CollectionNLCG Class Reference

#include <collection.hpp>

Inheritance diagram for CollectionNLCG:

Public Member Functions
virtual void	stepx (flt dx)
flt	get_length_squared ()
flt	fdota ()
flt	fdotf ()
flt	fdotv ()
flt	vdotv ()
	CollectionNLCG (sptr< OriginBox > box, sptr< AtomGroup > atoms, const flt dt, const flt P0, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >(), const flt kappa=10.0, const flt kmax=1000, const uint secmax=40, const flt seceps=1e-20)
flt	kinetic_energy ()
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...
flt	hamiltonian ()
void	set_forces (bool constraints_and_a=true)
	Set forces. More...
void	set_forces (bool constraints_and_a, bool setV)
void	timestep ()
	Take one step forward in time. More...
void	descend ()
void	reset ()
void	set_dt (flt newdt)
void	set_pressure_goal (flt P)
flt	get_pressure_goal ()
void	set_kappa (flt k)
void	set_max_alpha (flt a)
void	set_max_alpha_fraction (flt a)
void	set_max_dx (flt d)
void	set_max_step (flt m)
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 ()
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	virial ()
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 ()

Public Attributes
flt	dt
flt	seceps
uint	secmax
flt	kappa
flt	alphamax
flt	afrac
flt	dxmax
flt	stepmax
flt	kmax
flt	P0
flt	Knew
flt	k
flt	vl
flt	fl
flt	al
flt	alpha
flt	beta
flt	betaused
flt	dxsum
flt	alphavmax
flt	maxdV
uint	sec

Additional Inherited Members
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 inherited from Collection
sptr< Box >	box
sptr< AtomGroup >	atoms
vector< sptr< Interaction > >	interactions
vector< sptr< StateTracker > >	trackers
vector< sptr< Constraint > >	constraints

Detailed Description

Examples:

packer.cpp.

Constructor & Destructor Documentation

CollectionNLCG::CollectionNLCG	(	sptr< OriginBox >	box,
		sptr< AtomGroup >	atoms,
		const flt	dt,
		const flt	P0,
		vector< sptr< Interaction > >	interactions = vector<sptr<Interaction> >(),
		vector< sptr< StateTracker > >	trackers = vector<sptr<StateTracker> >(),
		vector< sptr< Constraint > >	constraints = vector<sptr<Constraint> >(),
		const flt	kappa = 10.0,
		const flt	kmax = 1000,
		const uint	secmax = 40,
		const flt	seceps = 1e-20
	)

Member Function Documentation

void CollectionNLCG::descend

(

)

flt CollectionNLCG::fdota

(

)

flt CollectionNLCG::fdotf

(

)

flt CollectionNLCG::fdotv

(

)

flt CollectionNLCG::get_length_squared

(

)

flt CollectionNLCG::get_pressure_goal ( )

inline

flt CollectionNLCG::hamiltonian

(

)

Examples:

packer.cpp.

flt CollectionNLCG::kinetic_energy ( )

virtual

Reimplemented from Collection.

Examples:

packer.cpp.

flt CollectionNLCG::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 from Collection.

Examples:

packer.cpp.

void CollectionNLCG::reset

(

)

void CollectionNLCG::set_dt ( flt  newdt )

inline

void CollectionNLCG::set_forces ( bool  constraints_and_a = true )

inlinevirtual

Set forces.

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

Reimplemented from Collection.

void CollectionNLCG::set_forces	(	bool	constraints_and_a,
		bool	setV
	)

void CollectionNLCG::set_kappa ( flt  k )

inline

void CollectionNLCG::set_max_alpha ( flt  a )

inline

void CollectionNLCG::set_max_alpha_fraction ( flt  a )

inline

void CollectionNLCG::set_max_dx ( flt  d )

inline

void CollectionNLCG::set_max_step ( flt  m )

inline

void CollectionNLCG::set_pressure_goal ( flt  P )

inline

Examples:

packer.cpp.

void CollectionNLCG::stepx ( flt  dx )

virtual

Reimplemented in CollectionNLCGFixedL.

void CollectionNLCG::timestep ( )

virtual

Take one step forward in time.

Secant stepping

Implements Collection.

Examples:

packer.cpp.

flt CollectionNLCG::vdotv

(

)

Member Data Documentation

flt CollectionNLCG::afrac

flt CollectionNLCG::al

flt CollectionNLCG::alpha

flt CollectionNLCG::alphamax

flt CollectionNLCG::alphavmax

flt CollectionNLCG::beta

flt CollectionNLCG::betaused

flt CollectionNLCG::dt

flt CollectionNLCG::dxmax

flt CollectionNLCG::dxsum

flt CollectionNLCG::fl

flt CollectionNLCG::k

flt CollectionNLCG::kappa

flt CollectionNLCG::kmax

flt CollectionNLCG::Knew

flt CollectionNLCG::maxdV

flt CollectionNLCG::P0

uint CollectionNLCG::sec

flt CollectionNLCG::seceps

uint CollectionNLCG::secmax

flt CollectionNLCG::stepmax

flt CollectionNLCG::vl

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

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