Generic type of scatterer: can be an atom, or a more complex assembly of atoms. More...

Inheritance diagram for ObjCryst::Scatterer:

Collaboration diagram for ObjCryst::Scatterer:

Public Member Functions
	Scatterer ()
	Constructor.

	Scatterer (const Scatterer &old)
	Copy Constructor.

virtual	~Scatterer ()
	Destructor.

virtual Scatterer *	CreateCopy () const =0

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

virtual int	GetNbComponent () const =0
	Number of components in the scatterer (eg number of point scatterers)

virtual const ScatteringComponentList &	GetScatteringComponentList () const =0
	Get the list of all scattering components for this scatterer. More...

virtual string	GetComponentName (const int i) const =0
	Name for the i-th component of this scatterer. More...

REAL	GetX () const
	X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...

REAL	GetY () const
	Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...

REAL	GetZ () const
	Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...

REAL	GetOccupancy () const
	Get the occupancy of the scatterer (0. More...

virtual void	SetX (const REAL x)
	X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...

virtual void	SetY (const REAL y)
	Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...

virtual void	SetZ (const REAL z)
	Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...

virtual void	SetOccupancy (const REAL occupancy)
	Change the occupancy of the scatterer (0. More...

	operator string () const
	Conversion function. More...

virtual void	Print () const =0
	Print some info about the scatterer (ideally this should be one line...).

virtual const string &	GetColour () const
	Colour associated to this scatterer (using POVRay names) More...

virtual const float *	GetColourRGB () const
	Colour associated to this scatterer, 3 RGB Coordinates.

virtual ostream &	POVRayDescription (ostream &os, const CrystalPOVRayOptions &options) const =0

virtual void	GLInitDisplayList (const bool noSymmetrics=false, const REAL xMin=-.1, const REAL xMax=1.1, const REAL yMin=-.1, const REAL yMax=1.1, const REAL zMin=-.1, const REAL zMax=1.1, const bool displayEnantiomer=false, const bool displayNames=false, const bool hideHydrogens=false) const =0

const RefinableObjClock &	GetClockScatterer () const
	Last time anything in the scatterer was changed (atoms, positions, scattering power)

RefinableObjClock &	GetClockScatterer ()
	Last time anything in the scatterer was changed (atoms, positions, scattering power)

void	SetCrystal (Crystal &)
	Set the crystal in which is included this Scatterer.

const Crystal &	GetCrystal () const
	In which crystal is this Scatterer included ?

Crystal &	GetCrystal ()
	In which crystal is this Scatterer included ?

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	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.

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

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

virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. More...

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.

Protected Member Functions
virtual void	InitRefParList ()=0

virtual void	InitRGBColour ()
	Get RGB Colour coordinates from Colour Name. More...

const RefinableObjClock &	GetClockScattCompList () const
	Last time the ScatteringComponentList was generated.

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
CrystVector_REAL	mXYZ
	coordinates of the scatterer (or of its center..)

REAL	mOccupancy
	Occupancy : 0 <= occ <= 1 For a multi-atom scatterer (polyhedron,..), this is the overall occupancy of the scatterer (affects all components of the scatterer).

string	mColourName
	Colour for this scatterer (from POVRay)

float	mColourRGB [3]
	Colour for this scatterer using RGB.

RefinableObjClock	mClockScatterer
	Last time anything (number of atoms, positions, scattering power) was changed.

RefinableObjClock	mClockScattCompList

Crystal *	mpCryst
	The crystal in which the Scatterer is This is needed so that we can know which scattering powers are available in the crystal, and also to convert fractionnal to orthonormal coordinates (for some scatterers only). 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

Generic type of scatterer: can be an atom, or a more complex assembly of atoms.

A Scatterer is able to give its position (in fractionnal coordinates) in the unit cell, and more generally the position of all point scattering centers (ScatteringComponent), along with the ScatteringPower associated with each position.

For simple atoms, there is only one scattering position with the associated scattering power (scattering factor, anomalous, thermic). For complex scatterers (molecules: ZScatterer) there are as many positions as atoms.

A scatterer also has a few functions to display itself in 3D

This is an abstract base class.

Definition at line 130 of file Scatterer.h.

Member Function Documentation

virtual Scatterer* ObjCryst::Scatterer::CreateCopy ( ) const

pure virtual

so-called Virtual copy constructor, needed to make copies of arrays of Scatterers

Implemented in ObjCryst::Molecule, ObjCryst::ZPolyhedron, ObjCryst::ZScatterer, and ObjCryst::Atom.

const string & ObjCryst::Scatterer::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::Molecule, ObjCryst::ZScatterer, and ObjCryst::Atom.

Definition at line 97 of file Scatterer.cpp.

const string & ObjCryst::Scatterer::GetColour ( ) const

virtual

Colour associated to this scatterer (using POVRay names)

Definition at line 130 of file Scatterer.cpp.

virtual string ObjCryst::Scatterer::GetComponentName ( const int i ) const

pure virtual

Name for the i-th component of this scatterer.

If the component is an Atom, Then the name is that of the atom. Else, it is the name of the scatterer plus the component number in the scatterer plus the name of the ScatteringPower.

Note: It would be better to return a reference, but we don't want to keep a name for all components... Weeelll, needs some more thinking... see what performance hit results (if any).

Bug:: does not take into account dummy atoms !!

Implemented in ObjCryst::Molecule, ObjCryst::ZScatterer, and ObjCryst::Atom.

REAL ObjCryst::Scatterer::GetOccupancy ( ) const

Get the occupancy of the scatterer (0.

-> 1.0)

The occupancy is given in %, and must take into account the 'special position' character of atoms (ie an atom on a 2fold axis should have at most a .5 population, etc...). For a multi-atom scatterer (polyhedra), this is the overall occupancy of the scatterer, affecting all atoms.

Definition at line 106 of file Scatterer.cpp.

virtual const ScatteringComponentList& ObjCryst::Scatterer::GetScatteringComponentList ( ) const

pure virtual

Get the list of all scattering components for this scatterer.

This is the most important function of this class, giving the list of scattering positions along with the associated ScatteringPower.

Implemented in ObjCryst::Molecule, ObjCryst::ZScatterer, and ObjCryst::Atom.

REAL ObjCryst::Scatterer::GetX ( ) const

X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer.

Definition at line 103 of file Scatterer.cpp.

REAL ObjCryst::Scatterer::GetY ( ) const

Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer.

Definition at line 104 of file Scatterer.cpp.

REAL ObjCryst::Scatterer::GetZ ( ) const

Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer.

Definition at line 105 of file Scatterer.cpp.

virtual void ObjCryst::Scatterer::GLInitDisplayList	(	const bool	noSymmetrics = `false`,
		const REAL	xMin = `-.1`,
		const REAL	xMax = `1.1`,
		const REAL	yMin = `-.1`,
		const REAL	yMax = `1.1`,
		const REAL	zMin = `-.1`,
		const REAL	zMax = `1.1`,
		const bool	displayEnantiomer = `false`,
		const bool	displayNames = `false`,
		const bool	hideHydrogens = `false`
	)		const

pure virtual

Create an OpenGL Display List of the scatterer. This should only be called by a Crystal object.

Parameters

noSymmetrics	if false (the default), then all symmetrics are shown in the 3D display, within the limits defined by the min/max parameters \ param xMin,xMax,yMin,yMax,zMin,zMax: in fractionnal coordinates, the region in which we want scaterrer to be displayed. The test is made on the center of the scatterer (eg a ZScatterer (molecule) will not be 'cut' on the border).
displayNames	if true, only the names of the scatterers will be displayed, at the position of the scatterers (to actually see them, they will have to be translated with respect to the drawing of the scatterers).
hideHydrogens	if true, do not display hydrogens/deuterium and their bonds

Implemented in ObjCryst::Molecule, ObjCryst::ZScatterer, and ObjCryst::Atom.

virtual void ObjCryst::Scatterer::InitRefParList ( )

protectedpure virtual

Prepare refinable parameters for the scatterer object

Implemented in ObjCryst::Molecule, ObjCryst::ZScatterer, and ObjCryst::Atom.

void ObjCryst::Scatterer::InitRGBColour ( )

protectedvirtual

Get RGB Colour coordinates from Colour Name.

Note that the colour used for display is usually that of the ScatteringPower, not that of the Scatterer

Definition at line 140 of file Scatterer.cpp.

ObjCryst::Scatterer::operator string ( ) const

Conversion function.

-> returns the scatt name

Warning: EXPERIMENTAL. DO NOT USE, as this may be removed.

Definition at line 118 of file Scatterer.cpp.

virtual ostream& ObjCryst::Scatterer::POVRayDescription	(	ostream &	os,
		const CrystalPOVRayOptions &	options
	)		const

pure virtual

Output a description of the scatterer for POVRay. This should only be called by the Crystal Object to which belongs this scatterer.

Implemented in ObjCryst::Molecule, ObjCryst::ZScatterer, and ObjCryst::Atom.

void ObjCryst::Scatterer::SetOccupancy ( const REAL occupancy )

virtual

Change the occupancy of the scatterer (0.

-> 1.0)

The occupancy is given in %, and must take into account the 'special position' character of atoms (ie an atom on a 2fold axis should have at most a .5 population, etc...). For a multi-atom scatterer (polyhedra), this is the overall occupancy of the scatterer, affecting all atoms.

Definition at line 112 of file Scatterer.cpp.

void ObjCryst::Scatterer::SetX ( const REAL x )

virtual

X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer.

Definition at line 109 of file Scatterer.cpp.

void ObjCryst::Scatterer::SetY ( const REAL y )

virtual

Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer.

Definition at line 110 of file Scatterer.cpp.

void ObjCryst::Scatterer::SetZ ( const REAL z )

virtual

Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer.

Definition at line 111 of file Scatterer.cpp.

Member Data Documentation

RefinableObjClock ObjCryst::Scatterer::mClockScattCompList

mutableprotected

Last time the ScatteringComponentList was generated

Definition at line 287 of file Scatterer.h.

Crystal* ObjCryst::Scatterer::mpCryst

protected

The crystal in which the Scatterer is This is needed so that we can know which scattering powers are available in the crystal, and also to convert fractionnal to orthonormal coordinates (for some scatterers only).

It cannot be const since some scatterers may want to modify the list of scattering powers of the crystal...

Definition at line 294 of file Scatterer.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation