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root/OpenMD/trunk/src/selection/HullFinder.cpp
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Comparing trunk/src/selection/HullFinder.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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;
92 –    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
96      OpenMDBitSet bsResult(nStuntDoubles_);
97   #ifdef HAVE_QHULL
98      surfaceMesh_->computeHull(localSites_);
99   #else
100      sprintf( painCave.errMsg,
101 <             "HullFinder error: Hull calculation is not possible without libqhull.\n",
102 <             "Please rebuild OpenMD with qhull enabled.");
101 >             "HullFinder : Hull calculation is not possible without libqhull.\n"
102 >             "\tPlease rebuild OpenMD with qhull enabled.");
103 >    painCave.severity = OPENMD_ERROR;
104 >    painCave.isFatal = 1;
105 >    simError();
106 > #endif
107 >    
108 >    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
109 >    // Loop over the mesh faces
110 >    std::vector<Triangle>::iterator face;
111 >    std::vector<StuntDouble*>::iterator vertex;
112 >
113 >    // This will work in parallel because the triangles returned by the mesh
114 >    // have a NULL stuntDouble if this processor doesn't own the
115 >    
116 >    for (face = sMesh.begin(); face != sMesh.end(); ++face) {
117 >      Triangle thisTriangle = *face;
118 >      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
119 >      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
120 >        if ((*vertex) != NULL) {
121 >          bsResult.setBitOn((*vertex)->getGlobalIndex());          
122 >        }
123 >      }
124 >    }
125 >    return bsResult;
126 >  }
127 >
128 >  OpenMDBitSet HullFinder::findHull(int frame) {
129 >    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
130 >    OpenMDBitSet bsResult(nStuntDoubles_);
131 > #ifdef HAVE_QHULL
132 >    surfaceMesh_->computeHull(localSites_);
133 > #else
134 >    sprintf( painCave.errMsg,
135 >             "HullFinder : Hull calculation is not possible without libqhull.\n"
136 >             "\tPlease rebuild OpenMD with qhull enabled.");
137        painCave.severity = OPENMD_ERROR;
138        painCave.isFatal = 1;
139        simError();
# Line 108 | Line 145 | namespace OpenMD {
145      std::vector<Triangle>::iterator face;
146      std::vector<StuntDouble*>::iterator vertex;
147  
148 +    // This will work in parallel because the triangles returned by the mesh
149 +    // have a NULL stuntDouble if this processor doesn't own the
150 +    
151      for (face = sMesh.begin(); face != sMesh.end(); ++face) {
152        Triangle thisTriangle = *face;
153        std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();

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