Base class for tempering Monte Carlo optimizations. More...

#include <TemperingBase.hh>

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

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

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

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

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

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

core::Real	temperature () const
	Return the temperature of the underlying MonteCarlo object. More...

core::Real	temperature (core::Size level) const
	Return the temperature of the given level. More...

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

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

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

	TemperatureController (TemperatureController const &)
	Copy constructor. 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 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 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

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 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...

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...

Static Public Member Functions
static void	register_options ()
	Register the options used by this mover with the global options system. More...

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...

Protected Member Functions
void	set_defaults ()
	Help the constructor initialize the object. More...

virtual void	init_from_options ()
	Assign user-specified command-line values to data members. More...

virtual bool	initialize_from_file (std::string const &filename)
	Initialize temperatures and weights from a file. More...

virtual void	write_to_file (std::string const &file_in, std::string const &output_name, utility::vector1< core::Real > const &wcounts)
	Save temperatures and weights to a file. More...

bool	check_temp_consistency ()
	Assert that the current temperature of the MonteCarlo object agrees with the current temperature level of this object. More...

virtual bool	time_for_temp_move ()
	Return true if a temperature move should be made on this iteration. More...

void	reset_temp_counter ()

core::Size	current_temp () const
	Return the current temperature level. Identical to temperature_level() as far as I can tell. More...

void	clear ()
	Forget all temperature levels and return to an uninitialized state. More...

void	set_temperatures (utility::vector1< core::Real > const &)
	Explicitly set the temperature levels. More...

virtual void	set_current_temp (core::Size new_temp)
	Set the temperature to the given level. More...

bool	stats_line_output () const
	Return true if a statistics summary should be written. More...

bool	stats_silent_output () const
	Return true if a statistics summary should be inserted into a silent file. More...

std::string const &	stats_file () const
	Return the name of the silent file into which statistics should be recorded. More...

void	generate_temp_range (core::Real temp_low, core::Real temp_high, core::Size n_levels, InterpolationType interpolation=linear)
	Explicitly set the temperature levels by interpolating the given parameters. More...

MultiTemperatureTrialCounter &	trial_counter ()

Protected Member Functions inherited from protocols::canonical_sampling::TemperatureController
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...

Protected Attributes
utility::vector1< core::Real >	temperatures_
	Temperature levels. More...

core::Size	temperature_stride_
	Frequency for attempting temperature moves (e.g. once every `io_stride_` steps). More...

core::Size	io_stride_
	Frequency with which statistics should be written (e.g. once every `io_stride_` steps). More...

bool	trust_current_temp_
	If false, look for current temperature in monte_carlo_ before each move. Set to true by default. More...

bool	stats_line_output_
	If true, a statistics summary will be written. More...

bool	stats_silent_output_
	If true, the statistics summary will be inserted in a silent file. More...

std::string	stats_file_
	Name of the silent file used for writing statistics. More...

protocols::jd2::JobOP	job_
	Job object to report on temperatures. More...

bool	instance_initialized_
	If false, init_from_options() will be called before the simulation starts. More...

core::Size	current_temp_
	Current temperature level. Not the current temperature! More...

core::Size	temp_trial_count_
	Number of times time_for_temp_move() has been called. This method is meant to be called every time temperature_move() is called. More...

MultiTemperatureTrialCounter	trial_counter_

Private Types
typedef TemperatureController	Parent

Static Private Attributes
static bool	options_registered_

Additional Inherited Members
Public Types inherited from protocols::canonical_sampling::TemperatureController
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

Detailed Description

Base class for tempering Monte Carlo optimizations.

Many important Monte Carlo optimization techniques, like simulated annealing and parallel tempering, depend on a changing temperature schedule. TemperatureController provides the essential interface for providing this functionality. This class provides a lot of useful protected member functions, especially with regard to input (i.e. command-line or file) and output (i.e. tracer or silent file).

That said, my first impression is that this class really limits what you can do in terms of output. The emphasis seems to be on silent files, so it would be hard to instead use (for example) database output. In general, putting IO code in a base class seems like a bad idea. Better to do that kind of stuff with object composition, so different IO formats can easily be swapped in and out. Perhaps this would be a good target for a small refactoring project.

Member Typedef Documentation

typedef TemperatureController protocols::canonical_sampling::TemperingBase::Parent

private

Constructor & Destructor Documentation

protocols::canonical_sampling::TemperingBase::TemperingBase ( )

Default constructor.

References set_defaults().

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

Copy constructor.

References canonical_sampling, current_temp_, instance_initialized_, job_, stats_file_, stats_line_output_, stats_silent_output_, temp_trial_count_, temperature_stride_, temperatures_, and trust_current_temp_.

Member Function Documentation

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

inlinevirtual

No-op implemented only to satisfy the Mover interface.

Reimplemented from protocols::canonical_sampling::TemperatureController.

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

bool protocols::canonical_sampling::TemperingBase::check_temp_consistency ( )

protected

Assert that the current temperature of the MonteCarlo object agrees with the current temperature level of this object.

References current_temp_, protocols::canonical_sampling::TemperatureController::monte_carlo(), runtime_assert, temperature(), temperatures_, and trust_current_temp_.

Referenced by protocols::canonical_sampling::SimulatedTempering::temperature_move(), and protocols::canonical_sampling::ParallelTempering::temperature_move().

void protocols::canonical_sampling::TemperingBase::clear ( )

protected

Forget all temperature levels and return to an uninitialized state.

References instance_initialized_, and temperatures_.

Referenced by protocols::canonical_sampling::HamiltonianExchange::clear(), and initialize_from_file().

core::Size protocols::canonical_sampling::TemperingBase::current_temp ( ) const

inlineprotected

Return the current temperature level. Identical to temperature_level() as far as I can tell.

References current_temp_.

Referenced by protocols::canonical_sampling::HamiltonianExchange::next_exchange_level(), and protocols::canonical_sampling::SimulatedTempering::temperature_move().

void protocols::canonical_sampling::TemperingBase::finalize_simulation	(	core::pose::Pose &	,
		protocols::canonical_sampling::MetropolisHastingsMover const &
	)

virtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

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

References job_, protocols::canonical_sampling::MetropolisHastingsMover::output_name(), stats_file_, tag, protocols::canonical_sampling::tr, trial_counter_, and protocols::canonical_sampling::MultiTemperatureTrialCounter::write_to_file().

Referenced by protocols::canonical_sampling::SimulatedTempering::finalize_simulation(), protocols::canonical_sampling::AsyncMPITemperingBase::finalize_simulation(), and protocols::canonical_sampling::ParallelTempering::finalize_simulation().

void protocols::canonical_sampling::TemperingBase::generate_temp_range	(	core::Real	temp_low,
		core::Real	temp_high,
		core::Size	n_levels,
		InterpolationType	interpolation = `linear`
	)

protected

Explicitly set the temperature levels by interpolating the given parameters.

References protocols::canonical_sampling::exponential, protocols::canonical_sampling::interpolation_type_enum_to_string(), protocols::canonical_sampling::linear, runtime_assert, temperatures_, and protocols::canonical_sampling::tr.

Referenced by init_from_options(), and parse_my_tag().

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

virtual

Return the name of this class.

Reimplemented from protocols::canonical_sampling::TemperatureController.

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

void protocols::canonical_sampling::TemperingBase::init_from_options ( )

protectedvirtual

bool protocols::canonical_sampling::TemperingBase::initialize_from_file ( std::string const & filename )

protectedvirtual

Initialize temperatures and weights from a file.

Return false if an IO error occurs.

Reimplemented in protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

References clear(), getline(), utility::io::izstream::good(), in, tag, temperatures_, and protocols::canonical_sampling::tr.

Referenced by init_from_options(), and parse_my_tag().

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

virtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::TemperatureController.

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

References protocols::jd2::Job::add_string_real_pair(), current_temp_, protocols::jd2::get_current_job(), init_from_options(), instance_initialized_, protocols::jd2::jd2_used(), job_, protocols::canonical_sampling::TemperatureController::monte_carlo(), protocols::canonical_sampling::MultiTemperatureTrialCounter::set_temperature_observer(), temp_trial_count_, temperature(), temperatures_, protocols::canonical_sampling::tr, and trial_counter_.

Referenced by protocols::canonical_sampling::AsyncMPITemperingBase::initialize_simulation(), protocols::canonical_sampling::SimulatedTempering::initialize_simulation(), initialize_simulation(), and protocols::canonical_sampling::ParallelTempering::initialize_simulation().

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

virtual

Reimplemented from protocols::canonical_sampling::TemperatureController.

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

References initialize_simulation(), set_current_temp(), temperature(), and utility_exit_with_message.

Size protocols::canonical_sampling::TemperingBase::n_temp_levels ( ) const

virtual

Return the number of temperature levels used by this controller.

See also: temperature_level()

Reimplemented from protocols::canonical_sampling::TemperatureController.

References temperatures_.

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

virtual

Callback executed after the Metropolis criterion is evaluated.

Reimplemented from protocols::canonical_sampling::TemperatureController.

References protocols::canonical_sampling::MetropolisHastingsMover::current_trial(), io_stride_, protocols::canonical_sampling::MetropolisHastingsMover::output_name(), stats_file_, utility::to_string(), trial_counter_, and protocols::canonical_sampling::MultiTemperatureTrialCounter::write_to_file().

void protocols::canonical_sampling::TemperingBase::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

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

References generate_temp_range(), initialize_from_file(), instance_initialized_, protocols::canonical_sampling::interpolation_type_string_to_enum(), io_stride_, stats_file_, stats_line_output_, stats_silent_output_, temperature_stride_, protocols::canonical_sampling::tr, and trust_current_temp_.

Referenced by protocols::canonical_sampling::HamiltonianExchange::parse_my_tag(), protocols::canonical_sampling::SimulatedTempering::parse_my_tag(), and protocols::canonical_sampling::ParallelTempering::parse_my_tag().

void protocols::canonical_sampling::TemperingBase::register_options ( )

static

Register the options used by this mover with the global options system.

References NEW_OPT, protocols::evaluation::options_registered_, and protocols::sic_dock::range().

Referenced by protocols::canonical_sampling::ParallelTempering::register_options(), and protocols::canonical_sampling::HamiltonianExchange::register_options().

void protocols::canonical_sampling::TemperingBase::reset_temp_counter ( )

inlineprotected

References temp_trial_count_.

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

void protocols::canonical_sampling::TemperingBase::set_current_temp ( core::Size new_temp )

protectedvirtual

Set the temperature to the given level.

Note that the argument is a temperature level, not a raw temperature.

References protocols::jd2::Job::add_string_real_pair(), current_temp_, job_, protocols::canonical_sampling::TemperatureController::monte_carlo(), and temperatures_.

Referenced by protocols::canonical_sampling::HamiltonianExchange::initialize_simulation(), initialize_simulation(), protocols::canonical_sampling::ParallelTempering::initialize_simulation(), set_temperatures(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), and protocols::canonical_sampling::ParallelTempering::temperature_move().

void protocols::canonical_sampling::TemperingBase::set_defaults ( )

protected

Help the constructor initialize the object.

handling of options including command-line

References trust_current_temp_.

Referenced by TemperingBase().

void protocols::canonical_sampling::TemperingBase::set_temperatures ( utility::vector1< core::Real > const & temps )

protected

Explicitly set the temperature levels.

References set_current_temp(), and temperatures_.

Referenced by protocols::canonical_sampling::SimulatedTempering::initialize_from_file(), and protocols::canonical_sampling::HamiltonianExchange::initialize_from_file().

std::string const& protocols::canonical_sampling::TemperingBase::stats_file ( ) const

inlineprotected

Return the name of the silent file into which statistics should be recorded.

See also: stats_line_output(); stats_silent_output()

References stats_file_.

Referenced by protocols::canonical_sampling::SimulatedTempering::finalize_simulation(), and protocols::canonical_sampling::SimulatedTempering::temperature_move().

bool protocols::canonical_sampling::TemperingBase::stats_line_output ( ) const

inlineprotected

Return true if a statistics summary should be written.

See also: stats_silent_output(); stats_file()

References stats_line_output_.

Referenced by protocols::canonical_sampling::SimulatedTempering::write_to_file().

bool protocols::canonical_sampling::TemperingBase::stats_silent_output ( ) const

inlineprotected

Return true if a statistics summary should be inserted into a silent file.

See also: stats_line_output(); stats_file()

References stats_silent_output_.

Referenced by protocols::canonical_sampling::SimulatedTempering::write_to_file().

core::Real protocols::canonical_sampling::TemperingBase::temperature ( ) const

virtual

Return the temperature of the underlying MonteCarlo object.

Implements protocols::canonical_sampling::TemperatureController.

References protocols::canonical_sampling::TemperatureController::monte_carlo().

Referenced by check_temp_consistency(), protocols::canonical_sampling::ParallelTempering::finalize_simulation(), initialize_simulation(), protocols::canonical_sampling::HamiltonianExchange::show(), protocols::canonical_sampling::ParallelTempering::shuffle_temperatures(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::canonical_sampling::ParallelTempering::temperature_move(), and protocols::canonical_sampling::SimulatedTempering::write_to_file().

core::Real protocols::canonical_sampling::TemperingBase::temperature ( core::Size level ) const

virtual

Return the temperature of the given level.

Implements protocols::canonical_sampling::TemperatureController.

References temperatures_.

core::Size protocols::canonical_sampling::TemperingBase::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 from protocols::canonical_sampling::TemperatureController.

References current_temp_.

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

virtual bool protocols::canonical_sampling::TemperingBase::time_for_temp_move ( )

inlineprotectedvirtual

Return true if a temperature move should be made on this iteration.

Reimplemented in protocols::canonical_sampling::AsyncMPITemperingBase.

References temp_trial_count_, and temperature_stride_.

Referenced by protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::canonical_sampling::ParallelTempering::temperature_move(), and protocols::canonical_sampling::AsyncMPITemperingBase::time_for_temp_move().

MultiTemperatureTrialCounter& protocols::canonical_sampling::TemperingBase::trial_counter ( )

inlineprotected

References trial_counter_.

void protocols::canonical_sampling::TemperingBase::write_to_file	(	std::string const &	file_in,
		std::string const &	output_name,
		utility::vector1< core::Real > const &	wcounts
	)