#include <collection.hpp>

Inheritance diagram for CollectionGear4NPH:

Public Member Functions
	CollectionGear4NPH (sptr< OriginBox > box, sptr< AtomGroup > atoms, const flt dt, const flt P, const flt Q, uint ncorrectionsteps, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >())

	CollectionGear4NPH (sptr< OriginBox > box, sptr< AtomGroup > atoms, const flt dt, const flt P, const flt Q, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >())

void	timestep ()
	Take one step forward in time. More...

flt	kinetic_energy ()

flt	temp (bool minuscomv=true)

flt	hamiltonian ()

flt	get_dV ()

flt	getddV ()

void	set_dt (flt newdt)

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	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	resetbs ()

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	P

flt	Q

flt	dV

flt	ddV

flt	dddV

uint	ncorrec

vector< Vec >	bs

Protected Attributes inherited from Collection
sptr< Box >	box

sptr< AtomGroup >	atoms

vector< sptr< Interaction > >	interactions

vector< sptr< StateTracker > >	trackers

vector< sptr< Constraint > >	constraints

Constructor & Destructor Documentation

CollectionGear4NPH::CollectionGear4NPH	(	sptr< OriginBox >	box,
		sptr< AtomGroup >	atoms,
		const flt	dt,
		const flt	P,
		const flt	Q,
		uint	ncorrectionsteps,
		vector< sptr< Interaction > >	interactions = `vector<sptr<Interaction> >()`,
		vector< sptr< StateTracker > >	trackers = `vector<sptr<StateTracker> >()`,
		vector< sptr< Constraint > >	constraints = `vector<sptr<Constraint> >()`
	)

inline

CollectionGear4NPH::CollectionGear4NPH	(	sptr< OriginBox >	box,
		sptr< AtomGroup >	atoms,
		const flt	dt,
		const flt	P,
		const flt	Q,
		vector< sptr< Interaction > >	interactions = `vector<sptr<Interaction> >()`,
		vector< sptr< StateTracker > >	trackers = `vector<sptr<StateTracker> >()`,
		vector< sptr< Constraint > >	constraints = `vector<sptr<Constraint> >()`
	)

inline

Member Function Documentation

flt CollectionGear4NPH::get_dV ( )

inline

flt CollectionGear4NPH::getddV ( )

inline

flt CollectionGear4NPH::hamiltonian ( )

inline

flt CollectionGear4NPH::kinetic_energy ( )

virtual

Reimplemented from Collection.

void CollectionGear4NPH::resetbs ( )

inlineprotected

void CollectionGear4NPH::set_dt ( flt newdt )

inline

flt CollectionGear4NPH::temp ( bool minuscomv = true )

virtual

Reimplemented from Collection.

void CollectionGear4NPH::timestep ( )

virtual

Take one step forward in time.

Prediction

Correction

Implements Collection.

Member Data Documentation

vector<Vec> CollectionGear4NPH::bs

protected

flt CollectionGear4NPH::dddV

protected

flt CollectionGear4NPH::ddV

protected

flt CollectionGear4NPH::dt

protected

flt CollectionGear4NPH::dV

protected

uint CollectionGear4NPH::ncorrec

protected

flt CollectionGear4NPH::P

protected

flt CollectionGear4NPH::Q

protected

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

src/collection.hpp
src/collection.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation