--- trunk/src/applications/staticProps/GofRZ.cpp	2010/04/29 14:48:10	1441
+++ trunk/src/applications/staticProps/GofRZ.cpp	2012/08/30 17:18:22	1790
@@ -36,7 +36,8 @@
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
  * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <algorithm>
@@ -47,31 +48,31 @@ 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){
+               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_ = len_ / (double)nZBins_;    
-      histogram_.resize(nRBins_);
-      avgGofr_.resize(nRBins_);
-      for (int i = 0 ; i < nRBins_; ++i) {
-        histogram_[i].resize(nZBins_);
-        avgGofr_[i].resize(nZBins_);
-      }
-    }
+    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(nZBins_);
+      avgGofr_[i].resize(nZBins_);
+    } 
+  }
 
   void GofRZ::preProcess() {
-    for (int i = 0; i < avgGofr_.size(); ++i) {
+    for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
       std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
     }
   }
 
-  void GofRZ::initalizeHistogram() {
+  void GofRZ::initializeHistogram() {
     npairs_ = 0;
-    for (int i = 0; i < histogram_.size(); ++i){
+    for (unsigned int i = 0; i < histogram_.size(); ++i){
       std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
     }
   }
@@ -79,17 +80,17 @@ namespace OpenMD {
   void GofRZ::processHistogram() {
     int nPairs = getNPairs();
     RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
-    RealType pairDensity = nPairs / volume;
+    RealType pairDensity = nPairs / volume * 2.0;
 
-    for(int i = 0 ; i < histogram_.size(); ++i){
+    for(unsigned 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;
 
-      for (int j = 0; j < histogram_[i].size(); ++j){
-	avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
+      for (unsigned int j = 0; j < histogram_[i].size(); ++j){
+        avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
       }
     }
 
@@ -108,14 +109,15 @@ namespace OpenMD {
 
     RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
 
-    int whichRBin = distance / deltaR_;
+    int whichRBin = int(distance / deltaR_);
 
     if (distance <= len_) {
      
-      RealType Z = abs(r12.z());
+      RealType Z = fabs(r12.z());
 
-      if (Z <= len_) {
-        int whichZBin = Z / deltaZ_;
+      if (Z <= zLen_) {
+        int whichZBin = int(Z / deltaZ_);
+              
         ++histogram_[whichRBin][whichZBin];        
         ++npairs_;
       }
@@ -129,16 +131,16 @@ namespace OpenMD {
       rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
       rdfStream << "selection2: (" << selectionScript2_ << ")\n";
       rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
-      rdfStream << "#nZBins =" << nZBins_ << "deltaZ = " << deltaZ_ << "\n";
-      for (int i = 0; i < avgGofr_.size(); ++i) {
-	RealType r = deltaR_ * (i + 0.5);
+      rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
+      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
+        RealType r = deltaR_ * (i + 0.5);
 
-	for(int j = 0; j < avgGofr_[i].size(); ++j) {
+        for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
           RealType z = deltaZ_ * (j + 0.5);
-	  rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
-	}
+          rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
+        }
 
-	rdfStream << "\n";
+        rdfStream << "\n";
       }
         
     } else {