Base class for controlling the temperature of a simulation. More...

#include <TemperatureController.hh>

Public Types
typedef utility::vector1 < core::Size >	GridCoord

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	TemperatureController ()
	Default constructor. More...

	TemperatureController (TemperatureController const &)
	Copy constructor. More...

virtual void	apply (core::pose::Pose &)
	No-op implemented only to satisfy the Mover interface. More...

virtual std::string	get_name () const
	Return the name of this class. More...

virtual bool	reinitialize_for_each_job () const
	Return false. This class does not need to be reinitialized for each job. More...

virtual bool	reinitialize_for_new_input () const
	Return false. This class does not need to be reinitialized for new input. More...

virtual void	observe_after_metropolis (MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after the Metropolis criterion is evaluated. More...

virtual core::Real	temperature_move (core::Real score)=0
	Execute the temperature move. More...

virtual core::Real	temperature_move (core::pose::Pose &pose)
	Execute a temperature move which depends on the current pose. More...

virtual core::Real	temperature () const =0
	Return the current temperature. More...

virtual core::Real	temperature (core::Size level) const =0
	Set the current temperature to match given level. More...

virtual core::Size	temperature_level () const
	Return the current temperature level. More...

virtual GridCoord	level_2_grid_coord (core::Size level) const

virtual core::Size	exchange_grid_dim () const

virtual core::Size	nlevels_per_dim (core::Size) const

virtual void	initialize_simulation (core::pose::Pose &pose, MetropolisHastingsMover const &metropolis_hastings_mover, core::Size level, core::Real temperature, core::Size cycle)

virtual void	initialize_simulation (core::pose::Pose &, MetropolisHastingsMover const &, core::Size)
	Callback executed before any Monte Carlo trials are attempted. More...

virtual core::Size	n_temp_levels () const
	Return the number of temperature levels used by this controller. More...

protocols::moves::MonteCarloCOP	monte_carlo () const
	Return const access to the MonteCarlo object being controlled. More...

virtual bool	finished_simulation (core::Size trials, core::Size ntrials)
	Return true if the simulation has been completed. More...

virtual void	set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)
	Set the MonteCarlo object to be controlled. More...

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
	ThermodynamicObserver ()
	Default constructor. More...

virtual	~ThermodynamicObserver ()
	Destructor. More...

virtual void	finalize_simulation (core::pose::Pose &, MetropolisHastingsMover const &)
	Callback executed after all Monte Carlo trials are completed. More...

virtual bool	restart_simulation (core::pose::Pose &, MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &)
	Attempt to restart the last simulation that was recorded by this observer. More...

virtual bool	requires_pose ()
	Return false if this observer does not require a valid pose. TrialCounterObserver is an example of such an observer. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Protected Member Functions
protocols::moves::MonteCarloOP	monte_carlo ()
	Return non-const access to the MonteCarlo object being controlled. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Private Attributes
protocols::moves::MonteCarloOP	monte_carlo_

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Detailed Description

Base class for controlling the temperature of a simulation.

Many schemes to improve the performance of condensed phase Monte Carlo simulations depends on changing the temperature of the system. Common examples include simulated annealing and parallel tempering. This class provides an interface for writing these algorithms. The most important method is temperature_move(), which is responsible for actually changing the temperature of the MonteCarlo object used for the underlying simulation. Methods like temperature_level() are also provided for managing a discrete number of different temperature levels, which is a common feature of these algorithms.

The TemperingBase class serves a similar role to this one, but is geared towards controllers that actually intend to change the temperature. This class also is parent to FixedTemperatureController, which is the default controller used by MetropolisHastingsMover.

Member Typedef Documentation

typedef utility::vector1< core::Size > protocols::canonical_sampling::TemperatureController::GridCoord

Constructor & Destructor Documentation

protocols::canonical_sampling::TemperatureController::TemperatureController ( )

Default constructor.

References canonical_sampling.

protocols::canonical_sampling::TemperatureController::TemperatureController ( TemperatureController const & other )

Copy constructor.

References canonical_sampling.

Member Function Documentation

virtual void protocols::canonical_sampling::TemperatureController::apply ( core::pose::Pose & )

inlinevirtual

No-op implemented only to satisfy the Mover interface.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::AsyncMPITemperingBase, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::TemperingBase, protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

virtual core::Size protocols::canonical_sampling::TemperatureController::exchange_grid_dim ( ) const

inlinevirtual

Reimplemented in protocols::canonical_sampling::HamiltonianExchange.

virtual bool protocols::canonical_sampling::TemperatureController::finished_simulation	(	core::Size	trials,
		core::Size	ntrials
	)

inlinevirtual

Return true if the simulation has been completed.

Reimplemented in protocols::canonical_sampling::AsyncMPITemperingBase.

Referenced by protocols::canonical_sampling::AsyncMPITemperingBase::finished_simulation().

std::string protocols::canonical_sampling::TemperatureController::get_name ( ) const

virtual

Return the name of this class.

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::FixedTemperatureController, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::TemperingBase, protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

void protocols::canonical_sampling::TemperatureController::initialize_simulation	(	core::pose::Pose &	pose,
		MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	level,
		core::Real	temperature,
		core::Size	cycle
	)

virtual

Reimplemented in protocols::canonical_sampling::HamiltonianExchange, protocols::canonical_sampling::TemperingBase, and protocols::canonical_sampling::AsyncMPITemperingBase.

References utility_exit_with_message.

virtual void protocols::canonical_sampling::TemperatureController::initialize_simulation	(	core::pose::Pose &	,
		MetropolisHastingsMover const &	,
		core::Size
	)

inlinevirtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::HamiltonianExchange, protocols::canonical_sampling::SimulatedTempering, protocols::canonical_sampling::TemperingBase, and protocols::canonical_sampling::AsyncMPITemperingBase.

virtual GridCoord protocols::canonical_sampling::TemperatureController::level_2_grid_coord ( core::Size level ) const

inlinevirtual

Reimplemented in protocols::canonical_sampling::HamiltonianExchange.

protocols::moves::MonteCarloCOP protocols::canonical_sampling::TemperatureController::monte_carlo ( ) const

Return const access to the MonteCarlo object being controlled.

References monte_carlo_.

Referenced by protocols::canonical_sampling::TemperingBase::check_temp_consistency(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::canonical_sampling::HamiltonianExchange::initialize_simulation(), protocols::canonical_sampling::TemperingBase::set_current_temp(), set_monte_carlo(), and protocols::canonical_sampling::TemperingBase::temperature().

protocols::moves::MonteCarloOP protocols::canonical_sampling::TemperatureController::monte_carlo ( )

protected

Return non-const access to the MonteCarlo object being controlled.

References monte_carlo_.

virtual core::Size protocols::canonical_sampling::TemperatureController::n_temp_levels ( ) const

inlinevirtual

Return the number of temperature levels used by this controller.

See also: temperature_level()

Reimplemented in protocols::canonical_sampling::TemperingBase.

Referenced by nlevels_per_dim().

virtual core::Size protocols::canonical_sampling::TemperatureController::nlevels_per_dim ( core::Size ) const

inlinevirtual

Reimplemented in protocols::canonical_sampling::HamiltonianExchange.

References n_temp_levels().

void protocols::canonical_sampling::TemperatureController::observe_after_metropolis ( MetropolisHastingsMover const & metropolis_hastings_mover )

virtual

Callback executed after the Metropolis criterion is evaluated.

Implements protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::TemperingBase.

References protocols::moves::MonteCarlo::last_accepted_score(), monte_carlo_, score, and temperature_move().

virtual bool protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job ( ) const

inlinevirtual

Return false. This class does not need to be reinitialized for each job.

Reimplemented from protocols::moves::Mover.

virtual bool protocols::canonical_sampling::TemperatureController::reinitialize_for_new_input ( ) const

inlinevirtual

Return false. This class does not need to be reinitialized for new input.

Reimplemented from protocols::moves::Mover.

void protocols::canonical_sampling::TemperatureController::set_monte_carlo ( protocols::moves::MonteCarloOP monte_carlo )

virtual

Set the MonteCarlo object to be controlled.

Reimplemented in protocols::canonical_sampling::HamiltonianExchange.

References monte_carlo(), and monte_carlo_.

Referenced by protocols::canonical_sampling::HamiltonianExchange::set_monte_carlo().

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature ( ) const

pure virtual

Return the current temperature.

Implemented in protocols::canonical_sampling::FixedTemperatureController, and protocols::canonical_sampling::TemperingBase.

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature ( core::Size level ) const

pure virtual

Set the current temperature to match given level.

Implemented in protocols::canonical_sampling::FixedTemperatureController, and protocols::canonical_sampling::TemperingBase.

virtual core::Size protocols::canonical_sampling::TemperatureController::temperature_level ( ) const

inlinevirtual

Return the current temperature level.

Tempering controllers often work with a handful of discrete temperature levels. This method makes it possible to work with levels, which are discrete, rather than temperatures, which are continuous.

See also: n_temp_levels(); temperature()

Reimplemented in protocols::canonical_sampling::TemperingBase.

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature_move ( core::Real score )

pure virtual

Execute the temperature move.

This method is called by observe_after_metropolis() and is expected to return the new temperature (in units of kT, to the extent that that is meaningful in the context of rosetta).

Implemented in protocols::canonical_sampling::FixedTemperatureController, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::SimulatedTempering, and protocols::canonical_sampling::HamiltonianExchange.

Referenced by observe_after_metropolis(), and temperature_move().

core::Real protocols::canonical_sampling::TemperatureController::temperature_move ( core::pose::Pose & pose )

virtual

Execute a temperature move which depends on the current pose.

The default implementation just calls the pose-independent temperature_pose() method with the energy of the given pose. However, the HamiltonianExchange temperature controller needs to evaluate the alternative Hamiltonian.

Reimplemented in protocols::canonical_sampling::HamiltonianExchange.

References core::pose::Pose::energies(), temperature_move(), and core::scoring::Energies::total_energy().

Member Data Documentation

protocols::moves::MonteCarloOP protocols::canonical_sampling::TemperatureController::monte_carlo_

private

Referenced by monte_carlo(), observe_after_metropolis(), and set_monte_carlo().

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

src/protocols/canonical_sampling/TemperatureController.hh
src/protocols/canonical_sampling/TemperatureController.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation