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:

Collaboration diagram for ObjCryst::PowderPattern:

Public Member Functions
	PowderPattern (const PowderPattern &)
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry.
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.
REAL	GetScaleFactor (const int i) const
	Access to the scale factor of components (will be 1 for background components).
REAL	GetScaleFactor (const PowderPatternComponent &comp) const
	Access to the scale factor of components (will be 1 for background components).
void	SetScaleFactor (const int i, REAL s)
	Access to the scale factor of components (will be 1 for background components).
void	SetScaleFactor (const PowderPatternComponent &comp, REAL s)
	Access to the scale factor of components (will be 1 for background components).
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)) ?
const RefinableObjClock &	GetClockNbPointUsed () const
	Clock corresponding to the last time the number of points used was changed.
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 $(2\theta)_{obs} = (2\theta)_{real} + a\cos(\theta)$ .
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.
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. If Iobs is missing, the column is omitted.
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.
REAL	GetIntegratedChi2 () const
	Return integrated Chi^2.
REAL	GetChi2_Option () const
	Return the conventionnal or integrated Chi^2, depending on the option.
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. 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).
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 ()
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
virtual void	SetMaxSinThetaOvLambda (const REAL max)
	Set the maximum value for sin(theta)/lambda. All data (reflections,..) still exist but are ignored for all calculations.
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. (zero, transparency,..).
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. either to 2theta or to TOF), depending on the type of radiation.
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.
PeakList	FindPeaks (const float dmin=2.0, const float maxratio=0.01, const unsigned int maxpeak=100)
	Find peaks in the pattern.
const CrystVector_REAL &	GetScaleFactor () const
	Access the scale factors (see PowderPattern::mScaleFactor).
CrystVector_REAL &	GetScaleFactor ()
	Access the scale factors (see PowderPattern::mScaleFactor).
void	ExportFullprof (const std::string &prefix) const
	Export powder pattern & crystal structure in Fullprof format.
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. It is mutable since it is completely defined by other parameters (eg it is not an 'independent parameter').
CrystVector_REAL	mPowderPatternIntegratedCalc
	The calculated powder pattern, integrated.
CrystVector_REAL	mPowderPatternBackgroundCalc
	The calculated powder pattern part which corresponds to 'background' (eg non-scalable components). It is already included in mPowderPatternCalc.
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. Integrated.
CrystVector_REAL	mChi2Cumul
	The cumulative Chi^2 (integrated or not, depending on the option).
CrystVector_REAL	mPowderPatternUsedCalc
	The calculated powder pattern. Cropped to the maximum sin(theta)/lambda for LSQ.
CrystVector_REAL	mPowderPatternUsedObs
	The calculated powder pattern. Cropped to the maximum sin(theta)/lambda for LSQ.
CrystVector_REAL	mPowderPatternUsedWeight
	The weight for each point of the pattern. Cropped to the maximum sin(theta)/lambda for LSQ.
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
ObjRegistry < PowderPatternComponent >	mPowderPatternComponentRegistry
	The components (crystalline phases, background,...) of the powder pattern.
CrystVector_REAL	mScaleFactor
	The scale factors for each component. For unscalable phases, this is set to 1 (constant).
bool	mUseFastLessPreciseFunc
	Use faster, less precise functions ?
bool	mStatisticsExcludeBackground
	Should Statistics (R, Rw,..) exclude the background ?
CrystVector_int	mScalableComponentIndex
CrystMatrix_REAL	mFitScaleFactorM
CrystMatrix_REAL	mFitScaleFactorB
CrystMatrix_REAL	mFitScaleFactorX
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	mIntegratedChi2
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. In practice, this is the sum of 1/2log(2pisig(i)^2), although we discard the 2pi terms.
REAL	mIntegratedChi2LikeNorm
REAL	mR
REAL	mRw
RefinableObjClock	mClockChi2
	Clock the last time Chi^2 was computed.
RefinableObjClock	mClockIntegratedChi2
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.

Definition at line 485 of file PowderPattern.h.

Member Function Documentation

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

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.

Definition at line 1707 of file PowderPattern.cpp.

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, 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,:

Deprecated:: 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.

Definition at line 4301 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::ExportFullprof ( const std::string & prefix ) const

Export powder pattern & crystal structure in Fullprof format.

This will create two files - the .pcr file (including the crystal structure and all pattern parameters), and the .dat file with the powder pattern, written using the "Ins=10" file format.

Parameters:

prefix,:

the prefix used to output the two files, 'prefix'.pcr and 'prefix'.dat

Note:: : in development. Only supports constant wavelength neutron & X-ray patterns.

Definition at line 4733 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::FitScaleFactorForR ( ) const

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

min is the *beginning* of the excluded region

Definition at line 3518 of file PowderPattern.cpp.

void ObjCryst::PowderPattern::FitScaleFactorForRw ( ) const

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

min is the *beginning* of the excluded region

Definition at line 3834 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetChi2 ( ) const

Return conventionnal Chi^2.

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

min is the *beginning* of the excluded region !

Definition at line 3377 of file PowderPattern.cpp.

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.

Definition at line 1905 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetIntegratedChi2 ( ) const

Return integrated Chi^2.

Definition at line 3456 of file PowderPattern.cpp.

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.

Definition at line 4357 of file PowderPattern.cpp.

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:

Definition at line 1888 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetR ( ) const

Unweighted R-factor.

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

min is the *beginning* of the excluded region !

Definition at line 2981 of file PowderPattern.cpp.

REAL ObjCryst::PowderPattern::GetRw ( ) const

Get the weighted R-factor.

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

min is the *beginning* of the excluded region !

Definition at line 3174 of file PowderPattern.cpp.

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.

Definition at line 4318 of file PowderPattern.cpp.

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)

Definition at line 2380 of file PowderPattern.cpp.

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)

Definition at line 2320 of file PowderPattern.cpp.

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

Import fullprof-style diffraction data.

Parameters:

fullprofFileName,:

filename

Definition at line 2091 of file PowderPattern.cpp.

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

Definition at line 2520 of file PowderPattern.cpp.

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)

Definition at line 2660 of file PowderPattern.cpp.

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

Definition at line 2438 of file PowderPattern.cpp.

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

Import *.cpi Sietronics diffraction data.

Parameters:

fileName,:

filename

Definition at line 2272 of file PowderPattern.cpp.

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

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

Parameters:

fileName,:

the filename

Definition at line 2583 of file PowderPattern.cpp.

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

Import *.xdd diffraction data (Topas,.

..).

Parameters:

fileName,:

filename

Definition at line 2229 of file PowderPattern.cpp.

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

For internal use only.

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

Reimplemented from ObjCryst::RefinableObj.

Definition at line 4437 of file PowderPattern.cpp.

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...

Definition at line 2946 of file PowderPattern.cpp.

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().

Definition at line 2921 of file PowderPattern.cpp.

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()

Definition at line 1790 of file PowderPattern.cpp.

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

Definition at line 1803 of file PowderPattern.cpp.

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.

Definition at line 1847 of file PowderPattern.cpp.

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.

Definition at line 1841 of file PowderPattern.cpp.

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

Definition at line 4285 of file PowderPattern.cpp.

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

Definition at line 4265 of file PowderPattern.cpp.

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

Definition at line 4528 of file PowderPattern.cpp.

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

Definition at line 4492 of file PowderPattern.cpp.

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.

Definition at line 2006 of file PowderPattern.cpp.

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.

Definition at line 2001 of file PowderPattern.cpp.

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

Definition at line 4509 of file PowderPattern.cpp.

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.

Definition at line 1991 of file PowderPattern.cpp.

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.

Definition at line 1898 of file ObjCryst/IO.cpp.

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.

Definition at line 1791 of file ObjCryst/IO.cpp.

Member Data Documentation

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

For internal use only.

Used to fit the components' scale factors

Definition at line 995 of file PowderPattern.h.

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.

Definition at line 1023 of file PowderPattern.h.

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

For internal use only.

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

Definition at line 993 of file PowderPattern.h.

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...

Definition at line 983 of file PowderPattern.h.

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.

Definition at line 932 of file PowderPattern.h.

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

ObjCryst::PowderPattern Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation