--- branches/development/src/brains/Snapshot.cpp	2010/07/09 23:08:25	1465
+++ branches/development/src/brains/Snapshot.cpp	2011/11/22 20:38:56	1665
@@ -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).
  */
   
 /**
@@ -59,7 +60,6 @@ namespace OpenMD {
     hmat_ = m;
     invHmat_ = hmat_.inverse();
     
-
     //prepare fortran Hmat 
     RealType fortranHmat[9];
     RealType fortranInvHmat[9];
@@ -115,49 +115,43 @@ namespace OpenMD {
     }    
 
     //notify fortran simulation box has changed
-    setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
+    // setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
   }
 
 
   void Snapshot::wrapVector(Vector3d& pos) {
+    
+    Vector3d scaled = scaleVector(pos);
+    
+    for (int i = 0; i < 3; i++) 
+      scaled[i] -= roundMe(scaled[i]);
 
-    int i;
-    Vector3d scaled;
+    if( !orthoRhombic_ )
+      pos = hmat_ * scaled;    
+    else {
 
-    if( !orthoRhombic_ ){
-
-      // calc the scaled coordinates.
-      scaled = invHmat_* pos;
-
-      // wrap the scaled coordinates
-      for (i = 0; i < 3; ++i) {
-	scaled[i] -= roundMe(scaled[i]);
-      }
-
       // calc the wrapped real coordinates from the wrapped scaled coordinates
-      pos = hmat_ * scaled;    
+      for (int i=0; i<3; i++) {
+	pos[i] = scaled[i] * hmat_(i, i);
+      }   
+    }
+  }
 
-    } else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
+  inline Vector3d Snapshot::scaleVector(Vector3d& pos) {   
     
-      // calc the scaled coordinates.
-      for (i=0; i<3; i++) {
-	scaled[i] = pos[i] * invHmat_(i, i);
-      }
-        
-      // wrap the scaled coordinates
-      for (i = 0; i < 3; ++i) {
-	scaled[i] -= roundMe(scaled[i]);
-      }
+    Vector3d scaled;
 
-      // calc the wrapped real coordinates from the wrapped scaled coordinates
-      for (i=0; i<3; i++) {
-	pos[i] = scaled[i] * hmat_(i, i);
-      }
-        
+    if( !orthoRhombic_ )
+      scaled = invHmat_* pos;
+    else {
+      // calc the scaled coordinates.
+      for (int i=0; i<3; i++) 
+        scaled[i] = pos[i] * invHmat_(i, i);
     }
 
+    return scaled;
   }
-
+  
   Vector3d Snapshot::getCOM() {
     if( !hasCOM_ ) {
       sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
@@ -184,6 +178,5 @@ namespace OpenMD {
     }
     return COMw_;
   }
- 
 }