\ brief ScatteringPower for a spherical particule More...

Inheritance diagram for ObjCryst::ScatteringPowerSphere:

Collaboration diagram for ObjCryst::ScatteringPowerSphere:

Public Member Functions
	ScatteringPowerSphere ()
	Default constructor.

	ScatteringPowerSphere (const string &name, const REAL radius, const REAL bIso=1.0)
	constructor More...

	ScatteringPowerSphere (const ScatteringPowerSphere &old)

void	Init (const string &name, const REAL radius, const REAL bIso=1.0)

virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...

virtual CrystVector_REAL	GetScatteringFactor (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the Scattering factor for all reflections of a given ScatteringData object. More...

virtual REAL	GetForwardScatteringFactor (const RadiationType) const
	Get the scattering factor at (0,0,0). More...

virtual CrystVector_REAL	GetTemperatureFactor (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the temperature factor for all reflections of a given ScatteringData object. More...

virtual CrystMatrix_REAL	GetResonantScattFactReal (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the real part of the resonant scattering factor. More...

virtual CrystMatrix_REAL	GetResonantScattFactImag (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the imaginary part of the resonant scattering factor. More...

REAL	GetRadius () const
	Return the physical radius of this type of scatterer (for 3D display purposes). More...

virtual void	Print () const

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...

Public Member Functions inherited from ObjCryst::ScatteringPower
	ScatteringPower (const ScatteringPower &old)

virtual void	operator= (const ScatteringPower &rhs)

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 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 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 RefinableObjClock &	GetMaximumLikelihoodParClock () 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()

RefinablePar &	GetPar (const long i)
	Access all parameters in the order they were inputted.

const RefinablePar &	GetPar (const long i) const
	Access all parameters in the order they were inputted.

RefinablePar &	GetPar (const string &name)
	Access all parameters from their name.

const RefinablePar &	GetPar (const string &name) const
	Access all parameters from their name.

RefinablePar &	GetPar (const REAL *)
	Access parameter from its adress.

const RefinablePar &	GetPar (const REAL *) const
	Access parameter from its adress.

RefinablePar &	GetParNotFixed (const long i)
	Access all parameters in the order they were inputted, skipping fixed parameters. More...

const RefinablePar &	GetParNotFixed (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...

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	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.

RefObjOpt &	GetOption (const unsigned int i)
	Access to the options.

const RefObjOpt &	GetOption (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 RefinableObjClock &	GetRefParListClock () 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 RefinableObjClock &	GetClockMaster () const
	This clocks records any change in the object. See refinableObj::mClockMaster.

Private Member Functions
virtual void	InitRefParList ()

void	Init ()
	Initialization of the object, used by all constructors, and operator=.

Private Attributes
REAL	mBiso
	Isotropic temperature B-factor.

REAL	mRadius
	Radius of the sphere.

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::ScatteringPower
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 inherited from ObjCryst::ScatteringPower
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< RefinableObj >	mSubObjRegistry
	Registry of RefinableObject needed for this object (owned by this object or not)

ObjRegistry< RefinableObj >	mClientObjRegistry
	Registry of RefinableObject using this object. More...

ObjRegistry< RefObjOpt >	mOptionRegistry
	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

\ brief ScatteringPower for a spherical particule

This can be used to modelize the form factor of disordered (or low-resolution) of fullerene-type compounds, where all atoms are located on a sphere.

This actually modelizes a spherical distribution of a single electron, so to modelize C60 the occupancy must be set to 60*6.

Definition at line 41 of file ScatteringPowerSphere.h.

Constructor & Destructor Documentation

ObjCryst::ScatteringPowerSphere::ScatteringPowerSphere	(	const string &	name,
		const REAL	radius,
		const REAL	bIso = `1.0`
	)

constructor

Parameters

name	: name of the ScatteringPower ('C60','France 98'...). The name can have any format
nbAtom	the number of atoms
biso	: Isotropic thermic coefficient
AxisLengthX,AxisLengthY,AxisLengthZ	length of the different main axis of the ellipsoid
symbol	the symbol of the element associated to this fullerene. By default it is assumed to be carbon

Definition at line 47 of file ScatteringPowerSphere.cpp.

Member Function Documentation

const string & ObjCryst::ScatteringPowerSphere::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::ScatteringPower.

Definition at line 80 of file ScatteringPowerSphere.cpp.

REAL ObjCryst::ScatteringPowerSphere::GetForwardScatteringFactor ( const RadiationType ) const

virtual

Get the scattering factor at (0,0,0).

Used for scatterer (electron, nucleus) density generation.

Implements ObjCryst::ScatteringPower.

Definition at line 138 of file ScatteringPowerSphere.cpp.

REAL ObjCryst::ScatteringPowerSphere::GetRadius ( ) const

virtual

Return the physical radius of this type of scatterer (for 3D display purposes).

Warning: this may be removed later.

Implements ObjCryst::ScatteringPower.

Definition at line 198 of file ScatteringPowerSphere.cpp.

CrystMatrix_REAL ObjCryst::ScatteringPowerSphere::GetResonantScattFactImag	(	const ScatteringData &	data,
		const int	spgSymPosIndex = `0`
	)		const

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.

Implements ObjCryst::ScatteringPower.

Definition at line 190 of file ScatteringPowerSphere.cpp.

CrystMatrix_REAL ObjCryst::ScatteringPowerSphere::GetResonantScattFactReal	(	const ScatteringData &	data,
		const int	spgSymPosIndex = `0`
	)		const

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.

Implements ObjCryst::ScatteringPower.

Definition at line 182 of file ScatteringPowerSphere.cpp.

CrystVector_REAL ObjCryst::ScatteringPowerSphere::GetScatteringFactor	(	const ScatteringData &	data,
		const int	spgSymPosIndex = `0`
	)		const

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.

Implements ObjCryst::ScatteringPower.

Definition at line 86 of file ScatteringPowerSphere.cpp.

CrystVector_REAL ObjCryst::ScatteringPowerSphere::GetTemperatureFactor	(	const ScatteringData &	data,
		const int	spgSymPosIndex = `0`
	)		const

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.

Implements ObjCryst::ScatteringPower.

Definition at line 143 of file ScatteringPowerSphere.cpp.

void ObjCryst::ScatteringPowerSphere::XMLInput	(	istream &	is,
		const XMLCrystTag &	tag
	)

virtual

Input From stream.

Todo:: Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 236 of file ScatteringPowerSphere.cpp.

void ObjCryst::ScatteringPowerSphere::XMLOutput	(	ostream &	os,
		int	indent = `0`
	)		const

virtual

Output to stream in well-formed XML.

Todo:: Use inheritance.. as for XMLInputTag()...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 205 of file ScatteringPowerSphere.cpp.

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation