#include <IMP/atom/TAMDParticle.h>

Inheritance diagram for IMP::atom::TAMDParticle:

Detailed Description

A decorator for a diffusing particle that is simulated in a TAMD BD simulation.

See Also: BrownianDynamicsBarak

TAMDParticle is used to decorate diffusing particle that are simulated as part of a TAMD simulation (Temperature-Accelerated MD), and exhibit elevated temperature and elevated friction coefficient (=actual diffusion coefficient reduced during TAMD BD simulation).

See: Maragliano and Vanden-Eijden, 2006; Abrams and Vanden-Eijden, PNAS 2011

Definition at line 39 of file TAMDParticle.h.

Public Member Functions
	TAMDParticle (::IMP::Model *m,::IMP::ParticleIndex id)

	TAMDParticle (const IMP::ParticleAdaptor &d)

double	get_friction_scale_factor () const

ParticleIndex	get_reference_particle_index () const

double	get_temperature_scale_factor () const

void	set_friction_scale_factor (float tsf)

void	set_temperature_scale_factor (float tsf)

void	show (std::ostream &out=std::cout) const

void	update_coordinates_from_ref ()

Public Member Functions inherited from IMP::Decorator
bool	get_is_valid () const
	Returns true if constructed with a non-default constructor. More...

Model *	get_model () const
	Returns the Model containing the particle. More...

Particle *	get_particle () const
	Returns the particle decorated by this decorator. More...

ParticleIndex	get_particle_index () const
	Returns the particle index decorated by this decorator. More...

	operator Particle * () const

	operator ParticleIndex () const

Particle *	operator-> () const

Static Public Member Functions
static FloatKey	get_friction_scale_factor_key ()
	Get the temperature scale factor key. More...

static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex p)
	Return true if the particle is an instance of an TAMDParticle. More...

static ParticleIndexKey	get_reference_particle_index_key ()
	Get the temperature scale factor key. More...

static FloatKey	get_temperature_scale_factor_key ()
	Get the temperature scale factor key. More...

static TAMDParticle	setup_particle (Model *m, ParticleIndex pi, ParticleIndex pi_ref, Float tsf, Float fsf)

static TAMDParticle	setup_particle (IMP::ParticleAdaptor pa, ParticleIndex pi_ref, Float tsf, Float fsf)

static TAMDParticle	setup_particle (Model m, ParticleIndex pi, Particle p_ref, Float tsf, Float fsf)

static TAMDParticle	setup_particle (IMP::ParticleAdaptor pa, Particle *p_ref, Float tsf, Float fsf)

Additional Inherited Members
Protected Member Functions inherited from IMP::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)

Member Function Documentation

double IMP::atom::TAMDParticle::get_friction_scale_factor ( ) const

get friction factoring for particle relative to particle diffusion coefficient / rotational diffusion coefficient

Definition at line 138 of file TAMDParticle.h.

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static FloatKey IMP::atom::TAMDParticle::get_friction_scale_factor_key ( )

static

Get the temperature scale factor key.

static bool IMP::atom::TAMDParticle::get_is_setup	(	Model *	m,
		ParticleIndex	p
	)

static

Return true if the particle is an instance of an TAMDParticle.

Definition at line 102 of file TAMDParticle.h.

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ParticleIndex IMP::atom::TAMDParticle::get_reference_particle_index ( ) const

returns the particle associated with this TAMD variable (eg, centroid of some particles)

Definition at line 112 of file TAMDParticle.h.

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static ParticleIndexKey IMP::atom::TAMDParticle::get_reference_particle_index_key ( )

static

Get the temperature scale factor key.

double IMP::atom::TAMDParticle::get_temperature_scale_factor ( ) const

get temperature factoring for particle relative to simulation temperature

Definition at line 125 of file TAMDParticle.h.

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static FloatKey IMP::atom::TAMDParticle::get_temperature_scale_factor_key ( )

static

Get the temperature scale factor key.

void IMP::atom::TAMDParticle::set_friction_scale_factor ( float tsf )

set friction factoring for particle relative to particle diffusion coefficient / rotational diffusion coefficient

Definition at line 132 of file TAMDParticle.h.

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void IMP::atom::TAMDParticle::set_temperature_scale_factor ( float tsf )

set temperature factoring for particle relative to simulation temperature

Definition at line 119 of file TAMDParticle.h.

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static TAMDParticle IMP::atom::TAMDParticle::setup_particle	(	IMP::ParticleAdaptor	pa,
		ParticleIndex	pi_ref,
		Float	tsf,
		Float	fsf
	)

static

Returns: a TAMDParticle object that decorates the particle specified by pa

See Also: setup_particle(m, pi, pi_ref , tsf , fsf )

Definition at line 80 of file TAMDParticle.h.

static TAMDParticle IMP::atom::TAMDParticle::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		ParticleIndex	pi_ref,
		Float	tsf,
		Float	fsf
	)

static

setup a TAMD variable associated with pi_ref, with temperature scaled by tsf and friction scaled by fsf.

Note: Particle is assumed to be decorated as diffusive, XYZ particle.

Parameters

m	the particle model
pi	the particle index to be setup
pi_ref	- reference particle index in same model with which this tamd particle is associate
tsf	- temperature scale factor
fsf	- friction scale factor

Returns: a TAMDParticle object that decorates particle pi

Definition at line 80 of file TAMDParticle.h.

static TAMDParticle IMP::atom::TAMDParticle::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		Particle *	p_ref,
		Float	tsf,
		Float	fsf
	)

static

setup a TAMD variable associated with pi_ref, with temperature scaled by tsf and friction scaled by fsf

Note: Particle is assumed to be decorated as diffusive, XYZ particle.

Parameters

m	the particle model
pi	the particle index to be setup
p_ref	- reference particle with which this tamd particle is associate
tsf	- temperature scale factor
fsf	- friction scale factor

Returns: a TAMDParticle object that decorates particle pi

Definition at line 97 of file TAMDParticle.h.

static TAMDParticle IMP::atom::TAMDParticle::setup_particle	(	IMP::ParticleAdaptor	pa,
		Particle *	p_ref,
		Float	tsf,
		Float	fsf
	)

static

Returns: a TAMDParticle object that decorates the particle specified by pa

See Also: setup_particle(m, pi, p_ref , tsf , fsf )

Definition at line 97 of file TAMDParticle.h.

void IMP::atom::TAMDParticle::update_coordinates_from_ref ( )

copy x,y,z coordinates from reference particle.

Note: Assumes both this particle and the reference particle are decorated by XYZ (no runtime check is made in release mode!)

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

TAMDParticle.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation