Unit Cell class: Unit cell with spacegroup information. More...

Inheritance diagram for ObjCryst::UnitCell:

Collaboration diagram for ObjCryst::UnitCell:

Public Member Functions
	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.

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

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 (ostream &os) const
	Prints some info about the UnitCell. 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	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization. More...

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...

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

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

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

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

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.

Protected Member Functions
virtual 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 UnitCell parameters. More...

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)

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

void	InitMatrices () const

void	UpdateLatticePar ()

Private Attributes
CrystVector_REAL	mCellDim
	a,b and c in Angstroems, angles (stored) in radians For cubic, rhomboedric UnitCells, only the 'a' parameter is relevant. More...

SpaceGroup	mSpaceGroup
	The space group of the UnitCell.

CrystMatrix_REAL	mBMatrix
	B Matrix (Orthogonalization matrix for reciprocal space) $B= \left[ \begin {array}{ccc} a^* & b^\cos(\gamma^) & c^\cos(\beta^) \\ 0 & b^\sin(\gamma^) & -c^\sin(\beta^)\cos(\alpha) \\ 0 & 0 & \frac{1}{c}\end{array} \right]$ $\left[ \begin{array}{c} k_x \\ k_y \\ k_z \end{array} \right]_{orthonormal} = B \times \left[ \begin{array}{c} h \\ k \\ l \end{array}\right]_{integer}$ . More...

CrystMatrix_REAL	mBMatrixInvert
	inverse of B Matrix (i.e. inverse of orthogonalization matrix for direct space)

CrystMatrix_REAL	mOrthMatrix
	Eucl Matrix (Orthogonalization matrix for direct space) $M_{orth}= \left[ \begin {array}{ccc} a & b\cos(\gamma) & c\cos(\beta) \\ 0 & b\sin(\gamma) & -c\sin(\beta)\cos(\alpha^) \\ 0 & 0 & \frac{1}{c^}\end{array} \right]$ $\left[ \begin{array}{c} x \\ y \\ z \end{array} \right]_{orthonormal} = M_{orth} \times \left[ \begin{array}{c} x \\ y \\ z \end{array} \right]_{fractional coords}$ . More...

CrystMatrix_REAL	mOrthMatrixInvert
	inverse of Eucl Matrix (i.e. inverse of de-orthogonalization matrix for direct space)

RefinableObjClock	mClockLatticePar
	Last time lattice parameters were changed.

RefinableObjClock	mClockMetricMatrix

RefinableObjClock	mClockLatticeParUpdate

RefObjOpt	mConstrainLatticeToSpaceGroup
	Option to override lattice parameters constraints from spacegroup choice. More...

Additional Inherited Members
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

Unit Cell class: Unit cell with spacegroup information.

Definition at line 71 of file UnitCell.h.

Constructor & Destructor Documentation

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

UnitCell Constructor (orthorombic)

Parameters

a,b,c	: unit cell dimension, in angstroems
SpaceGroupId	space group symbol or number

Definition at line 44 of file UnitCell.cpp.

ObjCryst::UnitCell::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)

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 55 of file UnitCell.cpp.

Member Function Documentation

void ObjCryst::UnitCell::FractionalToOrthonormalCoords	(	REAL &	x,
		REAL &	y,
		REAL &	z
	)		const

Get orthonormal cartesian coordinates for a set of (x,y,z) fractional coordinates.

X,y and z input are changed to Amgstroems values The convention is taken following : e1 is chosen along a, e2 in the (a,b) plane, then e3 is along c*

Definition at line 261 of file UnitCell.cpp.

const CrystMatrix_REAL & ObjCryst::UnitCell::GetBMatrix ( ) const

Get the 'B' matrix (UnitCell::mBMatrix)for the UnitCell (orthogonalization matrix for the given lattice, in the reciprocal space)

The convention is taken following Giacovazzo, "Fundamentals of Crystallography", p.69 "e1 is chosen along a*, e2 in the (a*,b*) plane, then e3 is along c".

Definition at line 235 of file UnitCell.cpp.

const string & ObjCryst::UnitCell::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::RefinableObj.

Reimplemented in ObjCryst::Crystal.

Definition at line 86 of file UnitCell.cpp.

CrystVector_REAL ObjCryst::UnitCell::GetLatticePar ( ) const

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

Definition at line 92 of file UnitCell.cpp.

REAL ObjCryst::UnitCell::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.

Definition at line 161 of file UnitCell.cpp.

const CrystMatrix_REAL & ObjCryst::UnitCell::GetOrthMatrix ( ) const

Get the orthogonalization matrix (UnitCell::mOrthMatrix)for the UnitCell in real space.

Definition at line 242 of file UnitCell.cpp.

CrystVector_REAL ObjCryst::UnitCell::GetOrthonormalCoords	(	const REAL	x,
		const REAL	y,
		const REAL	z
	)		const

Get orthonormal cartesian coordinates for a set of (x,y,z) fractional coordinates.

Results are given in Angstroems. The convention is taken following : e1 is chosen along a, e2 in the (a,b) plane, then e3 is along c*

Definition at line 249 of file UnitCell.cpp.

void ObjCryst::UnitCell::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
	)

protectedvirtual

Init all UnitCell 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 UnitCell, : '(TaSe4)2I'

Reimplemented in ObjCryst::Crystal.

