Class to compute the contribution to a powder pattern from a crystalline phase. More...

Inheritance diagram for ObjCryst::PowderPatternDiffraction:

Collaboration diagram for ObjCryst::PowderPatternDiffraction:

Classes
struct	ReflProfile
	Profile of a single reflection. More...

Public Member Functions
	PowderPatternDiffraction (const PowderPatternDiffraction &)

virtual PowderPatternDiffraction *	CreateCopy () const
	So-called virtual copy constructor.

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

virtual void	SetParentPowderPattern (PowderPattern &)
	Set the PowderPattern object which uses this component. More...

virtual const CrystVector_REAL &	GetPowderPatternCalc () const
	Get the calculated powder pattern for this component. More...

virtual pair< const CrystVector_REAL , const RefinableObjClock >	GetPowderPatternIntegratedCalc () const
	Get the integrated values of the powder pattern. More...

void	SetReflectionProfilePar (const ReflectionProfileType prof, const REAL fwhmCagliotiW, const REAL fwhmCagliotiU=0, const REAL fwhmCagliotiV=0, const REAL eta0=0.5, const REAL eta1=0.)
	Set reflection profile parameters. More...

void	SetProfile (ReflectionProfile *prof)
	Assign a new profile. More...

const ReflectionProfile &	GetProfile () const
	Get reflection profile.

ReflectionProfile &	GetProfile ()
	Get reflection profile.

virtual void	GenHKLFullSpace ()

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

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

virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. 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	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 const Radiation &	GetRadiation () const
	Get the radiation object for this data.

virtual const CrystVector_REAL &	GetPowderPatternCalcVariance () const
	Get the variance associated to each point of the calculated powder pattern, for this component. More...

virtual pair< const CrystVector_REAL , const RefinableObjClock >	GetPowderPatternIntegratedCalcVariance () const
	Get the variance associated to each point of the calculated powder pattern, for this component (integrated version). More...

virtual bool	HasPowderPatternCalcVariance () const
	Does this component have a variance associated with each calculated point ? i.e., do we use maximum likelihood to take into account incomplete models ?

virtual void	SetCrystal (Crystal &crystal)
	Set the crystal for this experiment. More...

void	SetExtractionMode (const bool extract=true, const bool init=false)
	Prepare intensity extraction (Le Bail or Pawley) More...

bool	GetExtractionMode () const
	Return true if in extraction mode, i.e. using extracted intensities instead of computed structure factors.

void	ExtractLeBail (unsigned int nbcycle=1)
	Extract intensities using Le Bail method. More...

virtual long	GetNbReflBelowMaxSinThetaOvLambda () const
	Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(theta)/lambda value set. More...

void	SetFrozenLatticePar (const unsigned int i, REAL v)
	Change one parameter in mFrozenLatticePar. This triggers a call to CalcLocalBMatrix() if the parameter has changed.

REAL	GetFrozenLatticePar (const unsigned int i) const
	Access to one parameter in mFrozenLatticePar.

void	FreezeLatticePar (const bool use)
	Set the use local cell parameters ? (see mFrozenLatticePar) If this changes mUseLocalLatticePar from false to true, this triggers a copy of the Crystal's lattice parameters into mFrozenLatticePar.

bool	FreezeLatticePar () const
	Do we use local cell parameters ? (see mFrozenLatticePar)

Public Member Functions inherited from ObjCryst::PowderPatternComponent
	PowderPatternComponent (const PowderPatternComponent &)

const PowderPattern &	GetParentPowderPattern () const
	Get the PowderPattern object which uses this component. More...

PowderPattern &	GetParentPowderPattern ()
	Get the PowderPattern object which uses this component. More...

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

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

bool	IsScalable () const
	Is this component scalable ? More...

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

const list< pair< const REAL,const string > > &	GetPatternLabelList () const
	Get a list of labels for the pattern (usually reflection indexes). 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	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

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.

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

virtual void	SetHKL (const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l)
	input H,K,L More...

virtual void	GenHKLFullSpace2 (const REAL maxsithsl, const bool unique=false)
	Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value. More...

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

const Crystal &	GetCrystal () const
	Const access to the data's crystal.

Crystal &	GetCrystal ()
	Access to the data's crystal.

bool	HasCrystal () const
	Has a Crystal structure associated yet ?

long	GetNbRefl () const
	Return the number of reflections in this experiment.

const CrystVector_REAL &	GetH () const
	Return the 1D array of H coordinates for all reflections.

const CrystVector_REAL &	GetK () const
	Return the 1D array of K coordinates for all reflections.

const CrystVector_REAL &	GetL () const
	Return the 1D array of L coordinates for all reflections.

const CrystVector_REAL &	GetH2Pi () const
	Return the 1D array of H coordinates for all reflections, multiplied by 2*pi. More...

const CrystVector_REAL &	GetK2Pi () const
	Return the 1D array of K coordinates for all reflections, multiplied by 2*pi. More...

const CrystVector_REAL &	GetL2Pi () const
	Return the 1D array of L coordinates for all reflections, multiplied by 2*pi. More...

const CrystVector_REAL &	GetReflX () const
	Return the 1D array of orthonormal x coordinates for all reflections (recipr. space)

const CrystVector_REAL &	GetReflY () const
	Return the 1D array of orthonormal y coordinates for all reflections (recipr. space)

const CrystVector_REAL &	GetReflZ () const
	Return the 1D array of orthonormal z coordinates for all reflections (recipr. space)

const CrystVector_REAL &	GetSinThetaOverLambda () const
	Return an array with $\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for all reflections.

const CrystVector_REAL &	GetTheta () const
	Return an array with theta values for all reflections.

const RefinableObjClock &	GetClockTheta () const
	Clock the last time the sin(theta)/lambda and theta arrays were re-computed.

const CrystVector_REAL &	GetFhklCalcSq () const
	Returns the Array of calculated \|F(hkl)\|^2 for all reflections.

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

const CrystVector_REAL &	GetFhklCalcReal () const
	Access to real part of F(hkl)calc.

const CrystVector_REAL &	GetFhklCalcImag () const
	Access to imaginary part of F(hkl)calc.

const CrystVector_REAL &	GetFhklObsSq () const
	Returns the Array of observed \|F(hkl)\|^2 for all reflections.

const map< const ScatteringPower *, CrystVector_REAL > &	GetScatteringFactor () const
	Scattering factors for each ScatteringPower, as vectors with NbRefl elements.

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

void	SetIsIgnoringImagScattFact (const bool b)
	If true, then the imaginary part of the scattering factor is ignored during Structure factor computation. More...

bool	IsIgnoringImagScattFact () const
	If true, then the imaginary part of the scattering factor is ignored during Structure factor computation. More...

virtual void	PrintFhklCalc (ostream &os=cout) const
	Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections. More...

virtual void	PrintFhklCalcDetail (ostream &os=cout) const
	Print H, K, L sin(theta)/lambda theta F^2 Re(F) Im(F) [Re(F) Im(F)]_i, where [Re(F) Im(F)]_i are the real and imaginary contribution of the different scattering powers to the overall structure factor.

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

const RefinableObjClock &	GetClockNbReflBelowMaxSinThetaOvLambda () const
	Clock the last time the number of reflections used was changed.

Protected Member Functions
virtual void	CalcPowderPattern () const
	Calc the powder pattern. More...

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

virtual void	CalcPowderPatternIntegrated () const

virtual void	CalcPowderPatternIntegrated_FullDeriv (std::set< RefinablePar * > &vPar)
	Calc the integrated powder pattern. More...

void	CalcPowderReflProfile () const

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

void	CalcIntensityCorr () const

virtual void	CalcIhkl () const

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

virtual void	Prepare ()

virtual void	InitOptions ()

virtual const CrystVector_long &	GetBraggLimits () const
	Get the pixel positions separating the integration intervals around reflections. More...

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

virtual const CrystMatrix_REAL &	GetBMatrix () const
	This can use either locally stored lattice parameters from mLocalLatticePar, or the Crystal's, depending on mUseLocalLatticePar. More...

void	CalcFrozenBMatrix () const
	Calculate the local BMatrix, used if mFreezeLatticePar is true.

void	PrepareIntegratedProfile () const

Protected Member Functions inherited from ObjCryst::PowderPatternComponent
const RefinableObjClock &	GetClockPowderPatternCalcVariance () const
	Last time the variance on the pattern was actually calculated.

const RefinableObjClock &	GetClockBraggLimits () const
	Get last time the Bragg Limits were changed.

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 Member Functions inherited from ObjCryst::ScatteringData
virtual void	PrepareHKLarrays ()

virtual CrystVector_long	SortReflectionBySinThetaOverLambda (const REAL maxSTOL=-1.)

CrystVector_long	EliminateExtinctReflections ()

virtual void	CalcSinThetaLambda () const

REAL	CalcSinThetaLambda (REAL h, REAL k, REAL l) const
	Calculate sin(theta)/lambda for a single reflection.

void	CalcScattFactor () const

void	CalcTemperatureFactor () const

virtual void	CalcResonantScattFactor () const

void	CalcGlobalTemperatureFactor () const
	Compute the overall temperature factor affecting all reflections.

void	CalcStructFactor () const
	Compute the overall structure factor (real and imaginary part). More...

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

void	CalcGeomStructFactor () const
	Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal. More...

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

void	CalcLuzzatiFactor () const
	Calculate the Luzzati factor associated to each ScatteringPower and each reflection, for maximum likelihood optimization.

void	CalcStructFactVariance () const
	Calculate the variance associated to the calculated structure factor. More...

Protected Attributes
RefinableObjClock	mClockProfilePar
	Last time the reflection parameters were changed.

RefinableObjClock	mClockLorentzPolarSlitCorrPar
	Last time the Lorentz-Polarization and slit parameters were changed.

RefinableObjClock	mClockIntensityCorr
	Last time the Lorentz-Polar-Slit correction was computed.

RefinableObjClock	mClockProfileCalc
	Last time the reflection profiles were computed.

RefinableObjClock	mClockIhklCalc
	Last time intensities were computed.

ReflectionProfile *	mpReflectionProfile
	Profile.

CrystVector_REAL	mIntensityCorr
	Calculated corrections for all reflections. More...

LorentzCorr	mCorrLorentz
	Lorentz correction.

PolarizationCorr	mCorrPolar
	Polarization correction.

PowderSlitApertureCorr	mCorrSlitAperture
	Slit aperture correction.

TextureMarchDollase	mCorrTextureMarchDollase
	Preferred orientation (texture) correction following the March-Dollase model.

TextureEllipsoid	mCorrTextureEllipsoid
	Preferred orientation (texture) correction following the Ellipsoidal function.

TOFCorr	mCorrTOF
	Time-Of-Flight intensity correction.

CrystVector_REAL	mIhklCalc
	Computed intensities for all reflections.

std::map< RefinablePar *, CrystVector_REAL >	mIhkl_FullDeriv

CrystVector_REAL	mIhklCalcVariance
	Variance on computed intensities for all reflections.

vector< ReflProfile >	mvReflProfile
	Reflection profiles for ALL reflections during the last powder pattern generation.

std::map< RefinablePar *, vector< CrystVector_REAL > >	mvReflProfile_FullDeriv
	Derivatives of reflection profiles versus a list of parameters. More...

vector< pair< unsigned long, CrystVector_REAL > >	mIntegratedProfileFactor
	For each reflection, store the integrated value of the normalized profile over all integration intervals. More...

RefinableObjClock	mClockIntegratedProfileFactor
	Last time the integrated values of normalized profiles was calculated.

bool	mExtractionMode
	Extraction mode (Le Bail, Pawley)

DiffractionDataSingleCrystal *	mpLeBailData
	Single crystal data extracted from the powder pattern.

CrystVector_REAL	mFrozenLatticePar
	a,b and c in Angstroems, angles (stored) in radians This is used to override lattice parameter from the Crystal structure, e.g. More...

bool	mFreezeLatticePar
	If true, use local cell parameters from mFrozenLatticePar rather than the Crystal.

CrystMatrix_REAL	mFrozenBMatrix
	Local B Matrix, used if mFreezeLatticePar is true.

Protected Attributes inherited from ObjCryst::PowderPatternComponent
CrystVector_REAL	mPowderPatternCalc
	The calculated component of a powder pattern. More...

