--- trunk/src/applications/staticProps/GofRAngle.cpp	2008/01/23 21:21:50	1213
+++ trunk/src/applications/staticProps/GofRAngle.cpp	2012/08/22 02:28:28	1782
@@ -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/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)
@@ -62,14 +63,14 @@ namespace oopse {
 
 
   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() {
     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 +81,14 @@ namespace oopse {
     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;    
       }
     }
@@ -127,10 +128,10 @@ namespace oopse {
       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) {
+      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
 	RealType r = deltaR_ * (i + 0.5);
 
-	for(int j = 0; j < avgGofr_[i].size(); ++j) {
+	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
 	  RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
 	  rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
 	}