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

Inheritance diagram for ObjCryst::Crystal:

Collaboration diagram for ObjCryst::Crystal:

Classes
struct	BumpMergePar
	Storage for anti-bump/merge parameters. More...

struct	Neighbour
	Interatomic distance for a given neighbour. More...

struct	NeighbourHood
	Table of neighbours for a given unique atom. More...

Public Types
typedef std::map< pair< const ScatteringPower , const ScatteringPower > , Crystal::BumpMergePar >	VBumpMergePar
	Anti-bump parameters. More...

Public Member Functions
	Crystal ()
	Default Constructor.

	Crystal (const REAL a, const REAL b, const REAL c, const string &SpaceGroupId)
	Crystal Constructor (orthorombic) More...

	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) More...

	Crystal (const Crystal &oldCryst)
	Crystal copy constructor.

	~Crystal ()
	Crystal destructor.

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

void	AddScatterer (Scatterer *scatt)
	Add a scatterer to the crystal. More...

void	RemoveScatterer (Scatterer *scatt, const bool del=true)
	Remove a Scatterer. This also deletes the scatterer unless del=false.

long	GetNbScatterer () const
	Number of scatterers in the crystal.

Scatterer &	GetScatt (const string &scattName)
	Provides an access to the scatterers. More...

const Scatterer &	GetScatt (const string &scattName) const
	Provides a const access to the scatterers. More...

Scatterer &	GetScatt (const long scattIndex)
	Provides an access to the scatterers. More...

const Scatterer &	GetScatt (const long scattIndex) const
	Provides a const access to the scatterers. More...

ObjRegistry< Scatterer > &	GetScattererRegistry ()
	Get the registry of scatterers.

const ObjRegistry< Scatterer > &	GetScattererRegistry () const
	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. More...

void	RemoveScatteringPower (ScatteringPower *scattPow, const bool del=true)
	Remove a ScatteringPower for this Crystal. More...

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. More...

CrystMatrix_REAL	GetMinDistanceTable (const REAL minDistance=0.1) const
	Minimum interatomic distance between all scattering components (atoms) in the crystal. More...

void	PrintMinDistanceTable (const REAL minDistance=0.1, ostream &os=cout) const
	Print the minimum distance table between all scattering centers (atoms) in the crystal. More...

ostream &	POVRayDescription (ostream &os, const CrystalPOVRayOptions &options) const
	XMLOutput POV-Ray Description for this Crystal. More...

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 bool hideHydrogens=false) const
	Create an OpenGL DisplayList of the crystal. More...

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. More...

void	ResetDynPopCorr () const
	Reset Dynamical Population Correction factors (ie set it to 1)

REAL	GetDynPopCorr (const Scatterer *pscatt, unsigned int component) const
	Access the Dynamical Occupancy Correction for a given component (atom) in a given Scatterer.

void	SetUseDynPopCorr (const int use)
	Set the use of dynamical population correction (Crystal::mUseDynPopCorr). More...

int	GetUseDynPopCorr () const
	Get dynamical population correction setting. More...

REAL	GetBumpMergeCost () const
	Get the Anti-bumping/pro-Merging cost function. More...

void	SetBumpMergeDistance (const ScatteringPower &scatt1, const ScatteringPower &scatt2, const REAL dist=1.5)
	Set the Anti-bumping distance between two scattering types. More...

void	SetBumpMergeDistance (const ScatteringPower &scatt1, const ScatteringPower &scatt2, const REAL dist, const bool allowMerge)
	Set the Anti-bumping distance between two scattering types.

void	RemoveBumpMergeDistance (const ScatteringPower &scatt1, const ScatteringPower &scatt2)
	Remove an Anti-bumping distance between two scattering types.

const VBumpMergePar &	GetBumpMergeParList () const

VBumpMergePar &	GetBumpMergeParList ()

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. More...

virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream. More...

virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration. More...

virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object. More...

virtual void	CIFOutput (ostream &os, double mindist=0.5) const
	output Crystal structure as a cif file (EXPERIMENTAL !) More...

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

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...

void	AddBondValenceRo (const ScatteringPower &, const ScatteringPower &, const REAL ro)

void	RemoveBondValenceRo (const ScatteringPower &, const ScatteringPower &)

REAL	GetBondValenceCost () const
	Get the Bond-Valence cost function, which compares the expected valence to the one computed from Bond-Valence Ro parameters.

std::map< pair< const ScatteringPower , const ScatteringPower >, REAL > &	GetBondValenceRoList ()

const std::map< pair< const ScatteringPower , const ScatteringPower >, REAL > &	GetBondValenceRoList () const

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. More...

void	SetDeleteSubObjInDestructor (const bool b)
	Set whether to delete the Scatterers and ScatteringPowers in the destructor. More...

void	ConnectAtoms (const REAL min_relat_dist=0.4, const REAL max_relat_dist=1.3, const bool warnuser_fail=false)
	Convert as much as possible the crystal's atoms to molecule(s). More...

Public Member Functions inherited from ObjCryst::UnitCell
	UnitCell ()
	Default Constructor.

	UnitCell (const REAL a, const REAL b, const REAL c, const string &SpaceGroupId)
	UnitCell Constructor (orthorombic) More...

	UnitCell (const REAL a, const REAL b, const REAL c, const REAL alpha, const REAL beta, const REAL gamma, const string &SpaceGroupId)
	UnitCell Constructor (triclinic) More...

	UnitCell (const UnitCell &oldCryst)
	UnitCell copy constructor.

	~UnitCell ()
	Destructor.

CrystVector_REAL	GetLatticePar () const
	Lattice parameters (a,b,c,alpha,beta,gamma) as a 6-element vector in Angstroems and radians. More...

REAL	GetLatticePar (const int whichPar) const
	Return one of the 6 Lattice parameters, 0<= whichPar <6 (a,b,c,alpha,beta,gamma), returned in Angstroems and radians. More...

const RefinableObjClock &	GetClockLatticePar () const
	last time the Lattice parameters were changed

const CrystMatrix_REAL &	GetBMatrix () const
	Get the 'B' matrix (UnitCell::mBMatrix)for the UnitCell (orthogonalization matrix for the given lattice, in the reciprocal space) More...

const CrystMatrix_REAL &	GetOrthMatrix () const
	Get the orthogonalization matrix (UnitCell::mOrthMatrix)for the UnitCell in real space. More...

const RefinableObjClock &	GetClockMetricMatrix () const
	last time the metric matrices were changed

CrystVector_REAL	GetOrthonormalCoords (const REAL x, const REAL y, const REAL z) const
	Get orthonormal cartesian coordinates for a set of (x,y,z) fractional coordinates. More...

void	FractionalToOrthonormalCoords (REAL &x, REAL &y, REAL &z) const
	Get orthonormal cartesian coordinates for a set of (x,y,z) fractional coordinates. More...

void	OrthonormalToFractionalCoords (REAL &x, REAL &y, REAL &z) const
	Get fractional cartesian coordinates for a set of (x,y,z) orthonormal coordinates. More...

void	MillerToOrthonormalCoords (REAL &x, REAL &y, REAL &z) const
	Get Miller H,K, L indices from orthonormal coordinates in reciprocal space. More...

void	OrthonormalToMillerCoords (REAL &x, REAL &y, REAL &z) const
	Get orthonormal coordinates given a set of H,K, L indices in reciprocal space. More...

virtual void	Print () const

const SpaceGroup &	GetSpaceGroup () const
	Access to the SpaceGroup object.

SpaceGroup &	GetSpaceGroup ()
	Access to the SpaceGroup object.

REAL	GetVolume () const
	Volume of Unit Cell (in Angstroems)

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	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...

void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj. 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	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

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.

Private Member Functions
void	InitOptions ()
	Init options. More...

int	FindScatterer (const string &scattName) const
	Find a scatterer (its index # in mpScatterrer[]) with a given name. More...

void	CalcDistTable (const bool fast) const
	Compute the distance Table (mDistTable) for all scattering components. More...

void	CalcBondValenceSum () const
	Calculate all Bond Valences.

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. More...

RefinableObjClock	mDistTableClock
	The time when the distance table was last calculated.

REAL	mDistTableMaxDistance
	The distance up to which the distance table & neighbours needs to be 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

RefinableObjClock	mClockNeighborTable

RefinableObjClock	mClockDynPopCorr

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). More...

map< pair< const ScatteringPower , const ScatteringPower >, REAL >	mvBondValenceRo
	Map of Bond Valence "Ro" parameters for each couple of ScatteringPower.

RefinableObjClock	mBondValenceParClock
	Last Time Bond Valence parameters were changed.

RefinableObjClock	mBondValenceCalcClock
	Last time Bond Valences were calculated.

RefinableObjClock	mBondValenceCostClock
	Last time the Bond Valence cost was calculated.

REAL	mBondValenceCost
	Current Bond Valence cost.

REAL	mBondValenceCostScale
	Bond Valence cost scale factor.

std::map< long, REAL >	mvBondValenceCalc
	List of calculated bond valences, as a map, the key being the index of the atom in Crystal::mScattCompList. More...

bool	mDeleteSubObjInDestructor

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::UnitCell
void	InitRefParList ()
	Prepare the refinable parameters list. More...

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 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

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.

Definition at line 97 of file Crystal.h.

Member Typedef Documentation

typedef std::map<pair<const ScatteringPower*, const ScatteringPower*>,Crystal::BumpMergePar > ObjCryst::Crystal::VBumpMergePar

Anti-bump parameters.

Each atom type (ScatteringPower is referenced using a reference number)

Definition at line 325 of file Crystal.h.

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

Definition at line 73 of file Crystal.cpp.

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

Definition at line 90 of file Crystal.cpp.

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())

Definition at line 174 of file Crystal.cpp.

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.

Definition at line 227 of file Crystal.cpp.

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, or for nested optimizations (e.g. least-squares optimizations inside a global one).; EndOptimization() must be called at the end of the optimization, the same number of time BeginOptimization() was called !

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	xrefitem deprecated 28.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1160 of file Crystal.cpp.

void ObjCryst::Crystal::CalcDistTable ( const bool fast ) const

private

Compute the distance Table (mDistTable) for all scattering components.

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 and mDistTableMaxDistance2) to make it even faster.

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.

Warning: not using the fast option has not been very much tested...

optimize again. Test if recomputation is needed using Clocks. Use a global option instead of asymUnitMargin.

Definition at line 1628 of file Crystal.cpp.

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.

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()

Definition at line 708 of file Crystal.cpp.

void ObjCryst::Crystal::CIFOutput	(	ostream &	os,
		double	mindist = `0.5`
	)		const

virtual

output Crystal structure as a cif file (EXPERIMENTAL !)

Parameters

mindist : minimum distance between atoms to consider them overlapping. Overlapping atoms are only included as comments in the CIF file.

Warning: This is very crude and EXPERIMENTAL so far: there is not much information beside atom positions...

Definition at line 930 of file Crystal.cpp.

void ObjCryst::Crystal::ConnectAtoms	(	const REAL	min_relat_dist = `0.4`,
		const REAL	max_relat_dist = `1.3`,
		const bool	warnuser_fail = `false`
	)

Convert as much as possible the crystal's atoms to molecule(s).

Parameters

min_relat_dist,max_relat_dist	this compares all interatomic distances with the sum of atomic covalent radii d_cov, if d_covmin_relat_dist < d < d_covmax_relat_dist, the atoms are assumed to be connected by a bond. This function only works if the Crystal contains only atoms.
warnuser_fail	if true, will pass a message to the end user that auto-creating at least one Molecule failed.

Warning: : experimental, unstable

Definition at line 1295 of file Crystal.cpp.

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()

Definition at line 803 of file Crystal.cpp.

REAL ObjCryst::Crystal::GetBumpMergeCost ( ) const

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().

Definition at line 820 of file Crystal.cpp.

const string & ObjCryst::Crystal::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::UnitCell.

Definition at line 168 of file Crystal.cpp.

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 , 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.

Definition at line 1141 of file Crystal.cpp.

REAL ObjCryst::Crystal::GetLogLikelihood ( ) const

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).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 925 of file Crystal.cpp.

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.

Definition at line 387 of file Crystal.cpp.

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

Provides an access to the scatterers.

Parameters

scattName the name of the scatterer to access

Definition at line 198 of file Crystal.cpp.

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

Definition at line 203 of file Crystal.cpp.

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

Provides an access to the scatterers.

Parameters

scattIndex the number of the scatterer to access

Definition at line 208 of file Crystal.cpp.

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

Definition at line 213 of file Crystal.cpp.

int ObjCryst::Crystal::GetUseDynPopCorr ( ) const

Get dynamical population correction setting.

See SetUseDynPopCorr.

Definition at line 798 of file Crystal.cpp.

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 bool	hideHydrogens = `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).
hideHydrogens	if true, do not display hydrogens/deuterium and their bonds

Definition at line 545 of file Crystal.cpp.

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.

Definition at line 894 of file Crystal.cpp.

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
	)

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.

Definition at line 1277 of file Crystal.cpp.

void ObjCryst::Crystal::InitOptions ( )

privatevirtual

Init options.

Need only be done once per Crystal.

Reimplemented from ObjCryst::UnitCell.

Definition at line 1576 of file Crystal.cpp.

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)

Definition at line 461 of file Crystal.cpp.

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.

Definition at line 324 of file Crystal.cpp.

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)

Definition at line 428 of file Crystal.cpp.

void ObjCryst::Crystal::RemoveScatteringPower	(	ScatteringPower *	scattPow,
		const bool	del = `true`
	)

Remove a ScatteringPower for this Crystal.

(the Scattering power is deleted unless del=false). This function should check that it is not used any more before removing it.

Definition at line 237 of file Crystal.cpp.

void ObjCryst::Crystal::SetBumpMergeDistance	(	const ScatteringPower &	scatt1,
		const ScatteringPower &	scatt2,
		const REAL	dist = `1.5`
	)

Set the Anti-bumping distance between two scattering types.

Definition at line 860 of file Crystal.cpp.

void ObjCryst::Crystal::SetDeleteSubObjInDestructor ( const bool b )

Set whether to delete the Scatterers and ScatteringPowers in the destructor.

By default these sub-objects are deleted.

Definition at line 1848 of file Crystal.cpp.

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.

Definition at line 791 of file Crystal.cpp.

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.

Definition at line 885 of file ObjCryst/IO.cpp.

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.

Definition at line 791 of file ObjCryst/IO.cpp.

Member Data Documentation

RefinableObjClock ObjCryst::Crystal::mClockDynPopCorr

mutableprivate

Last time the dynamical population correction was computed

Definition at line 486 of file Crystal.h.

RefinableObjClock ObjCryst::Crystal::mClockNeighborTable

mutableprivate

Last time the Neighbor Table was generated

Definition at line 484 of file Crystal.h.

RefinableObjClock ObjCryst::Crystal::mClockScattCompList

mutableprivate

Last time the ScatteringComponentList was generated

Definition at line 482 of file Crystal.h.

RefObjOpt ObjCryst::Crystal::mDisplayEnantiomer

private

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).

Definition at line 493 of file Crystal.h.

std::map<long, REAL> ObjCryst::Crystal::mvBondValenceCalc

mutableprivate

List of calculated bond valences, as a map, the key being the index of the atom in Crystal::mScattCompList.

Definition at line 511 of file Crystal.h.

std::vector<NeighbourHood> ObjCryst::Crystal::mvDistTableSq

mutableprivate

Interatomic distance table for all unique atoms.

Definition at line 460 of file Crystal.h.

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

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation