The base class for simulators. More...

#include <IMP/atom/Simulator.h>

Inheritance diagram for IMP::atom::Simulator:

Detailed Description

The base class for simulators.

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 given number of frames.

Definition at line 34 of file Simulator.h.

Public Member Functions
	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
	Return the simulator temperature in kelvin. More...

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

void	set_temperature (double d)
	Set the temperature of the simulator to d in kelvin units. More...

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::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	erase_optimizer_state (unsigned int i)

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

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

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
	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)

virtual double	do_step (const ParticleIndexes &sc, double dt)=0
	Perform a single time step. More...

virtual bool	get_is_simulation_particle (ParticleIndex p) const =0
	Return true if the passed particle is appropriate for the simulation. More...

virtual void	setup (const ParticleIndexes &)

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

virtual ModelObjectsTemp	do_get_outputs () const override
	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 ()

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
	Get the maximum allowed time step in fs. More...

double	get_last_time_step () const

Explicitly accessing the particles list
One can explicitly specify which particles should be used for the simulation, or retrieve information about the list of particles. Each particle must be a Mass and core::XYZ particle. If none are specified, the model is searched for appropriate particles, based on the get_simulation_particles() method, which can be overridden by child classes.
list	particles
	A Python list of Particles More...

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	erase_particle (unsigned int i)

void	reserve_particles (unsigned int sz)

Constructor & Destructor Documentation

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

Parameters

m	model associated with simulator
name	simulator 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 Float IMP::atom::Simulator::do_optimize ( unsigned int ns )

overrideprotectedvirtual

override this function to do actual optimization

Implements IMP::Optimizer.

virtual double IMP::atom::Simulator::do_simulate ( double time )

protectedvirtual

called by simulate() - calls setup() and then calls do_step() iteratively till given simulation time is completed

Parameters

time	time to simulate

Returns: score at end of simulation period

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

protectedvirtual

Calls the protected method setup() and then calls 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()

See Also: simulate_wave()

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

protectedpure virtual

Perform a single time step.

Parameters

[in]	sc	the particles that should be moved
[in]	dt	maximum time step value

Returns: the amount that time should be advanced.

Implemented in IMP::atom::MolecularDynamics, IMP::atom::BrownianDynamics, and IMP::spb::MolecularDynamicsWithWte.

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 126 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::atom::MolecularDynamics, IMP::atom::BrownianDynamics, IMP::spb::MolecularDynamicsWithWte, and IMP::isd::MolecularDynamics.

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

Get the time of the last simulated time step (or the maximal time step if the simulation has not started), in units of fs

Definition at line 107 of file Simulator.h.

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

Get the maximum allowed time step in fs.

Definition at line 103 of file Simulator.h.

ParticleIndexes IMP::atom::Simulator::get_simulation_particle_indexes ( ) const

Same as get_simulation_particles(), but returns particle model indexes.

See Also: get_simulation_particles()

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

Returns the set of particles used in the simulation.

If a non-empty set of particles was provided explicitly by earlier calls to the particles list accessor methods, eg, add_particles(), this set it returned. Otherwise, the associated Model object is searched for appropriate particles that have a mass and XYZ decorators.

See Also: add_particle(); add_particles(); remove_particle(); clear_particles(); set_particles(); set_particles_order()

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

Return the simulator temperature in kelvin.

Definition at line 79 of file Simulator.h.

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

Sets the current simulation time in femtoseconds to ct.

Definition at line 129 of file Simulator.h.

void IMP::atom::Simulator::set_temperature ( double d )

Set the temperature of the simulator to d in kelvin units.

Sets the temperature of the simulator. Note that some simulators (e.g. BrownianDynamics) may rely on other temperature-dependent constants (e.g. diffusion coefficients via Diffusion decorator) that will need to be updated independently to reflect the new temperature.

Parameters

d	temperature in K

Definition at line 91 of file Simulator.h.

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

protectedvirtual

Perform any setup operations needed before running a series of simulation steps

Note: Called by do_simulate() or do_simulate_wave() before iterative calls to do_step()

Reimplemented in IMP::atom::MolecularDynamics, IMP::atom::BrownianDynamics, and IMP::spb::MolecularDynamicsWithWte.

Definition at line 178 of file Simulator.h.

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

Simulate for a given time in fs.

simulate for at least the passed time, by calling do_simulate() with optimizing states turned on

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 at least the passed time, by calling do_simulate_wave() with optimizing states turned on

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.

Member Data Documentation

list IMP::atom::Simulator::particles

A Python list of Particles

Note: This class member is only available in Python.

Definition at line 166 of file Simulator.h.

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

Simulator.h

Detailed Description

Public Member Functions

Protected Member Functions

Time steps

Explicitly accessing the particles list

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation