf)colvar::cvc
cvc()colvar::cvc
cvc_featurescolvar::cvcstatic
data_begin_poscolvarparseprotected
data_end_poscolvarparseprotected
debug_gradients()colvar::cvcvirtual
decr_ref_count(int f)colvardeps
delete_features() (defined in colvar::cvc)colvar::cvcinlinestatic
description (defined in colvardeps)colvardeps
disable(int f)colvardeps
dist2(colvarvalue const &x1, colvarvalue const &x2) constcolvar::cvcvirtual
dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) constcolvar::cvcvirtual
dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) constcolvar::cvcvirtual
do_feature_side_effects(int)colvardepsinlinevirtual
enable(int f, bool dry_run=false, bool toplevel=true)colvardeps
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_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_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() constcolvar::cvcinlinevirtual
features_atomgroup enum namecolvardeps
features_biases enum namecolvardeps
features_colvar enum namecolvardeps
features_cvc enum namecolvardeps
free_children_deps()colvardeps
ftcolvar::cvcprotected
function_typecolvar::cvc
function_typescolvar::cvcprotected
get_atom_lists()colvar::cvcvirtual
get_config() constcolvarparseinline
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=(int) 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=(size_t) 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=(cvm::real) 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,(int) 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,(size_t) 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,(long) 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,(cvm::real) 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(std::string const &param_name)colvar::cvcvirtual
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
init(std::string const &conf)colvar::cvcvirtual
init_as_angle()colvar::cvcprotected
init_as_distance()colvar::cvcprotected
init_as_periodic_angle()colvar::cvcprotected
init_dependencies()colvar::cvcvirtual
init_feature(int feature_id, const char *description, feature_type type)colvardeps
init_scalar_boundaries(cvm::real lb, cvm::real ub)colvar::cvcprotected
init_total_force_params(std::string const &conf)colvar::cvcvirtual
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
Jacobian_derivative() constcolvar::cvcinline
jdcolvar::cvcprotected
key_already_set(std::string const &key_str)colvarparseprotected
key_lookup(std::string const &conf, char const *key, std::string *data=NULL, size_t *save_pos=NULL)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
lower_boundarycolvar::cvcprotected
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() (defined in colvar::cvc)colvar::cvcinlinevirtual
namecolvar::cvc
param_exists(std::string const &param_name)colvarparams
param_grad_mapcolvarparamsprotected
param_mapcolvarparamsprotected
parentscolvardepsprivate
parse_deprecated enum valuecolvarparse
parse_deprecation_warning enum valuecolvarparse
parse_echo enum valuecolvarparse
parse_echo_default enum valuecolvarparse
parse_group(std::string const &conf, char const *group_key, bool optional=false)colvar::cvc
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
periodcolvar::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::cvcvirtual
register_atom_group(cvm::atom_group *ag)colvar::cvc
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_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
set_param(std::string const &param_name, void const *new_value)colvar::cvcvirtual
set_string(std::string const &conf)colvarparse
set_value(colvarvalue const &new_value)colvar::cvcinline
setup()colvar::cvc
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest)colvarparsestatic
strip_values(std::string &conf)colvarparseprotected
sup_coeffcolvar::cvc
sup_npcolvar::cvc
time_step_factorcolvardepsprotected
to_lower_cppstr(std::string const &in)colvarparseinlinestatic
total_force() constcolvar::cvcinline
upper_boundarycolvar::cvcprotected
value() constcolvar::cvcinline
white_spacecolvarparsestatic
widthcolvar::cvcprotected
wrap(colvarvalue &x_unwrapped) constcolvar::cvcvirtual
wrap_centercolvar::cvc
xcolvar::cvcprotected
x_oldcolvar::cvcprotected
~colvardeps() (defined in colvardeps)colvardepsvirtual
~colvarparams()colvarparamsprotectedvirtual
~colvarparse()colvarparsevirtual
~cvc()colvar::cvcvirtual