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ObjCryst::Crystal Class Reference

Crystal class: Unit cell, spacegroup, scatterers. More...

Inheritance diagram for ObjCryst::Crystal:

List of all members.

Public Methods
	Crystal ()
	Default Constructor.
	Crystal (const REAL a, const REAL b, const REAL c, const string &SpaceGroupId)
	Crystal Constructor (orthorombic).
	Crystal (const REAL a, const REAL b, const REAL c, const REAL alpha, const REAL beta, const REAL gamma, const string &SpaceGroupId)
	Crystal Constructor (triclinic).
	Crystal (const Crystal &oldCryst)
	Crystal copy constructor.
	~Crystal ()
	Crystal destructor.
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...).
void	AddScatterer (Scatterer *scatt)
	Add a scatterer to the crystal.
void	RemoveScatterer (Scatterer *scatt)
	Remove a Scatterer. This also deletes the scatterer.
long	GetNbScatterer () const
	Number of scatterers in the crystal.
Scatterer &	GetScatt (const string &scattName)
	Provides an access to the scatterers.
const Scatterer &	GetScatt (const string &scattName) const
	Provides a const access to the scatterers.
Scatterer &	GetScatt (const long scattIndex)
	Provides an access to the scatterers.
const Scatterer &	GetScatt (const long scattIndex) const
	Provides a const access to the scatterers.
ObjRegistry< Scatterer > &	GetScattererRegistry ()
	Get the registry of scatterers.
ObjRegistry< ScatteringPower > &	GetScatteringPowerRegistry ()
	Get the registry of ScatteringPower included in this Crystal.
const ObjRegistry< ScatteringPower > &	GetScatteringPowerRegistry () const
	Get the registry of ScatteringPower included in this Crystal.
void	AddScatteringPower (ScatteringPower *scattPow)
	Add a ScatteringPower for this Crystal.
void	RemoveScatteringPower (ScatteringPower *scattPow)
	Remove a ScatteringPower for this Crystal.
ScatteringPower &	GetScatteringPower (const string &name)
	Find a ScatteringPower from its name. Names must be unique in a given Crystal.
const ScatteringPower &	GetScatteringPower (const string &name) const
	Find a ScatteringPower from its name. Names must be unique in a given Crystal.
const RefinableObjClock &	GetMasterClockScatteringPower () const
	Get the clock which reports all changes in ScatteringPowers.
virtual const ScatteringComponentList &	GetScatteringComponentList () const
	Get the list of all scattering components.
const RefinableObjClock &	GetClockScattCompList () const
	Get the list of all scattering components.
void	Print (ostream &os=cout) const
	Prints some info about the crystal.
CrystMatrix_REAL	GetMinDistanceTable (const REAL minDistance=0.1) const
	Minimum interatomic distance between all scattering components (atoms) in the crystal.
void	PrintMinDistanceTable (const REAL minDistance=0.1, ostream &os=cout) const
	Print the minimum distance table between all scattering centers (atoms) in the crystal.
ostream &	POVRayDescription (ostream &os, const CrystalPOVRayOptions &options) const
	XMLOutput POV-Ray Description for this Crystal.
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 displayNames=false) const
	Create an OpenGL DisplayList of the crystal.
void	CalcDynPopCorr (const REAL overlapDist=1., const REAL mergeDist=.0) const
	Compute the 'Dynamical population correction for all atoms. Atoms which are considered "equivalent" (ie currently with the same Z number) and which are overlapping see their Dynamical occupancy changed so that when they fully overlap, they are equivalent to 1 atom.
