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root/OpenMD/trunk/src/restraints/MolecularRestraint.cpp
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Comparing trunk/src/restraints/MolecularRestraint.cpp (file contents):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 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 "restraints/MolecularRestraint.hpp"
# Line 46 | Line 46
46  
47   //using namespace JAMA;
48  
49 < namespace oopse {
49 > namespace OpenMD {
50  
51 +
52    void MolecularRestraint::calcForce(std::vector<Vector3d> struc,
53                                       Vector3d molCom){
54  
# Line 141 | Line 142 | namespace oopse {
142  
143        Quat4d quat = A.toQuaternion();  
144  
144 –      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
145 –
145        RealType tw, sx, sy, ttw, swingX, swingY;
146 <      quat.toTwistSwing(tw, sx, sy);
148 <      quat.toSwingTwist(swingX, swingY, ttw);
146 >      quat.toSwingTwist(swingX, swingY, twistAngle);
147  
150 –      // std::cerr << eularAngles << "\t[" << twistAngle << "," << swingAngle <<
151 –      // "]\t[" << tw << "," << sx << "," << sy << "]\t[" << ttw <<
152 –      // "," << ssx << "," << ssy << "]" << std::endl;
153 –
148        RealType dVdtwist, dVdswing, dVdswingX, dVdswingY;
149        RealType dTwist, dSwing, dSwingX, dSwingY;
150        RealType p;

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