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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 ()
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_double & GetIcalc () const
 returns the calculated diffracted intensity. More...

const CrystVector_double & GetIobs () const
 Return the array of observed intensities for all peaks.

void SetIobs (const CrystVector_double &)
 Return the array of observed intensities for all peaks.

const CrystVector_double & GetSigma () const
 Return the array of sigmas for observed intensities, for all peaks.

void SetSigma (const CrystVector_double &)
 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_double & GetWeight () const
 Return the weights (for each reflection) used for computing Rw.

void SetWeight (const CrystVector_double &)
 Change the weights (for each reflection) used for computing Rw.

void SetHklIobs (CrystVector_long const &h, CrystVector_long const &k, CrystVector_long const &l, CrystVector_double const &iObs, CrystVector_double const &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 double GetRw () const
 Return the Crystal R-factor (weighted). More...

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

virtual double 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 double 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 double minRelatSigma=1e-4)
 Set the weight for all observed intensities to 1/sigma^2. More...

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

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.


Private Attributes

bool mHasObservedData
 Are there observed intensities ?

CrystVector_double mObsIntensity
 Observed intensity (after ABS and LP corrections). More...

CrystVector_double mObsSigma
 Sigma for observed intensities (either individual reflections or spectrum).

CrystVector_double mWeight
 weight for computing R-Factor, for each observed value.

CrystVector_double mCalcIntensity
 Calculated intensities.

double mScaleFactor
 Scale factor. It is applied when computing intensities. The scaleapplies to intensities.


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 FitScaleFactorForR   [virtual]
 

Compute the best scale factor minimising R.

The computed scale factor is immediatly applied to Icalc

virtual void FitScaleFactorForRw   [virtual]
 

Compute the best scale factor minimising Rw.

The computed scale factor is immediatly applied to Icalc

virtual double GetChi2   const [virtual]
 

Return conventionnal Chi^2.

Returns:

const CrystVector_double& 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 double GetR   const [virtual]
 

Return the Crystal R-factor (unweighted).

Returns:

virtual double GetRw   const [virtual]
 

Return the Crystal R-factor (weighted).

Returns:

void 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 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 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 SetHklIobs CrystVector_long const &    h,
CrystVector_long const &    k,
CrystVector_long const &    l,
CrystVector_double const &    iObs,
CrystVector_double const &    sigma
 

input H,K,L, Iobs and Sigma.

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

virtual void SetWeightToInvSigma2 const double    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 void 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 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_double 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 Wed Nov 14 19:48:37 2001 for ObjCryst++ by doxygen1.2.11.1 written by Dimitri van Heesch, © 1997-2001