Merge branch 'upstream-objcryst'

* upstream-objcryst:
  Avoid access to mpScattPow for dummy atom
  Add STL-type methods (begin, end, size) for ObjRegistry and Molecule objects
  Minor changes to be in sync with https://github.com/diffpy/libobjcryst
  Add access to Options in OptimizationObj, by number or name. Also provide access by name in RefinableObj
  MonteCarloObj: add public access to AutoLSQ option
  Radiation: fix automatic setting of options and used parameters

Author: vincefn

src/ObjCryst/ObjCryst/Atom.cpp

@@ -169,16 +169,23 @@ string Atom::GetComponentName(const int i) const{ return this->GetName();}
 void Atom::Print() const
 {
    VFN_DEBUG_MESSAGE("Atom::Print()",1)
-   cout << "Atom ("
-        << FormatString(mpScattPowAtom->GetSymbol(),4) << ") :"
-        << FormatString(this->GetName(),16)  << " at : "
-        << FormatFloat(this->GetX())
-        << FormatFloat(this->GetY())
-        << FormatFloat(this->GetZ());
-   if(this->IsDummy()) cout << " DUMMY! ";
+   if(this->IsDummy())
+   {
+      cout << "Atom (DUMMY) :"
+           << FormatString(this->GetName(),16)  << " at : "
+           << FormatFloat(this->GetX())
+           << FormatFloat(this->GetY())
+           << FormatFloat(this->GetZ());
+   }
    else
    {
-      cout << ", Biso="
+      cout << "Atom ("
+           << FormatString(mpScattPowAtom->GetSymbol(),4) << ") :"
+           << FormatString(this->GetName(),16)  << " at : "
+           << FormatFloat(this->GetX())
+           << FormatFloat(this->GetY())
+           << FormatFloat(this->GetZ())
+           << ", Biso="
            << FormatFloat(mpScattPowAtom->GetBiso())
            << ", Popu=" << FormatFloat(this->GetOccupancy());
    }
@@ -303,6 +310,7 @@ void Atom::GLInitDisplayList(const bool onlyIndependentAtoms,
                              const bool fullMoleculeInLimits)const
 {
    VFN_DEBUG_MESSAGE("Atom::GLInitDisplayList():"<<this->GetName(),5)
+   if(this->IsDummy()) return ;
    REAL en=1;
    if(displayEnantiomer==true) en=-1;
 
@@ -323,7 +331,6 @@ void Atom::GLInitDisplayList(const bool onlyIndependentAtoms,
    const REAL bb=this->GetCrystal().GetLatticePar(1);
    const REAL cc=this->GetCrystal().GetLatticePar(2);
 
-   if(this->IsDummy()) return ;
    if(hideHydrogens  && (mpScattPowAtom->GetForwardScatteringFactor(RAD_XRAY)<1.5)) return;
    GLUquadricObj* pQuadric = gluNewQuadric();
    if(true==onlyIndependentAtoms)

src/ObjCryst/ObjCryst/Molecule.cpp

@@ -937,6 +937,9 @@ void MolBondAngle::SetAtom3(MolAtom& at){mvpAtom[2]=&at;}
 //MolAtom& MolBondAngle::GetAtom1(){return *(mvpAtom[0]);}
 //MolAtom& MolBondAngle::GetAtom2(){return *(mvpAtom[1]);}
 //MolAtom& MolBondAngle::GetAtom3(){return *(mvpAtom[2]);}
+std::size_t MolBondAngle::size() const {return mvpAtom.size();}
+vector<MolAtom*>::const_iterator MolBondAngle::begin() const {return mvpAtom.begin();}
+vector<MolAtom*>::const_iterator MolBondAngle::end() const  {return mvpAtom.end();}
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolBondAngle::WXCreate(wxWindow* parent)
 {
@@ -1294,6 +1297,9 @@ MolAtom& MolDihedralAngle::GetAtom1(){return *(mvpAtom[0]);}
 MolAtom& MolDihedralAngle::GetAtom2(){return *(mvpAtom[1]);}
 MolAtom& MolDihedralAngle::GetAtom3(){return *(mvpAtom[2]);}
 MolAtom& MolDihedralAngle::GetAtom4(){return *(mvpAtom[3]);}
+std::size_t MolDihedralAngle::size() const {return mvpAtom.size();}
+vector<MolAtom*>::const_iterator MolDihedralAngle::begin() const {return mvpAtom.begin();}
+vector<MolAtom*>::const_iterator MolDihedralAngle::end() const  {return mvpAtom.end();}
 #ifdef __WX__CRYST__
 WXCrystObjBasic* MolDihedralAngle::WXCreate(wxWindow* parent)
 {

src/ObjCryst/ObjCryst/Molecule.h

@@ -229,6 +229,7 @@ class MolBond:public Restraint
       void SetBondOrder(const REAL length);
       bool IsFreeTorsion()const;
       void SetFreeTorsion(const bool isInRing);
+   
   private:
       pair<MolAtom*,MolAtom*> mAtomPair;
       REAL mLength0,mDelta,mSigma;
@@ -316,6 +317,9 @@ class MolBondAngle:public Restraint
       MolAtom& GetAtom3();
       bool IsFlexible()const;
       void SetFlexible(const bool isInRing);
+      std::size_t size() const;
+      vector<MolAtom*>::const_iterator begin() const;
+      vector<MolAtom*>::const_iterator end() const;
    private:
       /// The vector of the 3 atoms involved in the bond angle.
       vector<MolAtom*> mvpAtom;
@@ -408,6 +412,9 @@ class MolDihedralAngle:public Restraint
       MolAtom& GetAtom2();
       MolAtom& GetAtom3();
       MolAtom& GetAtom4();
+      std::size_t size() const;
+      vector<MolAtom*>::const_iterator begin() const;
+      vector<MolAtom*>::const_iterator end() const;
    private:
       /// The vector of the 4 atoms involved in the bond angle.
       vector<MolAtom*> mvpAtom;

src/ObjCryst/ObjCryst/ScatteringData.cpp

@@ -220,15 +220,23 @@ void Radiation::SetRadiationType(const RadiationType rad)
 {
    mRadiationType.SetChoice(rad);
    if(rad == RAD_NEUTRON) mLinearPolarRate=0;
-   if(rad == RAD_ELECTRON) mLinearPolarRate=0;
-   if(rad != RAD_XRAY) this->SetWavelengthType(WAVELENGTH_MONOCHROMATIC);
+   if(rad == RAD_ELECTRON)
+   {
+      mLinearPolarRate=0;
+      this->SetWavelengthType(WAVELENGTH_MONOCHROMATIC);
+   }
    else this->UpdateDisplay();
 }
 
 void Radiation::SetWavelengthType(const WavelengthType &type)
 {
    mWavelengthType.SetChoice((unsigned long) type);
-   if(type==WAVELENGTH_TOF) this->SetRadiationType(RAD_NEUTRON);
+   if(type==WAVELENGTH_TOF)
+   {
+      this->SetRadiationType(RAD_NEUTRON);
+      this->GetPar("XRayTubeDeltaLambda").SetIsUsed(false);
+      this->GetPar("XRayTubeAlpha2Alpha1Ratio").SetIsUsed(false);
+   }
    if(type==WAVELENGTH_ALPHA12)
    {
       this->SetRadiationType(RAD_XRAY);

src/ObjCryst/ObjCryst/ZScatterer.cpp

@@ -1530,6 +1530,21 @@ void ZScatterer::ExportFenskeHallZMatrix(ostream &os)
 void ZScatterer::SetCenterAtomIndex(const unsigned int ix){mCenterAtomIndex=ix;}
 unsigned int ZScatterer::GetCenterAtomIndex()const{return mCenterAtomIndex;}
 
+std::size_t ZScatterer::size() const
+{
+   return mZAtomRegistry.size();
+}
+
+vector<ZAtom*>::const_iterator ZScatterer::begin() const
+{
+   return mZAtomRegistry.begin();
+}
+
+vector<ZAtom*>::const_iterator ZScatterer::end() const
+{
+   return mZAtomRegistry.end();
+}
+
 void ZScatterer::GlobalOptRandomMove(const REAL mutationAmplitude,
                                      const RefParType *type)
 {

src/ObjCryst/ObjCryst/ZScatterer.h

@@ -350,6 +350,19 @@ class ZScatterer: public Scatterer
       void SetCenterAtomIndex(const unsigned int);
       /// Get the index of the central atom (around which the rotation is made)
       unsigned int GetCenterAtomIndex()const;
+      /** STL access to registry of Zatom size
+       */
+      std::size_t size() const;
+      /** low-level access to the underlying vector of ZAtom begin().
+       * Const access as we do not want the number and order of objects to change,
+       * but the objects themselves can be modified.
+       */
+      vector<ZAtom*>::const_iterator begin() const;
+      /** low-level access to the underlying vector of ZAtom end().
+       * Const access as we do not want the number and order of objects to change,
+       * but the objects themselves can be modified.
+       */
+      vector<ZAtom*>::const_iterator end() const;
    protected:
       /** Update the atom coordinates (in real units, in Angstroems).
       *

src/ObjCryst/RefinableObj/GlobalOptimObj.cpp

@@ -299,6 +299,59 @@ long& OptimizationObj::NbTrialPerRun() {return mNbTrialPerRun;}
 
 const long& OptimizationObj::NbTrialPerRun() const {return mNbTrialPerRun;}
 
+unsigned int OptimizationObj::GetNbOption()const
+{
+   return mOptionRegistry.GetNb();
+}
+
+ObjRegistry<RefObjOpt>& OptimizationObj::GetOptionList()
+{
+   return mOptionRegistry;
+}
+
+RefObjOpt& OptimizationObj::GetOption(const unsigned int i)
+{
+   VFN_DEBUG_MESSAGE("RefinableObj::GetOption()"<<i,3)
+   //:TODO: Check
+   return mOptionRegistry.GetObj(i);
+}
+
+RefObjOpt& OptimizationObj::GetOption(const string & name)
+{
+   VFN_DEBUG_MESSAGE("OptimizationObj::GetOption()"<<name,3)
+   const long i=mOptionRegistry.Find(name);
+   if(i<0)
+   {
+      this->Print();
+      throw ObjCrystException("OptimizationObj::GetOption(): cannot find option: "+name+" in object:"+this->GetName());
+   }
+   return mOptionRegistry.GetObj(i);
+}
+
+const RefObjOpt& OptimizationObj::GetOption(const unsigned int i)const
+{
+   VFN_DEBUG_MESSAGE("RefinableObj::GetOption()"<<i,3)
+   //:TODO: Check
+   return mOptionRegistry.GetObj(i);
+}
+
+const RefObjOpt& OptimizationObj::GetOption(const string & name)const
+{
+   VFN_DEBUG_MESSAGE("OptimizationObj::GetOption()"<<name,3)
+   const long i=mOptionRegistry.Find(name);
+   if(i<0)
+   {
+      this->Print();
+      throw ObjCrystException("OptimizationObj::GetOption(): cannot find option: "+name+" in object:"+this->GetName());
+   }
+   return mOptionRegistry.GetObj(i);
+}
+
+const ObjRegistry<RefinableObj>& OptimizationObj::GetRefinedObjList() const
+{
+   return mRefinedObjList;
+}
+
 void OptimizationObj::PrepareRefParList()
 {
    VFN_DEBUG_ENTRY("OptimizationObj::PrepareRefParList()",6)
@@ -375,6 +428,7 @@ void OptimizationObj::InitOptions()
       needInitNames=false;//Only once for the class
    }
    mXMLAutoSave.Init(6,&xmlAutoSaveName,xmlAutoSaveChoices);
+   this->AddOption(&mXMLAutoSave);
    VFN_DEBUG_MESSAGE("OptimizationObj::InitOptions():End",5)
 }
 
@@ -404,6 +458,13 @@ void OptimizationObj::BuildRecursiveRefObjList()
    }
 }
 
+void OptimizationObj::AddOption(RefObjOpt *opt)
+{
+   VFN_DEBUG_ENTRY("OptimizationObj::AddOption()",5)
+   mOptionRegistry.Register(*opt);
+   VFN_DEBUG_EXIT("OptimizationObj::AddOption()",5)
+}
+
 //#################################################################################
 //
 //       MonteCarloObj
@@ -2087,6 +2148,11 @@ void MonteCarloObj::InitOptions()
    mAnnealingScheduleMutation.Init(6,&AnnealingScheduleMutationName,AnnealingScheduleChoices);
    mSaveTrackedData.Init(2,&saveTrackedDataName,saveTrackedDataChoices);
    mAutoLSQ.Init(3,&runAutoLSQName,runAutoLSQChoices);
+   this->AddOption(&mGlobalOptimType);
+   this->AddOption(&mAnnealingScheduleTemp);
+   this->AddOption(&mAnnealingScheduleMutation);
+   this->AddOption(&mSaveTrackedData);
+   this->AddOption(&mAutoLSQ);
    VFN_DEBUG_MESSAGE("MonteCarloObj::InitOptions():End",5)
 }
 

src/ObjCryst/RefinableObj/GlobalOptimObj.h

@@ -222,6 +222,21 @@ class OptimizationObj
       virtual long& NbTrialPerRun();
       /// Number of trial per run
       virtual const long& NbTrialPerRun() const;
+      //Options
+      /// Access to the options registry
+      ObjRegistry<RefObjOpt>& GetOptionList();
+      /// Number of Options for this object
+      unsigned int GetNbOption()const;
+      /// Access to the options
+      RefObjOpt& GetOption(const unsigned int i);
+      /// Access to the options by name
+      RefObjOpt& GetOption(const string & name);
+      /// const access to the options
+      const RefObjOpt& GetOption(const unsigned int i)const;
+      /// const access to the options by name
+      const RefObjOpt& GetOption(const string & name)const;
+      /// Access the list of refined object
+      const ObjRegistry<RefinableObj>& GetRefinedObjList() const;
    protected:
       /// \internal Prepare mRefParList for the refinement
       void PrepareRefParList();
@@ -235,6 +250,8 @@ class OptimizationObj
       /// object has been added or modified. If no object has been
       /// added and no sub-object has been added/removed, then nothing is done.
       void BuildRecursiveRefObjList();
+      /// \internal Add an option for this parameter
+      void AddOption(RefObjOpt *opt);
       /// The refinable par list used during refinement. Only a condensed version
       /// of all objects. This is useful to keep an history of modifications, and to
       /// restore previous values.
@@ -308,6 +325,10 @@ class OptimizationObj
       /// MainTracker object to track the evolution of cost functions, likelihood,
       /// and individual parameters.
       MainTracker mMainTracker;
+      /// 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
+      ObjRegistry<RefObjOpt> mOptionRegistry;
    private:
    #ifdef __WX__CRYST__
    public:

src/ObjCryst/RefinableObj/RefinableObj.cpp

@@ -983,11 +983,13 @@ template<class T> void ObjRegistry<T>::DeleteAll()
 
 template<class T> T& ObjRegistry<T>::GetObj(const unsigned int i)
 {
+   if(i>=this->GetNb()) throw ObjCrystException("ObjRegistry<T>::GetObj(i): i >= nb!");
    return *(mvpRegistry[i]);
 }
 
 template<class T> const T& ObjRegistry<T>::GetObj(const unsigned int i) const
 {
+   if(i>=this->GetNb()) throw ObjCrystException("ObjRegistry<T>::GetObj(i): i >= nb!");
    return *(mvpRegistry[i]);
 }
 
@@ -1116,6 +1118,21 @@ template<class T> void ObjRegistry<T>::UpdateUI()
    #endif
 }
 
+template<class T> std::size_t ObjRegistry<T>::size() const
+{
+   return (std::size_t) mvpRegistry.size();
+}
+
+template<class T> typename vector<T*>::const_iterator ObjRegistry<T>::begin() const
+{
+   return mvpRegistry.begin();
+}
+
+template<class T> typename vector<T*>::const_iterator ObjRegistry<T>::end() const
+{
+   return mvpRegistry.end();
+}
+
 #ifdef __WX__CRYST__
 template<class T> WXRegistry<T>* ObjRegistry<T>::WXCreate(wxWindow *parent)
 {
@@ -1846,6 +1863,11 @@ void RefinableObj::ResetParList()
    VFN_DEBUG_MESSAGE("RefinableObj::ResetParList():End.",3)
 }
 
+ObjRegistry<RefObjOpt>& RefinableObj::GetOptionList()
+{
+    return mOptionRegistry;
+}
+
 unsigned int RefinableObj::GetNbOption()const
 {
    return mOptionRegistry.GetNb();
@@ -1858,12 +1880,36 @@ RefObjOpt& RefinableObj::GetOption(const unsigned int i)
    return mOptionRegistry.GetObj(i);
 }
 
+RefObjOpt& RefinableObj::GetOption(const string & name)
+{
+    VFN_DEBUG_MESSAGE("RefinableObj::GetOption()"<<name,3)
+    const long i=mOptionRegistry.Find(name);
+    if(i<0)
+    {
+        this->Print();
+        throw ObjCrystException("RefinableObj::GetOption(): cannot find option: "+name+" in object:"+this->GetName());
+    }
+    return mOptionRegistry.GetObj(i);
+}
+
 const RefObjOpt& RefinableObj::GetOption(const unsigned int i)const
 {
    //:TODO: Check
    return mOptionRegistry.GetObj(i);
 }
 
+const RefObjOpt& RefinableObj::GetOption(const string & name)const
+{
+    VFN_DEBUG_MESSAGE("RefinableObj::GetOption()"<<name,3)
+    const long i=mOptionRegistry.Find(name);
+    if(i<0)
+    {
+        this->Print();
+        throw ObjCrystException("RefinableObj::GetOption(): cannot find option: "+name+" in object:"+this->GetName());
+    }
+    return mOptionRegistry.GetObj(i);
+}
+
 void RefinableObj::GetGeneGroup(const RefinableObj &obj,
                                 CrystVector_uint & groupIndex,
                                 unsigned int &first) const