--- trunk/src/integrators/DLM.cpp	2006/05/17 21:51:42	963
+++ trunk/src/integrators/DLM.cpp	2013/06/16 15:15:42	1879
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,11 +28,21 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "DLM.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) {
     RealType dt2 = 0.5 * dt;    
@@ -77,7 +78,6 @@ namespace oopse {
 
       // rotate about the z-axis
       angle = dt * ji[2] / I(2, 2);
-      sd->addZangle(angle);
       rotateStep( 0, 1, angle, ji, A);
 
       // rotate about the y-axis
@@ -108,16 +108,19 @@ namespace oopse {
     RotMat3x3d rot = RotMat3x3d::identity(); // initalize rot as a unit matrix
 
     // use a small angle aproximation for sin and cosine
+    
+    angleSqr = angle * angle;
+    angleSqrOver4 = angleSqr / 4.0;
+    top = 1.0 - angleSqrOver4;
+    bottom = 1.0 + angleSqrOver4;
 
-    //angleSqr = angle * angle;
-    //angleSqrOver4 = angleSqr / 4.0;
-    //top = 1.0 - angleSqrOver4;
-    //bottom = 1.0 + angleSqrOver4;
+    cosAngle = top / bottom;
+    sinAngle = angle / bottom;
+    
+    // or don't use the small angle approximation:
+    //cosAngle = cos(angle);
+    //sinAngle = sin(angle);
 
-    //cosAngle = top / bottom;
-    //sinAngle = angle / bottom;
-    cosAngle = cos(angle);
-    sinAngle = sin(angle);
     rot(axes1, axes1) = cosAngle;
     rot(axes2, axes2) = cosAngle;
 
@@ -127,11 +130,26 @@ namespace oopse {
     // rotate the momentum acoording to: ji[] = rot[][] * ji[]
     ji = rot * ji;
 
-    // rotate the Rotation matrix acording to:
-    // A[][] = A[][] * transpose(rot[][])
-    // transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
+    // This code comes from converting an algorithm detailed in 
+    // J. Chem. Phys. 107 (15), pp. 5840-5851 by Dullweber, 
+    // Leimkuhler and McLachlan (DLM) for use in our code.
+    // In Appendix A, the DLM paper has the change to the rotation 
+    // matrix as: Q = Q * rot.transpose(), but our rotation matrix 
+    // A is actually equivalent to Q.transpose(). This fact can be 
+    // seen on page 5849 of the DLM paper where a lab frame 
+    // dipole \mu_i(t) is expressed in terms of a body-fixed
+    // reference orientation, \bar{\mu_i} and the rotation matrix, Q:
+    //  \mu_i(t) = Q * \bar{\mu_i}
+    // Our code computes lab frame vectors from body-fixed reference
+    // vectors using:
+    //   v_{lab} = A.transpose() * v_{body}
+    //  (See StuntDouble.hpp for confirmation of this fact).
+    //
+    // So, using the identity:
+    //  (A * B).transpose() = B.transpose() * A.transpose(),  we
+    // get the equivalent of Q = Q * rot.transpose() for our code to be:
 
-    A = rot * A; //? A = A* rot.transpose();
+    A = rot * A;
   
   }