--- trunk/src/applications/staticProps/GofAngle2.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/applications/staticProps/GofAngle2.cpp	2013/06/16 15:15:42	1879
@@ -35,13 +35,16 @@
  *                                                                      
  * [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>
 #include <fstream>
 #include "applications/staticProps/GofAngle2.hpp"
+#include "primitives/Atom.hpp"
+#include "types/MultipoleAdapter.hpp"
 #include "utils/simError.h"
 
 namespace OpenMD {
@@ -66,14 +69,14 @@ namespace OpenMD {
 
   void GofAngle2::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 GofAngle2::initalizeHistogram() {
+  void GofAngle2::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);
   }
 
@@ -95,8 +98,22 @@ namespace OpenMD {
     Vector3d r12 = pos1 - pos2;
     if (usePeriodicBoundaryConditions_) 
       currentSnapshot_->wrapVector(r12);
-    Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
-    Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
+
+    AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
+    AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
+    MultipoleAdapter ma1 = MultipoleAdapter(atype1);
+    MultipoleAdapter ma2 = MultipoleAdapter(atype2);
+
+    Vector3d dipole1, dipole2;
+    if (ma1.isDipole())         
+        dipole1 = sd1->getDipole();
+    else
+        dipole1 = sd1->getA().transpose() * V3Z;
+
+    if (ma2.isDipole())         
+        dipole2 = sd2->getDipole();
+    else
+        dipole2 = sd2->getA().transpose() * V3Z;
     
     r12.normalize();
     dipole1.normalize();    
@@ -107,8 +124,8 @@ namespace OpenMD {
     RealType cosAngle2 = dot(dipole1, dipole2);
 
     RealType halfBin = (nAngleBins_ - 1) * 0.5;
-    int angleBin1 = halfBin * (cosAngle1 + 1.0);
-    int angleBin2 = halfBin * (cosAngle2 + 1.0);
+    int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
+    int angleBin2 = int(halfBin * (cosAngle2 + 1.0));
 
     ++histogram_[angleBin1][angleBin2];    
     ++npairs_;
@@ -121,11 +138,11 @@ namespace OpenMD {
       rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
       rdfStream << "selection2: (" << selectionScript2_ << ")\n";
       rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
-      for (int i = 0; i < avgGofr_.size(); ++i) {
-	RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
-
-	for(int j = 0; j < avgGofr_[i].size(); ++j) {
-	  RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
+      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
+	// RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
+        
+	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
+	  // RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
 	  rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
 	}