Detailed Description

Maintains temperature during molecular dynamics by velocity scaling.

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 25 of file VelocityScalingOptimizerState.h.

Public Member Functions
	VelocityScalingOptimizerState (Model *m, ParticleIndexesAdaptor pis, double temperature)

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	rescale_velocities () const
	Rescale the velocities now. More...

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

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

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

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

Optimizer *	get_optimizer () const

unsigned int	get_period () const
	Get the periodicity of this state. More...

virtual void	reset ()
	Reset counters, as if at the start of an optimize run. More...

virtual void	set_is_optimizing (bool)
	Called by an Optimizer to signal begin/end of an optimize run. More...

void	set_number_of_updates (unsigned int n)
	Set the counter of number of times do_update() has been called. More...

void	set_period (unsigned int p)
	Set the periodicity of this state. More...

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

void	update_always ()
	Force the state to perform its action now, ignoring the periodicity. More...

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_update (unsigned int call)

Protected Member Functions inherited from IMP::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::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 ()

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::OptimizerState.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 40 of file VelocityScalingOptimizerState.h.

void IMP::atom::VelocityScalingOptimizerState::rescale_velocities ( ) const

Rescale the velocities now.

void IMP::atom::VelocityScalingOptimizerState::set_particles ( const Particles & pis )

Set the particles to use.

Definition at line 32 of file VelocityScalingOptimizerState.h.

void IMP::atom::VelocityScalingOptimizerState::set_temperature ( Float temperature )