ObjCryst::PowderPattern Class Reference

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

Inheritance diagram for ObjCryst::PowderPattern:

[legend]Collaboration diagram for ObjCryst::PowderPattern:

[legend]List of all members.


Public Member Functions
	PowderPattern ()
	PowderPattern (const PowderPattern &)
	~PowderPattern ()
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...).
void	AddPowderPatternComponent (PowderPatternComponent &)
	Add a component (phase, backround) to this pattern.
unsigned int	GetNbPowderPatternComponent () const
	Number of components.
const PowderPatternComponent &	GetPowderPatternComponent (const string &name) const
	Access to a component of the powder pattern.
const PowderPatternComponent &	GetPowderPatternComponent (const int) const
	Access to a component of the powder pattern.
PowderPatternComponent &	GetPowderPatternComponent (const string &name)
	Access to a component of the powder pattern.
PowderPatternComponent &	GetPowderPatternComponent (const int)
	Access to a component of the powder pattern.
void	SetPowderPatternPar (const REAL min, const REAL step, unsigned long nbPoint)
	the powder pattern angular range & resolution parameter.
void	SetPowderPatternX (const CrystVector_REAL &x)
	Set the x coordinate of the powder pattern : either the 2theta or time-of-flight values for each recorded point.
unsigned long	GetNbPoint () const
	Number of points ?
unsigned long	GetNbPointUsed () const
	Number of points actually calculated (below the chosen max(sin(theta)/lambda)) ?
void	SetRadiation (const Radiation &radiation)
	Set the radiation.
const Radiation &	GetRadiation () const
	Neutron or x-ray experiment ?
Radiation &	GetRadiation ()
	Neutron or x-ray experiment ?
void	SetRadiationType (const RadiationType radiation)
	Set the radiation type.
RadiationType	GetRadiationType () const
	Neutron or x-ray experiment ?
void	SetWavelength (const REAL lambda)
	Set the wavelength of the experiment (in Angstroems).
void	SetWavelength (const string &XRayTubeElementName, const REAL alpha12ratio=0.5)
	Set the wavelength of the experiment to that of an X-Ray tube.
void	SetEnergy (const REAL energy)
	Set the energy of the experiment [in keV, lambda(A)=12398/E(keV)].
REAL	GetWavelength () const
	wavelength of the experiment (in Angstroems)
const CrystVector_REAL &	GetPowderPatternCalc () const
	Get the calculated powder pattern.
const CrystVector_REAL &	GetPowderPatternObs () const
	Get the observed powder pattern.
const CrystVector_REAL &	GetPowderPatternObsSigma () const
	Get the sigma for each point of the observed powder pattern.
const CrystVector_REAL &	GetPowderPatternVariance () const
	Get the variance (obs+model) for each point of the powder pattern.
const CrystVector_REAL &	GetPowderPatternWeight () const
	Get the weight for each point of the powder pattern.
REAL	GetPowderPatternXMin () const
	Get the Minimum 2theta.
REAL	GetPowderPatternXStep () const
	Get the average step in 2theta.
REAL	GetPowderPatternXMax () const
	Get the maximum 2theta.
const CrystVector_REAL &	GetPowderPatternX () const
	Get the vector of X (2theta or time-of-flight) coordinates.
const CrystVector_REAL &	GetChi2Cumul () const
	Get the powder pattern cumulative Chi^2.
const RefinableObjClock &	GetClockPowderPatternCalc () const
	Last time the pattern was calculated.
const RefinableObjClock &	GetClockPowderPatternPar () const
	When were the pattern parameters (2theta range, step) changed ?
const RefinableObjClock &	GetClockPowderPatternRadiation () const
	When were the radiation parameter (radiation type, wavelength) changed ?
const RefinableObjClock &	GetClockPowderPatternXCorr () const
	When were the parameters for 2theta/TOF correction (zero, transparency, displacement) last changed ?
void	SetXZero (const REAL newZero)
	Change Zero in x (2theta,tof).
void	Set2ThetaDisplacement (const REAL displacement)
	Change displacement correction $(2\theta)_{obs} = (2\theta)_{real} + \frac{a}{\cos(\theta)}$ .
void	Set2ThetaTransparency (const REAL transparency)
	Change transparency correction $(2\theta)_{obs} = (2\theta)_{real} + b\sin(2\theta)$ .
void	ImportPowderPatternFullprof (const string &fullprofFileName)
	Import fullprof-style diffraction data.
void	ImportPowderPatternPSI_DMC (const string &filename)
	Import powder pattern, format DMC from PSI.
void	ImportPowderPatternILL_D1A5 (const string &filename)
	Import powder pattern, format from ILL D1A/D2B (format without counter info).
void	ImportPowderPatternXdd (const string &fileName)
	Import *.xdd diffraction data (Topas,...).
void	ImportPowderPatternSietronicsCPI (const string &fileName)
	Import *.cpi Sietronics diffraction data.
void	ImportPowderPattern2ThetaObsSigma (const string &fileName, const int nbSkip=0)
	Import file with 3 columns 2Theta Iobs Sigma.
void	ImportPowderPatternFullprof4 (const string &fileName)
	Import diffraction data from a file, with the first line has 2ThetaMin, step, 2thetaMax, and the following lines alternate 10 Iobs and 10 sigma. Ends with null entries (to fill last Iobs line to reach last sigme line).
void	ImportPowderPatternMultiDetectorLLBG42 (const string &fileName)
	diffraction data in a multi-detector format (fullprof format #6).
void	ImportPowderPattern2ThetaObs (const string &fileName, const int nbSkip=0)
	Import file with 2 columns 2Theta Iobs.
void	ImportPowderPatternTOF_ISIS_XYSigma (const string &fileName)
	Import TOF file (ISIS type, 3 columns t, Iobs, sigma(Iobs)).
void	ImportPowderPatternGSAS (const string &fileName)
	Import GSAS standard powder pattern data (see GSAS manual).
void	ImportPowderPatternCIF (const CIF &cif)
	Import CIF powder pattern data.
void	SetPowderPatternObs (const CrystVector_REAL &obs)
	Set observed powder pattern from vector array.
void	SavePowderPattern (const string &filename="powderPattern.out") const
	Save powder pattern to one file, text format, 3 columns theta Iobs Icalc.
void	PrintObsCalcData (ostream &os=cout) const
	Print to thee screen/console the observed and calculated pattern (long, mostly useful for debugging).
REAL	GetR () const
	Unweighted R-factor.
REAL	GetIntegratedR () const
REAL	GetRw () const
	Get the weighted R-factor.
REAL	GetIntegratedRw () const
REAL	GetChi2 () const
	Return conventionnal Chi^2.
void	FitScaleFactorForR () const
	Fit the scale(s) factor of each component to minimize R.
void	FitScaleFactorForIntegratedR () const
void	FitScaleFactorForRw () const
	Fit the scale(s) factor of each component to minimize Rw.
void	FitScaleFactorForIntegratedRw () const
void	SetSigmaToSqrtIobs ()
	Set sigma=sqrt(Iobs).
void	SetWeightToInvSigmaSq (const REAL minRelatSigma=1e-3)
	Set w = 1/sigma^2.
void	SetWeightToUnit ()
	Set w = 1.
void	SetWeightPolynomial (const REAL a, const REAL b, const REAL c, const REAL minRelatIobs=1e-3)
	Set w = 1/(a+ Iobs + bIobs^2+cIobs^3).
void	AddExcludedRegion (const REAL min2Theta, const REAL max2theta)
	Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be, as always, in radians.
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	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration.
virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object.
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 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.
void	Prepare ()
	Prepare everything (if necessary) for an optimization/calculation.
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter.
virtual void	SetMaxSinThetaOvLambda (const REAL max)
	Set the maximum value for sin(theta)/lambda.
REAL	GetMaxSinThetaOvLambda () const
	Get the maximum value for sin(theta)/lambda.
const CrystVector_long &	GetIntegratedProfileMin () const
	Get the list of first pixels for the integration intervals.
const CrystVector_long &	GetIntegratedProfileMax () const
	Get the list of last pixels for the integration intervals.
const RefinableObjClock &	GetIntegratedProfileLimitsClock () const
	When were the integration intervals last changed ?
REAL	X2XCorr (const REAL x) const
	Get the experimental x (2theta, tof) from the theoretical value, taking into account all corrections (zero, transparency,..).
REAL	X2PixelCorr (const REAL x) const
	Get the pixel number on the experimental pattern, from the theoretical (uncorrected) x coordinate, taking into account all corrections.
REAL	X2Pixel (const REAL x) const
	Get the pixel number on the experimental pattern, corresponding to a given (experimental) x coordinate.
REAL	STOL2X (const REAL stol) const
	Convert sin(theta)/lambda to X (i.e.
REAL	X2STOL (const REAL x) const
	Convert X (either 2theta or TOF) to sin(theta)/lambda, depending on the type of radiation.
REAL	STOL2Pixel (const REAL stol) const
	Convert sin(theta)/lambda to pixel, depending on the type of radiation.
Protected Member Functions
void	CalcPowderPattern () const
	Calc the powder pattern.
void	CalcPowderPatternIntegrated () const
	Calc the integrated powder pattern.
virtual void	Init ()
	Init parameters and options.
void	PrepareIntegratedRfactor () const
	Prepare the calculation of the integrated R-factors.
void	CalcNbPointUsed () const
	Calculate the number of points of the pattern actually used, from the maximum value of sin(theta)/lambda.
virtual void	InitOptions ()
	Initialize options.
Protected Attributes
CrystVector_REAL	mPowderPatternCalc
	The calculated powder pattern.
CrystVector_REAL	mPowderPatternIntegratedCalc
	The calculated powder pattern, integrated.
CrystVector_REAL	mPowderPatternBackgroundCalc
	The calculated powder pattern part which corresponds to 'background' (eg non-scalable components).
CrystVector_REAL	mPowderPatternBackgroundIntegratedCalc
	The calculated powder pattern part which corresponds to 'background' (eg non-scalable components), integrated.
CrystVector_REAL	mPowderPatternObs
	The observed powder pattern.
CrystVector_REAL	mPowderPatternObsSigma
	The sigma of the observed pattern.
CrystVector_REAL	mPowderPatternWeight
	The weight for each point of the pattern.
CrystVector_REAL	mPowderPatternVariance
	The complete variance associated to each point of the powder pattern, taking into account observation and model errors.
CrystVector_REAL	mPowderPatternVarianceIntegrated
	The complete variance associated to each point of the powder pattern, taking into account observation and model errors.
CrystVector_REAL	mChi2Cumul
	The cumulative Chi^2 (integrated or not, depending on the option).
CrystVector_REAL	mX
	Vector of x coordinates (either 2theta or time-of-flight) for the pattern.
bool	mIsXAscending
	Is the mX vector sorted in ascending order ? (true for 2theta, false for TOF).
unsigned long	mNbPoint
	Number of points in the pattern.
Radiation	mRadiation
	The Radiation corresponding to this experiment.
RefinableObjClock	mClockPowderPatternPar
	When were the pattern parameters (2theta or time-of-flight range) changed ?
RefinableObjClock	mClockPowderPatternRadiation
	When were the radiation parameter (radiation type, wavelength) changed ?
RefinableObjClock	mClockPowderPatternCalc
	When was the powder pattern last computed ?
RefinableObjClock	mClockPowderPatternIntegratedCalc
	When was the powder pattern (integrated) last computed ?
RefinableObjClock	mClockPowderPatternXCorr
	Corrections to 2Theta.
RefinableObjClock	mClockScaleFactor
	Last modification of the scale factor.
CrystVector_REAL	mExcludedRegionMinX
	Min coordinate for for all excluded regions.
CrystVector_REAL	mExcludedRegionMaxX
	Max coordinate for 2theta for all excluded regions.
REAL	mXZero
	Zero correction : $(2\theta)_{obs} = (2\theta)_{real} +(2\theta)_{0}$ Thus mPowderPattern2ThetaMin=(mPowderPattern2ThetaMin-m2ThetaZero).
REAL	m2ThetaDisplacement
	Displacement correction : $(2\theta)_{obs} = (2\theta)_{real} + \frac{a}{\cos(\theta)}$ .
REAL	m2ThetaTransparency
	Transparency correction : $(2\theta)_{obs} = (2\theta)_{real} + b\sin(2\theta)$ .
REAL	mDIFC
	Time Of Flight (TOF) parameters : $t = DIFC\frac{\sin(\theta)}{\lambda} + DIFA\left(\frac{\sin(\theta)}{\lambda}\right)^2 + mXZero$ .
REAL	mDIFA
	Time Of Flight (TOF) parameters : $t = DIFC\frac{\sin(\theta)}{\lambda} + DIFA\left(\frac{\sin(\theta)}{\lambda}\right)^2 + mXZero$ .
ObjRegistry< PowderPatternComponent >	mPowderPatternComponentRegistry
	The components (crystalline phases, background,...) of the powder pattern.
CrystVector_REAL	mScaleFactor
	The scale factors for each component.
bool	mUseFastLessPreciseFunc
	Use faster, less precise functions ?
bool	mStatisticsExcludeBackground
	Should Statistics (R, Rw,..) exclude the background ?
CrystVector_int	mScalableComponentIndex
CrystMatrix_REAL	mFitScaleFactorM
	Used to fit the components' scale factors.
CrystMatrix_REAL	mFitScaleFactorB
	Used to fit the components' scale factors.
CrystMatrix_REAL	mFitScaleFactorX
	Used to fit the components' scale factors.
RefObjOpt	mOptProfileIntegration
	Use Integrated profiles for Chi^2, R, Rwp...
CrystVector_long	mIntegratedPatternMin
CrystVector_long	mIntegratedPatternMax
CrystVector_REAL	mIntegratedObs
CrystVector_REAL	mIntegratedWeight
CrystVector_REAL	mIntegratedWeightObs
CrystVector_REAL	mIntegratedVarianceObs
RefinableObjClock	mClockIntegratedFactorsPrep
REAL	mChi2
REAL	mChi2LikeNorm
	This is the logarithm of the part of log(Likelihood) which corresponds to the normalization terms of gaussian distribution for each obs/calc point.
REAL	mR
REAL	mRw
RefinableObjClock	mClockChi2
	Clock the last time Chi^2 was computed.
REAL	mMaxSinThetaOvLambda
	Maximum sin(theta)/lambda for all calculations (10 by default).
unsigned long	mNbPointUsed
	Number of points actually used, due to the maximum value of sin(theta)/lambda.
unsigned long	mNbIntegrationUsed
	Number of integration intervals actually used, due to the maximum value of sin(theta)/lambda.
RefinableObjClock	mClockNbPointUsed
	Clock recording the last time the number of points used (PowderPattern::mNbPointUsed) was changed.

Detailed Description

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

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

Constructor & Destructor Documentation

ObjCryst::PowderPattern::PowderPattern ( )

ObjCryst::PowderPattern::PowderPattern ( const PowderPattern & )

ObjCryst::PowderPattern::~PowderPattern ( )

Member Function Documentation

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

const REAL max2theta

)

Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be, as always, in radians.
Does not work yet with integrated R factors. Note that the pattern is still computed in these regions. They are only ignored by statistics functions (R, Rws).

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

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

virtual void ObjCryst::PowderPattern::BeginOptimization ( const bool allowApproximations = false,

const bool enableRestraints = false

) [virtual]

This should be called by any optimization class at the begining of an optimization.
This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects.
Note:
this may be called several time for some objects which are used by several other objects.

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::RefinableObj.

void ObjCryst::PowderPattern::CalcNbPointUsed ( ) const [protected]

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

void ObjCryst::PowderPattern::CalcPowderPattern ( ) const [protected]

Calc the powder pattern.

void ObjCryst::PowderPattern::CalcPowderPatternIntegrated ( ) const [protected]

Calc the integrated powder pattern.

void ObjCryst::PowderPattern::FitScaleFactorForIntegratedR ( ) const

void ObjCryst::PowderPattern::FitScaleFactorForIntegratedRw ( ) const

void ObjCryst::PowderPattern::FitScaleFactorForR ( ) const

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

void ObjCryst::PowderPattern::FitScaleFactorForRw ( ) const

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

REAL ObjCryst::PowderPattern::GetChi2 ( ) const

Return conventionnal Chi^2.

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

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

Get the powder pattern cumulative Chi^2.
Depending on the chosen option, it will be calculated in an integrated manner or not.
The vector is recomputed on every call, so this is slow.

virtual const string& ObjCryst::PowderPattern::GetClassName ( ) const [virtual]

Name for this class ("RefinableObj", "Crystal",...).
This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry
Reimplemented from ObjCryst::RefinableObj.

const RefinableObjClock& ObjCryst::PowderPattern::GetClockPowderPatternCalc ( ) const

Last time the pattern was calculated.

const RefinableObjClock& ObjCryst::PowderPattern::GetClockPowderPatternPar ( ) const

When were the pattern parameters (2theta range, step) changed ?

const RefinableObjClock& ObjCryst::PowderPattern::GetClockPowderPatternRadiation ( ) const

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

const RefinableObjClock& ObjCryst::PowderPattern::GetClockPowderPatternXCorr ( ) const

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

virtual void ObjCryst::PowderPattern::GetGeneGroup ( const RefinableObj & obj,

CrystVector_uint & groupIndex,

unsigned int & firstGroup

) const [virtual]

Get the gene group assigned to each parameter.
Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life.
The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique.

Parameters:

obj the , supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object.

groupIndex a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned).

firstGroup this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group.

Note:
this function is not optimized, and should only be called at the beginning of a refinement.

Reimplemented from ObjCryst::RefinableObj.

const RefinableObjClock& ObjCryst::PowderPattern::GetIntegratedProfileLimitsClock ( ) const

When were the integration intervals last changed ?

const CrystVector_long& ObjCryst::PowderPattern::GetIntegratedProfileMax ( ) const

Get the list of last pixels for the integration intervals.

const CrystVector_long& ObjCryst::PowderPattern::GetIntegratedProfileMin ( ) const

Get the list of first pixels for the integration intervals.

REAL ObjCryst::PowderPattern::GetIntegratedR ( ) const

REAL ObjCryst::PowderPattern::GetIntegratedRw ( ) const

virtual REAL ObjCryst::PowderPattern::GetLogLikelihood ( ) const [virtual]

Get -log(likelihood) of the current configuration for the object.
By default (no likelihood evaluation available), this is equal to 0.
This call should not be recursive, it is the task of the algorithm to get the sum of likelihoods for all objects invlolved.

Note:
contrary to the old "Cost Function" approach, with log(Likelihood) there is no 'choice' of cost function, so that it is the task of the object to give the optimized likelihood (possibly with user options).

Warning:
: this is in under heavy development, so expect changes...

Reimplemented from ObjCryst::RefinableObj.

virtual const CrystVector_REAL& ObjCryst::PowderPattern::GetLSQCalc ( const unsigned int ) const [virtual]

Get the current calculated value for the LSQ function.

Reimplemented from ObjCryst::RefinableObj.

virtual const CrystVector_REAL& ObjCryst::PowderPattern::GetLSQObs ( const unsigned int ) const [virtual]

Get the observed values for the LSQ function.

Reimplemented from ObjCryst::RefinableObj.

virtual const CrystVector_REAL& ObjCryst::PowderPattern::GetLSQWeight ( const unsigned int ) const [virtual]

Get the weight values for the LSQ function.

Reimplemented from ObjCryst::RefinableObj.

REAL ObjCryst::PowderPattern::GetMaxSinThetaOvLambda ( ) const

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

virtual unsigned int ObjCryst::PowderPattern::GetNbLSQFunction ( ) const [virtual]

Number of LSQ functions.

Reimplemented from ObjCryst::RefinableObj.

unsigned long ObjCryst::PowderPattern::GetNbPoint ( ) const

Number of points ?

unsigned long ObjCryst::PowderPattern::GetNbPointUsed ( ) const

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

unsigned int ObjCryst::PowderPattern::GetNbPowderPatternComponent ( ) const

Number of components.

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

Get the calculated powder pattern.

PowderPatternComponent& ObjCryst::PowderPattern::GetPowderPatternComponent ( const int )

Access to a component of the powder pattern.

PowderPatternComponent& ObjCryst::PowderPattern::GetPowderPatternComponent ( const string & name )

Access to a component of the powder pattern.

const PowderPatternComponent& ObjCryst::PowderPattern::GetPowderPatternComponent ( const int ) const

Access to a component of the powder pattern.

const PowderPatternComponent& ObjCryst::PowderPattern::GetPowderPatternComponent ( const string & name ) const

Access to a component of the powder pattern.

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

Get the observed powder pattern.

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

Get the sigma for each point of the observed powder pattern.

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

Get the variance (obs+model) for each point of the powder pattern.

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

Get the weight for each point of the powder pattern.

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

Get the vector of X (2theta or time-of-flight) coordinates.

REAL ObjCryst::PowderPattern::GetPowderPatternXMax ( ) const

Get the maximum 2theta.

REAL ObjCryst::PowderPattern::GetPowderPatternXMin ( ) const

Get the Minimum 2theta.

REAL ObjCryst::PowderPattern::GetPowderPatternXStep ( ) const

Get the average step in 2theta.

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

Deprecated:

REAL ObjCryst::PowderPattern::GetR ( ) const

Unweighted R-factor.

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

Radiation& ObjCryst::PowderPattern::GetRadiation ( )

Neutron or x-ray experiment ?

const Radiation& ObjCryst::PowderPattern::GetRadiation ( ) const

Neutron or x-ray experiment ?

RadiationType ObjCryst::PowderPattern::GetRadiationType ( ) const

Neutron or x-ray experiment ?

REAL ObjCryst::PowderPattern::GetRw ( ) const

Get the weighted R-factor.

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

REAL ObjCryst::PowderPattern::GetWavelength ( ) const

wavelength of the experiment (in Angstroems)

virtual void ObjCryst::PowderPattern::GlobalOptRandomMove ( const REAL mutationAmplitude,

const RefParType * type = gpRefParTypeObjCryst

) [virtual]

Make a random move of the current configuration.
This is for global optimization algorithms. the moves for each parameter are less than their global optimization step, multiplied by the mutation amplitude.

Warning:
: this makes a random move for the parameter declared for this object, and it is the duty of the object to decide whether the included objects should be moved and how. (eg an algorithm should only call for a move with the top object, and this object decides how he and his sub-objects moves). By default (RefinableObj implementation) all included objects are moved recursively.
RefinableObj::
Parameters:

mutationAmplitude: multiplier for the maximum move amplitude, for all parameters

type: restrain the change exclusively to parameters of a given type (same type or descendant from this RefParType).

Reimplemented from ObjCryst::RefinableObj.

void ObjCryst::PowderPattern::ImportPowderPattern2ThetaObs ( const string & fileName,

const int nbSkip = 0

)

Import file with 2 columns 2Theta Iobs.

Parameters:

fileName: the filename (surprise!)

nbSkip: the number of lines to skip at the beginning of the file (default=0)

void ObjCryst::PowderPattern::ImportPowderPattern2ThetaObsSigma ( const string & fileName,

const int nbSkip = 0

)

Import file with 3 columns 2Theta Iobs Sigma.

Parameters:

fileName: the filename (surprise!)

nbSkip: the number of lines to skip at the beginning of the file (default=0)

void ObjCryst::PowderPattern::ImportPowderPatternCIF ( const CIF & cif )

Import CIF powder pattern data.

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

Import fullprof-style diffraction data.

Parameters:

fullprofFileName: filename

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

Import diffraction data from a file, with the first line has 2ThetaMin, step, 2thetaMax, and the following lines alternate 10 Iobs and 10 sigma. Ends with null entries (to fill last Iobs line to reach last sigme line).
That's fullprof format #4.
Parameters:

fileName: filename

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

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

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

void ObjCryst::PowderPattern::ImportPowderPatternILL_D1A5 ( const string & filename )

Import powder pattern, format from ILL D1A/D2B (format without counter info).

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

diffraction data in a multi-detector format (fullprof format #6).
First line is text. Third entry of second line is the 2theta step. Third line has the 2thetamin, fourth line has monitors and temperatures. Then each line has ten pairs (I2,I8)of NbCounters,intensity. Ends with negative entries.
Parameters:

fileName: filename

void ObjCryst::PowderPattern::ImportPowderPatternPSI_DMC ( const string & filename )

Import powder pattern, format DMC from PSI.

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

Import *.cpi Sietronics diffraction data.

Parameters:

fileName: filename

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

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

Parameters:

fileName: the filename

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

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

Parameters:

fileName: filename

virtual void ObjCryst::PowderPattern::Init ( ) [protected, virtual]

Init parameters and options.

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

Initialize options.

void ObjCryst::PowderPattern::Prepare ( ) [virtual]

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

Reimplemented from ObjCryst::RefinableObj.

void ObjCryst::PowderPattern::PrepareIntegratedRfactor ( ) const [protected]

Prepare the calculation of the integrated R-factors.

void ObjCryst::PowderPattern::PrintObsCalcData ( ostream & os = cout ) const

Print to thee screen/console the observed and calculated pattern (long, mostly useful for debugging).

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

Save powder pattern to one file, text format, 3 columns theta Iobs Icalc.
If Iobs is missing, the column is omitted.

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

void ObjCryst::PowderPattern::Set2ThetaDisplacement ( const REAL displacement )

Change displacement correction $(2\theta)_{obs} = (2\theta)_{real} + \frac{a}{\cos(\theta)}$ .

void ObjCryst::PowderPattern::Set2ThetaTransparency ( const REAL transparency )

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

void ObjCryst::PowderPattern::SetEnergy ( const REAL energy )

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

virtual void ObjCryst::PowderPattern::SetMaxSinThetaOvLambda ( const REAL max ) [virtual]

Set the maximum value for sin(theta)/lambda.
All data (reflections,..) still exist but are ignored for all calculations.

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

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

void ObjCryst::PowderPattern::SetPowderPatternPar ( const REAL min,

const REAL step,

unsigned long nbPoint

)

the powder pattern angular range & resolution parameter.
this will affect all components (phases) of the pattern.
Use this with caution, as the number of points must be correct with respect to the observed data (Iobs).

Parameters:

min: min 2theta (in radians) or time-of-flight (in microseconds) value,

step: step (assumed constant) in 2theta or time-of-flight (in microseconds).

nbPoints: number of points in the pattern.

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

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

Set the x coordinate of the powder pattern : either the 2theta or time-of-flight values for each recorded point.
The step need not be constant, but the variation must be strictly monotonous.
2theta must be in radians and time-of-flight in microseconds

void ObjCryst::PowderPattern::SetRadiation ( const Radiation & radiation )

Set the radiation.

void ObjCryst::PowderPattern::SetRadiationType ( const RadiationType radiation )

Set the radiation type.

void ObjCryst::PowderPattern::SetSigmaToSqrtIobs ( )

Set sigma=sqrt(Iobs).

void ObjCryst::PowderPattern::SetWavelength ( const string & XRayTubeElementName,

const REAL alpha12ratio = 0.5

)

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

Parameters:

XRayTubeElementName : name of the anticathode element name. Known ones are Cr, Fe, Cu, Mo, Ag.

alpha2Alpha2ratio: Kalpha2/Kalpha1 ratio (0.5 by default)

Alpha1 and alpha2 wavelength are taken from R. Grosse-Kunstleve package, and the average wavelength is calculated using the alpha2/alpha1 weight. All structure factors computation are made using the average wavelength, and for powder diffraction, profiles are output at the alpha1 and alpha2 ratio for the calculated pattern.
NOTE : if the name of the wavelength is generic (eg"Cu"), then the program considers that there are both Alpha1 and Alpha2, and thus automatically changes the WavelengthType to WAVELENGTH_ALPHA12. If instead either alpha1 or alpha2 (eg "CuA1") is asked for, the WavelengthType is set to WAVELENGTH_MONOCHROMATIC. In both cases, the radiation type is set to X-Ray.

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

Set the wavelength of the experiment (in Angstroems).

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

void ObjCryst::PowderPattern::SetWeightPolynomial ( const REAL a,

const REAL b,

const REAL c,

const REAL minRelatIobs = 1e-3

)

Set w = 1/(a+ Iobs + b*Iobs^2+c*Iobs^3).
To filter too small or null intensities: if Iobs < [minRelatIobs * max(Iobs)], then use Iobs=minRelatIobs * max(Iobs) to compute the weight.
Typical values: a=2*min(Iobs) b=2/max(Iobs) c=0

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

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

void ObjCryst::PowderPattern::SetWeightToUnit ( )

Set w = 1.

void ObjCryst::PowderPattern::SetXZero ( const REAL newZero )

Change Zero in x (2theta,tof).

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

Convert sin(theta)/lambda to pixel, depending on the type of radiation.
This does not take into account any zero/transparency, etc... correction

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

Convert sin(theta)/lambda to X (i.e.
either to 2theta or to TOF), depending on the type of radiation.
This does not take into account any zero/transparency, etc... correction

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

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

Parameters:

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

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

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

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

Get the pixel number on the experimental pattern, from the theoretical (uncorrected) x coordinate, taking into account all corrections.
(zero, transparency,..).
For internal use only.

Parameters:

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

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

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

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

Convert X (either 2theta or TOF) to sin(theta)/lambda, depending on the type of radiation.
This does not take into account any zero/transparency, etc... correction

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

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

For internal use only.

Parameters:

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

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

virtual void ObjCryst::PowderPattern::XMLInput ( istream & is,

const XMLCrystTag & tag

) [virtual]

Input From stream.

Todo:
Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc...

Reimplemented from ObjCryst::RefinableObj.

virtual void ObjCryst::PowderPattern::XMLOutput ( ostream & os,

int indent = 0

) const [virtual]

Output to stream in well-formed XML.

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

Reimplemented from ObjCryst::RefinableObj.

Member Data Documentation

REAL ObjCryst::PowderPattern::m2ThetaDisplacement [protected]

Displacement correction : $(2\theta)_{obs} = (2\theta)_{real} + \frac{a}{\cos(\theta)}$ .

REAL ObjCryst::PowderPattern::m2ThetaTransparency [protected]

Transparency correction : $(2\theta)_{obs} = (2\theta)_{real} + b\sin(2\theta)$ .

REAL ObjCryst::PowderPattern::mChi2 [mutable, protected]

CrystVector_REAL ObjCryst::PowderPattern::mChi2Cumul [mutable, protected]

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

REAL ObjCryst::PowderPattern::mChi2LikeNorm [mutable, protected]

This is the logarithm of the part of log(Likelihood) which corresponds to the normalization terms of gaussian distribution for each obs/calc point.
In practice, this is the sum of 1/2*log(2pi*sig(i)^2), although we discard the 2pi terms.

RefinableObjClock ObjCryst::PowderPattern::mClockChi2 [mutable, protected]

Clock the last time Chi^2 was computed.

RefinableObjClock ObjCryst::PowderPattern::mClockIntegratedFactorsPrep [mutable, protected]

RefinableObjClock ObjCryst::PowderPattern::mClockNbPointUsed [mutable, protected]

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

RefinableObjClock ObjCryst::PowderPattern::mClockPowderPatternCalc [mutable, protected]

When was the powder pattern last computed ?

RefinableObjClock ObjCryst::PowderPattern::mClockPowderPatternIntegratedCalc [mutable, protected]

When was the powder pattern (integrated) last computed ?

RefinableObjClock ObjCryst::PowderPattern::mClockPowderPatternPar [protected]

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

RefinableObjClock ObjCryst::PowderPattern::mClockPowderPatternRadiation [protected]

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

RefinableObjClock ObjCryst::PowderPattern::mClockPowderPatternXCorr [protected]

Corrections to 2Theta.

RefinableObjClock ObjCryst::PowderPattern::mClockScaleFactor [mutable, protected]

Last modification of the scale factor.

REAL ObjCryst::PowderPattern::mDIFA [protected]

Time Of Flight (TOF) parameters : $t = DIFC*\frac{\sin(\theta)}{\lambda} + DIFA*\left(\frac{\sin(\theta)}{\lambda}\right)^2 + mXZero$ .

REAL ObjCryst::PowderPattern::mDIFC [protected]

Time Of Flight (TOF) parameters : $t = DIFC*\frac{\sin(\theta)}{\lambda} + DIFA*\left(\frac{\sin(\theta)}{\lambda}\right)^2 + mXZero$ .

CrystVector_REAL ObjCryst::PowderPattern::mExcludedRegionMaxX [protected]

Max coordinate for 2theta for all excluded regions.

CrystVector_REAL ObjCryst::PowderPattern::mExcludedRegionMinX [protected]

Min coordinate for for all excluded regions.

CrystMatrix_REAL ObjCryst::PowderPattern::mFitScaleFactorB [mutable, protected]

Used to fit the components' scale factors.

CrystMatrix_REAL ObjCryst::PowderPattern::mFitScaleFactorM [mutable, protected]

Used to fit the components' scale factors.

CrystMatrix_REAL ObjCryst::PowderPattern::mFitScaleFactorX [mutable, protected]

Used to fit the components' scale factors.

CrystVector_REAL ObjCryst::PowderPattern::mIntegratedObs [mutable, protected]

CrystVector_long ObjCryst::PowderPattern::mIntegratedPatternMax [mutable, protected]

CrystVector_long ObjCryst::PowderPattern::mIntegratedPatternMin [mutable, protected]

CrystVector_REAL ObjCryst::PowderPattern::mIntegratedVarianceObs [mutable, protected]

CrystVector_REAL ObjCryst::PowderPattern::mIntegratedWeight [mutable, protected]

CrystVector_REAL ObjCryst::PowderPattern::mIntegratedWeightObs [mutable, protected]

bool ObjCryst::PowderPattern::mIsXAscending [protected]

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

REAL ObjCryst::PowderPattern::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.

unsigned long ObjCryst::PowderPattern::mNbIntegrationUsed [mutable, protected]

Number of integration intervals actually used, due to the maximum value of sin(theta)/lambda.

unsigned long ObjCryst::PowderPattern::mNbPoint [protected]

Number of points in the pattern.

unsigned long ObjCryst::PowderPattern::mNbPointUsed [mutable, protected]

Number of points actually used, due to the maximum value of sin(theta)/lambda.

RefObjOpt ObjCryst::PowderPattern::mOptProfileIntegration [protected]

Use Integrated profiles for Chi^2, R, Rwp...

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternBackgroundCalc [mutable, protected]

The calculated powder pattern part which corresponds to 'background' (eg non-scalable components).
It is already included in mPowderPatternCalc

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternBackgroundIntegratedCalc [mutable, protected]

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

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternCalc [mutable, protected]

The calculated powder pattern.
It is mutable since it is completely defined by other parameters (eg it is not an 'independent parameter')

ObjRegistry<PowderPatternComponent> ObjCryst::PowderPattern::mPowderPatternComponentRegistry [protected]

The components (crystalline phases, background,...) of the powder pattern.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternIntegratedCalc [mutable, protected]

The calculated powder pattern, integrated.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternObs [protected]

The observed powder pattern.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternObsSigma [protected]

The sigma of the observed pattern.

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternVariance [mutable, protected]

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

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternVarianceIntegrated [mutable, protected]

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

CrystVector_REAL ObjCryst::PowderPattern::mPowderPatternWeight [mutable, protected]

The weight for each point of the pattern.

REAL ObjCryst::PowderPattern::mR [mutable, protected]

Radiation ObjCryst::PowderPattern::mRadiation [protected]

The Radiation corresponding to this experiment.

REAL ObjCryst::PowderPattern::mRw [mutable, protected]

CrystVector_int ObjCryst::PowderPattern::mScalableComponentIndex [mutable, protected]

For internal use only.

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

CrystVector_REAL ObjCryst::PowderPattern::mScaleFactor [mutable, protected]

The scale factors for each component.
For unscalable phases, this is set to 1 (constant).
This is mutable because generally we use the 'best' scale factor, but it should not be...

bool ObjCryst::PowderPattern::mStatisticsExcludeBackground [protected]

Should Statistics (R, Rw,..) exclude the background ?

bool ObjCryst::PowderPattern::mUseFastLessPreciseFunc [protected]

Use faster, less precise functions ?

CrystVector_REAL ObjCryst::PowderPattern::mX [protected]

Vector of x coordinates (either 2theta or time-of-flight) for the pattern.
Stored in ascending order for 2theta, and descending for TOF, i.e. always in ascending order for the corresponding sin(theta)/lambda.

REAL ObjCryst::PowderPattern::mXZero [protected]

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

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

PowderPattern.h

Generated on Tue Nov 14 15:04:34 2006 for ObjCryst++ by

1.3.6

ObjCryst::PowderPattern Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation