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ObjCryst::OptimizationObj Class Reference

Base object for Optimization methods. More...

Inheritance diagram for ObjCryst::OptimizationObj:

List of all members.

Public Methods
	OptimizationObj (const string name="")
	Constructor.
virtual	~OptimizationObj ()
	Destructor.
virtual void	RandomizeStartingConfig ()
	Randomize starting configuration. Only affects limited and periodic parameters.
virtual void	Optimize (long &nbSteps, const bool silent=false, const REAL finalcost=0, const REAL maxTime=-1)=0
	Launch optimization for N steps.
void	FixAllPar ()
	Fix all parameters.
void	SetParIsFixed (const string &parName, const bool fix)
	Fix one parameter.
void	SetParIsFixed (const RefParType *type, const bool fix)
	Fix one family of parameters.
void	UnFixAllPar ()
	UnFix All parameters.
void	SetParIsUsed (const string &parName, const bool use)
	Set a parameter to be used.
void	SetParIsUsed (const RefParType *type, const bool use)
	Set a family of parameters to be used.
void	SetLimitsRelative (const string &parName, const REAL min, const REAL max)
	Change the relative limits for a parameter from its name.
void	SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
	Change the relative limits for a family of parameter.
void	SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
	Change the absolute limits for a parameter from its name.
void	SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
	Change the absolute limits for a family of parameter.
REAL	GetLogLikelihood ()
	The optimized (minimized, actually) function.
void	StopAfterCycle ()
	Stop after the current cycle. USed for interactive refinement.
virtual void	DisplayReport ()
	Show report to the user during refinement. Used for GUI update.
void	AddRefinableObj (RefinableObj &)
	Add a refined object. All sub-objects are also added.
virtual void	XMLOutput (ostream &os, int indent=0) const=0
	Output a description of the object in XML format to a stream.
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)=0
	Input in XML format from a stream, restoring the set of refined objects and the associated cost functions. Note that the corresponding objects must have been loaded in memory before, else shit happens.
const string &	GetName () const
	Get the name for this object.
void	SetName (const string &)
	Set the name for this object.
virtual const string	GetClassName () const
	Get the name for this class type.
virtual void	Print () const
	Print some information about this object.
void	RestoreBestConfiguration ()
	Restore the Best configuration.
bool	IsOptimizing () const
	Are we busy optimizing ?
void	TagNewBestConfig () const
	During a global optimization, tell all objects that the current config is the latest "best" config.
REAL	GetLastOptimElapsedTime () const
	Get the elapsed time (in seconds) during the last optimization.
Protected Methods
void	PrepareRefParList ()
	Prepare mRefParList for the refinement.
void	InitRandomSeedFromTime () const
	Initialize random seed from time.
virtual void	InitOptions ()
	Initialization of options.
virtual void	UpdateDisplay ()
	Update Display (if any display is available), when a new 'relevant' configuration is reached.
void	BuildRecursiveRefObjList ()
	(Re)build OptimizationObj::mRecursiveRefinedObjList, if an object has been added or modified.
Protected Attributes
RefinableObj	mRefParList
	The refinable par list used during refinement.
string	mName
	Name of the GlobalOptimization object.
string	mSaveFileName
	File name where refinement info is saved (NOT USED so far...).
long	mNbTrial
	Number of trials so far.
REAL	mBestCost
	Best value of the cost function so far.
long	mBestParSavedSetIndex
	Index of the 'best' saved parameter set.
unsigned long	mContext
	The current 'context', in the case the optimization is run in different parallel contexts.
map< unsigned long, map< const RefinableObj *, LogLikelihoodStats > >	mvContextObjStats
	Statistics for each context.
map< const RefinableObj *, DynamicObjWeight >	mvObjWeight
	Weights for each objects in each context.
bool	mIsOptimizing
	True if a refinement is being done. For multi-threaded environment.
bool	mStopAfterCycle
	If true, then stop at the end of the cycle. Used in multi-threaded environment.
ObjRegistry< RefinableObj >	mRefinedObjList
	The refined objects.
ObjRegistry< RefinableObj >	mRecursiveRefinedObjList
	The refined objects, recursively including all sub-objects.
RefObjOpt	mXMLAutoSave
	Periodic save of complete environment as an xml file.
REAL	mLastOptimTime
	The time elapsed after the last optimization, in seconds.

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Detailed Description

Base object for Optimization methods.

This is an abstract base class, derived for Monte-Cralo type algorithms (Simulated Annealing & Parallel Tempering), and hopefully soon for Genetic Algorithms.

Remarks:

Instead of keeping a copy of the list of parameters here, maybe it would be better to delegate all parameter handling to the refined objects (they would also have to keep in memory the saved parameter sets, so that could be difficult to administrate...).

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Member Function Documentation

void ObjCryst::OptimizationObj::BuildRecursiveRefObjList (    )  [protected]

(Re)build OptimizationObj::mRecursiveRefinedObjList, if an object has been added or modified. If no object has been added and no sub-object has been added/removed, then nothing is done.

REAL ObjCryst::OptimizationObj::GetLogLikelihood (    )

The optimized (minimized, actually) function. This function is the weighted sum of the chosen Cost Functions for the refined objects.

void ObjCryst::OptimizationObj::InitRandomSeedFromTime (    )  [protected]

Initialize random seed from time. For internal use only.

virtual void ObjCryst::OptimizationObj::Optimize (  long &    nbSteps, const bool    silent = false, const REAL    finalcost = 0, const REAL    maxTime = -1 )  [pure virtual]

Launch optimization for N steps. Parameters: nbSteps:  the number of steps to go. This number is modified (decreases!) as the refinement goes on. silent  : if true, absolutely no message should be printed (except debugging) finalcost:  the optimization will stop if overall cost fallse below this value maxTime:  the optimization will stop after the given number of seconds has been spent optimizing (ignored if <0). Implemented in ObjCryst::MonteCarloObj.

void ObjCryst::OptimizationObj::PrepareRefParList (    )  [protected]

Prepare mRefParList for the refinement. For internal use only.

virtual void ObjCryst::OptimizationObj::UpdateDisplay (    )  [protected, virtual]

Update Display (if any display is available), when a new 'relevant' configuration is reached. This calls all RefinableObj::UpdateDisplay()

virtual void ObjCryst::OptimizationObj::XMLOutput (  ostream &    os, int    indent = 0 )  const [pure virtual]

Output a description of the object in XML format to a stream. This saves the list of refined object and the cost functions, as well as options for the refinement. The refined objects are not saved, so this must be done somewhere else (they must be reloaded before this object). Implemented in ObjCryst::MonteCarloObj.

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Member Data Documentation

ObjRegistry<RefinableObj> ObjCryst::OptimizationObj::mRecursiveRefinedObjList [protected]

The refined objects, recursively including all sub-objects. This is mutable, since it is a function of mRefinedObjList only.

RefinableObj ObjCryst::OptimizationObj::mRefParList [protected]

The refinable par list used during refinement. Only a condensed version of all objects. This is useful to keep an history of modifications, and to restore previous values. Remarks: maybe this should be completely delegated to the refined objetcs.

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

• GlobalOptimObj.h

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