| 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). |
| 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 |
|
|
| 56 |
|
#include "brains/DataStorage.hpp" |
| 57 |
|
#include "brains/Stats.hpp" |
| 57 |
– |
#include "UseTheForce/DarkSide/simulation_interface.h" |
| 58 |
|
|
| 59 |
– |
|
| 59 |
|
namespace OpenMD{ |
| 60 |
|
|
| 61 |
|
/** |
| 150 |
|
|
| 151 |
|
/** Wrapping the vector according to periodic boundary condition*/ |
| 152 |
|
void wrapVector(Vector3d& v); |
| 153 |
+ |
/** Scaling a vector to multiples of the periodic box */ |
| 154 |
+ |
Vector3d scaleVector(Vector3d &v); |
| 155 |
+ |
|
| 156 |
+ |
|
| 157 |
|
Vector3d getCOM(); |
| 158 |
|
Vector3d getCOMvel(); |
| 159 |
|
Vector3d getCOMw(); |
| 212 |
|
hasCOM_ = true; |
| 213 |
|
} |
| 214 |
|
|
| 212 |
– |
Vector3d getAtomPosByIindex(int iIndex) { |
| 213 |
– |
#ifdef IS_MPI |
| 214 |
– |
return atomIData.position[iIndex]; |
| 215 |
– |
#else |
| 216 |
– |
return atomData.position[iIndex]; |
| 217 |
– |
#endif |
| 218 |
– |
} |
| 219 |
– |
Vector3d getAtomPosByJindex(int jIndex) { |
| 220 |
– |
#ifdef IS_MPI |
| 221 |
– |
return atomJData.position[jIndex]; |
| 222 |
– |
#else |
| 223 |
– |
return atomData.position[jIndex]; |
| 224 |
– |
#endif |
| 225 |
– |
} |
| 226 |
– |
|
| 227 |
– |
Vector3d getCutoffGroupPosByIindex(int iIndex) { |
| 228 |
– |
#ifdef IS_MPI |
| 229 |
– |
return cgIData.position[iIndex]; |
| 230 |
– |
#else |
| 231 |
– |
return cgData.position[iIndex]; |
| 232 |
– |
#endif |
| 233 |
– |
} |
| 234 |
– |
Vector3d getCutoffGroupPosByJindex(int jIndex) { |
| 235 |
– |
#ifdef IS_MPI |
| 236 |
– |
return cgJData.position[jIndex]; |
| 237 |
– |
#else |
| 238 |
– |
return cgData.position[jIndex]; |
| 239 |
– |
#endif |
| 240 |
– |
} |
| 241 |
– |
|
| 215 |
|
DataStorage atomData; |
| 216 |
|
DataStorage rigidbodyData; |
| 217 |
|
DataStorage cgData; |
| 218 |
|
Stats statData; |
| 219 |
|
|
| 247 |
– |
#ifdef IS_MPI |
| 248 |
– |
DataStorage atomIData; |
| 249 |
– |
DataStorage atomJData; |
| 250 |
– |
DataStorage cgIData; |
| 251 |
– |
DataStorage cgJData; |
| 252 |
– |
#endif |
| 253 |
– |
|
| 254 |
– |
|
| 220 |
|
private: |
| 221 |
|
RealType currentTime_; |
| 222 |
|
|
