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Comparing trunk/src/applications/staticProps/GofR.cpp (file contents):
Revision 306 by tim, Wed Feb 9 17:08:22 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>
43   #include <fstream>
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)
50 <    : RadialDistrFunc(info, filename, sele1, sele2, len){
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 <    histogram_.resize(nbins_);
53 <    avgGofr_.resize(nbins_);
54 < }
52 >      deltaR_ = len_ /nRBins_;
53 >    
54 >      histogram_.resize(nRBins_);
55 >      avgGofr_.resize(nRBins_);
56  
57 +      setOutputName(getPrefix(filename) + ".gofr");
58 +    }
59  
60 < void GofR::preProcess() {
61 <    avgGofr_.resize(nbins_);
60 >
61 >  void GofR::preProcess() {
62      std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);    
63 < }
63 >  }
64  
65 < void GofR::initalizeHistogram() {
62 <    npairs_ = 0;
65 >  void GofR::initalizeHistogram() {
66      std::fill(histogram_.begin(), histogram_.end(), 0);
67 < }
67 >  }
68  
69  
70 < void GofR::processHistogram() {
70 >  void GofR::processHistogram() {
71  
72 <    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
73 <    double pairDensity = npairs_ /volume;
74 <    double pairConstant = ( 4.0 * PI * pairDensity ) / 3.0;
72 >    int nPairs = getNPairs();
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 * delta_;
80 <        double rUpper = rLower + delta_;
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;    
84 >      avgGofr_[i] += histogram_[i] / nIdeal;    
85      }
86  
87 < }
87 >  }
88  
89 < void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
89 >  void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
90  
91      if (sd1 == sd2) {
92 <        return;
92 >      return;
93      }
94      
95      Vector3d pos1 = sd1->getPos();
96      Vector3d pos2 = sd2->getPos();
97 <    Vector3d r12 = pos1 - pos2;
98 <    
99 <    double distance = (pos1 - pos2).length();
97 >    Vector3d r12 = pos2 - pos1;
98 >    if (usePeriodicBoundaryConditions_)
99 >      currentSnapshot_->wrapVector(r12);
100  
101 <    int whichBin = distance / delta_;
98 <    histogram_[whichBin] ++;
99 <    npairs_++;
100 < }
101 >    RealType distance = r12.length();
102  
103 +    if (distance < len_) {
104 +      int whichBin = distance / deltaR_;
105 +      histogram_[whichBin] += 2;
106 +    }
107 +  }
108  
109 < void GofR::writeRdf() {
109 >
110 >  void GofR::writeRdf() {
111      std::ofstream rdfStream(outputFilename_.c_str());
112      if (rdfStream.is_open()) {
113 <        rdfStream << "#radial distribution function\n";
114 <        rdfStream << "#selection1: " << selectionScript1_;
115 <        rdfStream << "#selection2: " << selectionScript2_;
113 >      rdfStream << "#radial distribution function\n";
114 >      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
115 >      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
116 >      rdfStream << "#r\tcorrValue\n";
117 >      for (int i = 0; i < avgGofr_.size(); ++i) {
118 >        RealType r = deltaR_ * (i + 0.5);
119 >        rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
120 >      }
121          
122      } else {
123  
124 <
124 >      sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str());
125 >      painCave.isFatal = 1;
126 >      simError();  
127      }
114 – }
128  
129 +    rdfStream.close();
130 +  }
131 +
132   }
133  

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