--- trunk/src/applications/staticProps/GofRAngle.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/applications/staticProps/GofRAngle.cpp	2014/02/20 16:27:30	1968
@@ -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/GofRAngle.hpp"
+#include "primitives/Atom.hpp"
+#include "types/MultipoleAdapter.hpp"
 #include "utils/simError.h"
 
 namespace OpenMD {
@@ -62,14 +65,14 @@ namespace OpenMD {
 
 
   void GofRAngle::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 GofRAngle::initalizeHistogram() {
+  void GofRAngle::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);
     }
   }
@@ -80,14 +83,14 @@ namespace OpenMD {
     RealType pairDensity = nPairs /volume;
     RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
 
-    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 = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
       RealType nIdeal = volSlice * pairConstant;
 
-      for (int j = 0; j < histogram_[i].size(); ++j){
+      for (unsigned int j = 0; j < histogram_[i].size(); ++j){
 	avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
       }
     }
@@ -106,13 +109,13 @@ namespace OpenMD {
       currentSnapshot_->wrapVector(r12);
 
     RealType distance = r12.length();
-    int whichRBin = distance / deltaR_;
+    int whichRBin = int(distance / deltaR_);
 
     if (distance <= len_) {
 
       RealType cosAngle = evaluateAngle(sd1, sd2);
       RealType halfBin = (nAngleBins_ - 1) * 0.5;
-      int whichThetaBin = halfBin * (cosAngle + 1.0);
+      int whichThetaBin = int(halfBin * (cosAngle + 1.0));
       ++histogram_[whichRBin][whichThetaBin];
         
       ++npairs_;
@@ -127,11 +130,11 @@ namespace OpenMD {
       rdfStream << "selection2: (" << selectionScript2_ << ")\n";
       rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
       rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
-      for (int i = 0; i < avgGofr_.size(); ++i) {
-	RealType r = deltaR_ * (i + 0.5);
+      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
+	// RealType r = deltaR_ * (i + 0.5);
 
-	for(int j = 0; j < avgGofr_[i].size(); ++j) {
-	  RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
+	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
+	  // RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
 	  rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
 	}
 
@@ -156,14 +159,52 @@ namespace OpenMD {
       currentSnapshot_->wrapVector(r12);
 
     r12.normalize();
-    Vector3d dipole = sd1->getElectroFrame().getColumn(2);
-    dipole.normalize();    
-    return dot(r12, dipole);
+
+    Vector3d vec;    
+    
+    if (sd1->isAtom()) {
+      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
+      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
+      
+      if (ma1.isDipole() )
+        vec = sd1->getDipole();
+      else 
+        vec = sd1->getA().transpose() * V3Z;
+    } else {
+      vec = sd1->getA().transpose() * V3Z;
+    }
+
+    vec.normalize();    
+      
+    return dot(r12, vec);
   }
 
   RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
-    Vector3d v1 = sd1->getElectroFrame().getColumn(2);
-    Vector3d v2 = sd2->getElectroFrame().getColumn(2);    
+    Vector3d v1, v2;
+
+    if (sd1->isAtom()){
+      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
+      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
+      if (ma1.isDipole() )
+        v1 = sd1->getDipole();
+      else 
+        v1 = sd1->getA().transpose() * V3Z;
+    } else {
+      v1 = sd1->getA().transpose() * V3Z;
+    }
+    
+    if (sd2->isAtom()) {
+      AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
+      MultipoleAdapter ma2 = MultipoleAdapter(atype2);
+           
+      if (ma2.isDipole() )
+        v2 = sd2->getDipole();
+      else 
+        v2 = sd2->getA().transpose() * V3Z;
+    } else {
+      v2 = sd2->getA().transpose() * V3Z;
+    }
+      
     v1.normalize();
     v2.normalize();
     return dot(v1, v2);