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integrate_potential Member List

This is the complete list of members for integrate_potential, 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]
acc_value(std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0)	colvar_grid_scalar	[inline]
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)	colvarparse	[protected]
address(std::vector< int > const &ix) const	colvar_grid< cvm::real >	[inline, protected]
allowed_keywords	colvarparse	[protected]
atimes(const std::vector< cvm::real > &x, std::vector< cvm::real > &r)	integrate_potential	[protected]
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) const	colvar_grid< cvm::real >	[inline]
bin_to_value_scalar(int const &i_bin, colvarvalue const &new_offset, cvm::real const &new_width) const	colvar_grid< cvm::real >	[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< 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_scalar()	colvar_grid_scalar
colvar_grid_scalar(colvar_grid_scalar const &g)	colvar_grid_scalar
colvar_grid_scalar(std::vector< int > const &nx_i)	colvar_grid_scalar
colvar_grid_scalar(std::vector< colvar * > &colvars, bool add_extra_bin=false)	colvar_grid_scalar
colvarparams()	colvarparams	[protected]
colvarparse()	colvarparse
colvarparse(const std::string &conf)	colvarparse
config_string	colvarparse	[protected]
copy_grid(colvar_grid< cvm::real > const &other_grid)	colvar_grid< cvm::real >	[inline]
current_bin_scalar(int const i) const	colvar_grid< cvm::real >	[inline]
current_bin_scalar(int const i, int const iv) const	colvar_grid< cvm::real >	[inline]
current_bin_scalar_bound(int const i) const	colvar_grid< cvm::real >	[inline]
current_bin_scalar_fraction(int const i) const	colvar_grid< cvm::real >	[inline]
cv	colvar_grid< cvm::real >	[protected]
data	colvar_grid< cvm::real >	[protected]
data_begin_pos	colvarparse	[protected]
data_end_pos	colvarparse	[protected]
delta_grid(colvar_grid< cvm::real > const &other_grid)	colvar_grid< cvm::real >	[inline]
divergence	integrate_potential	[protected]
entropy() const	colvar_grid_scalar
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< cvm::real >	[inline]
get_colvars_index() const	colvar_grid< cvm::real >	[inline]
get_colvars_index_bound() const	colvar_grid< cvm::real >	[inline]
get_config() const	colvarparse	[inline]
get_grad(cvm::real *g, std::vector< int > &ix)	integrate_potential	[protected]
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 &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]
getline_nocomments(std::istream &is, std::string &s)	colvarparse	[static]
gradient_finite_diff(const std::vector< int > &ix0, int n=0)	colvar_grid_scalar	[inline]
gradients	integrate_potential	[protected]
hard_lower_boundaries	colvar_grid< cvm::real >
hard_upper_boundaries	colvar_grid< cvm::real >
has_data	colvar_grid< cvm::real >
has_parent_data	colvar_grid< cvm::real >
incr(std::vector< int > &ix) const	colvar_grid< cvm::real >	[inline]
index_ok(std::vector< int > const &ix) const	colvar_grid< cvm::real >	[inline]
init_from_boundaries()	colvar_grid< cvm::real >	[inline]
init_from_colvars(std::vector< colvar * > const &colvars, size_t mult_i=1, bool add_extra_bin=false)	colvar_grid< cvm::real >	[inline]
integral() const	colvar_grid_scalar
integrate(const int itmax, const cvm::real &tol, cvm::real &err)	integrate_potential
integrate_potential()	integrate_potential
integrate_potential(std::vector< colvar * > &colvars, colvar_grid_gradient *gradients)	integrate_potential
integrate_potential(colvar_grid_gradient *gradients)	integrate_potential
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]
l2norm(const std::vector< cvm::real > &x)	integrate_potential	[protected]
lower_boundaries	colvar_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)	colvarparse	[protected]
mark_key_set_user(std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode)	colvarparse	[protected]
maximum_value() const	colvar_grid_scalar
minimum_pos_value() const	colvar_grid_scalar
minimum_value() const	colvar_grid_scalar
mult	colvar_grid< cvm::real >	[protected]
multiplicity() const	colvar_grid< cvm::real >	[inline]
multiply_constant(cvm::real const &a)	colvar_grid< cvm::real >	[inline]
nd	colvar_grid< cvm::real >	[protected]
