ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/restraints/ObjectRestraint.cpp
(Generate patch)

Comparing trunk/src/restraints/ObjectRestraint.cpp (file contents):
Revision 1364 by cli2, Wed Oct 7 20:49:50 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/ObjectRestraint.hpp"
43  
44 < namespace oopse {
44 > namespace OpenMD {
45  
46    void ObjectRestraint::calcForce(Vector3d struc) {
47  
48      pot_ = 0.0;
49 –    
49      if (restType_ & rtDisplacement) {
50        Vector3d del = struc - refPos_;
51 <      RealType r = del.length();  
51 >      RealType r = del.length();
52        Vector3d frc = -kDisp_ * del;
53        RealType p = 0.5 * kDisp_ * del.lengthSquare();
54 <      pot_ += p;
54 >      pot_ = p;
55        force_ = frc * scaleFactor_;
56        restInfo_[rtDisplacement] = std::make_pair(r,p);
57      }
# Line 73 | Line 72 | namespace oopse {
72  
73        RealType twistAngle, swingAngle;
74        Vector3d swingAxis;
75 <      RealType tw, swingX, swingY;
75 >      RealType swingX, swingY;
76        
77 <      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
78 <      quat.toSwingTwist(tw, swingX, swingY);
79 <      
77 >      quat.toSwingTwist(swingX, swingY, twistAngle);
78 >
79 >
80        RealType dVdtwist, dVdswingX, dVdswingY;
81        RealType dTwist, dSwingX, dSwingY;
82        RealType p;

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines