Simple Brownian dynamics simulator. More...

#include <IMP/atom/BrownianDynamics.h>

Inheritance diagram for IMP::atom::BrownianDynamics:

Detailed Description

Simple Brownian dynamics simulator.

This is an implementation of a Brownian Dynamics simulator.

Input particles and score

Each optimized particle must have x,y,z attributes that are optimizable. In addition, each optimized particle must be decorated with the Diffusion decorator. Optionally, the RigidBodyDiffusion decorator can be used to specify a rotational diffusion coefficient for core::RigidBody particles. The optimizer assumes the scoring function to be energy in kcal/mol, and the xyz coordinates to be in angstroms and the diffusion coefficient of each particle be in \(A^2/fs\) (or \(Radian^2/fs\) for rotational diffusion coefficient). Particles without optimized x,y,z and nonoptimized D are skipped.

The optimizer can either automatically determine which particles to use from the model or be passed a SingletonContainer for the particles. If such a container is passed, particles added to it during optimization state updates are handled properly.

Simulation

At each simulation time step, each particle is translated in the direction of the sum of a random diffusion vector and the gradient of the scoring function (force field) at the particle coordinates. The translation is proportional to the particle diffusion coefficient, the time step size, and the inverse of kT. Note that particles masses are not considered, only their diffusion coefficients.

Similarly, rigid bodies are rotated by the sum of a random torque and a force field torque, proportionally to the rotational diffusion coefficient, the time step size, and inversely proportional kT.

If the skt (stochastic Runge Kutta) flag is true, the simulation is altered slightly to apply the SKT scheme.

See Also: Diffusion; RigidBodyDiffusion

Definition at line 74 of file BrownianDynamics.h.

Public Member Functions
	BrownianDynamics (Model *m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=500)
	Create the optimizer. More...

virtual std::string	get_type_name () const

virtual ::IMP::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

void	set_maximum_move (double ms)

void	set_use_stochastic_runge_kutta (bool tf)

Public Member Functions inherited from IMP::atom::Simulator
	Simulator (Model *m, std::string name="Simulator %1%", double wave_factor=1.0)

double	get_current_time () const

double	get_kt () const

ParticleIndexes	get_simulation_particle_indexes () const

ParticlesTemp	get_simulation_particles () const
	Returns the set of particles used in the simulation. More...

double	get_temperature () const

void	set_current_time (double ct)
	Sets the current simulation time in femtoseconds to ct. More...

void	set_temperature (double d)

double	simulate (double time_in_fs)
	Simulate for a given time in fs. More...

double	simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5)

void	set_maximum_time_step (double ts)

double	get_maximum_time_step () const

double	get_last_time_step () const

void	remove_particle (Particle *d)

void	remove_particles (const Particles &d)

void	set_particles (const Particles &ps)

void	set_particles_order (const Particles &objs)

unsigned int	add_particle (Particle *obj)

void	add_particles (const Particles &objs)

void	clear_particles ()

unsigned int	get_number_of_particles () const

bool	get_has_particles ()

Particle *	get_particle (unsigned int i) const

Particles	get_particles () const

void	reserve_particles (unsigned int sz)

Public Member Functions inherited from IMP::Optimizer
	Optimizer (Model *m, std::string name="Optimizer %1%")

double	get_last_score () const
	Return the score found in the last evaluate. More...

ScoringFunction *	get_scoring_function () const
	Return the scoring function that is being used. More...

bool	get_stop_on_good_score () const

double	optimize (unsigned int max_steps)
	Optimize the model for up to max_steps iterations. More...

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)
	Set the scoring function to use. More...

void	set_stop_on_good_score (bool tf)

void	remove_optimizer_state (OptimizerState *d)

void	remove_optimizer_states (const OptimizerStates &d)

void	set_optimizer_states (const OptimizerStates &ps)

void	set_optimizer_states_order (const OptimizerStates &objs)

unsigned int	add_optimizer_state (OptimizerState *obj)

void	add_optimizer_states (const OptimizerStates &objs)

void	clear_optimizer_states ()

unsigned int	get_number_of_optimizer_states () const

bool	get_has_optimizer_states ()

OptimizerState *	get_optimizer_state (unsigned int i) const

OptimizerStates	get_optimizer_states () const

void	reserve_optimizer_states (unsigned int sz)

Public Member Functions inherited from IMP::ModelObject
	ModelObject (Model *m, std::string name)

bool	get_has_dependencies () const
	Return whether this object has dependencies computed. More...

bool	get_has_required_score_states () const
	Return whether score states are computed. More...

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const
	Get the interacting sets induced by this ModelObject. More...

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const
	Get the score states that are ancestors of this in the dependency graph. More...

void	set_has_dependencies (bool tf)
	Either invalidate the dependencies or ensure they are correct. More...

void	set_has_required_score_states (bool tf)
	Compute the required score states. More...

Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

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

const std::string &	get_name () const

void	set_name (std::string name)

Protected Member Functions
virtual void	do_advance_chunk (double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)

virtual double	do_step (const ParticleIndexes &sc, double dt)

algebra::Vector3D const &	get_force (unsigned int i) const
	get the force felt on particle i More...

algebra::Vector3Ds const &	get_forces () const
	get the force felt on each particle More...

virtual bool	get_is_simulation_particle (ParticleIndex p) const
	Return true if the passed particle is appropriate for the simulation. More...

bool	get_is_srk () const

double	get_max_step () const
	returns the maximal step size allowed in this simulation More...

double	get_sample (double sigma)

void	reset_random_pool ()
	regenerate internal cached pool of random numbers More...

void	set_force (unsigned int i, algebra::Vector3D const &f)
	set the force felt on particle i to f More...

virtual void	setup (const ParticleIndexes &ps)

Protected Member Functions inherited from IMP::atom::Simulator
virtual Float	do_optimize (unsigned int max_steps)
	override this function to do actual optimization More...

virtual double	do_simulate (double time)

virtual double	do_simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5)

Protected Member Functions inherited from IMP::Optimizer
virtual ModelObjectsTemp	do_get_inputs () const

virtual ModelObjectsTemp	do_get_outputs () const
	don't return anything here to avoid pointless dependencies More...

ModelObjectsTemp	get_optimizer_state_inputs () const

void	update_states () const
	Update optimizer states, should be called at each successful step. More...

Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::atom::BrownianDynamics::BrownianDynamics	(	Model *	m,
		std::string	name = `"BrownianDynamics%1%"`,
		double	wave_factor = `1.0`,
		unsigned int	random_pool_size = `500`
	)

Create the optimizer.

If sc is not null, that container will be used to find particles to move, otherwise the model will be searched.

Parameters

m	model associated with bd
name	name of bd object
wave_factor	for wave step function, see Simulator object, if >1.001 or so, creates a wave of time steps that are larger by up to wave_factor from formal maximal time step
random_pool_size	number of random numbers in internal pool used to accelerate random number generation. Memory requirement scales accordingly.

Note: wave_factor is an advanced feature - if you're not sure, just use its default, see also Simulator::simulate_wave()

Member Function Documentation

virtual void IMP::atom::BrownianDynamics::do_advance_chunk	(	double	dtfs,
		double	ikt,
		const ParticleIndexes &	ps,
		unsigned int	begin,
		unsigned int	end
	)

protectedvirtual

advances a chunk of ps from index begin to end

Parameters

dtfs	time step in femtoseconds
ikt	inverse kT for current chunk step
ps	particle indexes to advance
begin	beginning index of chunk of ps
end	end index of chunk of ps

Reimplemented in IMP::atom::BrownianDynamicsTAMD.

virtual double IMP::atom::BrownianDynamics::do_step	(	const ParticleIndexes &	sc,
		double	dt
	)

protectedvirtual

Calls do_advance_chunk() to advance ps in chunks

Parameters

sc	particles to simulate in this step
dt	maximal step size in femtoseconds

Returns: the time step actually simulated (for this class, it is always equal to the inut dt)

Implements IMP::atom::Simulator.

algebra::Vector3D const& IMP::atom::BrownianDynamics::get_force ( unsigned int i ) const

protected

get the force felt on particle i

Definition at line 175 of file BrownianDynamics.h.

algebra::Vector3Ds const& IMP::atom::BrownianDynamics::get_forces ( ) const

protected

get the force felt on each particle

Definition at line 171 of file BrownianDynamics.h.

virtual bool IMP::atom::BrownianDynamics::get_is_simulation_particle ( ParticleIndex p ) const

protectedvirtual

Return true if the passed particle is appropriate for the simulation.

Implements IMP::atom::Simulator.

bool IMP::atom::BrownianDynamics::get_is_srk ( ) const

protected

returns true if implementing the Stochastic Runga-Kutta Brownian Dynamics variant

Definition at line 147 of file BrownianDynamics.h.

double IMP::atom::BrownianDynamics::get_max_step ( ) const

protected

returns the maximal step size allowed in this simulation

Definition at line 143 of file BrownianDynamics.h.

double IMP::atom::BrownianDynamics::get_sample ( double sigma )

protected

returns a normally distributed sample with mean zero and std-dev sigma

Definition at line 155 of file BrownianDynamics.h.

virtual ::IMP::VersionInfo IMP::atom::BrownianDynamics::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 107 of file BrownianDynamics.h.

void IMP::atom::BrownianDynamics::reset_random_pool ( )

protected

regenerate internal cached pool of random numbers

void IMP::atom::BrownianDynamics::set_force	(	unsigned int	i,
		algebra::Vector3D const &	f
	)

protected

set the force felt on particle i to f

Definition at line 166 of file BrownianDynamics.h.

virtual void IMP::atom::BrownianDynamics::setup ( const ParticleIndexes & ps )

protectedvirtual

a set of setup operations before a series of simulation steps

Reimplemented from IMP::atom::Simulator.

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

BrownianDynamics.h

Detailed Description

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation