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Comparing:
trunk/src/selection/HullFinder.cpp (file contents), Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
branches/development/src/selection/HullFinder.cpp (file contents), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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 81 | Line 82 | namespace OpenMD {
82          stuntdoubles_[rb->getGlobalIndex()] = rb;
83        }
84          
85 <    }    
86 <    surfaceMesh_ = new ConvexHull();    
85 >    }
86 > #ifdef HAVE_QHULL
87 >    surfaceMesh_ = new ConvexHull();
88 > #endif
89    }
90  
91 +  HullFinder::~HullFinder() {
92 +    delete surfaceMesh_;
93 +  }
94 +
95    OpenMDBitSet HullFinder::findHull() {
89 –    StuntDouble* sd;
96      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
97      OpenMDBitSet bsResult(nStuntDoubles_);
98 + #ifdef HAVE_QHULL
99 +    surfaceMesh_->computeHull(localSites_);
100 + #else
101 +    sprintf( painCave.errMsg,
102 +             "HullFinder : Hull calculation is not possible without libqhull.\n"
103 +             "\tPlease rebuild OpenMD with qhull enabled.");
104 +    painCave.severity = OPENMD_ERROR;
105 +    painCave.isFatal = 1;
106 +    simError();
107 + #endif
108 +    
109 +    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
110 +    int nTriangles = sMesh.size();
111 +    // Loop over the mesh faces
112 +    std::vector<Triangle>::iterator face;
113 +    std::vector<StuntDouble*>::iterator vertex;
114  
115 +    // This will work in parallel because the triangles returned by the mesh
116 +    // have a NULL stuntDouble if this processor doesn't own the
117 +    
118 +    for (face = sMesh.begin(); face != sMesh.end(); ++face) {
119 +      Triangle thisTriangle = *face;
120 +      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
121 +      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
122 +        if ((*vertex) != NULL) {
123 +          bsResult.setBitOn((*vertex)->getGlobalIndex());          
124 +        }
125 +      }
126 +    }
127 +    return bsResult;
128 +  }
129 +
130 +  OpenMDBitSet HullFinder::findHull(int frame) {
131 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
132 +    OpenMDBitSet bsResult(nStuntDoubles_);
133 + #ifdef HAVE_QHULL
134      surfaceMesh_->computeHull(localSites_);
135 + #else
136 +    sprintf( painCave.errMsg,
137 +             "HullFinder : Hull calculation is not possible without libqhull.\n"
138 +             "\tPlease rebuild OpenMD with qhull enabled.");
139 +      painCave.severity = OPENMD_ERROR;
140 +      painCave.isFatal = 1;
141 +      simError();
142 + #endif
143 +    
144      std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
145      int nTriangles = sMesh.size();
146      // Loop over the mesh faces
147      std::vector<Triangle>::iterator face;
148      std::vector<StuntDouble*>::iterator vertex;
149  
150 +    // This will work in parallel because the triangles returned by the mesh
151 +    // have a NULL stuntDouble if this processor doesn't own the
152 +    
153      for (face = sMesh.begin(); face != sMesh.end(); ++face) {
154        Triangle thisTriangle = *face;
155        std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();

Comparing:
trunk/src/selection/HullFinder.cpp (property svn:keywords), Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
branches/development/src/selection/HullFinder.cpp (property svn:keywords), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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