new_data	colvar_grid< cvm::real >	[protected]
new_index() const	colvar_grid< cvm::real >	[inline]
nr_linbcg_sym(const std::vector< cvm::real > &b, std::vector< cvm::real > &x, const cvm::real &tol, const int itmax, int &iter, cvm::real &err)	integrate_potential	[protected]
nt	colvar_grid< cvm::real >	[protected]
num_variables() const	colvar_grid< cvm::real >	[inline]
number_of_points(int const icv=-1) const	colvar_grid< cvm::real >	[inline]
number_of_points_vec() const	colvar_grid< cvm::real >	[inline]
nx	colvar_grid< cvm::real >	[protected]
nxc	colvar_grid< cvm::real >	[protected]
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_params(std::string const &conf, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)	colvar_grid< cvm::real >	[inline]
parse_required enum value	colvarparse
parse_restart enum value	colvarparse
parse_silent enum value	colvarparse
periodic	colvar_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)	colvar_grid< cvm::real >	[inline]
raw_data_num() const	colvar_grid< cvm::real >	[inline]
raw_data_out(cvm::real *out_data) const	colvar_grid< cvm::real >	[inline]
raw_data_out(std::vector< cvm::real > &out_data) const	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_scalar
read_multicol(std::string const &filename, std::string description="grid file", bool add=false)	colvar_grid_scalar
read_raw(std::istream &is)	colvar_grid< cvm::real >	[inline]
read_restart(std::istream &is)	colvar_grid< cvm::real >	[inline]
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_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]
samples	colvar_grid_scalar
set_div()	integrate_potential
set_param(std::string const &param_name, void const *new_value)	colvarparams	[virtual]
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]
set_zero_minimum()	integrate_potential	[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() const	colvar_grid< cvm::real >	[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]
update_div_local(const std::vector< int > &ix)	integrate_potential	[protected]
update_div_neighbors(const std::vector< int > &ix)	integrate_potential
upper_boundaries	colvar_grid< cvm::real >
use_actual_value	colvar_grid< cvm::real >	[protected]
value(std::vector< int > const &ix, size_t const &imult=0) const	colvar_grid< cvm::real >	[inline]
value(size_t i) const	colvar_grid< cvm::real >	[inline]
value_input(std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0, bool add=false)	colvar_grid_scalar	[inline, virtual]
value_output(std::vector< int > const &ix, size_t const &imult=0) const	colvar_grid_scalar	[inline, virtual]
value_to_bin_scalar(colvarvalue const &value, const int i) const	colvar_grid< cvm::real >	[inline]
value_to_bin_scalar(colvarvalue const &value, colvarvalue const &new_offset, cvm::real const &new_width) const	colvar_grid< cvm::real >	[inline]
value_to_bin_scalar_bound(colvarvalue const &value, const int i) const	colvar_grid< cvm::real >	[inline]
value_to_bin_scalar_fraction(colvarvalue const &value, const int i) const	colvar_grid< cvm::real >	[inline]
vector_gradient_finite_diff(const std::vector< int > &ix0, std::vector< cvm::real > &grad)	colvar_grid_scalar	[inline]
white_space	colvarparse	[static]
widths	colvar_grid< cvm::real >
wrap(std::vector< int > &ix) const	colvar_grid< cvm::real >	[inline]
wrap_edge(std::vector< int > &ix) const	colvar_grid< cvm::real >	[inline]
write_multicol(std::ostream &os) const	colvar_grid_scalar
write_multicol(std::string const &filename, std::string description="grid file") const	colvar_grid_scalar
write_opendx(std::ostream &os) const	colvar_grid_scalar
write_opendx(std::string const &filename, std::string description="grid file") const	colvar_grid_scalar
write_params(std::ostream &os)	colvar_grid< cvm::real >	[inline]
write_raw(std::ostream &os, size_t const buf_size=3) const	colvar_grid< cvm::real >	[inline]
write_restart(std::ostream &os)	colvar_grid< cvm::real >	[inline]
~colvar_grid()	colvar_grid< cvm::real >	[inline, virtual]
~colvar_grid_scalar()	colvar_grid_scalar	[virtual]
~colvarparams()	colvarparams	[protected, virtual]
~colvarparse()	colvarparse	[virtual]
~integrate_potential()	integrate_potential	[inline, virtual]

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