ObjCryst::DiffractionDataSingleCrystal Class Reference

DiffractionData object for Single Crystal analysis. More...

Inheritance diagram for ObjCryst::DiffractionDataSingleCrystal:

Collaboration diagram for ObjCryst::DiffractionDataSingleCrystal:

Public Member Functions
	DiffractionDataSingleCrystal (const bool regist=true)
	Default constructor.
	DiffractionDataSingleCrystal (Crystal &cryst, const bool regist=true)
	Constructor, with an assigned crystal structure.
	DiffractionDataSingleCrystal (const DiffractionDataSingleCrystal &old)
	Copy constructor.
virtual DiffractionDataSingleCrystal *	CreateCopy () const
	So-called virtual copy constructor.
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.
const CrystVector_REAL &	GetIcalc () const
	returns the calculated diffracted intensity.
const CrystVector_REAL &	GetIobs () const
	Return the array of observed intensities for all peaks.
void	SetIobs (const CrystVector_REAL &)
	Return the array of observed intensities for all peaks.
const CrystVector_REAL &	GetSigma () const
	Return the array of sigmas for observed intensities, for all peaks.
void	SetSigma (const CrystVector_REAL &)
	Return the array of sigmas for observed intensities, for all peaks.
void	SetIobsToIcalc ()
	Set Iobs to current values of Icalc. Mostly used for tests.
const CrystVector_REAL &	GetWeight () const
	Return the weights (for each reflection) used for computing Rw.
void	SetWeight (const CrystVector_REAL &)
	Change the weights (for each reflection) used for computing Rw.
void	SetHklIobs (const CrystVector_long &h, const CrystVector_long &k, const CrystVector_long &l, const CrystVector_REAL &iObs, const CrystVector_REAL &sigma)
	input H,K,L, Iobs and Sigma
void	ImportHklIobs (const string &fileName, const long nbRefl, const int skipLines=0)
	Import h,k,l,I from a file.
void	ImportHklIobsSigma (const string &fileName, const long nbRefl, const int skipLines=0)
	Import h,k,l,I,Sigma from a file.
void	ImportHklIobsSigmaJanaM91 (const string &fileName)
	Import h,k,l,I,Sigma from a Jana98 '*.m91' file.
void	ImportHklIobsGroup (const string &fileName, const unsigned int skipLines=0)
	Import h,k,l and grouped intensities from a file.
virtual REAL	GetRw () const
	Return the Crystal R-factor (weighted).
virtual REAL	GetR () const
	Return the Crystal R-factor (unweighted).
virtual REAL	GetChi2 () const
	Return conventionnal Chi^2.
virtual void	FitScaleFactorForRw () const
	Compute the best scale factor minimising Rw.
virtual void	FitScaleFactorForR () const
	Compute the best scale factor minimising R.
virtual REAL	GetBestRFactor () const
	Compute the best scale factor to minimize R, apply this scale factor and return the R value obtained.
virtual void	SetSigmaToSqrtIobs ()
	Set sigma for all observed intensities to sqrt(obs).
virtual void	SetWeightToInvSigma2 (const REAL minRelatSigma=1e-4)
	Set the weight for all observed intensities to 1/sigma^2.
REAL	GetScaleFactor () const
	Scale factor (applied to Icalc to match Iobs).
virtual void	PrintObsData () const
	Print H, K, L Iobs sigma for all reflections.
virtual void	PrintObsCalcData () const
	Print H, K, L Iobs sigma Icalc for all reflections Iobs and sigma (if given) are scaled to Icalc (if available).
virtual void	SetUseOnlyLowAngleData (const bool useOnlyLowAngle, const REAL angle=0.)
void	SaveHKLIobsIcalc (const string &filename="hklIobsIcalc.out")
	Save H,K,L Iobs Icalc to a file, text format, 3 columns theta Iobs Icalc. If Iobs is missing, the column is omitted.
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.
virtual const Radiation &	GetRadiation () const
	Get the radiation object for this data.
Radiation &	GetRadiation ()
virtual void	SetRadiationType (const RadiationType radiation)
	Set : neutron or x-ray experiment ? Wavelength ?
void	SetWavelength (const REAL)
	Set the (monochromatic) wavelength of the beam.
void	SetWavelength (const string &XRayTubeElementName, const REAL alpha2Alpha2ratio=0.5)
	\ brief Set X-Ray tube radiation.
void	SetEnergy (const REAL)
	Set the (monochromatic) energy of the beam.
Private Member Functions
virtual void	InitRefParList ()
void	CalcIcalc () const
	Calc intensities.
virtual CrystVector_long	SortReflectionBySinThetaOverLambda (const REAL maxTheta=-1.)
void	InitOptions ()
	Init options (currently only twinning).
void	PrepareTwinningCalc () const
	Determine the index of reflections to be summed because of twinning (GroupOption==1) The reflections must have been sorted by increasing theta beforehand.
Private Attributes
bool	mHasObservedData
	Are there observed intensities ?
CrystVector_REAL	mObsIntensity
	Observed intensity (after ABS and LP corrections).
CrystVector_REAL	mObsSigma
	Sigma for observed intensities (either individual reflections or spectrum).
CrystVector_REAL	mWeight
	weight for computing R-Factor, for each observed value.
CrystVector_REAL	mCalcIntensity
	Calculated intensities.
REAL	mScaleFactor
	Scale factor. It is applied when computing intensities. The scale applies to intensities.
REAL	mChi2
	Chi^2.
RefinableObjClock	mClockIcalc
	Last time Icalc was computed.
RefinableObjClock	mClockScaleFactor
	Last modification of the scale factor.
RefinableObjClock	mClockChi2
	Clock the last time Chi^2 was computed.
RefObjOpt	mGroupOption
	Option for the type of grouping (0:no, 1:by theta values (twinning), 2:user-supplied groups).
CrystVector_REAL	mGroupIobs
	The observed intensities summed on all reflections that are (or could be) overlapped dur to a twinning.
CrystVector_REAL	mGroupSigma
	The uncertainty on observed grouped intensities.
CrystVector_REAL	mGroupIcalc
	The calculated intensities summed on all reflections that are grouped.
CrystVector_REAL	mGroupWeight
	The weight on each reflection sum in case of grouped reflections. The sum is the inverse of the sum of all sigma^2.
CrystVector_long	mGroupIndex
	The index of reflections which need to be summed.
long	mNbGroup
	Number of groups.
long	mNbGroupUsed
	Number of groups below max[sin(theta)/lambda].
RefinableObjClock	mClockPrepareTwinningCorr
	Clock for twinning, when the preparation of twinning correction was last made.
Radiation	mRadiation

Detailed Description

DiffractionData object for Single Crystal analysis.

Currently this handles only in the simplest way single crystal dat: ie only data which has been completely corrected for Lorentz/Polarization and absorption.

What needs to be developped: define the geometry of the experiment (incident and emerging angles), the polarization of the beam, etc...

Definition at line 50 of file DiffractionDataSingleCrystal.h.

Constructor & Destructor Documentation

ObjCryst::DiffractionDataSingleCrystal::DiffractionDataSingleCrystal ( const bool regist = true )

Default constructor.

Parameters:

regist,:

if false, do not add to the global registry of single crystal data or refinable objects - this is only useful for data to be used internally only.

Deprecated:: Use the constructor passing a crystal structure instead.

Definition at line 55 of file DiffractionDataSingleCrystal.cpp.

ObjCryst::DiffractionDataSingleCrystal::DiffractionDataSingleCrystal	(	Crystal &	cryst,
		const bool	regist = `true`
	)

Constructor, with an assigned crystal structure.

Parameters:

regist,:

if false, do not add to the global registry of single crystal data or refinable objects - this is only useful for data to be used internally only.

Definition at line 66 of file DiffractionDataSingleCrystal.cpp.

Member Function Documentation

void ObjCryst::DiffractionDataSingleCrystal::FitScaleFactorForR ( ) const [virtual]

Compute the best scale factor minimising R.

The computed scale factor is immediatly applied to Icalc

Definition at line 746 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::FitScaleFactorForRw ( ) const [virtual]

Compute the best scale factor minimising Rw.

The computed scale factor is immediatly applied to Icalc

Definition at line 701 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetChi2 ( ) const [virtual]

Return conventionnal Chi^2.

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

Definition at line 623 of file DiffractionDataSingleCrystal.cpp.

const CrystVector_REAL & ObjCryst::DiffractionDataSingleCrystal::GetIcalc ( ) const

returns the calculated diffracted intensity.

This is an array of calculated intensities for each reflections in the single crystal case, and the array with the full powder powder profile for powder diffraction.

Definition at line 163 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::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 903 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetR ( ) const [virtual]

Return the Crystal R-factor (unweighted).

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

Definition at line 584 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetRw ( ) const [virtual]

Return the Crystal R-factor (weighted).

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

Definition at line 544 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::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 896 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobs	(	const string &	fileName,
		const long	nbRefl,
		const int	skipLines = `0`
	)

Import h,k,l,I from a file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters:

	fileName	The name of the data file. This file should be formatted with H,k,l, Iobs separated by spaces.
	nbRefl	The number of reflections to extract.
	skipLines	The number of lines to skip at the beginning of the file.

Definition at line 221 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobsGroup	(	const string &	fileName,
		const unsigned int	skipLines = `0`
	)

Import h,k,l and grouped intensities from a file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters:

	fileName	The name of the data file. This file should be formatted with H,k,l, Iobs separated by spaces.
	skipLines	The number of lines to skip at the beginning of the file.

File format (the reflection which has an intensity entry marks the end of the group) h k l Igroup -2 4 2 -2 -4 2 100.4 2 -4 1 2 4 1 193.2 ...

Definition at line 433 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobsSigma	(	const string &	fileName,
		const long	nbRefl,
		const int	skipLines = `0`
	)

Import h,k,l,I,Sigma from a file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters:

	fileName	The name of the data file. This file should be formatted with H,k,l, Iobs and Sigma separated by spaces.
	nbRefl	The number of reflections to extract.
	skipLines	The number of lines to skip at the beginning of the file.

Definition at line 284 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobsSigmaJanaM91 ( const string & fileName )

Import h,k,l,I,Sigma from a Jana98 '*.m91' file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters:

fileName

The name of the data file.

Definition at line 352 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::PrintObsData ( ) const [virtual]

Print H, K, L Iobs sigma for all reflections.

Definition at line 819 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetHklIobs	(	const CrystVector_long &	h,
		const CrystVector_long &	k,
		const CrystVector_long &	l,
		const CrystVector_REAL &	iObs,
		const CrystVector_REAL &	sigma
	)

input H,K,L, Iobs and Sigma

Parameters:

	h,k,l,:	REAL arrays (vectors with NbRefl elements -same size) with the h, k and l coordinates of all reflections.
	iobs,sigma,:	REAL arrays (vectors with NbRefl elements -same size) with the Observed intensity and sigma for all reflections.

Definition at line 120 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetSigmaToSqrtIobs ( ) [virtual]

Set sigma for all observed intensities to sqrt(obs).

Definition at line 796 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetWavelength	(	const string &	XRayTubeElementName,
		const REAL	alpha2Alpha2ratio = `0.5`
	)

\ brief Set X-Ray tube radiation.

Parameters:

	XRayTubeElementName	: name of the anticathode element name. Known ones are Cr, Fe, Cu, Mo, Ag.
	alpha2Alpha2ratio,:	Kalpha2/Kalpha1 ratio (0.5 by default)

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 946 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetWeightToInvSigma2 ( const REAL minRelatSigma = 1e-4 ) [virtual]

Set the weight for all observed intensities to 1/sigma^2.

For sigmas which are smaller than minRelatSigma times the max value of sigma, the output weight is set to 0.

Definition at line 803 of file DiffractionDataSingleCrystal.cpp.

CrystVector_long ObjCryst::DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda ( const REAL maxSTOL = -1. ) [private, virtual]

For internal use only.

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

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

Reimplemented from ObjCryst::ScatteringData.

Definition at line 989 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::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 1187 of file ObjCryst/IO.cpp.

void ObjCryst::DiffractionDataSingleCrystal::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 1087 of file ObjCryst/IO.cpp.

Member Data Documentation

CrystVector_long ObjCryst::DiffractionDataSingleCrystal::mGroupIndex [mutable, private]

The index of reflections which need to be summed.

They must have been sorted by increasing theta values. Each entry (the reflection index) marks the beginning of a new batch of reflections to be summed.

Here only the groups of reflections are roughly sorted by sin(theta)/lambda. It is assumed, howver, that grouped reflections are of approximately the same d_hkl. After ScatteringData::GetNbReflBelowMaxSinThetaOvLambda(), the number of groups for which *all* reflections are below the limit are taken into account for the statistics.

Note that DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda() is called (i.e. immediately after importing the reflections)

Definition at line 332 of file DiffractionDataSingleCrystal.h.

CrystVector_REAL ObjCryst::DiffractionDataSingleCrystal::mObsIntensity [private]

Observed intensity (after ABS and LP corrections).

In the single crystal case, this is a list of intensity corresponding to (h,k,l). For a powder sample, this is a list of all peaks intensities.

Definition at line 287 of file DiffractionDataSingleCrystal.h.

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

ObjCryst::DiffractionDataSingleCrystal Class Reference

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation