_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_constant(size_t const &t) | colvar_grid< size_t > | [inline] |
add_grid(colvar_grid< size_t > const &other_grid, cvm::real scale_factor=1.0) | colvar_grid< size_t > | [inline] |
add_keyword(char const *key) | colvarparse | [protected] |
address(std::vector< int > const &ix) const | colvar_grid< size_t > | [inline, protected] |
allowed_keywords | colvarparse | [protected] |
bin_distance_from_boundaries(std::vector< colvarvalue > const &values, bool skip_hard_boundaries=false) | colvar_grid< size_t > | [inline] |
bin_to_value_scalar(int const &i_bin, int const i) const | colvar_grid< size_t > | [inline] |
bin_to_value_scalar(int const &i_bin, colvarvalue const &new_offset, cvm::real const &new_width) const | colvar_grid< size_t > | [inline] |
check_ascii(std::string const &conf) | colvarparse | [static] |
check_braces(std::string const &conf, size_t const start_pos) | colvarparse | [static] |
check_consistency() | colvar_grid< size_t > | [inline] |
check_consistency(colvar_grid< size_t > const &other_grid) | colvar_grid< size_t > | [inline] |
check_keywords(std::string &conf, char const *key) | colvarparse | |
clear() | colvarparse | |
clear_keyword_registry() | colvarparse | |
colvar_grid() | colvar_grid< size_t > | [inline] |
colvar_grid(colvar_grid< size_t > const &g) | colvar_grid< size_t > | [inline] |
colvar_grid(std::vector< int > const &nx_i, size_t const &t=size_t(), size_t mult_i=1) | colvar_grid< size_t > | [inline] |
colvar_grid(std::vector< colvar * > const &colvars, size_t const &t=size_t(), size_t mult_i=1, bool add_extra_bin=false) | colvar_grid< size_t > | [inline] |
colvar_grid_count() | colvar_grid_count | |
colvar_grid_count(std::vector< int > const &nx_i, size_t const &def_count=0) | colvar_grid_count | |
colvar_grid_count(std::vector< colvar * > &colvars, size_t const &def_count=0, bool add_extra_bin=false) | colvar_grid_count | |
colvarparams() | colvarparams | [protected] |
colvarparse() | colvarparse | |
colvarparse(const std::string &conf) | colvarparse | |
config_string | colvarparse | [protected] |
copy_grid(colvar_grid< size_t > const &other_grid) | colvar_grid< size_t > | [inline] |
current_bin_scalar(int const i) const | colvar_grid< size_t > | [inline] |
current_bin_scalar(int const i, int const iv) const | colvar_grid< size_t > | [inline] |
current_bin_scalar_bound(int const i) const | colvar_grid< size_t > | [inline] |
current_bin_scalar_fraction(int const i) const | colvar_grid< size_t > | [inline] |
cv | colvar_grid< size_t > | [protected] |
data | colvar_grid< size_t > | [protected] |
data_begin_pos | colvarparse | [protected] |
data_end_pos | colvarparse | [protected] |
delta_grid(colvar_grid< size_t > const &other_grid) | colvar_grid< size_t > | [inline] |
error_key_required(std::string const &key_str, Parse_Mode const &parse_mode) | colvarparse | [protected] |
get_colvars_index(std::vector< colvarvalue > const &values) const | colvar_grid< size_t > | [inline] |
get_colvars_index() const | colvar_grid< size_t > | [inline] |
get_colvars_index_bound() const | colvar_grid< size_t > | [inline] |
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_param(std::string const ¶m_name) | colvarparams | [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] |
getline_nocomments(std::istream &is, std::string &s) | colvarparse | [static] |
gradient_finite_diff(const std::vector< int > &ix0, int n=0) | colvar_grid_count | [inline] |
hard_lower_boundaries | colvar_grid< size_t > | |
hard_upper_boundaries | colvar_grid< size_t > | |
has_data | colvar_grid< size_t > | |
has_parent_data | colvar_grid< size_t > | |
incr(std::vector< int > &ix) const | colvar_grid< size_t > | [inline] |
incr_count(std::vector< int > const &ix) | colvar_grid_count | [inline] |
index_ok(std::vector< int > const &ix) const | colvar_grid< size_t > | [inline] |
init_from_boundaries() | colvar_grid< size_t > | [inline] |
init_from_colvars(std::vector< colvar * > const &colvars, size_t mult_i=1, bool add_extra_bin=false) | colvar_grid< size_t > | [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] |
log_gradient_finite_diff(const std::vector< int > &ix0, int n=0) | colvar_grid_count | [inline] |
lower_boundaries | colvar_grid< size_t > | |
map_grid(colvar_grid< size_t > const &other_grid) | colvar_grid< size_t > | [inline] |
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] |
mult | colvar_grid< size_t > | [protected] |
multiplicity() const | colvar_grid< size_t > | [inline] |
multiply_constant(cvm::real const &a) | colvar_grid< size_t > | [inline] |
nd | colvar_grid< size_t > | [protected] |
new_count(std::vector< int > const &ix, size_t const &imult=0) | colvar_grid_count | [inline] |
new_data | colvar_grid< size_t > | [protected] |
new_index() const | colvar_grid< size_t > | [inline] |
nt | colvar_grid< size_t > | [protected] |
num_variables() const | colvar_grid< size_t > | [inline] |
number_of_points(int const icv=-1) const | colvar_grid< size_t > | [inline] |
number_of_points_vec() const | colvar_grid< size_t > | [inline] |
nx | colvar_grid< size_t > | [protected] |
nxc | colvar_grid< size_t > | [protected] |
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_Mode enum name | colvarparse | |
parse_normal enum value | colvarparse | |
parse_null enum value | colvarparse | |
parse_override enum value | colvarparse | |
parse_params(std::string const &conf, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal) | colvar_grid< size_t > | [inline] |
parse_required enum value | colvarparse | |
parse_restart enum value | colvarparse | |
parse_silent enum value | colvarparse | |
periodic | colvar_grid< size_t > | |
raw_data_in(const size_t *in_data) | colvar_grid< size_t > | [inline] |
raw_data_in(const std::vector< size_t > &in_data) | colvar_grid< size_t > | [inline] |
raw_data_num() const | colvar_grid< size_t > | [inline] |
raw_data_out(size_t *out_data) const | colvar_grid< size_t > | [inline] |
raw_data_out(std::vector< size_t > &out_data) const | colvar_grid< size_t > | [inline] |
read_config_line(std::istream &is, std::string &line) | colvarparse | |
read_multicol(std::istream &is, bool add=false) | colvar_grid_count | |
read_multicol(std::string const &filename, std::string description="grid file", bool add=false) | colvar_grid_count | |
read_raw(std::istream &is) | colvar_grid< size_t > | [inline] |
read_restart(std::istream &is) | colvar_grid< size_t > | [inline] |
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_small_values(cvm::real const &a) | colvar_grid< size_t > | [inline] |
request_actual_value(bool b=true) | colvar_grid< size_t > | [inline] |
reset(size_t const &t=size_t()) | colvar_grid< size_t > | [inline] |
set_param(std::string const ¶m_name, void const *new_value) | colvarparams | [virtual] |
set_sizes(std::vector< int > const &new_sizes) | colvar_grid< size_t > | [inline] |
set_string(std::string const &conf) | colvarparse | |
set_value(std::vector< int > const &ix, size_t const &t, size_t const &imult=0) | colvar_grid< size_t > | [inline] |
set_value(size_t i, size_t const &t) | colvar_grid< size_t > | [inline] |
setup(std::vector< int > const &nx_i, size_t const &t=size_t(), size_t const &mult_i=1) | colvar_grid< size_t > | [inline] |
setup() | colvar_grid< size_t > | [inline] |
sizes() const | colvar_grid< size_t > | [inline] |
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest) | colvarparse | [static] |
strip_values(std::string &conf) | colvarparse | [protected] |
to_lower_cppstr(std::string const &in) | colvarparse | [inline, static] |
upper_boundaries | colvar_grid< size_t > | |
use_actual_value | colvar_grid< size_t > | [protected] |
value(std::vector< int > const &ix, size_t const &imult=0) const | colvar_grid< size_t > | [inline] |
value(size_t i) const | colvar_grid< size_t > | [inline] |
value_input(std::vector< int > const &ix, size_t const &t, size_t const &imult=0, bool add=false) | colvar_grid_count | [inline, virtual] |
value_output(std::vector< int > const &ix, size_t const &imult=0) const | colvar_grid< size_t > | [inline, virtual] |
value_to_bin_scalar(colvarvalue const &value, const int i) const | colvar_grid< size_t > | [inline] |
value_to_bin_scalar(colvarvalue const &value, colvarvalue const &new_offset, cvm::real const &new_width) const | colvar_grid< size_t > | [inline] |
value_to_bin_scalar_bound(colvarvalue const &value, const int i) const | colvar_grid< size_t > | [inline] |
value_to_bin_scalar_fraction(colvarvalue const &value, const int i) const | colvar_grid< size_t > | [inline] |
white_space | colvarparse | [static] |
widths | colvar_grid< size_t > | |
wrap(std::vector< int > &ix) const | colvar_grid< size_t > | [inline] |
wrap_edge(std::vector< int > &ix) const | colvar_grid< size_t > | [inline] |
write_multicol(std::ostream &os) const | colvar_grid_count | |
write_multicol(std::string const &filename, std::string description="grid file") const | colvar_grid_count | |
write_opendx(std::ostream &os) const | colvar_grid_count | |
write_opendx(std::string const &filename, std::string description="grid file") const | colvar_grid_count | |
write_params(std::ostream &os) | colvar_grid< size_t > | [inline] |
write_raw(std::ostream &os, size_t const buf_size=3) const | colvar_grid< size_t > | [inline] |
write_restart(std::ostream &os) | colvar_grid< size_t > | [inline] |
~colvar_grid() | colvar_grid< size_t > | [inline, virtual] |
~colvar_grid_count() | colvar_grid_count | [inline, virtual] |
~colvarparams() | colvarparams | [protected, virtual] |
~colvarparse() | colvarparse | [virtual] |