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Collective Variables Module - Developer Documentation
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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) (defined in colvarparse) | 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 &) (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) | 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 |
| allowed_keywords | colvarparse | protected |
| atimes(const std::vector< cvm::real > &x, std::vector< cvm::real > &r) | integrate_potential | protected |
| b_smoothed | integrate_potential | |
| 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_flat_bound() const | 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 > | |
| data | colvar_grid< cvm::real > | |
| 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=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 ¶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 |
| get_state_params() const | colvar_grid_scalar | |
| get_value(size_t i) const | colvar_grid< cvm::real > | inline |
| 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 (defined in integrate_potential) | integrate_potential | protected |
| grid_rmsd(colvar_grid_scalar const &other_grid) const | colvar_grid_scalar | |
| 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 |
| integral() const | colvar_grid_scalar | |
| integrate(const int itmax, const cvm::real &tol, cvm::real &err, bool verbose=true) | integrate_potential | |
| integrate_potential() (defined in integrate_potential) | integrate_potential | |
| integrate_potential(std::vector< colvar * > &colvars, std::shared_ptr< colvar_grid_gradient > gradients) | integrate_potential | |
| integrate_potential(std::shared_ptr< 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=nullptr, size_t *save_pos=nullptr) | colvarparse | |
| key_not_set enum value (defined in colvarparse) | colvarparse | protected |
| key_set_default enum value (defined in colvarparse) | colvarparse | protected |
| key_set_mode enum name | colvarparse | protected |
| key_set_modes | colvarparse | protected |
| key_set_user enum value (defined in colvarparse) | colvarparse | protected |
| keyword_delimiters_left | colvarparse | protected |
| keyword_delimiters_right | colvarparse | protected |
| l2norm(const std::vector< cvm::real > &x) | integrate_potential | protected |
| log_gradient_finite_diff(const std::vector< int > &ix0, int n=0, int offset=0) | colvar_grid_scalar | inline |
| 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 > | |
| multiplicity() const | colvar_grid< cvm::real > | inline |
| multiply_constant(cvm::real const &a) | colvar_grid< cvm::real > | inline |
| nd | colvar_grid< cvm::real > | |
| new_data | colvar_grid< cvm::real > | |
| 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 > | |
| 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 > | |
| nxc | colvar_grid< cvm::real > | |
| 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_scalar | |
| 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_num() const | colvar_grid< cvm::real > | inline |
| raw_data_out(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_scalar | |
| read_raw(cvm::memory_stream &is) | colvar_grid_scalar | |
| read_restart(std::istream &is) | colvar_grid_scalar | |
| read_restart(cvm::memory_stream &is) | colvar_grid_scalar | |
| 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< 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 ¶m_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 | inlinestatic |
| update_div_local(const std::vector< int > &ix) | integrate_potential | |
| update_div_neighbors(const std::vector< int > &ix) | integrate_potential | |
| upper_boundaries | colvar_grid< cvm::real > | |
| use_actual_value | colvar_grid< cvm::real > | |
| 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) override | colvar_grid_scalar | inlinevirtual |
| value_output(std::vector< int > const &ix, size_t const &imult=0) const override | colvar_grid_scalar | inlinevirtual |
| 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_detect_edge(std::vector< int > &ix) const | colvar_grid< cvm::real > | inline |
| wrap_to_edge(std::vector< int > &ix, std::vector< int > &edge_bin) 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_raw(std::ostream &os, size_t const buf_size=3) const | colvar_grid_scalar | |
| write_raw(cvm::memory_stream &os, size_t const buf_size=3) const | colvar_grid_scalar | |
| write_restart(std::ostream &os) | colvar_grid_scalar | |
| write_restart(cvm::memory_stream &os) | colvar_grid_scalar | |
| ~colvar_grid() | colvar_grid< cvm::real > | inlinevirtual |
| ~colvar_grid_scalar() | colvar_grid_scalar | virtual |
| ~colvarparams() | colvarparams | protectedvirtual |
| ~colvarparse() override | colvarparse | |
| ~integrate_potential() (defined in integrate_potential) | integrate_potential | inlinevirtual |
1.9.5