Statistics and order parameters about the simulations. More...

#include <IMP/npctransport/Statistics.h>

Inheritance diagram for IMP::npctransport::Statistics:

Detailed Description

Statistics and order parameters about the simulations.

Definition at line 63 of file npctransport/Statistics.h.

Public Member Functions
	Statistics (SimulationData *sd, unsigned int statistics_interval_frames, std::string output_file_name)

void	add_fg_chain_stats (FGChain *fg_chain)
	add statistics about an FG chain More...

void	add_floater_stats (IMP::Particle *p)
	add statistics about a floater particle More...

void	add_interaction_stats (core::ParticleType type0, core::ParticleType type1)
	add statistics about interactions between particles of type 0 and 1 More...

OptimizerStates	add_optimizer_states (Optimizer *o=nullptr)
	add all statistics-related optimizer states to o More...

bool	get_is_activated ()

Model *	get_model ()

Model *	get_model () const

std::string	get_output_file_name () const

SimulationData *	get_sd ()

SimulationData const *	get_sd () const

virtual std::string	get_type_name () const override

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

void	remove_particle_type (core::ParticleType pt)
	Remove all statistics related to particle type pt. More...

void	reset_statistics_optimizer_states ()

void	set_interrupted (bool tf)
	Loads the stats file and set the interrupted flag to true. More...

void	update (const IMP::internal::SimpleTimer &timer, unsigned int nf_new=1, bool force_full_output=false)

void	update_particle_type_xyz_distribution_map (Particle *p)

void	update_particle_type_zr_distribution_map (Particle *p)

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)

Additional Inherited Members
Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::npctransport::Statistics::Statistics	(	SimulationData *	sd,
		unsigned int	statistics_interval_frames,
		std::string	output_file_name
	)

Parameters

sd	the sd that owns and uses this statistics object
statistics_interval_frames	the interval of simulation frames for gathering statistics
output_file_name	name of output file to which to dump statistics (or update if it already exists) when calling update()

Member Function Documentation

void IMP::npctransport::Statistics::add_fg_chain_stats ( FGChain * fg_chain )

add statistics about an FG chain

add statistics about an FG chains

Parameters

fg_chain the chain

void IMP::npctransport::Statistics::add_floater_stats ( IMP::Particle * p )

add statistics about a floater particle

Parameters

p	the particle

void IMP::npctransport::Statistics::add_interaction_stats	(	core::ParticleType	type0,
		core::ParticleType	type1
	)

add statistics about interactions between particles of type 0 and 1

add statistics about interactions between particles of type 0 and 1 (order does not matter)

Parameters

type0	type of first interacting particles
type1	type of other interacting particles

OptimizerStates IMP::npctransport::Statistics::add_optimizer_states ( Optimizer * o = nullptr )

add all statistics-related optimizer states to o

Parameters

o	optimizer to which optimizer states are added, use get_sd()->get_bd() if nullptr

Returns: the list of optimizer states that were added

Note: If called for more than one optimizer, only the last optimizer will be guaranteed to work well.

bool IMP::npctransport::Statistics::get_is_activated ( )

if true, statistics have been activated, so add_optimizer_states() was called such that statistics are being tracked

Definition at line 270 of file npctransport/Statistics.h.

Model* IMP::npctransport::Statistics::get_model ( )

returns the model associated with the owned SimulationData

Model* IMP::npctransport::Statistics::get_model ( ) const

returns the model associated with the owned SimulationData

SimulationData* IMP::npctransport::Statistics::get_sd ( )

return the SimulationData object that owns this ScoringFunction

Definition at line 264 of file npctransport/Statistics.h.

SimulationData const* IMP::npctransport::Statistics::get_sd ( ) const

return the SimulationData object that owns this ScoringFunction

Definition at line 276 of file npctransport/Statistics.h.

virtual ::IMP::VersionInfo IMP::npctransport::Statistics::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 359 of file npctransport/Statistics.h.

void IMP::npctransport::Statistics::remove_particle_type ( core::ParticleType pt )

Remove all statistics related to particle type pt.

Removes statistics of particle type pt from all internal maps and from the optimizer states of get_sd()->get_bd()

Parameters

pt	the particle type to be removed

void IMP::npctransport::Statistics::reset_statistics_optimizer_states ( )

resets all the counters of any statistics counters, and the simulation time to zero

void IMP::npctransport::Statistics::set_interrupted ( bool tf )

Loads the stats file and set the interrupted flag to true.

void IMP::npctransport::Statistics::update	(	const IMP::internal::SimpleTimer &	timer,
		unsigned int	nf_new = `1`,
		bool	force_full_output = `false`
	)

opens / creates statistics protobuf file, and update it with appropriate statistics, using statistics file originally specified in the constructor, and based on statistics gathered from the optimizer that was specified by add_optimizer_states().

Exceptions

UsageException If add_optimizer_states() was not called yet (= get_is_activated() is false)

Parameters

timer	the timer that was used to measure the time that has elapsed for statistics
nf_new	the number of frames by which the statistics file should be advanced. This is used to weight the contribution of average statistics over time.
force_full_output	if true, then full statistics are dumped to the output file, even if the number of calls to update does not divide by the value of full_output_statistics_interval_factor

Note: this method is not const cause it may invoke e.g., energy evaluation though it does not substantially change anything in the state of the object; if configuration file full_output_statistics_interval_factor is larger than 1, then full statistics are dumped every N calls to update(), where N is the value of full_output_statistics_interval_factor, and only the HDF5 file is updated at each call.

void IMP::npctransport::Statistics::update_particle_type_xyz_distribution_map ( Particle * p )

updates the map of x-y-z distributions of particle coordinates with p's binned position counts (if z-symmetry flag is on, z is absolute vertical location)

Comment: assume a pore geometry, no checks made that it is so

void IMP::npctransport::Statistics::update_particle_type_zr_distribution_map ( Particle * p )

updates the map of z-r distributions of particle coordinates with p's binned position counts (if z-symmetry flag is on, z is absolute vertical location; r is distance from pore axis)

Comment: assume a pore geometry, no checks made that it is so

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

npctransport/Statistics.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation