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Comparing trunk/src/applications/staticProps/NanoVolume.cpp (file contents):
Revision 1195 by cpuglis, Thu Dec 6 20:04:02 2007 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 1.4 2007-12-06 20:04:01 cpuglis 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/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 73 | Line 71 | void NanoVolume::process() {
71   }
72  
73   void NanoVolume::process() {
74 < #if defined(HAVE_CGAL)
74 > #if defined(HAVE_QHULL)
75    Molecule* mol;
76    Atom* atom;
77    RigidBody* rb;
# Line 85 | Line 83 | void NanoVolume::process() {
83    Vector3d vec;
84    int i,j;
85  
86 <  ConvexHull* hull = new ConvexHull();
86 > #ifdef HAVE_QHULL
87 >  // ConvexHull* thishull = new ConvexHull();
88 >  AlphaHull* thishull = new AlphaHull(2.0);
89 > #endif
90  
91    DumpReader reader(info_, dumpFilename_);
92    int nFrames = reader.getNFrames();
93    frameCounter_ = 0;
94  
95 <  pos_.reserve(info_->getNGlobalAtoms());
95 >  theAtoms_.reserve(info_->getNGlobalAtoms());
96  
97    for (int istep = 0; istep < nFrames; istep += step_) {
98      reader.readFrame(istep);
# Line 99 | Line 100 | void NanoVolume::process() {
100      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
101      
102      // Clear pos vector between each frame.
103 <    pos_.clear();
103 >    theAtoms_.clear();
104      
105      if (evaluator_.isDynamic()) {
106        seleMan_.setSelectionSet(evaluator_.evaluate());
# Line 118 | Line 119 | void NanoVolume::process() {
119      // outer loop is over the selected StuntDoubles:
120      
121      for (sd = seleMan_.beginSelected(i); sd != NULL;
122 <         sd = seleMan_.nextSelected(i)) {
122 >            sd = seleMan_.nextSelected(i)) {
123        
124 <      pos_.push_back(sd->getPos());
124 >     theAtoms_.push_back(sd);
125        myIndex = sd->getGlobalIndex();
126        
127      }
128 +    
129 +    /*
130 +    for (mol = info_->beginMolecule(mi); mol != NULL;
131 +                 mol = info_->nextMolecule(mi)) {
132 +              for (atom = mol->beginAtom(ai); atom != NULL;
133 +                   atom = mol->nextAtom(ai)) {
134 +                     theAtoms_.push_back(atom);
135 +              }
136 +            }
137 +    */
138      // Generate convex hull for this frame.
139 <    hull->genHull(pos_);
140 <    totalVolume_ += hull->getVolume();          
139 >    thishull->computeHull(theAtoms_);
140 >  //  totalVolume_ += hull->getVolume();                
141    }
142 <  RealType avgVolume = totalVolume_/(RealType) frameCounter_;
142 >  //RealType avgVolume = totalVolume_/(RealType) frameCounter_;
143    //std::cout.precision(7);
144    //std::cout  << avgVolume << std::endl;
145 <
145 > /*
146    std::ofstream osq(getOutputFileName().c_str());
147    osq.precision(7);
148    if (osq.is_open()){
# Line 139 | Line 150 | void NanoVolume::process() {
150  
151    }
152    osq.close();
153 + */
154   #else
155 <  sprintf(painCave.errMsg, "NanoVolume: CGAL support was not compiled in!\n");
155 >  sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
156    painCave.isFatal = 1;
157    simError();  
158 +
159   #endif
160 +
161   }

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