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colvarbias_restraint Member List

This is the complete list of members for colvarbias_restraint, 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) 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_colvar(std::string const &cv_name) colvarbias
add_keyword(char const *key) colvarparse [protected]
allowed_keywords colvarparse [protected]
analyze() colvarbias [inline, virtual]
b_output_energy colvarbias [protected]
bias_energy colvarbias [protected]
bias_type colvarbias
biasing_force_scaling_factors colvarbias [protected]
biasing_force_scaling_factors_bin colvarbias [protected]
bin_count(int bin_index) colvarbias [virtual]
bin_num() colvarbias [virtual]
calc_energy(std::vector< colvarvalue > const *values) colvarbias [virtual]
calc_forces(std::vector< colvarvalue > const *values) colvarbias [virtual]
can_accumulate_data() colvarbias [virtual]
change_configuration(std::string const &) colvarbias_restraint [inline, 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() colvarbias [virtual]
clear_keyword_registry() colvarparse
colvarbias::clear_state_data() colvarbias [virtual]
colvarbias_ti::clear_state_data() colvarbias_ti [virtual]
colvar_forces colvarbias [protected]
colvar_values colvarbias [protected]
colvarbias(char const *key) colvarbias
colvarbias_restraint(char const *key) colvarbias_restraint
colvarbias_ti(char const *key) colvarbias_ti
colvardeps() colvardeps
colvarparams() colvarparams [protected]
colvarparse() colvarparse
colvarparse(const std::string &conf) colvarparse
colvars colvarbias [protected]
communicate_forces() colvarbias
config_string colvarparse [protected]
current_bin() colvarbias [virtual]
cvb_features colvarbias [static]
d_restraint_potential_dk(size_t i) const=0 colvarbias_restraint [protected, pure virtual]
data_begin_pos colvarparse [protected]
data_end_pos colvarparse [protected]
decr_ref_count(int f) colvardeps
delete_features() colvarbias [inline, static]
description colvardeps
disable(int f) colvardeps
do_feature_side_effects(int) colvardeps [inline, virtual]
enable(int f, bool dry_run=false, bool toplevel=true) colvardeps
end_of_step() colvarbias [virtual]
energy_difference(std::string const &) colvarbias_restraint [inline, virtual]
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 colvarbias [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
get_config() const colvarparse [inline]
get_energy() colvarbias [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 &param_name) colvarparams [virtual]
get_param_grad_names() colvarparams [virtual]
get_param_grad_ptr(std::string const &param_name) colvarparams [virtual]
get_param_names() colvarparams [virtual]
get_param_ptr(std::string const &param_name) colvarparams [virtual]
get_state_params() const colvarbias_restraint [virtual]
get_time_step_factor() const colvardeps [inline]
getline_nocomments(std::istream &is, std::string &s) colvarparse [static]
has_data colvarbias [protected]
init(std::string const &conf) colvarbias_restraint [virtual]
init_dependencies() colvarbias [virtual]
init_feature(int feature_id, const char *description, feature_type type) colvardeps
init_grids() colvarbias_ti [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]
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]
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]
matching_state colvarbias [protected]
modify_features() colvarbias [inline, virtual]
name colvarbias
num_variables() const colvarbias [inline]
output_freq colvarbias
output_prefix colvarbias
param_exists(std::string const &param_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_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
previous_colvar_forces colvarbias [protected]
print_state() colvardeps
provide(int feature_id, bool truefalse=true) colvardeps
rank colvarbias
read_config_line(std::istream &is, std::string &line) colvarparse
read_state(std::istream &is) colvarbias
colvarbias::read_state_data(std::istream &is) colvarbias [inline, virtual]
colvarbias_ti::read_state_data(std::istream &is) colvarbias_ti [virtual]
read_state_data_key(std::istream &is, char const *key) colvarbias
read_state_prefix(std::string const &prefix) colvarbias
read_state_string(char const *buffer) colvarbias
register_param(std::string const &param_name, void *param_ptr) colvarparams [protected]
register_param_grad(std::string const &param_name, colvarvalue *param_grad_ptr) colvarparams [protected]
remove_all_children() colvardeps
remove_child(colvardeps *child) colvardeps
replica_share() colvarbias [virtual]
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() colvarbias [virtual]
restore_children_deps() colvardeps
restraint_force(size_t i) const=0 colvarbias_restraint [protected, pure virtual]
restraint_potential(size_t i) const=0 colvarbias_restraint [protected, pure virtual]
set_enabled(int feature_id, bool truefalse=true) colvardeps
set_param(std::string const &param_name, void const *new_value) colvarparams [virtual]
set_state_params(std::string const &conf) colvarbias_restraint [virtual]
set_string(std::string const &conf) colvarparse
setup_output() colvarbias [inline, virtual]
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest) colvarparse [static]
state_file_step colvarbias [protected]
state_keyword colvarbias
strip_values(std::string &conf) colvarparse [protected]
ti_avg_forces colvarbias_ti [protected]
ti_bin colvarbias_ti [protected]
ti_count colvarbias_ti [protected]
ti_system_forces colvarbias_ti [protected]
time_step_factor colvardeps [protected]
to_lower_cppstr(std::string const &in) colvarparse [inline, static]
update() colvarbias_restraint [virtual]
update_system_forces(std::vector< colvarvalue > const *subtract_forces) colvarbias_ti [virtual]
variables() colvarbias [inline]
variables(int i) const colvarbias [inline]
white_space colvarparse [static]
colvarbias::write_output_files() colvarbias [inline, virtual]
colvarbias_ti::write_output_files() colvarbias_ti [virtual]
write_state(std::ostream &os) colvarbias
colvarbias::write_state_data(std::ostream &os) colvarbias [inline, virtual]
colvarbias_ti::write_state_data(std::ostream &os) colvarbias_ti [virtual]
write_state_prefix(std::string const &prefix) colvarbias
write_state_string(std::string &output) colvarbias
write_state_to_replicas() colvarbias [inline, virtual]
write_traj(std::ostream &os) colvarbias_restraint [virtual]
write_traj_label(std::ostream &os) colvarbias_restraint [virtual]
~colvarbias() colvarbias [virtual]
~colvarbias_restraint() colvarbias_restraint [virtual]
~colvarbias_ti() colvarbias_ti [virtual]
~colvardeps() colvardeps [virtual]
~colvarparams() colvarparams [protected, virtual]
~colvarparse() colvarparse [virtual]
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