--- trunk/src/applications/staticProps/Hxy.cpp	2006/05/23 21:12:45	969
+++ trunk/src/applications/staticProps/Hxy.cpp	2012/09/10 18:38:44	1796
@@ -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 +29,19 @@
  * 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).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *
- *  Hxy.cpp
- *  OOPSE-2.0
- *
  *  Created by Xiuquan Sun on 05/09/06.
  *  @author  Xiuquan Sun 
- *  @version $Id: Hxy.cpp,v 1.6 2006-05-23 21:12:45 xsun Exp $
+ *  @version $Id$
  *
  */
 
@@ -61,7 +58,7 @@
 #include<stdlib.h>
 #include<math.h>
 
-namespace oopse {
+namespace OpenMD {
   
   Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins)
     : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){
@@ -103,9 +100,9 @@ namespace oopse {
       errbin_sum_sq.clear();
       errbin_sq.clear();
       
-      for(int i=0; i < bin.size(); i++)
+      for(unsigned int i=0; i < bin.size(); i++)
 	bin[i].clear();
-      for(int i=0; i < samples.size(); i++)
+      for(unsigned int i=0; i < samples.size(); i++)
 	samples[i].clear();
 
       mag.clear();
@@ -118,26 +115,24 @@ namespace oopse {
     int nFrames = reader.getNFrames();
     nProcessed_ = nFrames/step_;
     
-    for(int k=0; k < bin.size(); k++)
+    for(unsigned int k=0; k < bin.size(); k++)
       bin[k].resize(nFrames);
-    for(int k=0; k < samples.size(); k++)
+    for(unsigned int k=0; k < samples.size(); k++)
       samples[k].resize(nFrames);
 
     RealType lenX_, lenY_;
     RealType gridX_, gridY_;
     RealType halfBoxX_, halfBoxY_;
 
-    int binNoX, binNoY;
     RealType interpsum, value;
     int ninterp, px, py, newp;
-    int newx, newy, newindex, index;
+    int newindex, index;
     int new_i, new_j, new_index;
 
     RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
     RealType maxfreqx, maxfreqy, maxfreq;
 
     int whichbin;
-    int nMolecules;
 
     std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
     std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
@@ -148,17 +143,16 @@ namespace oopse {
     std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0);
     std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0);
     
-    for(int i=0; i < bin.size(); i++)
+    for(unsigned int i=0; i < bin.size(); i++)
       std::fill(bin[i].begin(), bin[i].end(), 0.0);
     
-    for(int i=0; i < samples.size(); i++)
+    for(unsigned int i=0; i < samples.size(); i++)
       std::fill(samples[i].begin(), samples[i].end(), 0);
     
     for (int istep = 0; istep < nFrames; istep += step_) {
       
       reader.readFrame(istep);
       currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
-      nMolecules = info_->getNGlobalMolecules();
       
       Mat3x3d hmat = currentSnapshot_->getHmat();
       
@@ -204,7 +198,8 @@ namespace oopse {
       //wrap the stuntdoubles into a cell     
       for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
 	Vector3d pos = sd->getPos();
-	currentSnapshot_->wrapVector(pos);
+        if (usePeriodicBoundaryConditions_)
+          currentSnapshot_->wrapVector(pos);
 	sd->setPos(pos);
       }