ObjCryst::PowderPatternDiffraction Class Reference

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

Inheritance diagram for ObjCryst::PowderPatternDiffraction:

[legend]Collaboration diagram for ObjCryst::PowderPatternDiffraction:

[legend]List of all members.


Public Member Functions
	PowderPatternDiffraction ()
	PowderPatternDiffraction (const PowderPatternDiffraction &)
virtual	~PowderPatternDiffraction ()
virtual PowderPatternDiffraction *	CreateCopy () const
	So-called virtual copy constructor.
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...).
virtual void	SetParentPowderPattern (const 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 ?
Protected Member Functions
virtual void	CalcPowderPattern () const
	Calc the powder pattern.
virtual void	CalcPowderPatternIntegrated () const
	Calc the integrated powder pattern.
void	CalcPowderReflProfile () const
	Calc reflection profiles for ALL reflections (powder diffraction).
void	CalcIntensityCorr () const
	Calc Lorentz-Polarisation-APerture correction.
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)
	exist but are ignored for all calculations.
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. Calc F^2 must be multiplied by this factor to yield intensities.
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
	First and last pixel for integrated R-factors around each reflection.
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.

Detailed Description

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

Constructor & Destructor Documentation

ObjCryst::PowderPatternDiffraction::PowderPatternDiffraction ( )

ObjCryst::PowderPatternDiffraction::PowderPatternDiffraction ( const PowderPatternDiffraction & )

virtual ObjCryst::PowderPatternDiffraction::~PowderPatternDiffraction ( ) [virtual]

Member Function Documentation

virtual 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.

virtual 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)

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

Calc Lorentz-Polarisation-APerture correction.

virtual 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.

virtual 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.

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

Calc reflection profiles for ALL reflections (powder diffraction).

virtual PowderPatternDiffraction* ObjCryst::PowderPatternDiffraction::CreateCopy ( ) const [virtual]

So-called virtual copy constructor.

Implements ObjCryst::ScatteringData.

virtual 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.

virtual void ObjCryst::PowderPatternDiffraction::GenHKLFullSpace ( ) [virtual]

virtual 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.

virtual 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.

virtual 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.

virtual 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.

virtual 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.

virtual 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.

virtual 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.

virtual const Radiation& ObjCryst::PowderPatternDiffraction::GetRadiation ( ) const [virtual]

Get the radiation object for this data.

Implements ObjCryst::ScatteringData.

virtual bool ObjCryst::PowderPatternDiffraction::HasPowderPatternCalcVariance ( ) const [virtual]

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

Implements ObjCryst::PowderPatternComponent.

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

virtual 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.

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

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

exist but are ignored for all calculations.
All data above still
Implements ObjCryst::PowderPatternComponent.

virtual void ObjCryst::PowderPatternDiffraction::SetParentPowderPattern ( const 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.

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

Assign a new profile.

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.

virtual 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.

virtual 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.

Member Data Documentation

RefinableObjClock ObjCryst::PowderPatternDiffraction::mClockIhklCalc [mutable, protected]

Last time intensities were computed.

RefinableObjClock ObjCryst::PowderPatternDiffraction::mClockIntegratedProfileFactor [mutable, protected]

Last time the integrated values of normalized profiles was calculated.

RefinableObjClock ObjCryst::PowderPatternDiffraction::mClockIntensityCorr [mutable, protected]

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

RefinableObjClock ObjCryst::PowderPatternDiffraction::mClockLorentzPolarSlitCorrPar [protected]

Last time the.

RefinableObjClock ObjCryst::PowderPatternDiffraction::mClockProfileCalc [mutable, protected]

Last time the reflection profiles were computed.

RefinableObjClock ObjCryst::PowderPatternDiffraction::mClockProfilePar [protected]

Last time the reflection parameters were changed.

LorentzCorr ObjCryst::PowderPatternDiffraction::mCorrLorentz [protected]

Lorentz correction.

PolarizationCorr ObjCryst::PowderPatternDiffraction::mCorrPolar [protected]

Polarization correction.

PowderSlitApertureCorr ObjCryst::PowderPatternDiffraction::mCorrSlitAperture [protected]

Slit aperture correction.

TextureMarchDollase ObjCryst::PowderPatternDiffraction::mCorrTextureMarchDollase [protected]

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

TOFCorr ObjCryst::PowderPatternDiffraction::mCorrTOF [protected]

Time-Of-Flight intensity correction.

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

Computed intensities for all reflections.

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

Variance on computed intensities for all reflections.

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.

CrystVector_long ObjCryst::PowderPatternDiffraction::mIntegratedReflMax [mutable, protected]

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

CrystVector_long ObjCryst::PowderPatternDiffraction::mIntegratedReflMin [mutable, protected]

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

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 ?).

ReflectionProfile* ObjCryst::PowderPatternDiffraction::mpReflectionProfile [protected]

Profile.

vector<ReflProfile> ObjCryst::PowderPatternDiffraction::mvReflProfile [mutable, protected]

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

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

PowderPattern.h

Generated on Tue Nov 14 15:04:31 2006 for ObjCryst++ by

1.3.6

ObjCryst::PowderPatternDiffraction Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation