--- trunk/src/applications/staticProps/NanoVolume.cpp	2007/09/17 20:11:47	1181
+++ trunk/src/applications/staticProps/NanoVolume.cpp	2010/01/08 17:15:27	1402
@@ -1,23 +1,14 @@
-/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
+/* Copyright (c) 2006, 2009, 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
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,41 +28,50 @@
  * University of Notre Dame has been advised of the possibility of
  * such damages.
  *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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).                        
  *
+ *
  *  NanoVolume.cpp
  *
- *  Purpose: To calculate convexhull, hull volume and radius
- *  using the CGAL library.
- *
  *  Created by Charles F. Vardeman II on 14 Dec 2006.
  *  @author  Charles F. Vardeman II
- *  @version $Id: NanoVolume.cpp,v 1.1 2007-09-17 20:11:47 chuckv Exp $
+ *  @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $
  *
  */
 
 #include "applications/staticProps/NanoVolume.hpp"
 #include "math/ConvexHull.hpp"
+#include "math/AlphaHull.hpp"
 #include "utils/simError.h"
 #include "io/DumpReader.hpp"
 #include "primitives/Molecule.hpp"
 #include "utils/NumericConstant.hpp"
 
-using namespace oopse;
+using namespace OpenMD;
 
 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()) {
     seleMan_.setSelectionSet(evaluator_.evaluate());
   }
+  frameCounter_ = 0;
+  totalVolume_ = 0.0;
 }
 
 void NanoVolume::process() {
-  
+#if defined(HAVE_QHULL)
   Molecule* mol;
   Atom* atom;
   RigidBody* rb;
@@ -83,13 +83,16 @@ void NanoVolume::process() {
   Vector3d vec;
   int i,j;
 
-  ConvexHull* hull = new ConvexHull();
+#ifdef HAVE_QHULL
+  // ConvexHull* thishull = new ConvexHull();
+  AlphaHull* thishull = new AlphaHull(2.0);
+#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);
@@ -97,7 +100,7 @@ void NanoVolume::process() {
     currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
     
     // Clear pos vector between each frame.
-    pos_.clear();
+    theAtoms_.clear();
     
     if (evaluator_.isDynamic()) {
       seleMan_.setSelectionSet(evaluator_.evaluate());
@@ -116,16 +119,43 @@ 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_);
-   // RealType hullVolume = hull->getVolume();
-		//std::cout <<"The volume for this hull is: "<< hullVolume << std::endl;
-		
+    thishull->computeHull(theAtoms_);
+  //  totalVolume_ += hull->getVolume();		
   }
+  //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: qhull support was not compiled in!\n");
+  painCave.isFatal = 1;
+  simError();  
+
+#endif
+
 }