colvarbias Class Reference

Collective variable bias, base class. More...

#include <colvarbias.h>

Inheritance diagram for colvarbias:

List of all members.

Public Member Functions
void	add_colvar (std::string const &cv_name)
	Add a new collective variable to this bias.
virtual void	update ()=0
	Retrieve colvar values and calculate their biasing forces.
virtual void	analyse ()
	Perform analysis tasks.
void	communicate_forces ()
	Send forces to the collective variables.
	colvarbias (std::string const &conf, char const *key)
	Constructor.
virtual	~colvarbias ()
	Destructor.
virtual std::istream &	read_restart (std::istream &is)=0
	Read the bias configuration from a restart file.
virtual std::ostream &	write_restart (std::ostream &os)=0
	Write the bias configuration to a restart file.
Public Attributes
int	id
	Numeric id of this bias.
std::string	name
	Name of this bias.
Protected Attributes
std::vector< colvar * >	colvars
	Pointers to collective variables to which the bias is applied; current values and metric functions will be obtained through each colvar object.
std::vector< colvarvalue >	colvar_forces
	Current forces from this bias to the colvars.
cvm::real	colvar_energy
	Current energy of this bias (colvar_forces should be obtained by deriving this).

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Detailed Description

Collective variable bias, base class.

Definition at line 9 of file colvarbias.h.

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Constructor & Destructor Documentation

colvarbias::colvarbias (  std::string const &  conf, char const *  key )

Constructor. Constructor of the base class colvarbias is protected, so that it can only be called from inherited classes Definition at line 6 of file colvarbias.C. References add_colvar(), colvars, colvarmodule::fatal_error(), colvarmodule::log(), name, and colvarparse::to_lower_cppstr(). : colvarparse() { cvm::log ("Initializing a new \""+std::string (key)+"\" instance.\n"); size_t rank = 1; std::string const key_str (key); if (colvarparse::to_lower_cppstr (key_str) == std::string ("abf")) { rank = cvm::n_abf_biases+1; } if (colvarparse::to_lower_cppstr (key_str) == std::string ("harmonic")) { rank = cvm::n_harm_biases+1; } if (colvarparse::to_lower_cppstr (key_str) == std::string ("histogram")) { rank = cvm::n_histo_biases+1; } if (colvarparse::to_lower_cppstr (key_str) == std::string ("metadynamics")) { rank = cvm::n_meta_biases+1; } get_keyval (conf, "name", name, key_str+cvm::to_str (rank)); // lookup the associated colvars std::vector<std::string> colvars_str; if (get_keyval (conf, "colvars", colvars_str)) { for (size_t i = 0; i < colvars_str.size(); i++) { add_colvar (colvars_str[i]); } } if (!colvars.size()) { cvm::fatal_error ("Error: no collective variables specified.\n"); } }

virtual colvarbias::~colvarbias (   )  [inline, virtual]

Destructor. Definition at line 37 of file colvarbias.h. {}

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Member Function Documentation

void colvarbias::add_colvar (  std::string const &  cv_name  )

Add a new collective variable to this bias. Definition at line 43 of file colvarbias.C. References colvar_forces, colvarmodule::colvar_p(), colvars, colvarmodule::debug(), colvar::enable(), colvarmodule::fatal_error(), colvarmodule::log(), colvar::name, and colvar::type(). Referenced by colvarbias(). { if (colvar *cvp = cvm::colvar_p (cv_name)) { cvp->enable (colvar::task_gradients); if (cvm::debug()) cvm::log ("Applying this bias to collective variable \""+ cvp->name+"\".\n"); colvars.push_back (cvp); colvar_forces.push_back (colvarvalue (cvp->type())); } else { cvm::fatal_error ("Error: cannot find a colvar named \""+ cv_name+"\".\n"); } }

virtual void colvarbias::analyse (   )  [inline, virtual]

Perform analysis tasks. Reimplemented in colvarbias_meta. Definition at line 25 of file colvarbias.h. {}

void colvarbias::communicate_forces (   )

Send forces to the collective variables. Definition at line 59 of file colvarbias.C. References colvar::add_bias_force(), colvar_forces, colvars, colvarmodule::debug(), colvarmodule::log(), and name. { for (size_t i = 0; i < colvars.size(); i++) { if (cvm::debug()) { cvm::log ("Communicating a force to colvar \""+ colvars[i]->name+"\", of type \""+ colvarvalue::type_desc[colvars[i]->type()]+"\".\n"); } colvars[i]->add_bias_force (colvar_forces[i]); } }

virtual std::istream& colvarbias::read_restart (  std::istream &  is  )  [pure virtual]

Read the bias configuration from a restart file. Implemented in colvarbias_harmonic, and colvarbias_meta.

virtual void colvarbias::update (   )  [pure virtual]

Retrieve colvar values and calculate their biasing forces. Implemented in colvarbias_harmonic, colvarbias_abf, colvarbias_histogram, and colvarbias_meta.

virtual std::ostream& colvarbias::write_restart (  std::ostream &  os  )  [pure virtual]

Write the bias configuration to a restart file. Implemented in colvarbias_harmonic, and colvarbias_meta.

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Member Data Documentation

cvm::real colvarbias::colvar_energy [protected]

Current energy of this bias (colvar_forces should be obtained by deriving this). Definition at line 57 of file colvarbias.h.

std::vector<colvarvalue> colvarbias::colvar_forces [protected]

Current forces from this bias to the colvars. Definition at line 53 of file colvarbias.h. Referenced by add_colvar(), and communicate_forces().

std::vector<colvar *> colvarbias::colvars [protected]

Pointers to collective variables to which the bias is applied; current values and metric functions will be obtained through each colvar object. Definition at line 50 of file colvarbias.h. Referenced by add_colvar(), colvarbias(), and communicate_forces().

int colvarbias::id

Numeric id of this bias. Definition at line 13 of file colvarbias.h.

std::string colvarbias::name

Name of this bias. Definition at line 16 of file colvarbias.h. Referenced by colvarbias(), and communicate_forces().

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

• colvarbias.h
• colvarbias.C

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