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Comparing trunk/src/primitives/DirectionalAtom.cpp (file contents):
Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 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/DirectionalAtom.hpp"
43   #include "utils/simError.h"
44 < namespace oopse {
44 > namespace OpenMD {
45    
46    DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
47      : Atom(dAtomType){
# Line 55 | Line 55 | namespace oopse {
55      int nLinearAxis = 0;
56      Mat3x3d inertiaTensor = getI();
57      for (int i = 0; i < 3; i++) {    
58 <      if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
58 >      if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
59          linear_ = true;
60          linearAxis_ = i;
61          ++ nLinearAxis;
# Line 65 | Line 65 | namespace oopse {
65      if (nLinearAxis > 1) {
66        sprintf( painCave.errMsg,
67                 "Directional Atom warning.\n"
68 <               "\tOOPSE found more than one axis in this directional atom with a vanishing \n"
68 >               "\tOpenMD found more than one axis in this directional atom with a vanishing \n"
69                 "\tmoment of inertia.");
70        painCave.isFatal = 0;
71        simError();
# Line 134 | Line 134 | namespace oopse {
134      ephi[1] = 0.0;
135      ephi[2] = 1.0;
136      
137 <    etheta[0] = cphi;
138 <    etheta[1] = sphi;
139 <    etheta[2] = 0.0;
137 >    etheta[0] = -sphi;
138 >    etheta[1] =  cphi;
139 >    etheta[2] =  0.0;
140      
141      epsi[0] = stheta * cphi;
142      epsi[1] = stheta * sphi;

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