--- trunk/src/selection/HullFinder.cpp	2010/04/22 19:44:57	1439
+++ trunk/src/selection/HullFinder.cpp	2013/06/17 18:28:30	1880
@@ -35,8 +35,9 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include "selection/HullFinder.hpp"
@@ -52,7 +53,7 @@ namespace OpenMD {
     
     SimInfo::MoleculeIterator mi;
     Molecule* mol;
-    StuntDouble* integrableObject;
+    StuntDouble* sd;
     Molecule::IntegrableObjectIterator  ioi;
     Molecule::AtomIterator ai;
     Atom* atom;
@@ -63,10 +64,10 @@ namespace OpenMD {
          mol = info_->nextMolecule(mi)) {
         
       // Hull is constructed from all known integrable objects.
-      for (integrableObject = mol->beginIntegrableObject(ioi);
-           integrableObject != NULL;
-           integrableObject = mol->nextIntegrableObject(ioi)) {
-        localSites_.push_back(integrableObject);
+      for (sd = mol->beginIntegrableObject(ioi);
+           sd != NULL;
+           sd = mol->nextIntegrableObject(ioi)) {
+        localSites_.push_back(sd);
       }
       
       // selection can include atoms (which may be a subset of the IOs)
@@ -87,27 +88,64 @@ namespace OpenMD {
 #endif
   }
 
+  HullFinder::~HullFinder() {
+    delete surfaceMesh_;
+  }
+
   OpenMDBitSet HullFinder::findHull() {
-    StuntDouble* sd;
-    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
     OpenMDBitSet bsResult(nStuntDoubles_);
 #ifdef HAVE_QHULL
     surfaceMesh_->computeHull(localSites_);
 #else
     sprintf( painCave.errMsg,
-             "Hullfinder error: Hull calculation not possible without libqhull.\n",
-              "Please rebuild with Qhull");
+             "HullFinder : Hull calculation is not possible without libqhull.\n"
+             "\tPlease rebuild OpenMD with qhull enabled.");
+    painCave.severity = OPENMD_ERROR;
+    painCave.isFatal = 1;
+    simError();
+#endif
+    
+    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
+    // Loop over the mesh faces
+    std::vector<Triangle>::iterator face;
+    std::vector<StuntDouble*>::iterator vertex;
+
+    // This will work in parallel because the triangles returned by the mesh
+    // have a NULL stuntDouble if this processor doesn't own the 
+    
+    for (face = sMesh.begin(); face != sMesh.end(); ++face) {
+      Triangle thisTriangle = *face;
+      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
+      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
+        if ((*vertex) != NULL) {
+          bsResult.setBitOn((*vertex)->getGlobalIndex());          
+        }
+      }
+    }
+    return bsResult;
+  }
+
+  OpenMDBitSet HullFinder::findHull(int frame) {
+    OpenMDBitSet bsResult(nStuntDoubles_);
+#ifdef HAVE_QHULL
+    surfaceMesh_->computeHull(localSites_);
+#else
+    sprintf( painCave.errMsg,
+             "HullFinder : Hull calculation is not possible without libqhull.\n"
+             "\tPlease rebuild OpenMD with qhull enabled.");
       painCave.severity = OPENMD_ERROR;
       painCave.isFatal = 1;
       simError();
 #endif
     
     std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
-    int nTriangles = sMesh.size();
     // Loop over the mesh faces
     std::vector<Triangle>::iterator face;
     std::vector<StuntDouble*>::iterator vertex;
 
+    // This will work in parallel because the triangles returned by the mesh
+    // have a NULL stuntDouble if this processor doesn't own the 
+    
     for (face = sMesh.begin(); face != sMesh.end(); ++face) {
       Triangle thisTriangle = *face;
       std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();