Merge branch 'upstream-objcryst':

* PowderPatternDiffraction: add GetFhklObsSq() and HasFhklObsSq()
* Use a valid XML output for a Molecule RigidGroup, writing atoms as Atom1, Atom2 etc... instead of repeating the Atom attribute. Fixes vincefn/objcryst#52. The saved files will not be backwards-compatible (readable but the list of atoms in the rigid group will not be read)
* Fix double loop in PowderPattern::PrepareIntegratedRfactor.

Author: vincefn

src/ObjCryst/ObjCryst/Molecule.cpp

@@ -25,6 +25,7 @@
 #include <algorithm>
 #include <iomanip>
 #include <ctime>
+#include <boost/format.hpp>
 
 #include "ObjCryst/Quirks/VFNStreamFormat.h"
 #include "ObjCryst/ObjCryst/Molecule.h"
@@ -2292,8 +2293,12 @@ void Molecule::XMLOutput(ostream &os,int indent)const
       for(pos=mvRigidGroup.begin();pos!=mvRigidGroup.end();++pos)
       {
          XMLCrystTag tagg("RigidGroup",false,true);
-         for(set<MolAtom *>::const_iterator at=(*pos)->begin();at!=(*pos)->end();++at)
-            tagg.AddAttribute("Atom",(*at)->GetName());
+         // Need to use Atom1, Atom2 etc.. so a valid XML is produced
+         // See https://github.com/vincefn/objcryst/issues/52
+         // This won't be backwards-compatible
+         int idx = 0;
+         for (set<MolAtom*>::const_iterator at = (*pos)->begin(); at != (*pos)->end(); ++at)
+             tagg.AddAttribute((boost::format("Atom%d") %idx++).str(), (*at)->GetName());
          /*
          tagg.AddAttribute("Q0",(*pos)->mQuat.Q0());
          tagg.AddAttribute("Q1",(*pos)->mQuat.Q1());
@@ -2384,7 +2389,7 @@ void Molecule::XMLInput(istream &is,const XMLCrystTag &tag)
       {
          RigidGroup s;
          for(unsigned int i=0;i<tagg.GetNbAttribute();i++)
-            if("Atom"==tagg.GetAttributeName(i))
+            if(tagg.GetAttributeName(i).rfind("Atom", 0)==0)
                s.insert(&(this->GetAtom(tagg.GetAttributeValue(i))));
          this->AddRigidGroup(s);
       }

src/ObjCryst/ObjCryst/PowderPattern.cpp

@@ -1298,6 +1298,19 @@ unsigned int PowderPatternDiffraction::GetProfileFitNetNbObs()const
    return nb;
 }
 
+bool PowderPatternDiffraction::HasFhklObsSq() const
+{
+  if(mpLeBailData==NULL) return false;
+  return mpLeBailData->GetFhklObsSq().size() > 0;
+}
+
+const CrystVector_REAL& PowderPatternDiffraction::GetFhklObsSq() const
+{
+  if(mpLeBailData==NULL)
+    throw ObjCrystException("PowderPatternDiffraction::GetFhklObsSq(): no extracted intensities available");
+   return mpLeBailData->GetFhklObsSq();
+}
+
 void PowderPatternDiffraction::CalcPowderPattern() const
 {
    this->GetNbReflBelowMaxSinThetaOvLambda();
@@ -6559,7 +6572,7 @@ void PowderPattern::PrepareIntegratedRfactor()const
       for(int i=0;i<mPowderPatternComponentRegistry.GetNb();i++)
       {
          const CrystVector_long vLim=mPowderPatternComponentRegistry.GetObj(i).GetBraggLimits();
-         for(i=0;i<vLim.numElements();i++) vLimits.push_back(vLim(i));
+         for(int j=0;j<vLim.numElements();j++) vLimits.push_back(vLim(j));
       }
       if(vLimits.size()<2)
       {

src/ObjCryst/ObjCryst/PowderPattern.h

@@ -420,6 +420,16 @@ class PowderPatternDiffraction : virtual public PowderPatternComponent,public Sc
       * No over paremeters (profile, background) are taken into account
       */
       unsigned int GetProfileFitNetNbObs()const;
+      /// Return true if there are extracted (le Bail) squared structure factors, false otherwise
+      bool HasFhklObsSq() const;
+      /** Get the extracted structure factors modulus (squared), e.g. using the Le Bail method.
+      *
+      * Note that the number of reflections listed is limited to the evaluated ones,
+      *which is usually smaller than the H,K and L arrays.
+      *
+      * Raises an exception if this is not available.
+      */
+      const CrystVector_REAL& GetFhklObsSq() const;
    protected:
       virtual void CalcPowderPattern() const;
       virtual void CalcPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);