CollectionDamped Class Reference

A damped Collection, equivalent to CollectionSol but without the random forces. More...

#include <collection.hpp>

Inheritance diagram for CollectionDamped:

Public Member Functions
	CollectionDamped (sptr< Box > box, sptr< AtomGroup > atoms, const flt dt, const flt damping, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >())
void	change_damping (const flt damp)
void	set_dt (const flt newdt)
void	timestep ()
	Take one step forward in time. More...
Public Member Functions inherited from 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 void	initialize ()
virtual void	set_forces (bool constraints_and_a=true)
	Set forces. 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	set_constants ()
Protected Member Functions inherited from Collection
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
flt	dt
flt	damping
flt	c0
flt	c1
flt	c2
Protected Attributes inherited from Collection
sptr< Box >	box
sptr< AtomGroup >	atoms
vector< sptr< Interaction > >	interactions
vector< sptr< StateTracker > >	trackers
vector< sptr< Constraint > >	constraints

Detailed Description

A damped Collection, equivalent to CollectionSol but without the random forces.

Uses the Langevin Equation (modified with \(\vec{f}\)):

\(\dot{\vec{p}} = - \xi \vec{p} + \vec{f} + \overset{\circ}{\vec{p}}\)

Except that here, we use \(\overset{\circ}{\vec{p}} = 0\).

Constructor & Destructor Documentation

CollectionDamped::CollectionDamped	(	sptr< Box >	box,
		sptr< AtomGroup >	atoms,
		const flt	dt,
		const flt	damping,
		vector< sptr< Interaction > >	interactions = vector<sptr<Interaction> >(),
		vector< sptr< StateTracker > >	trackers = vector<sptr<StateTracker> >(),
		vector< sptr< Constraint > >	constraints = vector<sptr<Constraint> >()
	)

Member Function Documentation

void CollectionDamped::change_damping ( const flt  damp )

inline

void CollectionDamped::set_constants ( )

protected

void CollectionDamped::set_dt ( const flt  newdt )

inline

void CollectionDamped::timestep ( )

virtual

Take one step forward in time.

Implements Collection.

Member Data Documentation

flt CollectionDamped::c0

protected

flt CollectionDamped::c1

protected

flt CollectionDamped::c2

protected

flt CollectionDamped::damping

protected

flt CollectionDamped::dt

protected

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

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