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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]
acfcolvar [protected]
acf_colvar_namecolvar [protected]
acf_coor enum valuecolvar [protected]
acf_lengthcolvar [protected]
acf_nframescolvar [protected]
acf_normalizecolvar [protected]
acf_notset enum valuecolvar [protected]
acf_offsetcolvar [protected]
acf_outfilecolvar [protected]
acf_p2coor enum valuecolvar [protected]
acf_stridecolvar [protected]
acf_typecolvar [protected]
acf_type_e enum namecolvar [protected]
acf_v_historycolvar [protected]
acf_v_history_pcolvar [protected]
acf_vel enum valuecolvar [protected]
acf_x_historycolvar [protected]
acf_x_history_pcolvar [protected]
active_cvc_square_normcolvar [protected]
actual_value() constcolvar [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_restartcolvar [protected]
allowed_keywordscolvarparse [protected]
analyze()colvar
applied_force() constcolvar [inline]
atom_idscolvar
atomic_gradientscolvar
biasescolvar
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) constcolvardeps [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_stringcolvarparse [protected]
cv_featurescolvar [static]
cvc_flagscolvar [protected]
cvc_param_exists(std::string const &param_name)colvar
cvcscolvar [protected]
data_begin_poscolvarparse [protected]
data_end_poscolvarparse [protected]
decr_ref_count(int f)colvardeps
delete_features()colvar [inline, static]
descriptioncolvardeps
disable(int f)colvardeps
dist2(colvarvalue const &x1, colvarvalue const &x2) constcolvar
dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) constcolvar
dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) constcolvar
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_boundariescolvar
ext_force_kcolvar [protected]
ext_gammacolvar [protected]
ext_masscolvar [protected]
ext_sigmacolvar [protected]
fcolvar
f_ag_active enum valuecolvardeps
f_ag_atom_forces enum valuecolvardeps
f_ag_center enum valuecolvardeps
f_ag_center_origin enum valuecolvardeps
f_ag_collect_atom_ids enum valuecolvardeps
f_ag_explicit_gradient enum valuecolvardeps
f_ag_fit_gradients enum valuecolvardeps
f_ag_fitting_group enum valuecolvardeps
f_ag_ntot enum valuecolvardeps
f_ag_rotate enum valuecolvardeps
f_ag_scalable enum valuecolvardeps
f_ag_scalable_com enum valuecolvardeps
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 valuecolvardeps
f_cv_Jacobian enum valuecolvardeps
f_cv_Langevin enum valuecolvardeps
f_cv_linear enum valuecolvardeps
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 valuecolvardeps
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_oldcolvar
f_type_dynamic enum valuecolvardeps [protected]
f_type_not_set enum valuecolvardeps [protected]
f_type_static enum valuecolvardeps [protected]
f_type_user enum valuecolvardeps [protected]
fbcolvar
fb_actualcolvar
fdiff_velocity(colvarvalue const &xold, colvarvalue const &xnew)colvar [inline, protected]
feature_statescolvardeps [protected]
feature_type enum namecolvardeps [protected]
features() constcolvar [inline, virtual]
features_atomgroup enum namecolvardeps
features_biases enum namecolvardeps
features_colvar enum namecolvardeps
features_cvc enum namecolvardeps
fjcolvar [protected]
force_constant() constcolvar [inline]
frcolvar [protected]
free_children_deps()colvardeps
ftcolvar
ft_reportedcolvar [protected]
get_atom_lists()colvar [virtual]
get_config() constcolvarparse [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() constcolvardeps [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) constcolvardeps [inline]
is_dynamic(int id)colvardeps [inline]
is_enabled(int f=f_cv_active) constcolvardeps [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 valuecolvarparse [protected]
key_set_default enum valuecolvarparse [protected]
key_set_mode enum namecolvarparse [protected]
key_set_modescolvarparse [protected]
key_set_user enum valuecolvarparse [protected]
keyword_delimiters_leftcolvarparse [protected]
keyword_delimiters_rightcolvarparse [protected]
kinetic_energycolvar [protected]
lower_boundarycolvar
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_cvcscolvar [protected]
namecolvar
num_active_cvcs() constcolvar [inline]
num_cvcs() constcolvar [inline]
num_dimensions() constcolvar [inline]
param_exists(std::string const &param_name)colvarparams
param_grad_mapcolvarparams [protected]
param_mapcolvarparams [protected]
parse_analysis(std::string const &conf)colvar
parse_deprecated enum valuecolvarparse
parse_deprecation_warning enum valuecolvarparse
parse_echo enum valuecolvarparse
parse_echo_default enum valuecolvarparse
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
periodic_boundaries() constcolvar
periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) constcolvar
potential_energycolvar [protected]
prev_timestepcolvar [protected]
prev_v_extcolvar [protected]
prev_x_extcolvar [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() constcolvar [inline]
runavecolvar [protected]
runave_lengthcolvar [protected]
runave_outfilecolvar [protected]
runave_stridecolvar [protected]
runave_variancecolvar [protected]
scripted_functioncolvar [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_valuescolvar [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_factorcolvardeps [protected]
to_lower_cppstr(std::string const &in)colvarparse [inline, static]
total_force() constcolvar [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_boundarycolvar
v_extcolvar [protected]
v_fdiffcolvar [protected]
v_reportedcolvar [protected]
value() constcolvar [inline]
velocity() constcolvar [inline]
volmap_ids_colvar [protected]
white_spacecolvarparse [static]
widthcolvar
wrap(colvarvalue &x_unwrapped) constcolvar
wrap_centercolvar
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
xcolvar [protected]
x_extcolvar [protected]
x_historycolvar [protected]
x_history_pcolvar [protected]
x_oldcolvar [protected]
x_reportedcolvar [protected]
x_restartcolvar [protected]
~colvar()colvar
~colvardeps()colvardeps [virtual]
~colvarparams()colvarparams [protected, virtual]
~colvarparse()colvarparse [virtual]

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