ObjCryst::RefinableObj Class Reference

Generic Refinable Object. More...

Inheritance diagram for ObjCryst::RefinableObj:

Collaboration diagram for ObjCryst::RefinableObj:

List of all members.

Public Member Functions

RefinableObj ()

Constructor.

RefinableObj (const bool internalUseOnly)

Constructor.

RefinableObj (const RefinableObj &old)

Defined not implemented.

virtual ~RefinableObj ()

Destructor.

virtual const string & GetClassName () const

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

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.

void PrepareForRefinement () const

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

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.

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.

const RefinablePar & GetParNotFixed (const long i) const

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

void AddPar (const RefinablePar &newRefPar)

Add a refinable parameter.

void AddPar (RefinablePar *newRefPar)

Add a refinable parameter.

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

Add all the parameters in another RefinableObj.

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

Remove a refinable parameter.

virtual void Print () const

unsigned long CreateParamSet (const string name="") const

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

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.

void RestoreParamSet (const unsigned long id)

Restore a saved set of values.

const CrystVector_REAL & GetParamSet (const unsigned long setId) const

Access one save refpar set.

CrystVector_REAL & GetParamSet (const unsigned long setId)

Access one save refpar set.

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.

const void EraseAllParamSet ()

Erase all saved refpar sets.

const string & GetParamSetName (const unsigned long setId) const

Get the name associated to a refpar set.

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.

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).

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

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

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

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

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.

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.

virtual void EndOptimization ()

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

virtual void RandomizeConfiguration ()

Randomize Configuration (before a global optimization).

virtual void GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)

Make a random move of the current configuration.

void BeginGlobalOptRandomMove ()

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

virtual REAL GetLogLikelihood () const

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

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.

void ResetParList ()

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

virtual void XMLOutput (ostream &os, int indent=0) const

Output to stream in well-formed XML.

virtual void XMLInput (istream &is, const XMLCrystTag &tag)

Input From stream.

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.

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.

void SetDeleteRefParInDestructor (const bool b)

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

const RefinableObjClock & GetRefParListClock () const

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

virtual REAL GetRestraintCost () const

Get the restraint cost (overall penalty of all restraints).

void AddRestraint (Restraint *pNewRestraint)

Add a new restraint.

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

Remove a restraint from the list of known restraints.

virtual void TagNewBestConfig () const

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

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.

map< unsigned long, pair
< CrystVector_REAL, string > > mvpSavedValuesSet

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

long mNbRefParNotFixed

Total of not-fixed parameters.

CrystVector_long mRefparNotFixedIndex

Index of not-fixed parameters.

bool mIsbeingRefined

Is the object being refined ?

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.

ObjRegistry< RefObjOpt > mOptionRegistry

List of options for this object.

bool mDeleteRefParInDestructor

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

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.

RefinableObjClock mClockMaster

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

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 730 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 1157 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.

Member Function Documentation

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

Definition at line 1210 of file RefinableObj.cpp.

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

Defined not implemented.

.. Should never be called

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 1240 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 1315 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 1385 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 1390 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.

Definition at line 1395 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.

Definition at line 1402 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

Definition at line 1409 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 1421 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 1461 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 1485 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 and not fixed. Others remain unchanged.

Definition at line 1494 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 1507 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 1514 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.

For internal use only.

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 1521 of file RefinableObj.cpp.

const void ObjCryst::RefinableObj::EraseAllParamSet ( )

Erase all saved refpar sets.

Definition at line 1529 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 1534 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 1555 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 1560 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 1573 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 1578 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 1602 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.

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,:	if true, then restrained parameters will be allowed to go beyond theur hard limits. This implies that the algorithm will take into account the cost (penalty) related to the restraints. Objects which do not use restraints will simply ignore this. WARNING: this parameter may be removed with the new likelihood scheme.

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

Definition at line 1615 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::PowderPatternDiffraction, ObjCryst::ScatteringData, and ObjCryst::ZScatterer.

Definition at line 1636 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 1655 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::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPattern, ObjCryst::TextureMarchDollase, and ObjCryst::ZScatterer.

Definition at line 1680 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 1696 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).

Warning:: : this is in under heavy development, so expect changes...

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

Definition at line 1705 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::CellExplorer.

Definition at line 1746 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 1758 of file RefinableObj.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::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ReflectionProfile, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::TextureMarchDollase, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::ZScatterer.

Definition at line 322 of file RefinableObj/IO.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::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ReflectionProfile, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::TextureMarchDollase, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::ZScatterer.

Definition at line 327 of file RefinableObj/IO.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.

Definition at line 1846 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::Atom, ObjCryst::Crystal, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ScatteringPower, and ObjCryst::ZScatterer.

Definition at line 1796 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 1805 of file RefinableObj.cpp.

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

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

Definition at line 1807 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 1809 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 1818 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 1824 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 1840 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddSubRefObj ( RefinableObj & obj ) [protected]

For internal use only.

Add an object in the registry of used objects.

Definition at line 1905 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::RemoveSubRefObj ( RefinableObj & obj ) [protected]

For internal use only.

Remove an object in the registry of used objects.

Definition at line 1912 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::AddOption ( RefObjOpt * opt ) [protected]

For internal use only.

Add an option for this parameter

Definition at line 1919 of file RefinableObj.cpp.

void ObjCryst::RefinableObj::Prepare ( ) [protected, virtual]

For internal use only.

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

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

Definition at line 1928 of file RefinableObj.cpp.

Member Data Documentation

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 1156 of file RefinableObj.h.

map<unsigned long,pair<CrystVector_REAL,string> > ObjCryst::RefinableObj::mvpSavedValuesSet [mutable, protected]

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 1164 of file RefinableObj.h.

ObjRegistry<RefinableObj> ObjCryst::RefinableObj::mClientObjRegistry [mutable, protected]

Registry of RefinableObject using this object.

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

Definition at line 1178 of file RefinableO


Public Member Functions
	RefinableObj ()
	Constructor.
	RefinableObj (const bool internalUseOnly)
	Constructor.
	RefinableObj (const RefinableObj &old)
	Defined not implemented.
virtual	~RefinableObj ()
	Destructor.
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",.
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.
void	PrepareForRefinement () const
	Find which parameters are used and not fixed, for a refinement /optimization.
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.
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.
const RefinablePar &	GetParNotFixed (const long i) const
	Access all parameters in the order they were inputed, skipping fixed parameters.
void	AddPar (const RefinablePar &newRefPar)
	Add a refinable parameter.
void	AddPar (RefinablePar *newRefPar)
	Add a refinable parameter.
void	AddPar (RefinableObj &newRefParList, const bool copyParam=false)
	Add all the parameters in another RefinableObj.
vector< RefinablePar * >::iterator	RemovePar (RefinablePar *refPar)
	Remove a refinable parameter.
virtual void	Print () const
unsigned long	CreateParamSet (const string name="") const
	Save the current set of refined values in a new set.
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.
void	RestoreParamSet (const unsigned long id)
	Restore a saved set of values.
const CrystVector_REAL &	GetParamSet (const unsigned long setId) const
	Access one save refpar set.
CrystVector_REAL &	GetParamSet (const unsigned long setId)
	Access one save refpar set.
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.
const void	EraseAllParamSet ()
	Erase all saved refpar sets.
const string &	GetParamSetName (const unsigned long setId) const
	Get the name associated to a refpar set.
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.
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).
void	SetLimitsProportional (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, proportionnaly to the current value.
void	SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, proportionnaly to their current value.
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.
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.
virtual void	EndOptimization ()
	This should be called by any optimization class at the end of an optimization.
virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization).
virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration.
void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj.
virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object.
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.
void	ResetParList ()
	Re-init the list of refinable parameters, removing all parameters.
virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML.
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream.
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.
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.
void	SetDeleteRefParInDestructor (const bool b)
	Set this object not to delete its list of parameters when destroyed.
const RefinableObjClock &	GetRefParListClock () const
	What was the last time a RefinablePar was added/removed ?
virtual REAL	GetRestraintCost () const
	Get the restraint cost (overall penalty of all restraints).
void	AddRestraint (Restraint *pNewRestraint)
	Add a new restraint.
vector< Restraint * >::iterator	RemoveRestraint (Restraint *pRestraint)
	Remove a restraint from the list of known restraints.
virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config.
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.
map< unsigned long, pair < CrystVector_REAL, string > >	mvpSavedValuesSet
	Map of (index,pointers to arrays) used to save sets of values for all parameters.
long	mNbRefParNotFixed
	Total of not-fixed parameters.
CrystVector_long	mRefparNotFixedIndex
	Index of not-fixed parameters.
bool	mIsbeingRefined
	Is the object being refined ?
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.
ObjRegistry< RefObjOpt >	mOptionRegistry
	List of options for this object.
bool	mDeleteRefParInDestructor
	If true (the default), then all RefinablePar will be deleted when the the object is deleted.
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.
RefinableObjClock	mClockMaster
	Master clock, which is changed whenever the object has been altered.