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ObjCryst::ScatteringData Class Reference

Class to compute structure factors for a set of reflections and a Crystal. More...

Inheritance diagram for ObjCryst::ScatteringData:

ObjCryst::RefinableObj ObjCryst::DiffractionDataSingleCrystal ObjCryst::PowderPatternDiffraction List of all members.

Public Methods

virtual ScatteringData * CreateCopy () const=0
 So-called virtual copy constructor.

virtual void SetHKL (const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l)
 input H,K,L

virtual void GenHKLFullSpace (const REAL maxTheta, const bool useMultiplicity=false)
 Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value.

RadiationType GetRadiationType () const
 Neutron or x-ray experiment ? Wavelength ?

virtual const RadiationGetRadiation () const=0
 Get the radiation object for this data.

virtual void SetCrystal (Crystal &crystal)
 Set the crystal for this experiment.

const CrystalGetCrystal () const
 Const access to the data's crystal.

CrystalGetCrystal ()
 Access to the data's crystal.

long GetNbRefl () const
 Return the number of reflections in this experiment.

const CrystVector_REAL & GetH () const
 Return the 1D array of H coordinates for all reflections.

const CrystVector_REAL & GetK () const
 Return the 1D array of K coordinates for all reflections.

const CrystVector_REAL & GetL () const
 Return the 1D array of L coordinates for all reflections.

const CrystVector_REAL & GetH2Pi () const
 Return the 1D array of H coordinates for all reflections, multiplied by 2*pi.

const CrystVector_REAL & GetK2Pi () const
 Return the 1D array of K coordinates for all reflections, multiplied by 2*pi.

const CrystVector_REAL & GetL2Pi () const
 Return the 1D array of L coordinates for all reflections, multiplied by 2*pi.

const CrystVector_REAL & GetReflX () const
 Return the 1D array of orthonormal x coordinates for all reflections (recipr. space).

const CrystVector_REAL & GetReflY () const
 Return the 1D array of orthonormal y coordinates for all reflections (recipr. space).

const CrystVector_REAL & GetReflZ () const
 Return the 1D array of orthonormal z coordinates for all reflections (recipr. space).

const CrystVector_REAL & GetSinThetaOverLambda () const
 Return an array with for all reflections.

const CrystVector_REAL & GetTheta () const
 Return an array with theta values for all reflections.

const RefinableObjClockGetClockTheta () const
 Clock the last time the sin(theta)/lambda and theta arrays were re-computed.

const CrystVector_REAL & GetFhklCalcSq () const
 Returns the Array of calculated |F(hkl)|^2 for all reflections.

const CrystVector_REAL & GetFhklCalcReal () const
 Access to real part of F(hkl)calc.

const CrystVector_REAL & GetFhklCalcImag () const
 Access to imaginary part of F(hkl)calc.

CrystVector_REAL GetWavelength () const
 wavelength of the experiment (in Angstroems)

void SetIsIgnoringImagScattFact (const bool b)
 If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.

bool IsIgnoringImagScattFact () const
 If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.

virtual void PrintFhklCalc (ostream &os=cout) const
 Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections.

virtual void PrintFhklCalcDetail (ostream &os=cout) const
 Print H, K, L sin(theta)/lambda theta F^2 Re(F) Im(F) [Re(F) Im(F)]_i, where [Re(F) Im(F)]_i are the real and imaginary contribution of the different scattering powers to the overall structure factor.

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 EndOptimization ()
 This should be called by any optimization class at the end of an optimization.

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.

long GetNbReflBelowMaxSinThetaOvLambda () const
 Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(theta)/lambda value set.

const RefinableObjClockGetClockNbReflBelowMaxSinThetaOvLambda () const
 Clock the last time the number of reflections used was changed.


Protected Methods

virtual void PrepareHKLarrays ()
virtual CrystVector_long SortReflectionByTheta (const REAL maxTheta=-1.)
CrystVector_long EliminateExtinctReflections ()
virtual void PrepareCalcStructFactor () const
virtual void CalcSinThetaLambda () const
void CalcScattFactor () const
 Get scattering factors for all ScatteringPower & reflections.

void CalcTemperatureFactor () const
 Compute thermic factors for all ScatteringPower & reflections.

virtual void CalcResonantScattFactor () const
void CalcGlobalTemperatureFactor () const
 Compute the overall temperature factor affecting all reflections.

void CalcStructFactor () const
 Compute the overall structure factor (real and imaginary part). This function is optimized for speed (geometrical structure factors are computed for all atoms and all reflections in two loops, avoiding re-calculation). So use this function for repetitive calculations.

void CalcGeomStructFactor (const ScatteringComponentList &scattCompList, const SpaceGroup &spg, const CrystVector_long &structFactorIndex, CrystVector_REAL *rsf2, CrystVector_REAL *isf2, bool useFastTabulatedTrigFunctions=false) const
 Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal.

void CalcLuzzatiFactor () const
 Calculate the Luzzati factor associated to each ScatteringPower and each reflection, for maximum likelihood optimization.

void CalcStructFactVariance () const
 Calculate the variance associated to the calculated structure factor.


Protected Attributes

long mNbRefl
 Number of H,K,L reflections.

CrystVector_REAL mH
 H,K,L coordinates.

CrystVector_REAL mK
 H,K,L coordinates.

CrystVector_REAL mL
 H,K,L coordinates.

CrystVector_long mIntH
 H,K,L integer coordinates.

CrystVector_long mIntK
 H,K,L integer coordinates.

CrystVector_long mIntL
 H,K,L integer coordinates.

CrystVector_REAL mH2Pi
 H,K,L coordinates, multiplied by 2PI.

CrystVector_REAL mK2Pi
 H,K,L coordinates, multiplied by 2PI.

CrystVector_REAL mL2Pi
 H,K,L coordinates, multiplied by 2PI.

CrystVector_REAL mX
 reflection coordinates in an orthonormal base

CrystVector_REAL mY
 reflection coordinates in an orthonormal base

CrystVector_REAL mZ
 reflection coordinates in an orthonormal base

CrystVector_int mMultiplicity
 Multiplicity for each reflections (mostly for powder diffraction).

CrystVector_int mExpectedIntensityFactor
 Expected intensity factor for all reflections.

CrystVector_REAL mFhklCalcReal
 real &imaginary parts of F(HKL)calc

CrystVector_REAL mFhklCalcImag
 real &imaginary parts of F(HKL)calc

CrystVector_REAL mFhklCalcSq
 F(HKL)^2 calc for each reflection.

CrystalmpCrystal
 Pointer to the crystal corresponding to this experiment.

REAL mGlobalBiso
 Global Biso, affecting the overall structure factor for all reflections (but not the structure factors of individual atoms or type of atomes).

CrystVector_REAL mGlobalTemperatureFactor
 Global Biso factor.

bool mUseFastLessPreciseFunc
 Use faster, but less precise, approximations for functions? (integer approximations to compute sin and cos in structure factors, and also to compute interatomic distances).

CrystVector_REAL mSinThetaLambda
  for the crystal and the reflections in ReciprSpace

CrystVector_REAL mTheta
 theta for the crystal and the HKL in ReciprSpace (in radians)

CrystVector_REAL mFprime
 Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We assume yet that data is monochromatic, but this could be specialized.

CrystVector_REAL mFsecond
 Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We assume yet that data is monochromatic, but this could be specialized.

CrystVector_REAL * mpTemperatureFactor
 Thermic factors as mNbScatteringPower vectors with NbRefl elements.

CrystVector_REAL * mpScatteringFactor
 Scattering factors as mNbScatteringPower vectors with NbRefl elements.

CrystVector_REAL * mpRealGeomSF
 Geometrical Structure factor for all reflection and ScatteringPower.

CrystVector_REAL * mpImagGeomSF
 Geometrical Structure factor for all reflection and ScatteringPower.

RefinableObjClock mClockHKL
 Clock for the list of hkl.

RefinableObjClock mClockStructFactor
 Clock for the structure factor.

RefinableObjClock mClockStructFactorSq
 Clock for the square modulus of the structure factor.

RefinableObjClock mClockTheta
 Clock the last time theta was computed.

RefinableObjClock mClockScattFactor
 Clock the last time scattering factors were computed.

RefinableObjClock mClockScattFactorResonant
 Clock the last time resonant scattering factors were computed.

RefinableObjClock mClockGeomStructFact
 Clock the last time the geometrical structure factors were computed.

RefinableObjClock mClockThermicFact
 Clock the last time temperature factors were computed.

RefinableObjClock mClockGlobalBiso
 last time the global Biso factor was modified

RefinableObjClock mClockGlobalTemperatureFact
 last time the global temperature factor was computed

const ScatteringComponentListmpScattCompList
 Pointer to the ScatteringComponentList of the crystal.

CrystVector_long mScatteringPowerIndex
 Index of the storage for scattering information.

CrystVector_long mScatteringPowerIndex2
 This is the reverse index. KLUDGEEEEEEEE !!!

long mNbScatteringPower
 Total number os ScatteringPower used for this DiffractionData.

bool mIgnoreImagScattFact
 Ignore imaginary part of scattering factor.

REAL mMaxSinThetaOvLambda
 Maximum sin(theta)/lambda for all calculations (10 by default).

long mNbReflUsed
 Number of reflections which are below the max.

RefinableObjClock mClockNbReflUsed
 Clock recording the last time the number of reflections used has increased.

vector< CrystVector_REAL > mvLuzzatiFactor
 The Luzzati 'D' factor for each scattering power and each reflection.

CrystVector_REAL mFhklCalcVariance
 The variance on all calculated structure factors, taking into account the positionnal errors and the expected intensity factor.


Detailed Description

Class to compute structure factors for a set of reflections and a Crystal.

This class only computes structure factor, but no intensity. i.e. it does not include any correction such as absorption, Lorentz or Polarization.

Does this really need to be a RefinableObj ?

Todo:
Optimize computation for Bijvoet/Friedel mates. To do this, generate an internal list of 'true independent reflections', with two entries for each, for both mates, and make the 'real' reflections only a reference to these reflections.

a lot of cleaning is necessary in the computing of structure factors, for (1) the 'preparation' part (deciding what needs to be recomputed) and (2) to allow anisotropic temperature factors (or other anisotropic parts)


Member Function Documentation

virtual void ObjCryst::ScatteringData::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.

Reimplemented in ObjCryst::PowderPatternDiffraction.

virtual void ObjCryst::ScatteringData::CalcResonantScattFactor   [protected, virtual]
 

For internal use only.

get f' and f" for ScatteringPower of the crystal, at the exp. wavelength

This could be specialized for multi-wavelength experiments...

void ObjCryst::ScatteringData::CalcScattFactor   [protected]
 

Get scattering factors for all ScatteringPower & reflections.

For internal use only.

virtual void ObjCryst::ScatteringData::CalcSinThetaLambda   [protected, virtual]
 

For internal use only.

Compute sin(theta)/lambda as well a orthonormal coordinates for all reflections. theta and tan(theta), are also re-computed, provided a wavelength has been supplied.

void ObjCryst::ScatteringData::CalcStructFactor   [protected]
 

Compute the overall structure factor (real and imaginary part). This function is optimized for speed (geometrical structure factors are computed for all atoms and all reflections in two loops, avoiding re-calculation). So use this function for repetitive calculations.

This function recognizes the type of radiation (XRay or neutron) and uses the corresponding scattering factor/length.

Returns:
the result (real and imaginary part of the structure factor) (mRealFhklCalc, mImagFhklCalc) are stored within ScatteringData.

void ObjCryst::ScatteringData::CalcTemperatureFactor   [protected]
 

Compute thermic factors for all ScatteringPower & reflections.

For internal use only.

CrystVector_long ObjCryst::ScatteringData::EliminateExtinctReflections   [protected]
 

For internal use only.

Get rid of extinct reflections. Useful after GenHKLFullSpace(). Do not use this if you have a list of observed reflections !

Currently done using (brute-force) numerical evaluation. Should rather use SpaceGroup info... To do !

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

virtual void ObjCryst::ScatteringData::EndOptimization   [virtual]
 

This should be called by any optimization class at the end of an optimization.

This also affects all sub-objects.

Note:
this may be called several time for some objects which are used by several other objects.

Reimplemented from ObjCryst::RefinableObj.

Reimplemented in ObjCryst::PowderPatternDiffraction.

virtual void ObjCryst::ScatteringData::GenHKLFullSpace const REAL    maxTheta,
const bool    useMultiplicity = false
[virtual]
 

Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value.

Parameters:
maxTheta:maximum  theta value
useMultiplicity:  if set to true, equivalent reflections will be removed. Bijvoet (Friedel) pairs are NOT merged, for 'anomalous' reasons, unless you have chosen to ignore the imaginary part of the scattering factor. If true, then multiplicity is stored in the mMultiplicity data member.
Warning:
The ScatteringData object must already have been assigned a crystal object using SetCrystal(), and the experimental wavelength must also have been set before calling this function.
Todo:
smarter generation, using spacegroup information to remove extinct reflection rather than brute-force computation.

const CrystVector_REAL& ObjCryst::ScatteringData::GetH2Pi  
 

Return the 1D array of H coordinates for all reflections, multiplied by 2*pi.

For internal use only.

Should be private

const CrystVector_REAL& ObjCryst::ScatteringData::GetK2Pi  
 

Return the 1D array of K coordinates for all reflections, multiplied by 2*pi.

For internal use only.

Should be private

const CrystVector_REAL& ObjCryst::ScatteringData::GetL2Pi  
 

Return the 1D array of L coordinates for all reflections, multiplied by 2*pi.

For internal use only.

Should be private

virtual void ObjCryst::ScatteringData::PrepareCalcStructFactor   [protected, virtual]
 

For internal use only.

Get the list of scattering components, and check what needs to be recomputed to get the new structure factors. No calculation is made in this function. Just getting prepared...

Todo:
Clean up the code, which is a really unbelievable mess (but working!)

Currently using flags to decide what should be recomputed, whereas Clocks should be used. a LOT of cleaning is necessary

virtual void ObjCryst::ScatteringData::PrepareHKLarrays   [protected, virtual]
 

For internal use only.

This function is called after H,K and L arrays have been initialized or modified.

virtual void ObjCryst::ScatteringData::SetHKL const CrystVector_REAL &    h,
const CrystVector_REAL &    k,
const CrystVector_REAL &    l
[virtual]
 

input H,K,L

Parameters:
h,k,l:  REAL arrays (vectors with NbRefl elements -same size), with the h, k and l coordinates of all reflections.

void ObjCryst::ScatteringData::SetIsIgnoringImagScattFact const bool    b
 

If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.

(default value=false)

Todo:
this should become useless once we take fully advantage of coupled computation of Structure Factors for Fridel/Bijvoet mates using an internal list of 'fully unique' reflections. Then only one of the mates need to be computed..

virtual void ObjCryst::ScatteringData::SetMaxSinThetaOvLambda const REAL    max [virtual]
 

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

All data (reflections,..) still exist but are ignored for all calculations.

Reimplemented in ObjCryst::PowderPatternDiffraction.

virtual CrystVector_long ObjCryst::ScatteringData::SortReflectionByTheta const REAL    maxTheta = -1. [protected, virtual]
 

For internal use only.

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)

Reimplemented in ObjCryst::DiffractionDataSingleCrystal.


Member Data Documentation

CrystVector_int ObjCryst::ScatteringData::mExpectedIntensityFactor [protected]
 

Expected intensity factor for all reflections.

See SpaceGroup::GetExpectedIntensityFactor()

CrystVector_REAL ObjCryst::ScatteringData::mFhklCalcVariance [protected]
 

The variance on all calculated structure factors, taking into account the positionnal errors and the expected intensity factor.

Actually this is the variance on both real and imaginary parts.

bool ObjCryst::ScatteringData::mIgnoreImagScattFact [protected]
 

Ignore imaginary part of scattering factor.

This can be used either to speed up computation, or when f" has a small effect on calculated intensities, mostly for powder diffraction (GenHKLFullSpace will not generate Friedel pairs, reducing the number of reflections by a factor up to 2 for some structures).

Practically this makes f"=0 during computation. The real resonant contribution (f') is not affected.

This may be removed later on...

REAL ObjCryst::ScatteringData::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.

This affects the computing of structure factors, intensities (for single crystal and powder patterns), R and Rw.

The reflections must be sorted by increasing sin(theta)/lambda for this to work correctly.

long ObjCryst::ScatteringData::mNbReflUsed [protected]
 

Number of reflections which are below the max.

This is updated automatically from ScatteringData::mMaxSinThetaOvLambda

Crystal* ObjCryst::ScatteringData::mpCrystal [protected]
 

Pointer to the crystal corresponding to this experiment.

This gives an access to the UB matrix for the crystal, as well as to the list of Scatterer.

CrystVector_long ObjCryst::ScatteringData::mScatteringPowerIndex [protected]
 

Index of the storage for scattering information.

This array as the same size as the total number of ScatteringPower, and for each we give the index of where their scattering, temperature and resonant factors are stored. THIS IS AWFULLY KLUDGE-ESQUE !!!

bool ObjCryst::ScatteringData::mUseFastLessPreciseFunc [protected]
 

Use faster, but less precise, approximations for functions? (integer approximations to compute sin and cos in structure factors, and also to compute interatomic distances).

This is activated by global optimization algortithms, only during the optimization.


The documentation for this class was generated from the following file:
Generated on Wed Jun 25 23:26:26 2003 for ObjCryst++ by doxygen1.2.18