ObjCryst::ScatteringPowerAtom Class Reference

The Scattering Power for an Atom. More...

Inheritance diagram for ObjCryst::ScatteringPowerAtom:

Collaboration diagram for ObjCryst::ScatteringPowerAtom:

List of all members.

Public Member Functions

ScatteringPowerAtom (const string &name, const string &symbol, const REAL bIso=1.0)

Atom constructor.

ScatteringPowerAtom (const ScatteringPowerAtom &old)

virtual const string & GetClassName () const

Name for this class ("RefinableObj", "Crystal",.

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

Re-initialize parameters (after using the default constructor).

virtual CrystVector_REAL GetScatteringFactor (const ScatteringData &data, const int spgSymPosIndex=0) const

Get the Scattering factor for all reflections of a given ScatteringData object.

virtual REAL GetForwardScatteringFactor (const RadiationType) const

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

virtual CrystVector_REAL GetTemperatureFactor (const ScatteringData &data, const int spgSymPosIndex=0) const

Get the temperature factor for all reflections of a given ScatteringData object.

virtual CrystMatrix_REAL GetResonantScattFactReal (const ScatteringData &data, const int spgSymPosIndex=0) const

Get the real part of the resonant scattering factor.

virtual CrystMatrix_REAL GetResonantScattFactImag (const ScatteringData &data, const int spgSymPosIndex=0) const

Get the imaginary part of the resonant scattering factor.

void SetSymbol (const string &symbol)

Set the symbol for this atom.

virtual const string & GetSymbol () const

Returns the symbol ('Ta', 'O2-',...) of the atom.

string GetElementName () const

Returns the standard name of the element (ie "hydrogen", "tantalum",.

int GetAtomicNumber () const

Atomic number for this atom.

REAL GetRadius () const

Atomic radius for this atom, in Angstroems.

virtual void Print () const

virtual void XMLOutput (ostream &os, int indent=0) const

Output to stream in well-formed XML.

virtual void XMLInput (istream &is, const XMLCrystTag &tag)

Input From stream.

Protected Member Functions

void InitAtScattCoeffsWK95 ()

void InitAtNeutronScattCoeffs ()

virtual void InitRefParList ()

Protected Attributes

string mSymbol

Symbol of this atom.

int mAtomicNumber

atomic number (Z) for the atom

cctbx::eltbx::xray_scattering::gaussian * mpGaussian

Pointer to cctbx's gaussian describing the thomson x-ray scattering factor.

REAL mNeutronScattLengthReal

Neutron Bond Coherent Scattering lengths.

REAL mNeutronScattLengthImag

REAL mRadius

Radius of the atom, in Angstroems.

REAL mNeutronAbsCrossSection

Neutron Absorption cross section (barn).

Detailed Description

The Scattering Power for an Atom.

Definition at line 295 of file ScatteringPower.h.

Constructor & Destructor Documentation

ObjCryst::ScatteringPowerAtom::ScatteringPowerAtom	(	const string &	name,
		const string &	symbol,
		const REAL	bIso = `1.0`
	)

Atom constructor.

Parameters:

	symbol	: 'Ti' , 'Ti4+', 'Cl1-' These symbols must correspond to one of the entries of the international tables for crystallography (1995) giving the analytical approximation for scattering factors.
	name	: name of the atom ('Ta1','Sm2', 'Tungsten_1'...). The name can have any format but spaces should be avoided, since it will generate problems when reading the names from a file...
	biso	: Isotropic thermic coefficient

Definition at line 223 of file ScatteringPower.cpp.

Member Function Documentation

const string & ObjCryst::ScatteringPowerAtom::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 250 of file ScatteringPower.cpp.

CrystVector_REAL ObjCryst::ScatteringPowerAtom::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 405 of file ScatteringPower.cpp.

REAL ObjCryst::ScatteringPowerAtom::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 451 of file ScatteringPower.cpp.

CrystVector_REAL ObjCryst::ScatteringPowerAtom::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 478 of file ScatteringPower.cpp.

CrystMatrix_REAL ObjCryst::ScatteringPowerAtom::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 574 of file ScatteringPower.cpp.

CrystMatrix_REAL ObjCryst::ScatteringPowerAtom::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 618 of file ScatteringPower.cpp.

string ObjCryst::ScatteringPowerAtom::GetElementName ( ) const

Returns the standard name of the element (ie "hydrogen", "tantalum",.

.).

Names are extracted form Grosse-Kunstleve 'atominfo' package, which uses data from the CRC Handbook of Chemistry & Physics, 63rd & 70th editions

Definition at line 673 of file ScatteringPower.cpp.

void ObjCryst::ScatteringPowerAtom::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 237 of file ObjCryst/IO.cpp.

void ObjCryst::ScatteringPowerAtom::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 274 of file ObjCryst/IO.cpp.

void ObjCryst::ScatteringPowerAtom::InitAtScattCoeffsWK95 ( ) [protected]

For internal use only.

Fetch the coefficients for analytical approximation of the atomic scattering factor.

void ObjCryst::ScatteringPowerAtom::InitAtNeutronScattCoeffs ( ) [protected]

For internal use only.

Fetch the coefficients neutron scattering.

Definition at line 701 of file ScatteringPower.cpp.

Member Data Documentation

string ObjCryst::ScatteringPowerAtom::mSymbol [protected]

Symbol of this atom.

This symbol must correspond to one of the entries of the international tables for crystallography (1995) giving the analytical approximation for scattering factors.

Definition at line 357 of file ScatteringPower.h.

REAL ObjCryst::ScatteringPowerAtom::mNeutronScattLengthReal [protected]

Neutron Bond Coherent Scattering lengths.

Real and imaginary (for atoms who have an imaginary part)

Reference : Neutron News, Vol. 3, No. 3, 1992, pp. 29-37.

Definition at line 372 of file ScatteringPower.h.

REAL ObjCryst::ScatteringPowerAtom::mNeutronAbsCrossSection [protected]

Neutron Absorption cross section (barn).

For 2200 m/s neutrons.

Reference : Neutron News, Vol. 3, No. 3, 1992, pp. 29-37.

Definition at line 383 of file ScatteringPower.h.

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


Public Member Functions
	ScatteringPowerAtom (const string &name, const string &symbol, const REAL bIso=1.0)
	Atom constructor.
	ScatteringPowerAtom (const ScatteringPowerAtom &old)
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",.
void	Init (const string &name, const string &symbol, const REAL bIso=1.0)
	Re-initialize parameters (after using the default constructor).
virtual CrystVector_REAL	GetScatteringFactor (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the Scattering factor for all reflections of a given ScatteringData object.
virtual REAL	GetForwardScatteringFactor (const RadiationType) const
	Get the scattering factor at (0,0,0).
virtual CrystVector_REAL	GetTemperatureFactor (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the temperature factor for all reflections of a given ScatteringData object.
virtual CrystMatrix_REAL	GetResonantScattFactReal (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the real part of the resonant scattering factor.
virtual CrystMatrix_REAL	GetResonantScattFactImag (const ScatteringData &data, const int spgSymPosIndex=0) const
	Get the imaginary part of the resonant scattering factor.
void	SetSymbol (const string &symbol)
	Set the symbol for this atom.
virtual const string &	GetSymbol () const
	Returns the symbol ('Ta', 'O2-',...) of the atom.
string	GetElementName () const
	Returns the standard name of the element (ie "hydrogen", "tantalum",.
int	GetAtomicNumber () const
	Atomic number for this atom.
REAL	GetRadius () const
	Atomic radius for this atom, in Angstroems.
virtual void	Print () const
virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML.
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream.
Protected Member Functions
void	InitAtScattCoeffsWK95 ()
void	InitAtNeutronScattCoeffs ()
virtual void	InitRefParList ()
Protected Attributes
string	mSymbol
	Symbol of this atom.
int	mAtomicNumber
	atomic number (Z) for the atom
cctbx::eltbx::xray_scattering::gaussian *	mpGaussian
	Pointer to cctbx's gaussian describing the thomson x-ray scattering factor.
REAL	mNeutronScattLengthReal
	Neutron Bond Coherent Scattering lengths.
REAL	mNeutronScattLengthImag
REAL	mRadius
	Radius of the atom, in Angstroems.
REAL	mNeutronAbsCrossSection
	Neutron Absorption cross section (barn).