Inheritance diagram for ObjCryst::RefinableObj:
Public Member Functions | |
RefinableObj () | |
Constructor. | |
RefinableObj (const bool internalUseOnly) | |
Constructor. | |
RefinableObj (const RefinableObj &old) | |
Defined not implemented... | |
virtual | ~RefinableObj () |
Destructor. | |
virtual const string & | GetClassName () const |
Name for this class ("RefinableObj", "Crystal",...). | |
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... | |
void | PrepareForRefinement () const |
Find which parameters are used and not fixed, for a refinement /optimization. | |
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. | |
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. | |
const RefinablePar & | GetParNotFixed (const long i) const |
Access all parameters in the order they were inputed, skipping fixed parameters. | |
void | AddPar (const RefinablePar &newRefPar) |
Add a refinable parameter. | |
void | AddPar (RefinablePar *newRefPar) |
Add a refinable parameter. | |
void | AddPar (RefinableObj &newRefParList) |
Add all the parameters in another RefinableObj. | |
vector< RefinablePar * >::iterator | RemovePar (RefinablePar *refPar) |
Remove a refinable parameter. | |
virtual void | Print () const |
unsigned long | CreateParamSet (const string name="") const |
Save the current set of refined values in a new set. | |
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. | |
void | RestoreParamSet (const unsigned long id) |
Restore a saved set of values. | |
const CrystVector_REAL & | GetParamSet (const unsigned long setId) const |
Access one save refpar set. | |
CrystVector_REAL & | GetParamSet (const unsigned long setId) |
Access one save refpar set. | |
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. | |
const void | EraseAllParamSet () |
Erase all saved refpar sets. | |
const string & | GetParamSetName (const unsigned long setId) const |
Get the name associated to a refpar set. | |
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. | |
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). | |
void | SetLimitsProportional (const string &parName, const REAL min, const REAL max) |
Change the limits for a given parameter, proportionnaly to the current value. | |
void | SetLimitsProportional (const RefParType *type, const REAL min, const REAL max) |
Change the limits for a category of parameters, proportionnaly to their current value. | |
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. | |
virtual void | DeRegisterClient (RefinableObj &) const |
Deregister an object (which not any more) using this object. | |
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. | |
virtual void | EndOptimization () |
This should be called by any optimization class at the end of an optimization. | |
virtual void | RandomizeConfiguration () |
Randomize Configuration (before a global optimization). | |
virtual void | GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst) |
Make a random move of the current configuration. | |
void | BeginGlobalOptRandomMove () |
Raise a flag, to be sure not to make a random change more than once in each RefinableObj. | |
virtual REAL | GetLogLikelihood () const |
Get -log(likelihood) of the current configuration for the object. | |
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. | |
void | ResetParList () |
Re-init the list of refinable parameters, removing all parameters. | |
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 | UpdateDisplay () const |
If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. | |
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. | |
void | SetDeleteRefParInDestructor (const bool b) |
Set this object not to delete its list of parameters when destroyed. | |
const RefinableObjClock & | GetRefParListClock () const |
What was the last time a RefinablePar was added/removed ? | |
virtual REAL | GetRestraintCost () const |
Get the restraint cost (overall penalty of all restraints). | |
void | AddRestraint (Restraint *pNewRestraint) |
Add a new restraint. | |
vector< Restraint * >::iterator | RemoveRestraint (Restraint *pRestraint) |
Remove a restraint from the list of known restraints. | |
virtual void | TagNewBestConfig () const |
During a global optimization, tells the object that the current config is the latest "best" config. | |
const RefinableObjClock & | GetClockMaster () const |
This clocks records _any_ change in the object. See refinableObj::mClockMaster. | |
Protected Member Functions | |
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 &) |
Add an object in the registry of used objects. | |
void | RemoveSubRefObj (RefinableObj &) |
Remove an object in the registry of used objects. | |
void | AddOption (RefObjOpt *opt) |
Add an option for this parameter. | |
virtual void | Prepare () |
Prepare everything (if necessary) for an optimization/calculation. | |
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 | |
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. | |
map< unsigned long, pair< CrystVector_REAL, string > > | mvpSavedValuesSet |
Map of (index,pointers to arrays) used to save sets of values for all parameters. | |
long | mNbRefParNotFixed |
Total of not-fixed parameters. | |
CrystVector_long | mRefparNotFixedIndex |
Index of not-fixed parameters. | |
bool | mIsbeingRefined |
Is the object being refined ? | |
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. | |
ObjRegistry< RefObjOpt > | mOptionRegistry |
List of options for this object. | |
bool | mDeleteRefParInDestructor |
If true (the default), then all RefinablePar will be deleted when the the object is deleted. | |
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. | |
RefinableObjClock | mClockMaster |
Master clock, which is changed whenever the object has been altered. |
This is basically a list of refinable parameters, with other basic common properties such as a name,. etc... This allows optimization/refinement algorithms to access the parameters without knowing what the object really is.
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Constructor.
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Constructor. Using internalUseOnly=true will avoid registering the the object to any registry, and thus (for example) no display will be created, nor will this object be automatically be saved. |
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Defined not implemented... Should never be called (copying the refinable parameters would allow you to modify the input object). Use the default constructor and RefinableObj::AddPar(RefinableObj&) instead. |
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Destructor.
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Add an option for this parameter.
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Add all the parameters in another RefinableObj. Parameters are copied, so they should be allocated in the heap.
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Add a refinable parameter. The parameter is not copied, so it should be allocated in the heap. |
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Add a refinable parameter. The parameter is copied, so it need only be allocated temporarily.
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Add a new restraint. This returns an iterator pointing to the next Restraint in the vector. |
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Add an object in the registry of used objects.
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Raise a flag, to be sure not to make a random change more than once in each RefinableObj. This calls recursively all sub-objects. This is necessary since one object may be included in several others. This must be called before making a random configuration change on a list of objects. |
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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.
Reimplemented in ObjCryst::Crystal, ObjCryst::Molecule, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::TextureMarchDollase, and ObjCryst::ScatteringData. |
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Erase the param set with the given id, releasing memory.
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Save the current set of refined values in a new set.
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Deregister an object (which not any more) using this object.
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This should be called by any optimization class at the end of an optimization. This also affects all sub-objects.
Reimplemented in ObjCryst::PowderPatternDiffraction, ObjCryst::ScatteringData, and ObjCryst::ZScatterer. |
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Erase all saved refpar sets.
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Find a refinable parameter from the adress of its value.
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Find a refinable parameter with a given name.
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Find a parameter set with a given id (and check if it is there).
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Fix All parameters.
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Name for this class ("RefinableObj", "Crystal",...). This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPatternComponent, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::PowderPatternBackgroundBayesianMinimiser, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::Scatterer, ObjCryst::TextureMarchDollase, ObjCryst::Radiation, ObjCryst::ScatteringPower, ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, ObjCryst::UnitCell, and ObjCryst::ZScatterer. |
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This clocks records _any_ change in the object. See refinableObj::mClockMaster.
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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.
Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ScatteringPower, and ObjCryst::ZScatterer. |
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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.
Reimplemented in ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPattern, ObjCryst::PowderPatternBackgroundBayesianMinimiser, and ObjCryst::ZMoveMinimizer. |
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Get the current calculated value for the LSQ function.
Reimplemented in ObjCryst::DiffractionDataSingleCrystal, and ObjCryst::PowderPattern. |
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Get the first derivative values for the LSQ function, for a given parameter. Note that the default method in the base RefinableObj class is to use numerical derivatives, so it should be overridden for better precision.
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Get the observed values for the LSQ function.
Reimplemented in ObjCryst::DiffractionDataSingleCrystal, and ObjCryst::PowderPattern. |
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Get the weight values for the LSQ function.
Reimplemented in ObjCryst::DiffractionDataSingleCrystal, and ObjCryst::PowderPattern. |
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Name of the object.
Reimplemented in ObjCryst::TextureMarchDollase. |
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Number of LSQ functions.
Reimplemented in ObjCryst::DiffractionDataSingleCrystal, and ObjCryst::PowderPattern. |
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Number of Options for this object.
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Total number of refinable parameter in the object. Note that some may be actually fixed or even not used !! For refinement use PrepareForRefinement(), NbRefParNotFixed(), and ParNotFixed(i) |
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Total number of non-fixed parameters. Is initialized by PrepareForRefinement().
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const access to the options
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Access to the options.
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Access parameter from its adress.
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Access parameter from its adress.
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Access all parameters from their name.
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Access all parameters from their name.
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Access all parameters in the order they were inputted.
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Access all parameters in the order they were inputted.
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Access one save refpar set.
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Access one save refpar set.
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Access the (human) value of one refined parameter in a saved set of parameters.
For internal use only.
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Get the name associated to a refpar set.
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Access all parameters in the order they were inputed, skipping fixed parameters. Must call PrepareForRefinement() before ! |
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Access all parameters in the order they were inputted, skipping fixed parameters. Must call PrepareForRefinement() before ! |
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What was the last time a RefinablePar was added/removed ?
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Get the restraint cost (overall penalty of all restraints). By default this returns 0, so this must be overloaded by any object which actually uses restraint.
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Access to the registry of RefinableObj used by this object.
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Access to the registry of RefinableObj used by this object.
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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.
Reimplemented in ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPattern, ObjCryst::TextureMarchDollase, and ObjCryst::ZScatterer. |
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Is the object being refined ? (Can be refined by one algorithm at a time only.).
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Defined not implemented... Should never be called |
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Prepare everything (if necessary) for an optimization/calculation.
Reimplemented in ObjCryst::PowderPatternComponent, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPattern. |
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Find which parameters are used and not fixed, for a refinement /optimization. This must be called before any refinement... |
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Reimplemented in ObjCryst::Atom, ObjCryst::Molecule, ObjCryst::Scatterer, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::ZScatterer. |
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Randomize Configuration (before a global optimization). This Affects only parameters which are limited and not fixed. The randomization also affects all sub-objects (recursive). Reimplemented in ObjCryst::Molecule. |
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Register a new object using this object.
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Remove a refinable parameter. This returns an iterator to the next parameter in the vector. |
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Remove a restraint from the list of known restraints. This does not delete the Restraint object. |
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Remove an object in the registry of used objects.
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Re-init the list of refinable parameters, removing all parameters. This does not delete the RefinablePar if RefinableObj::mDeleteRefParInDestructor is false |
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Restore a saved set of values.
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Save the current set of refined values over a previously-created set of saved values.
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Set this object not to delete its list of parameters when destroyed. This is used for the RefinableObj in algorithms objects (OptimizationObj), which only hold copies of parameters from the refined objects. |
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Change the maximum step to use during Global Optimization algorithms.
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Change the limits for a category of parameters, giving absolute new limits.
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Change the limits for a given parameter, giving absolute new limits.
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Change the limits for a category of parameters, proportionnaly to their current value. min should be < 1. and max > 1. |
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Change the limits for a given parameter, proportionnaly to the current value. min should be < 1. and max > 1. |
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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). Thus min should logically be <0 and max >0. |
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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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Name of the object.
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Fix/un-fix one family of parameters.
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Fix/un-fix one parameter from its name.
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Fix/un-fix one parameter from its #.
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Set whether a family of parameters is used.
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Set whether a parameter is used.
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During a global optimization, tells the object that the current config is the latest "best" config. This can be used by the object to make more intellingent random moves (use with caution: highly experimental !). Reimplemented in ObjCryst::Molecule, ObjCryst::PowderPatternBackground, and ObjCryst::TextureMarchDollase. |
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UnFix All parameters.
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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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Input From stream.
Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ReflectionProfile, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::TextureMarchDollase, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::ZScatterer. |
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Output to stream in well-formed XML.
Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::Molecule, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ReflectionProfile, ObjCryst::ReflectionProfilePseudoVoigt, ObjCryst::ReflectionProfileDoubleExponentialPseudoVoigt, ObjCryst::TextureMarchDollase, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, ObjCryst::ScatteringPowerSphere, and ObjCryst::ZScatterer. |
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Registry of RefinableObject using this object. This is mutable so that client can modify it (kludge?) |
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Master clock, which is changed whenever the object has been altered. It should be parent to all clocks recording changes in derived classes. |
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If true (the default), then all RefinablePar will be deleted when the the object is deleted. The opposite option (false) should only be used in RefinableObj holding 'copies' of other objects, such as in algorithms. |
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Is the object being refined ?
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Temporary array used to return derivative values of the LSQ function for given parameters.
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Name for this RefinableObject. Should be unique, at least in the same scope.+.
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Total of not-fixed parameters.
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List of options for this object. Note that these are just references, to options allocated by the object, to have a simple global access to all options |
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For internal use only. This true is false if RefinableObj::GlobalOptRandomMove() has been called since RefinableObj::BeginGlobalOptRandomMove() was called. |
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Last time the RefinableParList was modified (a parameter added or removed).
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Index of not-fixed parameters.
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Registry of RefinableObject needed for this object (owned by this object or not).
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Vector of pointers to the refinable parameters.
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Vector of pointers to the restraints for this object. This excludes all RefinablePar declared in RefinableObj::mpRefPar, which also are Restraint. |
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Map of (index,pointers to arrays) used to save sets of values for all parameters. Currently there is no limit to the number of saved sets. This is mutable since creating/storing a param set does not affect the 'real' part of the object. |