A decorator for a diffusing particle with a diffusion coefficient. More...

#include <IMP/atom/Diffusion.h>

Inheritance diagram for IMP::atom::Diffusion:

Detailed Description

A decorator for a diffusing particle with a diffusion coefficient.

Diffusion is used to decorate a particle with XYZ coordinates (since it inhertis from XYZ) and a translational diffusion coefficient D. D is specified in units of \(A^2/fs\), and it is used by eg IMP's Brownian dynamics simulator. It can be set explicitly or inferred implicitly from the radius.

 ## \example atom/Diffusion_decorator.py
 # This is a simple example using the Diffusion decorator to set the coordinates
 # and translational diffusion coefficient of some particles
 
 import IMP
 import IMP.core
 import IMP.atom
 import IMP.algebra
 import sys
 
 C0=[0,1,2] # in A
 C1=[1,2,3] # in A
 D1 = 3.0 # in A^2/fs
 R0=5 # in A
 IMP.setup_from_argv(sys.argv, "Diffusion decorator example")
 m = IMP.Model()
 
 # Setup a diffusion particle with an implicitly-set diffusion coefficient
 # using the Stokes-Einstein equation, treating radius as the Stokes radius
 p0 = m.add_particle("diffusion0")
 xyzr0 = IMP.core.XYZR.setup_particle(m, p0,
                                      IMP.algebra.Sphere3D(C0, R0))
 d0 = IMP.atom.Diffusion.setup_particle(m, p0)
 print("D automatically set to {:.2e} A^2/fs for radius {:.1f} A"
       .format(d0.get_diffusion_coefficient(), xyzr0.get_radius()))
 
 # Explicitly change the diffusion coefficient:
 d0.set_diffusion_coefficient(d0.get_diffusion_coefficient()/2.0)
 print("D reset to {:.2e} A^2/fs".format(d0.get_diffusion_coefficient()))
 
 # Setup a diffusion particle with an explicitly-set diffusion coefficient
 p1 = m.add_particle("diffusion1")
 d1 = IMP.atom.Diffusion.setup_particle(m, p1, C1, D1)
 print("D explicitly set to {:.2e} A^2/fs for coordinates {} A"
       .format(d1.get_diffusion_coefficient(), d1.get_coordinates()))

See Also: RigidBodyDiffusion; BrownianDynamics

Definition at line 36 of file Diffusion.h.

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

	Diffusion (const IMP::ParticleAdaptor &d)

double	get_diffusion_coefficient () const
	get diffusion coefficient in \(A^2/fs\) More...

void	set_diffusion_coefficient (double d)
	set diffusion coefficient in \(A^2/fs\) More...

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 FloatKey	get_diffusion_coefficient_key ()
	Get the D 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 Diffusion. More...

static Diffusion	setup_particle (Model *m, ParticleIndex pi, Float D)
	Setup the particle with the specified diffusion coefficient. More...

static Diffusion	setup_particle (IMP::ParticleAdaptor pa, Float D)

static Diffusion	setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D v, Float D)

static Diffusion	setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v, Float D)
	Setup the particle with the specified coordinates and diffusion coefficient. More...

static Diffusion	setup_particle (Model *m, ParticleIndex pi)

static Diffusion	setup_particle (IMP::ParticleAdaptor pa)

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 pa)

static XYZ	setup_particle (Model *m, ParticleIndex pi)

static XYZ	setup_particle (IMP::ParticleAdaptor pa, 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

double IMP::atom::Diffusion::get_diffusion_coefficient ( ) const

get diffusion coefficient in \(A^2/fs\)

Definition at line 107 of file Diffusion.h.

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static FloatKey IMP::atom::Diffusion::get_diffusion_coefficient_key ( )

static

Get the D key.

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

static

Return true if the particle is an instance of Diffusion.

Definition at line 97 of file Diffusion.h.

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void IMP::atom::Diffusion::set_diffusion_coefficient ( double d )

set diffusion coefficient in \(A^2/fs\)

Definition at line 102 of file Diffusion.h.

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static Diffusion IMP::atom::Diffusion::setup_particle	(	IMP::ParticleAdaptor	pa,
		Float	D
	)

static

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

See Also: setup_particle(m, pi, D )

Definition at line 76 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		Float	D
	)

static

Setup the particle with the specified diffusion coefficient.

If the particle does not have coordinates, it is decorated as XYZ and its coordinates are set to [0,0,0], otherwise the coordinates remain the same.

Returns: a Diffusion object that decorates particle pi

Definition at line 76 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		algebra::Vector3D	v,
		Float	D
	)

static

Setup the particle with the specified coordinates and diffusion coefficient.

Returns: a Diffusion object that decorates particle pi

Definition at line 78 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle	(	IMP::ParticleAdaptor	pa,
		algebra::Vector3D	v,
		Float	D
	)

static

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

See Also: setup_particle(m, p, v , D )

Definition at line 78 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle ( IMP::ParticleAdaptor pa )

static

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

See Also: setup_particle(m, p)

Definition at line 94 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle	(	Model *	m,
		ParticleIndex	pi
	)

static

Setup the particle with a diffusion coefficient automatically inferred from its radius using the Stokes-Einstein equation. The diffusion coefficient is computed implicitly using the Stokes-Einstein equation by calling IMP::atom::get_einstein_diffusion_coefficient(R), where the Stokes radius R is core::XYZR::get_radius() and the temperature is the default IMP temperature of 297.15K.

Note: If the simulation temperature or particle radius change, the diffusion coefficient must be changed explicitly e.g., using set_diffusion_coefficient(); This constructor can be used only on particles that have a radius field, e.g. decorated as IMP::core::XYZR.

Returns: a Diffusion object that decorates particle pi

Definition at line 94 of file Diffusion.h.

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

Diffusion.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation