ObjCryst::Atom Class Reference

The basic atom scatterer, in a crystal. More...

Inheritance diagram for ObjCryst::Atom:

[legend]Collaboration diagram for ObjCryst::Atom:

[legend]List of all members.

Public Member Functions
	Atom ()
	Default constructor.
	Atom (const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *pow)
	Atom constructor.
	Atom (const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *pow, const REAL popu)
	Atom constructor.
	Atom (const Atom &old)
	Copy constructor.
virtual Atom *	CreateCopy () const
	~Atom ()
	Destructor...
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...).
virtual void	operator= (const Atom &rhs)
void	Init (const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *pow, const REAL popu=1)
	initialize the atom (used for arrays of atoms).
virtual int	GetNbComponent () const
	Number of components in the scatterer (eg number of point scatterers).
virtual const ScatteringComponentList &	GetScatteringComponentList () const
	Get the list of all scattering components for this scatterer.
virtual string	GetComponentName (const int i) const
	Name for the i-th component of this scatterer.
virtual void	Print () const
	Print some info about the scatterer (ideally this should be one line...).
REAL	GetMass () const
	Returns the molar mass of the atom.
REAL	GetRadius () const
	Returns the radius (in Angstroems) of the atom.
virtual ostream &	POVRayDescription (ostream &os, const CrystalPOVRayOptions &options) const
	XMLOutput a description of the scatterer for POVRay.
virtual void	GLInitDisplayList (const bool onlyIndependentAtoms=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	IsDummy () const
	Is this a dummy atom ? (ie no ScatteringPower) Dummy atoms should not exist !
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.
const ScatteringPower &	GetScatteringPower () const
	Get the ScatteringPowerAtom corresponding to this atom.
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter.
Private Member Functions
virtual void	InitRefParList ()
	Prepare refinable parameters for the scatterer object.
Private Attributes
ScatteringComponentList	mScattCompList
	The list of scattering components.
const ScatteringPower *	mpScattPowAtom
	The ScatteringPowerAtom associated to that atom.

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Detailed Description

The basic atom scatterer, in a crystal.

This class records the position of the atom, and has a pointer to its ScatteringPowerAtom.

Note:

there can be 'Dummy' atoms, for which the used symbol is "X", and which have no scattering power (use with caution: dummy atoms are only supposed to be used within ZScatterer) ####################################################################

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Constructor & Destructor Documentation

ObjCryst::Atom::Atom (   )

Default constructor. The Atom must be initialized thereafter using Atom::Init()

ObjCryst::Atom::Atom (  const REAL  x, const REAL  y, const REAL  z, const string &  name, const ScatteringPower *  pow )

Atom constructor. Parameters: x,y,z  : fractional coordinates of the atom pow  : the ScatteringPower associated to this atom. Must be allocated separately. name  : name of the atom ('Ta1','Sm2', 'Tungsten_1'...). The name can have any format but spaces should be avoided.

ObjCryst::Atom::Atom (  const REAL  x, const REAL  y, const REAL  z, const string &  name, const ScatteringPower *  pow, const REAL  popu )

Atom constructor. Parameters: x,y,z  : fractional coordinates of the atom popu  : the population of the atom (0.0->1.0) This should take into account the multiplicity of the atom. For an atom in group P2 and on the 2 axis, this should be set to 0.5, unless you are using the dynamical occupancy correction (recommended for global optimizations). See Crystal::CalcDynPopCorr() and Crystal::mUseDynPopCorr pow  : the ScatteringPower associated to this atom. Must be allocated separatly. name  : name of the atom ('Ta1','Sm2', 'Tungsten_1'...). The name can have any format but spaces should be avoided (just a precaution)

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Member Function Documentation

virtual Atom* ObjCryst::Atom::CreateCopy (   )  const [virtual]

For internal use only. so-called Virtual copy constructor, needed to make copies of arrays of Scatterers Implements ObjCryst::Scatterer.

virtual const string& ObjCryst::Atom::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::Scatterer.

virtual string ObjCryst::Atom::GetComponentName (  const int  i  )  const [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 !! Implements ObjCryst::Scatterer.

virtual void ObjCryst::Atom::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: obj  the , 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. groupIndex  a 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). firstGroup  this 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.

REAL ObjCryst::Atom::GetMass (   )  const

Returns the molar mass of the atom. Values are extracted from the 'atominfo' package, which uses data from the CRC Handbook of Chemistry & Physics, 63rd & 70th editions The Mass is actually extracted from the ScatteringPowerAtom.

REAL ObjCryst::Atom::GetRadius (   )  const

Returns the radius (in Angstroems) of the atom. Values are extracted from the 'atominfo' package, which uses data from the ICSD/CRYSTIN Manual The Radius is extracted from the ScatteringPowerAtom.

virtual const ScatteringComponentList& ObjCryst::Atom::GetScatteringComponentList (   )  const [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. Implements ObjCryst::Scatterer.

virtual void ObjCryst::Atom::GLInitDisplayList (  const bool  onlyIndependentAtoms = 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 [virtual]

For internal use only. 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). Implements ObjCryst::Scatterer.

void ObjCryst::Atom::Init (  const REAL  x, const REAL  y, const REAL  z, const string &  name, const ScatteringPower *  pow, const REAL  popu = 1 )

initialize the atom (used for arrays of atoms). Parameters: x,y,z  : fractional coordinates of the atom pow  : the ScatteringPower associated to this atom. Must be allocated separately. name  : name of the atom ('Ta1','Sm2', 'Tungsten_1'...).

virtual void ObjCryst::Atom::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.

virtual void ObjCryst::Atom::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.

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

• Atom.h

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