--- trunk/src/applications/staticProps/GofXyz.cpp	2012/03/15 13:50:52	1693
+++ trunk/src/applications/staticProps/GofXyz.cpp	2013/06/16 15:15:42	1879
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <algorithm>
@@ -44,6 +45,8 @@
 #include "applications/staticProps/GofXyz.hpp"
 #include "utils/simError.h"
 #include "primitives/Molecule.hpp"
+#include "types/MultipoleAdapter.hpp"
+
 namespace OpenMD {
 
   GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
@@ -78,7 +81,7 @@ namespace OpenMD {
   }
 
 
-  void GofXyz::initalizeHistogram() {
+  void GofXyz::initializeHistogram() {
     //calculate the center of mass of the molecule of selected stuntdouble in selection1
 
     if (!evaluator3_.isDynamic()) {
@@ -103,12 +106,21 @@ namespace OpenMD {
 	 sd1 != NULL || sd3 != NULL;
 	 sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
 
-      Vector3d r3 =sd3->getPos();
+      Vector3d r3 = sd3->getPos();
       Vector3d r1 = sd1->getPos();
       Vector3d v1 =  r3 - r1;
       if (usePeriodicBoundaryConditions_)
         info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
-      Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
+
+      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
+      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
+
+      Vector3d zaxis;
+      if (ma1.isDipole()) 
+        zaxis = sd1->getDipole();
+      else
+        zaxis = sd1->getA().transpose() * V3Z;
+
       Vector3d xaxis = cross(v1, zaxis);
       Vector3d yaxis = cross(zaxis, xaxis);
 
@@ -139,9 +151,9 @@ namespace OpenMD {
     
     Vector3d newR12 = i->second * r12;
     // x, y and z's possible values range -halfLen_ to halfLen_
-    int xbin = (newR12.x()+ halfLen_) / deltaR_;
-    int ybin = (newR12.y() + halfLen_) / deltaR_;
-    int zbin = (newR12.z() + halfLen_) / deltaR_;
+    int xbin = int( (newR12.x() + halfLen_) / deltaR_);
+    int ybin = int( (newR12.y() + halfLen_) / deltaR_);
+    int zbin = int( (newR12.z() + halfLen_) / deltaR_);
 
     if (xbin < nRBins_ && xbin >=0 &&
         ybin < nRBins_ && ybin >= 0 &&
@@ -158,12 +170,11 @@ namespace OpenMD {
       //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
       //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
       //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
-      for (int i = 0; i < histogram_.size(); ++i) {
- 
-	for(int j = 0; j < histogram_[i].size(); ++j) {
- 
-	  for(int k = 0;k < histogram_[i][j].size(); ++k) {
-	    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
+      for (unsigned int i = 0; i < histogram_.size(); ++i) { 
+	for(unsigned int j = 0; j < histogram_[i].size(); ++j) { 
+	  for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
+	    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ),
+                            sizeof(histogram_[i][j][k] ));
 	  }
 	}
       }