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root/group/trunk/OOPSE-3.0/src/applications/staticProps/GofXyz.cpp
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Comparing trunk/OOPSE-3.0/src/applications/staticProps/GofXyz.cpp (file contents):
Revision 2135 by tim, Mon Mar 28 15:54:04 2005 UTC vs.
Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC

# Line 46 | Line 46 | GofXyz::GofXyz(SimInfo* info, const std::string& filen
46   #include "primitives/Molecule.hpp"
47   namespace oopse {
48  
49 < GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins)
49 >  GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins)
50      : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
51 <    setOutputName(getPrefix(filename) + ".gxyz");
51 >      setOutputName(getPrefix(filename) + ".gxyz");
52  
53 <    evaluator3_.loadScriptString(sele3);
54 <    if (!evaluator3_.isDynamic()) {
53 >      evaluator3_.loadScriptString(sele3);
54 >      if (!evaluator3_.isDynamic()) {
55          seleMan3_.setSelectionSet(evaluator3_.evaluate());
56 <    }    
56 >      }    
57  
58 <    deltaR_ =  len_ / nRBins_;
58 >      deltaR_ =  len_ / nRBins_;
59      
60 <    histogram_.resize(nRBins_);
61 <    for (int i = 0 ; i < nRBins_; ++i) {
60 >      histogram_.resize(nRBins_);
61 >      for (int i = 0 ; i < nRBins_; ++i) {
62          histogram_[i].resize(nRBins_);
63          for(int j = 0; j < nRBins_; ++j) {
64 <            histogram_[i][j].resize(nRBins_);
64 >          histogram_[i][j].resize(nRBins_);
65          }
66 <    }  
66 >      }  
67    
68 < }
68 >    }
69  
70  
71 < void GofXyz::preProcess() {
71 >  void GofXyz::preProcess() {
72      for (int i = 0 ; i < nRBins_; ++i) {
73 <        histogram_[i].resize(nRBins_);
74 <        for(int j = 0; j < nRBins_; ++j) {
75 <            std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
76 <        }
73 >      histogram_[i].resize(nRBins_);
74 >      for(int j = 0; j < nRBins_; ++j) {
75 >        std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
76 >      }
77      }  
78 < }
78 >  }
79  
80  
81 < void GofXyz::initalizeHistogram() {
81 >  void GofXyz::initalizeHistogram() {
82      //calculate the center of mass of the molecule of selected stuntdouble in selection1
83  
84      if (!evaluator3_.isDynamic()) {
85 <        seleMan3_.setSelectionSet(evaluator3_.evaluate());
85 >      seleMan3_.setSelectionSet(evaluator3_.evaluate());
86      }    
87  
88      assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
# Line 100 | Line 100 | void GofXyz::initalizeHistogram() {
100      StuntDouble* sd3;
101      
102      for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
103 <        sd1 != NULL, sd3 != NULL;
104 <        sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
103 >         sd1 != NULL, sd3 != NULL;
104 >         sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
105  
106 <        Vector3d r3 =sd3->getPos();
107 <        Vector3d r1 = sd1->getPos();
108 <        Vector3d v1 =  r3 - r1;
109 <        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
110 <        Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
111 <        Vector3d xaxis = cross(v1, zaxis);
112 <        Vector3d yaxis = cross(zaxis, xaxis);
106 >      Vector3d r3 =sd3->getPos();
107 >      Vector3d r1 = sd1->getPos();
108 >      Vector3d v1 =  r3 - r1;
109 >      info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
110 >      Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
111 >      Vector3d xaxis = cross(v1, zaxis);
112 >      Vector3d yaxis = cross(zaxis, xaxis);
113  
114 <        xaxis.normalize();
115 <        yaxis.normalize();
116 <        zaxis.normalize();
114 >      xaxis.normalize();
115 >      yaxis.normalize();
116 >      zaxis.normalize();
117  
118 <        RotMat3x3d rotMat;
119 <        rotMat.setRow(0, xaxis);
120 <        rotMat.setRow(1, yaxis);
121 <        rotMat.setRow(2, zaxis);
118 >      RotMat3x3d rotMat;
119 >      rotMat.setRow(0, xaxis);
120 >      rotMat.setRow(1, yaxis);
121 >      rotMat.setRow(2, zaxis);
122          
123 <        rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
123 >      rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
124      }
125  
126 < }
126 >  }
127  
128 < void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
128 >  void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
129  
130      Vector3d pos1 = sd1->getPos();
131      Vector3d pos2 = sd2->getPos();
# Line 144 | Line 144 | void GofXyz::collectHistogram(StuntDouble* sd1, StuntD
144      if (xbin < nRBins_ && xbin >=0 &&
145          ybin < nRBins_ && ybin >= 0 &&
146          zbin < nRBins_ && zbin >=0 ) {
147 <        ++histogram_[xbin][ybin][zbin];
147 >      ++histogram_[xbin][ybin][zbin];
148      }
149      
150 < }
150 >  }
151  
152 < void GofXyz::writeRdf() {
152 >  void GofXyz::writeRdf() {
153      std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
154      if (rdfStream.is_open()) {
155 <        //rdfStream << "#g(x, y, z)\n";
156 <        //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
157 <        //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
158 <        //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
159 <        for (int i = 0; i < histogram_.size(); ++i) {
155 >      //rdfStream << "#g(x, y, z)\n";
156 >      //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
157 >      //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
158 >      //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
159 >      for (int i = 0; i < histogram_.size(); ++i) {
160  
161 <            for(int j = 0; j < histogram_[i].size(); ++j) {
161 >        for(int j = 0; j < histogram_[i].size(); ++j) {
162  
163 <                for(int k = 0;k < histogram_[i][j].size(); ++k) {
164 <                    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
165 <                }
166 <            }
167 <        }
163 >          for(int k = 0;k < histogram_[i][j].size(); ++k) {
164 >            rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
165 >          }
166 >        }
167 >      }
168          
169      } else {
170  
171 <        sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
172 <        painCave.isFatal = 1;
173 <        simError();  
171 >      sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
172 >      painCave.isFatal = 1;
173 >      simError();  
174      }
175  
176      rdfStream.close();
177 < }
177 >  }
178  
179   }

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