ObjCryst::ScatteringPower Class Reference

Abstract Base Class to describe the scattering power of any Scatterer component in a crystal. More...

Inheritance diagram for ObjCryst::ScatteringPower:

[legend]Collaboration diagram for ObjCryst::ScatteringPower:

[legend]List of all members.

Public Member Functions
	ScatteringPower ()
	ScatteringPower (const ScatteringPower &old)
virtual	~ScatteringPower ()
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...).
virtual void	operator= (const ScatteringPower &rhs)
virtual CrystVector_REAL	GetScatteringFactor (const ScatteringData &data, const int spgSymPosIndex=-1) const=0
	Get the Scattering factor for all reflections of a given ScatteringData object.
virtual REAL	GetForwardScatteringFactor (const RadiationType) const=0
	Get the scattering factor at (0,0,0).
virtual CrystVector_REAL	GetTemperatureFactor (const ScatteringData &data, const int spgSymPosIndex=-1) const=0
	Get the temperature factor for all reflections of a given ScatteringData object.
virtual CrystMatrix_REAL	GetResonantScattFactReal (const ScatteringData &data, const int spgSymPosIndex=-1) const=0
	Get the real part of the resonant scattering factor.
virtual CrystMatrix_REAL	GetResonantScattFactImag (const ScatteringData &data, const int spgSymPosIndex=-1) const=0
	Get the imaginary part of the resonant scattering factor.
virtual bool	IsScatteringFactorAnisotropic () const
	Is the scattering factor anisotropic ?
virtual bool	IsTemperatureFactorAnisotropic () const
	Is the thermic factor anisotropic ?
virtual bool	IsResonantScatteringAnisotropic () const
	Are the resonant scattering terms anisotropic ?
virtual const string &	GetSymbol () const
	Symbol for this Scattering power (the atom name for atoms).
REAL	GetBiso () const
	Returns the isotropic temperature B factor.
REAL &	GetBiso ()
	Returns the isotropic temperature B factor.
virtual void	SetBiso (const REAL newB)
	Sets the isotropic temperature B factor.
bool	IsIsotropic () const
	Returns true if the scattering power is isotropic, else false.
long	GetDynPopCorrIndex () const
	Get the number identifying this kind of scatterer, used to decide whether two scatterers are equivalent, for the dynamical occupancy correction.
long	GetNbScatteringPower () const
	Total number of ScatteringPower object.
const RefinableObjClock &	GetLastChangeClock () const
	ObjCrystClock time when the last modification was made to the object.
const string &	GetColourName () const
	Get the (POV-Ray) name associated to the color (if any).
const float *	GetColourRGB () const
	Get the float[3] array of RGB components defining the colour of this scattering power.
void	SetColour (const string &colorName)
	Set the colour from the associated POV-Ray name.
void	SetColour (const float r, const float g, const float b)
	Set the colour from RGB components (all between 0 and 1.).
virtual REAL	GetRadius () const=0
	Return the physical radius of this type of scatterer (for 3D display purposes).
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter.
REAL	GetMaximumLikelihoodPositionError () const
	Maximum Likelihood: get the estimated error (sigma) on the positions for this kind of element.
void	SetMaximumLikelihoodPositionError (const REAL mle)
	Maximum Likelihood: set the estimated error (sigma) on the positions for this kind of element.
REAL	GetMaximumLikelihoodNbGhostAtom () const
	Maximum Likelihood: get the number of ghost elements per asymmetric unit.
void	SetMaximumLikelihoodNbGhostAtom (const REAL nb)
	Maximum Likelihood: set the number of ghost elements per asymmetric unit.
const RefinableObjClock &	GetMaximumLikelihoodParClock () const
	Get the clock value for the last change on the maximum likelihood parameters (positionnal error, number of ghost atoms).
virtual REAL	GetFormalCharge () const
virtual void	SetFormalCharge (const REAL charge)
Protected Member Functions
virtual void	InitRefParList ()=0
virtual void	Init ()
	Initialization of the object, used by all constructors, and operator=.
virtual void	InitRGBColour ()
	Get RGB Colour coordinates from Colour Name.
Protected Attributes
long	mDynPopCorrIndex
	number identifying this kind of scatterer, for the dynamical occupancy correction.
REAL	mBiso
	Temperature isotropic B factor.
bool	mIsIsotropic
	Is the scattering isotropic ?
CrystVector_REAL	mBeta
	Anisotropic Beta(ij).
RefinableObjClock	mClock
	Clock.
string	mColourName
	Colour for this ScatteringPower (from POVRay).
float	mColourRGB [3]
	Colour for this ScatteringPower using RGB.
REAL	mMaximumLikelihoodPositionError
	estimated error (sigma) on the positions for this type of element.
RefinableObjClock	mMaximumLikelihoodParClock
REAL	mMaximumLikelihoodNbGhost
	Number of ghost atoms in the asymmetric unit.
REAL	mFormalCharge
	Formal Charge.

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Detailed Description

Abstract Base Class to describe the scattering power of any Scatterer component in a crystal.

This includes:

• the scattering factor,
• the temperature factor
• real and imaginary parts of the resonant scattering factor.

The interface is independent of the radiation type.

This base class is designed to handle both isotropic and anisotropic versions of scattering, temperature and anomalous factors.

Todo:

Anisotropic scattering (temperature factor especially) code, using derived classes

Clarify organization by removing any 'real' data from the top, abstract base class (eg remove Biso and Betaij), and by creating derived classes. Optionnaly 3 classes (used as members of ScatteringPower) could be created, TemperatureFactor, ScatteringFactor, and ResonantScatteringFactor. In any way the design of this class should not evolve, so that code using the ScatteringPower interface will remain compatible whatever modifications are made.

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Constructor & Destructor Documentation

ObjCryst::ScatteringPower::ScatteringPower (   )

ObjCryst::ScatteringPower::ScatteringPower (  const ScatteringPower &  old  )

virtual ObjCryst::ScatteringPower::~ScatteringPower (   )  [virtual]

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Member Function Documentation

REAL& ObjCryst::ScatteringPower::GetBiso (   )

Returns the isotropic temperature B factor.

REAL ObjCryst::ScatteringPower::GetBiso (   )  const

Returns the isotropic temperature B factor.

virtual const string& ObjCryst::ScatteringPower::GetClassName (   )  const [virtual]

Name for this class ("RefinableObj", "Crystal",...). This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry Reimplemented from ObjCryst::RefinableObj. Reimplemented in ObjCryst::ScatteringPowerAtom, and ObjCryst::ScatteringPowerSphere.

const string& ObjCryst::ScatteringPower::GetColourName (   )  const

Get the (POV-Ray) name associated to the color (if any).

const float* ObjCryst::ScatteringPower::GetColourRGB (   )  const

Get the float[3] array of RGB components defining the colour of this scattering power.

long ObjCryst::ScatteringPower::GetDynPopCorrIndex (   )  const

Get the number identifying this kind of scatterer, used to decide whether two scatterers are equivalent, for the dynamical occupancy correction.

virtual REAL ObjCryst::ScatteringPower::GetFormalCharge (   )  const [virtual]

virtual REAL ObjCryst::ScatteringPower::GetForwardScatteringFactor (  const  RadiationType  )  const [pure virtual]

Get the scattering factor at (0,0,0). Used for scatterer (electron, nucleus) density generation. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual void ObjCryst::ScatteringPower::GetGeneGroup (  const RefinableObj &  obj, CrystVector_uint &  groupIndex, unsigned int &  firstGroup )  const [virtual]

Get the gene group assigned to each parameter. Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life. The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique. Parameters: obj  the , supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object. groupIndex  a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned). firstGroup  this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group. Note: this function is not optimized, and should only be called at the beginning of a refinement. Reimplemented from ObjCryst::RefinableObj.

const RefinableObjClock& ObjCryst::ScatteringPower::GetLastChangeClock (   )  const

ObjCrystClock time when the last modification was made to the object.

REAL ObjCryst::ScatteringPower::GetMaximumLikelihoodNbGhostAtom (   )  const

Maximum Likelihood: get the number of ghost elements per asymmetric unit.

const RefinableObjClock& ObjCryst::ScatteringPower::GetMaximumLikelihoodParClock (   )  const

Get the clock value for the last change on the maximum likelihood parameters (positionnal error, number of ghost atoms).

REAL ObjCryst::ScatteringPower::GetMaximumLikelihoodPositionError (   )  const

Maximum Likelihood: get the estimated error (sigma) on the positions for this kind of element.

long ObjCryst::ScatteringPower::GetNbScatteringPower (   )  const

Total number of ScatteringPower object.

virtual REAL ObjCryst::ScatteringPower::GetRadius (   )  const [pure virtual]

Return the physical radius of this type of scatterer (for 3D display purposes). Warning: this may be removed later. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual CrystMatrix_REAL ObjCryst::ScatteringPower::GetResonantScattFactImag (  const ScatteringData &  data, const int  spgSymPosIndex = -1 )  const [pure virtual]

Get the imaginary part of the resonant scattering factor. Returns: a matrix where each row corresponds to each wavelength (currently only monochromatic experiments are made so there is only one row), and each column corresponds to each reflection only if the scattering term is anisotropic, which is not the case so far... Parameters: data:  the ScatteringData object, giving access to all the reflections, and a list of wavelengths. spgSymPosIndex:  if the ScatteringPower is anisotropic, then the different symmetrics will not have the same scattering power for all reflections. This parameter is the index of the symmetric position in the Spacegroup. If spgSymPosIndex=-1, the isotropic values are returned. Warning: There is no anisotropic code yet, so spgSymPosIndex is simply ignored so far , but the design of this function is general for any anisotropic scattering. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual CrystMatrix_REAL ObjCryst::ScatteringPower::GetResonantScattFactReal (  const ScatteringData &  data, const int  spgSymPosIndex = -1 )  const [pure virtual]

Get the real part of the resonant scattering factor. Returns: a matrix where each row corresponds to each wavelength (currently only monochromatic experiments are made so there is only one row), and each column corresponds to each reflection only if the scattering term is anisotropic, which is not the case so far... Parameters: data:  the ScatteringData object, giving access to all the reflections and a list of wavelengths). spgSymPosIndex:  if the ScatteringPower is anisotropic, then the different symmetrics will not have the same scattering power for all reflections. This parameter is the index of the symmetric position in the Spacegroup. If spgSymPosIndex=-1, the isotropic values are returned. Warning: There is no anisotropic code yet, so spgSymPosIndex is simply ignored so far , but the design of this function is general for any anisotropic scattering. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual CrystVector_REAL ObjCryst::ScatteringPower::GetScatteringFactor (  const ScatteringData &  data, const int  spgSymPosIndex = -1 )  const [pure virtual]

Get the Scattering factor for all reflections of a given ScatteringData object. Returns: a vector with the scattering factor for all reflections, in the same order as in the ScatteringData object. This format is independent of the radiation type (X-Ray, neutron..). Parameters: data:  the ScatteringData object, giving access to all the reflections. spgSymPosIndex:  if the ScatteringPower is anisotropic, then the different symmetrics will not have the same scattering power for all reflections. This parameter is the index of the symmetric position in the Spacegroup. If spgSymPosIndex=-1, the isotropic values are returned. Warning: There is no anisotropic code yet, so spgSymPosIndex is simply ignored so far , but the design of this function is general for any anisotropic scattering. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual const string& ObjCryst::ScatteringPower::GetSymbol (   )  const [virtual]

Symbol for this Scattering power (the atom name for atoms). Reimplemented in ObjCryst::ScatteringPowerAtom.

virtual CrystVector_REAL ObjCryst::ScatteringPower::GetTemperatureFactor (  const ScatteringData &  data, const int  spgSymPosIndex = -1 )  const [pure virtual]

Get the temperature factor for all reflections of a given ScatteringData object. Returns: a vector with the temperature factor for all reflections, in the same order as in the ScatteringData object. Parameters: data:  the ScatteringData object, giving access to all the reflections. spgSymPosIndex:  if the ScatteringPower is anisotropic, then the different symmetrics will not have the same scattering power for all reflections. This parameter is the index of the symmetric position in the Spacegroup. If spgSymPosIndex=-1, the isotropic values are returned. Warning: There is no anisotropic code yet, so spgSymPosIndex is simply ignored so far , but the design of this function is general for any anisotropic scattering. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual void ObjCryst::ScatteringPower::Init (   )  [protected, virtual]

Initialization of the object, used by all constructors, and operator=.

virtual void ObjCryst::ScatteringPower::InitRefParList (   )  [protected, pure virtual]

Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower.

virtual void ObjCryst::ScatteringPower::InitRGBColour (   )  [protected, virtual]

Get RGB Colour coordinates from Colour Name.

bool ObjCryst::ScatteringPower::IsIsotropic (   )  const

Returns true if the scattering power is isotropic, else false.

virtual bool ObjCryst::ScatteringPower::IsResonantScatteringAnisotropic (   )  const [virtual]

Are the resonant scattering terms anisotropic ?

virtual bool ObjCryst::ScatteringPower::IsScatteringFactorAnisotropic (   )  const [virtual]

Is the scattering factor anisotropic ?

virtual bool ObjCryst::ScatteringPower::IsTemperatureFactorAnisotropic (   )  const [virtual]

Is the thermic factor anisotropic ?

virtual void ObjCryst::ScatteringPower::operator= (  const ScatteringPower &  rhs  )  [virtual]

virtual void ObjCryst::ScatteringPower::SetBiso (  const REAL  newB  )  [virtual]

Sets the isotropic temperature B factor.

void ObjCryst::ScatteringPower::SetColour (  const float  r, const float  g, const float  b )

Set the colour from RGB components (all between 0 and 1.).

void ObjCryst::ScatteringPower::SetColour (  const string &  colorName  )

Set the colour from the associated POV-Ray name.

virtual void ObjCryst::ScatteringPower::SetFormalCharge (  const REAL  charge  )  [virtual]

void ObjCryst::ScatteringPower::SetMaximumLikelihoodNbGhostAtom (  const REAL  nb  )

Maximum Likelihood: set the number of ghost elements per asymmetric unit.

void ObjCryst::ScatteringPower::SetMaximumLikelihoodPositionError (  const REAL  mle  )

Maximum Likelihood: set the estimated error (sigma) on the positions for this kind of element.

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Member Data Documentation

CrystVector_REAL ObjCryst::ScatteringPower::mBeta [protected]

Anisotropic Beta(ij).

REAL ObjCryst::ScatteringPower::mBiso [protected]

Temperature isotropic B factor. Reimplemented in ObjCryst::ScatteringPowerSphere.

RefinableObjClock ObjCryst::ScatteringPower::mClock [protected]

Clock.

string ObjCryst::ScatteringPower::mColourName [protected]

Colour for this ScatteringPower (from POVRay).

float ObjCryst::ScatteringPower::mColourRGB[3] [protected]

Colour for this ScatteringPower using RGB.

long ObjCryst::ScatteringPower::mDynPopCorrIndex [protected]

number identifying this kind of scatterer, for the dynamical occupancy correction. Right now it is the atomic number.

REAL ObjCryst::ScatteringPower::mFormalCharge [protected]

Formal Charge. This can be used for bond valence analysis, or energy calculations. Default value is 0.

bool ObjCryst::ScatteringPower::mIsIsotropic [protected]

Is the scattering isotropic ?

REAL ObjCryst::ScatteringPower::mMaximumLikelihoodNbGhost [protected]

Number of ghost atoms in the asymmetric unit. These contribute to the variance of the structure factor, but not to the structure factor as the uncertainty on their position is infinite.

RefinableObjClock ObjCryst::ScatteringPower::mMaximumLikelihoodParClock [protected]

REAL ObjCryst::ScatteringPower::mMaximumLikelihoodPositionError [protected]

estimated error (sigma) on the positions for this type of element.

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

• ScatteringPower.h

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