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virtual int | init (std::string const &conf) |
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virtual void | calc_value () |
| Calculate the variable. More...
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virtual void | calc_gradients () |
| Calculate the atomic gradients, to be reused later in order to apply forces. More...
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template<int flags> |
int | compute_coordnum () |
| Workhorse function.
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template<int flags> |
void | main_loop (bool **pairlist_elem) |
| Workhorse function.
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std::string | function_type () const |
| String identifier for the type of collective variable.
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| cvc () |
| Constructor.
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virtual | ~cvc () |
| Destructor.
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virtual int | init (std::string const &conf) |
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virtual int | init_dependencies () |
| Initialize dependency tree. More...
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int | setup () |
| After construction, set data related to dependency handling.
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virtual const std::vector< feature * > & | features () const |
| Implementation of the feature list accessor for colvar. More...
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virtual std::vector< feature * > & | modify_features () |
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virtual std::vector< std::vector< int > > | get_atom_lists () |
| Get vector of vectors of atom IDs for all atom groups.
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virtual void | read_data () |
| Obtain data needed for the calculation for the backend.
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virtual void | calc_value ()=0 |
| Calculate the variable. More...
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virtual void | calc_gradients () |
| Calculate the atomic gradients, to be reused later in order to apply forces. More...
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void | calc_fit_gradients () |
| Calculate the atomic fit gradients.
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virtual void | debug_gradients () |
| Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component.
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virtual void | collect_gradients (std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients) |
| Calculate atomic gradients and add them to the corresponding item in gradient vector May be overridden by CVCs that do not store their gradients in the classic way, see dihedPC. More...
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virtual void | calc_force_invgrads () |
| Calculate the total force from the system using the inverse atomic gradients. More...
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virtual void | calc_Jacobian_derivative () |
| Calculate the divergence of the inverse atomic gradients. More...
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colvarvalue const & | value () const |
| Return the previously calculated value.
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colvarvalue const & | total_force () const |
| Return the previously calculated total force.
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colvarvalue const & | Jacobian_derivative () const |
| Return the previously calculated divergence of the inverse atomic gradients.
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virtual void | apply_force (colvarvalue const &cvforce) |
| Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) More...
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virtual cvm::real | dist2 (colvarvalue const &x1, colvarvalue const &x2) const |
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virtual colvarvalue | dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const |
| Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities) More...
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virtual colvarvalue | dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const |
| Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities) More...
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virtual void | wrap (colvarvalue &x_unwrapped) const |
| Wrap value (for periodic/symmetric cvcs) More...
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void | register_atom_group (cvm::atom_group *ag) |
| Store a pointer to new atom group, and list as child for dependencies.
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virtual colvarvalue const * | get_param_grad (std::string const ¶m_name) |
| Pointer to the gradient of parameter param_name.
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virtual int | set_param (std::string const ¶m_name, void const *new_value) |
| Set the named parameter to the given value. More...
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void | set_value (colvarvalue const &new_value, bool now=false) |
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| colvarparse () |
| Default constructor.
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| colvarparse (const std::string &conf) |
| Constructor that stores the object's config string.
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void | clear () |
| Set the object ready to parse a new configuration string.
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void | set_string (std::string const &conf) |
| Set a new config string for this object.
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| ~colvarparse () override |
| Default destructor.
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std::string const & | get_config () const |
| Get the configuration string (includes comments)
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int | check_keywords (std::string &conf, char const *key) |
| Check that all the keywords within "conf" are in the list of allowed keywords; this will invoke strip_values() first and then loop over all words.
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void | clear_keyword_registry () |
| Use this after parsing a config string (note that check_keywords() calls it already)
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bool | get_keyval (std::string const &conf, char const *key, int &value, int const &def_value=0, Parse_Mode const parse_mode=parse_normal) |
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bool | 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) |
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bool | get_keyval (std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | get_keyval (std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | 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) |
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bool | key_lookup (std::string const &conf, char const *key, std::string *data=nullptr, size_t *save_pos=nullptr) |
| Low-level function for parsing configuration strings; automatically adds the requested keyword to the list of valid ones. More...
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std::istream & | read_config_line (std::istream &is, std::string &line) |
| Reads a configuration line, adds it to config_string, and returns the stream. More...
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template<> |
int | _get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, bool &value, bool const &) |
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template<> |
int | _get_keyval_scalar_novalue_ (std::string const &key_str, bool &value, Parse_Mode const &parse_mode) |
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int | param_exists (std::string const ¶m_name) |
| Whether the parameter param_name exists.
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virtual std::vector< std::string > | get_param_names () |
| Get a copy of the names of registered parameters.
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virtual std::vector< std::string > | get_param_grad_names () |
| Get a copy of the names of registered parameter gradients.
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virtual void const * | get_param_ptr (std::string const ¶m_name) |
| Pointer to the parameter param_name.
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virtual void const * | get_param_grad_ptr (std::string const ¶m_name) |
| Pointer to the gradient of parameter param_name.
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virtual cvm::real | get_param (std::string const ¶m_name) |
| Value of the parameter param_name (must be a scalar)
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virtual int | set_param (std::string const ¶m_name, void const *new_value) |
| Set the named parameter to the given value. More...
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int | get_time_step_factor () const |
| returns time_step_factor
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void | init_feature (int feature_id, const char *description, feature_type type) |
| Pair a numerical feature ID with a description and type.
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bool | is_not_set (int id) |
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bool | is_dynamic (int id) |
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bool | is_static (int id) |
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bool | is_user (int id) |
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virtual const std::vector< feature * > & | features () const =0 |
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virtual std::vector< feature * > & | modify_features ()=0 |
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void | add_child (colvardeps *child) |
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void | remove_child (colvardeps *child) |
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void | remove_all_children () |
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bool | is_enabled (int f=f_cv_active) const |
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bool | is_available (int f=f_cv_active) const |
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void | provide (int feature_id, bool truefalse=true) |
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void | set_enabled (int feature_id, bool truefalse=true) |
| Enable or disable, depending on flag value.
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int | enable (int f, bool dry_run=false, bool toplevel=true, bool error=false) |
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int | disable (int f) |
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void | free_children_deps () |
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void | restore_children_deps () |
| re-enable children features (to be used when object becomes active)
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int | decr_ref_count (int f) |
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virtual void | do_feature_side_effects (int) |
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virtual int | init_dependencies ()=0 |
| Initialize dependency tree for object of a derived class. More...
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void | require_feature_self (int f, int g) |
| Make feature f require feature g within the same object.
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void | exclude_feature_self (int f, int g) |
| Make features f and g mutually exclusive within the same object.
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void | require_feature_children (int f, int g) |
| Make feature f require feature g within children.
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void | require_feature_alt (int f, int g, int h) |
| Make feature f require either g or h within the same object.
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void | require_feature_alt (int f, int g, int h, int i) |
| Make feature f require any of g, h, or i within the same object.
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void | require_feature_alt (int f, int g, int h, int i, int j) |
| Make feature f require any of g, h, i, or j within the same object.
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void | print_state () |
| print all enabled features and those of children, for debugging
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void | check_enabled (int f, std::string const &reason) const |
| Check that a feature is enabled, raising COLVARS_BUG_ERROR if not.
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