Pseudo-Voigt reflection profile, with 6-parameters anisotropic Lorentzian broadening and Toraya asymmetric modelling. More...

Inheritance diagram for ObjCryst::ReflectionProfilePseudoVoigtAnisotropic:

Collaboration diagram for ObjCryst::ReflectionProfilePseudoVoigtAnisotropic:

Public Member Functions
	ReflectionProfilePseudoVoigtAnisotropic (const ReflectionProfilePseudoVoigtAnisotropic &old)

virtual ReflectionProfilePseudoVoigtAnisotropic *	CreateCopy () const

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

CrystVector_REAL	GetProfile (const CrystVector_REAL &x, const REAL xcenter, const REAL h, const REAL k, const REAL l) const
	Get the reflection profile. More...

void	SetProfilePar (const REAL fwhmCagliotiW, const REAL fwhmCagliotiU=0, const REAL fwhmCagliotiV=0, const REAL fwhmGaussP=0, const REAL fwhmLorentzX=0, const REAL fwhmLorentzY=0, const REAL fwhmLorentzGammaHH=0, const REAL fwhmLorentzGammaKK=0, const REAL fwhmLorentzGammaLL=0, const REAL fwhmLorentzGammaHK=0, const REAL fwhmLorentzGammaHL=0, const REAL fwhmLorentzGammaKL=0, const REAL pseudoVoigtEta0=0, const REAL pseudoVoigtEta1=0, const REAL asymA0=0, const REAL asymA1=0, const REAL asymA2=0)
	Set reflection profile parameters. More...

virtual REAL	GetFullProfileWidth (const REAL relativeIntensity, const REAL xcenter, const REAL h, const REAL k, const REAL l)
	Get the (approximate) full profile width at a given percentage of the profile maximum (e.g. More...

bool	IsAnisotropic () const
	Is the profile anisotropic ?

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...

Public Member Functions inherited from ObjCryst::ReflectionProfile
	ReflectionProfile (const ReflectionProfile &old)

Public Member Functions inherited from ObjCryst::RefinableObj
	RefinableObj ()
	Constructor.

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

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

virtual	~RefinableObj ()
	Destructor.

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	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.

Private Member Functions
void	InitParameters ()
	Initialize parameters.

Private Attributes
REAL	mCagliotiU
	FWHM parameters: More...

REAL	mCagliotiV

REAL	mCagliotiW

REAL	mScherrerP

REAL	mLorentzX

REAL	mLorentzY

REAL	mLorentzGammaHH

REAL	mLorentzGammaKK

REAL	mLorentzGammaLL

REAL	mLorentzGammaHK

REAL	mLorentzGammaHL

REAL	mLorentzGammaKL

REAL	mPseudoVoigtEta0
	Pseudo-Voigt mixing parameter : $\eta=\eta_0 +2\vartheta\eta_1$ eta=1 -> pure Lorentzian ; eta=0 -> pure Gaussian.

REAL	mPseudoVoigtEta1

REAL	mAsym0
	Asymmetry parameters, following the analytical function for asymmetric pseudo-voigt given by Toraya in J. More...

REAL	mAsym1

REAL	mAsym2

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::RefinableObj
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 inherited from ObjCryst::RefinableObj
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

Pseudo-Voigt reflection profile, with 6-parameters anisotropic Lorentzian broadening and Toraya asymmetric modelling.

Definition at line 163 of file ReflectionProfile.h.

Member Function Documentation

const string & ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::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 from ObjCryst::RefinableObj.

Definition at line 517 of file ReflectionProfile.cpp.

REAL ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::GetFullProfileWidth	(	const REAL	relativeIntensity,
		const REAL	xcenter,
		const REAL	h,
		const REAL	k,
		const REAL	l
	)

virtual

Get the (approximate) full profile width at a given percentage of the profile maximum (e.g.

FWHM=GetFullProfileWidth(0.5)).

Implements ObjCryst::ReflectionProfile.

Definition at line 596 of file ReflectionProfile.cpp.

CrystVector_REAL ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::GetProfile	(	const CrystVector_REAL &	x,
		const REAL	xcenter,
		const REAL	h,
		const REAL	k,
		const REAL	l
	)		const

virtual

Get the reflection profile.

Parameters

x	the vector of x coordinates (i.e. either 2theta or time-of-flight)
xcenter	coordinate (2theta, tof) of the center of the peak
h,k,l	reflection Miller indices

Note: : derived classes who need either d_hkl or the orthonormal coordinates of the scattering vector should be passed a ObjCryst::UnitCell object in the constructor so that they can use ObjCryst::UnitCell::MillerToOrthonormalCoords()

Implements ObjCryst::ReflectionProfile.

Definition at line 523 of file ReflectionProfile.cpp.

void ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::SetProfilePar	(	const REAL	fwhmCagliotiW,
		const REAL	fwhmCagliotiU = `0`,
		const REAL	fwhmCagliotiV = `0`,
		const REAL	fwhmGaussP = `0`,
		const REAL	fwhmLorentzX = `0`,
		const REAL	fwhmLorentzY = `0`,
		const REAL	fwhmLorentzGammaHH = `0`,
		const REAL	fwhmLorentzGammaKK = `0`,
		const REAL	fwhmLorentzGammaLL = `0`,
		const REAL	fwhmLorentzGammaHK = `0`,
		const REAL	fwhmLorentzGammaHL = `0`,
		const REAL	fwhmLorentzGammaKL = `0`,
		const REAL	pseudoVoigtEta0 = `0`,
		const REAL	pseudoVoigtEta1 = `0`,
		const REAL	asymA0 = `0`,
		const REAL	asymA1 = `0`,
		const REAL	asymA2 = `0`
	)

Set reflection profile parameters.

if only W is given, the width is constant

See documentation for mCagliotiU,mCagliotiV,mCagliotiW,mScherrerP,mLorentzX,mLorentzY, mLorentzGammaHH,mLorentzGammaKK,mLorentzGammaLL,mLorentzGammaHK,mLorentzGammaHL,mLorentzGammaKL mAsym0,mAsym1,mAsym2.

Definition at line 558 of file ReflectionProfile.cpp.

void ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::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...

Implements ObjCryst::ReflectionProfile.

Definition at line 712 of file ReflectionProfile.cpp.

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

virtual

Output to stream in well-formed XML.

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

Implements ObjCryst::ReflectionProfile.

Definition at line 647 of file ReflectionProfile.cpp.

Member Data Documentation

REAL ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::mAsym0

private

Asymmetry parameters, following the analytical function for asymmetric pseudo-voigt given by Toraya in J.

Appl. Cryst 23(1990),485-491

Asymmetric coefficient:

$A=A_0+A_1/\sin(2\vartheta)+A_2/\sin^2(2\vartheta)$

Asymmetric profile:

$Prof(\vartheta-\vartheta_{max}<=0)=Prof_0(\frac{1+A}{A})(\vartheta-\vartheta_{max}))$

$Prof(\vartheta-\vartheta_{max}>=0)=Prof_0((1+A) (\vartheta-\vartheta_{max}))$

Definition at line 242 of file ReflectionProfile.h.

REAL ObjCryst::ReflectionProfilePseudoVoigtAnisotropic::mCagliotiU

private

FWHM parameters:

Profile: $Prof(\vartheta) = \eta Lorentz(\vartheta) + (1-\eta) Gauss(\vartheta)$

This pseudo-Voigt profile is the linear combination of a Gaussian and a Lorentzian:

$Profile(\vartheta)= Lorentz(\vartheta) + Gauss(\vartheta)$

Gaussian FWHM parameters, following Caglioti's law and Scherrer broadening coefficient:

$fwhm_g^2= U \tan^2(\theta) + V \tan(\theta) +W +\frac{P}{\cos^2\vartheta}$

See Cagliotti, Pauletti & Ricci, Nucl. Instrum. 3 (1958), 223.

Lorentzian FWHM parameters

$fwhm_l= \frac{X}{\cos\vartheta} +(Y + \frac{\gamma_L}{\sin^2\vartheta})\tan\vartheta$

with anisotropic broadening factor:

$\gamma_L = \gamma_{HH}h^2 + \gamma_{KK}k^2 + \gamma_{LL}l^2 + 2\gamma_{HK}hk + 2\gamma_{hl} + 2\gamma_{kl}kl$

Note: : in the above formula we use $\frac{\gamma_L}{\sin^2\vartheta}$ rather than the more usual $\gamma_L d^2$ for computing purposes (the model being purely phenomenological).

Definition at line 227 of file ReflectionProfile.h.

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

Member Data Documentation