Collective Variables Module - Developer Documentation
Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Attributes | List of all members
colvar::cvc Class Referenceabstract

Colvar component (base class for collective variables) More...

#include <colvarcomp.h>

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Public Member Functions

 cvc (std::string const &conf)
 Constructor. More...
 
virtual int init (std::string const &conf)
 
virtual int init_dependencies ()
 Initialize dependency tree.
 
cvm::atom_groupparse_group (std::string const &conf, char const *group_key, bool optional=false)
 Within the constructor, make a group parse its own options from the provided configuration string Returns reference to new group.
 
virtual int init_total_force_params (std::string const &conf)
 Parse options pertaining to total force calculation.
 
int setup ()
 After construction, set data related to dependency handling.
 
 cvc ()
 Default constructor (used when colvar::cvc objects are declared within other ones)
 
virtual ~cvc ()
 Destructor.
 
virtual const std::vector< feature * > & features () const
 Implementation of the feature list accessor for colvar.
 
virtual std::vector< feature * > & modify_features ()
 
virtual std::vector< std::vector< int > > get_atom_lists ()
 Get vector of vectors of atom IDs for all atom groups.
 
virtual void read_data ()
 Obtain data needed for the calculation for the backend.
 
virtual void calc_value ()=0
 Calculate the variable.
 
virtual void calc_gradients ()
 Calculate the atomic gradients, to be reused later in order to apply forces.
 
void calc_fit_gradients ()
 Calculate the atomic fit gradients.
 
virtual void debug_gradients ()
 Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component.
 
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.
 
virtual void calc_force_invgrads ()
 Calculate the total force from the system using the inverse atomic gradients.
 
virtual void calc_Jacobian_derivative ()
 Calculate the divergence of the inverse atomic gradients.
 
colvarvalue const & value () const
 Return the previously calculated value.
 
colvarvalue const & total_force () const
 Return the previously calculated total force.
 
colvarvalue const & Jacobian_derivative () const
 Return the previously calculated divergence of the inverse atomic gradients.
 
virtual void apply_force (colvarvalue const &cvforce)=0
 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...
 
virtual cvm::real dist2 (colvarvalue const &x1, colvarvalue const &x2) const
 Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities) More...
 
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)
 
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)
 
virtual void wrap (colvarvalue &x_unwrapped) const
 Wrap value (for periodic/symmetric cvcs)
 
void register_atom_group (cvm::atom_group *ag)
 Store a pointer to new atom group, and list as child for dependencies.
 
- Public Member Functions inherited from colvarparse
 colvarparse ()
 Default constructor.
 
 colvarparse (const std::string &conf)
 Constructor that stores the object's config string.
 
void init ()
 Set the object ready to parse a new configuration string.
 
void init (std::string const &conf)
 Set a new config string for this object.
 
std::string const & get_config () const
 Get the configuration string (includes comments)
 
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.
 
void clear_keyword_registry ()
 Use this after parsing a config string (note that check_keywords() calls it already)
 
bool get_keyval (std::string const &conf, char const *key, int &value, int const &def_value=(int) 0, Parse_Mode const parse_mode=parse_normal)
 
bool 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)
 
bool get_keyval (std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal)
 
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)
 
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)
 
bool 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)
 
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)
 
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)
 
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)
 
bool get_keyval (std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal)
 
bool 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)
 
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,(size_t) 0), Parse_Mode const parse_mode=parse_normal)
 
bool 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)
 
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)
 
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,(cvm::real) 0.0), Parse_Mode const parse_mode=parse_normal)
 
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)
 
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)
 
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)
 
bool key_lookup (std::string const &conf, char const *key, std::string *data=NULL, size_t *save_pos=NULL)
 Low-level function for parsing configuration strings; automatically adds the requested keyword to the list of valid ones. More...
 
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...
 
template<>
int _get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, bool &value, bool const &def_value)
 
template<>
int _get_keyval_scalar_novalue_ (std::string const &key_str, bool &value, Parse_Mode const &parse_mode)
 
- Public Member Functions inherited from colvardeps
int get_time_step_factor () const
 returns time_step_factor
 
void init_feature (int feature_id, const char *description, feature_type type)
 Pair a numerical feature ID with a description and type.
 
bool is_not_set (int id)
 
bool is_dynamic (int id)
 
bool is_static (int id)
 
bool is_user (int id)
 
void add_child (colvardeps *child)
 
void remove_child (colvardeps *child)
 
void remove_all_children ()
 
bool is_enabled (int f=f_cv_active) const
 
bool is_available (int f=f_cv_active) const
 
void provide (int feature_id, bool truefalse=true)
 
void set_enabled (int feature_id, bool truefalse=true)
 Enable or disable, depending on flag value.
 
int enable (int f, bool dry_run=false, bool toplevel=true)
 
int disable (int f)
 
void free_children_deps ()
 
void restore_children_deps ()
 re-enable children features (to be used when object becomes active)
 
int decr_ref_count (int f)
 
virtual void do_feature_side_effects (int id)
 
void require_feature_self (int f, int g)
 Make feature f require feature g within the same object.
 
void exclude_feature_self (int f, int g)
 Make features f and g mutually exclusive within the same object.
 
void require_feature_children (int f, int g)
 Make feature f require feature g within children.
 
void require_feature_alt (int f, int g, int h)
 Make feature f require either g or h within the same object.
 
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.
 
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.
 
void print_state ()
 print all enabled features and those of children, for debugging
 
void check_enabled (int f, std::string const &reason) const
 Check that a feature is enabled, raising BUG_ERROR if not.
 

Static Public Member Functions

static void delete_features ()
 
- Static Public Member Functions inherited from colvarparse
static std::string to_lower_cppstr (std::string const &in)
 Return a lowercased copy of the string.
 
static std::istream & getline_nocomments (std::istream &is, std::string &s)
 Works as std::getline() but also removes everything between a comment character and the following newline.
 
static int check_braces (std::string const &conf, size_t const start_pos)
 Check if the content of a config string has matching braces. More...
 

Public Attributes

std::string name
 The name of the object (helps to identify this cvc instance when debugging)
 
std::string function_type
 Description of the type of collective variable. More...
 
std::string config_key
 Keyword used in the input to denote this CVC.
 
cvm::real sup_coeff
 Coefficient in the polynomial combination (default: 1.0)
 
int sup_np
 Exponent in the polynomial combination (default: 1)
 
bool b_periodic
 Is this a periodic component?
 
cvm::real period
 Period of this cvc value, (default: 0.0, non periodic)
 
cvm::real wrap_center
 If the component is periodic, wrap around this value (default: 0.0)
 
std::vector< cvm::atom_group * > atom_groups
 Pointers to all atom groups, to let colvars collect info e.g. atomic gradients.
 
bool b_try_scalable
 Whether or not this CVC will be computed in parallel whenever possible.
 
- Public Attributes inherited from colvardeps
std::string description
 

Static Public Attributes

static std::vector< feature * > cvc_features
 Implementation of the feature list for colvar.
 
- Static Public Attributes inherited from colvarparse
static const char *const white_space = " \t"
 Accepted white space delimiters, used in key_lookup()
 

Protected Attributes

colvarvalue x
 Cached value.
 
colvarvalue x_old
 Value at the previous step.
 
colvarvalue ft
 Calculated total force (Note: this is calculated from the total atomic forces read from the program, subtracting fromt the "internal" forces of the system the "external" forces from the colvar biases)
 
colvarvalue jd
 Calculated Jacobian derivative (divergence of the inverse gradients): serves to calculate the phase space correction.
 
- Protected Attributes inherited from colvarparse
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()
 
std::map< std::string, key_set_modekey_set_modes
 Track which keywords have been already set, and how.
 
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.
 
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.
 
std::string config_string
 Configuration string of the object (includes comments)
 
- Protected Attributes inherited from colvardeps
int time_step_factor
 
std::vector< feature_statefeature_states
 List of the states of all features.
 

Additional Inherited Members

- Public Types inherited from colvarparse
enum  Parse_Mode {
  parse_null = 0, parse_echo = (1<<1), parse_echo_default = (1<<2), parse_silent = 0,
  parse_required = (1<<16), parse_override = (1<<17), parse_restart = (1<<18), parse_normal = (1<<2) | (1<<1) | (1<<17)
}
 How a keyword is parsed in a string. More...
 
- Public Types inherited from colvardeps
enum  features_biases {
  f_cvb_active, f_cvb_awake, f_cvb_apply_force, f_cvb_get_total_force,
  f_cvb_output_acc_work, f_cvb_history_dependent, f_cvb_time_dependent, f_cvb_scalar_variables,
  f_cvb_calc_pmf, f_cvb_calc_ti_samples, f_cvb_write_ti_samples, f_cvb_write_ti_pmf,
  f_cvb_ntot
}
 
