Detailed Description

A decorator for a center of mass particle that is part of a TAMD simulation (so simulators can recognize it as such)

See Also: BrownianDynamicsBarak

TAMDCentroid is almost identical to IMP::core::Centroid, used to decorate particles that represent centers of mass of their children. It also contains some flags that are useful for TAMD simulations (Temperature-Accelerated MD).

See Also: IMP::core::Centroid

Definition at line 38 of file TAMDCentroid.h.

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

	TAMDCentroid (const IMP::ParticleAdaptor &d)

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

Public Member Functions inherited from IMP::core::Centroid
	Centroid (const IMP::ParticleAdaptor &d)

	Centroid (::IMP::Model *m,::IMP::ParticleIndex id)

Constraint *	get_constraint () const

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

Public Member Functions inherited from IMP::core::XYZ
	XYZ (::IMP::Model *m,::IMP::ParticleIndex id)

	XYZ (const IMP::ParticleAdaptor &d)

void	add_to_derivative (int i, Float v, DerivativeAccumulator &d)

void	add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add the vector v to the derivative vector of the x,y,z coordinates. More...

Float	get_coordinate (int i) const
	Get the ith coordinate. More...

const algebra::Vector3D &	get_coordinates () const
	Convert it to a vector. More...

bool	get_coordinates_are_optimized () const
	Get whether the coordinates are optimized. More...

Float	get_derivative (int i) const

algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives accumulated by add_to_derivatives(). More...

algebra::Vector3D	get_vector_to (const XYZ &b) const
	Get the vector from this particle to another. More...

Float	get_x () const

Float	get_y () const

Float	get_z () const

void	set_coordinate (unsigned int i, Float v)
	set the ith coordinate More...

void	set_coordinates (const algebra::Vector3D &v)
	set all coordinates from a vector More...

void	set_coordinates_are_optimized (bool tf) const
	Set whether the coordinates are optimized. More...

void	set_x (Float t)

void	set_y (Float t)

void	set_z (Float t)

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

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 bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex pi)

static TAMDCentroid	setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)

static TAMDCentroid	setup_particle (IMP::ParticleAdaptor decorator, ParticleIndexesAdaptor members)

static TAMDCentroid	setup_particle (Model m, ParticleIndex pi, Refiner refiner)

static TAMDCentroid	setup_particle (IMP::ParticleAdaptor decorator, Refiner *refiner)

Static Public Member Functions inherited from IMP::core::Centroid
static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex pi)

static Centroid	setup_particle (IMP::ParticleAdaptor decorator, Refiner *refiner)

static Centroid	setup_particle (Model m, ParticleIndex pi, Refiner refiner)

static Centroid	setup_particle (IMP::ParticleAdaptor decorator, ParticleIndexesAdaptor members)

static Centroid	setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)

Static Public Member Functions inherited from IMP::core::XYZ
static FloatKey	get_coordinate_key (unsigned int i)

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

static bool	get_is_setup (Model *m, ParticleIndex pi)

static const FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...

static XYZ	setup_particle (IMP::ParticleAdaptor decorator)

static XYZ	setup_particle (Model *m, ParticleIndex pi)

static XYZ	setup_particle (IMP::ParticleAdaptor decorator, algebra::Vector3D v)

static XYZ	setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v)

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

	Decorator (ParticleAdaptor p)

Member Function Documentation

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle	(	IMP::ParticleAdaptor	decorator,
		ParticleIndexesAdaptor	members
	)

static

See Also: setup_particle(m, pi, members )

Definition at line 63 of file TAMDCentroid.h.

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		ParticleIndexesAdaptor	members
	)

static

Sets up TAMDCentroid over members, and constrains TAMDCentroid to be computed before model evaluation and to propagate derivatives following model evaluation. SetupDocSetup the particle so that it can be used with this decorator

Definition at line 63 of file TAMDCentroid.h.

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle	(	IMP::ParticleAdaptor	decorator,
		Refiner *	refiner
	)

static

See Also: setup_particle(m, pi, refiner )

Definition at line 71 of file TAMDCentroid.h.

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		Refiner *	refiner
	)

static

Sets up TAMDCentroid over particles passed by applying the refiner over the particle pi, and constrains TAMDCentroid to be computed before model evaluation and to propagate derivatives following model evaluation. SetupDocSetup the particle so that it can be used with this decorator

Definition at line 71 of file TAMDCentroid.h.

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

TAMDCentroid.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation