A collective variable (main class); to be defined, it needs at least one object of a derived class of colvar::cvc; it calculates and returns a colvarvalue object.
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colvarvalue const & | value () const |
| Current value (previously set by calc() or by read_traj())
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colvarvalue const & | actual_value () const |
| Current actual value (not extended DOF)
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colvarvalue const & | run_ave () const |
| Current running average (if calculated as set by analysis flag)
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cvm::real const & | force_constant () const |
| Force constant of the spring.
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colvarvalue const & | velocity () const |
| Current velocity (previously set by calc() or by read_traj())
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colvarvalue const & | total_force () const |
| Current total force (previously obtained from calc() or read_traj()). Note: this is calculated using the atomic forces from the last simulation step. More...
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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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void | do_feature_side_effects (int id) |
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bool | periodic_boundaries () const |
| Is the interval defined by the two boundaries periodic?
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bool | periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub) const |
| Is the interval defined by the two boundaries periodic?
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| colvar () |
| Constructor.
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int | init (std::string const &conf) |
| Main init function.
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void | define_component_types () |
| Populate the map of available CVC types.
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int | init_components (std::string const &conf) |
| Parse the CVC configuration and allocate their data.
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int | init_custom_function (std::string const &conf) |
| Parse parameters for custom function with Lepton.
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int | init_grid_parameters (std::string const &conf) |
| Init defaults for grid options.
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int | init_extended_Lagrangian (std::string const &conf) |
| Init extended Lagrangian parameters.
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int | init_output_flags (std::string const &conf) |
| Init output flags.
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virtual int | init_dependencies () |
| Initialize dependency tree. More...
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void | setup () |
| Get ready for a run and re-initialize internal data if needed.
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| ~colvar () |
| Destructor.
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int | calc () |
| Calculate the colvar's value and related quantities.
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int | end_of_step () |
| Carry out operations needed before next step is run.
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int | calc_cvcs (int first=0, size_t num_cvcs=0) |
| Calculate a subset of the colvar components (CVCs) currently active (default: all active CVCs) Note: both arguments refer to the sect of active CVCs, not all CVCs.
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int | check_cvc_range (int first_cvc, size_t num_cvcs) |
| Ensure that the selected range of CVCs is consistent.
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int | calc_cvc_values (int first, size_t num_cvcs) |
| Calculate the values of the given subset of CVCs.
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int | calc_cvc_gradients (int first, size_t num_cvcs) |
| Same as colvar::calc_cvc_values but for gradients.
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int | calc_cvc_total_force (int first, size_t num_cvcs) |
| Same as colvar::calc_cvc_values but for total forces.
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int | calc_cvc_Jacobians (int first, size_t num_cvcs) |
| Same as colvar::calc_cvc_values but for Jacobian derivatives/forces.
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int | collect_cvc_data () |
| Collect quantities from CVCs and update aggregated data for the colvar.
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int | collect_cvc_values () |
| Collect the values of the CVCs.
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int | collect_cvc_gradients () |
| Same as colvar::collect_cvc_values but for gradients.
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int | collect_cvc_total_forces () |
| Same as colvar::collect_cvc_values but for total forces.
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int | collect_cvc_Jacobians () |
| Same as colvar::collect_cvc_values but for Jacobian derivatives/forces.
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int | calc_colvar_properties () |
| Calculate the quantities associated to the colvar (but not to the CVCs)
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colvarvalue const | applied_force () const |
| Get the current applied force.
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void | reset_bias_force () |
| Set the total biasing force to zero.
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void | add_bias_force (colvarvalue const &force) |
| Add to the total force from biases.
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void | add_bias_force_actual_value (colvarvalue const &force) |
| Apply a force to the actual value (only meaningful with extended Lagrangian)
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cvm::real | update_forces_energy () |
| Collect all forces on this colvar, integrate internal equations of motion of internal degrees of freedom; see also colvar::communicate_forces() return colvar energy if extended Lagrandian active.
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void | update_extended_Lagrangian () |
| Integrate equations of motion of extended Lagrangian coordinate if needed.
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void | communicate_forces () |
| Communicate forces (previously calculated in colvar::update()) to the external degrees of freedom.
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int | set_cvc_flags (std::vector< bool > const &flags) |
| Enables and disables individual CVCs based on the given array.
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int | update_cvc_flags () |
| Updates the flags in the CVC objects, and their number.
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int | update_cvc_config (std::vector< std::string > const &confs) |
| Modify the configuration of CVCs (currently, only base class data)
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int | cvc_param_exists (std::string const ¶m_name) |
| Whether this named parameter exists (in the first and only component)
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cvm::real | get_cvc_param (std::string const ¶m_name) |
| Get the value of the named parameter (from the first and only component)
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void const * | get_cvc_param_ptr (std::string const ¶m_name) |
| Get a pointer to the named parameter (from the first and only component)
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colvarvalue const * | get_cvc_param_grad (std::string const ¶m_name) |
| Pointer to the derivative of the variable with respect to param_name.
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int | set_cvc_param (std::string const ¶m_name, void const *new_value) |
| Set the named parameter in the first and only component to the given value.
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size_t | num_dimensions () const |
| Number of dimensions of the value of this colvar.
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size_t | num_cvcs () const |
| Number of CVC objects defined.
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size_t | num_active_cvcs () const |
| number of CVC objects with an active flag (as set by update_cvc_flags)
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cvm::real | dist2 (colvarvalue const &x1, colvarvalue const &x2) const |
| Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients. More...
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colvarvalue | dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const |
| Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients. More...
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colvarvalue | dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const |
| Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients. More...
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void | wrap (colvarvalue &x_unwrapped) const |
| Use the internal metrics (as from colvar::cvc objects) to wrap a value into a standard interval. More...
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int | parse_analysis (std::string const &conf) |
| Read the analysis tasks.
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int | analyze () |
| Perform analysis tasks.
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std::istream & | read_traj (std::istream &is) |
| Read the value from a collective variable trajectory file.
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std::ostream & | write_traj (std::ostream &os) |
| Output formatted values to the trajectory file.
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std::ostream & | write_traj_label (std::ostream &os) |
| Write a label to the trajectory file (comment line)
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std::istream & | read_state (std::istream &is) |
| Read the colvar's state from a formatted input stream.
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cvm::memory_stream & | read_state (cvm::memory_stream &is) |
| Read the colvar's state from an unformatted input stream.
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int | check_matching_state (std::string const &state_conf) |
| Check the name of the bias vs. the given string, set the matching_state flag accordingly.
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int | set_state_params (std::string const &state_conf) |
| Read the values of colvar mutable data from a string (used by both versions of read_state())
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std::string const | get_state_params () const |
| Write the state information of this colvar in a block of text, suitable for later parsing.
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std::ostream & | write_state (std::ostream &os) const |
| Write the colvar's state to a formatted output stream.
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cvm::memory_stream & | write_state (cvm::memory_stream &os) const |
| Write the colvar's state to an unformatted output stream.
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int | write_output_files () |
| Write output files (if defined, e.g. in analysis mode)
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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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std::vector< int > const & | get_volmap_ids () |
| Volmap numeric IDs, one for each CVC (-1 if not available)
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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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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) |
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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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colvarvalue | fdiff_velocity (colvarvalue const &xold, colvarvalue const &xnew) |
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void | update_active_cvc_square_norm () |
| Update the sum of square coefficients for active cvcs.
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void | calc_vel_acf (std::list< colvarvalue > &v_history, colvarvalue const &v) |
| Velocity ACF, scalar product between v(0) and v(t)
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void | calc_coor_acf (std::list< colvarvalue > &x_history, colvarvalue const &x) |
| Coordinate ACF, scalar product between x(0) and x(t) (does not work with scalar numbers)
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void | calc_p2coor_acf (std::list< colvarvalue > &x_history, colvarvalue const &x) |
| Coordinate ACF, second order Legendre polynomial between x(0) and x(t) (does not work with scalar numbers)
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int | calc_acf () |
| Calculate the auto-correlation function (ACF)
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int | write_acf (std::ostream &os) |
| Save the ACF to a file.
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int | calc_runave () |
| Calculate the running average and its standard deviation.
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void | build_atom_list (void) |
| Initialize the sorted list of atom IDs for atoms involved in all cvcs (called when enabling f_cv_collect_gradients)
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bool | get_key_string_value (std::string const &conf, char const *key, std::string &data) |
| Get the string value of a keyword, and save it for later parsing.
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bool | get_key_string_multi_value (std::string const &conf, char const *key, std::vector< std::string > &data) |
| Get multiple strings from repeated instances of a same keyword.
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template<typename TYPE > |
bool | _get_keyval_scalar_ (std::string const &conf, char const *key, TYPE &value, TYPE const &def_value, Parse_Mode const &parse_mode) |
| Template for single-value keyword parsers.
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template<typename TYPE > |
bool | _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) |
| Template for multiple-value keyword parsers.
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template<typename TYPE > |
int | _get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, TYPE &value, TYPE const &def_value) |
| Extract the value of a variable from a string.
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template<typename TYPE > |
int | _get_keyval_scalar_novalue_ (std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode) |
| Handle the case where the user provides a keyword without value.
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template<typename TYPE > |
void | mark_key_set_user (std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode) |
| Record that the keyword has just been user-defined.
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template<typename TYPE > |
void | mark_key_set_default (std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode) |
| Record that the keyword has just been set to its default value.
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void | error_key_required (std::string const &key_str, Parse_Mode const &parse_mode) |
| Raise error condition due to the keyword being required!
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bool | key_already_set (std::string const &key_str) |
| True if the keyword has been set already.
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void | add_keyword (char const *key) |
| Add a new valid keyword to the list.
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void | strip_values (std::string &conf) |
| Remove all the values from the config string.
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| colvarparams () |
| Default constructor.
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virtual | ~colvarparams () |
| Default destructor.
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void | register_param (std::string const ¶m_name, void *param_ptr) |
| Register the given parameter.
