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colvar::map_total Class Reference

#include <colvarcomp.h>

Inheritance diagram for colvar::map_total:

List of all members.

Public Methods
	map_total ()
	map_total (std::string const &conf)
virtual	~map_total ()
virtual int	init (std::string const &conf)
	An init function should be defined for every class inheriting from cvc Parameters: conf  Contents of the configuration file pertaining to this cvc. More...
virtual void	calc_value ()
	\brief Calculate the variable. More...
virtual void	calc_gradients ()
	\brief Calculate the atomic gradients, to be reused later in order to apply forces. More...
virtual void	apply_force (colvarvalue const &force)
	\brief 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: cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object. More...
Protected Attributes
std::string	volmap_name
	String identifier of the map object (as used by the simulation engine). More...
int	volmap_id
	Numeric identifier of the map object (as used by the simulation engine). More...
int	volmap_index
	Index of the map objet in the proxy arrays. More...
cvm::atom_group *	atoms
	Group of atoms selected internally (optional). More...
std::vector< cvm::real >	atom_weights
	Weights assigned to each atom (default: uniform weights). More...

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Constructor & Destructor Documentation

colvar::map_total::map_total (    )

Definition at line 18 of file colvarcomp_volmaps.C. References atoms, NULL, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, volmap_id, volmap_index, and colvar::cvc::x.

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

Definition at line 29 of file colvarcomp_volmaps.C. References atoms, conf, NULL, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, volmap_id, volmap_index, and colvar::cvc::x.

virtual colvar::map_total::~map_total (    )  [inline, virtual]

Definition at line 1848 of file colvarcomp.h.

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Member Function Documentation

void colvar::map_total::apply_force (  colvarvalue const &    force )  [virtual]

\brief 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: cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object. Implements colvar::cvc. Definition at line 134 of file colvarcomp_volmaps.C. References colvarproxy_volmaps::apply_volmap_force, atoms, force, colvarmodule::main, colvarmodule::proxy, colvarvalue::real_value, and volmap_index.

void colvar::map_total::calc_gradients (    )  [virtual]

\brief Calculate the atomic gradients, to be reused later in order to apply forces. Reimplemented from colvar::cvc. Definition at line 128 of file colvarcomp_volmaps.C.

void colvar::map_total::calc_value (    )  [virtual]

\brief Calculate the variable. Implements colvar::cvc. Definition at line 104 of file colvarcomp_volmaps.C. References atom_weights, atoms, colvarproxy_volmaps::compute_volmap, colvardeps::f_cvc_gradient, colvarproxy_volmaps::get_volmap_value, colvardeps::is_enabled, colvarmodule::main, NULL, colvarmodule::proxy, colvarvalue::real_value, colvarproxy_volmaps::volmap_flag_gradients, colvarproxy_volmaps::volmap_flag_null, colvarproxy_volmaps::volmap_flag_use_atom_field, volmap_id, volmap_index, and colvar::cvc::x.

int colvar::map_total::init (  std::string const &    conf )  [virtual]

An init function should be defined for every class inheriting from cvc Parameters: conf  Contents of the configuration file pertaining to this cvc. Reimplemented from colvar::cvc. Definition at line 41 of file colvarcomp_volmaps.C. References atom_weights, atoms, colvarproxy_volmaps::check_volmap_by_id, colvarproxy_volmaps::check_volmap_by_name, colvarmodule::cite_feature, COLVARS_INPUT_ERROR, conf, colvarmodule::error, colvarparse::get_keyval, colvarproxy_volmaps::get_volmap_id_from_name, colvarproxy_volmaps::init_volmap_by_id, colvarproxy_volmaps::init_volmap_by_name, colvarmodule::main, NULL, colvar::cvc::parse_group, colvarmodule::proxy, colvarparams::register_param, colvarmodule::to_str, volmap_id, volmap_index, and volmap_name.

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Member Data Documentation

std::vector<cvm::real> colvar::map_total::atom_weights [protected]

Weights assigned to each atom (default: uniform weights). Definition at line 1869 of file colvarcomp.h. Referenced by calc_value, and init.

cvm::atom_group* colvar::map_total::atoms [protected]

Group of atoms selected internally (optional). Definition at line 1866 of file colvarcomp.h. Referenced by apply_force, calc_value, init, and map_total.

int colvar::map_total::volmap_id [protected]

Numeric identifier of the map object (as used by the simulation engine). Definition at line 1860 of file colvarcomp.h. Referenced by calc_value, init, and map_total.

int colvar::map_total::volmap_index [protected]

Index of the map objet in the proxy arrays. Definition at line 1863 of file colvarcomp.h. Referenced by apply_force, calc_value, init, and map_total.

std::string colvar::map_total::volmap_name [protected]

String identifier of the map object (as used by the simulation engine). Definition at line 1857 of file colvarcomp.h. Referenced by init.

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

• colvarcomp.h
• colvarcomp_volmaps.C

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