Definition at line 339 of file UnitCell.cpp.

void ObjCryst::UnitCell::InitMatrices ( ) const

private

.Init the (de)orthogonalization matrices. They are re-computed only if parameters have changed since last call.

Definition at line 388 of file UnitCell.cpp.

void ObjCryst::UnitCell::InitOptions ( )

privatevirtual

Init options.

Need only be done once per UnitCell.

Reimplemented in ObjCryst::Crystal.

Definition at line 365 of file UnitCell.cpp.

void ObjCryst::UnitCell::InitRefParList ( )

protected

Prepare the refinable parameters list.

This is called once when creating the UnitCell.

Definition at line 521 of file UnitCell.cpp.

void ObjCryst::UnitCell::MillerToOrthonormalCoords	(	REAL &	x,
		REAL &	y,
		REAL &	z
	)		const

Get Miller H,K, L indices from orthonormal coordinates in reciprocal space.

Result is stored into x,y and z

Definition at line 284 of file UnitCell.cpp.

void ObjCryst::UnitCell::OrthonormalToFractionalCoords	(	REAL &	x,
		REAL &	y,
		REAL &	z
	)		const

Get fractional cartesian coordinates for a set of (x,y,z) orthonormal coordinates.

Result is stored into x,y and z The convention is taken following : e1 is chosen along a, e2 in the (a,b) plane, then e3 is along c*

Definition at line 271 of file UnitCell.cpp.

void ObjCryst::UnitCell::OrthonormalToMillerCoords	(	REAL &	x,
		REAL &	y,
		REAL &	z
	)		const

Get orthonormal coordinates given a set of H,K, L indices in reciprocal space.

Result is stored into x,y and z

Definition at line 294 of file UnitCell.cpp.

void ObjCryst::UnitCell::Print ( ostream & os ) const

virtual

Prints some info about the UnitCell.

Parameters

os	the stream to which the information is outputed (default=cout)

Reimplemented in ObjCryst::Crystal.

Definition at line 304 of file UnitCell.cpp.

void ObjCryst::UnitCell::UpdateLatticePar ( )

private

Update cell parameters for tetragonal, trigonal, hexagonal, cubic lattices. Also set angular parameters for those group which need it. This is needed during Refinement, since for example in a quadratic spg, only a is refined and we need to have b=a...

Definition at line 443 of file UnitCell.cpp.

Member Data Documentation

CrystMatrix_REAL ObjCryst::UnitCell::mBMatrix

mutableprivate

B Matrix (Orthogonalization matrix for reciprocal space)

$B= \left[ \begin {array}{ccc} a^* & b^*\cos(\gamma^*) & c^*\cos(\beta^*) \\ 0 & b^*\sin(\gamma^*) & -c^*\sin(\beta^*)\cos(\alpha) \\ 0 & 0 & \frac{1}{c}\end{array} \right]$

$\left[ \begin{array}{c} k_x \\ k_y \\ k_z \end{array} \right]_{orthonormal} = B \times \left[ \begin{array}{c} h \\ k \\ l \end{array}\right]_{integer}$

.

Note: this matrix is and must remain upper triangular. this is assumed for some optimizations.

Definition at line 219 of file UnitCell.h.

CrystVector_REAL ObjCryst::UnitCell::mCellDim

private

a,b and c in Angstroems, angles (stored) in radians For cubic, rhomboedric UnitCells, only the 'a' parameter is relevant.

For quadratic and hexagonal UnitCells, only a and c parameters are relevant. The MUTABLE is temporary ! It should not be !

Definition at line 206 of file UnitCell.h.

RefinableObjClock ObjCryst::UnitCell::mClockLatticeParUpdate

mutableprivate

Last time the lattice parameters whre updated

Definition at line 241 of file UnitCell.h.

RefinableObjClock ObjCryst::UnitCell::mClockMetricMatrix

mutableprivate

Last time metric matrices were computed

Definition at line 239 of file UnitCell.h.

RefObjOpt ObjCryst::UnitCell::mConstrainLatticeToSpaceGroup

private

Option to override lattice parameters constraints from spacegroup choice.

Warning: EXPERIMENTAL

Normally lattice parameters are constrained by the space group choice (e.g. a=b=c and angles =90� for cubic spacegroups). Using this option allows you to override this, and choose any lattice parameter. THis works as long as symmetry operations are applied to fractionnal coordinates.

This is useful duting global optimization when searching the structure in a UnitCell which has (or is expected to have) a known pseudo-crystallographic symmetry, to reduce dramatically the number of parameters. Of course for final refinement the 'real' symmetry should be imposed.

Definition at line 257 of file UnitCell.h.

CrystMatrix_REAL ObjCryst::UnitCell::mOrthMatrix

mutableprivate

Eucl Matrix (Orthogonalization matrix for direct space)

$M_{orth}= \left[ \begin {array}{ccc} a & b\cos(\gamma) & c\cos(\beta) \\ 0 & b\sin(\gamma) & -c\sin(\beta)\cos(\alpha^*) \\ 0 & 0 & \frac{1}{c^*}\end{array} \right]$

$\left[ \begin{array}{c} x \\ y \\ z \end{array} \right]_{orthonormal} = M_{orth} \times \left[ \begin{array}{c} x \\ y \\ z \end{array} \right]_{fractional coords}$

.

Note: this matrix is and must remain upper triangular. this is assumed for some optimizations.

Definition at line 232 of file UnitCell.h.

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation