Collection Class Reference

#include <collection.hpp>

Inheritance diagram for Collection:

Public Member Functions
	Collection (sptr< Box > box, sptr< AtomGroup > atoms, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >(), bool should_initialize=true)
virtual void	initialize ()
virtual void	set_forces (bool constraints_and_a=true)
	Set forces. More...
virtual void	timestep ()=0
	Take one step forward in time. More...
flt	degrees_of_freedom ()
	Total degrees of freedom. More...
flt	potential_energy ()
flt	energy ()
	Total energy, including both potential and kinetic_energy. More...
virtual flt	temp (bool minuscomv=true)
virtual flt	kinetic_energy ()
virtual flt	virial ()
virtual flt	pressure ()
	Returns (1/d V) Σ ri dot fi where d is number of dimensions note that Interaction->pressure just returns Σ ri dot fi. More...
sptr< Box >	get_box ()
Vec	com ()
Vec	com_velocity ()
Vec	angular_momentum (const Vec &loc)
	Shortcut to AtomGroup method of the same name. More...
Vec	angular_momentum ()
	Shortcut to AtomGroup method of the same name. More...
flt	gyradius ()
virtual	~Collection ()
void	reset_com_velocity ()
	Shortcut to AtomGroup method of the same name. More...
void	reset_L ()
	Shortcut to AtomGroup method of the same name. More...
void	scale_velocities (flt scaleby)
	Scale all velocities by a factor. More...
void	scale_velocities_to_temp (flt T, bool minuscomv=true)
	Scale all velocities to get to a specific temperature. More...
void	scale_velocities_to_energy (flt E)
	Scale all velocities to get to a specific total energy. More...
void	add_interaction (sptr< Interaction > inter)
void	add_tracker (sptr< StateTracker > track)
void	add_constraint (sptr< Constraint > c)
void	add (sptr< Interaction > a)
void	add (sptr< StateTracker > a)
void	add (sptr< Constraint > a)
vector< sptr< Interaction > >	get_interactions ()

Protected Member Functions
void	update_trackers ()
	To be called immediately after setting particle positions and velocities; lets StateTracker instances stay updated automatically. More...
void	update_constraint_positions ()
	To be called approximately after forces have been set. More...
void	update_constraint_velocities ()
void	update_constraint_forces ()
virtual flt	set_forces_get_pressure (bool constraints_and_a=true)

Protected Attributes
sptr< Box >	box
sptr< AtomGroup >	atoms
vector< sptr< Interaction > >	interactions
vector< sptr< StateTracker > >	trackers
vector< sptr< Constraint > >	constraints

Detailed Description

A "Collection" of atoms, the box, and an integrator. Provides general simulation time-stepping as well as statistical tracking.

The most useful method is timestep(), which takes one step forward in time; this is defined by each subclass separately, as each subclass uses a different integration scheme.

Constructor & Destructor Documentation

Collection::Collection	(	sptr< Box >	box,
		sptr< AtomGroup >	atoms,
		vector< sptr< Interaction > >	interactions = vector<sptr<Interaction> >(),
		vector< sptr< StateTracker > >	trackers = vector<sptr<StateTracker> >(),
		vector< sptr< Constraint > >	constraints = vector<sptr<Constraint> >(),
		bool	should_initialize = true
	)

virtual Collection::~Collection ( )

inlinevirtual

Member Function Documentation

void Collection::add ( sptr< Interaction >  a )

inline

Examples:

hardspheres.cpp.

void Collection::add ( sptr< StateTracker >  a )

inline

void Collection::add ( sptr< Constraint >  a )

inline

void Collection::add_constraint ( sptr< Constraint >  c )

inline

void Collection::add_interaction ( sptr< Interaction >  inter )

inline

Examples:

hardspheres.cpp, LJatoms.cpp, and packer.cpp.

void Collection::add_tracker ( sptr< StateTracker >  track )

inline

Examples:

hardspheres.cpp, LJatoms.cpp, and packer.cpp.

Vec Collection::angular_momentum ( const Vec &  loc )

inline

Shortcut to AtomGroup method of the same name.

Vec Collection::angular_momentum ( )

inline

Shortcut to AtomGroup method of the same name.

Vec Collection::com ( )

inline

Vec Collection::com_velocity ( )

inline

flt Collection::degrees_of_freedom

(

)

Total degrees of freedom.

This takes into account constraints, and whether the center-of-mass is free.

flt Collection::energy

(

)

Total energy, including both potential and kinetic_energy.

Examples:

LJatoms.cpp.

sptr<Box> Collection::get_box ( )

inline

vector<sptr<Interaction> > Collection::get_interactions ( )

inline

flt Collection::gyradius

(

)

void Collection::initialize ( )

virtual

virtual flt Collection::kinetic_energy ( )

inlinevirtual

Reimplemented in CollectionGear4NPH, and CollectionNLCG.

Examples:

LJatoms.cpp.

flt Collection::potential_energy

(

)

Examples:

hardspheres.cpp.

flt Collection::pressure ( )

virtual

Returns (1/d V) Σ ri dot fi where d is number of dimensions note that Interaction->pressure just returns Σ ri dot fi.

Reimplemented in CollectionNLCGV, and CollectionNLCG.

void Collection::reset_com_velocity ( )

inline

Shortcut to AtomGroup method of the same name.

Examples:

hardspheres.cpp, and LJatoms.cpp.

void Collection::reset_L ( )

inline

Shortcut to AtomGroup method of the same name.

void Collection::scale_velocities

(

flt

scaleby

)

Scale all velocities by a factor.

void Collection::scale_velocities_to_energy

(

flt

E

)

Scale all velocities to get to a specific total energy.

Examples:

LJatoms.cpp.

void Collection::scale_velocities_to_temp	(	flt	T,
		bool	minuscomv = true
	)

Scale all velocities to get to a specific temperature.

void Collection::set_forces ( bool  constraints_and_a = true )

virtual

Set forces.

This should be called at the beginning of the simulation, and will also be called by timestep()

Reimplemented in CollectionGear4NPT, CollectionGaussianT, and CollectionNLCG.

flt Collection::set_forces_get_pressure ( bool  constraints_and_a = true )

protectedvirtual

flt Collection::temp ( bool  minuscomv = true )

virtual

Reimplemented in CollectionGear4NPH.

virtual void Collection::timestep ( )

pure virtual

Take one step forward in time.

Implemented in CollectionCDBDgrid, CollectionCDBD, CollectionCDgrid, CollectionCD, CollectionVerletNPT, CollectionGear4NPT, CollectionGear4NPH, CollectionRK4, CollectionGear6A, CollectionGear5A, CollectionGear4A, CollectionGear3A, CollectionGaussianT, CollectionNoseHoover, CollectionNLCGV, CollectionNLCG, CollectionOverdamped, CollectionVerlet, CollectionSolHT, CollectionDamped, CollectionSol, and StaticCollec.

void Collection::update_constraint_forces ( )

protected

void Collection::update_constraint_positions ( )

protected

To be called approximately after forces have been set.

Constraints will typically set forces / velocities in some direction to zero, so update_constraints should be called after all forces have been set, and any external velocity changes have been made.

void Collection::update_constraint_velocities ( )

protected

void Collection::update_trackers ( )

protected

To be called immediately after setting particle positions and velocities; lets StateTracker instances stay updated automatically.

flt Collection::virial ( )

virtual

Member Data Documentation

sptr<AtomGroup> Collection::atoms

protected

sptr<Box> Collection::box

protected

vector<sptr<Constraint> > Collection::constraints

protected

vector<sptr<Interaction> > Collection::interactions

protected

vector<sptr<StateTracker> > Collection::trackers

protected

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

• src/collection.hpp
• src/collection.cpp