Public Member Functions |
| ScatteringPowerSphere () |
| Default constructor.
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| ScatteringPowerSphere (const string &name, const REAL radius, const REAL bIso=1.0) |
| constructor
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| ScatteringPowerSphere (const ScatteringPowerSphere &old) |
void | Init (const string &name, const REAL radius, const REAL bIso=1.0) |
virtual const string & | GetClassName () const |
| Name for this class ("RefinableObj", "Crystal",...).
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virtual CrystVector_REAL | GetScatteringFactor (const ScatteringData &data, const int spgSymPosIndex=0) const |
| Get the Scattering factor for all reflections of a given ScatteringData object.
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virtual REAL | GetForwardScatteringFactor (const RadiationType) const |
| Get the scattering factor at (0,0,0).
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virtual CrystVector_REAL | GetTemperatureFactor (const ScatteringData &data, const int spgSymPosIndex=0) const |
| Get the temperature factor for all reflections of a given ScatteringData object.
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virtual CrystMatrix_REAL | GetResonantScattFactReal (const ScatteringData &data, const int spgSymPosIndex=0) const |
| Get the real part of the resonant scattering factor.
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virtual CrystMatrix_REAL | GetResonantScattFactImag (const ScatteringData &data, const int spgSymPosIndex=0) const |
| Get the imaginary part of the resonant scattering factor.
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REAL | GetRadius () const |
| Return the physical radius of this type of scatterer (for 3D display purposes).
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virtual void | Print () const |
virtual void | XMLOutput (ostream &os, int indent=0) const |
| Output to stream in well-formed XML.
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virtual void | XMLInput (istream &is, const XMLCrystTag &tag) |
| Input From stream.
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| ScatteringPower (const ScatteringPower &old) |
virtual void | operator= (const ScatteringPower &rhs) |
virtual bool | IsScatteringFactorAnisotropic () const |
| Is the scattering factor anisotropic ?
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virtual bool | IsTemperatureFactorAnisotropic () const |
| Is the thermic factor anisotropic ?
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virtual bool | IsResonantScatteringAnisotropic () const |
| Are the resonant scattering terms anisotropic ?
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virtual const string & | GetSymbol () const |
| Symbol for this Scattering power (the atom name for atoms)
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REAL | GetBiso () const |
| Returns the isotropic temperature B factor.
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REAL & | GetBiso () |
| Returns the isotropic temperature B factor.
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virtual void | SetBiso (const REAL newB) |
| Sets the isotropic temperature B factor.
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REAL | GetBij (const size_t &i, const size_t &j) const |
| Returns the anisotropic temperature B factor for (i, j) pair.
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REAL | GetBij (const size_t &idx) const |
| Returns the anisotropic temperature B factor for given index.
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virtual void | SetBij (const size_t &i, const size_t &j, const REAL newB) |
| Sets the anisotropic temperature B factor for (i, j) pair.
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virtual void | SetBij (const size_t &idx, const REAL newB) |
| Sets the anisotropic temperature B factor for given index.
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bool | IsIsotropic () const |
| Returns true if the scattering power is isotropic, else false.
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long | GetDynPopCorrIndex () const |
| Get the number identifying this kind of scatterer, used to decide whether two scatterers are equivalent, for the dynamical occupancy correction.
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long | GetNbScatteringPower () const |
| Total number of ScatteringPower object.
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const RefinableObjClock & | GetLastChangeClock () const |
| ObjCrystClock time when the last modification was made to the object.
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const string & | GetColourName () const |
| Get the (POV-Ray) name associated to the color (if any)
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const float * | GetColourRGB () const |
| Get the float[3] array of RGB components defining the colour of this scattering power.
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void | SetColour (const string &colorName) |
| Set the colour from the associated POV-Ray name.
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void | SetColour (const float r, const float g, const float b) |
| Set the colour from RGB components (all between 0 and 1.)
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virtual void | GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const |
| Get the gene group assigned to each parameter.
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REAL | GetMaximumLikelihoodPositionError () const |
| Maximum Likelihood: get the estimated error (sigma) on the positions for this kind of element.
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void | SetMaximumLikelihoodPositionError (const REAL mle) |
| Maximum Likelihood: set the estimated error (sigma) on the positions for this kind of element.
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REAL | GetMaximumLikelihoodNbGhostAtom () const |
| Maximum Likelihood: get the number of ghost elements per asymmetric unit.
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void | SetMaximumLikelihoodNbGhostAtom (const REAL nb) |
| Maximum Likelihood: set the number of ghost elements per asymmetric unit.
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const RefinableObjClock & | GetMaximumLikelihoodParClock () const |
| Get the clock value for the last change on the maximum likelihood parameters (positionnal error, number of ghost atoms).
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virtual REAL | GetFormalCharge () const |
virtual void | SetFormalCharge (const REAL charge) |
| RefinableObj () |
| Constructor.
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| RefinableObj (const bool internalUseOnly) |
| Constructor.
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| RefinableObj (const RefinableObj &old) |
| Defined not implemented...
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virtual | ~RefinableObj () |
| Destructor.
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virtual const string & | GetName () const |
| Name of the object.
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virtual void | SetName (const string &name) |
| Name of the object.
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void | operator= (const RefinableObj &old) |
| Defined not implemented...
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void | PrepareForRefinement () const |
| Find which parameters are used and not fixed, for a refinement /optimization.
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void | FixAllPar () |
| Fix All parameters.
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void | UnFixAllPar () |
| UnFix All parameters.
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void | SetParIsFixed (const long parIndex, const bool fix) |
| Fix/un-fix one parameter from its #.
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void | SetParIsFixed (const string &parName, const bool fix) |
| Fix/un-fix one parameter from its name.
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void | SetParIsFixed (const RefParType *type, const bool fix) |
| Fix/un-fix one family of parameters.
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void | SetParIsUsed (const string &parName, const bool use) |
| Set whether a parameter is used.
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void | SetParIsUsed (const RefParType *type, const bool use) |
| Set whether a family of parameters is used.
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long | GetNbPar () const |
| Total number of refinable parameter in the object.
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long | GetNbParNotFixed () const |
| Total number of non-fixed parameters. Is initialized by PrepareForRefinement()
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RefinablePar & | GetPar (const long i) |
| Access all parameters in the order they were inputted.
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const RefinablePar & | GetPar (const long i) const |
| Access all parameters in the order they were inputted.
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RefinablePar & | GetPar (const string &name) |
| Access all parameters from their name.
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const RefinablePar & | GetPar (const string &name) const |
| Access all parameters from their name.
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RefinablePar & | GetPar (const REAL *) |
| Access parameter from its adress.
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const RefinablePar & | GetPar (const REAL *) const |
| Access parameter from its adress.
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long | GetParIndex (const string &name, const bool nothrow=false) const |
| Get a parameter index (the order it was inputted) from its name.
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long | GetParIndex (const REAL *, const bool nothrow=false) const |
| Get a parameter index (the order it was inputted) from its adress.
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RefinablePar & | GetParNotFixed (const long i) |
| Access all parameters in the order they were inputted, skipping fixed parameters.
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const RefinablePar & | GetParNotFixed (const long i) const |
| Access all parameters in the order they were inputed, skipping fixed parameters.
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void | AddPar (const RefinablePar &newRefPar) |
| Add a refinable parameter.
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void | AddPar (RefinablePar *newRefPar) |
| Add a refinable parameter.
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void | AddPar (RefinableObj &newRefParList, const bool copyParam=false) |
| Add all the parameters in another RefinableObj.
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vector< RefinablePar * >::iterator | RemovePar (RefinablePar *refPar) |
| Remove a refinable parameter.
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unsigned long | CreateParamSet (const string name="") const |
| Save the current set of refined values in a new set.
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void | ClearParamSet (const unsigned long id) const |
| Erase the param set with the given id, releasing memory.
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void | SaveParamSet (const unsigned long id) const |
| Save the current set of refined values over a previously-created set
*of saved values.
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void | RestoreParamSet (const unsigned long id) |
| Restore a saved set of values.
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const CrystVector_REAL & | GetParamSet (const unsigned long setId) const |
| Access one save refpar set.
