--- trunk/src/brains/Snapshot.cpp	2009/11/25 20:02:06	1390
+++ branches/development/src/brains/Snapshot.cpp	2011/05/25 16:20:37	1568
@@ -51,13 +51,14 @@
 #include "utils/NumericConstant.hpp"
 #include "utils/simError.h"
 #include "utils/Utility.hpp"
+#include <cstdio>
+
 namespace OpenMD {
 
   void  Snapshot::setHmat(const Mat3x3d& m) {
     hmat_ = m;
     invHmat_ = hmat_.inverse();
     
-
     //prepare fortran Hmat 
     RealType fortranHmat[9];
     RealType fortranInvHmat[9];
@@ -113,49 +114,43 @@ 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");
@@ -182,6 +177,5 @@ namespace OpenMD {
     }
     return COMw_;
   }
- 
 }