void	ResetDynPopCorr () const
	Reset Dynamical Population Correction factors (ie set it to 1).
void	SetUseDynPopCorr (const int use)
	Set the use of dynamical population correction (Crystal::mUseDynPopCorr).
REAL	GetBumpMergeCost () const
	Get the Anti-bumping/pro-Merging cost function.
void	SetBumpMergeDistance (const ScatteringPower &scatt1, const ScatteringPower &scatt2, const REAL dist=1.5)
	Set the Anti-bumping distance between two scattering types.
void	SetBumpMergeDistance (const ScatteringPower &scatt1, const ScatteringPower &scatt2, const REAL dist, const bool allowMerge)
	Set the Anti-bumping distance between two scattering types.
const RefinableObjClock &	GetClockScattererList () const
	When was the list of scatterers last changed ?
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.
virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration.
virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object.
virtual void	CIFOutput (ostream &os) const
	output Crystal structure as a cif file (EXPERIMENTAL !)
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter.
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.
Private Types
typedef std::vector< pair< pair< const ScatteringPower *, const ScatteringPower * >, Crystal::BumpMergePar > >	VBumpMergePar
	Anti-bump parameters.
Private Methods
void	Init (const REAL a, const REAL b, const REAL c, const REAL alpha, const REAL beta, const REAL gamma, const string &SpaceGroupId, const string &name)
	Init all Crystal parameters.
void	InitOptions ()
	Init options.
int	FindScatterer (const string &scattName) const
	Find a scatterer (its index # in mpScatterrer[]) with a given name.
void	CalcDistTable (const bool fast, const REAL asymUnitMargin=4) const
	Compute the distance Table (mDistTable) for all scattering components.
Private Attributes
ObjRegistry< Scatterer >	mScattererRegistry
	The registry of scatterers for this UnitCell.
VBumpMergePar	mvBumpMergePar
	Anti-bump parameters map.
RefinableObjClock	mBumpMergeParClock
	Last Time Anti-bump parameters were changed.
RefinableObjClock	mBumpMergeCostClock
	Last Time Anti-bump parameters were changed.
REAL	mBumpMergeCost
	Current bump-merge cost.
REAL	mBumpMergeScale
	Bump-merge scale factor.
std::vector< NeighbourHood >	mvDistTableSq
	Interatomic distance table for all unique atoms.
RefinableObjClock	mDistTableClock
	The time when the distance table was last calculated.
ScatteringComponentList	mScattCompList
	The list of all scattering components in the crystal.
RefinableObjClock	mLatticeClock
	Clock for lattice paramaters.
RefObjOpt	mUseDynPopCorr
	Use Dynamical population correction (ScatteringComponent::mDynPopCorr) during Structure factor calculation ?
ObjRegistry< ScatteringPower >	mScatteringPowerRegistry
	The registry of ScatteringPower for this Crystal.
RefinableObjClock	mClockScattererList
	Last time the list of Scatterers was changed.
RefinableObjClock	mClockScattCompList
	Last time the ScatteringComponentList was generated.
RefinableObjClock	mClockNeighborTable
	Last time the Neighbor Table was generated.
RefinableObjClock	mClockDynPopCorr
	Last time the dynamical population correction was computed.
RefinableObjClock	mMasterClockScatteringPower
	master clock recording every change in Scattering Powers
RefObjOpt	mDisplayEnantiomer
	Display the enantiomeric (mirror along x) structure in 3D? This can be helpful for non-centrosymmetric structure which have been solved using powder diffraction (which only gives the relative configuration).

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Detailed Description

Crystal class: Unit cell, spacegroup, scatterers.

A Crystal object has several main characteristics : (1) a unit cell, (2) a Spacegroup and (3) a list of Scatterer. Also stored in the Crystal is a list of the ScttaringPower used by all the scatterers of this crystal.

The crystal is capable of giving a list of all scattering components (ie the list of all unique scattering 'points' (ScatteringComponent, ie atoms) in the unit cell, each associated to a ScatteringPower).

When those scattering components are on a special position or overlapping with another component of the same type, it is possible to correct dynamically the occupancy of this/these components to effectively have only one component instead of several due to the overlapping. This method is interesting for global optimization where atoms must not be "locked" on a special position. If this "Dynamical Occupancy Correction" is used then no occupancy should be corrected for special positions, since this will be done dynamically.

A crystal structure can be viewed in 3D using OpenGL.

Todo:

exporting (and importing) crystal structures to/from other files format than ObjCryst's XML (eg CIF, and format used by refinement software)

Currently only 3D crystal structures can be handled, with no magnetic structure (that may be done later) and no incommensurate structure.

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Constructor & Destructor Documentation

ObjCryst::Crystal::Crystal (  const REAL    a, const REAL    b, const REAL    c, const string &    SpaceGroupId )

Crystal Constructor (orthorombic). Parameters: a,b,c  : unit cell dimension, in angstroems SpaceGroupId:  space group symbol or number

ObjCryst::Crystal::Crystal (  const REAL    a, const REAL    b, const REAL    c, const REAL    alpha, const REAL    beta, const REAL    gamma, const string &    SpaceGroupId )

Crystal Constructor (triclinic). Parameters: a,b,c  : unit cell dimension, in angstroems alpha,beta,gamma  : unit cell angles, in radians. SpaceGroupId:  space group symbol or number

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Member Function Documentation

void ObjCryst::Crystal::AddScatterer (  Scatterer *    scatt )

Add a scatterer to the crystal. Warning: the scatterer must be allocated in the heap, since the scatterer will not be copied but used directly. A Scatterer can only belong to one Crystal. It will be detroyed when removed or when the Crystal is destroyed. Parameters: scatt  : the address of the scatterer to be included in the crystal scatterer names must be unique in a given crystal. Note: that the ScatteringPower used in the Scatterer should be one of the Crystal (see Crystal::AddScatteringPower())

void ObjCryst::Crystal::AddScatteringPower (  ScatteringPower *    scattPow )

Add a ScatteringPower for this Crystal. It must be allocated in the heap, and not used by any other Crystal.

virtual void ObjCryst::Crystal::BeginOptimization (  const bool    allowApproximations = false, const bool    enableRestraints = false )  [virtual]

This should be called by any optimization class at the begining of an optimization. This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects. Note: this may be called several time for some objects which are used by several other objects. Parameters: allowApproximations:  if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives. enableRestraints:  if true, then restrained parameters will be allowed to go beyond theur hard limits. This implies that the algorithm will take into account the cost (penalty) related to the restraints. Objects which do not use restraints will simply ignore this. WARNING: this parameter may be removed with the new likelihood scheme. Reimplemented from ObjCryst::RefinableObj.

void ObjCryst::Crystal::CalcDistTable (  const bool    fast, const REAL    asymUnitMargin = 4 )  const [private]

Compute the distance Table (mDistTable) for all scattering components. \internal Parameters: fast  : if true, the distance calculations will be made using integers, thus with a lower precision but faster. Less atoms will also be involved (using the AsymmetricUnit) to make it even faster. asymUnitMargin  (in Angstroem). This is used only if fast=true. In that case, the distance is calculated between (i) independent atoms in the asymmetric unit cell and (ii) all atoms which are inside the asymmetric unit cell or less than 'asymUnitMargin' distant from the asymmetric unit borders. This parameter should be used when only the shortest distances need to be calculated (typically for dynamical population correction). Using a too short margin will result in having some distances calculated wrongly (ie one atom1 in the unit cell could have an atom2 neighbor just outside the sym unit: if margin=0, then the distance is calculated between atom1 and the atom2 symmetric inside the asym unit). Warning: Crystal::GetScatteringComponentList() must be called beforehand, since this will not be done here. Returns: see Crystal::mDistTableSq and Crystal::mDistTableIndex Todo: sanitize the result distance table in a more usable structure than the currently used Crystal::mDistTableSq and Crystal::mDistTableIndex. optimize again. Test if recomputation is needed using Clocks. Use a global option instead of asymUnitMargin. Warning: not using the fast option has not been very much tested...

void ObjCryst::Crystal::CalcDynPopCorr (  const REAL    overlapDist = 1., const REAL    mergeDist = .0 )  const

Compute the 'Dynamical population correction for all atoms. Atoms which are considered "equivalent" (ie currently with the same Z number) and which are overlapping see their Dynamical occupancy changed so that when they fully overlap, they are equivalent to 1 atom. For internal use only. Parameters: overlapDist  : distance below which atoms (ScatteringComponents, to be more precise) are considered overlapping and should be corrected. The correction changes the dynamical occupancy from 1 to 1/nbAtomOverlapping, progressively as the distance falls from overlapDist to mergeDist. mergeDist  : distance below which atoms are considered fully overlapping. If 3 atoms are 'fully' overlapping, then all have a dynamical population correction equal to 1/3 This is const since ScatteringComponent::mDynPopCorr is mutable. \warning. Do not call this function, which will turn private. This is called by only Crystal::GetScatteringComponentList()

virtual void ObjCryst::Crystal::CIFOutput (  ostream &    os )  const [virtual]

output Crystal structure as a cif file (EXPERIMENTAL !) Warning: This is very crude and EXPERIMENTAL so far: only isotropic scattering power are supported, and there is not much information beside atom positions...

int ObjCryst::Crystal::FindScatterer (  const string &    scattName )  const [private]

Find a scatterer (its index # in mpScatterrer[]) with a given name. Warning: There should be no duplicate names !!! :TODO: test in AddScatterer()

REAL ObjCryst::Crystal::GetBumpMergeCost (    )

Get the Anti-bumping/pro-Merging cost function. Only works (ie returnes a non-null value) if you have added antibump distances using Crystal::SetBumpMergeDistance().

virtual const string& ObjCryst::Crystal::GetClassName (    )  [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::UnitCell.

virtual void ObjCryst::Crystal::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 \RefinableObj, 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.

virtual REAL ObjCryst::Crystal::GetLogLikelihood (    )  [virtual]

Get -log(likelihood) of the current configuration for the object. By default (no likelihood evaluation available), this is equal to 0. This call should not be recursive, it is the task of the algorithm to get the sum of likelihoods for all objects invlolved. Note: contrary to the old "Cost Function" approach, with log(Likelihood) there is no 'choice' of cost function, so that it is the task of the object to give the optimized likelihood (possibly with user options). \warning: this is in under heavy development, so expect changes... Reimplemented from ObjCryst::RefinableObj.

CrystMatrix_REAL ObjCryst::Crystal::GetMinDistanceTable (  const REAL    minDistance = 0.1 )  const

Minimum interatomic distance between all scattering components (atoms) in the crystal. This will return a symmetrical matrix with NbComp rows and cols, where NbComp is the number of independent scattering components in the unit cell. All distances are given in Angstroems. Note that the distance of a given atom with 'itself' is not generally equal to 0 (except full special position), but equal to the min distance with its symmetrics. Parameters: minDistance  : atoms who are less distant than (minDistance,in Angstroems) are considered equivalent. So the smallest distance between any atoms will be at least minDistance.

const Scatterer& ObjCryst::Crystal::GetScatt (  const long    scattIndex )  const

Provides a const access to the scatterers. Parameters: scattIndex  the number of the scatterer to access

Scatterer& ObjCryst::Crystal::GetScatt (  const long    scattIndex )

Provides an access to the scatterers. Parameters: scattIndex  the number of the scatterer to access

const Scatterer& ObjCryst::Crystal::GetScatt (  const string &    scattName )  const

Provides a const access to the scatterers. Parameters: scattName  the name of the scatterer to access

Scatterer& ObjCryst::Crystal::GetScatt (  const string &    scattName )

Provides an access to the scatterers. Parameters: scattName  the name of the scatterer to access

virtual void ObjCryst::Crystal::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    displayNames = false )  const [virtual]

