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.
branches/development/src/restraints/ObjectRestraint.cpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 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, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "restraints/ObjectRestraint.hpp"
44  
45 < namespace oopse {
45 > namespace OpenMD {
46  
47    void ObjectRestraint::calcForce(Vector3d struc) {
48  
49      pot_ = 0.0;
49 –    
50      if (restType_ & rtDisplacement) {
51        Vector3d del = struc - refPos_;
52 <      RealType r = del.length();  
52 >      RealType r = del.length();
53        Vector3d frc = -kDisp_ * del;
54        RealType p = 0.5 * kDisp_ * del.lengthSquare();
55 <      pot_ += p;
55 >      pot_ = p;
56        force_ = frc * scaleFactor_;
57        restInfo_[rtDisplacement] = std::make_pair(r,p);
58      }
# Line 71 | Line 71 | namespace oopse {
71  
72        Quat4d quat = temp.toQuaternion();
73  
74 <      RealType twistAngle, swingAngle;
74 >      RealType twistAngle;
75        Vector3d swingAxis;
76 <      RealType tw, swingX, swingY;
76 >      RealType swingX, swingY;
77        
78 <      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
79 <      quat.toSwingTwist(tw, swingX, swingY);
80 <      
81 <      RealType dVdtwist, dVdswingX, dVdswingY;
82 <      RealType dTwist, dSwingX, dSwingY;
78 >      quat.toSwingTwist(swingX, swingY, twistAngle);
79 >
80        RealType p;
81        Vector3d tTwist, tSwing;
82  
83        if (restType_ & rtTwist){
84 <        dTwist = twistAngle - twist0_;
85 <        dVdtwist = kTwist_ * sin(dTwist);
84 >        RealType dTwist = twistAngle - twist0_;
85 >        RealType dVdtwist = kTwist_ * sin(dTwist);
86          p = kTwist_ * (1.0 - cos(dTwist) );
87          pot_ += p;
88          tBody -= dVdtwist * V3Z;
# Line 93 | Line 90 | namespace oopse {
90        }
91  
92        if (restType_ & rtSwingX){
93 <        dSwingX = swingX - swingX0_;
94 <        dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
93 >        RealType dSwingX = swingX - swingX0_;
94 >        RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
95          p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
96          pot_ += p;
97          tBody -= dVdswingX * V3X;
# Line 102 | Line 99 | namespace oopse {
99        }
100  
101        if (restType_ & rtSwingY){
102 <        dSwingY = swingY - swingY0_;
103 <        dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
102 >        RealType dSwingY = swingY - swingY0_;
103 >        RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
104          p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
105          pot_ += p;
106          tBody -= dVdswingY * V3Y;

Comparing:
trunk/src/restraints/ObjectRestraint.cpp (property svn:keywords), Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
branches/development/src/restraints/ObjectRestraint.cpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

Diff Legend

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