--- trunk/src/integrators/DLM.cpp	2005/01/12 22:41:40	246
+++ trunk/src/integrators/DLM.cpp	2009/04/23 18:31:05	1339
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -43,9 +43,9 @@ namespace oopse {
 
 namespace oopse {
 
-void DLM::doRotate(StuntDouble* sd, Vector3d& ji, double dt) {
-    double dt2 = 0.5 * dt;    
-    double angle;
+  void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) {
+    RealType dt2 = 0.5 * dt;    
+    RealType angle;
 
     RotMat3x3d A = sd->getA();
     Mat3x3d I = sd->getI();
@@ -53,54 +53,54 @@ void DLM::doRotate(StuntDouble* sd, Vector3d& ji, doub
     // use the angular velocities to propagate the rotation matrix a full time step
     if (sd->isLinear()) {
 
-        int i = sd->linearAxis();
-        int j = (i+1)%3;
-        int k = (i+2)%3;
+      int i = sd->linearAxis();
+      int j = (i+1)%3;
+      int k = (i+2)%3;
 
-        angle = dt2 * ji[j] / I(j, j);
-        rotateStep( k, i, angle, ji, A );
+      angle = dt2 * ji[j] / I(j, j);
+      rotateStep( k, i, angle, ji, A );
 
-        angle = dt * ji[k] / I(k, k);
-        rotateStep( i, j, angle, ji, A);
+      angle = dt * ji[k] / I(k, k);
+      rotateStep( i, j, angle, ji, A);
 
-        angle = dt2 * ji[j] / I(j, j);
-        rotateStep( k, i, angle, ji, A );
+      angle = dt2 * ji[j] / I(j, j);
+      rotateStep( k, i, angle, ji, A );
 
     } else {
-        // rotate about the x-axis
-        angle = dt2 * ji[0] / I(0, 0);
-        rotateStep( 1, 2, angle, ji, A );
+      // rotate about the x-axis
+      angle = dt2 * ji[0] / I(0, 0);
+      rotateStep( 1, 2, angle, ji, A );
 
-        // rotate about the y-axis
-        angle = dt2 * ji[1] / I(1, 1);
-        rotateStep( 2, 0, angle, ji, A );
+      // rotate about the y-axis
+      angle = dt2 * ji[1] / I(1, 1);
+      rotateStep( 2, 0, angle, ji, A );
 
-        // rotate about the z-axis
-        angle = dt * ji[2] / I(2, 2);
-        sd->addZangle(angle);
-        rotateStep( 0, 1, angle, ji, A);
+      // 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
-        angle = dt2 * ji[1] / I(1, 1);
-        rotateStep( 2, 0, angle, ji, A );
+      // rotate about the y-axis
+      angle = dt2 * ji[1] / I(1, 1);
+      rotateStep( 2, 0, angle, ji, A );
 
-        // rotate about the x-axis
-        angle = dt2 * ji[0] / I(0, 0);
-        rotateStep( 1, 2, angle, ji, A );
+      // rotate about the x-axis
+      angle = dt2 * ji[0] / I(0, 0);
+      rotateStep( 1, 2, angle, ji, A );
 
     }
 
     sd->setA( A  );
-}
+  }
 
 
-void DLM::rotateStep(int axes1, int axes2, double angle, Vector3d& ji, RotMat3x3d& A) {
+  void DLM::rotateStep(int axes1, int axes2, RealType angle, Vector3d& ji, RotMat3x3d& A) {
 
-    double sinAngle;
-    double cosAngle;
-    double angleSqr;
-    double angleSqrOver4;
-    double top, bottom;
+    RealType sinAngle;
+    RealType cosAngle;
+    RealType angleSqr;
+    RealType angleSqrOver4;
+    RealType top, bottom;
 
     RotMat3x3d tempA(A);  // initialize the tempA
     Vector3d tempJ(0.0);
@@ -117,6 +117,9 @@ void DLM::rotateStep(int axes1, int axes2, double angl
     cosAngle = top / bottom;
     sinAngle = angle / bottom;
 
+    // or don't use the small angle approximation:
+    //cosAngle = cos(angle);
+    //sinAngle = sin(angle);
     rot(axes1, axes1) = cosAngle;
     rot(axes2, axes2) = cosAngle;
 
@@ -126,13 +129,28 @@ void DLM::rotateStep(int axes1, int axes2, double angl
     // 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;
   
-}
+  }
 
 
 }