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Comparing branches/development/src/selection/HullFinder.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
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 87 | Line 88 | namespace OpenMD {
88   #endif
89    }
90  
91 +  HullFinder::~HullFinder() {
92 +    delete surfaceMesh_;
93 +  }
94 +
95    OpenMDBitSet HullFinder::findHull() {
91 –    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 error: Hull calculation is not possible without libqhull.\n",
103 <             "Please rebuild OpenMD with qhull enabled.");
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();
# Line 108 | Line 147 | namespace OpenMD {
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();

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