Powder pattern class, with an observed pattern and several calculated components to modelize the pattern. More...

Inheritance diagram for ObjCryst::PowderPattern:

Collaboration diagram for ObjCryst::PowderPattern:

Public Member Functions
	PowderPattern (const PowderPattern &)

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

void	AddPowderPatternComponent (PowderPatternComponent &)
	Add a component (phase, backround) to this pattern. More...

unsigned int	GetNbPowderPatternComponent () const
	Number of components.

const PowderPatternComponent &	GetPowderPatternComponent (const string &name) const
	Access to a component of the powder pattern.

const PowderPatternComponent &	GetPowderPatternComponent (const int) const
	Access to a component of the powder pattern.

PowderPatternComponent &	GetPowderPatternComponent (const string &name)
	Access to a component of the powder pattern.

PowderPatternComponent &	GetPowderPatternComponent (const int)
	Access to a component of the powder pattern.

REAL	GetScaleFactor (const int i) const
	Access to the scale factor of components (will be 1 for background components)

REAL	GetScaleFactor (const PowderPatternComponent &comp) const
	Access to the scale factor of components (will be 1 for background components)

void	SetScaleFactor (const int i, REAL s)
	Access to the scale factor of components (will be 1 for background components)

void	SetScaleFactor (const PowderPatternComponent &comp, REAL s)
	Access to the scale factor of components (will be 1 for background components)

void	SetPowderPatternPar (const REAL min, const REAL step, unsigned long nbPoint)
	the powder pattern angular range & resolution parameter. More...

void	SetPowderPatternX (const CrystVector_REAL &x)
	Set the x coordinate of the powder pattern : either the 2theta or time-of-flight values for each recorded point. More...

unsigned long	GetNbPoint () const
	Number of points ?

unsigned long	GetNbPointUsed () const
	Number of points actually calculated (below the chosen max(sin(theta)/lambda)) ?

const RefinableObjClock &	GetClockNbPointUsed () const
	Clock corresponding to the last time the number of points used was changed.

void	SetRadiation (const Radiation &radiation)
	Set the radiation.

const Radiation &	GetRadiation () const
	Neutron or x-ray experiment ?

Radiation &	GetRadiation ()
	Neutron or x-ray experiment ?

void	SetRadiationType (const RadiationType radiation)
	Set the radiation type.

RadiationType	GetRadiationType () const
	Neutron or x-ray experiment ?

void	SetWavelength (const REAL lambda)
	Set the wavelength of the experiment (in Angstroems). More...

void	SetWavelength (const string &XRayTubeElementName, const REAL alpha12ratio=0.5)
	Set the wavelength of the experiment to that of an X-Ray tube. More...

void	SetEnergy (const REAL energy)
	Set the energy of the experiment [in keV, lambda(A)=12398/E(keV)].

REAL	GetWavelength () const
	wavelength of the experiment (in Angstroems)

const CrystVector_REAL &	GetPowderPatternCalc () const
	Get the calculated powder pattern.

std::map< RefinablePar *, CrystVector_REAL > &	GetPowderPattern_FullDeriv (std::set< RefinablePar * > &vPar)

const CrystVector_REAL &	GetPowderPatternObs () const
	Get the observed powder pattern.

const CrystVector_REAL &	GetPowderPatternObsSigma () const
	Get the sigma for each point of the observed powder pattern.

const CrystVector_REAL &	GetPowderPatternVariance () const
	Get the variance (obs+model) for each point of the powder pattern.

const CrystVector_REAL &	GetPowderPatternWeight () const
	Get the weight for each point of the powder pattern.

REAL	GetPowderPatternXMin () const
	Get the Minimum 2theta.

REAL	GetPowderPatternXStep () const
	Get the average step in 2theta. More...

REAL	GetPowderPatternXMax () const
	Get the maximum 2theta.

const CrystVector_REAL &	GetPowderPatternX () const
	Get the vector of X (2theta or time-of-flight) coordinates.

const CrystVector_REAL &	GetChi2Cumul () const
	Get the powder pattern cumulative Chi^2. More...

const RefinableObjClock &	GetClockPowderPatternCalc () const
	Last time the pattern was calculated.

const RefinableObjClock &	GetClockPowderPatternPar () const
	When were the pattern parameters (2theta range, step) changed ?

const RefinableObjClock &	GetClockPowderPatternRadiation () const
	When were the radiation parameter (radiation type, wavelength) changed ?

const RefinableObjClock &	GetClockPowderPatternXCorr () const
	When were the parameters for 2theta/TOF correction (zero, transparency, displacement) last changed ?

void	SetXZero (const REAL newZero)
	Change Zero in x (2theta,tof)

void	Set2ThetaDisplacement (const REAL displacement)
	Change displacement correction $(2\theta)_{obs} = (2\theta)_{real} + a\cos(\theta)$ .

void	Set2ThetaTransparency (const REAL transparency)
	Change transparency correction $(2\theta)_{obs} = (2\theta)_{real} + b\sin(2\theta)$ .

void	ImportPowderPatternFullprof (const string &fullprofFileName)
	Import fullprof-style diffraction data. More...

void	ImportPowderPatternPSI_DMC (const string &filename)
	Import powder pattern, format DMC from PSI.

void	ImportPowderPatternILL_D1A5 (const string &filename)
	Import powder pattern, format from ILL D1A/D2B (format without counter info)

void	ImportPowderPatternXdd (const string &fileName)
	Import *.xdd diffraction data (Topas,...). More...

void	ImportPowderPatternSietronicsCPI (const string &fileName)
	Import *.cpi Sietronics diffraction data. More...

void	ImportPowderPattern2ThetaObsSigma (const string &fileName, const int nbSkip=0)
	Import file with 3 columns 2Theta Iobs Sigma. More...

void	ImportPowderPatternFullprof4 (const string &fileName)
	Import diffraction data from a file, with the first line has 2ThetaMin, step, 2thetaMax, and the following lines alternate 10 Iobs and 10 sigma. More...

void	ImportPowderPatternMultiDetectorLLBG42 (const string &fileName)
	diffraction data in a multi-detector format (fullprof format #6). More...

void	ImportPowderPattern2ThetaObs (const string &fileName, const int nbSkip=0)
	Import file with 2 columns 2Theta Iobs. More...

void	ImportPowderPatternTOF_ISIS_XYSigma (const string &fileName)
	Import TOF file (ISIS type, 3 columns t, Iobs, sigma(Iobs)) More...

void	ImportPowderPatternGSAS (const string &fileName)
	Import GSAS standard powder pattern data (see GSAS manual). More...

void	ImportPowderPatternCIF (const CIF &cif)
	Import CIF powder pattern data.

void	SetPowderPatternObs (const CrystVector_REAL &obs)
	Set observed powder pattern from vector array. More...

void	SavePowderPattern (const string &filename="powderPattern.out") const
	Save powder pattern to one file, text format, 3 columns theta Iobs Icalc. More...

void	PrintObsCalcData (ostream &os=cout) const
	Print to thee screen/console the observed and calculated pattern (long, mostly useful for debugging)

REAL	GetR () const
	Unweighted R-factor. More...

REAL	GetIntegratedR () const

REAL	GetRw () const
	Get the weighted R-factor. More...

REAL	GetIntegratedRw () const

REAL	GetChi2 () const
	Return conventionnal Chi^2. More...

REAL	GetIntegratedChi2 () const
	Return integrated Chi^2. More...

REAL	GetChi2_Option () const
	Return the conventionnal or integrated Chi^2, depending on the option.

void	FitScaleFactorForR () const
	Fit the scale(s) factor of each component to minimize R. More...

void	FitScaleFactorForIntegratedR () const

void	FitScaleFactorForRw () const
	Fit the scale(s) factor of each component to minimize Rw. More...

void	FitScaleFactorForIntegratedRw () const

void	SetSigmaToSqrtIobs ()
	Set sigma=sqrt(Iobs)

void	SetWeightToInvSigmaSq (const REAL minRelatSigma=1e-3)
	Set w = 1/sigma^2. More...

void	SetWeightToUnit ()
	Set w = 1.

void	SetWeightPolynomial (const REAL a, const REAL b, const REAL c, const REAL minRelatIobs=1e-3)
	Set w = 1/(a+ Iobs + bIobs^2+cIobs^3) More...

void	AddExcludedRegion (const REAL min2Theta, const REAL max2theta)
	Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be, as always, in radians. More...

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

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...

void	Prepare ()

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

virtual void	SetMaxSinThetaOvLambda (const REAL max)
	Set the maximum value for sin(theta)/lambda. More...

REAL	GetMaxSinThetaOvLambda () const
	Get the maximum value for sin(theta)/lambda.

const CrystVector_long &	GetIntegratedProfileMin () const
	Get the list of first pixels for the integration intervals.

const CrystVector_long &	GetIntegratedProfileMax () const
	Get the list of last pixels for the integration intervals.

const RefinableObjClock &	GetIntegratedProfileLimitsClock () const
	When were the integration intervals last changed ?

REAL	X2XCorr (const REAL x) const
	Get the experimental x (2theta, tof) from the theoretical value, taking into account all corrections (zero, transparency,..). More...

REAL	X2PixelCorr (const REAL x) const
	Get the pixel number on the experimental pattern, from the theoretical (uncorrected) x coordinate, taking into account all corrections. More...

REAL	X2Pixel (const REAL x) const
	Get the pixel number on the experimental pattern, corresponding to a given (experimental) x coordinate. More...

REAL	STOL2X (const REAL stol) const
	Convert sin(theta)/lambda to X (i.e. More...

REAL	X2STOL (const REAL x) const
	Convert X (either 2theta or TOF) to sin(theta)/lambda, depending on the type of radiation. More...

REAL	STOL2Pixel (const REAL stol) const
	Convert sin(theta)/lambda to pixel, depending on the type of radiation. More...

PeakList	FindPeaks (const float dmin=2.0, const float maxratio=0.01, const unsigned int maxpeak=100)
	Find peaks in the pattern.

const CrystVector_REAL &	GetScaleFactor () const
	Access the scale factors (see PowderPattern::mScaleFactor)

CrystVector_REAL &	GetScaleFactor ()
	Access the scale factors (see PowderPattern::mScaleFactor)

void	ExportFullprof (const std::string &prefix) const
	Export powder pattern & crystal structure in Fullprof format. More...

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	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...

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

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

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
void	CalcPowderPattern () const
	Calc the powder pattern.

void	CalcPowderPattern_FullDeriv (std::set< RefinablePar * > &vPar)

void	CalcPowderPatternIntegrated () const
	Calc the integrated powder pattern.

void	CalcPowderPatternIntegrated_FullDeriv (std::set< RefinablePar * > &vPar)

virtual void	Init ()
	Init parameters and options.

void	PrepareIntegratedRfactor () const
	Prepare the calculation of the integrated R-factors.

void	CalcNbPointUsed () const
	Calculate the number of points of the pattern actually used, from the maximum value of sin(theta)/lambda.

virtual void	InitOptions ()
	Initialize options.

Number of points actually due to the maximum value of	sin (theta)/lambda.mutable unsigned long mNbPointUsed

Number of integration intervals actually due to the maximum value of	sin (theta)/lambda.mutable unsigned long mNbIntegrationUsed

Clock recording the last time the number of points	used (PowderPattern::mNbPointUsed) was changed.mutable RefinableObjClock mClockNbPointUsed

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)

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
CrystVector_REAL	mPowderPatternCalc
	The calculated powder pattern. More...

std::map< RefinablePar *, CrystVector_REAL >	mPowderPattern_FullDeriv

CrystVector_REAL	mPowderPatternIntegratedCalc
	The calculated powder pattern, integrated.

std::map< RefinablePar *, CrystVector_REAL >	mPowderPatternIntegrated_FullDeriv

CrystVector_REAL	mPowderPatternBackgroundCalc
	The calculated powder pattern part which corresponds to 'background' (eg non-scalable components). More...

CrystVector_REAL	mPowderPatternBackgroundIntegratedCalc
	The calculated powder pattern part which corresponds to 'background' (eg non-scalable components), integrated.

CrystVector_REAL	mPowderPatternObs
	The observed powder pattern.

CrystVector_REAL	mPowderPatternObsSigma
	The sigma of the observed pattern.

CrystVector_REAL	mPowderPatternWeight
	The weight for each point of the pattern.

CrystVector_REAL	mPowderPatternVariance
	The complete variance associated to each point of the powder pattern, taking into account observation and model errors. More...

CrystVector_REAL	mPowderPatternVarianceIntegrated
	The complete variance associated to each point of the powder pattern, taking into account observation and model errors. More...

CrystVector_REAL	mChi2Cumul
	The cumulative Chi^2 (integrated or not, depending on the option)

CrystVector_REAL	mPowderPatternUsedCalc
	The calculated powder pattern. Cropped to the maximum sin(theta)/lambda for LSQ.

std::map< RefinablePar *, CrystVector_REAL >	mPowderPatternUsed_FullDeriv

CrystVector_REAL	mPowderPatternUsedObs
	The calculated powder pattern. Cropped to the maximum sin(theta)/lambda for LSQ.

CrystVector_REAL	mPowderPatternUsedWeight
	The weight for each point of the pattern. Cropped to the maximum sin(theta)/lambda for LSQ.

CrystVector_REAL	mX
	Vector of x coordinates (either 2theta or time-of-flight) for the pattern. More...

bool	mIsXAscending
	Is the mX vector sorted in ascending order ? (true for 2theta, false for TOF)

unsigned long	mNbPoint
	Number of points in the pattern.

Radiation	mRadiation
	The Radiation corresponding to this experiment.

RefinableObjClock	mClockPowderPatternPar
	When were the pattern parameters (2theta or time-of-flight range) changed ?

RefinableObjClock	mClockPowderPatternRadiation
	When were the radiation parameter (radiation type, wavelength) changed ?

RefinableObjClock	mClockPowderPatternCalc
	When was the powder pattern last computed ?

RefinableObjClock	mClockPowderPatternIntegratedCalc
	When was the powder pattern (integrated) last computed ?

RefinableObjClock	mClockPowderPatternXCorr
	Corrections to 2Theta.

RefinableObjClock	mClockScaleFactor
	Last modification of the scale factor.

CrystVector_REAL	mExcludedRegionMinX
	Min coordinate for for all excluded regions.

CrystVector_REAL	mExcludedRegionMaxX
	Max coordinate for 2theta for all excluded regions.

REAL	mXZero
	Zero correction : $(2\theta)_{obs} = (2\theta)_{real} +(2\theta)_{0}$ Thus mPowderPattern2ThetaMin=(mPowderPattern2ThetaMin-m2ThetaZero)

REAL	mMaxSinThetaOvLambda
	Displacement correction : $(2\theta)_{obs} = (2\theta)_{real} + \frac{a}{\cos(\theta)}$ REAL m2ThetaDisplacement; Transparency correction : $(2\theta)_{obs} = (2\theta)_{real} + b\sin(2\theta)$ REAL m2ThetaTransparency; Time Of Flight (TOF) parameters : $t = DIFC\frac{\sin(\theta)}{\lambda} + DIFA\left(\frac{\sin(\theta)}{\lambda}\right)^2 + mXZero$ REAL mDIFC,mDIFA; Components of the powder pattern The components (crystalline phases, background,...) of the powder pattern ObjRegistry<PowderPatternComponent> mPowderPatternComponentRegistry; The scale factors for each component. More...

Number of points actually	used

Number of integration intervals actually	used

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

Powder pattern class, with an observed pattern and several calculated components to modelize the pattern.

This can also be used for simulation, using a fake Iobs. Supports multiple phases.

Definition at line 534 of file PowderPattern.h.

Member Function Documentation

void ObjCryst::PowderPattern::AddExcludedRegion	(	const REAL	min2Theta,
		const REAL	max2theta
	)

Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be, as always, in radians.

Does not work yet with integrated R factors. Note that the pattern is still computed in these regions. They are only ignored by statistics functions (R, Rws).

Definition at line 5062 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::AddPowderPatternComponent ( PowderPatternComponent & comp )

Add a component (phase, backround) to this pattern.

It must have been allocated in the heap. The pattern parameters (2theta min, step, nbpoints, wavelength, radiation type) of the component are automatically changed to that of the PowderPattern object.

Definition at line 2430 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::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 from ObjCryst::RefinableObj.

Definition at line 5038 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ExportFullprof ( const std::string & prefix ) const

Export powder pattern & crystal structure in Fullprof format.

This will create two files - the .pcr file (including the crystal structure and all pattern parameters), and the .dat file with the powder pattern, written using the "Ins=10" file format.

Parameters

prefix the prefix used to output the two files, 'prefix'.pcr and 'prefix'.dat

Note: : in development. Only supports constant wavelength neutron & X-ray patterns.

Definition at line 5500 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::FitScaleFactorForR ( ) const

Fit the scale(s) factor of each component to minimize R.

min is the beginning of the excluded region

Definition at line 4245 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::FitScaleFactorForRw ( ) const

Fit the scale(s) factor of each component to minimize Rw.

min is the beginning of the excluded region

Definition at line 4561 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetChi2 ( ) const

Return conventionnal Chi^2.

Returns: $\chi^2 = \sum_i w_i \left(I_i^{obs}-I_i^{calc} \right)^2$

min is the beginning of the excluded region !

Definition at line 4106 of file PowderPattern.cpp.

const CrystVector_REAL & ObjCryst::PowderPattern::GetChi2Cumul ( ) const

Get the powder pattern cumulative Chi^2.

Depending on the chosen option, it will be calculated in an integrated manner or not.

The vector is recomputed on every call, so this is slow.

Definition at line 2634 of file PowderPattern.cpp.

const string & ObjCryst::PowderPattern::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 2424 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::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 from ObjCryst::RefinableObj.

Definition at line 5213 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetIntegratedChi2 ( ) const

Return integrated Chi^2.

Definition at line 4185 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::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 from ObjCryst::RefinableObj.

Definition at line 5094 of file PowderPattern.cpp.

std::map< RefinablePar *, CrystVector_REAL > & ObjCryst::PowderPattern::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 from ObjCryst::RefinableObj.

Definition at line 5174 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetPowderPatternXStep ( ) const

Get the average step in 2theta.

Warning: : this will only return (2ThetaMax-2ThetaMin)/(nbPoints-1), so this is the 2theta step only if the step is fixed.

Deprecated:

Definition at line 2617 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetR ( ) const

Unweighted R-factor.

Returns: $R= \sqrt {\frac{\sum_i \left( I_i^{obs}-I_i^{calc} \right)^2} {\sum_i (I_i^{obs})^2} }$

min is the beginning of the excluded region !

Definition at line 3710 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetRw ( ) const

Get the weighted R-factor.

Returns: $R_{w}= \sqrt {\frac{\sum_i w_i\left( I_i^{obs}-I_i^{calc} \right)^2} {\sum_i w_i (I_i^{obs})^2} }$

min is the beginning of the excluded region !

Definition at line 3903 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::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 from ObjCryst::RefinableObj.

Definition at line 5055 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPattern2ThetaObs	(	const string &	fileName,
		const int	nbSkip = `0`
	)

Import file with 2 columns 2Theta Iobs.

Parameters

fileName	the filename (surprise!)
nbSkip	the number of lines to skip at the beginning of the file (default=0)

Definition at line 3109 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPattern2ThetaObsSigma	(	const string &	fileName,
		const int	nbSkip = `0`
	)

Import file with 3 columns 2Theta Iobs Sigma.

Parameters

fileName	the filename (surprise!)
nbSkip	the number of lines to skip at the beginning of the file (default=0)

Definition at line 3049 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternFullprof ( const string & fullprofFileName )

Import fullprof-style diffraction data.

Parameters

fullprofFileName filename

Definition at line 2820 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternFullprof4 ( const string & fileName )

Import diffraction data from a file, with the first line has 2ThetaMin, step, 2thetaMax, and the following lines alternate 10 Iobs and 10 sigma.

Ends with null entries (to fill last Iobs line to reach last sigme line).

That's fullprof format #4.

Parameters

fileName filename

Definition at line 3249 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternGSAS ( const string & fileName )

Import GSAS standard powder pattern data (see GSAS manual).

Warning: : partial support (only CONST-constant wavelength- data so far)

Definition at line 3389 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternMultiDetectorLLBG42 ( const string & fileName )

diffraction data in a multi-detector format (fullprof format #6).

First line is text. Third entry of second line is the 2theta step. Third line has the 2thetamin, fourth line has monitors and temperatures. Then each line has ten pairs (I2,I8)of NbCounters,intensity. Ends with negative entries.

Parameters

fileName filename

Definition at line 3167 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternSietronicsCPI ( const string & fileName )

Import *.cpi Sietronics diffraction data.

Parameters

fileName filename

Definition at line 3001 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternTOF_ISIS_XYSigma ( const string & fileName )

Import TOF file (ISIS type, 3 columns t, Iobs, sigma(Iobs))

Parameters

fileName the filename

Definition at line 3312 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ImportPowderPatternXdd ( const string & fileName )

Import *.xdd diffraction data (Topas,...).

Parameters

fileName filename

Definition at line 2958 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::Prepare ( )

virtual

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

Reimplemented from ObjCryst::RefinableObj.

Definition at line 5204 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SavePowderPattern ( const string & filename = "powderPattern.out" ) const

Save powder pattern to one file, text format, 3 columns theta Iobs Icalc.

If Iobs is missing, the column is omitted.

Todo:: export in other formats (.prf,...), with a list of reflection position for all phases...

Definition at line 3675 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetMaxSinThetaOvLambda ( const REAL max )

virtual

Set the maximum value for sin(theta)/lambda.

All data (reflections,..) still exist but are ignored for all calculations.

Definition at line 5238 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetPowderPatternObs ( const CrystVector_REAL & obs )

Set observed powder pattern from vector array.

Note: powder pattern parameters must have been set before calling this function, for example by calling DiffractionDataPowder::InitPowderPatternPar().

Definition at line 3650 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetPowderPatternPar	(	const REAL	min,
		const REAL	step,
		unsigned long	nbPoint
	)

the powder pattern angular range & resolution parameter.

this will affect all components (phases) of the pattern.

Use this with caution, as the number of points must be correct with respect to the observed data (Iobs).

Parameters

min	min 2theta (in radians) or time-of-flight (in microseconds) value,
step	step (assumed constant) in 2theta or time-of-flight (in microseconds).
nbPoints	number of points in the pattern.

Warning: : use only this for constant-step patterns. Otherwise, use PowderPattern::SetPowderPatternX()

Definition at line 2513 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetPowderPatternX ( const CrystVector_REAL & x )

Set the x coordinate of the powder pattern : either the 2theta or time-of-flight values for each recorded point.

The step need not be constant, but the variation must be strictly monotonous.

2theta must be in radians and time-of-flight in microseconds

Definition at line 2526 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetWavelength ( const REAL lambda )

Set the wavelength of the experiment (in Angstroems).

Note: : this is only useful for a monochromatic (X-Ray or neutron) powder pattern.

Definition at line 2564 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetWavelength	(	const string &	XRayTubeElementName,
		const REAL	alpha12ratio = `0.5`
	)

Set the wavelength of the experiment to that of an X-Ray tube.

Parameters

XRayTubeElementName	: name of the anticathode element name. Known ones are Cr, Fe, Cu, Mo, Ag.
alpha2Alpha2ratio	Kalpha2/Kalpha1 ratio (0.5 by default)

Alpha1 and alpha2 wavelength are taken from R. Grosse-Kunstleve package, and the average wavelength is calculated using the alpha2/alpha1 weight. All structure factors computation are made using the average wavelength, and for powder diffraction, profiles are output at the alpha1 and alpha2 ratio for the calculated pattern.

NOTE : if the name of the wavelength is generic (eg"Cu"), then the program considers that there are both Alpha1 and Alpha2, and thus automatically changes the WavelengthType to WAVELENGTH_ALPHA12. If instead either alpha1 or alpha2 (eg "CuA1") is asked for, the WavelengthType is set to WAVELENGTH_MONOCHROMATIC. In both cases, the radiation type is set to X-Ray.

Definition at line 2570 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetWeightPolynomial	(	const REAL	a,
		const REAL	b,
		const REAL	c,
		const REAL	minRelatIobs = `1e-3`
	)

Set w = 1/(a+ Iobs + b*Iobs^2+c*Iobs^3)

To filter too small or null intensities: if Iobs < [minRelatIobs * max(Iobs)], then use Iobs=minRelatIobs * max(Iobs) to compute the weight.

Typical values: a=2*min(Iobs) b=2/max(Iobs) c=0

Definition at line 5022 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::SetWeightToInvSigmaSq ( const REAL minRelatSigma = 1e-3 )

Set w = 1/sigma^2.

To filter too small or null intensities :If sigma< minRelatSigma* max(sigma), then w=1/(minRelatSigma* max(sigma))^2

Definition at line 5002 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::STOL2Pixel ( const REAL stol ) const

Convert sin(theta)/lambda to pixel, depending on the type of radiation.

This does not take into account any zero/transparency, etc... correction

Definition at line 5295 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::STOL2X ( const REAL stol ) const

Convert sin(theta)/lambda to X (i.e.

either to 2theta or to TOF), depending on the type of radiation.

This does not take into account any zero/transparency, etc... correction

Definition at line 5259 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::X2Pixel ( const REAL x ) const

Get the pixel number on the experimental pattern, corresponding to a given (experimental) x coordinate.

Parameters

x	the x (2theta, tof) value.

Returns: the x (2theta, tof) value as it appears on the pattern.

Warning: : this can be real slow, especially for non-fixed steps.; : this returns the exact pixel coordinate, as a floating-point value, and not the closest pixel coordinate.

Definition at line 2735 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::X2PixelCorr ( const REAL x ) const

Get the pixel number on the experimental pattern, from the theoretical (uncorrected) x coordinate, taking into account all corrections.

(zero, transparency,..).

Parameters

x	the theoretical x (2theta, tof) value.

Returns: the x (2theta, tof) value as it appears on the pattern.

Warning: : this can be real slow, especially for non-fixed steps.; : this returns the exact pixel coordinate, as a floating-point value, and not the closest pixel coordinate.

Definition at line 2730 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::X2STOL ( const REAL x ) const

Convert X (either 2theta or TOF) to sin(theta)/lambda, depending on the type of radiation.

This does not take into account any zero/transparency, etc... correction

Definition at line 5276 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::X2XCorr ( const REAL x ) const

Get the experimental x (2theta, tof) from the theoretical value, taking into account all corrections (zero, transparency,..).

Parameters

ttheta the theoretical x (2theta, tof) value.

Returns: the x (2theta, tof) value as it appears on the pattern.

Definition at line 2720 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::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 from ObjCryst::RefinableObj.

Definition at line 2084 of file ObjCryst/IO.cpp.

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

virtual

Output to stream in well-formed XML.

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

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1977 of file ObjCryst/IO.cpp.

Member Data Documentation

REAL ObjCryst::PowderPattern::mMaxSinThetaOvLambda

protected

Displacement correction : $(2\theta)_{obs} = (2\theta)_{real} + \frac{a}{\cos(\theta)}$ REAL m2ThetaDisplacement; Transparency correction : $(2\theta)_{obs} = (2\theta)_{real} + b\sin(2\theta)$ REAL m2ThetaTransparency; Time Of Flight (TOF) parameters : $t = DIFC*\frac{\sin(\theta)}{\lambda} + DIFA*\left(\frac{\sin(\theta)}{\lambda}\right)^2 + mXZero$ REAL mDIFC,mDIFA; Components of the powder pattern The components (crystalline phases, background,...) of the powder pattern ObjRegistry<PowderPatternComponent> mPowderPatternComponentRegistry; The scale factors for each component.

For unscalable phases, this is set to 1 (constant).

This is mutable because generally we use the 'best' scale factor, but it should not be... mutable CrystVector_REAL mScaleFactor;

Use faster, less precise functions ? bool mUseFastLessPreciseFunc;

For statistics Should Statistics (R, Rw,..) exclude the background ? bool mStatisticsExcludeBackground;

To compute scale factors, which are the components (phases) that can be scaled ? mutable CrystVector_int mScalableComponentIndex;

Used to fit the components' scale factors mutable CrystMatrix_REAL mFitScaleFactorM,mFitScaleFactorB,mFitScaleFactorX;

Use Integrated profiles for Chi^2, R, Rwp... RefObjOpt mOptProfileIntegration;

Integrated R-factors mutable CrystVector_long mIntegratedPatternMin,mIntegratedPatternMax; mutable CrystVector_REAL mIntegratedObs; mutable CrystVector_REAL mIntegratedWeight; mutable CrystVector_REAL mIntegratedWeightObs; mutable CrystVector_REAL mIntegratedVarianceObs; mutable RefinableObjClock mClockIntegratedFactorsPrep; Statistical indicators mutable REAL mChi2,mIntegratedChi2; This is the logarithm of the part of log(Likelihood) which corresponds to the normalization terms of gaussian distribution for each obs/calc point. In practice, this is the sum of 1/2*log(2pi*sig(i)^2), although we discard the 2pi terms. mutable REAL mChi2LikeNorm,mIntegratedChi2LikeNorm; mutable REAL mR; mutable REAL mRw; Clock the last time Chi^2 was computed mutable RefinableObjClock mClockChi2,mClockIntegratedChi2; /** Maximum sin(theta)/lambda for all calculations (10 by default).

This keeps all data in memory, but only the part which is below the max is calculated.

Definition at line 1079 of file PowderPattern.h.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternBackgroundCalc

mutableprotected

The calculated powder pattern part which corresponds to 'background' (eg non-scalable components).

It is already included in mPowderPatternCalc

Definition at line 955 of file PowderPattern.h.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternCalc

mutableprotected

The calculated powder pattern.

It is mutable since it is completely defined by other parameters (eg it is not an 'independent parameter')

Definition at line 948 of file PowderPattern.h.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternVariance

mutableprotected

The complete variance associated to each point of the powder pattern, taking into account observation and model errors.

Definition at line 967 of file PowderPattern.h.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternVarianceIntegrated

mutableprotected

The complete variance associated to each point of the powder pattern, taking into account observation and model errors.

Integrated.

Definition at line 970 of file PowderPattern.h.

CrystVector_REAL ObjCryst::PowderPattern::mX

protected

Vector of x coordinates (either 2theta or time-of-flight) for the pattern.

Stored in ascending order for 2theta, and descending for TOF, i.e. always in ascending order for the corresponding sin(theta)/lambda.

Definition at line 988 of file PowderPattern.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation