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colvar Member List

This is the complete list of members for colvar, 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]
acf	colvar	[protected]
acf_colvar_name	colvar	[protected]
acf_coor enum value	colvar	[protected]
acf_length	colvar	[protected]
acf_nframes	colvar	[protected]
acf_normalize	colvar	[protected]
acf_notset enum value	colvar	[protected]
acf_offset	colvar	[protected]
acf_outfile	colvar	[protected]
acf_p2coor enum value	colvar	[protected]
acf_stride	colvar	[protected]
acf_type	colvar	[protected]
acf_type_e enum name	colvar	[protected]
acf_v_history	colvar	[protected]
acf_v_history_p	colvar	[protected]
acf_vel enum value	colvar	[protected]
acf_x_history	colvar	[protected]
acf_x_history_p	colvar	[protected]
active_cvc_square_norm	colvar	[protected]
actual_value() const	colvar	[inline]
add_bias_force(colvarvalue const &force)	colvar	[inline]
add_bias_force_actual_value(colvarvalue const &force)	colvar	[inline]
add_child(colvardeps *child)	colvardeps
add_keyword(char const *key)	colvarparse	[protected]
after_restart	colvar	[protected]
allowed_keywords	colvarparse	[protected]
analyze()	colvar
applied_force() const	colvar	[inline]
atom_ids	colvar
atomic_gradients	colvar
biases	colvar
build_atom_list(void)	colvar	[protected]
calc()	colvar
calc_acf()	colvar	[protected]
calc_colvar_properties()	colvar
calc_coor_acf(std::list< colvarvalue > &x_history, colvarvalue const &x)	colvar	[protected]
calc_cvc_gradients(int first, size_t num_cvcs)	colvar
calc_cvc_Jacobians(int first, size_t num_cvcs)	colvar
calc_cvc_total_force(int first, size_t num_cvcs)	colvar
calc_cvc_values(int first, size_t num_cvcs)	colvar
calc_cvcs(int first=0, size_t num_cvcs=0)	colvar
calc_p2coor_acf(std::list< colvarvalue > &x_history, colvarvalue const &x)	colvar	[protected]
calc_runave()	colvar	[protected]
calc_vel_acf(std::list< colvarvalue > &v_history, colvarvalue const &v)	colvar	[protected]
check_ascii(std::string const &conf)	colvarparse	[static]
check_braces(std::string const &conf, size_t const start_pos)	colvarparse	[static]
check_cvc_range(int first_cvc, size_t num_cvcs)	colvar
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_cvc_data()	colvar
collect_cvc_gradients()	colvar
collect_cvc_Jacobians()	colvar
collect_cvc_total_forces()	colvar
collect_cvc_values()	colvar
colvar()	colvar
colvardeps()	colvardeps
colvarparams()	colvarparams	[protected]
colvarparse()	colvarparse
colvarparse(const std::string &conf)	colvarparse
communicate_forces()	colvar
compare_cvc(const colvar::cvc *const i, const colvar::cvc *const j)	colvar	[static]
config_string	colvarparse	[protected]
cv_features	colvar	[static]
cvc_flags	colvar	[protected]
cvc_param_exists(std::string const &param_name)	colvar
cvcs	colvar	[protected]
data_begin_pos	colvarparse	[protected]
data_end_pos	colvarparse	[protected]
decr_ref_count(int f)	colvardeps
delete_features()	colvar	[inline, static]
description	colvardeps
disable(int f)	colvardeps
dist2(colvarvalue const &x1, colvarvalue const &x2) const	colvar
dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const	colvar
dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const	colvar
do_feature_side_effects(int id)	colvar	[virtual]
enable(int f, bool dry_run=false, bool toplevel=true)	colvardeps
end_of_step()	colvar
error_key_required(std::string const &key_str, Parse_Mode const &parse_mode)	colvarparse	[protected]
exclude_feature_self(int f, int g)	colvardeps
expand_boundaries	colvar
ext_force_k	colvar	[protected]
ext_gamma	colvar	[protected]
ext_mass	colvar	[protected]
ext_sigma	colvar	[protected]
f	colvar
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_old	colvar
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]
fb	colvar
fb_actual	colvar
fdiff_velocity(colvarvalue const &xold, colvarvalue const &xnew)	colvar	[inline, protected]
feature_states	colvardeps	[protected]
feature_type enum name	colvardeps	[protected]
features() const	colvar	[inline, virtual]
features_atomgroup enum name	colvardeps
features_biases enum name	colvardeps
features_colvar enum name	colvardeps
features_cvc enum name	colvardeps
fj	colvar	[protected]
force_constant() const	colvar	[inline]
fr	colvar	[protected]
free_children_deps()	colvardeps
ft	colvar
ft_reported	colvar	[protected]
get_atom_lists()	colvar	[virtual]
get_config() const	colvarparse	[inline]
get_cvc_param(std::string const &param_name)	colvar
get_cvc_param_grad(std::string const &param_name)	colvar
get_cvc_param_ptr(std::string const &param_name)	colvar
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_time_step_factor() const	colvardeps	[inline]
get_volmap_ids()	colvar
getline_nocomments(std::istream &is, std::string &s)	colvarparse	[static]
init(std::string const &conf)	colvar
init_components(std::string const &conf)	colvar
init_custom_function(std::string const &conf)	colvar
init_dependencies()	colvar	[virtual]
init_extended_Lagrangian(std::string const &conf)	colvar
init_feature(int feature_id, const char *description, feature_type type)	colvardeps
init_grid_parameters(std::string const &conf)	colvar
init_output_flags(std::string const &conf)	colvar
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]
kinetic_energy	colvar	[protected]
lower_boundary	colvar
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	[inline, virtual]
n_active_cvcs	colvar	[protected]
name	colvar
num_active_cvcs() const	colvar	[inline]
num_cvcs() const	colvar	[inline]
num_dimensions() const	colvar	[inline]
param_exists(std::string const &param_name)	colvarparams
param_grad_map	colvarparams	[protected]
param_map	colvarparams	[protected]
parse_analysis(std::string const &conf)	colvar
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
period	colvar
periodic_boundaries() const	colvar
periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) const	colvar
potential_energy	colvar	[protected]
prev_timestep	colvar	[protected]
prev_v_ext	colvar	[protected]
prev_x_ext	colvar	[protected]
print_state()	colvardeps
provide(int feature_id, bool truefalse=true)	colvardeps
read_config_line(std::istream &is, std::string &line)	colvarparse
read_state(std::istream &is)	colvar
read_traj(std::istream &is)	colvar
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
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_bias_force()	colvar	[inline]
restore_children_deps()	colvardeps
run_ave() const	colvar	[inline]
runave	colvar	[protected]
runave_length	colvar	[protected]
runave_outfile	colvar	[protected]
runave_stride	colvar	[protected]
runave_variance	colvar	[protected]
scripted_function	colvar	[protected]
set_cvc_flags(std::vector< bool > const &flags)	colvar
set_cvc_param(std::string const &param_name, void const *new_value)	colvar
set_enabled(int feature_id, bool truefalse=true)	colvardeps
set_param(std::string const &param_name, void const *new_value)	colvarparams	[virtual]
set_string(std::string const &conf)	colvarparse
setup()	colvar
sorted_cvc_values	colvar	[protected]
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	[inline, static]
total_force() const	colvar	[inline]
update_active_cvc_square_norm()	colvar	[protected]
update_cvc_config(std::vector< std::string > const &confs)	colvar
update_cvc_flags()	colvar
update_extended_Lagrangian()	colvar
update_forces_energy()	colvar
upper_boundary	colvar
v_ext	colvar	[protected]
v_fdiff	colvar	[protected]
v_reported	colvar	[protected]
value() const	colvar	[inline]
velocity() const	colvar	[inline]
volmap_ids_	colvar	[protected]
white_space	colvarparse	[static]
width	colvar
wrap(colvarvalue &x_unwrapped) const	colvar
wrap_center	colvar
write_acf(std::ostream &os)	colvar	[protected]
write_output_files()	colvar
write_state(std::ostream &os)	colvar
write_traj(std::ostream &os)	colvar
write_traj_label(std::ostream &os)	colvar
x	colvar	[protected]
x_ext	colvar	[protected]
x_history	colvar	[protected]
x_history_p	colvar	[protected]
x_old	colvar	[protected]
x_reported	colvar	[protected]
x_restart	colvar	[protected]
~colvar()	colvar
~colvardeps()	colvardeps	[virtual]
~colvarparams()	colvarparams	[protected, virtual]
~colvarparse()	colvarparse	[virtual]

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