--- trunk/src/applications/staticProps/ObjectCount.cpp	2010/10/19 18:40:54	1513
+++ trunk/src/applications/staticProps/ObjectCount.cpp	2012/08/22 02:28:28	1782
@@ -36,7 +36,8 @@
  * [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).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <algorithm>
@@ -68,8 +69,13 @@ void ObjectCount::process() {
   SimInfo::MoleculeIterator mi;
   Molecule::RigidBodyIterator rbIter;
   
+  counts_.clear();
+  counts_.resize(10, 0);
   DumpReader reader(info_, dumpFilename_);    
   int nFrames = reader.getNFrames();
+  unsigned long int nsum = 0;
+  unsigned long int n2sum = 0;
+
   for (int i = 0; i < nFrames; i += step_) {
     reader.readFrame(i);
     currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
@@ -87,30 +93,20 @@ void ObjectCount::process() {
 	seleMan_.setSelectionSet(evaluator_.evaluate());
     }
         
-    int count = 0;
-    int k; 
+    unsigned int count = seleMan_.getSelectionCount();
 
-    for (StuntDouble* sd = seleMan_.beginSelected(k); 
-         sd != NULL; sd = seleMan_.nextSelected(k)) {
-      count++;
+    if (counts_.size() <= count)  {
+      counts_.resize(count, 0);
     }
-    
-    if (counts_.size() < count) counts_.resize(count);
+
     counts_[count]++;
+
+    nsum += count;
+    n2sum += count * count;
   }
    
   int nProcessed = nFrames /step_;
 
-  vector<int>::iterator it;
-  unsigned long int n;
-  unsigned long int nsum = 0;
-  unsigned long int n2sum = 0;
-  for (it = counts_.begin(); it != counts_.end(); ++it) {
-    n = (*it);
-    nsum += n;
-    n2sum += n*n;
-  }
-
   nAvg = nsum / nProcessed;
   n2Avg = n2sum / nProcessed;
   sDev = sqrt(n2Avg - nAvg*nAvg);
@@ -125,11 +121,11 @@ void ObjectCount::process() {
       ofs << "# <N> = "<< nAvg << "\n";
       ofs << "# <N^2> = " << n2Avg << "\n";
       ofs << "# sqrt(<N^2> - <N>^2)  = " << sDev << "\n";
-      ofs << "# N\tcount(N)\n";
+      ofs << "# N\tcounts[N]\n";
+      for (unsigned int i = 0; i < counts_.size(); ++i) {
+        ofs << i << "\t" << counts_[i] << "\n";
+      }
       
-      for (int i = 0; i < counts_.size(); ++i) {
-        ofs << i <<"\t" << counts_[i]<< std::endl;
-      }        
     } else {
       
       sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str());