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root/OpenMD/trunk/src/applications/staticProps/NanoVolume.cpp
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Comparing trunk/src/applications/staticProps/NanoVolume.cpp (file contents):
Revision 1207 by chuckv, Tue Jan 8 19:36:28 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 5 | Line 5
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 1.6 2008-01-08 19:36:28 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"
54 – #include "math/AlphaShape.hpp"
51   #include "utils/simError.h"
52   #include "io/DumpReader.hpp"
53   #include "primitives/Molecule.hpp"
54   #include "utils/NumericConstant.hpp"
55  
56 < using namespace oopse;
56 > using namespace OpenMD;
57  
58   NanoVolume::NanoVolume(SimInfo* info,
59                         const std::string& filename,
# Line 74 | Line 70 | void NanoVolume::process() {
70   }
71  
72   void NanoVolume::process() {
73 < #if defined(HAVE_CGAL) || defined(HAVE_QHULL)
73 > #if defined(HAVE_QHULL)
74    Molecule* mol;
75    Atom* atom;
76    RigidBody* rb;
# Line 87 | Line 83 | void NanoVolume::process() {
83    int i,j;
84  
85   #ifdef HAVE_QHULL
86 <  ConvexHull* hull = new ConvexHull();
86 >  ConvexHull* thishull = new ConvexHull();
87   #endif
92 – #ifdef HAVE_CGAL
93 –  AlphaShape* hull = new AlphaShape();
94 – #endif
88  
89    DumpReader reader(info_, dumpFilename_);
90    int nFrames = reader.getNFrames();
91    frameCounter_ = 0;
92  
93 <  pos_.reserve(info_->getNGlobalAtoms());
93 >  theAtoms_.reserve(info_->getNGlobalAtoms());
94  
95    for (int istep = 0; istep < nFrames; istep += step_) {
96      reader.readFrame(istep);
# Line 105 | Line 98 | void NanoVolume::process() {
98      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
99      
100      // Clear pos vector between each frame.
101 <    pos_.clear();
101 >    theAtoms_.clear();
102      
103      if (evaluator_.isDynamic()) {
104        seleMan_.setSelectionSet(evaluator_.evaluate());
# Line 124 | Line 117 | void NanoVolume::process() {
117      // outer loop is over the selected StuntDoubles:
118      
119      for (sd = seleMan_.beginSelected(i); sd != NULL;
120 <         sd = seleMan_.nextSelected(i)) {
120 >            sd = seleMan_.nextSelected(i)) {
121        
122 <      pos_.push_back(sd->getPos());
122 >     theAtoms_.push_back(sd);
123        myIndex = sd->getGlobalIndex();
124        
125      }
126 +    
127 +    /*
128 +    for (mol = info_->beginMolecule(mi); mol != NULL;
129 +                 mol = info_->nextMolecule(mi)) {
130 +              for (atom = mol->beginAtom(ai); atom != NULL;
131 +                   atom = mol->nextAtom(ai)) {
132 +                     theAtoms_.push_back(atom);
133 +              }
134 +            }
135 +    */
136      // Generate convex hull for this frame.
137 <    hull->genHull(pos_);
137 >    thishull->computeHull(theAtoms_);
138    //  totalVolume_ += hull->getVolume();                
139    }
140    //RealType avgVolume = totalVolume_/(RealType) frameCounter_;
# Line 147 | Line 150 | void NanoVolume::process() {
150    osq.close();
151   */
152   #else
153 <  sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n");
153 >  sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
154    painCave.isFatal = 1;
155    simError();  
156  

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