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Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 UTC vs.
Revision 1424 by gezelter, Tue Mar 30 15:05:38 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   #include <algorithm>
42   #include <math.h>
43   #include "primitives/RigidBody.hpp"
44   #include "utils/simError.h"
45   #include "utils/NumericConstant.hpp"
46 < namespace oopse {
46 > namespace OpenMD {
47    
48    RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData),
49                             inertiaTensor_(0.0){    
# Line 117 | Line 117 | namespace oopse {
117      ephi[0] = 0.0;
118      ephi[1] = 0.0;
119      ephi[2] = 1.0;
120 +    
121 +    //etheta[0] = -sphi;
122 +    //etheta[1] =  cphi;
123 +    //etheta[2] =  0.0;
124      
125      etheta[0] = cphi;
126      etheta[1] = sphi;
127 <    etheta[2] = 0.0;
127 >    etheta[2] =  0.0;
128      
129      epsi[0] = stheta * cphi;
130      epsi[1] = stheta * sphi;
# Line 193 | Line 197 | namespace oopse {
197          
198      int nLinearAxis = 0;
199      for (int i = 0; i < 3; i++) {    
200 <      if (fabs(evals[i]) < oopse::epsilon) {
200 >      if (fabs(evals[i]) < OpenMD::epsilon) {
201          linear_ = true;
202          linearAxis_ = i;
203          ++ nLinearAxis;
# Line 203 | Line 207 | namespace oopse {
207      if (nLinearAxis > 1) {
208        sprintf( painCave.errMsg,
209                 "RigidBody error.\n"
210 <               "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
210 >               "\tOpenMD found more than one axis in this rigid body with a vanishing \n"
211                 "\tmoment of inertia.  This can happen in one of three ways:\n"
212                 "\t 1) Only one atom was specified, or \n"
213                 "\t 2) All atoms were specified at the same location, or\n"

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