--- trunk/src/math/ConvexHull.cpp	2010/02/24 15:22:03	1410
+++ branches/development/src/math/ConvexHull.cpp	2013/01/09 19:27:52	1825
@@ -1,4 +1,4 @@
-/* Copyright (c) 2008, 2009, 2010 The University of Notre Dame. All Rights Reserved.
+/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
@@ -35,16 +35,16 @@
  * [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).                        
+ * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *
- *
  *  ConvexHull.cpp
  *
  *  Purpose: To calculate convexhull, hull volume libqhull.
  *
  *  Created by Charles F. Vardeman II on 11 Dec 2006.
  *  @author  Charles F. Vardeman II
- *  @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $
+ *  @version $Id$
  *
  */
 
@@ -62,20 +62,10 @@
 #include <mpi.h>
 #endif
 
-using namespace OpenMD;
+#include "math/qhull.hpp"
 
 #ifdef HAVE_QHULL
-extern "C"
-{
-#include <qhull/qhull.h>
-#include <qhull/mem.h>
-#include <qhull/qset.h>
-#include <qhull/geom.h>
-#include <qhull/merge.h>
-#include <qhull/poly.h>
-#include <qhull/io.h>
-#include <qhull/stat.h>
-}
+using namespace OpenMD;
 
 ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
 }
@@ -90,13 +80,14 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
   facetT *facet;
   setT *vertices;
   int curlong, totlong;
-  pointT *intPoint;
+  // pointT *intPoint;
   
   std::vector<double> ptArray(numpoints*dim_);
 
   // Copy the positon vector into a points vector for qhull.
   std::vector<StuntDouble*>::iterator SD;
   int i = 0;
+
   for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
     Vector3d pos = (*SD)->getPos();      
     ptArray[dim_ * i] = pos.x();
@@ -105,12 +96,14 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
     i++;
   }
   
+  /* Clean up memory from previous convex hull calculations */
   boolT ismalloc = False;
-  /* Clean up memory from previous convex hull calculations*/
   
+  /* compute the hull for our local points (or all the points for single
+     processor versions) */
   if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
-
+    
     sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
     painCave.isFatal = 1;
     simError();
@@ -194,9 +187,13 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
   // Free previous hull
   qh_freeqhull(!qh_ALL);
   qh_memfreeshort(&curlong, &totlong);
-  if (curlong || totlong)
-    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
-	      << totlong << curlong << std::endl;
+  if (curlong || totlong) {
+    sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
+            "\tdid not free %d bytes of long memory (%d pieces)", 
+            totlong, curlong);
+    painCave.isFatal = 1;
+    simError();
+  }
   
   if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
                    const_cast<char *>(options_.c_str()), NULL, stderr)){
@@ -208,8 +205,9 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
   } //qh_new_qhull
 
 #endif
-  intPoint = qh interior_point;
-  RealType calcvol = 0.0;
+  // commented out below, so comment out here also.
+  // intPoint = qh interior_point;
+  // RealType calcvol = 0.0;
   FORALLfacets {  
     Triangle face;
     //Qhull sets the unit normal in facet->normal
@@ -260,10 +258,7 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
       vel = bodydoubles[id]->getVel();
       mass = bodydoubles[id]->getMass();
       face.addVertexSD(bodydoubles[id]);      
-
-
-#endif
-	
+#endif	
       faceVel = faceVel + vel;
       faceMass = faceMass + mass;
       ver++;      
@@ -271,7 +266,7 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
 
     face.addVertices(p[0], p[1], p[2]);
     face.setFacetMass(faceMass);
-    face.setFacetVelocity(faceVel/3.0);
+    face.setFacetVelocity(faceVel / RealType(3.0));
     /*
     RealType comparea = face.computeArea();
     realT calcarea = qh_facetarea (facet);
@@ -292,9 +287,13 @@ void ConvexHull::computeHull(std::vector<StuntDouble*>
   //  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl; 
   qh_freeqhull(!qh_ALL);
   qh_memfreeshort(&curlong, &totlong);
-  if (curlong || totlong)
-    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
-              << totlong << curlong << std::endl;    
+  if (curlong || totlong) {
+    sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
+            "\tdid not free %d bytes of long memory (%d pieces)", 
+            totlong, curlong);
+    painCave.isFatal = 1;
+    simError();
+  }
 }
 
 void ConvexHull::printHull(const std::string& geomFileName) {