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Comparing:
trunk/src/primitives/Inversion.cpp (file contents), Revision 1309 by gezelter, Tue Oct 21 18:23:31 2008 UTC vs.
branches/development/src/primitives/Inversion.cpp (file contents), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "primitives/Inversion.hpp"
44  
45 < namespace oopse {
45 > namespace OpenMD {
46  
47    Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3,
48                         Atom *atom4, InversionType *it) :
49      atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4),
50      inversionType_(it) { }
51    
52 <  void Inversion::calcForce(RealType& angle) {
52 >  void Inversion::calcForce(RealType& angle, bool doParticlePot) {
53      
54 <    // In OOPSE's version of an inversion, the central atom
54 >    // In OpenMD's version of an inversion, the central atom
55      // comes first.  However, to get the planarity in a typical cosine
56      // version of this potential (i.e. Amber-style), the central atom
57      // is treated as atom *3* in a standard torsion form:
# Line 94 | Line 95 | namespace oopse {
95      f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
96      f3 = dVdcosPhi * cross(dcosdB, r43);
97  
98 <    // In OOPSE's version of an improper torsion, the central atom
98 >    // In OpenMD's version of an improper torsion, the central atom
99      // comes first.  However, to get the planarity in a typical cosine
100      // version of this potential (i.e. Amber-style), the central atom
101      // is treated as atom *3* in a standard torsion form:
102  
103      //  AMBER:   I - J - K - L   (e.g. K is sp2 hybridized carbon)
104 <    //  OOPSE:   I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
104 >    //  OpenMD:  I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
105  
106      // Confusing enough?  Good.
107  
# Line 109 | Line 110 | namespace oopse {
110      atom4_->addFrc(-f2);
111      atom3_->addFrc(-f3);
112  
113 <    atom1_->addParticlePot(potential_);
114 <    atom2_->addParticlePot(potential_);
115 <    atom3_->addParticlePot(potential_);
116 <    atom4_->addParticlePot(potential_);
117 <
113 >    if (doParticlePot) {
114 >      atom1_->addParticlePot(potential_);
115 >      atom2_->addParticlePot(potential_);
116 >      atom3_->addParticlePot(potential_);
117 >      atom4_->addParticlePot(potential_);
118 >    }
119 >    
120      angle = acos(cos_phi) /M_PI * 180.0;
121    }
122  

Comparing:
trunk/src/primitives/Inversion.cpp (property svn:keywords), Revision 1309 by gezelter, Tue Oct 21 18:23:31 2008 UTC vs.
branches/development/src/primitives/Inversion.cpp (property svn:keywords), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

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