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Comparing branches/development/src/selection/HullFinder.cpp (file contents):
Revision 1618 by gezelter, Mon Sep 12 17:09:26 2011 UTC vs.
Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "selection/HullFinder.hpp"
# Line 52 | Line 53 | namespace OpenMD {
53      
54      SimInfo::MoleculeIterator mi;
55      Molecule* mol;
56 <    StuntDouble* integrableObject;
56 >    StuntDouble* sd;
57      Molecule::IntegrableObjectIterator  ioi;
58      Molecule::AtomIterator ai;
59      Atom* atom;
# Line 63 | Line 64 | namespace OpenMD {
64           mol = info_->nextMolecule(mi)) {
65          
66        // Hull is constructed from all known integrable objects.
67 <      for (integrableObject = mol->beginIntegrableObject(ioi);
68 <           integrableObject != NULL;
69 <           integrableObject = mol->nextIntegrableObject(ioi)) {
70 <        localSites_.push_back(integrableObject);
67 >      for (sd = mol->beginIntegrableObject(ioi);
68 >           sd != NULL;
69 >           sd = mol->nextIntegrableObject(ioi)) {
70 >        localSites_.push_back(sd);
71        }
72        
73        // selection can include atoms (which may be a subset of the IOs)
# Line 88 | Line 89 | namespace OpenMD {
89    }
90  
91    OpenMDBitSet HullFinder::findHull() {
91 –    StuntDouble* sd;
92      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
93      OpenMDBitSet bsResult(nStuntDoubles_);
94   #ifdef HAVE_QHULL
# Line 108 | Line 108 | namespace OpenMD {
108      std::vector<Triangle>::iterator face;
109      std::vector<StuntDouble*>::iterator vertex;
110  
111 +    // This will work in parallel because the triangles returned by the mesh
112 +    // have a NULL stuntDouble if this processor doesn't own the
113 +    
114      for (face = sMesh.begin(); face != sMesh.end(); ++face) {
115        Triangle thisTriangle = *face;
116        std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();

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