--- trunk/src/applications/staticProps/GofAngle2.cpp	2006/05/17 21:51:42	963
+++ trunk/src/applications/staticProps/GofAngle2.cpp	2012/09/10 18:38:44	1796
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,16 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <algorithm>
@@ -44,7 +45,7 @@
 #include "applications/staticProps/GofAngle2.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 
   GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, 
 		       const std::string& sele2, int nangleBins)
@@ -66,14 +67,14 @@ namespace oopse {
 
   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);
   }
 
@@ -93,7 +94,8 @@ namespace oopse {
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
     Vector3d r12 = pos1 - pos2;
-    currentSnapshot_->wrapVector(r12);
+    if (usePeriodicBoundaryConditions_) 
+      currentSnapshot_->wrapVector(r12);
     Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
     Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
     
@@ -106,10 +108,10 @@ namespace oopse {
     RealType cosAngle2 = dot(dipole1, dipole2);
 
     RealType halfBin = (nAngleBins_ - 1) * 0.5;
-    int angleBin1 = halfBin * (cosAngle1 + 1.0);
-    int angleBin2 = halfBin * (cosAngle1 + 1.0);
+    int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
+    int angleBin2 = int(halfBin * (cosAngle2 + 1.0));
 
-    ++histogram_[angleBin1][angleBin1];    
+    ++histogram_[angleBin1][angleBin2];    
     ++npairs_;
   }
 
@@ -120,11 +122,11 @@ namespace oopse {
       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";
 	}