--- trunk/src/applications/staticProps/RhoZ.cpp	2008/06/30 17:53:42	1267
+++ trunk/src/applications/staticProps/RhoZ.cpp	2013/06/16 15:15:42	1879
@@ -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.
@@ -38,13 +29,18 @@
  * University of Notre Dame has been advised of the possibility of
  * such damages.
  *
- *
- *  RhoZ.cpp
- *  OOPSE-2.0
- *
+ * 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, 234107 (2008).          
+ * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *  Created by Charles F. Vardeman II on 11/26/05.
  *  @author  Charles F. Vardeman II 
- *  @version $Id: RhoZ.cpp,v 1.7 2008-06-30 17:53:42 gpuliti Exp $
+ *  @version $Id$
  *
  */
 
@@ -56,7 +52,7 @@
 #include "utils/simError.h"
 #include "io/DumpReader.hpp"
 #include "primitives/Molecule.hpp"
-namespace oopse {
+namespace OpenMD {
   
   RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins)
     : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), nZBins_(nzbins){
@@ -130,7 +126,7 @@ namespace oopse {
       //loop over the slices to calculate the densities
       for (i = 0; i < nZBins_; i++) {
         RealType totalMass = 0;
-        for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
+        for (unsigned int k = 0; k < sliceSDLists_[i].size(); ++k) {
           totalMass += sliceSDLists_[i][k]->getMass();
         }
         density_[i] += totalMass/sliceVolume;
@@ -159,7 +155,7 @@ namespace oopse {
       rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
       rdfStream << "#selection: (" << selectionScript_ << ")\n";
       rdfStream << "#z\tdensity\n";
-      for (int i = 0; i < density_.size(); ++i) {
+      for (unsigned int i = 0; i < density_.size(); ++i) {
         RealType z = zAve * (i+0.5)/density_.size();
         rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
       }