--- trunk/src/applications/staticProps/NanoVolume.cpp	2008/10/15 18:26:01	1304
+++ trunk/src/applications/staticProps/NanoVolume.cpp	2013/06/16 15:15:42	1879
@@ -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.
@@ -37,27 +28,35 @@
  * 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, 234107 (2008).          
+ * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *
  *  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 1.8 2008-10-15 18:26:01 chuckv Exp $
+ *  @version $Id$
  *
  */
 
 #include "applications/staticProps/NanoVolume.hpp"
+#if defined(HAVE_QHULL)
 #include "math/ConvexHull.hpp"
-//#include "math/AlphaShape.hpp"
+#include "math/AlphaHull.hpp"
+#endif
 #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,
@@ -74,7 +73,7 @@ void NanoVolume::process() {
 }
 
 void NanoVolume::process() {
-#if defined(HAVE_CGAL) || defined(HAVE_QHULL)
+#if defined(HAVE_QHULL)
   Molecule* mol;
   Atom* atom;
   RigidBody* rb;
@@ -86,13 +85,8 @@ void NanoVolume::process() {
   Vector3d vec;
   int i,j;
 
-#ifdef HAVE_QHULL
-  ConvexHull* thishull = new ConvexHull();
-#endif
-#ifdef HAVE_CGAL
-  //  AlphaShape* hull = new AlphaShape();
-  ConvexHull* thishull = new ConvexHull();
-#endif
+   //ConvexHull* thishull = new ConvexHull();
+   AlphaHull* thishull = new AlphaHull(2.0);
 
   DumpReader reader(info_, dumpFilename_);
   int nFrames = reader.getNFrames();
@@ -158,10 +152,9 @@ void NanoVolume::process() {
   osq.close();
 */
 #else
-  sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n");
+  sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
   painCave.isFatal = 1;
   simError();  
-
 #endif
 
 }