Class to compute structure factors for a set of reflections and a Crystal. More...

Inheritance diagram for ObjCryst::ScatteringData:

Collaboration diagram for ObjCryst::ScatteringData:

Public Member Functions
	ScatteringData (const ScatteringData &old)

virtual ScatteringData *	CreateCopy () const =0
	So-called virtual copy constructor.

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...

virtual void	GenHKLFullSpace (const REAL maxTheta, 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 ?

virtual const Radiation &	GetRadiation () const =0
	Get the radiation object for this data.

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

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.

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

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

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

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

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

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...

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

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

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

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

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

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

void	FixAllPar ()
	Fix All parameters.

void	UnFixAllPar ()
	UnFix All parameters.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	Print () const

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Protected Member Functions
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.

virtual const CrystMatrix_REAL &	GetBMatrix () const
	Get access to the B matrix used to compute reflection positions. More...

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 Member Functions inherited from ObjCryst::RefinableObj
long	FindPar (const string &name) const
	Find a refinable parameter with a given name.

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

void	AddSubRefObj (RefinableObj &)

void	RemoveSubRefObj (RefinableObj &)

void	AddOption (RefObjOpt *opt)

virtual void	Prepare ()

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

Protected Attributes
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.

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

Class to compute structure factors for a set of reflections and a Crystal.

This class only computes structure factor, but no intensity. i.e. it does not include any correction such as absorption, Lorentz or Polarization.

Does this really need to be a RefinableObj ?

Todo:: Optimize computation for Bijvoet/Friedel mates. To do this, generate an internal list of 'true independent reflections', with two entries for each, for both mates, and make the 'real' reflections only a reference to these reflections.

Todo:: a lot of cleaning is necessary in the computing of structure factors, for (1) the 'preparation' part (deciding what needs to be recomputed) and (2) to allow anisotropic temperature factors (or other anisotropic parts)

Definition at line 305 of file ScatteringData.h.

Member Function Documentation

void ObjCryst::ScatteringData::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.

Reimplemented in ObjCryst::PowderPatternDiffraction.

Definition at line 826 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcGeomStructFactor ( ) const

protected

Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal.

Definition at line 1579 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcResonantScattFactor ( ) const

protectedvirtual

get f' and f" for ScatteringPower of the crystal, at the exp. wavelength

This could be specialized for multi-wavelength experiments...

Definition at line 1221 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcScattFactor ( ) const

protected

Get scattering factors for all ScatteringPower & reflections

Definition at line 1172 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcSinThetaLambda ( ) const

protectedvirtual

Compute sin(theta)/lambda as well a orthonormal coordinates for all reflections. theta and tan(theta), are also re-computed, provided a wavelength has been supplied.

Definition at line 1064 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcStructFactor ( ) const

protected

Compute the overall structure factor (real and imaginary part).

This function is optimized for speed (geometrical structure factors are computed for all atoms and all reflections in two loops, avoiding re-calculation). So use this function for repetitive calculations.

This function recognizes the type of radiation (XRay or neutron) and uses the corresponding scattering factor/length.

Returns: the result (real and imaginary part of the structure factor) (mRealFhklCalc, mImagFhklCalc) are stored in ScatteringData.

Definition at line 1272 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcStructFactVariance ( ) const

protected

Calculate the variance associated to the calculated structure factor.

Definition at line 2365 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::CalcTemperatureFactor ( ) const

protected

Compute thermic factors for all ScatteringPower & reflections

Definition at line 1198 of file ScatteringData.cpp.

CrystVector_long ObjCryst::ScatteringData::EliminateExtinctReflections ( )

protected

Get rid of extinct reflections. Useful after GenHKLFullSpace(). Do not use this if you have a list of observed reflections !

Currently done using (brute-force) numerical evaluation. Should rather use SpaceGroup info... To do !

Returns: an array with the subscript of the kept reflections (for inherited classes)

Definition at line 1020 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::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::RefinableObj.

Reimplemented in ObjCryst::PowderPatternDiffraction.

Definition at line 838 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::GenHKLFullSpace	(	const REAL	maxTheta,
		const bool	unique = `false`
	)

virtual

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 in ObjCryst::PowderPatternDiffraction.

Definition at line 579 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::GenHKLFullSpace2	(	const REAL	maxsithsl,
		const bool	unique = `false`
	)

virtual

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

Parameters

maxTheta:maximum	theta 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.

Definition at line 483 of file ScatteringData.cpp.

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

protectedvirtual

Get access to the B matrix used to compute reflection positions.

May be overridden by derived classes to use different lattice parameters than the Crystal's unitcell (used for multiple datasets).

Reimplemented in ObjCryst::PowderPatternDiffraction.

Definition at line 1167 of file ScatteringData.cpp.

const CrystVector_REAL & ObjCryst::ScatteringData::GetH2Pi ( ) const

Return the 1D array of H coordinates for all reflections, multiplied by 2*pi.

Should be private

Definition at line 616 of file ScatteringData.cpp.

const CrystVector_REAL & ObjCryst::ScatteringData::GetK2Pi ( ) const

Return the 1D array of K coordinates for all reflections, multiplied by 2*pi.

Should be private

Definition at line 617 of file ScatteringData.cpp.

const CrystVector_REAL & ObjCryst::ScatteringData::GetL2Pi ( ) const

Return the 1D array of L coordinates for all reflections, multiplied by 2*pi.

Should be private

Definition at line 618 of file ScatteringData.cpp.

long ObjCryst::ScatteringData::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 in ObjCryst::PowderPatternDiffraction.

Definition at line 920 of file ScatteringData.cpp.

bool ObjCryst::ScatteringData::IsIgnoringImagScattFact ( ) const

If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.

Definition at line 763 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::PrepareHKLarrays ( )

protectedvirtual

This function is called after H,K and L arrays have been initialized or modified.

Definition at line 865 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::PrintFhklCalc ( ostream & os = cout ) const

virtual

Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections.

Definition at line 765 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::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::RefinableObj.

Reimplemented in ObjCryst::PowderPatternDiffraction.

Definition at line 853 of file ScatteringData.cpp.

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

virtual

Set the crystal for this experiment.

Reimplemented in ObjCryst::PowderPatternDiffraction.

Definition at line 593 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::SetHKL	(	const CrystVector_REAL &	h,
		const CrystVector_REAL &	k,
		const CrystVector_REAL &	l
	)

virtual

input H,K,L

Parameters

h,k,l REAL arrays (vectors with NbRefl elements -same size), with the h, k and l coordinates of all reflections.

Definition at line 469 of file ScatteringData.cpp.

void ObjCryst::ScatteringData::SetIsIgnoringImagScattFact ( const bool b )

If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.

(default value=false)

Todo:: this should become useless once we take fully advantage of coupled computation of Structure Factors for Fridel/Bijvoet mates using an internal list of 'fully unique' reflections. Then only one of the mates need to be computed..

Definition at line 756 of file ScatteringData.cpp.

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

virtual

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

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

Reimplemented in ObjCryst::PowderPatternDiffraction.

Definition at line 918 of file ScatteringData.cpp.

CrystVector_long ObjCryst::ScatteringData::SortReflectionBySinThetaOverLambda ( const REAL maxSTOL = -1. )

protectedvirtual

sort reflections by theta values (also get rid of [0,0,0] if present) If maxSTOL >0, then only reflections where sin(theta)/lambda<maxSTOL are kept

Returns: an array with the subscript of the kept reflections (for inherited classes)

Reimplemented in ObjCryst::DiffractionDataSingleCrystal.

Definition at line 947 of file ScatteringData.cpp.

Member Data Documentation

CrystVector_int ObjCryst::ScatteringData::mExpectedIntensityFactor

protected

Expected intensity factor for all reflections.

See SpaceGroup::GetExpectedIntensityFactor()

Definition at line 549 of file ScatteringData.h.

CrystVector_REAL ObjCryst::ScatteringData::mFhklCalcVariance

mutableprotected

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

Actually this is the variance on both real and imaginary parts.

Definition at line 672 of file ScatteringData.h.

bool ObjCryst::ScatteringData::mIgnoreImagScattFact

protected

Ignore imaginary part of scattering factor.

This can be used either to speed up computation, or when f" has a small effect on calculated intensities, mostly for powder diffraction (GenHKLFullSpace will not generate Friedel pairs, reducing the number of reflections by a factor up to 2 for some structures).

Practically this makes f"=0 during computation. The real resonant contribution (f') is not affected.

This may be removed later on...

Definition at line 643 of file ScatteringData.h.

REAL ObjCryst::ScatteringData::mMaxSinThetaOvLambda

protected

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.

This affects the computing of structure factors, intensities (for single crystal and powder patterns), R and Rw.

The reflections must be sorted by increasing sin(theta)/lambda for this to work correctly.

Definition at line 657 of file ScatteringData.h.

long ObjCryst::ScatteringData::mNbReflUsed

mutableprotected

Number of reflections which are below the max.

This is updated automatically from ScatteringData::mMaxSinThetaOvLambda

Definition at line 660 of file ScatteringData.h.

Crystal* ObjCryst::ScatteringData::mpCrystal

protected

Pointer to the crystal corresponding to this experiment.

This gives an access to the UB matrix for the crystal, as well as to the list of Scatterer.

Definition at line 563 of file ScatteringData.h.

bool ObjCryst::ScatteringData::mUseFastLessPreciseFunc

protected

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

This is activated by global optimization algortithms, only during the optimization.

Definition at line 579 of file ScatteringData.h.

map<const ScatteringPower*,REAL> ObjCryst::ScatteringData::mvFprime

mutableprotected

Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value.

For multi-wavelength support this should be changed to a vector... or to a matrix to take into account anisotropy of anomalous scattering...

Definition at line 595 of file ScatteringData.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