Collective Variables Module - Developer Documentation
colvar_grid_gradient Member List

This is the complete list of members for colvar_grid_gradient, 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
acc_force(std::vector< int > const &ix, cvm::real const *forces)colvar_grid_gradientinline
acc_value(std::vector< int > const &ix, std::vector< colvarvalue > const &values)colvar_grid_gradientinline
add_constant(cvm::real const &t)colvar_grid< cvm::real >inline
add_grid(colvar_grid< cvm::real > const &other_grid, cvm::real scale_factor=1.0)colvar_grid< cvm::real >inline
add_keyword(char const *key)colvarparseprotected
address(std::vector< int > const &ix) constcolvar_grid< cvm::real >inline
allowed_keywordscolvarparseprotected
average(bool smoothed=false)colvar_grid_gradientinline
bin_distance_from_boundaries(std::vector< colvarvalue > const &values, bool skip_hard_boundaries=false)colvar_grid< cvm::real >inline
bin_to_value_scalar(int const &i_bin, int const i) constcolvar_grid< cvm::real >inline
bin_to_value_scalar(int const &i_bin, colvarvalue const &new_offset, cvm::real const &new_width) constcolvar_grid< cvm::real >inline
check_ascii(std::string const &conf)colvarparsestatic
check_braces(std::string const &conf, size_t const start_pos)colvarparsestatic
check_consistency()colvar_grid< cvm::real >inline
check_consistency(colvar_grid< cvm::real > const &other_grid)colvar_grid< cvm::real >inline
check_keywords(std::string &conf, char const *key)colvarparse
clear()colvarparse
clear_keyword_registry()colvarparse
colvar_grid()colvar_grid< cvm::real >inline
colvar_grid(colvar_grid< cvm::real > const &g)colvar_grid< cvm::real >inline
colvar_grid(std::vector< int > const &nx_i, cvm::real const &t=cvm::real(), size_t mult_i=1)colvar_grid< cvm::real >inline
colvar_grid(std::vector< colvar * > const &colvars, cvm::real const &t=cvm::real(), size_t mult_i=1, bool add_extra_bin=false)colvar_grid< cvm::real >inline
colvar_grid_gradient()colvar_grid_gradient
colvar_grid_gradient(std::vector< int > const &nx_i)colvar_grid_gradient
colvar_grid_gradient(std::vector< colvar *> &colvars)colvar_grid_gradient
colvar_grid_gradient(std::string &filename)colvar_grid_gradient
colvar_grid_gradient(std::vector< colvar *> &colvars, std::shared_ptr< colvar_grid_count > samples_in)colvar_grid_gradient
colvarparams()colvarparamsprotected
colvarparse()colvarparse
colvarparse(const std::string &conf)colvarparse
config_stringcolvarparseprotected
copy_grid(colvar_grid< cvm::real > const &other_grid)colvar_grid< cvm::real >inline
current_bin_flat_bound() constcolvar_grid< cvm::real >inline
current_bin_scalar(int const i) constcolvar_grid< cvm::real >inline
current_bin_scalar(int const i, int const iv) constcolvar_grid< cvm::real >inline
current_bin_scalar_bound(int const i) constcolvar_grid< cvm::real >inline
current_bin_scalar_fraction(int const i) constcolvar_grid< cvm::real >inline
cvcolvar_grid< cvm::real >
datacolvar_grid< cvm::real >
data_begin_poscolvarparseprotected
data_end_poscolvarparseprotected
delta_grid(colvar_grid< cvm::real > const &other_grid)colvar_grid< cvm::real >inline
error_key_required(std::string const &key_str, Parse_Mode const &parse_mode)colvarparseprotected
full_samplescolvar_grid_gradient
get_colvars_index(std::vector< colvarvalue > const &values) constcolvar_grid< cvm::real >inline
get_colvars_index() constcolvar_grid< cvm::real >inline
get_colvars_index_bound() constcolvar_grid< cvm::real >inline
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=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=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=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, 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, 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, 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, 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_param(std::string const &param_name)colvarparamsvirtual
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_state_params() constcolvar_grid_gradient
get_value(size_t i) constcolvar_grid< cvm::real >inline
getline_nocomments(std::istream &is, std::string &s)colvarparsestatic
grid_rmsd(colvar_grid_gradient const &other_grid) constcolvar_grid_gradient
hard_lower_boundariescolvar_grid< cvm::real >
hard_upper_boundariescolvar_grid< cvm::real >
has_datacolvar_grid< cvm::real >
has_parent_datacolvar_grid< cvm::real >
incr(std::vector< int > &ix) constcolvar_grid< cvm::real >inline
index_ok(std::vector< int > const &ix) constcolvar_grid< cvm::real >inline
init_from_boundaries() (defined in colvar_grid< cvm::real >)colvar_grid< cvm::real >inline
init_from_colvars(std::vector< colvar * > const &colvars, size_t mult_i=1, bool add_extra_bin=false) (defined in colvar_grid< cvm::real >)colvar_grid< cvm::real >inline
key_already_set(std::string const &key_str)colvarparseprotected
key_lookup(std::string const &conf, char const *key, std::string *data=nullptr, size_t *save_pos=nullptr)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_boundariescolvar_grid< cvm::real >
map_grid(colvar_grid< cvm::real > const &other_grid)colvar_grid< cvm::real >inline
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
min_samples (defined in colvar_grid_gradient)colvar_grid_gradient
multcolvar_grid< cvm::real >
multiplicity() constcolvar_grid< cvm::real >inline
multiply_constant(cvm::real const &a)colvar_grid< cvm::real >inline
ndcolvar_grid< cvm::real >
new_datacolvar_grid< cvm::real >
new_index() constcolvar_grid< cvm::real >inline
ntcolvar_grid< cvm::real >
num_variables() constcolvar_grid< cvm::real >inline
number_of_points(int const icv=-1) constcolvar_grid< cvm::real >inline
number_of_points_vec() constcolvar_grid< cvm::real >inline
nxcolvar_grid< cvm::real >
nxccolvar_grid< cvm::real >
param_exists(std::string const &param_name)colvarparams
param_grad_mapcolvarparamsprotected
param_mapcolvarparamsprotected
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_params(std::string const &conf, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)colvar_grid_gradient
parse_required enum valuecolvarparse
parse_restart enum valuecolvarparse
parse_silent enum valuecolvarparse
periodiccolvar_grid< cvm::real >
raw_data_in(const cvm::real *in_data)colvar_grid< cvm::real >inline
raw_data_in(const std::vector< cvm::real > &in_data) (defined in colvar_grid< cvm::real >)colvar_grid< cvm::real >inline
raw_data_num() constcolvar_grid< cvm::real >inline
raw_data_out(cvm::real *out_data) constcolvar_grid< cvm::real >inline
raw_data_out(std::vector< cvm::real > &out_data) const (defined in colvar_grid< cvm::real >)colvar_grid< cvm::real >inline
read_config_line(std::istream &is, std::string &line)colvarparse
read_multicol(std::istream &is, bool add=false)colvar_grid_gradient
read_multicol(std::string const &filename, std::string description="grid file", bool add=false)colvar_grid_gradient
read_raw(std::istream &is)colvar_grid_gradient
read_raw(cvm::memory_stream &is)colvar_grid_gradient
read_restart(std::istream &is)colvar_grid_gradient
read_restart(cvm::memory_stream &is)colvar_grid_gradient
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_small_values(cvm::real const &a)colvar_grid< cvm::real >inline
request_actual_value(bool b=true)colvar_grid< cvm::real >inline
reset(cvm::real const &t=cvm::real())colvar_grid< cvm::real >inline
samplescolvar_grid_gradient
set_param(std::string const &param_name, void const *new_value)colvarparamsvirtual
set_sizes(std::vector< int > const &new_sizes)colvar_grid< cvm::real >inline
set_string(std::string const &conf)colvarparse
set_value(std::vector< int > const &ix, cvm::real const &t, size_t const &imult=0)colvar_grid< cvm::real >inline
set_value(size_t i, cvm::real const &t)colvar_grid< cvm::real >inline
setup(std::vector< int > const &nx_i, cvm::real const &t=cvm::real(), size_t const &mult_i=1)colvar_grid< cvm::real >inline
setup()colvar_grid< cvm::real >inline
sizes() constcolvar_grid< cvm::real >inline
smooth_inverse_weight(cvm::real weight)colvar_grid_gradientinline
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest)colvarparsestatic
strip_values(std::string &conf)colvarparseprotected
to_lower_cppstr(std::string const &in)colvarparseinlinestatic
upper_boundariescolvar_grid< cvm::real >
use_actual_valuecolvar_grid< cvm::real >
value(std::vector< int > const &ix, size_t const &imult=0) constcolvar_grid< cvm::real >inline
value(size_t i) constcolvar_grid< cvm::real >inline
value_input(std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0, bool add=false) overridecolvar_grid_gradientinlinevirtual
value_output(std::vector< int > const &ix, size_t const &imult=0) const overridecolvar_grid_gradientinlinevirtual
value_output_smoothed(std::vector< int > const &ix, bool smoothed=true)colvar_grid_gradientinlinevirtual
value_to_bin_scalar(colvarvalue const &value, const int i) constcolvar_grid< cvm::real >inline
value_to_bin_scalar(colvarvalue const &value, colvarvalue const &new_offset, cvm::real const &new_width) constcolvar_grid< cvm::real >inline
value_to_bin_scalar_bound(colvarvalue const &value, const int i) constcolvar_grid< cvm::real >inline
value_to_bin_scalar_fraction(colvarvalue const &value, const int i) constcolvar_grid< cvm::real >inline
vector_value(std::vector< int > const &ix, std::vector< cvm::real > &v) constcolvar_grid_gradientinline
vector_value_smoothed(std::vector< int > const &ix, cvm::real *grad, bool smoothed=true)colvar_grid_gradientinline
white_spacecolvarparsestatic
widthscolvar_grid< cvm::real >
wrap(std::vector< int > &ix) constcolvar_grid< cvm::real >inline
wrap_detect_edge(std::vector< int > &ix) constcolvar_grid< cvm::real >inline
wrap_to_edge(std::vector< int > &ix, std::vector< int > &edge_bin) constcolvar_grid< cvm::real >inline
write_1D_integral(std::ostream &os)colvar_grid_gradient
write_multicol(std::ostream &os) constcolvar_grid_gradient
write_multicol(std::string const &filename, std::string description="grid file") constcolvar_grid_gradient
write_opendx(std::ostream &os) constcolvar_grid_gradient
write_opendx(std::string const &filename, std::string description="grid file") constcolvar_grid_gradient
write_raw(std::ostream &os, size_t const buf_size=3) constcolvar_grid_gradient
write_raw(cvm::memory_stream &os, size_t const buf_size=3) constcolvar_grid_gradient
write_restart(std::ostream &os)colvar_grid_gradient
write_restart(cvm::memory_stream &os)colvar_grid_gradient
~colvar_grid()colvar_grid< cvm::real >inlinevirtual
~colvar_grid_gradient()colvar_grid_gradientinlinevirtual
~colvarparams()colvarparamsprotectedvirtual
~colvarparse() overridecolvarparse