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CrystVector_REAL & | GetParamSet (const unsigned long setId) |
| Access one save refpar set.
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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.
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const void | EraseAllParamSet () |
| Erase all saved refpar sets.
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const string & | GetParamSetName (const unsigned long setId) const |
| Get the name associated to a refpar set.
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void | SetLimitsAbsolute (const string &parName, const REAL min, const REAL max) |
| Change the limits for a given parameter, giving absolute new limits.
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void | SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max) |
| Change the limits for a category of parameters, giving absolute new limits.
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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.
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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).
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void | SetLimitsProportional (const string &parName, const REAL min, const REAL max) |
| Change the limits for a given parameter, proportionnaly to the current value.
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void | SetLimitsProportional (const RefParType *type, const REAL min, const REAL max) |
| Change the limits for a category of parameters, proportionnaly to their current value.
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void | SetGlobalOptimStep (const RefParType *type, const REAL step) |
| Change the maximum step to use during Global Optimization algorithms.
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ObjRegistry< RefinableObj > & | GetSubObjRegistry () |
| Access to the registry of RefinableObj used by this object.
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const ObjRegistry< RefinableObj > & | GetSubObjRegistry () const |
| Access to the registry of RefinableObj used by this object.
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virtual void | RegisterClient (RefinableObj &) const |
| Register a new object using this object.
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virtual void | DeRegisterClient (RefinableObj &) const |
| Deregister an object (which not any more) using this object.
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virtual const ObjRegistry
< RefinableObj > & | GetClientRegistry () const |
| Get the list of clients.
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virtual ObjRegistry
< RefinableObj > & | GetClientRegistry () |
| Get the list of clients.
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bool | IsBeingRefined () const |
| Is the object being refined ? (Can be refined by one algorithm at a time only.)
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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.
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virtual void | EndOptimization () |
| This should be called by any optimization class at the end of an optimization.
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virtual void | SetApproximationFlag (const bool allow) |
| Enable or disable numerical approximations.
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virtual void | RandomizeConfiguration () |
| Randomize Configuration (before a global optimization).
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virtual void | GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst) |
| Make a random move of the current configuration.
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void | BeginGlobalOptRandomMove () |
| Raise a flag, to be sure not to make a random change more than once in each RefinableObj.
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virtual REAL | GetLogLikelihood () const |
| Get -log(likelihood) of the current configuration for the object.
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virtual unsigned int | GetNbLSQFunction () const |
| Number of LSQ functions.
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virtual const CrystVector_REAL & | GetLSQCalc (const unsigned int) const |
| Get the current calculated value for the LSQ function.
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virtual const CrystVector_REAL & | GetLSQObs (const unsigned int) const |
| Get the observed values for the LSQ function.
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virtual const CrystVector_REAL & | GetLSQWeight (const unsigned int) const |
| Get the weight values for the LSQ function.
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virtual const CrystVector_REAL & | GetLSQDeriv (const unsigned int, RefinablePar &) |
| Get the first derivative values for the LSQ function, for a given parameter.
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void | ResetParList () |
| Re-init the list of refinable parameters, removing all parameters.
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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.
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unsigned int | GetNbOption () const |
| Number of Options for this object.
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RefObjOpt & | GetOption (const unsigned int i) |
| Access to the options.
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const RefObjOpt & | GetOption (const unsigned int i) const |
| const access to the options
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void | SetDeleteRefParInDestructor (const bool b) |
| Set this object not to delete its list of parameters when destroyed.
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const RefinableObjClock & | GetRefParListClock () const |
| What was the last time a RefinablePar was added/removed ?
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virtual REAL | GetRestraintCost () const |
| Get the restraint cost (overall penalty of all restraints)
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void | AddRestraint (Restraint *pNewRestraint) |
| Add a new restraint.
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vector< Restraint * >::iterator | RemoveRestraint (Restraint *pRestraint) |
| Remove a restraint from the list of known restraints.
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virtual void | TagNewBestConfig () const |
| During a global optimization, tells the object that the current config is the latest "best" config.
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const RefinableObjClock & | GetClockMaster () const |
| This clocks records any change in the object. See refinableObj::mClockMaster.
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