--- trunk/src/applications/staticProps/GofRAngle.cpp	2006/05/17 21:51:42	963
+++ trunk/src/applications/staticProps/GofRAngle.cpp	2009/11/25 20:02:06	1390
@@ -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 +28,15 @@
  * 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]  Vardeman & Gezelter, in progress (2009).                        
  */
 
 #include <algorithm>
@@ -44,15 +44,14 @@
 #include "applications/staticProps/GofRAngle.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 
   GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, 
 		       const std::string& sele2, RealType len, int nrbins, int nangleBins)
     : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
 
-      deltaR_ = len_ /nRBins_;             
-      deltaCosAngle_ = 2.0 / nAngleBins_;    
-
+      deltaR_ = len_ /(double) nRBins_;
+      deltaCosAngle_ = 2.0 / (double)nAngleBins_;    
       histogram_.resize(nRBins_);
       avgGofr_.resize(nRBins_);
       for (int i = 0 ; i < nRBins_; ++i) {
@@ -63,7 +62,6 @@ namespace oopse {
 
 
   void GofRAngle::preProcess() {
-
     for (int i = 0; i < avgGofr_.size(); ++i) {
       std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
     }
@@ -71,13 +69,12 @@ namespace oopse {
 
   void GofRAngle::initalizeHistogram() {
     npairs_ = 0;
-    for (int i = 0; i < histogram_.size(); ++i)
+    for (int i = 0; i < histogram_.size(); ++i){
       std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
+    }
   }
 
-
   void GofRAngle::processHistogram() {
-
     int nPairs = getNPairs();
     RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
     RealType pairDensity = nPairs /volume;
@@ -102,16 +99,17 @@ namespace oopse {
     if (sd1 == sd2) {
       return;
     }
-    
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
     Vector3d r12 = pos2 - pos1;
-    currentSnapshot_->wrapVector(r12);
+    if (usePeriodicBoundaryConditions_)
+      currentSnapshot_->wrapVector(r12);
 
     RealType distance = r12.length();
     int whichRBin = distance / deltaR_;
 
     if (distance <= len_) {
+
       RealType cosAngle = evaluateAngle(sd1, sd2);
       RealType halfBin = (nAngleBins_ - 1) * 0.5;
       int whichThetaBin = halfBin * (cosAngle + 1.0);
@@ -153,7 +151,10 @@ namespace oopse {
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
     Vector3d r12 = pos2 - pos1;
-    currentSnapshot_->wrapVector(r12);
+  
+    if (usePeriodicBoundaryConditions_)
+      currentSnapshot_->wrapVector(r12);
+
     r12.normalize();
     Vector3d dipole = sd1->getElectroFrame().getColumn(2);
     dipole.normalize();