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Comparing trunk/src/applications/staticProps/GofRAngle.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/GofRAngle.hpp"
45   #include "utils/simError.h"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
50 <                       const std::string& sele2, double len, int nrbins, int nangleBins)
50 >                       const std::string& sele2, RealType len, int nrbins, int nangleBins)
51      : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
52  
53 <      deltaR_ = len_ /nRBins_;            
54 <      deltaCosAngle_ = 2.0 / nAngleBins_;    
55 <
53 >      deltaR_ = len_ /(double) nRBins_;
54 >      deltaCosAngle_ = 2.0 / (double)nAngleBins_;    
55        histogram_.resize(nRBins_);
56        avgGofr_.resize(nRBins_);
57        for (int i = 0 ; i < nRBins_; ++i) {
# Line 63 | Line 62 | namespace oopse {
62  
63  
64    void GofRAngle::preProcess() {
66 –
65      for (int i = 0; i < avgGofr_.size(); ++i) {
66        std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
67      }
# Line 71 | Line 69 | namespace oopse {
69  
70    void GofRAngle::initalizeHistogram() {
71      npairs_ = 0;
72 <    for (int i = 0; i < histogram_.size(); ++i)
72 >    for (int i = 0; i < histogram_.size(); ++i){
73        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
74 +    }
75    }
76  
78 –
77    void GofRAngle::processHistogram() {
80 –
78      int nPairs = getNPairs();
79 <    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
80 <    double pairDensity = nPairs /volume;
81 <    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
79 >    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
80 >    RealType pairDensity = nPairs /volume;
81 >    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
82  
83      for(int i = 0 ; i < histogram_.size(); ++i){
84  
85 <      double rLower = i * deltaR_;
86 <      double rUpper = rLower + deltaR_;
87 <      double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
88 <      double nIdeal = volSlice * pairConstant;
85 >      RealType rLower = i * deltaR_;
86 >      RealType rUpper = rLower + deltaR_;
87 >      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
88 >      RealType nIdeal = volSlice * pairConstant;
89  
90        for (int j = 0; j < histogram_[i].size(); ++j){
91          avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
# Line 102 | Line 99 | namespace oopse {
99      if (sd1 == sd2) {
100        return;
101      }
105 –    
102      Vector3d pos1 = sd1->getPos();
103      Vector3d pos2 = sd2->getPos();
104      Vector3d r12 = pos2 - pos1;
105 <    currentSnapshot_->wrapVector(r12);
105 >    if (usePeriodicBoundaryConditions_)
106 >      currentSnapshot_->wrapVector(r12);
107  
108 <    double distance = r12.length();
108 >    RealType distance = r12.length();
109      int whichRBin = distance / deltaR_;
110  
111      if (distance <= len_) {
112 <      double cosAngle = evaluateAngle(sd1, sd2);
113 <      double halfBin = (nAngleBins_ - 1) * 0.5;
112 >
113 >      RealType cosAngle = evaluateAngle(sd1, sd2);
114 >      RealType halfBin = (nAngleBins_ - 1) * 0.5;
115        int whichThetaBin = halfBin * (cosAngle + 1.0);
116        ++histogram_[whichRBin][whichThetaBin];
117          
# Line 130 | Line 128 | namespace oopse {
128        rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
129        rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
130        for (int i = 0; i < avgGofr_.size(); ++i) {
131 <        double r = deltaR_ * (i + 0.5);
131 >        RealType r = deltaR_ * (i + 0.5);
132  
133          for(int j = 0; j < avgGofr_[i].size(); ++j) {
134 <          double cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
134 >          RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
135            rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
136          }
137  
# Line 149 | Line 147 | namespace oopse {
147      rdfStream.close();
148    }
149  
150 <  double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
150 >  RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
151      Vector3d pos1 = sd1->getPos();
152      Vector3d pos2 = sd2->getPos();
153      Vector3d r12 = pos2 - pos1;
154 <    currentSnapshot_->wrapVector(r12);
154 >  
155 >    if (usePeriodicBoundaryConditions_)
156 >      currentSnapshot_->wrapVector(r12);
157 >
158      r12.normalize();
159      Vector3d dipole = sd1->getElectroFrame().getColumn(2);
160      dipole.normalize();    
161      return dot(r12, dipole);
162    }
163  
164 <  double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
164 >  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
165      Vector3d v1 = sd1->getElectroFrame().getColumn(2);
166      Vector3d v2 = sd2->getElectroFrame().getColumn(2);    
167      v1.normalize();

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