ObjCryst::ZMoveMinimizer Class Reference
Class to minimize conformation changes for random moves. More...
Inheritance diagram for ObjCryst::ZMoveMinimizer:
Collaboration diagram for ObjCryst::ZMoveMinimizer:
Public Member Functions | |
| ZMoveMinimizer (ZScatterer &scatt) | |
| virtual REAL | GetLogLikelihood () const |
| Get -log(likelihood) of the current configuration for the object. More... | |
| void | RecordConformation () |
| void | SetZAtomWeight (const CrystVector_REAL weight) |
| void | MinimizeChange (long nbTrial=10000) |
| 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 & | GetClassName () const |
| Name for this class ("RefinableObj", "Crystal",...). More... | |
| 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... | |
| virtual void | Print () const |
| 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 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. | |
Private Attributes | |
| ZScatterer * | mpZScatt |
| MonteCarloObj | mOptimObj |
| CrystVector_REAL | mXCoord0 |
| CrystVector_REAL | mYCoord0 |
| CrystVector_REAL | mZCoord0 |
| CrystVector_REAL | mAtomWeight |
Additional Inherited Members | |
| 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
Class to minimize conformation changes for random moves.
Very experimental !!!
Only used within ZScatterer.
Definition at line 168 of file ZScatterer.h.
Member Function Documentation
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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 153 of file ZScatterer.cpp.
The documentation for this class was generated from the following files:
