Merge remote-tracking branch 'objcryst/master' into upstream-objcryst

* objcryst/master:
  Crystal::XMLInput(): add a hook to re-use atomic scattering power when mDeleteSubObjInDestructor is False. This is useful when re-loading Crystal configurations using their xml descriptions repeatedly, notably in python.

Author: vincefn

ObjCryst/ObjCryst/Crystal.h

@@ -341,19 +341,26 @@ class Crystal:public UnitCell
       const RefinableObjClock& GetClockScattererList()const;
 
       virtual void XMLOutput(ostream &os,int indent=0)const;
+      /** \brief Input the crystal structure from a stream.
+      *
+      * This will destroy any Scatterer of ScatteringPower if
+      * mDeleteSubObjInDestructor is true. Otherwise they will just
+      * be de-registered and should be deleted somewhere else,
+      * but there is a special hook implemented where any
+      * previously existing ScatteringPowerAtom will be re-used if
+      * equivalent to the one in the input.
+      */
       virtual void XMLInput(istream &is,const XMLCrystTag &tag);
       //virtual void XMLInputOld(istream &is,const IOCrystTag &tag);
 
       virtual void GlobalOptRandomMove(const REAL mutationAmplitude,
                                        const RefParType *type=gpRefParTypeObjCryst);
       virtual REAL GetLogLikelihood()const;
-      /** \brief output Crystal structure as a cif file (EXPERIMENTAL !)
+      /** \brief output Crystal structure as a cif file
       *  \param mindist : minimum distance between atoms to consider them
       *  overlapping. Overlapping atoms are only included as comments in the
       *  CIF file.
       *
-      * \warning This is very crude and EXPERIMENTAL so far:  there is not much
-      * information beside atom positions...
       */
       virtual void CIFOutput(ostream &os, double mindist = 0.5)const;
 

ObjCryst/ObjCryst/IO.cpp

@@ -896,13 +896,37 @@ void Crystal::XMLInput(istream &is,const XMLCrystTag &tagg)
          this->RemoveSubRefObj(mScatteringPowerRegistry.GetObj(i));
          mScatteringPowerRegistry.GetObj(i).DeRegisterClient(*this);
       }
-      mScatteringPowerRegistry.DeleteAll();
+
+      std::list<ScatteringPowerAtom*> vold_scattpow;
+      if(mDeleteSubObjInDestructor)
+      {
+         mScatteringPowerRegistry.DeleteAll();
+      }
+      else
+      {
+         // Keep track of the old atomic scattering powers to see if they can be re-used
+         for(std::vector<ScatteringPower*>::const_iterator pos=mScatteringPowerRegistry.begin() ;
+            pos!=mScatteringPowerRegistry.end(); ++pos)
+         {
+            if((*pos)->GetClassName().compare("ScatteringPowerAtom")!=0) continue;
+            vold_scattpow.push_back(dynamic_cast<ScatteringPowerAtom*>(*pos));
+         }
+         mScatteringPowerRegistry.DeRegisterAll();
+      }
+
       for(long i=0;i<mScattererRegistry.GetNb();i++)
       {
          this->RemoveSubRefObj(mScattererRegistry.GetObj(i));
          mScattererRegistry.GetObj(i).DeRegisterClient(*this);
       }
-      mScattererRegistry.DeleteAll();
+      if(mDeleteSubObjInDestructor)
+      {
+         mScattererRegistry.DeleteAll();
+      }
+      else
+      {
+         mScattererRegistry.DeRegisterAll();
+      }
 
    for(unsigned int i=0;i<tagg.GetNbAttribute();i++)
    {
@@ -1011,6 +1035,33 @@ void Crystal::XMLInput(istream &is,const XMLCrystTag &tagg)
          VFN_DEBUG_MESSAGE("Crystal::XMLInput():reading a ScatteringPowerAtom",5)
          ScatteringPowerAtom *sc=new ScatteringPowerAtom;
          sc->XMLInput(is,tag);
+         if(!mDeleteSubObjInDestructor)
+         {
+            // Can we re-use a previous scattering power since we did not delete them ?
+            for(std::list<ScatteringPowerAtom*>::iterator pos= vold_scattpow.begin();
+                pos!=vold_scattpow.end();++pos)
+            {
+               if((*pos)->GetSymbol() != sc->GetSymbol()) continue;
+               if((*pos)->GetName() != sc->GetName()) continue;
+               if((*pos)->GetFormalCharge() != sc->GetFormalCharge()) continue;
+               if((*pos)->GetMaximumLikelihoodNbGhostAtom() != sc->GetMaximumLikelihoodNbGhostAtom()) continue;
+               if((*pos)->GetMaximumLikelihoodPositionError() != sc->GetMaximumLikelihoodPositionError()) continue;
+               if((*pos)->IsIsotropic() != sc->IsIsotropic()) continue;
+               if(fabs((*pos)->GetBiso() - sc->GetBiso()) > 1e-4f) continue;
+               if(!(*pos)->IsIsotropic())
+               {
+                  if(fabs((*pos)->GetBij(0) - sc->GetBij(0)) > 1e-4f) continue;
+                  if(fabs((*pos)->GetBij(1) - sc->GetBij(1)) > 1e-4f) continue;
+                  if(fabs((*pos)->GetBij(2) - sc->GetBij(2)) > 1e-4f) continue;
+                  if(fabs((*pos)->GetBij(3) - sc->GetBij(3)) > 1e-4f) continue;
+                  if(fabs((*pos)->GetBij(4) - sc->GetBij(4)) > 1e-4f) continue;
+                  if(fabs((*pos)->GetBij(5) - sc->GetBij(5)) > 1e-4f) continue;
+               }
+               VFN_DEBUG_MESSAGE("Crystal::XMLInput(): reusing scattering power: "<<sc->GetName(),5);
+               delete sc;
+               sc = *pos;
+            }
+         }
          this->AddScatteringPower(sc);
          VFN_DEBUG_EXIT("Crystal::XMLInput():reading a ScatteringPowerAtom",5)
          continue;