CrystVector_REAL	mPowderPatternIntegratedCalc
	The calculated powder pattern, integrated.

CrystVector_REAL	mPowderPatternCalcVariance
	The variance associated to each point of the calculated powder pattern.

CrystVector_REAL	mPowderPatternIntegratedCalcVariance
	The variance associated to each point of the calculated powder pattern, integrated.

CrystVector_long	mIntegratedReflLimits
	Interval limits around each reflection, for integrated R-factors.

bool	mIsScalable
	Scalable ? (crystal phase = scalable, background= not scalable)

RefinableObjClock	mClockPowderPatternCalc
	When was the powder pattern last computed ?

RefinableObjClock	mClockPowderPatternIntegratedCalc
	When was the 'integrated' powder pattern last computed ?

RefinableObjClock	mClockPowderPatternVarianceCalc
	When was the powder pattern variance last computed ?

RefinableObjClock	mClockPowderPatternIntegratedVarianceCalc
	When was the 'integrated' powder pattern variance last computed ?

PowderPattern *	mpParentPowderPattern
	The PowderPattern object in which this component is included.

RefinableObjClock	mClockBraggLimits
	Get last time the Bragg Limits were changed.

list< pair< const REAL,const string > >	mvLabel
	The labels associated to different points of the pattern.

std::map< RefinablePar *, CrystVector_REAL >	mPowderPattern_FullDeriv

std::map< RefinablePar *, CrystVector_REAL >	mPowderPatternIntegrated_FullDeriv

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...

Protected Attributes inherited from ObjCryst::ScatteringData
long	mNbRefl
	Number of H,K,L reflections.

CrystVector_REAL	mH
	H,K,L coordinates.

CrystVector_REAL	mK

CrystVector_REAL	mL

CrystVector_long	mIntH
	H,K,L integer coordinates.

CrystVector_long	mIntK

CrystVector_long	mIntL

CrystVector_REAL	mH2Pi
	H,K,L coordinates, multiplied by 2PI.

CrystVector_REAL	mK2Pi

CrystVector_REAL	mL2Pi

CrystVector_REAL	mX
	reflection coordinates in an orthonormal base

CrystVector_REAL	mY

CrystVector_REAL	mZ

CrystVector_int	mMultiplicity
	Multiplicity for each reflections (mostly for powder diffraction)

CrystVector_int	mExpectedIntensityFactor
	Expected intensity factor for all reflections. More...

CrystVector_REAL	mFhklCalcReal
	real &imaginary parts of F(HKL)calc

CrystVector_REAL	mFhklCalcImag

std::map< RefinablePar *, CrystVector_REAL >	mFhklCalcReal_FullDeriv

std::map< RefinablePar *, CrystVector_REAL >	mFhklCalcImag_FullDeriv

CrystVector_REAL	mFhklCalcSq
	F(HKL)^2 calc for each reflection.

std::map< RefinablePar *, CrystVector_REAL >	mFhklCalcSq_FullDeriv

Crystal *	mpCrystal
	Pointer to the crystal corresponding to this experiment. More...

REAL	mGlobalBiso
	Global Biso, affecting the overall structure factor for all reflections (but not the structure factors of individual atoms or type of atomes).

CrystVector_REAL	mGlobalTemperatureFactor
	Global Biso factor.

bool	mUseFastLessPreciseFunc
	Use faster, but less precise, approximations for functions? (integer approximations to compute sin and cos in structure factors, and also to compute interatomic distances). More...

CrystVector_REAL	mSinThetaLambda
	$\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for the crystal and the reflections in ReciprSpace

CrystVector_REAL	mTheta
	theta for the crystal and the HKL in ReciprSpace (in radians)

map< const ScatteringPower *, REAL >	mvFprime
	Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value. More...

map< const ScatteringPower *, REAL >	mvFsecond

map< const ScatteringPower *, CrystVector_REAL >	mvTemperatureFactor
	Thermic factors for each ScatteringPower, as vectors with NbRefl elements.

map< const ScatteringPower *, CrystVector_REAL >	mvScatteringFactor
	Scattering factors for each ScatteringPower, as vectors with NbRefl elements.

map< const ScatteringPower *, CrystVector_REAL >	mvRealGeomSF
	Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements.

map< const ScatteringPower *, CrystVector_REAL >	mvImagGeomSF

map< RefinablePar , map < const ScatteringPower , CrystVector_REAL > >	mvRealGeomSF_FullDeriv

map< RefinablePar , map < const ScatteringPower , CrystVector_REAL > >	mvImagGeomSF_FullDeriv

RefinableObjClock	mClockHKL
	Clock for the list of hkl.

RefinableObjClock	mClockStructFactor
	Clock for the structure factor.

RefinableObjClock	mClockStructFactorSq
	Clock for the square modulus of the structure factor.

RefinableObjClock	mClockTheta
	Clock the last time theta was computed.

RefinableObjClock	mClockScattFactor
	Clock the last time scattering factors were computed.

RefinableObjClock	mClockScattFactorResonant
	Clock the last time resonant scattering factors were computed.

RefinableObjClock	mClockGeomStructFact
	Clock the last time the geometrical structure factors were computed.

RefinableObjClock	mClockThermicFact
	Clock the last time temperature factors were computed.

RefinableObjClock	mClockGlobalBiso
	last time the global Biso factor was modified

RefinableObjClock	mClockGlobalTemperatureFact
	last time the global temperature factor was computed

bool	mIgnoreImagScattFact
	Ignore imaginary part of scattering factor. More...

REAL	mMaxSinThetaOvLambda
	Maximum sin(theta)/lambda for all calculations (10 by default). More...

long	mNbReflUsed
	Number of reflections which are below the max. More...

RefinableObjClock	mClockNbReflUsed
	Clock recording the last time the number of reflections used has increased.

map< const ScatteringPower *, CrystVector_REAL >	mvLuzzatiFactor
	The Luzzati 'D' factor for each scattering power and each reflection.

CrystVector_REAL	mFhklCalcVariance
	The variance on all calculated structure factors, taking into account the positionnal errors and the expected intensity factor. More...

RefinableObjClock	mClockLuzzatiFactor

RefinableObjClock	mClockFhklCalcVariance

CrystVector_REAL	mFhklObsSq
	Observed squared structure factors (zero-sized if none)

RefinableObjClock	mClockFhklObsSq
	Last time observed squared structure factors were altered.

Private Member Functions
void	GenHKLFullSpace (const REAL, const bool)
	Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value. More...

Detailed Description

Class to compute the contribution to a powder pattern from a crystalline phase.

Definition at line 306 of file PowderPattern.h.

Member Function Documentation

void ObjCryst::PowderPatternDiffraction::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::ScatteringData.

Definition at line 872 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcIhkl ( ) const

protectedvirtual

Compute the intensity for all reflections (taking into account corrections, but not the multiplicity)

Definition at line 2022 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcIntensityCorr ( ) const

protected

Calc Lorentz-Polarisation-Aperture correction

Definition at line 1944 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcPowderPattern ( ) const

protectedvirtual

Calc the powder pattern.

As always, recomputation is only done if necessary (ie if a parameter has changed since the last computation)

Implements ObjCryst::PowderPatternComponent.

Definition at line 1203 of file PowderPattern.cpp.

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

protectedvirtual

Calc the integrated powder pattern.

This should be optimized so that the full powder pattern is not explicitely computed.

Reimplemented from ObjCryst::PowderPatternComponent.

Definition at line 1529 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcPowderReflProfile ( ) const

protected

Calc reflection profiles for ALL reflections (powder diffraction)

Definition at line 1614 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcPowderReflProfile_FullDeriv ( std::set< RefinablePar * > & vPar )

protected

Calc derivatives of reflection profiles for all used reflections, for a given list of refinable parameters

Definition at line 1789 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::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 from ObjCryst::ScatteringData.

Definition at line 886 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::ExtractLeBail ( unsigned int nbcycle = 1 )

Extract intensities using Le Bail method.

Parameters

nbcycle number of cycles

Definition at line 1053 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::GenHKLFullSpace	(	const REAL	maxTheta,
		const bool	unique
	)

privatevirtual

Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value.

Parameters

maxsithsl:maximum	sin(theta)/lambda=1/2d value
unique	if set to true, only unique reflections will be listed. Bijvoet (Friedel) pairs are NOT merged, for 'anomalous' reasons, unless you have chosen to ignore the imaginary part of the scattering factor.

The multiplicity is always stored in ScatteringData::mMultiplicity.

Warning: The ScatteringData object must already have been assigned a crystal object using SetCrystal(), and the experimental wavelength must also have been set before calling this function.

Deprecated:: Rather use PowderPattern::GenHKLFullSpace2, with a maximum sin(theta)/lambda value, which also works for dispersive experiments.

Reimplemented from ObjCryst::ScatteringData.

Definition at line 846 of file PowderPattern.cpp.

const CrystMatrix_REAL & ObjCryst::PowderPatternDiffraction::GetBMatrix ( ) const

protectedvirtual

This can use either locally stored lattice parameters from mLocalLatticePar, or the Crystal's, depending on mUseLocalLatticePar.

Reimplemented from ObjCryst::ScatteringData.

Definition at line 2244 of file PowderPattern.cpp.

const CrystVector_long & ObjCryst::PowderPatternDiffraction::GetBraggLimits ( ) const

protectedvirtual

Get the pixel positions separating the integration intervals around reflections.

Returns: : an array with the pixel positions, empty if this component has no peaks. The positions should be in increasing order, but could go beyond the pattern limits.

Implements ObjCryst::PowderPatternComponent.

Definition at line 2222 of file PowderPattern.cpp.

const string & ObjCryst::PowderPatternDiffraction::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::PowderPatternComponent.

Definition at line 777 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::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 917 of file PowderPattern.cpp.

long ObjCryst::PowderPatternDiffraction::GetNbReflBelowMaxSinThetaOvLambda ( ) const

virtual

Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(theta)/lambda value set.

Reimplemented from ObjCryst::ScatteringData.

Definition at line 1147 of file PowderPattern.cpp.

const CrystVector_REAL & ObjCryst::PowderPatternDiffraction::GetPowderPatternCalc ( ) const

virtual

Get the calculated powder pattern for this component.

Note that the pattern is not scaled.

Implements ObjCryst::PowderPatternComponent.

Definition at line 799 of file PowderPattern.cpp.

const CrystVector_REAL & ObjCryst::PowderPatternDiffraction::GetPowderPatternCalcVariance ( ) const

virtual

Get the variance associated to each point of the calculated powder pattern, for this component.

Warning: : this is experimental, with the aim of using Maximum Likelihood to improve structure determination.

Implements ObjCryst::PowderPatternComponent.

Definition at line 937 of file PowderPattern.cpp.

pair< const CrystVector_REAL *, const RefinableObjClock * > ObjCryst::PowderPatternDiffraction::GetPowderPatternIntegratedCalc ( ) const

virtual

Get the integrated values of the powder pattern.

Note: : the integration intervals are those given by the parent PowderPattern, so that all PowderPatternComponent's intervals are taken into account

This avoids explicitely calculating the full profile powder pattern.

Implements ObjCryst::PowderPatternComponent.

Definition at line 806 of file PowderPattern.cpp.

pair< const CrystVector_REAL *, const RefinableObjClock * > ObjCryst::PowderPatternDiffraction::GetPowderPatternIntegratedCalcVariance ( ) const

virtual

Get the variance associated to each point of the calculated powder pattern, for this component (integrated version).

Warning: : this is experimental, with the aim of using Maximum Likelihood to improve structure determination.

Implements ObjCryst::PowderPatternComponent.

Definition at line 944 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::Prepare ( )

protectedvirtual

This will be called by the parent PowderPattern object, before calculating the first powder pattern. Or maybe it should be called automatically by the object itself...

Implements ObjCryst::PowderPatternComponent.

Definition at line 2192 of file PowderPattern.cpp.

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

virtual

Enable or disable numerical approximations.

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

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

Also see:

Reimplemented from ObjCryst::ScatteringData.

Definition at line 903 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetCrystal ( Crystal & crystal )

virtual

Set the crystal for this experiment.

Reimplemented from ObjCryst::ScatteringData.

Definition at line 956 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetExtractionMode	(	const bool	extract = `true`,
		const bool	init = `false`
	)

Prepare intensity extraction (Le Bail or Pawley)

Parameters

extract	if true, begin extraction mode, else enable structure factor calculations
init	if true and extract=true, intensities are set to 100. Otherwise if extract==true and init=false, the program will try to re-use existing extracted data (in mpLeBailData), but only if the list of HKL is unchanged. Otherwise initilization to 100 will be forced.

Definition at line 975 of file PowderPattern.cpp.

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

protectedvirtual

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

All data above still exist but are ignored for all calculations.

Implements ObjCryst::PowderPatternComponent.

Definition at line 2241 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetParentPowderPattern ( PowderPattern & )

virtual

Set the PowderPattern object which uses this component.

This sets all necessary pattern parameters (2theta/tof range, wavelength, radiation type...) accordingly.

Implements ObjCryst::PowderPatternComponent.

Definition at line 788 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetProfile ( ReflectionProfile * prof )

Assign a new profile.

Definition at line 822 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetReflectionProfilePar	(	const ReflectionProfileType	prof,
		const REAL	fwhmCagliotiW,
		const REAL	fwhmCagliotiU = `0`,
		const REAL	fwhmCagliotiV = `0`,
		const REAL	eta0 = `0.5`,
		const REAL	eta1 = `0.`
	)

Set reflection profile parameters.

:TODO: assymmetric profiles

Parameters

fwhmCagliotiW,fwhmCagliotiU,fwhmCagliotiV	: these are the U,V and W parameters in the Caglioti's law : $fwhm^2= U \tan^2(\theta) + V \tan(\theta) +W$ if only W is given, the width is constant
eta0,eta1	these are the mixing parameters in the case of a pseudo-Voigt function.

Definition at line 812 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::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 1689 of file ObjCryst/IO.cpp.

void ObjCryst::PowderPatternDiffraction::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 1617 of file ObjCryst/IO.cpp.

Member Data Documentation

CrystVector_REAL ObjCryst::PowderPatternDiffraction::mFrozenLatticePar

mutableprotected

a,b and c in Angstroems, angles (stored) in radians This is used to override lattice parameter from the Crystal structure, e.g.

for multiple datasets collected at different temperatures Ignored unless mFreezeLatticePar is true

Definition at line 509 of file PowderPattern.h.

vector< pair<unsigned long, CrystVector_REAL> > ObjCryst::PowderPatternDiffraction::mIntegratedProfileFactor

mutableprotected

For each reflection, store the integrated value of the normalized profile over all integration intervals.

The first field is the first integration interval to which the reflection contributes, and the second field is a vector with all the integrated values for the intervals, listed in ascending 2theta(tof) order.

Definition at line 498 of file PowderPattern.h.

CrystVector_REAL ObjCryst::PowderPatternDiffraction::mIntensityCorr

mutableprotected

Calculated corrections for all reflections.

Calc F^2 must be multiplied by this factor to yield intensities.

Thus we have : $I_{hkl} = L \times P \times SlitAp \times F_{hkl}^2$

with $L = \frac{1}{\sin(2\theta)}$ (Lorentz factor). $P = \frac{1}{1+A}\left(1+A\cos^2(2\theta)\right)$ (Polarization factor), with $A = \frac{1-f}{1+f}$ , where f is the polarization rate of the incident beam in the plane which (i) includes the incident beam, and (ii) is perpendicular to the diffracting plane. For an X-Ray Tube without monochromator, A=1, and if there is a monochromator : $A = \cos^2(2\theta_{mono})$ The factor $SlitAp = \frac{1}{\sin(\theta)}$ takes into account the fraction of the diffracted cone which falls in the detector slit.

If there is prefereed orientation, this also holds the associated correction.

Todo:: : store all corrections in a registry, so that other corrections can more easily be added (? Maybe not that useful, especially since these correction do not need to be displayed to the user ?).

Definition at line 452 of file PowderPattern.h.

std::map<RefinablePar*,vector<CrystVector_REAL> > ObjCryst::PowderPatternDiffraction::mvReflProfile_FullDeriv

mutableprotected

Derivatives of reflection profiles versus a list of parameters.

This will be limited to the reflections actually used. First and last point of each profile are the same as in mvReflProfile.

Definition at line 488 of file PowderPattern.h.

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Member Function Documentation

Member Data Documentation