--- trunk/src/applications/staticProps/GofR.cpp	2006/05/17 21:51:42	963
+++ trunk/src/applications/staticProps/GofR.cpp	2012/08/22 18:43:27	1785
@@ -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/GofR.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 
   GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
     : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
@@ -62,7 +63,7 @@ namespace oopse {
     std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);    
   }
 
-  void GofR::initalizeHistogram() {
+  void GofR::initializeHistogram() {
     std::fill(histogram_.begin(), histogram_.end(), 0);
   }
 
@@ -74,7 +75,7 @@ namespace oopse {
     RealType pairDensity = nPairs /volume * 2.0;
     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_;
@@ -95,7 +96,8 @@ namespace oopse {
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
     Vector3d r12 = pos2 - pos1;
-    currentSnapshot_->wrapVector(r12);
+    if (usePeriodicBoundaryConditions_)
+      currentSnapshot_->wrapVector(r12);
 
     RealType distance = r12.length();
 
@@ -113,11 +115,10 @@ namespace oopse {
       rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
       rdfStream << "selection2: (" << selectionScript2_ << ")\n";
       rdfStream << "#r\tcorrValue\n";
-      for (int i = 0; i < avgGofr_.size(); ++i) {
+      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
 	RealType r = deltaR_ * (i + 0.5);
 	rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
       }
-        
     } else {
 
       sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str());