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void | register_param_grad (std::string const ¶m_name, colvarvalue *param_grad_ptr) |
| Register the gradient of the given parameter.
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bool | get_keyval_feature (colvarparse *cvp, std::string const &conf, char const *key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal) |
| Parse a keyword and enable a feature accordingly.
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colvarvalue | x |
| Value of the colvar.
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colvarvalue | x_reported |
| Cached reported value (x may be manipulated)
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colvarvalue | v_fdiff |
| Finite-difference velocity.
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colvarvalue | v_reported |
| Cached reported velocity.
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colvarvalue | x_ext |
| Restraint center.
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colvarvalue | prev_x_ext |
| Previous value of the restraint center;.
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colvarvalue | v_ext |
| Velocity of the restraint center.
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colvarvalue | prev_v_ext |
| Previous velocity of the restraint center.
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cvm::real | ext_mass = 0.0 |
| Mass of the restraint center.
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cvm::real | ext_force_k = 0.0 |
| Restraint force constant.
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cvm::real | ext_gamma = 0.0 |
| Friction coefficient for Langevin extended dynamics.
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cvm::real | ext_sigma = 0.0 |
| Amplitude of Gaussian white noise for Langevin extended dynamics.
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colvarvalue | fr |
| Applied force on extended DOF, for output (unscaled if using MTS)
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colvarvalue | fj |
| Jacobian force, when Jacobian_force is enabled.
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colvarvalue | ft_reported |
| Cached reported total force.
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size_t | n_active_cvcs = 0 |
| Number of CVC objects with an active flag.
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cvm::real | active_cvc_square_norm = 0.0 |
| Sum of square coefficients for active cvcs.
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cvm::step_number | prev_timestep |
| Absolute timestep number when this colvar was last updated.
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bool | matching_state |
| Flag used to tell if the state string being read is for this colvar.
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colvarvalue | x_old |
| Previous value (to calculate velocities during analysis)
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colvarvalue | x_restart |
| Value read from the most recent state file (if any)
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bool | after_restart |
| True if a state file was just read.
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std::list< std::list< colvarvalue > > | acf_x_history |
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std::list< std::list< colvarvalue > > | acf_v_history |
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std::list< std::list< colvarvalue > >::iterator | acf_x_history_p |
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std::list< std::list< colvarvalue > >::iterator | acf_v_history_p |
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std::list< std::list< colvarvalue > > | x_history |
| Time series of values and velocities used in running averages.
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std::list< std::list< colvarvalue > >::iterator | x_history_p |
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std::string | acf_colvar_name |
| Collective variable with which the correlation is calculated (default: itself)
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size_t | acf_length |
| Length of autocorrelation function (ACF)
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size_t | acf_offset |
| After how many steps the ACF starts.
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size_t | acf_stride |
| How many timesteps separate two ACF values.
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size_t | acf_nframes |
| Number of frames for each ACF point.
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bool | acf_normalize |
| Normalize the ACF to a maximum value of 1?
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std::vector< cvm::real > | acf |
| ACF values.
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std::string | acf_outfile |
| Name of the file to write the ACF.
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acf_type_e | acf_type |
| Type of autocorrelation function (ACF)
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size_t | runave_length |
| Length of running average series.
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size_t | runave_stride |
| Timesteps to skip between two values in the running average series.
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std::string | runave_outfile |
| Name of the file to write the running average.
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colvarvalue | runave |
| Current value of the running average.
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cvm::real | runave_variance = 0.0 |
| Current value of the square deviation from the running average.
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cvm::real | kinetic_energy = 0.0 |
| If extended Lagrangian active: colvar kinetic energy.
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cvm::real | potential_energy = 0.0 |
| If extended Lagrangian active: colvar harmonic potential.
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std::vector< std::shared_ptr< colvar::cvc > > | cvcs |
| Array of components objects.
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std::vector< bool > | cvc_flags |
| Flags to enable or disable cvcs at next colvar evaluation.
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std::string | scripted_function |
| Name of scripted function to be used.
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std::vector< const colvarvalue * > | sorted_cvc_values |
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std::vector< int > | volmap_ids_ |
| Volmap numeric IDs, one for each CVC (-1 if not available)
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std::string const | keyword_delimiters_left |
| Characters allowed immediately to the left of a kewyord.
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std::string const | keyword_delimiters_right |
| Characters allowed immediately to the right of a kewyord.
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std::list< std::string > | allowed_keywords |
| List of legal keywords for this object: this is updated by each call to colvarparse::get_keyval() or colvarparse::key_lookup()
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std::map< std::string, key_set_mode > | key_set_modes |
| Track which keywords have been already set, and how.
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std::list< size_t > | data_begin_pos |
| List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.
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std::list< size_t > | data_end_pos |
| List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.
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std::string | config_string |
| Configuration string of the object (includes comments)
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std::map< std::string, void const * > | param_map |
| Pointers to relevant parameters that may be accessed by other objects.
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std::map< std::string, colvarvalue const * > | param_grad_map |
| Derivatives of the object with respect to internal parameters.
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int | time_step_factor |
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std::vector< feature_state > | feature_states |
| List of the states of all features.
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