--- trunk/src/applications/staticProps/RhoR.cpp	2008/10/16 18:25:36	1306
+++ trunk/src/applications/staticProps/RhoR.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.
@@ -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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 /* Calculates Rho(R) for nanoparticle with radius R*/
@@ -47,9 +48,10 @@
 #include "utils/NumericConstant.hpp"
 #include "io/DumpReader.hpp"
 #include "primitives/Molecule.hpp"
+#include "brains/Thermo.hpp"
 #include <math.h>
 
-namespace oopse {
+namespace OpenMD {
 
      
   RhoR::RhoR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins, RealType particleR)
@@ -72,9 +74,8 @@ namespace oopse {
   
 
   void RhoR::process() {
-    
-
-    
+   
+    Thermo thermo(info_);
     DumpReader reader(info_, dumpFilename_);    
     int nFrames = reader.getNFrames();
     nProcessed_ = nFrames/step_;
@@ -88,11 +89,8 @@ namespace oopse {
       StuntDouble* sd;
       reader.readFrame(istep);
       currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
-      Vector3d CenterOfMass = info_->getCom();      
+      Vector3d CenterOfMass = thermo.getCom();      
       
-      
-      
-      
       if (evaluator_.isDynamic()) {
 	seleMan_.setSelectionSet(evaluator_.evaluate());
       }
@@ -105,7 +103,7 @@ namespace oopse {
 	RealType distance = r12.length();
 	
 	if (distance < len_) {
-	  int whichBin = distance / deltaR_;
+	  int whichBin = int(distance / deltaR_);
 	  histogram_[whichBin] += 1;
 	}
 	
@@ -124,7 +122,7 @@ namespace oopse {
     RealType particleDensity =  3.0 * info_->getNGlobalMolecules() / (4.0 * NumericConstant::PI * pow(particleR_,3));
     RealType pairConstant = ( 4.0 * NumericConstant::PI * particleDensity ) / 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_;
@@ -143,7 +141,7 @@ namespace oopse {
     if (rdfStream.is_open()) {
       rdfStream << "#radial density function rho(r)\n";
       rdfStream << "#r\tcorrValue\n";
-      for (int i = 0; i < avgRhoR_.size(); ++i) {
+      for (unsigned int i = 0; i < avgRhoR_.size(); ++i) {
 	RealType r = deltaR_ * (i + 0.5);
 	rdfStream << r << "\t" << avgRhoR_[i]/nProcessed_ << "\n";
       }