Generic Refinable Object. More...

Inheritance diagram for ObjCryst::RefinableObj:

Collaboration diagram for ObjCryst::RefinableObj:

Public Member Functions
	RefinableObj ()
	Constructor.

	RefinableObj (const bool internalUseOnly)
	Constructor. More...

	RefinableObj (const RefinableObj &old)
	Defined not implemented... More...

virtual	~RefinableObj ()
	Destructor.

virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...

virtual const string &	GetName () const
	Name of the object.

virtual void	SetName (const string &name)
	Name of the object.

void	operator= (const RefinableObj &old)
	Defined not implemented... More...

void	PrepareForRefinement () const
	Find which parameters are used and not fixed, for a refinement /optimization. More...

void	FixAllPar ()
	Fix All parameters.

void	UnFixAllPar ()
	UnFix All parameters.

void	SetParIsFixed (const long parIndex, const bool fix)
	Fix/un-fix one parameter from its #.

void	SetParIsFixed (const string &parName, const bool fix)
	Fix/un-fix one parameter from its name.

void	SetParIsFixed (const RefParType *type, const bool fix)
	Fix/un-fix one family of parameters.

void	SetParIsUsed (const string &parName, const bool use)
	Set whether a parameter is used.

void	SetParIsUsed (const RefParType *type, const bool use)
	Set whether a family of parameters is used.

long	GetNbPar () const
	Total number of refinable parameter in the object. More...

long	GetNbParNotFixed () const
	Total number of non-fixed parameters. Is initialized by PrepareForRefinement()

RefinablePar &	GetPar (const long i)
	Access all parameters in the order they were inputted.

const RefinablePar &	GetPar (const long i) const
	Access all parameters in the order they were inputted.

RefinablePar &	GetPar (const string &name)
	Access all parameters from their name.

const RefinablePar &	GetPar (const string &name) const
	Access all parameters from their name.

RefinablePar &	GetPar (const REAL *)
	Access parameter from its adress.

const RefinablePar &	GetPar (const REAL *) const
	Access parameter from its adress.

RefinablePar &	GetParNotFixed (const long i)
	Access all parameters in the order they were inputted, skipping fixed parameters. More...

const RefinablePar &	GetParNotFixed (const long i) const
	Access all parameters in the order they were inputed, skipping fixed parameters. More...

void	AddPar (const RefinablePar &newRefPar)
	Add a refinable parameter. More...

void	AddPar (RefinablePar *newRefPar)
	Add a refinable parameter. More...

void	AddPar (RefinableObj &newRefParList, const bool copyParam=false)
	Add all the parameters in another RefinableObj. More...

vector< RefinablePar * >::iterator	RemovePar (RefinablePar *refPar)
	Remove a refinable parameter. More...

virtual void	Print () const

unsigned long	CreateParamSet (const string name="") const
	Save the current set of refined values in a new set. More...

void	ClearParamSet (const unsigned long id) const
	Erase the param set with the given id, releasing memory.

void	SaveParamSet (const unsigned long id) const
	Save the current set of refined values over a previously-created set of saved values. More...

void	RestoreParamSet (const unsigned long id)
	Restore a saved set of values. More...

const CrystVector_REAL &	GetParamSet (const unsigned long setId) const
	Access one save refpar set. More...

CrystVector_REAL &	GetParamSet (const unsigned long setId)
	Access one save refpar set. More...

REAL	GetParamSet_ParNotFixedHumanValue (const unsigned long setId, const long parNumber) const
	Access the (human) value of one refined parameter in a saved set of parameters. More...

const void	EraseAllParamSet ()
	Erase all saved refpar sets. More...

const string &	GetParamSetName (const unsigned long setId) const
	Get the name associated to a refpar set. More...

void	SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving absolute new limits.

void	SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving absolute new limits.

void	SetLimitsRelative (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0. More...

void	SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). More...

void	SetLimitsProportional (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, proportionnaly to the current value. More...

void	SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, proportionnaly to their current value. More...

void	SetGlobalOptimStep (const RefParType *type, const REAL step)
	Change the maximum step to use during Global Optimization algorithms.

ObjRegistry< RefinableObj > &	GetSubObjRegistry ()
	Access to the registry of RefinableObj used by this object.

const ObjRegistry< RefinableObj > &	GetSubObjRegistry () const
	Access to the registry of RefinableObj used by this object.

virtual void	RegisterClient (RefinableObj &) const
	Register a new object using this object. More...

virtual void	DeRegisterClient (RefinableObj &) const
	Deregister an object (which not any more) using this object.

virtual const ObjRegistry < RefinableObj > &	GetClientRegistry () const
	Get the list of clients.

virtual ObjRegistry < RefinableObj > &	GetClientRegistry ()
	Get the list of clients.

bool	IsBeingRefined () const
	Is the object being refined ? (Can be refined by one algorithm at a time only.)

virtual void	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization. More...

virtual void	EndOptimization ()
	This should be called by any optimization class at the end of an optimization. More...

virtual void	SetApproximationFlag (const bool allow)
	Enable or disable numerical approximations. More...

virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization). More...

virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration. More...

void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More...

virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object. More...

virtual unsigned int	GetNbLSQFunction () const
	Number of LSQ functions.

virtual const CrystVector_REAL &	GetLSQCalc (const unsigned int) const
	Get the current calculated value for the LSQ function.

virtual const CrystVector_REAL &	GetLSQObs (const unsigned int) const
	Get the observed values for the LSQ function.

virtual const CrystVector_REAL &	GetLSQWeight (const unsigned int) const
	Get the weight values for the LSQ function.

virtual const CrystVector_REAL &	GetLSQDeriv (const unsigned int, RefinablePar &)
	Get the first derivative values for the LSQ function, for a given parameter. More...

virtual std::map< RefinablePar *, CrystVector_REAL > &	GetLSQ_FullDeriv (const unsigned int, std::set< RefinablePar * > &vPar)
	Get the first derivative for the LSQ function for each parameter supplied in a list. More...

void	ResetParList ()
	Re-init the list of refinable parameters, removing all parameters. More...

virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML. More...

virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream. More...

virtual void	UpdateDisplay () const
	If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. More...

unsigned int	GetNbOption () const
	Number of Options for this object.

RefObjOpt &	GetOption (const unsigned int i)
	Access to the options.

const RefObjOpt &	GetOption (const unsigned int i) const
	const access to the options

virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. More...

void	SetDeleteRefParInDestructor (const bool b)
	Set this object not to delete its list of parameters when destroyed. More...

const RefinableObjClock &	GetRefParListClock () const
	What was the last time a RefinablePar was added/removed ? More...

virtual REAL	GetRestraintCost () const
	Get the restraint cost (overall penalty of all restraints) More...

void	AddRestraint (Restraint *pNewRestraint)
	Add a new restraint. More...

vector< Restraint * >::iterator	RemoveRestraint (Restraint *pRestraint)
	Remove a restraint from the list of known restraints. More...

virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config. More...

const RefinableObjClock &	GetClockMaster () const
	This clocks records any change in the object. See refinableObj::mClockMaster.

Protected Member Functions
long	FindPar (const string &name) const
	Find a refinable parameter with a given name.

long	FindPar (const REAL *) const
	Find a refinable parameter from the adress of its value.

void	AddSubRefObj (RefinableObj &)

void	RemoveSubRefObj (RefinableObj &)

void	AddOption (RefObjOpt *opt)

virtual void	Prepare ()

map< unsigned long, pair < CrystVector_REAL, string > >::iterator	FindParamSet (unsigned long id) const
	Find a parameter set with a given id (and check if it is there)

Protected Attributes
string	mName
	Name for this RefinableObject. Should be unique, at least in the same scope.+.

vector< RefinablePar * >	mvpRefPar
	Vector of pointers to the refinable parameters.

vector< Restraint * >	mvpRestraint
	Vector of pointers to the restraints for this object. More...

map< unsigned long, pair < CrystVector_REAL, string > >	mvpSavedValuesSet
	Map of (index,pointers to arrays) used to save sets of values for all parameters. More...

long	mNbRefParNotFixed
	Total of not-fixed parameters.

CrystVector_long	mRefparNotFixedIndex
	Index of not-fixed parameters.

int	mOptimizationDepth
	Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place. More...

ObjRegistry< RefinableObj >	mSubObjRegistry
	Registry of RefinableObject needed for this object (owned by this object or not)

ObjRegistry< RefinableObj >	mClientObjRegistry
	Registry of RefinableObject using this object. More...

ObjRegistry< RefObjOpt >	mOptionRegistry
	List of options for this object. More...

bool	mDeleteRefParInDestructor
	If true (the default), then all RefinablePar will be deleted when the the object is deleted. More...

