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root/OpenMD/trunk/src/applications/staticProps/GofR.cpp
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Comparing trunk/src/applications/staticProps/GofR.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <algorithm>
# Line 44 | Line 44
44   #include "applications/staticProps/GofR.hpp"
45   #include "utils/simError.h"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49 <  GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
49 >  GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
50      : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
51  
52        deltaR_ = len_ /nRBins_;
# Line 70 | Line 70 | namespace oopse {
70    void GofR::processHistogram() {
71  
72      int nPairs = getNPairs();
73 <    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
74 <    double pairDensity = nPairs /volume * 2.0;
75 <    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
73 >    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
74 >    RealType pairDensity = nPairs /volume * 2.0;
75 >    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
76  
77      for(int i = 0 ; i < histogram_.size(); ++i){
78  
79 <      double rLower = i * deltaR_;
80 <      double rUpper = rLower + deltaR_;
81 <      double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
82 <      double nIdeal = volSlice * pairConstant;
79 >      RealType rLower = i * deltaR_;
80 >      RealType rUpper = rLower + deltaR_;
81 >      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
82 >      RealType nIdeal = volSlice * pairConstant;
83  
84        avgGofr_[i] += histogram_[i] / nIdeal;    
85      }
# Line 95 | Line 95 | namespace oopse {
95      Vector3d pos1 = sd1->getPos();
96      Vector3d pos2 = sd2->getPos();
97      Vector3d r12 = pos2 - pos1;
98 <    currentSnapshot_->wrapVector(r12);
98 >    if (usePeriodicBoundaryConditions_)
99 >      currentSnapshot_->wrapVector(r12);
100  
101 <    double distance = r12.length();
101 >    RealType distance = r12.length();
102  
103      if (distance < len_) {
104        int whichBin = distance / deltaR_;
# Line 114 | Line 115 | namespace oopse {
115        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
116        rdfStream << "#r\tcorrValue\n";
117        for (int i = 0; i < avgGofr_.size(); ++i) {
118 <        double r = deltaR_ * (i + 0.5);
118 >        RealType r = deltaR_ * (i + 0.5);
119          rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
120        }
121          

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