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root/OpenMD/trunk/src/applications/staticProps/RhoZ.cpp
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Comparing trunk/src/applications/staticProps/RhoZ.cpp (file contents):
Revision 840 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 44 | Line 44
44   *
45   *  Created by Charles F. Vardeman II on 11/26/05.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: RhoZ.cpp,v 1.2 2006-01-09 22:14:32 tim Exp $
47 > *  @version $Id: RhoZ.cpp,v 1.5 2006-05-17 21:51:42 tim Exp $
48   *
49   */
50  
# Line 58 | Line 58 | namespace oopse {
58   #include "primitives/Molecule.hpp"
59   namespace oopse {
60    
61 <  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int len, int nrbins)
62 <  : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
61 >  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins)
62 >    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
63  
64      evaluator_.loadScriptString(sele);
65      if (!evaluator_.isDynamic()) {
# Line 67 | Line 67 | namespace oopse {
67      }
68        
69      
70 <    deltaR_ = len_ /nRBins_;
70 >    deltaR_ = len_ /(nRBins_);
71      
72      sliceSDLists_.resize(nRBins_);
73      density_.resize(nRBins_);
# Line 78 | Line 78 | namespace oopse {
78    void RhoZ::process() {
79      DumpReader reader(info_, dumpFilename_);    
80      int nFrames = reader.getNFrames();
81 <    nProcessed_ = nFrames / step_;
81 >    nProcessed_ = nFrames/step_;
82  
83 –
83      for (int istep = 0; istep < nFrames; istep += step_) {
84  
85 <        StuntDouble* sd;
86 <        int i;    
87 <        reader.readFrame(istep);
88 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
85 >      int i;    
86 >      for (i=0; i < nRBins_; i++) {
87 >        sliceSDLists_[i].clear();
88 >      }
89  
90 <        double sliceVolume = currentSnapshot_->getVolume() /nRBins_;
91 <        //assume simulation box will never change
92 <        //Mat3x3d hmat = currentSnapshot_->getHmat();
93 <        double halfBoxZ = len_ /2;      
90 >      StuntDouble* sd;
91 >      reader.readFrame(istep);
92 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
93 >      
94 >      RealType sliceVolume = currentSnapshot_->getVolume() /nRBins_;
95 >      //assume simulation box will never change
96 >      //Mat3x3d hmat = currentSnapshot_->getHmat();
97 >      RealType halfBoxZ_ = len_ / 2.0;      
98          
99          if (evaluator_.isDynamic()) {
100            seleMan_.setSelectionSet(evaluator_.evaluate());
# Line 104 | Line 107 | namespace oopse {
107              sd->setPos(pos);
108          }
109  
110 <        //determine which atom belong to which slice
110 >        //determine which atom belongs to which slice
111          for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
112             Vector3d pos = sd->getPos();
113 <           int binNo = (pos.z() + halfBoxZ) /deltaR_;
113 >           //int binNo = (pos.z() /deltaR_) - 1;
114 >           int binNo = (pos.z() + halfBoxZ_) /deltaR_   ;
115 >           //std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = "  << deltaR_ << " binNo = " << binNo << "\n";
116             sliceSDLists_[binNo].push_back(sd);
117          }
118  
119          //loop over the slices to calculate the densities
120 <        for (std::size_t j = 0; j < sliceSDLists_.size(); ++j) {
121 <            double totalMass = 0;
122 <            for (int k = 0; k < sliceSDLists_[j].size(); ++k) {
123 <                totalMass += sliceSDLists_[j][k]->getMass();
120 >        for (i = 0; i < nRBins_; i++) {
121 >            RealType totalMass = 0;
122 >            for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
123 >                totalMass += sliceSDLists_[i][k]->getMass();
124              }
125 <            density_[j] += totalMass/sliceVolume;
125 >            density_[i] += totalMass/sliceVolume;
126          }
127      }
128  
124 –    
129      writeDensity();
130  
131    }
# Line 132 | Line 136 | namespace oopse {
136      std::ofstream rdfStream(outputFilename_.c_str());
137      if (rdfStream.is_open()) {
138        rdfStream << "#RhoZ\n";
139 <      rdfStream << "#selection: (" << selectionScript_ << ")\t";
139 >      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
140 >      rdfStream << "#selection: (" << selectionScript_ << ")\n";
141        rdfStream << "#z\tdensity\n";
142        for (int i = 0; i < density_.size(); ++i) {
143 <        double r = deltaR_ * (i + 0.5);
144 <        rdfStream << r << "\t" << density_[i]/nProcessed_ << "\n";
143 >        RealType r = deltaR_ * (i + 0.5);
144 >        rdfStream << r << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
145        }
146        
147      } else {

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