SubGroup Class Reference

#include <box.hpp>

Inheritance diagram for SubGroup:

Public Member Functions
	SubGroup (sptr< AtomVec > atoms)
AtomVec &	vec ()
Atom &	operator[] (cuint n)
Atom &	operator[] (cuint n) const
Atom &	get (cuint n)
void	add (AtomID a)
AtomID	get_id (cuint n)
uint	size () const
	Number of atoms in the group. More...
Public Member Functions inherited from AtomGroup
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 ()

Protected Attributes
sptr< AtomVec >	atoms
vector< AtomID >	ids

Detailed Description

A class for representing any grouping of atoms that is not the whole set of atoms, such as a molecule, a side-chain, etc.

Constructor & Destructor Documentation

SubGroup::SubGroup ( sptr< AtomVec >  atoms )

inline

Member Function Documentation

void SubGroup::add ( AtomID  a )

inline

Atom& SubGroup::get ( cuint  n )

inlinevirtual

Reimplemented from AtomGroup.

AtomID SubGroup::get_id ( cuint  n )

inlinevirtual

Implements AtomGroup.

Atom& SubGroup::operator[] ( cuint  n )

inlinevirtual

Implements AtomGroup.

Atom& SubGroup::operator[] ( cuint  n ) const

inlinevirtual

Implements AtomGroup.

uint SubGroup::size ( ) const

inlinevirtual

Number of atoms in the group.

Implements AtomGroup.

AtomVec& SubGroup::vec ( )

inlinevirtual

Implements AtomGroup.

Member Data Documentation

sptr<AtomVec> SubGroup::atoms

protected

vector<AtomID> SubGroup::ids

protected

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

• src/box.hpp