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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
IMP::atom::TAMDParticle Class Reference

#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...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_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
 
Particleoperator-> () 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
mthe particle model
pithe 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
mthe particle model
pithe 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: