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colvar::map_total Class Reference

#include <colvarcomp.h>

Inheritance diagram for colvar::map_total:

colvar::cvc colvarparse colvardeps colvarparams 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::realatom_weights
 Weights assigned to each atom (default: uniform weights). More...


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.


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.


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.


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