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root/OpenMD/trunk/src/primitives/Torsion.cpp
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Comparing trunk/src/primitives/Torsion.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 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 "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) :
48      atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { }
49  
50 <  void Torsion::calcForce(double& angle) {
50 >  void Torsion::calcForce(RealType& angle) {
51  
52      Vector3d pos1 = atom1_->getPos();
53      Vector3d pos2 = atom2_->getPos();
# Line 60 | Line 60 | namespace oopse {
60  
61      //  Calculate the cross products and distances
62      Vector3d A = cross(r21, r32);
63 <    double rA = A.length();
63 >    RealType rA = A.length();
64      Vector3d B = cross(r32, r43);
65 <    double rB = B.length();
65 >    RealType rB = B.length();
66      Vector3d C = cross(r32, A);
67 <    double rC = C.length();
67 >    RealType rC = C.length();
68  
69      A.normalize();
70      B.normalize();
71      C.normalize();
72      
73      //  Calculate the sin and cos
74 <    double cos_phi = dot(A, B) ;
74 >    RealType cos_phi = dot(A, B) ;
75      if (cos_phi > 1.0) cos_phi = 1.0;
76      if (cos_phi < -1.0) cos_phi = -1.0;
77  
78 <    double dVdcosPhi;
78 >    RealType dVdcosPhi;
79      torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
80 <    Vector3d f1;
81 <    Vector3d f2;
82 <    Vector3d f3;
80 >    Vector3d f1 ;
81 >    Vector3d f2 ;
82 >    Vector3d f3 ;
83  
84      Vector3d dcosdA = (cos_phi * A - B) /rA;
85      Vector3d dcosdB = (cos_phi * B - A) /rB;
# Line 92 | Line 92 | namespace oopse {
92      atom2_->addFrc(f2 - f1);
93      atom3_->addFrc(f3 - f2);
94      atom4_->addFrc(-f3);
95 +
96 +    atom1_->addParticlePot(potential_);
97 +    atom2_->addParticlePot(potential_);
98 +    atom3_->addParticlePot(potential_);
99 +    atom4_->addParticlePot(potential_);
100 +
101      angle = acos(cos_phi) /M_PI * 180.0;
102    }
103  

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