The base class for simulators. More...

#include <IMP/atom/Simulator.h>

Inheritance diagram for IMP::atom::Simulator:

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

double	get_current_time () const

double	get_kt () const

kernel::ParticleIndexes	get_simulation_particle_indexes () const

kernel::ParticlesTemp	get_simulation_particles () const

double	get_temperature () const

void	set_current_time (double ct)

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)

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

	Optimizer ()

void	clear_range_cache ()

Float	get_derivative (FloatIndex fi) const

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

FloatIndexes	get_optimized_attributes () const

Restraints	get_restraints () const

double	get_scaled_derivative (FloatIndex fi) const

double	get_scaled_value (FloatIndex fi) const

double	get_score_threshold () const

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

bool	get_stop_on_good_score () const

Float	get_value (FloatIndex fi) const

double	get_width (FloatKey k) const

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

void	set_restraints (const RestraintsTemp &rs)

void	set_scaled_value (FloatIndex fi, Float v) const

void	set_score_threshold (double s)

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)

void	set_stop_on_good_score (bool tf)

void	set_value (FloatIndex fi, double v) const

double	width (FloatKey k) const

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::kernel::ModelObject
	ModelObject (kernel::Model *m, std::string name)

	ModelObject (std::string name)

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

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

bool	get_is_part_of_model () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const

void	set_has_dependencies (bool tf)

void	set_has_required_score_states (bool tf)

virtual void	set_model (kernel::Model *m)

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

virtual void	do_destroy ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

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

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)

virtual std::string	get_type_name () const

Protected Member Functions
virtual Float	do_optimize (unsigned int max_steps)
	override this function to do actual optimization

virtual double	do_step (const kernel::ParticleIndexes &sc, double dt)=0

virtual bool	get_is_simulation_particle (kernel::ParticleIndex p) const =0

virtual void	setup (const kernel::ParticleIndexes &)

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

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

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::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

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

	Object ()

Time steps
The simulator has a maximum allowed time step. It can take shorter ones if needed due to stability concerns. As with all times in `IMP`, the time step is in fs.
void	set_maximum_time_step (double ts)

double	get_maximum_time_step () const

double	get_last_time_step () const

Explicitly specifying particles
One can explicitly specify which particles should be used for molecular dynamics. Each particle must be a Mass and core::XYZ particle. If none are specified, the model is searched for appropriate particles.
void	remove_particle (kernel::Particle *d)

void	remove_particles (const kernel::Particles &d)

void	set_particles (const kernel::Particles &ps)

void	set_particles_order (const kernel::Particles &objs)

unsigned int	add_particle (kernel::Particle *obj)

void	add_particles (const kernel::Particles &objs)

void	clear_particles ()

unsigned int	get_number_of_particles () const

bool	get_has_particles ()

kernel::Particle *	get_particle (unsigned int i) const

kernel::Particles	get_particles () const

void	reserve_particles (unsigned int sz)

Detailed Description

A simulator is an optimizer with dynamic tracking of time, such that each frame is associated with a (possibly variable size) time step.

The simulation can be invoked directly by calling simulate(fs) for a given time in femtoseconds, or by calling Optimizer::optimize(nf) for a give number of frames.

Definition at line 34 of file Simulator.h.

Constructor & Destructor Documentation

IMP::atom::Simulator::Simulator	(	kernel::Model *	m,
		std::string	name = `"Simulator %1%"`,
		double	wave_factor = `1.0`
	)

Parameters

m	model associated with simulater
name	simulater name where %1% is a joker
wave_factor	if >=1.001, use wave time step size with larger maximal time step, using simulate_wave() when calling optimize()

Note: wave_factor is an advanced feature - if you're not sure, just use its default, see also simulate_wave(); wave_factor is experimental and liable to change at any time.

See Also: simulate()

Member Function Documentation

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

protectedpure virtual

Perform a single time step and return the amount that time should be advanced. A maximum time step value is passed.

Implemented in IMP::atom::MolecularDynamics.

double IMP::atom::Simulator::get_current_time ( ) const

returns the simulation time in femtoseconds that was performed by this simulator since it was constructed

Note: this time can be tweaked using set_current_time() )

Definition at line 109 of file Simulator.h.

virtual bool IMP::atom::Simulator::get_is_simulation_particle ( kernel::ParticleIndex p ) const

protectedpure virtual

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

Implemented in IMP::atom::MolecularDynamics, and IMP::isd::MolecularDynamics.

kernel::ParticlesTemp IMP::atom::Simulator::get_simulation_particles ( ) const

Get the set of particles used in the simulation. This may be different then the stored set, eg if no particles are stored, the kernel::Model is searched for appropriate particles.

void IMP::atom::Simulator::set_current_time ( double ct )

Sets the current simulation time in femtoseconds to ct.

Definition at line 114 of file Simulator.h.

virtual void IMP::atom::Simulator::setup ( const kernel::ParticleIndexes & )

protectedvirtual

A Simulator class can perform setup operations before a series of simulation steps is taken.

Reimplemented in IMP::atom::MolecularDynamics.

Definition at line 141 of file Simulator.h.

double IMP::atom::Simulator::simulate ( double time_in_fs )

simulate for a given time, by calling the protected method do_step() iteratively.

Parameters

time_in_fs time in femtoseconds

double IMP::atom::Simulator::simulate_wave	(	double	time_in_fs,
		double	max_time_step_factor = `10.0`,
		double	base = `1.5`
	)

Simulate for a given time in fs using a wave step function with maximal time step increased by up to max_time_step_factor simulate for a given time, by calling the protected method do_step() iteratively, and using a self adjusting time step that can grow up to max_time_step_factor times than the default time step returned by get_maximum_time_step()

Parameters

time_in_fs	time_in_fs in femtoseconds
max_time_step_factor	the maximal factor by which the maximum time step is exceeded
base	base by which time step increases or decreases during the wave

Note: This function is experimental and liable to change at any time.

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

Simulator.h

Public Member Functions

Protected Member Functions

Time steps

Explicitly specifying particles

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation