colvarmodule::atom Class Reference

Stores numeric id, mass and all mutable data for an atom, mostly used by a colvar::cvc. More...

#include <colvaratoms.h>

Collaboration diagram for colvarmodule::atom:

Public Member Functions
	atom ()
	Default constructor (sets index and id both to -1)
	atom (int atom_number)
	Initialize an atom for collective variable calculation and get its internal identifier. More...
	atom (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id)
	Initialize an atom for collective variable calculation and get its internal identifier. More...
	atom (atom const &a)
	Copy constructor.
	~atom ()
	Destructor.
atom &	operator= (atom const &a)
	Assignment operator (added to appease LGTM)
void	reset_data ()
	Set mutable data (everything except id and mass) to zero.
void	update_mass ()
	Get the latest value of the mass.
void	update_charge ()
	Get the latest value of the charge.
void	read_position ()
	Get the current position.
void	read_velocity ()
	Get the current velocity.
void	read_total_force ()
	Get the total force.
void	apply_force (cvm::rvector const &new_force) const
	Apply a force to the atom. More...

Public Attributes
int	id
	Identifier for the MD program (0-based)
cvm::real	mass
	Mass.
cvm::real	charge
	Charge.
cvm::atom_pos	pos
	Current position (copied from the program, can be modified if necessary)
cvm::rvector	vel
	Current velocity (copied from the program, can be modified if necessary)
cvm::rvector	total_force
	System force at the previous step (copied from the program, can be modified if necessary)
cvm::rvector	grad
	Gradient of a scalar collective variable with respect to this atom. More...

Protected Attributes
int	index
	Index in the colvarproxy arrays (NOT in the global topology!)

Detailed Description

Stores numeric id, mass and all mutable data for an atom, mostly used by a colvar::cvc.

This class may be used to keep atomic data such as id, mass, position and collective variable derivatives) altogether. There may be multiple instances with identical numeric id, all acting independently: forces communicated through these instances will be summed together.

Constructor & Destructor Documentation

atom() [1/2]

cvm::atom::atom

(

int

atom_number

)

Initialize an atom for collective variable calculation and get its internal identifier.

Parameters

atom_number

Atom index in the system topology (1-based)

atom() [2/2]

cvm::atom::atom	(	cvm::residue_id const &	residue,
		std::string const &	atom_name,
		std::string const &	segment_id
	)

Initialize an atom for collective variable calculation and get its internal identifier.

Parameters

residue	Residue number
atom_name	Name of the atom in the residue
segment_id	For PSF topologies, the segment identifier; for other type of topologies, may not be required

Member Function Documentation

apply_force()

void colvarmodule::atom::apply_force ( cvm::rvector const &  new_force ) const

inline

Apply a force to the atom.

Note: the force is not applied instantly, but will be used later by the MD integrator (the colvars module does not integrate equations of motion.

Multiple calls to this function by either the same atom object or different objects with identical id will all be added together.

Member Data Documentation

grad

cvm::rvector colvarmodule::atom::grad

Gradient of a scalar collective variable with respect to this atom.

This can only handle a scalar collective variable (i.e. when the colvarvalue::real_value member is used from the colvarvalue class), which is also the most frequent case. For more complex types of colvarvalue objects, atomic gradients should be defined within the specific colvar::cvc implementation

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

• colvaratoms.h
• colvaratoms.cpp