RefinableObjClock	mRefParListClock
	Last time the RefinableParList was modified (a parameter added or removed).

bool	mRandomMoveIsDone

CrystVector_REAL	mLSQDeriv
	Temporary array used to return derivative values of the LSQ function for given parameters. More...

std::map< unsigned int, std::map< RefinablePar *, CrystVector_REAL > >	mLSQ_FullDeriv
	Temporary map to return the derivative of the LSQ function versus a list of parameters. More...

RefinableObjClock	mClockMaster
	Master clock, which is changed whenever the object has been altered. More...

Detailed Description

Generic Refinable Object.

This is basically a list of refinable parameters, with other basic common properties such as a name,. etc... This allows optimization/refinement algorithms to access the parameters without knowing what the object really is.

Todo:: Define more clearly which operations are recursive (ie also modify sub-objects).

Definition at line 752 of file RefinableObj.h.

Constructor & Destructor Documentation

ObjCryst::RefinableObj::RefinableObj ( const bool internalUseOnly )

Constructor.

Using internalUseOnly=true will avoid registering the the object to any registry, and thus (for example) no display will be created, nor will this object be automatically be saved.

Definition at line 1188 of file RefinableObj.cpp.

ObjCryst::RefinableObj::RefinableObj ( const RefinableObj & old )

Defined not implemented...

Should never be called (copying the refinable parameters would allow you to modify the input object). Use the default constructor and RefinableObj::AddPar(RefinableObj&) instead.

Definition at line 1203 of file RefinableObj.cpp.

Member Function Documentation

void ObjCryst::RefinableObj::AddOption ( RefObjOpt * opt )

protected

Add an option for this parameter

Definition at line 1973 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddPar ( const RefinablePar & newRefPar )

Add a refinable parameter.

The parameter is copied, so it need only be allocated temporarily.

Deprecated:

Use the next function, which supplies the parameter as a pointer, and avoids a useless copy.

Note: : if a parameter is added and its name is already used by another, its name will be automatically appended with an ~

Definition at line 1416 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddPar ( RefinablePar * newRefPar )

Add a refinable parameter.

The parameter is not copied, so it should be allocated in the heap.

Note: : if a parameter is added and its name is already used by another, its name will be automatically appended with an ~

Definition at line 1434 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddPar	(	RefinableObj &	newRefParList,
		const bool	copyParam = `false`
	)

Add all the parameters in another RefinableObj.

Parameters are copied, so they should be allocated in the heap.

Warning: If a copy of another RefinableObj parameter list is made, such as in the OptimizationObj class, make sure that upon deletion of this object the parameters will not be destroyed. To do this use RefinableObj::SetDeleteRefParInDestructor(false).

Parameters

copyParam if false (default), then parameters are not copied from the object but just referenced. Use RefinableObj::SetDeleteRefParInDestructor(false) accordingly. If true, then the parameters are copied, so that any modification to the fixed/limited/used attributes do not affect the original parameter. Only the value and the parameter's clock can then be modified by the copied parameter

Note: : if a parameter is added and its name is already used by another, its name will be automatically appended with an ~

Definition at line 1451 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddRestraint ( Restraint * pNewRestraint )

Add a new restraint.

This returns an iterator pointing to the next Restraint in the vector.

Definition at line 1889 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddSubRefObj ( RefinableObj & obj )

protected

Add an object in the registry of used objects.

Definition at line 1959 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::BeginGlobalOptRandomMove ( )

Raise a flag, to be sure not to make a random change more than once in each RefinableObj.

This calls recursively all sub-objects.

This is necessary since one object may be included in several others. This must be called before making a random configuration change on a list of objects.

Definition at line 1750 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::BeginOptimization	(	const bool	allowApproximations = `false`,
		const bool	enableRestraints = `false`
	)

virtual

This should be called by any optimization class at the begining of an optimization.

This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects.

Note: this may be called several time for some objects which are used by several other objects, or for nested optimizations (e.g. least-squares optimizations inside a global one).; EndOptimization() must be called at the end of the optimization, the same number of time BeginOptimization() was called !

Parameters

allowApproximations	if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives.
enableRestraints	xrefitem deprecated 28.

Reimplemented in ObjCryst::PowderPattern, ObjCryst::Molecule, ObjCryst::ScatteringData, ObjCryst::Crystal, ObjCryst::PowderPatternDiffraction, ObjCryst::CellExplorer, ObjCryst::TextureEllipsoid, ObjCryst::PowderPatternBackground, and ObjCryst::TextureMarchDollase.

Definition at line 1661 of file RefinableObj.cpp.

unsigned long ObjCryst::RefinableObj::CreateParamSet ( const string name = "" ) const

Save the current set of refined values in a new set.

Parameters

name	: the name associated to this set of values. Names should be unique.

Returns: an number identifying the set of saved values.

Warning: : there is no limit to the number of parameters sets, so try to release them when you don't need them.

Definition at line 1503 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::EndOptimization ( )

virtual

This should be called by any optimization class at the end of an optimization.

This also affects all sub-objects.

Note: this may be called several time for some objects which are used by several other objects.

Reimplemented in ObjCryst::Molecule, ObjCryst::ScatteringData, ObjCryst::PowderPatternDiffraction, and ObjCryst::ZScatterer.

Definition at line 1682 of file RefinableObj.cpp.

const void ObjCryst::RefinableObj::EraseAllParamSet ( )

Erase all saved refpar sets.

Definition at line 1572 of file RefinableObj.cpp.

const string & ObjCryst::RefinableObj::GetClassName ( ) const

virtual

Name for this class ("RefinableObj", "Crystal",...).

This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry

Reimplemented in ObjCryst::Molecule, ObjCryst::PowderPattern, ObjCryst::ScatteringPowerAtom, ObjCryst::PowderPatternDiffraction, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::CellExplorer, ObjCryst::TextureEllipsoid, ObjCryst::ZScatterer, ObjCryst::Radiation, ObjCryst::PowderPatternBackground, ObjCryst::ReflectionProfilePseudoVoigtAnisotropic, ObjCryst::TextureMarchDollase, ObjCryst::Scatterer, ObjCryst::Crystal, ObjCryst::ScatteringPower, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::UnitCell, ObjCryst::Atom, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::ScatteringPowerSphere, ObjCryst::PowderPatternComponent, and ObjCryst::PowderPatternBackgroundBayesianMinimiser.

Definition at line 1243 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::GetGeneGroup	(	const RefinableObj &	obj,
		CrystVector_uint &	groupIndex,
		unsigned int &	firstGroup
	)		const

virtual

Get the gene group assigned to each parameter.

Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life.

The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique.

Parameters

obj	the , supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object.
groupIndex	a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned).
firstGroup	this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group.

Note: this function is not optimized, and should only be called at the beginning of a refinement.

Reimplemented in ObjCryst::PowderPattern, ObjCryst::Crystal, ObjCryst::PowderPatternDiffraction, ObjCryst::ZScatterer, ObjCryst::ScatteringPower, ObjCryst::PowderPatternBackground, and ObjCryst::Atom.

Definition at line 1867 of file RefinableObj.cpp.

REAL ObjCryst::RefinableObj::GetLogLikelihood ( ) const

virtual

Get -log(likelihood) of the current configuration for the object.

By default (no likelihood evaluation available), this is equal to 0.

This call should not be recursive, it is the task of the algorithm to get the sum of likelihoods for all objects invlolved.

Note: contrary to the old "Cost Function" approach, with log(Likelihood) there is no 'choice' of cost function, so that it is the task of the object to give the optimized likelihood (possibly with user options).

Reimplemented in ObjCryst::PowderPattern, ObjCryst::Molecule, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::ZMoveMinimizer, and ObjCryst::PowderPatternBackgroundBayesianMinimiser.

Definition at line 1759 of file RefinableObj.cpp.

std::map< RefinablePar *, CrystVector_REAL > & ObjCryst::RefinableObj::GetLSQ_FullDeriv	(	const unsigned int	n,
		std::set< RefinablePar * > &	vPar
	)

virtual

Get the first derivative for the LSQ function for each parameter supplied in a list.

Returns: : a map, with a RefinablePar pointer as key, and as value the corresponding derivative vector. Note that the value of the map for the NULL key is the current value for the LSQ function, which is also returned. The map will include derivatives only for parameters which have been supplied in vPar - but if a parameter is listed in vPar and has a null derivative, the returned vecor will be empty.

Warning: : currently in development, to provide faster, analytic derivatives

Note: :ideally, this function should be const - but since numerical derivatives may be used before all analytical formulas are entered, a non-const version is required.

Todo:

Reimplemented in ObjCryst::PowderPattern, and ObjCryst::DiffractionDataSingleCrystal.

Definition at line 1819 of file RefinableObj.cpp.

const CrystVector_REAL & ObjCryst::RefinableObj::GetLSQDeriv	(	const unsigned int	n,
		RefinablePar &	par
	)

virtual

Get the first derivative values for the LSQ function, for a given parameter.

Note that the default method in the base RefinableObj class is to use numerical derivatives, so it should be overridden for better precision.

Todo:: This should be a const method, and the given RefPar should be const too...

Reimplemented in ObjCryst::Molecule, and ObjCryst::CellExplorer.

Definition at line 1806 of file RefinableObj.cpp.

long ObjCryst::RefinableObj::GetNbPar ( ) const

Total number of refinable parameter in the object.

Note that some may be actually fixed or even not used !! For refinement use PrepareForRefinement(), NbRefParNotFixed(), and ParNotFixed(i)

Definition at line 1348 of file RefinableObj.cpp.

const CrystVector_REAL & ObjCryst::RefinableObj::GetParamSet ( const unsigned long setId ) const

Access one save refpar set.

Parameters

setId : the number identifying the set.

Definition at line 1550 of file RefinableObj.cpp.

CrystVector_REAL & ObjCryst::RefinableObj::GetParamSet ( const unsigned long setId )

Access one save refpar set.

Parameters

setId : the number identifying the set.

Definition at line 1557 of file RefinableObj.cpp.

REAL ObjCryst::RefinableObj::GetParamSet_ParNotFixedHumanValue	(	const unsigned long	setId,
		const long	parNumber
	)		const

Access the (human) value of one refined parameter in a saved set of parameters.

Parameters

setId	: the number identifying the set.
parNumber	: the number identifying the parameter in the list of refined parameters

Returns: if parNumber=5 and setId=37, then the returned value will be the value (scaled if it is an angle) value of the 5th not-fixed parameter in the saved set #37.

Definition at line 1564 of file RefinableObj.cpp.

const string & ObjCryst::RefinableObj::GetParamSetName ( const unsigned long setId ) const

Get the name associated to a refpar set.

Parameters

setId : the number identifying the set.

Definition at line 1577 of file RefinableObj.cpp.

RefinablePar & ObjCryst::RefinableObj::GetParNotFixed ( const long i )

Access all parameters in the order they were inputted, skipping fixed parameters.

Must call PrepareForRefinement() before !

Definition at line 1406 of file RefinableObj.cpp.

const RefinablePar & ObjCryst::RefinableObj::GetParNotFixed ( const long i ) const

Access all parameters in the order they were inputed, skipping fixed parameters.

Must call PrepareForRefinement() before !

Definition at line 1411 of file RefinableObj.cpp.

const RefinableObjClock & ObjCryst::RefinableObj::GetRefParListClock ( ) const

What was the last time a RefinablePar was added/removed ?

Definition at line 1878 of file RefinableObj.cpp.

REAL ObjCryst::RefinableObj::GetRestraintCost ( ) const

virtual

Get the restraint cost (overall penalty of all restraints)

By default this returns 0, so this must be overloaded by any object which actually uses restraint.

Note: Instead, we could return by default the sum of the restraints, but this is dangerous since we want to have derived objects fully responsible for handling restraints.

Definition at line 1880 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::GlobalOptRandomMove	(	const REAL	mutationAmplitude,
		const RefParType *	type = `gpRefParTypeObjCryst`
	)

virtual

Make a random move of the current configuration.

This is for global optimization algorithms. the moves for each parameter are less than their global optimization step, multiplied by the mutation amplitude.

Warning: : this makes a random move for the parameter declared for this object, and it is the duty of the object to decide whether the included objects should be moved and how. (eg an algorithm should only call for a move with the top object, and this object decides how he and his sub-objects moves). By default (RefinableObj implementation) all included objects are moved recursively.

RefinableObj::

Parameters

mutationAmplitude	multiplier for the maximum move amplitude, for all parameters
type	restrain the change exclusively to parameters of a given type (same type or descendant from this RefParType).

Reimplemented in ObjCryst::PowderPattern, ObjCryst::Molecule, ObjCryst::Crystal, ObjCryst::ZScatterer, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::TextureEllipsoid, and ObjCryst::TextureMarchDollase.

Definition at line 1734 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::operator= ( const RefinableObj & old )

Defined not implemented...

Should never be called

void ObjCryst::RefinableObj::Prepare ( )

protectedvirtual

Prepare everything (if necessary) for an optimization/calculation.

Reimplemented in ObjCryst::PowderPattern, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPatternBackground, and ObjCryst::PowderPatternComponent.

Definition at line 1982 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::PrepareForRefinement ( ) const

Find which parameters are used and not fixed, for a refinement /optimization.

This must be called before any refinement...

Definition at line 1273 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::RandomizeConfiguration ( )

virtual

Randomize Configuration (before a global optimization).

This Affects only parameters which are limited and not fixed. The randomization also affects all sub-objects (recursive).

Reimplemented in ObjCryst::Molecule.

Definition at line 1709 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::RegisterClient ( RefinableObj & obj ) const

virtual

Register a new object using this object.

Todo:: : the clients should be const, but are not... This need to be fixed...

Definition at line 1648 of file RefinableObj.cpp.

vector< RefinablePar * >::iterator ObjCryst::RefinableObj::RemovePar ( RefinablePar * refPar )

Remove a refinable parameter.

This returns an iterator to the next parameter in the vector.

Definition at line 1463 of file RefinableObj.cpp.

vector< Restraint * >::iterator ObjCryst::RefinableObj::RemoveRestraint ( Restraint * pRestraint )

Remove a restraint from the list of known restraints.

This does not delete the Restraint object.

Definition at line 1895 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::RemoveSubRefObj ( RefinableObj & obj )

protected

Remove an object in the registry of used objects.

Definition at line 1966 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::ResetParList ( )

Re-init the list of refinable parameters, removing all parameters.

This does not delete the RefinablePar if RefinableObj::mDeleteRefParInDestructor is false

Definition at line 1829 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::RestoreParamSet ( const unsigned long id )

Restore a saved set of values.

Parameters

id	: the number identifying the set.

Warning: this only affects parameters which are used. Others remain unchanged. Parameters which are fixed are also restored, although generally they will not be altered.

Definition at line 1536 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SaveParamSet ( const unsigned long id ) const

Save the current set of refined values over a previously-created set of saved values.

Parameters

id	the number identifying the set of saved values.

Definition at line 1527 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SetApproximationFlag ( const bool allow )

virtual

Enable or disable numerical approximations.

This can be used for global optimization to get faster calculations. Depending on the type of object, this may do something or not (it does not do anything in a base RefinableObj, except calling this function for all sub-objects).

Note: Currently there is no mApproximationFlag in the base class, but maybe there should...

Also see:

Reimplemented in ObjCryst::ScatteringData, and ObjCryst::PowderPatternDiffraction.

Definition at line 1703 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SetDeleteRefParInDestructor ( const bool b )

Set this object not to delete its list of parameters when destroyed.

This is used for the RefinableObj in algorithms objects (OptimizationObj), which only hold copies of parameters from the refined objects.

Definition at line 1876 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SetLimitsProportional	(	const string &	parName,
		const REAL	min,
		const REAL	max
	)

Change the limits for a given parameter, proportionnaly to the current value.

min should be < 1. and max > 1.

Definition at line 1618 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SetLimitsProportional	(	const RefParType *	type,
		const REAL	min,
		const REAL	max
	)

Change the limits for a category of parameters, proportionnaly to their current value.

min should be < 1. and max > 1.

Definition at line 1624 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SetLimitsRelative	(	const string &	parName,
		const REAL	min,
		const REAL	max
	)

Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0.

Definition at line 1599 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::SetLimitsRelative	(	const RefParType *	type,
		const REAL	min,
		const REAL	max
	)

Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max).

Thus min should logically be <0 and max >0.

Definition at line 1605 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::TagNewBestConfig ( ) const

virtual

During a global optimization, tells the object that the current config is the latest "best" config.

This can be used by the object to make more intellingent random moves (use with caution: highly experimental !).

Reimplemented in ObjCryst::Molecule, ObjCryst::PowderPatternBackground, and ObjCryst::TextureMarchDollase.

Definition at line 1911 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::UpdateDisplay ( ) const

virtual

If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report.

Reimplemented in ObjCryst::Molecule.

Definition at line 1917 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::XMLInput	(	istream &	is,
		const XMLCrystTag &	tag
	)

virtual

Input From stream.

Todo:: Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc...

Reimplemented in ObjCryst::PowderPattern, ObjCryst::Molecule, ObjCryst::ScatteringPowerAtom, ObjCryst::PowderPatternDiffraction, ObjCryst::Crystal, ObjCryst::ZScatterer, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Radiation, ObjCryst::TextureEllipsoid, ObjCryst::PowderPatternBackground, ObjCryst::ReflectionProfilePseudoVoigtAnisotropic, ObjCryst::TextureMarchDollase, ObjCryst::Atom, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfile, and ObjCryst::ScatteringPowerSphere.

Definition at line 341 of file RefinableObj/IO.cpp.

void ObjCryst::RefinableObj::XMLOutput	(	ostream &	os,
		int	indent = `0`
	)		const

virtual

Output to stream in well-formed XML.

Todo:: Use inheritance.. as for XMLInputTag()...

Reimplemented in ObjCryst::PowderPattern, ObjCryst::Molecule, ObjCryst::ScatteringPowerAtom, ObjCryst::PowderPatternDiffraction, ObjCryst::Crystal, ObjCryst::ZScatterer, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Radiation, ObjCryst::TextureEllipsoid, ObjCryst::PowderPatternBackground, ObjCryst::ReflectionProfilePseudoVoigtAnisotropic, ObjCryst::TextureMarchDollase, ObjCryst::Atom, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfile, and ObjCryst::ScatteringPowerSphere.

Definition at line 336 of file RefinableObj/IO.cpp.

Member Data Documentation

ObjRegistry<RefinableObj> ObjCryst::RefinableObj::mClientObjRegistry

mutableprotected

Registry of RefinableObject using this object.

This is mutable so that client can modify it (kludge?)

Definition at line 1258 of file RefinableObj.h.

RefinableObjClock ObjCryst::RefinableObj::mClockMaster

protected

Master clock, which is changed whenever the object has been altered.

It should be parent to all clocks recording changes in derived classes.

Definition at line 1291 of file RefinableObj.h.

bool ObjCryst::RefinableObj::mDeleteRefParInDestructor

protected

If true (the default), then all RefinablePar will be deleted when the the object is deleted.

The opposite option (false) should only be used in RefinableObj holding 'copies' of other objects, such as in algorithms.

Definition at line 1268 of file RefinableObj.h.

std::map< unsigned int,std::map<RefinablePar*, CrystVector_REAL> > ObjCryst::RefinableObj::mLSQ_FullDeriv

mutableprotected

Temporary map to return the derivative of the LSQ function versus a list of parameters.

Several LSQ functions can be stored.

Todo:: In development

Definition at line 1282 of file RefinableObj.h.

CrystVector_REAL ObjCryst::RefinableObj::mLSQDeriv

mutableprotected

Temporary array used to return derivative values of the LSQ function for given parameters.

Definition at line 1276 of file RefinableObj.h.

int ObjCryst::RefinableObj::mOptimizationDepth

protected

Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place.

mOptimizationDepth>0 indicates the object is being optimized. Values larger than 1 indicate that several level of optimizations are taking place, e.g. one least-square optimization during a global optimization, etc...

Definition at line 1252 of file RefinableObj.h.

ObjRegistry<RefObjOpt> ObjCryst::RefinableObj::mOptionRegistry

protected

List of options for this object.

Note that these are just references, to options allocated by the object, to have a simple global access to all options

Definition at line 1264 of file RefinableObj.h.

bool ObjCryst::RefinableObj::mRandomMoveIsDone

protected

This true is false if RefinableObj::GlobalOptRandomMove() has been called since RefinableObj::BeginGlobalOptRandomMove() was called.

Definition at line 1273 of file RefinableObj.h.

vector<Restraint*> ObjCryst::RefinableObj::mvpRestraint

protected

Vector of pointers to the restraints for this object.

This excludes all RefinablePar declared in RefinableObj::mpRefPar, which also are Restraint.

Definition at line 1232 of file RefinableObj.h.

map<unsigned long,pair<CrystVector_REAL,string> > ObjCryst::RefinableObj::mvpSavedValuesSet

mutableprotected

Map of (index,pointers to arrays) used to save sets of values for all parameters.

Currently there is no limit to the number of saved sets.

This is mutable since creating/storing a param set does not affect the 'real' part of the object.

Definition at line 1240 of file RefinableObj.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation