FOX/ObjCryst++  1.10.X (development)
ObjCryst::ScatteringPower Class Referenceabstract

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

+ Inheritance diagram for ObjCryst::ScatteringPower:
+ Collaboration diagram for ObjCryst::ScatteringPower:

Public Member Functions

 ScatteringPower (const ScatteringPower &old)
 
virtual const string & GetClassName () const
 Name for this class ("RefinableObj", "Crystal",...). More...
 
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. More...
 
virtual REAL GetForwardScatteringFactor (const RadiationType) const =0
 Get the scattering factor at (0,0,0). More...
 
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. More...
 
virtual CrystMatrix_REAL GetResonantScattFactReal (const ScatteringData &data, const int spgSymPosIndex=-1) const =0
 Get the real part of the resonant scattering factor. More...
 
virtual CrystMatrix_REAL GetResonantScattFactImag (const ScatteringData &data, const int spgSymPosIndex=-1) const =0
 Get the imaginary part of the resonant scattering factor. More...
 
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) More...
 
REAL GetBiso () const
 Returns the isotropic temperature B factor. More...
 
REAL & GetBiso ()
 Returns the isotropic temperature B factor. More...
 
virtual void SetBiso (const REAL newB)
 Sets the isotropic temperature B factor. More...
 
REAL GetBij (const size_t &i, const size_t &j) const
 Returns the anisotropic temperature B factor for (i, j) pair. More...
 
REAL GetBij (const size_t &idx) const
 Returns the anisotropic temperature B factor for given index. More...
 
virtual void SetBij (const size_t &i, const size_t &j, const REAL newB)
 Sets the anisotropic temperature B factor for (i, j) pair. More...
 
virtual void SetBij (const size_t &idx, const REAL newB)
 Sets the anisotropic temperature B factor for given index. More...
 
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. More...
 
long GetNbScatteringPower () const
 Total number of ScatteringPower object.
 
const RefinableObjClockGetLastChangeClock () 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). More...
 
virtual void GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
 Get the gene group assigned to each parameter. More...
 
REAL GetMaximumLikelihoodPositionError () const
 Maximum Likelihood: get the estimated error (sigma) on the positions for this kind of element. More...
 
void SetMaximumLikelihoodPositionError (const REAL mle)
 Maximum Likelihood: set the estimated error (sigma) on the positions for this kind of element. More...
 
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 RefinableObjClockGetMaximumLikelihoodParClock () const
 Get the clock value for the last change on the maximum likelihood parameters (positionnal error, number of ghost atoms). More...
 
virtual REAL GetFormalCharge () const
 
virtual void SetFormalCharge (const REAL charge)
 
- Public Member Functions inherited from ObjCryst::RefinableObj
 RefinableObj ()
 Constructor.
 
 RefinableObj (const bool internalUseOnly)
 Constructor. More...
 
 RefinableObj (const RefinableObj &old)
 Defined not implemented... More...
 
virtual ~RefinableObj ()
 Destructor.
 
virtual const string & GetName () const
 Name of the object.
 
virtual void SetName (const string &name)
 Name of the object.
 
void operator= (const RefinableObj &old)
 Defined not implemented... More...
 
void PrepareForRefinement () const
 Find which parameters are used and not fixed, for a refinement /optimization. More...
 
void FixAllPar ()
 Fix All parameters.
 
void UnFixAllPar ()
 UnFix All parameters.
 
void SetParIsFixed (const long parIndex, const bool fix)
 Fix/un-fix one parameter from its #.
 
void SetParIsFixed (const string &parName, const bool fix)
 Fix/un-fix one parameter from its name.
 
void SetParIsFixed (const RefParType *type, const bool fix)
 Fix/un-fix one family of parameters.
 
void SetParIsUsed (const string &parName, const bool use)
 Set whether a parameter is used.
 
void SetParIsUsed (const RefParType *type, const bool use)
 Set whether a family of parameters is used.
 
long GetNbPar () const
 Total number of refinable parameter in the object. More...
 
long GetNbParNotFixed () const
 Total number of non-fixed parameters. Is initialized by PrepareForRefinement()
 
RefinableParGetPar (const long i)
 Access all parameters in the order they were inputted.
 
const RefinableParGetPar (const long i) const
 Access all parameters in the order they were inputted.
 
RefinableParGetPar (const string &name)
 Access all parameters from their name.
 
const RefinableParGetPar (const string &name) const
 Access all parameters from their name.
 
RefinableParGetPar (const REAL *)
 Access parameter from its adress.
 
const RefinableParGetPar (const REAL *) const
 Access parameter from its adress.
 
RefinableParGetParNotFixed (const long i)
 Access all parameters in the order they were inputted, skipping fixed parameters. More...
 
const RefinableParGetParNotFixed (const long i) const
 Access all parameters in the order they were inputed, skipping fixed parameters. More...
 
void AddPar (const RefinablePar &newRefPar)
 Add a refinable parameter. More...
 
void AddPar (RefinablePar *newRefPar)
 Add a refinable parameter. More...
 
void AddPar (RefinableObj &newRefParList, const bool copyParam=false)
 Add all the parameters in another RefinableObj. More...
 
vector< RefinablePar * >::iterator RemovePar (RefinablePar *refPar)
 Remove a refinable parameter. More...
 
virtual void Print () const
 
unsigned long CreateParamSet (const string name="") const
 Save the current set of refined values in a new set. More...
 
void ClearParamSet (const unsigned long id) const
 Erase the param set with the given id, releasing memory.
 
void SaveParamSet (const unsigned long id) const
 Save the current set of refined values over a previously-created set of saved values. More...
 
void RestoreParamSet (const unsigned long id)
 Restore a saved set of values. More...
 
const CrystVector_REAL & GetParamSet (const unsigned long setId) const
 Access one save refpar set. More...
 
CrystVector_REAL & GetParamSet (const unsigned long setId)
 Access one save refpar set. More...
 
REAL GetParamSet_ParNotFixedHumanValue (const unsigned long setId, const long parNumber) const
 Access the (human) value of one refined parameter in a saved set of parameters. More...
 
const void EraseAllParamSet ()
 Erase all saved refpar sets. More...
 
const string & GetParamSetName (const unsigned long setId) const
 Get the name associated to a refpar set. More...
 
void SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
 Change the limits for a given parameter, giving absolute new limits.
 
void SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
 Change the limits for a category of parameters, giving absolute new limits.
 
void SetLimitsRelative (const string &parName, const REAL min, const REAL max)
 Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0. More...
 
void SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
 Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). More...
 
void SetLimitsProportional (const string &parName, const REAL min, const REAL max)
 Change the limits for a given parameter, proportionnaly to the current value. More...
 
void SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
 Change the limits for a category of parameters, proportionnaly to their current value. More...
 
void SetGlobalOptimStep (const RefParType *type, const REAL step)
 Change the maximum step to use during Global Optimization algorithms.
 
ObjRegistry< RefinableObj > & GetSubObjRegistry ()
 Access to the registry of RefinableObj used by this object.
 
const ObjRegistry< RefinableObj > & GetSubObjRegistry () const
 Access to the registry of RefinableObj used by this object.
 
virtual void RegisterClient (RefinableObj &) const
 Register a new object using this object. More...
 
virtual void DeRegisterClient (RefinableObj &) const
 Deregister an object (which not any more) using this object.
 
virtual const ObjRegistry
< RefinableObj > & 
GetClientRegistry () const
 Get the list of clients.
 
virtual ObjRegistry
< RefinableObj > & 
GetClientRegistry ()
 Get the list of clients.
 
bool IsBeingRefined () const
 Is the object being refined ? (Can be refined by one algorithm at a time only.)
 
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. More...
 
virtual void EndOptimization ()
 This should be called by any optimization class at the end of an optimization. More...
 
virtual void SetApproximationFlag (const bool allow)
 Enable or disable numerical approximations. More...
 
virtual void RandomizeConfiguration ()
 Randomize Configuration (before a global optimization). More...
 
virtual void GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
 Make a random move of the current configuration. More...
 
void BeginGlobalOptRandomMove ()
 Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More...
 
virtual REAL GetLogLikelihood () const
 Get -log(likelihood) of the current configuration for the object. More...
 
virtual unsigned int GetNbLSQFunction () const
 Number of LSQ functions.
 
virtual const CrystVector_REAL & GetLSQCalc (const unsigned int) const
 Get the current calculated value for the LSQ function.
 
virtual const CrystVector_REAL & GetLSQObs (const unsigned int) const
 Get the observed values for the LSQ function.
 
virtual const CrystVector_REAL & GetLSQWeight (const unsigned int) const
 Get the weight values for the LSQ function.
 
virtual const CrystVector_REAL & GetLSQDeriv (const unsigned int, RefinablePar &)
 Get the first derivative values for the LSQ function, for a given parameter. More...
 
virtual std::map< RefinablePar
*, CrystVector_REAL > & 
GetLSQ_FullDeriv (const unsigned int, std::set< RefinablePar * > &vPar)
 Get the first derivative for the LSQ function for each parameter supplied in a list. More...
 
void ResetParList ()
 Re-init the list of refinable parameters, removing all parameters. More...
 
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...
 
virtual void UpdateDisplay () const
 If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. More...
 
unsigned int GetNbOption () const
 Number of Options for this object.
 
RefObjOptGetOption (const unsigned int i)
 Access to the options.
 
const RefObjOptGetOption (const unsigned int i) const
 const access to the options
 
void SetDeleteRefParInDestructor (const bool b)
 Set this object not to delete its list of parameters when destroyed. More...
 
const RefinableObjClockGetRefParListClock () const
 What was the last time a RefinablePar was added/removed ? More...
 
virtual REAL GetRestraintCost () const
 Get the restraint cost (overall penalty of all restraints) More...
 
void AddRestraint (Restraint *pNewRestraint)
 Add a new restraint. More...
 
vector< Restraint * >::iterator RemoveRestraint (Restraint *pRestraint)
 Remove a restraint from the list of known restraints. More...
 
virtual void TagNewBestConfig () const
 During a global optimization, tells the object that the current config is the latest "best" config. More...
 
const RefinableObjClockGetClockMaster () const
 This clocks records any change in the object. See refinableObj::mClockMaster.
 

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 Member Functions inherited from ObjCryst::RefinableObj
long FindPar (const string &name) const
 Find a refinable parameter with a given name.
 
long FindPar (const REAL *) const
 Find a refinable parameter from the adress of its value.
 
void AddSubRefObj (RefinableObj &)
 
void RemoveSubRefObj (RefinableObj &)
 
void AddOption (RefObjOpt *opt)
 
virtual void Prepare ()
 
map< unsigned long, pair
< CrystVector_REAL, string >
>::iterator 
FindParamSet (unsigned long id) const
 Find a parameter set with a given id (and check if it is there)
 

Protected Attributes

long mDynPopCorrIndex
 number identifying this kind of scatterer, for the dynamical occupancy correction. More...
 
REAL mBiso
 Temperature isotropic B factor.
 
bool mIsIsotropic
 Is the scattering isotropic ?
 
CrystVector_REAL mBeta
 Anisotropic Beta(ij) More...
 
CrystVector_REAL mB
 Anisotropic B(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. More...
 
REAL mFormalCharge
 Formal Charge. More...
 
- Protected Attributes inherited from ObjCryst::RefinableObj
string mName
 Name for this RefinableObject. Should be unique, at least in the same scope.+.
 
vector< RefinablePar * > mvpRefPar
 Vector of pointers to the refinable parameters.
 
vector< Restraint * > mvpRestraint
 Vector of pointers to the restraints for this object. More...
 
map< unsigned long, pair
< CrystVector_REAL, string > > 
mvpSavedValuesSet
 Map of (index,pointers to arrays) used to save sets of values for all parameters. More...
 
long mNbRefParNotFixed
 Total of not-fixed parameters.
 
CrystVector_long mRefparNotFixedIndex
 Index of not-fixed parameters.
 
int mOptimizationDepth
 Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place. More...
 
ObjRegistry< RefinableObjmSubObjRegistry
 Registry of RefinableObject needed for this object (owned by this object or not)
 
ObjRegistry< RefinableObjmClientObjRegistry
 Registry of RefinableObject using this object. More...
 
ObjRegistry< RefObjOptmOptionRegistry
 List of options for this object. More...
 
bool mDeleteRefParInDestructor
 If true (the default), then all RefinablePar will be deleted when the the object is deleted. More...
 
RefinableObjClock mRefParListClock
 Last time the RefinableParList was modified (a parameter added or removed).
 
bool mRandomMoveIsDone
 
CrystVector_REAL mLSQDeriv
 Temporary array used to return derivative values of the LSQ function for given parameters. More...
 
std::map< unsigned int,
std::map< RefinablePar
*, CrystVector_REAL > > 
mLSQ_FullDeriv
 Temporary map to return the derivative of the LSQ function versus a list of parameters. More...
 