Create an OpenGL DisplayList of the crystal. Parameters: onlyIndependentAtoms  if false (the default), then all symmetrics are displayed within the given limits \ param xMin,xMax,yMin,yMax,zMin,zMax: in fractionnal coordinates, the region in which we want scaterrers 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).

virtual void ObjCryst::Crystal::GlobalOptRandomMove (  const REAL    mutationAmplitude, const RefParType *    type = gpRefParTypeObjCryst )  [virtual]

Make a random move of the current configuration. This is for global optimization algorithms. the moves for each parameter are less than their global optimization step, multiplied by the mutation amplitude. \warning: this makes a random move for the parameter declared for this object, and it is the duty of the object to decide whether the included objects should be moved and how. (eg an algorithm should only call for a move with the top object, and this object decides how he and his sub-objects moves). By default (RefinableObj implementation) all included objects are moved recursively. RefinableObj:: Parameters: mutationAmplitude:  multiplier for the maximum move amplitude, for all parameters type:  restrain the change exclusively to parameters of a given type (same type or descendant from this RefParType). Reimplemented from ObjCryst::RefinableObj.

void ObjCryst::Crystal::Init (  const REAL    a, const REAL    b, const REAL    c, const REAL    alpha, const REAL    beta, const REAL    gamma, const string &    SpaceGroupId, const string &    name )  [private, virtual]

Init all Crystal parameters. Parameters: a,b,c  : unit cell dimension, in angstroems alpha,beta,gamma  : unit cell angles SpcGroup:  space group number (1..230) name:  name for the crystal, : '(TaSe4)2I' Reimplemented from ObjCryst::UnitCell.

void ObjCryst::Crystal::InitOptions (    )  [private, virtual]

Init options. Need only be done once per Crystal. Reimplemented from ObjCryst::UnitCell.

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

XMLOutput POV-Ray Description for this Crystal. Parameters: onlyIndependentAtoms  if false, all symmetrics are showed in the drawing. Warning: This currently needs some fixing (ZScatterer does not work ?) Use rather the OpenGL 3D display which is more useful. Parameters: os  the stream to which the information is outputed (default=cout)

void ObjCryst::Crystal::Print (  ostream &    os = cout )  const [virtual]

Prints some info about the crystal. Todo: one function to print on one line and a PrintLong() function Parameters: os  the stream to which the information is outputed (default=cout) Reimplemented from ObjCryst::UnitCell.

void ObjCryst::Crystal::PrintMinDistanceTable (  const REAL    minDistance = 0.1, ostream &    os = cout )  const

Print the minimum distance table between all scattering centers (atoms) in the crystal. Parameters: os  the stream to which the information is outputed (default=cout)

void ObjCryst::Crystal::RemoveScatteringPower (  ScatteringPower *    scattPow )

Remove a ScatteringPower for this Crystal. (the Scattering power is deleted). This function should check that it is not used any more before removing it.

void ObjCryst::Crystal::SetUseDynPopCorr (  const int    use )

Set the use of dynamical population correction (Crystal::mUseDynPopCorr). Atoms which are considered "equivalent" (ie currently with the same Z number) and which are overlapping see their Dynamical occupancy changed so that when they fully overlap, they are equivalent to 1 atom. The Dynamical Occupancy correction will be performed in Crystal::GetScatteringComponentList() automatically. This seriously affects the speed of the calculation, since computing interatomic distances is lenghty. Parameters: use  set to 1 to use, 0 not to use it.

virtual void ObjCryst::Crystal::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::Crystal::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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Member Data Documentation

RefinableObjClock ObjCryst::Crystal::mClockDynPopCorr [private]

Last time the dynamical population correction was computed. For internal use only.

RefinableObjClock ObjCryst::Crystal::mClockNeighborTable [private]

Last time the Neighbor Table was generated. For internal use only.

RefinableObjClock ObjCryst::Crystal::mClockScattCompList [private]

Last time the ScatteringComponentList was generated. For internal use only.

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

• Crystal.h

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