--- trunk/OOPSE/libmdtools/ExtendedSystem.cpp	2003/04/08 12:44:18	475
+++ trunk/OOPSE/libmdtools/ExtendedSystem.cpp	2003/04/08 12:50:18	476
@@ -172,6 +172,7 @@ void ExtendedSystem::AffineTransform( double oldBox[3]
   double r[3];
   double boxNum[3];
   double percentScale[3];
+  double delta[3];
   double rxi, ryi, rzi;
 
   molecules = entry_plug->molecules;
@@ -181,9 +182,6 @@ void ExtendedSystem::AffineTransform( double oldBox[3]
   percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
   percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
   
-  std::cerr << "ps = " << percentScale[0] <<" " << percentScale[1] << " " << percentScale[2] << "\n";
-
-
   for (i=0; i < entry_plug->n_mol; i++) {
     
     molecules[i].getCOM(r);
@@ -199,9 +197,6 @@ void ExtendedSystem::AffineTransform( double oldBox[3]
     boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * 
       (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
 
-
-    std::cerr << "boxNum = " << boxNum[0] << " " << boxNum[1] << " " << boxNum[2] << "\n";
-
     rxi = r[0] - boxNum[0];
     ryi = r[1] - boxNum[1];
     rzi = r[2] - boxNum[2];
@@ -211,10 +206,10 @@ void ExtendedSystem::AffineTransform( double oldBox[3]
     ryi += ryi*percentScale[1];
     rzi += rzi*percentScale[2];
 
-    r[0] = rxi + boxNum[0];
-    r[1] = ryi + boxNum[1];
-    r[2] = rzi + boxNum[2];
+    delta[0] = r[0] - (rxi + boxNum[0]);
+    delta[1] = r[1] - (ryi + boxNum[1]);
+    delta[2] = r[2] - (rzi + boxNum[2]);
 
-    molecules[i].moveCOM(r);
+    molecules[i].moveCOM(delta);
   }
 }