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Comparing trunk/src/integrators/DLM.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include "DLM.hpp"
43  
44 < namespace oopse {
44 > namespace OpenMD {
45  
46    void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) {
47      RealType dt2 = 0.5 * dt;    
# Line 109 | Line 109 | namespace oopse {
109  
110      // use a small angle aproximation for sin and cosine
111  
112 <    //angleSqr = angle * angle;
113 <    //angleSqrOver4 = angleSqr / 4.0;
114 <    //top = 1.0 - angleSqrOver4;
115 <    //bottom = 1.0 + angleSqrOver4;
112 >    angleSqr = angle * angle;
113 >    angleSqrOver4 = angleSqr / 4.0;
114 >    top = 1.0 - angleSqrOver4;
115 >    bottom = 1.0 + angleSqrOver4;
116  
117 <    //cosAngle = top / bottom;
118 <    //sinAngle = angle / bottom;
119 <    cosAngle = cos(angle);
120 <    sinAngle = sin(angle);
117 >    cosAngle = top / bottom;
118 >    sinAngle = angle / bottom;
119 >
120 >    // or don't use the small angle approximation:
121 >    //cosAngle = cos(angle);
122 >    //sinAngle = sin(angle);
123      rot(axes1, axes1) = cosAngle;
124      rot(axes2, axes2) = cosAngle;
125  
# Line 127 | Line 129 | namespace oopse {
129      // rotate the momentum acoording to: ji[] = rot[][] * ji[]
130      ji = rot * ji;
131  
132 <    // rotate the Rotation matrix acording to:
133 <    // A[][] = A[][] * transpose(rot[][])
134 <    // transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
132 >    // This code comes from converting an algorithm detailed in
133 >    // J. Chem. Phys. 107 (15), pp. 5840-5851 by Dullweber,
134 >    // Leimkuhler and McLachlan (DLM) for use in our code.
135 >    // In Appendix A, the DLM paper has the change to the rotation
136 >    // matrix as: Q = Q * rot.transpose(), but our rotation matrix
137 >    // A is actually equivalent to Q.transpose(). This fact can be
138 >    // seen on page 5849 of the DLM paper where a lab frame
139 >    // dipole \mu_i(t) is expressed in terms of a body-fixed
140 >    // reference orientation, \bar{\mu_i} and the rotation matrix, Q:
141 >    //  \mu_i(t) = Q * \bar{\mu_i}
142 >    // Our code computes lab frame vectors from body-fixed reference
143 >    // vectors using:
144 >    //   v_{lab} = A.transpose() * v_{body}
145 >    //  (See StuntDouble.hpp for confirmation of this fact).
146 >    //
147 >    // So, using the identity:
148 >    //  (A * B).transpose() = B.transpose() * A.transpose(),  we
149 >    // get the equivalent of Q = Q * rot.transpose() for our code to be:
150  
151 <    A = rot * A; //? A = A* rot.transpose();
151 >    A = rot * A;
152    
153    }
154  

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