ObjCryst::ScatteringData Class Reference

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

Inheritance diagram for ObjCryst::ScatteringData:

[legend]Collaboration diagram for ObjCryst::ScatteringData:

[legend]List of all members.


Public Member Functions
	ScatteringData ()
	ScatteringData (const ScatteringData &old)
	~ScatteringData ()
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	GenHKLFullSpace2 (const REAL maxsithsl, const bool unique=false)
	Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value.
virtual void	GenHKLFullSpace (const REAL maxTheta, const bool unique=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 Radiation &	GetRadiation () const=0
	Get the radiation object for this data.
virtual void	SetCrystal (Crystal &crystal)
	Set the crystal for this experiment.
const Crystal &	GetCrystal () const
	Const access to the data's crystal.
Crystal &	GetCrystal ()
	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 $\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for all reflections.
const CrystVector_REAL &	GetTheta () const
	Return an array with theta values for all reflections.
const RefinableObjClock &	GetClockTheta () 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 RefinableObjClock &	GetClockNbReflBelowMaxSinThetaOvLambda () const
	Clock the last time the number of reflections used was changed.
Protected Member Functions
virtual void	PrepareHKLarrays ()
virtual CrystVector_long	SortReflectionBySinThetaOverLambda (const REAL maxSTOL=-1.)
CrystVector_long	EliminateExtinctReflections ()
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
	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.
Crystal *	mpCrystal
	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
	$\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for the crystal and the reflections in ReciprSpace
CrystVector_REAL	mTheta
	theta for the crystal and the HKL in ReciprSpace (in radians)
map< const ScatteringPower *, REAL >	mvFprime
	Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value.
map< const ScatteringPower *, REAL >	mvFsecond
	Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value.
map< const ScatteringPower *, CrystVector_REAL >	mvTemperatureFactor
	Thermic factors for each ScatteringPower, as vectors with NbRefl elements.
map< const ScatteringPower *, CrystVector_REAL >	mvScatteringFactor
	Scattering factors for each ScatteringPower, as vectors with NbRefl elements.
map< const ScatteringPower *, CrystVector_REAL >	mvRealGeomSF
	Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements.
map< const ScatteringPower *, CrystVector_REAL >	mvImagGeomSF
	Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements.
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
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.
map< const ScatteringPower *, 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.
RefinableObjClock	mClockLuzzatiFactor
RefinableObjClock	mClockFhklCalcVariance

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)

Constructor & Destructor Documentation

ObjCryst::ScatteringData::ScatteringData ( )

ObjCryst::ScatteringData::ScatteringData ( const ScatteringData & old )

ObjCryst::ScatteringData::~ScatteringData ( )

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.

void ObjCryst::ScatteringData::CalcGeomStructFactor ( ) const [protected]

Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal.

void ObjCryst::ScatteringData::CalcGlobalTemperatureFactor ( ) const [protected]

Compute the overall temperature factor affecting all reflections.

void ObjCryst::ScatteringData::CalcLuzzatiFactor ( ) const [protected]

Calculate the Luzzati factor associated to each ScatteringPower and each reflection, for maximum likelihood optimization.

virtual void ObjCryst::ScatteringData::CalcResonantScattFactor ( ) const [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 ( ) const [protected]

Get scattering factors for all ScatteringPower & reflections.

virtual void ObjCryst::ScatteringData::CalcSinThetaLambda ( ) const [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 ( ) const [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 in ScatteringData.

void ObjCryst::ScatteringData::CalcStructFactVariance ( ) const [protected]

Calculate the variance associated to the calculated structure factor.

void ObjCryst::ScatteringData::CalcTemperatureFactor ( ) const [protected]

Compute thermic factors for all ScatteringPower & reflections.

virtual ScatteringData* ObjCryst::ScatteringData::CreateCopy ( ) const [pure virtual]

So-called virtual copy constructor.

Implemented in ObjCryst::DiffractionDataSingleCrystal, and ObjCryst::PowderPatternDiffraction.

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 unique = false

) [virtual]

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

Parameters:

maxsithsl:maximum sin(theta)/lambda=1/2d value

unique: if set to true, only unique reflections will be listed. Bijvoet (Friedel) pairs are NOT merged, for 'anomalous' reasons, unless you have chosen to ignore the imaginary part of the scattering factor.

The multiplicity is always stored in ScatteringData::mMultiplicity.

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.

Deprecated:
Rather use PowderPattern::GenHKLFullSpace2, with a maximum sin(theta)/lambda value, which also works for dispersive experiments.

virtual void ObjCryst::ScatteringData::GenHKLFullSpace2 ( const REAL maxsithsl,

const bool unique = 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

unique: if set to true, only unique reflections will be listed. Bijvoet (Friedel) pairs are NOT merged, for 'anomalous' reasons, unless you have chosen to ignore the imaginary part of the scattering factor.

The multiplicity is always stored in ScatteringData::mMultiplicity.

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.

const RefinableObjClock& ObjCryst::ScatteringData::GetClockNbReflBelowMaxSinThetaOvLambda ( ) const

Clock the last time the number of reflections used was changed.

const RefinableObjClock& ObjCryst::ScatteringData::GetClockTheta ( ) const

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

Crystal& ObjCryst::ScatteringData::GetCrystal ( )

Access to the data's crystal.

const Crystal& ObjCryst::ScatteringData::GetCrystal ( ) const

Const access to the data's crystal.

const CrystVector_REAL& ObjCryst::ScatteringData::GetFhklCalcImag ( ) const

Access to imaginary part of F(hkl)calc.

const CrystVector_REAL& ObjCryst::ScatteringData::GetFhklCalcReal ( ) const

Access to real part of F(hkl)calc.

const CrystVector_REAL& ObjCryst::ScatteringData::GetFhklCalcSq ( ) const

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

const CrystVector_REAL& ObjCryst::ScatteringData::GetH ( ) const

Return the 1D array of H coordinates for all reflections.

const CrystVector_REAL& ObjCryst::ScatteringData::GetH2Pi ( ) const

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::GetK ( ) const

Return the 1D array of K coordinates for all reflections.

const CrystVector_REAL& ObjCryst::ScatteringData::GetK2Pi ( ) const

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::GetL ( ) const

Return the 1D array of L coordinates for all reflections.

const CrystVector_REAL& ObjCryst::ScatteringData::GetL2Pi ( ) const

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

For internal use only.

Should be private

REAL ObjCryst::ScatteringData::GetMaxSinThetaOvLambda ( ) const

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

long ObjCryst::ScatteringData::GetNbRefl ( ) const

Return the number of reflections in this experiment.

long ObjCryst::ScatteringData::GetNbReflBelowMaxSinThetaOvLambda ( ) const

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

virtual const Radiation& ObjCryst::ScatteringData::GetRadiation ( ) const [pure virtual]

Get the radiation object for this data.

Implemented in ObjCryst::DiffractionDataSingleCrystal, and ObjCryst::PowderPatternDiffraction.

RadiationType ObjCryst::ScatteringData::GetRadiationType ( ) const

Neutron or x-ray experiment ? Wavelength ?

const CrystVector_REAL& ObjCryst::ScatteringData::GetReflX ( ) const

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

const CrystVector_REAL& ObjCryst::ScatteringData::GetReflY ( ) const

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

const CrystVector_REAL& ObjCryst::ScatteringData::GetReflZ ( ) const

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

const CrystVector_REAL& ObjCryst::ScatteringData::GetSinThetaOverLambda ( ) const

Return an array with $\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for all reflections.

const CrystVector_REAL& ObjCryst::ScatteringData::GetTheta ( ) const

Return an array with theta values for all reflections.

CrystVector_REAL ObjCryst::ScatteringData::GetWavelength ( ) const

wavelength of the experiment (in Angstroems)

bool ObjCryst::ScatteringData::IsIgnoringImagScattFact ( ) const

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

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::PrintFhklCalc ( ostream & os = cout ) const [virtual]

Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections.

virtual void ObjCryst::ScatteringData::PrintFhklCalcDetail ( ostream & os = cout ) const [virtual]

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 ObjCryst::ScatteringData::SetCrystal ( Crystal & crystal ) [virtual]

Set the crystal for this experiment.

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::SortReflectionBySinThetaOverLambda ( const REAL maxSTOL = -1. ) [protected, 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 in ObjCryst::DiffractionDataSingleCrystal.

Member Data Documentation

RefinableObjClock ObjCryst::ScatteringData::mClockFhklCalcVariance [mutable, protected]

RefinableObjClock ObjCryst::ScatteringData::mClockGeomStructFact [mutable, protected]

Clock the last time the geometrical structure factors were computed.

RefinableObjClock ObjCryst::ScatteringData::mClockGlobalBiso [protected]

last time the global Biso factor was modified

RefinableObjClock ObjCryst::ScatteringData::mClockGlobalTemperatureFact [mutable, protected]

last time the global temperature factor was computed

RefinableObjClock ObjCryst::ScatteringData::mClockHKL [protected]

Clock for the list of hkl.

RefinableObjClock ObjCryst::ScatteringData::mClockLuzzatiFactor [mutable, protected]

RefinableObjClock ObjCryst::ScatteringData::mClockNbReflUsed [mutable, protected]

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

RefinableObjClock ObjCryst::ScatteringData::mClockScattFactor [mutable, protected]

Clock the last time scattering factors were computed.

RefinableObjClock ObjCryst::ScatteringData::mClockScattFactorResonant [mutable, protected]

Clock the last time resonant scattering factors were computed.

RefinableObjClock ObjCryst::ScatteringData::mClockStructFactor [mutable, protected]

Clock for the structure factor.

RefinableObjClock ObjCryst::ScatteringData::mClockStructFactorSq [mutable, protected]

Clock for the square modulus of the structure factor.

RefinableObjClock ObjCryst::ScatteringData::mClockThermicFact [mutable, protected]

Clock the last time temperature factors were computed.

RefinableObjClock ObjCryst::ScatteringData::mClockTheta [mutable, protected]

Clock the last time theta was computed.

CrystVector_int ObjCryst::ScatteringData::mExpectedIntensityFactor [protected]

Expected intensity factor for all reflections.
See SpaceGroup::GetExpectedIntensityFactor()

CrystVector_REAL ObjCryst::ScatteringData::mFhklCalcImag [mutable, protected]

real &imaginary parts of F(HKL)calc

CrystVector_REAL ObjCryst::ScatteringData::mFhklCalcReal [mutable, protected]

real &imaginary parts of F(HKL)calc

CrystVector_REAL ObjCryst::ScatteringData::mFhklCalcSq [mutable, protected]

F(HKL)^2 calc for each reflection.

CrystVector_REAL ObjCryst::ScatteringData::mFhklCalcVariance [mutable, 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.

REAL ObjCryst::ScatteringData::mGlobalBiso [protected]

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

CrystVector_REAL ObjCryst::ScatteringData::mGlobalTemperatureFactor [mutable, protected]

Global Biso factor.

CrystVector_REAL ObjCryst::ScatteringData::mH [protected]

H,K,L coordinates.

CrystVector_REAL ObjCryst::ScatteringData::mH2Pi [mutable, protected]

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

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...

CrystVector_long ObjCryst::ScatteringData::mIntH [mutable, protected]

H,K,L integer coordinates.

CrystVector_long ObjCryst::ScatteringData::mIntK [mutable, protected]

H,K,L integer coordinates.

CrystVector_long ObjCryst::ScatteringData::mIntL [mutable, protected]

H,K,L integer coordinates.

CrystVector_REAL ObjCryst::ScatteringData::mK [protected]

H,K,L coordinates.

CrystVector_REAL ObjCryst::ScatteringData::mK2Pi [mutable, protected]

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

CrystVector_REAL ObjCryst::ScatteringData::mL [protected]

H,K,L coordinates.

CrystVector_REAL ObjCryst::ScatteringData::mL2Pi [mutable, protected]

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

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.

CrystVector_int ObjCryst::ScatteringData::mMultiplicity [protected]

Multiplicity for each reflections (mostly for powder diffraction).

long ObjCryst::ScatteringData::mNbRefl [protected]

Number of H,K,L reflections.

long ObjCryst::ScatteringData::mNbReflUsed [mutable, 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_REAL ObjCryst::ScatteringData::mSinThetaLambda [mutable, protected]

$\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for the crystal and the reflections in ReciprSpace

CrystVector_REAL ObjCryst::ScatteringData::mTheta [mutable, protected]

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

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.

map<const ScatteringPower*,REAL> ObjCryst::ScatteringData::mvFprime [mutable, protected]

Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value.
For multi-wavelength support this should be changed to a vector... or to a matrix to take into account anisotropy of anomalous scattering...

map<const ScatteringPower*,REAL> ObjCryst::ScatteringData::mvFsecond [mutable, protected]

Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value.
For multi-wavelength support this should be changed to a vector... or to a matrix to take into account anisotropy of anomalous scattering...

map<const ScatteringPower*,CrystVector_REAL> ObjCryst::ScatteringData::mvImagGeomSF [mutable, protected]

Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements.

map<const ScatteringPower*,CrystVector_REAL> ObjCryst::ScatteringData::mvLuzzatiFactor [mutable, protected]

The Luzzati 'D' factor for each scattering power and each reflection.

map<const ScatteringPower*,CrystVector_REAL> ObjCryst::ScatteringData::mvRealGeomSF [mutable, protected]

Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements.

map<const ScatteringPower*,CrystVector_REAL> ObjCryst::ScatteringData::mvScatteringFactor [mutable, protected]

Scattering factors for each ScatteringPower, as vectors with NbRefl elements.

map<const ScatteringPower*,CrystVector_REAL> ObjCryst::ScatteringData::mvTemperatureFactor [mutable, protected]

Thermic factors for each ScatteringPower, as vectors with NbRefl elements.

CrystVector_REAL ObjCryst::ScatteringData::mX [mutable, protected]

reflection coordinates in an orthonormal base

CrystVector_REAL ObjCryst::ScatteringData::mY [mutable, protected]

reflection coordinates in an orthonormal base

CrystVector_REAL ObjCryst::ScatteringData::mZ [mutable, protected]

reflection coordinates in an orthonormal base

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

ScatteringData.h

Generated on Tue Nov 14 15:05:11 2006 for ObjCryst++ by

1.3.6

ObjCryst::ScatteringData Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation