Atomic shape function object. More...

#include <atomsf.h>

Inheritance diagram for clipper::AtomShapeFn:

Public Types
enum	TYPE { X, Y, Z, Uiso, Occ, U11, U22, U33, U12, U13, U23 }
Public Member Functions
	AtomShapeFn ()
	null constructor
	AtomShapeFn (const Atom &atom)
	constructor: from atom object
	AtomShapeFn (const Coord_orth &xyz, const String &element, const ftype u_iso=0.0, const ftype occ=1.0)
	constructor: from coord, element, isotropic U, occupancy
	AtomShapeFn (const Coord_orth &xyz, const String &element, const U_aniso_orth &u_aniso, const ftype occ=1.0)
	constructor: from coord, element, anisotropic U, occupancy
void	init (const Atom &atom)
	initialiser: from atom object
void	init (const Coord_orth &xyz, const String &element, const ftype u_iso=0.0, const ftype occ=1.0)
	initialiser: from coord, element, isotropic U, occupancy
void	init (const Coord_orth &xyz, const String &element, const U_aniso_orth &u_aniso, const ftype occ=1.0)
	initialiser: from coord, element, anisotropic U, occupancy
ftype	f (const Coord_reci_orth &rfl) const
	return scattering factor as a function of reflection posn
ftype	rho (const Coord_orth &xyz) const
	return electron density as a function of coordinate
bool	rho_grad (const Coord_orth &xyz, ftype &rho, std::vector< ftype > &grad) const
	return Agarwal density gradients as a function of coordinate
bool	rho_curv (const Coord_orth &xyz, ftype &rho, std::vector< ftype > &grad, Matrix< ftype > &curv) const
	return Agarwal density gradient/curvature as a function of coordinate
bool	rho_grad (const Coord_orth &xyz, std::vector< ftype > &grad) const
ftype	f (const ftype &invresolsq) const
	return (isotropic) scattering factor as a function of resolution
ftype	rho (const ftype &rsq) const
	return (isotropic) electron density as a function of radius
std::vector< TYPE > &	agarwal_params ()
	define parameters for Agarwal gradient/curvature calcs

Detailed Description

Atomic shape function object.

The atomic scattering factor object is instantiated for each atom in turn, giving the atom parameters: position, element, occupancy and the isotropic or anisotropic U-value. (See clipper::Util for conversion from B-factors.). The methods of the class may then be called to return the scattering in reciprocal space or density in real space using either isotropic or anistropic models as required.

If the atom only has an isotropic U, the faster isotropic methods will be used where available.

This implementation uses the coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431. The source data can be found at: ftp://wrzx02.rz.uni-wuerzburg.de/pub/local/Crystallography/sfac.dat

Constructor & Destructor Documentation

clipper::AtomShapeFn::AtomShapeFn ( const Atom & atom )

constructor: from atom object

If the atom has an anisotropic U (even if the values are isotropic), then it is initialised as anisotropic, otherwise it is isotropic.

Parameters:

atom	The atom object.

References init().

clipper::AtomShapeFn::AtomShapeFn	(	const Coord_orth &	xyz,
		const String &	element,
		const ftype	u_iso = `0.0`,
		const ftype	occ = `1.0`
	)

constructor: from coord, element, isotropic U, occupancy

The atom is initialised as isotropic.

Parameters:

xyz	The atom coordinate.
element	The atom element.
u_iso	The isotropic U-value.
occ	The occupancy.

References init().

clipper::AtomShapeFn::AtomShapeFn	(	const Coord_orth &	xyz,
		const String &	element,
		const U_aniso_orth &	u_aniso,
		const ftype	occ = `1.0`
	)

constructor: from coord, element, anisotropic U, occupancy

The atom is initialised as anisotropic.

Parameters:

xyz	The atom coordinate.
element	The atom element.
u_aniso	The anisotropic U-value.
occ	The occupancy.

References init().

Member Function Documentation

void clipper::AtomShapeFn::init ( const Atom & atom )

initialiser: from atom object

If the atom has an anisotropic U (even if the values are isotropic), then it is initialised as anisotropic, otherwise it is isotropic.

Parameters:

atom	The atom object.

References clipper::Atom::coord_orth(), clipper::Atom::element(), clipper::Util::is_nan(), clipper::Mat33sym< T >::is_null(), clipper::Atom::occupancy(), clipper::Atom::u_aniso_orth(), and clipper::Atom::u_iso().

Referenced by AtomShapeFn(), and init().

void clipper::AtomShapeFn::init	(	const Coord_orth &	xyz,
		const String &	element,
		const ftype	u_iso = `0.0`,
		const ftype	occ = `1.0`
	)

initialiser: from coord, element, isotropic U, occupancy

The atom is initialised as isotropic.

Parameters:

xyz	The atom coordinate.
element	The atom element.
u_iso	The isotropic U-value.
occ	The occupancy.

References init().

void clipper::AtomShapeFn::init	(	const Coord_orth &	xyz,
		const String &	element,
		const U_aniso_orth &	u_aniso,
		const ftype	occ = `1.0`
	)

initialiser: from coord, element, anisotropic U, occupancy

The atom is initialised as anisotropic.

Parameters:

xyz	The atom coordinate.
element	The atom element.
u_aniso	The anisotropic U-value.
occ	The occupancy.

References clipper::Mat33sym< T >::det(), init(), clipper::Mat33sym< T >::mat00(), clipper::Mat33sym< T >::mat01(), clipper::Mat33sym< T >::mat02(), clipper::Mat33sym< T >::mat11(), clipper::Mat33sym< T >::mat12(), clipper::Mat33sym< T >::mat22(), clipper::Util::pi(), clipper::Util::twopi(), and clipper::U_aniso_orth::u_iso().

ftype clipper::AtomShapeFn::f ( const Coord_reci_orth & rfl ) const

return scattering factor as a function of reflection posn

Return the scattering factor as a function of position in reciprocal space in electrons.

Parameters:

rfl	Position in reciprocal space.

Returns:: The scattering factor in electrons.

References clipper::Coord_reci_orth::invresolsq(), clipper::Mat33sym< T >::quad_form(), and clipper::Util::twopi2().

ftype clipper::AtomShapeFn::rho ( const Coord_orth & xyz ) const

return electron density as a function of coordinate

Return the density as a function of position in real space in electrons.

Parameters:

xyz	Position in real space.
The	density in electrons.

References clipper::Coord_orth::lengthsq().

Referenced by clipper::Test_core::operator()().

bool clipper::AtomShapeFn::rho_grad	(	const Coord_orth &	xyz,
		ftype &	rho,
		std::vector< ftype > &	grad
	)		const

return Agarwal density gradients as a function of coordinate

Return the Agarwal gradients of the density with respect to tha atomic parameters as a function of position in real space in electrons. The parameter list is defined by assignment to agarwal_params().

Parameters:

xyz	Position in real space. rho The density in electrons.
grad	Vector gradient in electrons (pre-size for best performance).

References clipper::Coord_orth::lengthsq(), clipper::Coord_orth::x(), clipper::Coord_orth::y(), and clipper::Coord_orth::z().

bool clipper::AtomShapeFn::rho_curv	(	const Coord_orth &	xyz,
		ftype &	rho,
		std::vector< ftype > &	grad,
		Matrix< ftype > &	curv
	)		const

return Agarwal density gradient/curvature as a function of coordinate

Return the Agarwal gradients of the density with respect to tha atomic parameters as a function of position in real space in electrons. The parameter list is defined by assignment to agarwal_params().

Parameters:

xyz	Position in real space. rho The density in electrons.
grad	Vector gradient in electrons (pre-size for best performance).
curv	Matrix curvature in electrons (pre-size for best performance).

References clipper::Coord_orth::lengthsq(), clipper::Message::message(), clipper::Util::nan(), clipper::Coord_orth::x(), clipper::Coord_orth::y(), and clipper::Coord_orth::z().

Referenced by clipper::Test_core::operator()().