Maintains temperature during molecular dynamics by velocity scaling. More...

#include <IMP/atom/VelocityScalingOptimizerState.h>

Inheritance diagram for IMP::atom::VelocityScalingOptimizerState:

Public Member Functions
	VelocityScalingOptimizerState (const kernel::Particles &pis, Float temperature, unsigned skip_steps)

	VelocityScalingOptimizerState (kernel::Model *m, kernel::ParticleIndexesAdaptor pis, double temperature)

virtual std::string	get_type_name () const

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

void	rescale_velocities () const
	Rescale the velocities now.

void	set_particles (const kernel::Particles &pis)
	Set the particles to use.

void	set_temperature (Float temperature)
	Set the temperature to use.

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

	OptimizerState (std::string name="OptimizerState %1%")

unsigned int	get_number_of_updates () const
	Return the number of times update has been called.

Optimizer *	get_optimizer () const

unsigned int	get_period () const

virtual void	reset ()

virtual void	set_is_optimizing (bool)

void	set_number_of_updates (unsigned int n)
	Set the counter.

void	set_period (unsigned int p)

virtual void	update ()
	Called when the Optimizer accepts a new conformation. More...

void	update_always ()

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

	ModelObject (std::string name)

virtual void	do_set_model (kernel::Model *)

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

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_update (unsigned int call)

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

virtual ModelObjectsTemp	do_get_outputs () const

virtual void	do_set_is_optimizing (bool)

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 ()

Detailed Description

This OptimizerState, when used with the MolecularDynamics optimizer, implements a simple thermostat by periodically rescaling the velocities. (Note that this results in discontinuous dynamics.)

See Also: MolecularDynamics

Definition at line 26 of file VelocityScalingOptimizerState.h.

Constructor & Destructor Documentation

IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState	(	const kernel::Particles &	pis,
		Float	temperature,
		unsigned	skip_steps
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_period() instead.

Member Function Documentation

virtual void IMP::atom::VelocityScalingOptimizerState::do_update ( unsigned int )

protectedvirtual

This method is called every get_period() update calls. The number of times this method has been called since the last reset or start of the optimization run is passed.

Reimplemented from IMP::kernel::OptimizerState.

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

VelocityScalingOptimizerState.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation