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Comparing trunk/src/applications/staticProps/GofRAngle.cpp (file contents):
Revision 356 by tim, Wed Feb 16 21:00:39 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)
49 >  GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
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 <
56 <    histogram_.resize(nRBins_);
57 <    avgGofr_.resize(nRBins_);
58 <    for (int i = 0 ; i < nRBins_; ++i) {
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) {
58          histogram_[i].resize(nAngleBins_);
59          avgGofr_[i].resize(nAngleBins_);
60 +      }
61      }
62 – }
62  
63  
64 < void GofRAngle::preProcess() {
66 <
64 >  void GofRAngle::preProcess() {
65      for (int i = 0; i < avgGofr_.size(); ++i) {
66 <        std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
66 >      std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
67      }
68 < }
68 >  }
69  
70 < void GofRAngle::initalizeHistogram() {
70 >  void GofRAngle::initalizeHistogram() {
71      npairs_ = 0;
72 <    for (int i = 0; i < histogram_.size(); ++i)
73 <        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
74 < }
72 >    for (int i = 0; i < histogram_.size(); ++i){
73 >      std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
74 >    }
75 >  }
76  
77 <
79 < void GofRAngle::processHistogram() {
80 <
77 >  void GofRAngle::processHistogram() {
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;    
92 <        }
90 >      for (int j = 0; j < histogram_[i].size(); ++j){
91 >        avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
92 >      }
93      }
94  
95 < }
95 >  }
96  
97 < void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
97 >  void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
98  
99      if (sd1 == sd2) {
100 <        return;
100 >      return;
101      }
105 –    
102      Vector3d pos1 = sd1->getPos();
103      Vector3d pos2 = sd2->getPos();
104 <    Vector3d r12 = pos1 - pos2;
105 <    currentSnapshot_->wrapVector(r12);
104 >    Vector3d r12 = pos2 - pos1;
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;
114 <        int whichThetaBin = halfBin * (cosAngle + 1.0);
115 <        ++histogram_[whichRBin][whichThetaBin];
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          
118 <        ++npairs_;
118 >      ++npairs_;
119      }
120 < }
120 >  }
121  
122 < void GofRAngle::writeRdf() {
122 >  void GofRAngle::writeRdf() {
123      std::ofstream rdfStream(outputFilename_.c_str());
124      if (rdfStream.is_open()) {
125 <        rdfStream << "#radial distribution function\n";
126 <        rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
127 <        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
128 <        rdfStream << "#r\tcorrValue\n";
129 <        for (int i = 0; i < avgGofr_.size(); ++i) {
130 <            double r = deltaR_ * (i + 0.5);
125 >      rdfStream << "#radial distribution function\n";
126 >      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
127 >      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
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 >        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_;
135 <                rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
136 <            }
137 <        }
133 >        for(int j = 0; j < avgGofr_[i].size(); ++j) {
134 >          RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
135 >          rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
136 >        }
137 >
138 >        rdfStream << "\n";
139 >      }
140          
141      } else {
142 <
143 <
142 >      sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
143 >      painCave.isFatal = 1;
144 >      simError();  
145      }
146  
147      rdfStream.close();
148 < }
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 = pos1 - pos2;
154 <    currentSnapshot_->wrapVector(r12);
153 >    Vector3d r12 = pos2 - pos1;
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 < }
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 = sd1->getElectroFrame().getColumn(2);    
166 >    Vector3d v2 = sd2->getElectroFrame().getColumn(2);    
167      v1.normalize();
168      v2.normalize();
169      return dot(v1, v2);
170 < }
170 >  }
171  
172  
173   }

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