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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp
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Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1861 by gezelter, Tue Apr 9 19:45:54 2013 UTC vs.
Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

# Line 556 | Line 556 | namespace OpenMD {
556              slabWidth_ = hmat(2,2) / 10.0;
557          
558            if (hasSlabBCenter)
559 <            slabBCenter_ = rnemdParams->getSlabACenter();
559 >            slabBCenter_ = rnemdParams->getSlabBCenter();
560            else
561              slabBCenter_ = hmat(2,2) / 2.0;
562          
# Line 577 | Line 577 | namespace OpenMD {
577          }
578        }
579      }
580 +
581      // object evaluator:
582      evaluator_.loadScriptString(rnemdObjectSelection_);
583      seleMan_.setSelectionSet(evaluator_.evaluate());
583 –    
584      evaluatorA_.loadScriptString(selectionA_);
585      evaluatorB_.loadScriptString(selectionB_);
586 –    
586      seleManA_.setSelectionSet(evaluatorA_.evaluate());
587      seleManB_.setSelectionSet(evaluatorB_.evaluate());
589 –    
588      commonA_ = seleManA_ & seleMan_;
589 <    commonB_ = seleManB_ & seleMan_;    
589 >    commonB_ = seleManB_ & seleMan_;  
590    }
591    
592      
# Line 1732 | Line 1730 | namespace OpenMD {
1730        int isd;
1731        StuntDouble* sd;
1732        vector<StuntDouble*> aSites;
1735 –      ConvexHull* surfaceMeshA = new ConvexHull();
1733        seleManA_.setSelectionSet(evaluatorA_.evaluate());
1734        for (sd = seleManA_.beginSelected(isd); sd != NULL;
1735             sd = seleManA_.nextSelected(isd)) {
1736          aSites.push_back(sd);
1737        }
1738 +      ConvexHull* surfaceMeshA = new ConvexHull();
1739        surfaceMeshA->computeHull(aSites);
1740        areaA = surfaceMeshA->getArea();
1741 +      delete surfaceMeshA;
1742 +
1743      } else {
1744        if (usePeriodicBoundaryConditions_) {
1745          // in periodic boundaries, the surface area is twice the x-y
# Line 1753 | Line 1753 | namespace OpenMD {
1753        }
1754      }
1755  
1756 +
1757 +
1758      if (hasSelectionB_) {
1759        int isd;
1760        StuntDouble* sd;
1761        vector<StuntDouble*> bSites;
1760 –      ConvexHull* surfaceMeshB = new ConvexHull();
1762        seleManB_.setSelectionSet(evaluatorB_.evaluate());
1763        for (sd = seleManB_.beginSelected(isd); sd != NULL;
1764             sd = seleManB_.nextSelected(isd)) {
1765          bSites.push_back(sd);
1766        }
1767 +      ConvexHull* surfaceMeshB = new ConvexHull();    
1768        surfaceMeshB->computeHull(bSites);
1769        areaB = surfaceMeshB->getArea();
1770 +      delete surfaceMeshB;
1771 +
1772      } else {
1773        if (usePeriodicBoundaryConditions_) {
1774          // in periodic boundaries, the surface area is twice the x-y

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