| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 55 |
|
#define ISZERO(a,eps) ( (a)>-(eps) && (a)<(eps) ) |
| 56 |
|
const RealType tiny=1.0e-6; |
| 57 |
|
|
| 58 |
< |
namespace oopse{ |
| 58 |
> |
namespace OpenMD{ |
| 59 |
|
|
| 60 |
|
/** |
| 61 |
|
* @class Quaternion Quaternion.hpp "math/Quaternion.hpp" |
| 255 |
|
return rotation angle from -PI to PI |
| 256 |
|
*/ |
| 257 |
|
inline Real get_rotation_angle() const{ |
| 258 |
< |
if( w < (Real)0.0 ) |
| 258 |
> |
if( w() < (Real)0.0 ) |
| 259 |
|
return 2.0*atan2(-sqrt( x()*x() + y()*y() + z()*z() ), -w() ); |
| 260 |
|
else |
| 261 |
|
return 2.0*atan2( sqrt( x()*x() + y()*y() + z()*z() ), w() ); |
| 274 |
|
v.x()*sin_a, |
| 275 |
|
v.y()*sin_a, |
| 276 |
|
v.z()*sin_a); |
| 277 |
+ |
return *this; |
| 278 |
|
} |
| 279 |
|
|
| 280 |
|
/** |
| 313 |
|
c.z()); |
| 314 |
|
|
| 315 |
|
this->normalize(); // if "from" or "to" not unit, normalize quat |
| 316 |
< |
w += 1.0f; // reducing angle to halfangle |
| 317 |
< |
if( w <= 1e-6 ) { // angle close to PI |
| 316 |
> |
w() += 1.0f; // reducing angle to halfangle |
| 317 |
> |
if( w() <= 1e-6 ) { // angle close to PI |
| 318 |
|
if( ( from.z()*from.z() ) > ( from.x()*from.x() ) ) { |
| 319 |
< |
this->data_[0] = w; |
| 319 |
> |
this->data_[0] = w(); |
| 320 |
|
this->data_[1] = 0.0; //cross(from , Vector3d(1,0,0)) |
| 321 |
|
this->data_[2] = from.z(); |
| 322 |
|
this->data_[3] = -from.y(); |
| 323 |
|
} else { |
| 324 |
< |
this->data_[0] = w; |
| 324 |
> |
this->data_[0] = w(); |
| 325 |
|
this->data_[1] = from.y(); //cross(from, Vector3d(0,0,1)) |
| 326 |
|
this->data_[2] = -from.x(); |
| 327 |
|
this->data_[3] = 0.0; |
