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Comparing trunk/src/applications/staticProps/BondAngleDistribution.cpp (file contents):
Revision 1180 by chuckv, Mon Sep 17 20:05:51 2007 UTC vs.
Revision 1919 by jmarr, Wed Jul 31 18:03:35 2013 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 38 | Line 29
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31   *
32 < *  BondAngleDistribution.cpp
33 < *  OOPSE-4
34 < *
32 > * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 > * research, please cite the appropriate papers when you publish your
34 > * work.  Good starting points are:
35 > *                                                                      
36 > * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 > * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41   *  Created by J. Daniel Gezelter on 07/27/07.
42   *  @author  J. Daniel Gezelter
43 < *  @version $Id: BondAngleDistribution.cpp,v 1.1 2007-09-17 20:05:51 chuckv Exp $
43 > *  @version $Id$
44   *
45   */
46  
# Line 53 | Line 50
50   #include "primitives/Molecule.hpp"
51   #include "utils/NumericConstant.hpp"
52  
53 < namespace oopse {
53 > using namespace std;
54 > namespace OpenMD {
55  
56    BondAngleDistribution::BondAngleDistribution(SimInfo* info,
57 <                                              const std::string& filename,
58 <                                              const std::string& sele,
59 <                                              double rCut, int nbins) : StaticAnalyser(info, filename),
60 <                                              selectionScript_(sele),
61 <                                                                evaluator_(info), seleMan_(info){
57 >                                               const string& filename,
58 >                                               const string& sele,
59 >                                               double rCut, int nbins)
60 >  : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info),
61 >    seleMan_(info) {
62      
63      setOutputName(getPrefix(filename) + ".bad");
64      
# Line 84 | Line 82 | namespace oopse {
82      histogram_.clear();
83    }
84    
85 <  void BondAngleDistribution::initalizeHistogram() {
85 >  void BondAngleDistribution::initializeHistogram() {
86      for (int bin = 0; bin < nBins_; bin++) {      
87        histogram_[bin] = 0;
88      }
# Line 101 | Line 99 | namespace oopse {
99      StuntDouble* sd;
100      Vector3d vec;
101      std::vector<Vector3d> bondvec;
102 <    std::vector<RealType> bonddist;
103 <    RealType costheta;
104 <    RealType r;
107 <    RealType dist;
102 >    RealType r;    
103 >    int nBonds;    
104 >    int i;
105      
109 –    int nBonds;
110 –    
111 –    int i, j;
112 –    
106      DumpReader reader(info_, dumpFilename_);    
107      int nFrames = reader.getNFrames();
108      frameCounter_ = 0;
# Line 181 | Line 174 | namespace oopse {
174                Vector3d vec2 = bondvec[j];
175                
176                vec2.normalize();
177 <            
177 >              
178                RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI;
186 –              
179                
180 +              
181                if (theta > 180.0){
182                  theta = 360.0 - theta;
183                }
184 <              int whichBin = theta/deltaTheta_;
184 >              int whichBin = int(theta/deltaTheta_);
185                
186                histogram_[whichBin] += 2;
187              }

Comparing trunk/src/applications/staticProps/BondAngleDistribution.cpp (property svn:keywords):
Revision 1180 by chuckv, Mon Sep 17 20:05:51 2007 UTC vs.
Revision 1919 by jmarr, Wed Jul 31 18:03:35 2013 UTC

# Line 0 | Line 1
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