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

#include <TemperatureController.hh>

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

	TemperatureController (TemperatureController const &other)
	Default constructor. More...

virtual void	apply (core::pose::Pose &)
	No-op implemented only to satisfy the Mover interface. 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	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, MetropolisHastingsMover const &mover, core::Size cycle)
	Callback executed before any Monte Carlo trials are attempted. More...

virtual core::Real	temperature_move (core::pose::Pose &pose, MetropolisHastingsMover &mover, core::Real score)=0
	Execute a temperature move if necessary. More...

virtual void	finalize_simulation (core::pose::Pose &pose, MetropolisHastingsMover const &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...

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

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

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 std::string	get_name () const =0
	Each derived class must specify its name. The class name. 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
protocols::moves::MonteCarloOP	monte_carlo ()
	Return non-const access to the MonteCarlo object being controlled. More...

void	set_defaults ()
	Help the constructor initialize new objects. More...

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

virtual bool	init_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...

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...

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

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

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

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

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

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

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_
	The underlying monte carlo simulation. More...

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

core::Size	temperature_stride_
	Frequency for attempting temperature moves. 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...

Static Private Attributes
static bool	options_registered_
	If false, the options used by this class have not yet been added to the global options system. More...

Additional Inherited Members
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 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 are also get and set generally useful parameters. These methods include get_high_temp(), get_low_temp(), get_temp_levels(), get_stride(), and temperature_level(). Temperature levels are provided for managing a number of discrete temperature levels. Not all of these parameters are respected by and/or make sense for all temperature controllers. For example, FixedTemperatureController ignores all of this information.

Constructor & Destructor Documentation

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

Default constructor.

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

Default constructor.

References 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::TemperatureController::apply ( core::pose::Pose & )

inlinevirtual

No-op implemented only to satisfy the Mover interface.

Implements protocols::moves::Mover.

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

bool protocols::canonical_sampling::TemperatureController::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_, monte_carlo(), runtime_assert, temperature(), temperatures_, and trust_current_temp_.

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

void protocols::canonical_sampling::TemperatureController::clear ( )

protected

Forget all temperature levels and return to an uninitialized state.

References instance_initialized_, and temperatures_.

Referenced by protocols::canonical_sampling::MpiHamiltonianExchange::clear(), and init_from_file().

core::Size protocols::canonical_sampling::TemperatureController::current_temp ( )

inlineprotected

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

References current_temp_.

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

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

virtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented in protocols::canonical_sampling::MpiParallelTempering, protocols::canonical_sampling::MpiHamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

References job_.

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

void protocols::canonical_sampling::TemperatureController::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().

bool protocols::canonical_sampling::TemperatureController::init_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::SimulatedTempering, and protocols::canonical_sampling::MpiHamiltonianExchange.

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::TemperatureController::init_from_options ( )

protectedvirtual

Assign user-specified command-line values to data members.

Reimplemented in protocols::canonical_sampling::MpiHamiltonianExchange, protocols::canonical_sampling::SimulatedTempering, and protocols::canonical_sampling::FixedTemperatureController.

References generate_temp_range(), init_from_file(), instance_initialized_, option, options_registered_, protocols::sic_dock::range(), stats_file_, stats_line_output_, stats_silent_output_, temperature_stride_, protocols::canonical_sampling::tr, user, and utility_exit_with_message.

Referenced by protocols::canonical_sampling::SimulatedTempering::init_from_options(), protocols::canonical_sampling::MpiHamiltonianExchange::init_from_options(), and initialize_simulation().

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

virtual

Callback executed before any Monte Carlo trials are attempted.

The cycle parameter gives the number of times that the simulation has been restarted. Since the restart feature is currently commented out, cycle should always be 0.

Reimplemented in protocols::canonical_sampling::MpiParallelTempering, protocols::canonical_sampling::MpiHamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

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_, monte_carlo(), temp_trial_count_, temperature(), temperatures_, and protocols::canonical_sampling::tr.

Referenced by protocols::canonical_sampling::SimulatedTempering::initialize_simulation(), protocols::canonical_sampling::MpiHamiltonianExchange::initialize_simulation(), and protocols::canonical_sampling::MpiParallelTempering::initialize_simulation().

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

Return const access to the MonteCarlo object being controlled.

References monte_carlo_.

Referenced by check_temp_consistency(), protocols::canonical_sampling::MpiHamiltonianExchange::initialize_simulation(), initialize_simulation(), set_current_temp(), set_monte_carlo(), temperature(), and protocols::canonical_sampling::MpiHamiltonianExchange::temperature_move().

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

protected

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

References monte_carlo_.

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

Return the number of temperature levels used by this controller.

This parameter must be set from the command line using the -tempering:temp:levels flag. The default value is 10. In some cases (e.g. when using MpiParallelTempering), this parameter must also match the number of processes allocated to your app by mpirun. For example:

mpirun -np 32 my_parallel_tempering_app -tempering:temp:levels 32

I'm not sure why this requirement exists. It's simple enough to ask MPI how many threads are available; why not just set that many temperature levels? Perhaps this would make things harder to reproduce, because the behavior of the program would depend on options passed to mpirun.

See also: temperature_level(); temperature()

References temperatures_.

void protocols::canonical_sampling::TemperatureController::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::MpiHamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

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

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

void protocols::canonical_sampling::TemperatureController::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::docking::TemperedDocking::register_options().

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_current_temp ( core::Size new_temp )

protected

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_, monte_carlo(), and temperatures_.

Referenced by protocols::canonical_sampling::MpiHamiltonianExchange::initialize_simulation(), protocols::canonical_sampling::MpiParallelTempering::initialize_simulation(), set_temperatures(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::canonical_sampling::MpiHamiltonianExchange::temperature_move(), and protocols::canonical_sampling::MpiParallelTempering::temperature_move().

void protocols::canonical_sampling::TemperatureController::set_defaults ( )

protected

Help the constructor initialize new objects.

References instance_initialized_, and trust_current_temp_.

Referenced by protocols::canonical_sampling::MpiParallelTempering::MpiParallelTempering().

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

Set the MonteCarlo object to be controlled.

References monte_carlo(), and monte_carlo_.

void protocols::canonical_sampling::TemperatureController::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::FixedTemperatureController::FixedTemperatureController(), protocols::canonical_sampling::MpiHamiltonianExchange::init_from_file(), and protocols::canonical_sampling::SimulatedTempering::init_from_file().

std::string const& protocols::canonical_sampling::TemperatureController::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::TemperatureController::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::TemperatureController::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().

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

Return the temperature of the underlying MonteCarlo object.

References monte_carlo().

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

Return the temperature of the given level.

References temperatures_.

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

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. Higher temperature levels correspond to higher temperatures, and as usual in rosetta, counting starts at one. So the lowest temperature being simulated will always be level 1.

See also: n_temp_levels(); temperature()

References current_temp_.

Referenced by protocols::canonical_sampling::MpiHamiltonianExchange::temperature_move().

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature_move	(	core::pose::Pose &	pose,
		MetropolisHastingsMover &	mover,
		core::Real	score
	)

pure virtual

Execute a temperature move if necessary.

This method is expected to return the new temperature (in units of kT, although kT doesn't mean much in the context of rosetta).

Implemented in protocols::canonical_sampling::MpiParallelTempering, protocols::canonical_sampling::MpiHamiltonianExchange, protocols::canonical_sampling::SimulatedTempering, and protocols::canonical_sampling::FixedTemperatureController.

bool protocols::canonical_sampling::TemperatureController::time_for_temp_move ( )

inlineprotected

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

References temp_trial_count_, and temperature_stride_.

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

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