--- trunk/src/applications/staticProps/NanoVolume.cpp	2007/11/22 16:39:45	1188
+++ trunk/src/applications/staticProps/NanoVolume.cpp	2008/10/15 18:26:01	1304
@@ -45,12 +45,13 @@
  *
  *  Created by Charles F. Vardeman II on 14 Dec 2006.
  *  @author  Charles F. Vardeman II
- *  @version $Id: NanoVolume.cpp,v 1.2 2007-11-22 16:39:44 chuckv Exp $
+ *  @version $Id: NanoVolume.cpp,v 1.8 2008-10-15 18:26:01 chuckv Exp $
  *
  */
 
 #include "applications/staticProps/NanoVolume.hpp"
 #include "math/ConvexHull.hpp"
+//#include "math/AlphaShape.hpp"
 #include "utils/simError.h"
 #include "io/DumpReader.hpp"
 #include "primitives/Molecule.hpp"
@@ -62,7 +63,7 @@ NanoVolume::NanoVolume(SimInfo* info,
                        const std::string& filename,
                        const std::string& sele)
   : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
-  setOutputName(getPrefix(filename) + ".off");
+  setOutputName(getPrefix(filename) + ".avol");
   
   evaluator_.loadScriptString(sele);
   if (!evaluator_.isDynamic()) {
@@ -73,7 +74,7 @@ void NanoVolume::process() {
 }
 
 void NanoVolume::process() {
-  
+#if defined(HAVE_CGAL) || defined(HAVE_QHULL)
   Molecule* mol;
   Atom* atom;
   RigidBody* rb;
@@ -85,13 +86,19 @@ void NanoVolume::process() {
   Vector3d vec;
   int i,j;
 
-  ConvexHull* hull = new ConvexHull();
+#ifdef HAVE_QHULL
+  ConvexHull* thishull = new ConvexHull();
+#endif
+#ifdef HAVE_CGAL
+  //  AlphaShape* hull = new AlphaShape();
+  ConvexHull* thishull = new ConvexHull();
+#endif
 
   DumpReader reader(info_, dumpFilename_);
   int nFrames = reader.getNFrames();
   frameCounter_ = 0;
 
-  pos_.reserve(info_->getNGlobalAtoms());
+  theAtoms_.reserve(info_->getNGlobalAtoms());
 
   for (int istep = 0; istep < nFrames; istep += step_) {
     reader.readFrame(istep);
@@ -99,7 +106,7 @@ void NanoVolume::process() {
     currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
     
     // Clear pos vector between each frame.
-    pos_.clear();
+    theAtoms_.clear();
     
     if (evaluator_.isDynamic()) {
       seleMan_.setSelectionSet(evaluator_.evaluate());
@@ -118,16 +125,43 @@ void NanoVolume::process() {
     // outer loop is over the selected StuntDoubles:
     
     for (sd = seleMan_.beginSelected(i); sd != NULL;
-	 sd = seleMan_.nextSelected(i)) {
+	    sd = seleMan_.nextSelected(i)) {
       
-      pos_.push_back(sd->getPos());
+     theAtoms_.push_back(sd);
       myIndex = sd->getGlobalIndex();
       
     }
+    
+    /*
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+                 mol = info_->nextMolecule(mi)) {
+              for (atom = mol->beginAtom(ai); atom != NULL; 
+                   atom = mol->nextAtom(ai)) {
+                     theAtoms_.push_back(atom);
+              }
+            }
+    */
     // Generate convex hull for this frame.
-    hull->genHull(pos_);
-    totalVolume_ += hull->getVolume();		
+    thishull->computeHull(theAtoms_);
+  //  totalVolume_ += hull->getVolume();		
   }
-  RealType avgVolume = totalVolume_/(RealType) frameCounter_;
-  std::cout << avgVolume << std::endl;
+  //RealType avgVolume = totalVolume_/(RealType) frameCounter_;
+  //std::cout.precision(7);
+  //std::cout  << avgVolume << std::endl;
+/*
+  std::ofstream osq(getOutputFileName().c_str());
+  osq.precision(7);
+  if (osq.is_open()){
+      osq << avgVolume << std::endl;
+
+  }
+  osq.close();
+*/
+#else
+  sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n");
+  painCave.isFatal = 1;
+  simError();  
+
+#endif
+
 }