enum  features_colvar {
  f_cv_active, f_cv_awake, f_cv_gradient, f_cv_collect_gradient,
  f_cv_fdiff_velocity, f_cv_total_force, f_cv_total_force_calc, f_cv_subtract_applied_force,
  f_cv_Jacobian, f_cv_hide_Jacobian, f_cv_extended_Lagrangian, f_cv_Langevin,
  f_cv_output_energy, f_cv_output_value, f_cv_output_velocity, f_cv_output_applied_force,
  f_cv_output_total_force, f_cv_lower_boundary, f_cv_upper_boundary, f_cv_grid,
  f_cv_runave, f_cv_corrfunc, f_cv_scripted, f_cv_custom_function,
  f_cv_periodic, f_cv_scalar, f_cv_linear, f_cv_homogeneous,
  f_cv_multiple_ts, f_cv_ntot
}
 
enum  features_cvc {
  f_cvc_active, f_cvc_scalar, f_cvc_gradient, f_cvc_explicit_gradient,
  f_cvc_inv_gradient, f_cvc_debug_gradient, f_cvc_Jacobian, f_cvc_pbc_minimum_image,
  f_cvc_one_site_total_force, f_cvc_com_based, f_cvc_scalable, f_cvc_scalable_com,
  f_cvc_ntot
}
 
enum  features_atomgroup {
  f_ag_active, f_ag_center, f_ag_rotate, f_ag_fitting_group,
  f_ag_explicit_gradient, f_ag_fit_gradients, f_ag_atom_forces, f_ag_scalable,
  f_ag_scalable_com, f_ag_ntot
}
 
- Protected Types inherited from colvarparse
enum  key_set_mode { key_not_set = 0, key_set_user = 1, key_set_default = 2 }
 How a keyword has been set.
 
- Protected Types inherited from colvardeps
enum  feature_type { f_type_not_set, f_type_dynamic, f_type_user, f_type_static }
 Enum of possible feature types.
 
- Protected Member Functions inherited from colvarparse
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.
 
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.
 
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.
 
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.
 
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.
 
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.
 
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.
 
void error_key_required (std::string const &key_str, Parse_Mode const &parse_mode)
 Raise error condition due to the keyword being required!
 
bool key_already_set (std::string const &key_str)
 True if the keyword has been set already.
 
void add_keyword (char const *key)
 Add a new valid keyword to the list.
 
void strip_values (std::string &conf)
 Remove all the values from the config string.
 
- Protected Member Functions inherited from colvardeps
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.
 

Detailed Description

Colvar component (base class for collective variables)

A colvar::cvc object (or an object of a cvc-derived class) implements the calculation of a collective variable, its gradients and any other related physical quantities that depend on microscopic degrees of freedom.

No restriction is set to what kind of calculation a colvar::cvc object performs (usually an analytical function of atomic coordinates). The only constraints are that:

If you wish to implement a new collective variable component, you should write your own class by inheriting directly from colvar::cvc, or one of its derived classes (for instance, colvar::distance is frequently used, because it provides useful data and function members for any colvar based on two atom groups).

The steps are:

  1. Declare the new class as a derivative of colvar::cvc in the file colvarcomp.h
  2. Implement the new class in a file named colvarcomp_<something>.cpp
  3. Declare the name of the new class inside the colvar class in colvar.h (see "list of available components")
  4. Add a call for the new class in colvar::init_components() (file: colvar.cpp)

Constructor & Destructor Documentation

◆ cvc()

colvar::cvc::cvc ( std::string const &  conf)

Constructor.

Calls the init() function of the class

Member Function Documentation

◆ apply_force()

virtual void colvar::cvc::apply_force ( colvarvalue const &  cvforce)
pure virtual

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function)

Note: multiple calls to this function within the same simulation step will add the forces altogether

Parameters
cvforceThe collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object

Implemented in colvar::cartesian, colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_pairs, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, and colvar::distance.

◆ dist2()

cvm::real colvar::cvc::dist2 ( colvarvalue const &  x1,
colvarvalue const &  x2 
) const
virtual

Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities)

colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object.

If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients.

If constraints are present (and not already implemented by any of the colvarvalue types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface.

Finally, another useful application, if you are performing very many operations with these functions, could be to override the colvarvalue member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar colvarvalue type.

Reimplemented in colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, and colvar::distance.

◆ init()

int colvar::cvc::init ( std::string const &  conf)
virtual

An init function should be defined for every class inheriting from cvc

Parameters
confContents of the configuration file pertaining to this cvc

Reimplemented in colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, and colvar::orientation.

Member Data Documentation

◆ function_type

std::string colvar::cvc::function_type

Description of the type of collective variable.

Normally this string is set by the parent colvar object within its constructor, when all colvar::cvc objects are initialized; therefore the main "config string" constructor does not need to define it. If a colvar::cvc is initialized and/or a different constructor is used, this variable definition should be set within the constructor.


The documentation for this class was generated from the following files: