ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/staticProps/NanoVolume.cpp
(Generate patch)

Comparing trunk/src/applications/staticProps/NanoVolume.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1402 by chuckv, Fri Jan 8 17:15:27 2010 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2006, 2009, 2010 The University of Notre Dame. All Rights Reserved.
2   *
3   * The University of Notre Dame grants you ("Licensee") a
4   * non-exclusive, royalty free, license to use, modify and
5   * redistribute this software in source and binary code form, provided
6   * that the following conditions are met:
7   *
8 < * 1. Acknowledgement of the program authors must be made in any
9 < *    publication of scientific results based in part on use of the
10 < *    program.  An acceptable form of acknowledgement is citation of
11 < *    the article in which the program was described (Matthew
12 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14 < *    Parallel Simulation Engine for Molecular Dynamics,"
15 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
16 < *
17 < * 2. Redistributions of source code must retain the above copyright
8 > * 1. Redistributions of source code must retain the above copyright
9   *    notice, this list of conditions and the following disclaimer.
10   *
11 < * 3. Redistributions in binary form must reproduce the above copyright
11 > * 2. Redistributions in binary form must reproduce the above copyright
12   *    notice, this list of conditions and the following disclaimer in the
13   *    documentation and/or other materials provided with the
14   *    distribution.
# Line 37 | Line 28
28   * University of Notre Dame has been advised of the possibility of
29   * such damages.
30   *
31 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
32 + * research, please cite the appropriate papers when you publish your
33 + * work.  Good starting points are:
34 + *                                                                      
35 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
36 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
37 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 + * [4]  Vardeman & Gezelter, in progress (2009).                        
39   *
40 + *
41   *  NanoVolume.cpp
42   *
43 – *  Purpose: To calculate convexhull, hull volume and radius
44 – *  using the CGAL library.
45 – *
43   *  Created by Charles F. Vardeman II on 14 Dec 2006.
44   *  @author  Charles F. Vardeman II
45 < *  @version $Id: NanoVolume.cpp,v 1.7 2008-09-14 01:32:23 chuckv Exp $
45 > *  @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $
46   *
47   */
48  
49   #include "applications/staticProps/NanoVolume.hpp"
50   #include "math/ConvexHull.hpp"
51 < //#include "math/AlphaShape.hpp"
51 > #include "math/AlphaHull.hpp"
52   #include "utils/simError.h"
53   #include "io/DumpReader.hpp"
54   #include "primitives/Molecule.hpp"
55   #include "utils/NumericConstant.hpp"
56  
57 < using namespace oopse;
57 > using namespace OpenMD;
58  
59   NanoVolume::NanoVolume(SimInfo* info,
60                         const std::string& filename,
# Line 74 | Line 71 | void NanoVolume::process() {
71   }
72  
73   void NanoVolume::process() {
74 < #if defined(HAVE_CGAL) || defined(HAVE_QHULL)
74 > #if defined(HAVE_QHULL)
75    Molecule* mol;
76    Atom* atom;
77    RigidBody* rb;
# Line 87 | Line 84 | void NanoVolume::process() {
84    int i,j;
85  
86   #ifdef HAVE_QHULL
87 <  ConvexHull* thishull = new ConvexHull();
87 >  // ConvexHull* thishull = new ConvexHull();
88 >  AlphaHull* thishull = new AlphaHull(2.0);
89   #endif
92 – #ifdef HAVE_CGAL
93 –  //  AlphaShape* hull = new AlphaShape();
94 –  ConvexHull* thishull = new ConvexHull();
95 – #endif
90  
91    DumpReader reader(info_, dumpFilename_);
92    int nFrames = reader.getNFrames();
# Line 123 | Line 117 | void NanoVolume::process() {
117      }
118      
119      // outer loop is over the selected StuntDoubles:
120 <    /*
120 >    
121      for (sd = seleMan_.beginSelected(i); sd != NULL;
122              sd = seleMan_.nextSelected(i)) {
123        
124 <      pos_.push_back(sd->getPos());
124 >     theAtoms_.push_back(sd);
125        myIndex = sd->getGlobalIndex();
126        
127      }
128 <    */
128 >    
129 >    /*
130      for (mol = info_->beginMolecule(mi); mol != NULL;
131                   mol = info_->nextMolecule(mi)) {
132                for (atom = mol->beginAtom(ai); atom != NULL;
# Line 139 | Line 134 | void NanoVolume::process() {
134                       theAtoms_.push_back(atom);
135                }
136              }
137 <    
137 >    */
138      // Generate convex hull for this frame.
139      thishull->computeHull(theAtoms_);
140    //  totalVolume_ += hull->getVolume();                
# Line 157 | Line 152 | void NanoVolume::process() {
152    osq.close();
153   */
154   #else
155 <  sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n");
155 >  sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
156    painCave.isFatal = 1;
157    simError();  
158  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines