IMP  2.0.0
The Integrative Modeling Platform
IMP::atom::Diffusion Class Reference

A decorator for a diffusing particle. More...

#include <IMP/atom/Diffusion.h>

+ Inheritance diagram for IMP::atom::Diffusion:

Public Member Functions

 Diffusion (Model *m, ParticleIndex id)
 
 Diffusion (::IMP::kernel::Particle *p)
 
double get_diffusion_coefficient () const
 
void set_diffusion_coefficient (double d)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::core::XYZ
 XYZ (Model *m, ParticleIndex id)
 
 XYZ (::IMP::kernel::Particle *p)
 
void add_to_derivative (int i, Float v, DerivativeAccumulator &d)
 Add something to the derivative of the ith coordinate.
 
void add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
 Add something to the derivative of the coordinates.
 
Float get_coordinate (int i) const
 Get the ith coordinate.
 
const algebra::Vector3Dget_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
 Get the ith coordinate derivative.
 
algebra::Vector3D get_derivatives () const
 Get the vector of derivatives. More...
 
algebra::Vector3D get_vector_to (const XYZ &b) const
 Get the vector from this particle to another.
 
Float get_x () const
 
Float get_y () const
 
Float get_z () const
 
void set_coordinate (unsigned int i, Float v)
 set the ith coordinate
 
void set_coordinates (const algebra::Vector3D &v)
 set all coordinates from a vector
 
void set_coordinates_are_optimized (bool tf) const
 Set whether the coordinates are optimized.
 
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::kernel::Decorator
ParticleIndex get_particle_index () const
 
Particleget_particle () const
 
Modelget_model () const
 Returns the Model containing the particle.
 
 Decorator (Particle *p)
 
 Decorator ()
 

Static Public Member Functions

static Diffusion decorate_particle (::IMP::kernel::Particle *p)
 
static FloatKey get_diffusion_coefficient_key ()
 Get the D key.
 
static bool particle_is_instance (Particle *p)
 Return true if the particle is an instance of an Diffusion.
 
static bool particle_is_instance (Model *m, ParticleIndex p)
 Return true if the particle is an instance of an Diffusion.
 
static Diffusion setup_particle (Particle *p, const algebra::Vector3D &v, Float D)
 
static Diffusion setup_particle (Particle *p, Float D)
 
static Diffusion setup_particle (Particle *p)
 
- Static Public Member Functions inherited from IMP::core::XYZ
static XYZ decorate_particle (::IMP::kernel::Particle *p)
 
static FloatKey get_coordinate_key (unsigned int i)
 
static const FloatKeysget_xyz_keys ()
 Get a vector containing the keys for x,y,z. More...
 
static bool particle_is_instance (Particle *p)
 
static bool particle_is_instance (Model *m, ParticleIndex pi)
 
static XYZ setup_particle (Model *m, ParticleIndex pi, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0))
 
static XYZ setup_particle (Particle *p, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0))
 
- Static Public Member Functions inherited from IMP::kernel::Decorator
static bool particle_is_instance (Particle *p)
 Return true if the particle can be cast to the decorator. More...
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (Particle *p)
 

Detailed Description

See Also
BrownianDynamics
Warning: Diffusion has not been stabilized and is likely to change without notice. The name really should be fixed.

D is assumed to be in \(A^2/fs\)

Definition at line 31 of file Diffusion.h.

Member Function Documentation

static Diffusion IMP::atom::Diffusion::setup_particle ( Particle p,
const algebra::Vector3D v,
Float  D 
)
static

Create a decorator with the passed coordinates and D.

Definition at line 39 of file Diffusion.h.

+ Here is the call graph for this function:

static Diffusion IMP::atom::Diffusion::setup_particle ( Particle p,
Float  D 
)
static

Create a decorator with the a given D. The particle is assumed to already have x,y,z attributes

Definition at line 51 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle ( Particle p)
static

Create a decorator with the D determined from its radius.


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