--- trunk/src/applications/staticProps/GofRZ.cpp	2010/06/08 18:35:22	1444
+++ trunk/src/applications/staticProps/GofRZ.cpp	2010/06/08 20:26:50	1445
@@ -46,121 +46,111 @@ namespace OpenMD {
 
 namespace OpenMD {
 
-  GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1, 
-		       const std::string& sele2, RealType len, int nrbins, int nZBins)
-    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nZBins_(nZBins){
+    GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1, 
+		 const std::string& sele2, RealType len, RealType zlen, int nrbins, int nZBins)
+	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){
 
-      setOutputName(getPrefix(filename) + ".gofrz");
+	setOutputName(getPrefix(filename) + ".gofrz");
 
-      deltaR_ = len_ / (double) nRBins_;
-      deltaZ_ = 86.52361692 / (double)nZBins_;    // for solvated_NVT.md4
+	deltaR_ = len_ / (double) nRBins_;
+	deltaZ_ = zLen_ / (double)nZBins_;    // for solvated_NVT.md4
 
-      histogram_.resize(nRBins_);
-      avgGofr_.resize(nRBins_);
-      for (int i = 0 ; i < nRBins_; ++i) {
-        histogram_[i].resize(nRBins_);
-        avgGofr_[i].resize(nRBins_);
-        for (int j = 0 ; j < nZBins_; ++j) {
-        histogram_[i][j].resize(nZBins_);
-        avgGofr_[i][j].resize(nZBins_);
-      }
+	histogram_.resize(nRBins_);
+	avgGofr_.resize(nRBins_);
+	for (int i = 0 ; i < nRBins_; ++i) {
+	    histogram_[i].resize(nZBins_);
+	    avgGofr_[i].resize(nZBins_);
+	} 
     }
- 
-  }
-  void GofRZ::preProcess() {
-    for (int i = 0; i < avgGofr_[i].size(); ++i) {
-      avgGofr_[i].resize(nRBins_);
-      for (int j = 0; j < avgGofr_[i][j].size(); ++j) {
-      std::fill(avgGofr_[i][j].begin(), avgGofr_[i][j].end(), 0);
-      }
+
+    void GofRZ::preProcess() {
+	for (int i = 0; i < avgGofr_.size(); ++i) {
+	    std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
+	}
     }
-  }
 
-  void GofRZ::initalizeHistogram() {
-    npairs_ = 0;
-    for (int i = 0; i < histogram_[i].size(); ++i){
-      histogram_[i].resize(nRBins_);
-      for (int j = 0; j < histogram_[i][j].size(); ++j){
-      std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
-      }
+    void GofRZ::initalizeHistogram() {
+	npairs_ = 0;
+	for (int i = 0; i < histogram_.size(); ++i){
+	    std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
+	}
     }
-  }
   
-  void GofRZ::processHistogram() {
-    int nPairs = getNPairs();
-    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
-    RealType pairDensity = nPairs / volume * 2.0;
+    void GofRZ::processHistogram() {
+	int nPairs = getNPairs();
+	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
+	RealType pairDensity = nPairs / volume * 2.0;
 
-    for(int i = 0 ; i < histogram_[i].size(); ++i){
+	for(int i = 0 ; i < histogram_.size(); ++i){
 
-      RealType rLower = i * deltaR_;
-      RealType rUpper = rLower + deltaR_;
-      RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
-      RealType nIdeal = volSlice * pairDensity;
+	    RealType rLower = i * deltaR_;
+	    RealType rUpper = rLower + deltaR_;
+	    RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
+	    RealType nIdeal = volSlice * pairDensity;
 
-      for (int j = 0; j < histogram_[i][j].size(); ++j){
-	avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
-      }
+	    for (int j = 0; j < histogram_[i].size(); ++j){
+		avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
+	    }
+	}
+
     }
 
-  }
+    void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
 
-  void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
+	if (sd1 == sd2) {
+	    return;
+	}
+	Vector3d pos1 = sd1->getPos();
+	Vector3d pos2 = sd2->getPos();
+	Vector3d r12 = pos2 - pos1;
+	if (usePeriodicBoundaryConditions_)
+	    currentSnapshot_->wrapVector(r12);
 
-    if (sd1 == sd2) {
-      return;
-    }
-    Vector3d pos1 = sd1->getPos();
-    Vector3d pos2 = sd2->getPos();
-    Vector3d r12 = pos2 - pos1;
-    if (usePeriodicBoundaryConditions_)
-      currentSnapshot_->wrapVector(r12);
+	RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
 
-    RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
+	int whichRBin = distance / deltaR_;
 
-    int whichRBin = distance / deltaR_;
-
-    if (distance <= len_) {
+	if (distance <= len_) {
      
-      RealType Z = fabs(r12.z());
+	    RealType Z = fabs(r12.z());
 
-      if (Z <= 86.52361692) {
-        int whichZBin = Z / deltaZ_;
+	    if (Z <= zLen_) {
+		int whichZBin = Z / deltaZ_;
 
-        ++histogram_[whichRBin][whichZBin];        
-        ++npairs_;
-      }
+		++histogram_[whichRBin][whichZBin];        
+		++npairs_;
+	    }
+	}
     }
-  }
 
-  void GofRZ::writeRdf() {
-    std::ofstream rdfStream(outputFilename_.c_str());
-    if (rdfStream.is_open()) {
-      rdfStream << "#radial distribution function\n";
-      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
-      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
-      rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
-      rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
-      for (int i = 0; i < avgGofr_[i].size(); ++i) {
-	RealType r = deltaR_ * (i + 0.5);
+    void GofRZ::writeRdf() {
+	std::ofstream rdfStream(outputFilename_.c_str());
+	if (rdfStream.is_open()) {
+	    rdfStream << "#radial distribution function\n";
+	    rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
+	    rdfStream << "selection2: (" << selectionScript2_ << ")\n";
+	    rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
+	    rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
+	    for (int i = 0; i < avgGofr_.size(); ++i) {
+		RealType r = deltaR_ * (i + 0.5);
 
-	for(int j = 0; j < avgGofr_[i][j].size(); ++j) {
-          RealType z = deltaZ_ * (j + 0.5);
-	  rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
-	}
+		for(int j = 0; j < avgGofr_[i].size(); ++j) {
+		    RealType z = deltaZ_ * (j + 0.5);
+		    rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
+		}
 
-	rdfStream << "\n";
-      }
+		rdfStream << "\n";
+	    }
         
-    } else {
-      sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
-      painCave.isFatal = 1;
-      simError();  
+	} else {
+	    sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
+	    painCave.isFatal = 1;
+	    simError();  
+	}
+
+	rdfStream.close();
     }
 
-    rdfStream.close();
-  }
-
 }