AtomGroup Class Reference

a group of atoms, such as all of them (AtomVec), or a smaller group such as a molecule, sidebranch, etc. More...

#include <box.hpp>

Inheritance diagram for AtomGroup:

Public Member Functions
virtual AtomVec &	vec ()=0
virtual Atom &	operator[] (cuint n)=0
virtual Atom &	operator[] (cuint n) const =0
virtual Atom &	get (cuint n)
virtual AtomID	get_id (cuint n)=0
virtual uint	size () const =0
	Number of atoms in the group. More...
virtual AtomIter	begin ()
	For use in a for loop. More...
virtual AtomIter	end ()
Vec	com () const
	center of mass More...
Vec	com_force () const
	center of mass force (i.e., sum of all forces) More...
Vec	com_velocity () const
	center of mass velocity More...
flt	mass () const
	Mass of the whole group. More...
flt	kinetic_energy (const Vec originvelocity=Vec::Zero()) const
	Total kinetic_energy energy of the group. More...
Vec	momentum () const
	Total momentum. More...
flt	gyradius () const
	\(R_g\) More...
Vec	torque (const Vec loc) const
	Total torque about a given location. More...
Vec	torque () const
flt	moment_about (const Vec axis, const Vec loc) const
	Moment of inertia of the atoms about an axis. More...
flt	moment_about (const Vec axis) const
Vec	angular_momentum (const Vec loc) const
	Angular momentum. More...
Vec	angular_momentum () const
Matrix	moment (const Vec loc) const
	Moment of inertia of the atoms as a whole. More...
Matrix	moment () const
Vec	omega (const Vec loc) const
	Angular velocity. More...
Vec	omega () const
void	add_omega (Vec w, Vec origin)
	Add a given angular velocity to all atoms, by adding to their velocity. More...
void	add_omega (Vec w)
void	reset_L ()
	Reset angular momentum to 0. More...
void	add_velocity (Vec v)
	for resetting. Adds a fixed velocity to all atoms More...
void	reset_com_velocity ()
	Subtracts the center of mass velocity from all atoms. More...
void	randomize_velocities (flt T)
	Randomize velocities, for a specific temperature. More...
void	reset_forces ()
	for timestepping More...
virtual	~AtomGroup ()

Detailed Description

a group of atoms, such as all of them (AtomVec), or a smaller group such as a molecule, sidebranch, etc.

Constructor & Destructor Documentation

virtual AtomGroup::~AtomGroup ( )

inlinevirtual

Member Function Documentation

void AtomGroup::add_omega	(	Vec	w,
		Vec	origin
	)

Add a given angular velocity to all atoms, by adding to their velocity.

void AtomGroup::add_omega ( Vec  w )

inline

void AtomGroup::add_velocity

(

Vec

v

)

for resetting. Adds a fixed velocity to all atoms

Vec AtomGroup::angular_momentum

(

const Vec

loc

)

const

Angular momentum.

Vec AtomGroup::angular_momentum ( ) const

inline

virtual AtomIter AtomGroup::begin ( )

inlinevirtual

For use in a for loop.

Vec AtomGroup::com

(

)

const

center of mass

Vec AtomGroup::com_force

(

)

const

center of mass force (i.e., sum of all forces)

Vec AtomGroup::com_velocity

(

)

const

center of mass velocity

virtual AtomIter AtomGroup::end ( )

inlinevirtual

virtual Atom& AtomGroup::get ( cuint  n )

inlinevirtual

Reimplemented in SubGroup.

virtual AtomID AtomGroup::get_id ( cuint  n )

pure virtual

Implemented in SCAtomVec, SubGroup, and AtomVec.

flt AtomGroup::gyradius

(

)

const

\(R_g\)

flt AtomGroup::kinetic_energy

(

const Vec

originvelocity = Vec::Zero()

)

const

Total kinetic_energy energy of the group.

This is normally with reference to a "lab" reference frame (velocity (0,0,0)), but can optionally take a different origin velocity, e.g. com_velocity().

flt AtomGroup::mass

(

)

const

Mass of the whole group.

Matrix AtomGroup::moment

(

const Vec

loc

)

const

Moment of inertia of the atoms as a whole.

Matrix AtomGroup::moment ( ) const

inline

flt AtomGroup::moment_about	(	const Vec	axis,
		const Vec	loc
	)		const

Moment of inertia of the atoms about an axis.

flt AtomGroup::moment_about ( const Vec  axis ) const

inline

Vec AtomGroup::momentum

(

)

const

Total momentum.

Vec AtomGroup::omega

(

const Vec

loc

)

const

Angular velocity.

Vec AtomGroup::omega ( ) const

inline

virtual Atom& AtomGroup::operator[] ( cuint  n )

pure virtual

Implemented in SCAtomVec, SubGroup, and AtomVec.

virtual Atom& AtomGroup::operator[] ( cuint  n ) const

pure virtual

Implemented in SCAtomVec, SubGroup, and AtomVec.

void AtomGroup::randomize_velocities

(

flt

T

)

Randomize velocities, for a specific temperature.

void AtomGroup::reset_com_velocity ( )

inline

Subtracts the center of mass velocity from all atoms.

void AtomGroup::reset_forces

(

)

for timestepping

void AtomGroup::reset_L ( )

inline

Reset angular momentum to 0.

virtual uint AtomGroup::size ( ) const

pure virtual

Number of atoms in the group.

Implemented in SCAtomVec, SubGroup, and AtomVec.

Vec AtomGroup::torque

(

const Vec

loc

)

const

Total torque about a given location.

Vec AtomGroup::torque ( ) const

inline

virtual AtomVec& AtomGroup::vec ( )

pure virtual

Implemented in SCAtomVec, SubGroup, and AtomVec.

---

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

• src/box.hpp
• src/box.cpp