The base class for simulators.

#include <IMP/atom/Simulator.h>

Inheritance diagram for IMP::atom::Simulator:

Public Member Functions
	Simulator (Model *m, std::string name="Simulator %1%")
	Create the optimizer. More...

double	get_current_time () const

double	get_kt () const

ParticleIndexes	get_simulation_particle_indexes () const

ParticlesTemp	get_simulation_particles () const

double	get_temperature () const

	IMP_OPTIMIZER (Simulator)

void	set_temperature (double d)

double	simulate (double time_in_fs)
	Simulate until the given time in fs.

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

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

Model *	get_model () const
	Get the model being optimized.

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

bool	get_stop_on_good_score () const

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

void	set_model (Model *m)
	Set the model being optimized. More...

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)

void	set_stop_on_good_score (bool tf)

virtual void	show (std::ostream &out=std::cout) const
	Print info about the optimizer state. More...

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::base::Object
virtual void	clear_caches ()

virtual IMP::base::VersionInfo	get_version_info () const =0
	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)

Protected Member Functions
virtual double	do_step (const ParticleIndexes &sc, double dt)=0

virtual bool	get_is_simulation_particle (ParticleIndex p) const =0

virtual void	setup (const ParticleIndexes &)

Protected Member Functions inherited from IMP::kernel::Optimizer
virtual double	do_optimize (unsigned int ns)=0
	override this function to do actual optimization

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

double	width (FloatKey k) const

FloatIndexes	get_optimized_attributes () const

void	set_value (FloatIndex fi, double v) const

Float	get_value (FloatIndex fi) const

Float	get_derivative (FloatIndex fi) const

void	set_scaled_value (FloatIndex fi, Float v) const

double	get_scaled_value (FloatIndex fi) const

double	get_scaled_derivative (FloatIndex fi) const

void	clear_range_cache ()
	Clear the cache of range information. Do this at the start of optimization.

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

Related Functions
(Note that these are not member functions.)
void	set_current_time (double ct)

typedef IMP::base::Vector < IMP::base::WeakPointer < Simulator > >	SimulatorsTemp

Related Functions inherited from IMP::kernel::Optimizer
typedef IMP::base::Vector < IMP::base::WeakPointer < Optimizer > >	OptimizersTemp

Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

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 (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)

Detailed Description

Definition at line 25 of file Simulator.h.

Constructor & Destructor Documentation

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

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

Member Function Documentation

virtual double IMP::atom::Simulator::do_step	(	const 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.

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 74 of file Simulator.h.

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

protectedpure virtual

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

Implemented in IMP::isd::MolecularDynamics.

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 Model is searched for appropriate particles.

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

protectedvirtual

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

Definition at line 106 of file Simulator.h.

Friends And Related Function Documentation

void set_current_time ( double ct )

Definition at line 82 of file Simulator.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Simulator > > SimulatorsTemp

Definition at line 125 of file Simulator.h.

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

Simulator.h

Public Member Functions

Protected Member Functions

Related Functions

Time steps

Explicitly specifying particles

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation