ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/primitives/Torsion.cpp
(Generate patch)

Comparing trunk/src/primitives/Torsion.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1446 by gezelter, Thu Jun 17 14:48:02 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 "primitives/Torsion.hpp"
43  
44 < namespace oopse {
44 > namespace OpenMD {
45  
46    Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4,
47                     TorsionType *tt) :
# Line 63 | Line 63 | namespace oopse {
63      RealType rA = A.length();
64      Vector3d B = cross(r32, r43);
65      RealType rB = B.length();
66 –    Vector3d C = cross(r32, A);
67 –    RealType rC = C.length();
66  
67 +    /*
68 +       If either of the two cross product vectors is tiny, that means
69 +       the three atoms involved are colinear, and the torsion angle is
70 +       going to be undefined.  The easiest check for this problem is
71 +       to use the product of the two lengths.
72 +    */
73 +    if (rA * rB < OpenMD::epsilon) return;
74 +    
75      A.normalize();
76 <    B.normalize();
71 <    C.normalize();
76 >    B.normalize();  
77      
78      //  Calculate the sin and cos
79      RealType cos_phi = dot(A, B) ;
80      if (cos_phi > 1.0) cos_phi = 1.0;
81      if (cos_phi < -1.0) cos_phi = -1.0;
82 <
82 >    
83      RealType dVdcosPhi;
84      torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
85 <    Vector3d f1;
86 <    Vector3d f2;
87 <    Vector3d f3;
88 <
85 >    Vector3d f1 ;
86 >    Vector3d f2 ;
87 >    Vector3d f3 ;
88 >    
89      Vector3d dcosdA = (cos_phi * A - B) /rA;
90      Vector3d dcosdB = (cos_phi * B - A) /rB;
91 <
91 >    
92      f1 = dVdcosPhi * cross(r32, dcosdA);
93      f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
94      f3 = dVdcosPhi * cross(dcosdB, r32);
# Line 92 | Line 97 | namespace oopse {
97      atom2_->addFrc(f2 - f1);
98      atom3_->addFrc(f3 - f2);
99      atom4_->addFrc(-f3);
100 <    angle = acos(cos_phi) /M_PI * 180.0;
101 <  }
102 <
100 >    
101 >    atom1_->addParticlePot(potential_);
102 >    atom2_->addParticlePot(potential_);
103 >    atom3_->addParticlePot(potential_);
104 >    atom4_->addParticlePot(potential_);
105 >    
106 >    angle = acos(cos_phi) /M_PI * 180.0;    
107 >  }  
108   }

Comparing trunk/src/primitives/Torsion.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1446 by gezelter, Thu Jun 17 14:48:02 2010 UTC

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

Diff Legend

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