Inheritance diagram for ObjCryst::ScatteringPower:
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. |
This includes:
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.
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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Returns the isotropic temperature B factor.
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Returns the isotropic temperature B factor.
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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. |
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Get the (POV-Ray) name associated to the color (if any).
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Get the float[3] array of RGB components defining the colour of this scattering power.
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Get the number identifying this kind of scatterer, used to decide whether two scatterers are equivalent, for the dynamical occupancy correction.
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Get the scattering factor at (0,0,0). Used for scatterer (electron, nucleus) density generation. Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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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.
Reimplemented from ObjCryst::RefinableObj. |
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ObjCrystClock time when the last modification was made to the object.
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Maximum Likelihood: get the number of ghost elements per asymmetric unit.
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Get the clock value for the last change on the maximum likelihood parameters (positionnal error, number of ghost atoms).
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Maximum Likelihood: get the estimated error (sigma) on the positions for this kind of element.
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Total number of ScatteringPower object.
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Return the physical radius of this type of scatterer (for 3D display purposes).
Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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Get the imaginary part of the resonant scattering factor.
Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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Get the real part of the resonant scattering factor.
Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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Get the Scattering factor for all reflections of a given ScatteringData object.
Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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Symbol for this Scattering power (the atom name for atoms).
Reimplemented in ObjCryst::ScatteringPowerAtom. |
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Get the temperature factor for all reflections of a given ScatteringData object.
Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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Initialization of the object, used by all constructors, and operator=.
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Implemented in ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::GlobalScatteringPower. |
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Get RGB Colour coordinates from Colour Name.
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Returns true if the scattering power is isotropic, else false.
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Are the resonant scattering terms anisotropic ?
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Is the scattering factor anisotropic ?
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Is the thermic factor anisotropic ?
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Sets the isotropic temperature B factor.
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Set the colour from RGB components (all between 0 and 1.).
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Set the colour from the associated POV-Ray name.
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Maximum Likelihood: set the number of ghost elements per asymmetric unit.
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Maximum Likelihood: set the estimated error (sigma) on the positions for this kind of element.
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Anisotropic Beta(ij).
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Temperature isotropic B factor.
Reimplemented in ObjCryst::ScatteringPowerSphere. |
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Clock.
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Colour for this ScatteringPower (from POVRay).
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Colour for this ScatteringPower using RGB.
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number identifying this kind of scatterer, for the dynamical occupancy correction. Right now it is the atomic number. |
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Formal Charge. This can be used for bond valence analysis, or energy calculations. Default value is 0. |
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Is the scattering isotropic ?
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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. |
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estimated error (sigma) on the positions for this type of element.
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