--- trunk/src/applications/staticProps/P2OrderParameter.cpp	2011/03/03 20:32:49	1542
+++ trunk/src/applications/staticProps/P2OrderParameter.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 "applications/staticProps/P2OrderParameter.hpp"
@@ -61,7 +62,6 @@ namespace OpenMD {
     if (!evaluator1_.isDynamic()) {
       seleMan1_.setSelectionSet(evaluator1_.evaluate());
     }
-    
   }
 
   P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, 
@@ -122,8 +122,7 @@ namespace OpenMD {
     SimInfo::MoleculeIterator mi;
     Molecule::RigidBodyIterator rbIter;
     StuntDouble* sd;
-    int i;
-
+    int ii;
   
     DumpReader reader(info_, dumpFilename_);    
     int nFrames = reader.getNFrames();
@@ -131,7 +130,7 @@ namespace OpenMD {
     for (int i = 0; i < nFrames; i += step_) {
       reader.readFrame(i);
       currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
-
+      
       for (mol = info_->beginMolecule(mi); mol != NULL; 
            mol = info_->nextMolecule(mi)) {
         //change the positions of atoms which belong to the rigidbodies
@@ -148,8 +147,8 @@ namespace OpenMD {
         if  (evaluator1_.isDynamic()) 
           seleMan1_.setSelectionSet(evaluator1_.evaluate());
         
-        for (sd = seleMan1_.beginSelected(i); sd != NULL; 
-             sd = seleMan1_.nextSelected(i)) {
+        for (sd = seleMan1_.beginSelected(ii); sd != NULL; 
+             sd = seleMan1_.nextSelected(ii)) {
           if (sd->isDirectional()) {
             Vector3d vec = sd->getA().getColumn(2);
             vec.normalize();
@@ -173,10 +172,12 @@ namespace OpenMD {
         orderTensor /= sdPairs_.size();
       }
       
+
       orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();  
       
       Vector3d eigenvalues;
       Mat3x3d eigenvectors;    
+
       Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
       
       int which;
@@ -196,11 +197,10 @@ namespace OpenMD {
       }   
 
       RealType angle = 0.0;
-
       
       if (doVect_) {
-        for (sd = seleMan1_.beginSelected(i); sd != NULL; 
-             sd = seleMan1_.nextSelected(i)) {
+        for (sd = seleMan1_.beginSelected(ii); sd != NULL; 
+             sd = seleMan1_.nextSelected(ii)) {
           if (sd->isDirectional()) {
             Vector3d vec = sd->getA().getColumn(2);
             vec.normalize();
@@ -214,8 +214,7 @@ namespace OpenMD {
           Vector3d vec = j->first->getPos() - j->second->getPos();
           if (usePeriodicBoundaryConditions_)
             currentSnapshot_->wrapVector(vec);
-          vec.normalize();
-          
+          vec.normalize();          
           angle += acos(dot(vec, director)) ;
         }
         angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;