| 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. |
| 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 "DLM.hpp" |
| 43 |
|
|
| 44 |
< |
namespace oopse { |
| 44 |
> |
namespace OpenMD { |
| 45 |
|
|
| 46 |
|
void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) { |
| 47 |
|
RealType dt2 = 0.5 * dt; |
| 108 |
|
RotMat3x3d rot = RotMat3x3d::identity(); // initalize rot as a unit matrix |
| 109 |
|
|
| 110 |
|
// use a small angle aproximation for sin and cosine |
| 111 |
< |
|
| 111 |
> |
/* |
| 112 |
|
angleSqr = angle * angle; |
| 113 |
|
angleSqrOver4 = angleSqr / 4.0; |
| 114 |
|
top = 1.0 - angleSqrOver4; |
| 116 |
|
|
| 117 |
|
cosAngle = top / bottom; |
| 118 |
|
sinAngle = angle / bottom; |
| 119 |
< |
|
| 119 |
> |
*/ |
| 120 |
|
// or don't use the small angle approximation: |
| 121 |
< |
//cosAngle = cos(angle); |
| 122 |
< |
//sinAngle = sin(angle); |
| 121 |
> |
cosAngle = cos(angle); |
| 122 |
> |
sinAngle = sin(angle); |
| 123 |
> |
|
| 124 |
|
rot(axes1, axes1) = cosAngle; |
| 125 |
|
rot(axes2, axes2) = cosAngle; |
| 126 |
|
|
