--- trunk/src/applications/staticProps/Hxy.cpp	2006/05/22 15:30:42	967
+++ trunk/src/applications/staticProps/Hxy.cpp	2009/11/25 20:02:06	1390
@@ -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]  Vardeman & Gezelter, in progress (2009).                        
  *
- *  Hxy.cpp
- *  OOPSE-2.0
  *
  *  Created by Xiuquan Sun on 05/09/06.
  *  @author  Xiuquan Sun 
- *  @version $Id: Hxy.cpp,v 1.5 2006-05-22 15:30:42 xsun Exp $
+ *  @version $Id: Hxy.cpp,v 1.8 2009-11-25 20:01:59 gezelter Exp $
  *
  */
 
@@ -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){
@@ -139,6 +136,21 @@ namespace oopse {
     int whichbin;
     int nMolecules;
 
+    std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
+    std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
+    std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0);
+    std::fill(errbin.begin(), errbin.end(), 0.0);
+    std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0);
+    std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0);
+    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++)
+      std::fill(bin[i].begin(), bin[i].end(), 0.0);
+    
+    for(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);
@@ -163,27 +175,13 @@ namespace oopse {
 #else
       p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE);
 #endif
-      
-      int i, j;   
-      
+
       std::fill(gridsample_.begin(), gridsample_.end(), 0);
       std::fill(gridZ_.begin(), gridZ_.end(), 0.0);
-      std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
-      std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
-      std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0);
-      std::fill(errbin.begin(), errbin.end(), 0.0);
-      std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0);
-      std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0);
-      std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0);
-      std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0);
       std::fill(mag.begin(), mag.end(), 0.0);
       std::fill(newmag.begin(), newmag.end(), 0.0);
 
-      for(i=0; i < bin.size(); i++)
-	std::fill(bin[i].begin(), bin[i].end(), 0.0);
-
-      for(i=0; i < samples.size(); i++)
-	std::fill(samples[i].begin(), samples[i].end(), 0);
+      int i, j;   
       
       StuntDouble* sd;
       
@@ -203,7 +201,8 @@ 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);
       } 
       
@@ -387,7 +386,7 @@ namespace oopse {
       
       for ( i = 0; i < nbins_; i++) {
 	if ( samples[i][istep] > 0) {
-	  bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nMolecules;
+	  bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_;
 	}
       }    
     }