RefinableObjClock mClockMaster
 Master clock, which is changed whenever the object has been altered. More...
 

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.

Warning
: there is currently a storage for Anisotropic Displacement Parameters, but Debye-Waller calculation is only isotropic.

Definition at line 110 of file ScatteringPower.h.

Member Function Documentation

REAL ObjCryst::ScatteringPower::GetBij ( const size_t &  i,
const size_t &  j 
) const

Returns the anisotropic temperature B factor for (i, j) pair.

Warning
: this is ambiguous, as it is Beta_ij which are stored, and not Bij...

Definition at line 146 of file ScatteringPower.cpp.

REAL ObjCryst::ScatteringPower::GetBij ( const size_t &  idx) const

Returns the anisotropic temperature B factor for given index.

0 -> (1, 1) 1 -> (2, 2) 2 -> (3, 3) 3 -> (1, 2) 4 -> (1, 3) 5 -> (2, 3)

Warning
: this is ambiguous, as it is Beta_ij which are stored, and not Bij...

Definition at line 159 of file ScatteringPower.cpp.

REAL ObjCryst::ScatteringPower::GetBiso ( ) const

Returns the isotropic temperature B factor.

Definition at line 143 of file ScatteringPower.cpp.

REAL & ObjCryst::ScatteringPower::GetBiso ( )

Returns the isotropic temperature B factor.

Definition at line 144 of file ScatteringPower.cpp.

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.

Definition at line 122 of file ScatteringPower.cpp.

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.

Definition at line 183 of file ScatteringPower.cpp.

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.

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
objthe , 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.
groupIndexa 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).
firstGroupthis 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.

Definition at line 200 of file ScatteringPower.cpp.

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).

Definition at line 219 of file ScatteringPower.cpp.

REAL ObjCryst::ScatteringPower::GetMaximumLikelihoodPositionError ( ) const

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

Definition at line 216 of file ScatteringPower.cpp.

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
datathe ScatteringData object, giving access to all the reflections, and a list of wavelengths.
spgSymPosIndexif 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
datathe ScatteringData object, giving access to all the reflections and a list of wavelengths).
spgSymPosIndexif 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
datathe ScatteringData object, giving access to all the reflections.
spgSymPosIndexif 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.

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

Symbol for this Scattering power (the atom name for atoms)

Reimplemented in ObjCryst::ScatteringPowerAtom.

Definition at line 142 of file ScatteringPower.cpp.

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
datathe ScatteringData object, giving access to all the reflections.
spgSymPosIndexif 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.

void ObjCryst::ScatteringPower::SetBij ( const size_t &  i,
const size_t &  j,
const REAL  newB 
)
virtual

Sets the anisotropic temperature B factor for (i, j) pair.

Warning
: this is ambiguous, as it is Beta_ij which are stored, and not Bij...

Definition at line 163 of file ScatteringPower.cpp.

void ObjCryst::ScatteringPower::SetBij ( const size_t &  idx,
const REAL  newB 
)
virtual

Sets the anisotropic temperature B factor for given index.

0 -> (1, 1) 1 -> (2, 2) 2 -> (3, 3) 3 -> (1, 2) 4 -> (1, 3) 5 -> (2, 3)

Warning
: this is ambiguous, as it is Beta_ij which are stored, and not Bij...

Definition at line 176 of file ScatteringPower.cpp.

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

Sets the isotropic temperature B factor.

Definition at line 145 of file ScatteringPower.cpp.

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

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

Definition at line 222 of file ScatteringPower.cpp.

Member Data Documentation

CrystVector_REAL ObjCryst::ScatteringPower::mBeta
mutableprotected

Anisotropic Beta(ij)

These are stored temporarily, and derived from the Bij

Definition at line 301 of file ScatteringPower.h.

long ObjCryst::ScatteringPower::mDynPopCorrIndex
protected

number identifying this kind of scatterer, for the dynamical occupancy correction.

Right now it is the atomic number.

Definition at line 291 of file ScatteringPower.h.

REAL ObjCryst::ScatteringPower::mFormalCharge
protected

Formal Charge.

This can be used for bond valence analysis, or energy calculations.

Default value is 0.

Definition at line 324 of file ScatteringPower.h.

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.

Definition at line 318 of file ScatteringPower.h.


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