Main Page   Namespace List   Class Hierarchy   Alphabetical List   Compound List   Namespace Members   Compound Members   Related Pages  

ObjCryst::DiffractionDataSingleCrystal Class Reference

DiffractionData object for Single Crystal analysis. More...

#include <DiffractionDataSingleCrystal.h>

Inheritance diagram for ObjCryst::DiffractionDataSingleCrystal::

ObjCryst::ScatteringData ObjCryst::RefinableObj List of all members.

Public Methods

 DiffractionDataSingleCrystal ()
 DiffractionDataSingleCrystal (Crystal &cryst)
 Constructor, with an assigned crystal structure.

 DiffractionDataSingleCrystal (const DiffractionDataSingleCrystal &old)
 Copy constructor.

 ~DiffractionDataSingleCrystal ()
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. More...

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. More...

void ImportHklIobs (const string &fileName, const long nbRefl, const int skipLines=0)
 Import h,k,l,I form a file. More...

void ImportHklIobsSigma (const string &fileName, const long nbRefl, const int skipLines=0)
 Import h,k,l,I,Sigma form a file. More...

void ImportHklIobsSigmaJanaM91 (const string &fileName)
 Import h,k,l,I,Sigma form a Jana98 '*.m91' file. More...

virtual REAL GetRw () const
 Return the Crystal R-factor (weighted). More...

virtual REAL GetR () const
 Return the Crystal R-factor (unweighted). More...

virtual REAL GetChi2 () const
 Return conventionnal Chi^2. More...

virtual void FitScaleFactorForRw ()
 Compute the best scale factor minimising Rw. More...

virtual void FitScaleFactorForR ()
 Compute the best scale factor minimising R. More...

virtual REAL GetBestRFactor ()
 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. More...

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.

unsigned int GetNbCostFunction () const
 Number of Cost functions.

const string & GetCostFunctionName (const unsigned int) const
 Get a Cost function name from its id#.

const string & GetCostFunctionDescription (const unsigned int) const
 Get the (short) description of a cost function.

virtual REAL GetCostFunctionValue (const unsigned int)
 Get the current value of a cost function this should be const...

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. More...

virtual void XMLInput (istream &is, const XMLCrystTag &tag)
 Input From stream. More...


Private Methods

virtual void InitRefParList ()
void CalcIcalc () const
 Calc intensities.

virtual CrystVector_long SortReflectionByTheta (const REAL maxTheta=-1.)
 sort reflections by theta values (also get rid of [0,0,0] if present) If maxTheta >0, then only reflections where theta<maxTheta are kept
Returns:
an array with the subscript of the kept reflections (for inherited classes).
More...


void InitOptions ()
 Init options (currently only twinning).

void PrepareTwinningCalc () const
 Determine the index of reflections to be summed because of twinning. 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). More...

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 scaleapplies to intensities.

RefinableObjClock mClockIcalc
 Last time Icalc was computed.

RefinableObjClock mClockScaleFactor
 Last modification of the scale factor.

RefObjOpt mTwinningOption
 Option for the type of twinning.

CrystVector_REAL mTwinnedIobsSum
 The observed intensities summed on all reflections that are (or could be) overlapped dur to a twinning.

CrystVector_REAL mTwinnedIcalcSum
 The calculated intensities summed on all reflections that are (or could be) overlapped dur to a twinning.

CrystVector_REAL mTwinnedWeight
 The weight on each reflection sum in case of twinning. The sum is the inverse of the sum of all sigma^2.

CrystVector_long mTwinnedGroupIndex
 The index of reflections which need to be summed. They must have been sorted by increasing theta values. Each entry marks the beginning of a new batch of reflections to be summed.

RefinableObjClock mClockPrepareTwinningCorr
 Clock for twinning, when the preparation of twiinning correction was last made.


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...


Member Function Documentation

virtual void ObjCryst::DiffractionDataSingleCrystal::FitScaleFactorForR   [virtual]
 

Compute the best scale factor minimising R.

The computed scale factor is immediatly applied to Icalc

virtual void ObjCryst::DiffractionDataSingleCrystal::FitScaleFactorForRw   [virtual]
 

Compute the best scale factor minimising Rw.

The computed scale factor is immediatly applied to Icalc

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

Return conventionnal Chi^2.

Returns:

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.

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

Return the Crystal R-factor (unweighted).

Returns:

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

Return the Crystal R-factor (weighted).

Returns:

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

Import h,k,l,I form 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.

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

Import h,k,l,I,Sigma form 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.

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

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

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

Parameters:
fileName  The name of the data file.

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.

virtual 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.

virtual CrystVector_long ObjCryst::DiffractionDataSingleCrystal::SortReflectionByTheta const REAL    maxTheta = -1. [private, virtual]
 

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

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

For internal use only.

Reimplemented from ObjCryst::ScatteringData.

virtual 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.

virtual 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.


Member Data Documentation

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.


The documentation for this class was generated from the following file:
Generated on Tue Feb 5 17:37:21 2002 for ObjCryst++ by doxygen1.2.13.1 written by Dimitri van Heesch, © 1997-2001