ObjCryst::PowderPatternDiffraction Class Reference

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

Inheritance diagram for ObjCryst::PowderPatternDiffraction:

Collaboration diagram for ObjCryst::PowderPatternDiffraction:

List of all members.

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",.

virtual void SetParentPowderPattern (PowderPattern &)

Set the PowderPattern object which uses this component.

virtual const CrystVector_REAL & GetPowderPatternCalc () const

Get the calculated powder pattern for this component.

virtual pair< const
CrystVector_REAL *, const
RefinableObjClock * > GetPowderPatternIntegratedCalc () const

Get the integrated values of the powder pattern.

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.

void SetProfile (ReflectionProfile *prof)

Assign a new profile.

virtual void GenHKLFullSpace ()

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

Output to stream in well-formed XML.

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

Input From stream.

virtual void GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const

Get the gene group assigned to each parameter.

virtual void BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)

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

virtual void EndOptimization ()

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

virtual 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.

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).

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.

void SetExtractionMode (const bool extract=true, const bool init=false)

Prepare intensity extraction (Le Bail or Pawley).

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.

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.

Protected Member Functions

virtual void CalcPowderPattern () const

Calc the powder pattern.

virtual void CalcPowderPatternIntegrated () const

Calc the integrated powder pattern.

void CalcPowderReflProfile () const

void CalcIntensityCorr () const

virtual void CalcIhkl () const

virtual void Prepare ()

virtual void InitOptions ()

virtual void GetBraggLimits (CrystVector_long *&min, CrystVector_long *&max) const

Get the integration limits (first and last pixels) around each reflection, if this component has Bragg reflections.

virtual void SetMaxSinThetaOvLambda (const REAL max)

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

void PrepareIntegratedProfile () const

Protected Attributes

RefinableObjClock mClockProfilePar

Last time the reflection parameters were changed.

RefinableObjClock mClockLorentzPolarSlitCorrPar

Last time the.

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.

LorentzCorr mCorrLorentz

Lorentz correction.

PolarizationCorr mCorrPolar

Polarization correction.

PowderSlitApertureCorr mCorrSlitAperture

Slit aperture correction.

TextureMarchDollase mCorrTextureMarchDollase

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

TOFCorr mCorrTOF

Time-Of-Flight intensity correction.

CrystVector_REAL mIhklCalc

Computed intensities for all reflections.

CrystVector_REAL mIhklCalcVariance

Variance on computed intensities for all reflections.

vector< ReflProfile > mvReflProfile

Reflection profiles for ALL reflections during the last powder pattern generation.

CrystVector_long mIntegratedReflMin

First and last pixel for integrated R-factors around each reflection.

CrystVector_long mIntegratedReflMax

vector< pair< unsigned long,
CrystVector_REAL > > mIntegratedProfileFactor

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

RefinableObjClock mClockIntegratedProfileFactor

Last time the integrated values of normalized profiles was calculated.

bool mExtractionMode

Classes

struct ReflProfile

Profile of a single reflection. More...

Detailed Description

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

Definition at line 295 of file PowderPattern.h.

Member Function Documentation

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 628 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 639 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 650 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 657 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 663 of file PowderPattern.cpp.

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

Assign a new profile.

Definition at line 673 of file PowderPattern.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 1499 of file ObjCryst/IO.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 1551 of file ObjCryst/IO.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 718 of file PowderPattern.cpp.

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.

Parameters:

	allowApproximations,:	if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives.
	enableRestraints,:	if true, then restrained parameters will be allowed to go beyond theur hard limits. This implies that the algorithm will take into account the cost (penalty) related to the restraints. Objects which do not use restraints will simply ignore this. WARNING: this parameter may be removed with the new likelihood scheme.

Reimplemented from ObjCryst::ScatteringData.

Definition at line 700 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 710 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 738 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 745 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetCrystal ( Crystal & crystal ) [virtual]

Set the crystal for this experiment.

Reimplemented from ObjCryst::ScatteringData.

Definition at line 757 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

Definition at line 773 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 784 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 851 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcPowderPattern ( ) const [protected, virtual]

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 884 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcPowderPatternIntegrated ( ) const [protected, virtual]

Calc the integrated powder pattern.

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

Implements ObjCryst::PowderPatternComponent.

Definition at line 974 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcPowderReflProfile ( ) const [protected]

For internal use only.

Calc reflection profiles for ALL reflections (powder diffraction)

Definition at line 1076 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcIntensityCorr ( ) const [protected]

For internal use only.

Calc Lorentz-Polarisation-APerture correction

Definition at line 1251 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::CalcIhkl ( ) const [protected, virtual]

For internal use only.

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

Definition at line 1302 of file PowderPattern.cpp.

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

For internal use only.

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 1397 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::GetBraggLimits	(	CrystVector_long *&	min,
		CrystVector_long *&	max
	)			const `[protected, virtual]`

Get the integration limits (first and last pixels) around each reflection, if this component has Bragg reflections.

Used for integrated R(w) factors. The limits currently go from -2*FWHM to +2*FWHM. returns a pointer to the min and max pixels arrays (null pointers if no reflection for this phase).

Implements ObjCryst::PowderPatternComponent.

Definition at line 1427 of file PowderPattern.cpp.

void ObjCryst::PowderPatternDiffraction::SetMaxSinThetaOvLambda ( const REAL max ) [protected, virtual]

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 1450 of file PowderPattern.cpp.

Member Data Documentation

CrystVector_REAL ObjCryst::PowderPatternDiffraction::mIntensityCorr [mutable, protected]

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 412 of file PowderPattern.h.

vector< pair<unsigned long, CrystVector_REAL> > ObjCryst::PowderPatternDiffraction::mIntegratedProfileFactor [mutable, protected]

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 453 of file PowderPattern.h.

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


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",.
virtual void	SetParentPowderPattern (PowderPattern &)
	Set the PowderPattern object which uses this component.
virtual const CrystVector_REAL &	GetPowderPatternCalc () const
	Get the calculated powder pattern for this component.
virtual pair< const CrystVector_REAL , const RefinableObjClock >	GetPowderPatternIntegratedCalc () const
	Get the integrated values of the powder pattern.
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.
void	SetProfile (ReflectionProfile *prof)
	Assign a new profile.
virtual void	GenHKLFullSpace ()
virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML.
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream.
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter.
virtual void	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization.
virtual void	EndOptimization ()
	This should be called by any optimization class at the end of an optimization.
virtual 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.
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).
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.
void	SetExtractionMode (const bool extract=true, const bool init=false)
	Prepare intensity extraction (Le Bail or Pawley).
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.
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.
Protected Member Functions
virtual void	CalcPowderPattern () const
	Calc the powder pattern.
virtual void	CalcPowderPatternIntegrated () const
	Calc the integrated powder pattern.
void	CalcPowderReflProfile () const
void	CalcIntensityCorr () const
virtual void	CalcIhkl () const
virtual void	Prepare ()
virtual void	InitOptions ()
virtual void	GetBraggLimits (CrystVector_long &min, CrystVector_long &max) const
	Get the integration limits (first and last pixels) around each reflection, if this component has Bragg reflections.
virtual void	SetMaxSinThetaOvLambda (const REAL max)
	Set the maximum value for sin(theta)/lambda.
void	PrepareIntegratedProfile () const
Protected Attributes
RefinableObjClock	mClockProfilePar
	Last time the reflection parameters were changed.
RefinableObjClock	mClockLorentzPolarSlitCorrPar
	Last time the.
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.
LorentzCorr	mCorrLorentz
	Lorentz correction.
PolarizationCorr	mCorrPolar
	Polarization correction.
PowderSlitApertureCorr	mCorrSlitAperture
	Slit aperture correction.
TextureMarchDollase	mCorrTextureMarchDollase
	Preferred orientation (texture) correction following the March-Dollase model.
TOFCorr	mCorrTOF
	Time-Of-Flight intensity correction.
CrystVector_REAL	mIhklCalc
	Computed intensities for all reflections.
CrystVector_REAL	mIhklCalcVariance
	Variance on computed intensities for all reflections.
vector< ReflProfile >	mvReflProfile
	Reflection profiles for ALL reflections during the last powder pattern generation.
CrystVector_long	mIntegratedReflMin
	First and last pixel for integrated R-factors around each reflection.
CrystVector_long	mIntegratedReflMax
vector< pair< unsigned long, CrystVector_REAL > >	mIntegratedProfileFactor
	For each reflection, store the integrated value of the normalized profile over all integration intervals.
RefinableObjClock	mClockIntegratedProfileFactor
	Last time the integrated values of normalized profiles was calculated.
bool	mExtractionMode
Classes
struct	ReflProfile
	Profile of a single reflection. More...