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root/OpenMD/trunk/src/applications/staticProps/GofAngle2.cpp
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Comparing trunk/src/applications/staticProps/GofAngle2.cpp (file contents):
Revision 311 by tim, Thu Feb 10 22:37:21 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/GofAngle2.hpp"
45   #include "utils/simError.h"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49 < GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50 <    : RadialDistrFunc(info, filename, sele1, sele2){
51 <    setOutputName(getPrefix(filename) + ".gto");
49 >  GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
50 >                       const std::string& sele2, int nangleBins)
51 >    : RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {
52  
53 < }
53 >      setOutputName(getPrefix(filename) + ".gto");
54  
55 +      deltaCosAngle_ = 2.0 / nAngleBins_;
56  
57 < void GofAngle2::preProcess() {
57 >      histogram_.resize(nAngleBins_);
58 >      avgGofr_.resize(nAngleBins_);
59 >      for (int i = 0 ; i < nAngleBins_; ++i) {
60 >        histogram_[i].resize(nAngleBins_);
61 >        avgGofr_[i].resize(nAngleBins_);
62 >      }    
63  
64 +    }
65 +
66 +
67 +  void GofAngle2::preProcess() {
68 +
69      for (int i = 0; i < avgGofr_.size(); ++i) {
70 <        std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
70 >      std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
71      }
72 < }
72 >  }
73  
74 < void GofAngle2::initalizeHistogram() {
74 >  void GofAngle2::initalizeHistogram() {
75      npairs_ = 0;
76      for (int i = 0; i < histogram_.size(); ++i)
77 <        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
78 < }
77 >      std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
78 >  }
79  
80  
81 < void GofAngle2::processHistogram() {
81 >  void GofAngle2::processHistogram() {
82  
83      //std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)
84  
85 < }
85 >  }
86  
87 < void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
87 >  void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
88  
89      if (sd1 == sd2) {
90 <        return;
90 >      return;
91      }
92  
93      Vector3d pos1 = sd1->getPos();
94      Vector3d pos2 = sd2->getPos();
95      Vector3d r12 = pos1 - pos2;
96 <    currentSnapshot_->wrapVector(r12);
96 >    if (usePeriodicBoundaryConditions_)
97 >      currentSnapshot_->wrapVector(r12);
98      Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
99      Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
100      
# Line 91 | Line 103 | void GofAngle2::collectHistogram(StuntDouble* sd1, Stu
103      dipole2.normalize();    
104      
105  
106 <    double cosAngle1 = dot(r12, dipole1);
107 <    double cosAngle2 = dot(dipole1, dipole2);
106 >    RealType cosAngle1 = dot(r12, dipole1);
107 >    RealType cosAngle2 = dot(dipole1, dipole2);
108  
109 <   double halfBin = (nAngleBins_ - 1) * 0.5;
109 >    RealType halfBin = (nAngleBins_ - 1) * 0.5;
110      int angleBin1 = halfBin * (cosAngle1 + 1.0);
111 <    int angleBin2 = halfBin * (cosAngle1 + 1.0);
111 >    int angleBin2 = halfBin * (cosAngle2 + 1.0);
112  
113 <    ++histogram_[angleBin1][angleBin1];    
113 >    ++histogram_[angleBin1][angleBin2];    
114      ++npairs_;
115 < }
115 >  }
116  
117 < void GofAngle2::writeRdf() {
117 >  void GofAngle2::writeRdf() {
118      std::ofstream rdfStream(outputFilename_.c_str());
119      if (rdfStream.is_open()) {
120 <        rdfStream << "#radial distribution function\n";
121 <        rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
122 <        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
123 <        rdfStream << "#r\tcorrValue\n";
124 <        for (int i = 0; i < avgGofr_.size(); ++i) {
125 <            double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
120 >      rdfStream << "#radial distribution function\n";
121 >      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
122 >      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
123 >      rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
124 >      for (int i = 0; i < avgGofr_.size(); ++i) {
125 >        RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
126  
127 <            for(int j = 0; j < avgGofr_[i].size(); ++j) {
128 <                double cosAngle2 = -1.0 + (i + 0.5)*deltaCosAngle_;
129 <                rdfStream << cosAngle1 << "\t" << cosAngle2 << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
130 <            }
131 <        }
127 >        for(int j = 0; j < avgGofr_[i].size(); ++j) {
128 >          RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
129 >          rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
130 >        }
131 >
132 >        rdfStream << "\n";
133 >      }
134          
135      } else {
136  
137 <
137 >      sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
138 >      painCave.isFatal = 1;
139 >      simError();  
140      }
141  
142      rdfStream.close();
143 < }
143 >  }
144  
145   }

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