#include <collection.hpp>

Inheritance diagram for CollectionSolHT:

Public Member Functions
	CollectionSolHT (sptr< Box > box, sptr< AtomGroup > atoms, const flt dt, const flt damping, const flt desired_temperature, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >())

void	change_temperature (const flt newdt, const flt damp, const flt desired_temperature)

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_gauss ()

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	desT

GaussVec	gauss

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

for use in solution, with damped forces and random forces.

This uses the same physics as CollectionSol, but a different algorithm from Honeycutt and Thirumalai.

Note that the Honeycutt and Thirumalai algorithm is flawed, and this fixes it to some degree.

Treats Atom.f as the "configurational force", and Atom.a as the acceleration due to Atom.f + random force. Note that d²r/dt² = Atom.f + random force (- damping*v), but we don't include that.

1) find positions: (x0,v0,a0,f0) -> (x, v, a, f) sets Atom.x from previous force, velocity, and position x = x0 + dt v0 + 1/2 dt^2 a0 - damping*dt²/2m * v0 2) intermediate v: (v0,f0) -> (v1, f0) v1 = damped(v0) + dt/2 f0/m where damped(vo) = v0*(1-h*damping/2m + (h*damping/m)²/4) 3) set_forces(): (x, f0) -> (x,f) reset and set the forces f = grad(V(x)) 4) Acceleration: (f, a0) -> (f, a1) a1 = f/m + gaussian set acceleration given the forces, adding in random pieces, no damping 5) Finish v and a: (v1, f, a1) -> (v, f, a) v = v1 + dt/2 a1

Constructor & Destructor Documentation

CollectionSolHT::CollectionSolHT	(	sptr< Box >	box,
		sptr< AtomGroup >	atoms,
		const flt	dt,
		const flt	damping,
		const flt	desired_temperature,
		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 CollectionSolHT::change_temperature	(	const flt	newdt,
		const flt	damp,
		const flt	desired_temperature
	)

inline

void CollectionSolHT::set_gauss ( )

protected

void CollectionSolHT::timestep ( )

virtual

Take one step forward in time.

Implements Collection.

Member Data Documentation

flt CollectionSolHT::damping

protected

flt CollectionSolHT::desT

protected

flt CollectionSolHT::dt

protected

GaussVec CollectionSolHT::gauss

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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation