--- trunk/src/applications/staticProps/GofR.cpp	2005/02/09 17:08:22	306
+++ trunk/src/applications/staticProps/GofR.cpp	2005/02/13 20:36:24	328
@@ -42,19 +42,23 @@
 #include <algorithm>
 #include <fstream>
 #include "applications/staticProps/GofR.hpp"
+#include "utils/simError.h"
 
 namespace oopse {
 
-GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len)
-    : RadialDistrFunc(info, filename, sele1, sele2, len){
+GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
+    : RadialDistrFunc(info, filename, sele1, sele2){
 
-    histogram_.resize(nbins_);
-    avgGofr_.resize(nbins_);
+    deltaR_ = len_ /nRBins_;
+    
+    histogram_.resize(nRBins_);
+    avgGofr_.resize(nRBins_);
+
+    setOutputName(getPrefix(filename) + ".gr");
 }
 
 
 void GofR::preProcess() {
-    avgGofr_.resize(nbins_);
     std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);    
 }
 
@@ -68,12 +72,12 @@ void GofR::processHistogram() {
 
     double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
     double pairDensity = npairs_ /volume;
-    double pairConstant = ( 4.0 * PI * pairDensity ) / 3.0;
+    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
 
     for(int i = 0 ; i < histogram_.size(); ++i){
 
-        double rLower = i * delta_;
-        double rUpper = rLower + delta_;
+        double rLower = i * deltaR_;
+        double rUpper = rLower + deltaR_;
         double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
         double nIdeal = volSlice * pairConstant;
 
@@ -91,12 +95,15 @@ void GofR::collectHistogram(StuntDouble* sd1, StuntDou
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
     Vector3d r12 = pos1 - pos2;
-    
-    double distance = (pos1 - pos2).length();
+    currentSnapshot_->wrapVector(r12);
 
-    int whichBin = distance / delta_;
-    histogram_[whichBin] ++;
-    npairs_++;
+    double distance = r12.length();
+
+    if (distance < len_) {
+        int whichBin = distance / deltaR_;
+        ++histogram_[whichBin];
+        ++npairs_;
+    }
 }
 
 
@@ -104,13 +111,20 @@ void GofR::writeRdf() {
     std::ofstream rdfStream(outputFilename_.c_str());
     if (rdfStream.is_open()) {
         rdfStream << "#radial distribution function\n";
-        rdfStream << "#selection1: " << selectionScript1_;
-        rdfStream << "#selection2: " << selectionScript2_;
+        rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
+        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
+        rdfStream << "#r\tcorrValue\n";
+        for (int i = 0; i < avgGofr_.size(); ++i) {
+            double r = deltaR_ * (i + 0.5);
+            rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
+        }
         
     } else {
 
 
     }
+
+    rdfStream.close();
 }
 
 }