| 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 |
|
/** |
| 78 |
|
chi_(0.0), |
| 79 |
|
integralOfChiDt_(0.0), |
| 80 |
|
eta_(0.0), id_(-1), hasCOM_(false), |
| 81 |
< |
hasVolume_(false), volume_(0.0) { |
| 81 |
> |
volume_(0.0), hasVolume_(false) { |
| 82 |
|
|
| 83 |
|
} |
| 84 |
|
|
| 89 |
|
currentTime_(0), orthoTolerance_(1e-6), |
| 90 |
|
orthoRhombic_(0), chi_(0.0), |
| 91 |
|
integralOfChiDt_(0.0), eta_(0.0), id_(-1), |
| 92 |
< |
hasCOM_(false), hasVolume_(false), |
| 93 |
< |
volume_(0.0) { |
| 92 |
> |
hasCOM_(false), volume_(0.0), |
| 93 |
> |
hasVolume_(false) { |
| 94 |
|
} |
| 95 |
|
|
| 96 |
|
/** Returns the id of this Snapshot */ |
| 117 |
|
return rigidbodyData.getSize(); |
| 118 |
|
} |
| 119 |
|
|
| 120 |
+ |
/** Returns the number of rigid bodies */ |
| 121 |
+ |
int getNumberOfCutoffGroups() { |
| 122 |
+ |
return cgData.getSize(); |
| 123 |
+ |
} |
| 124 |
+ |
|
| 125 |
|
/** Returns the H-Matrix */ |
| 126 |
|
Mat3x3d getHmat() { |
| 127 |
|
return hmat_; |
| 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(); |
| 210 |
|
COMvel_ = COMvel; |
| 211 |
|
COMw_ = COMw; |
| 212 |
|
hasCOM_ = true; |
| 205 |
– |
} |
| 206 |
– |
|
| 207 |
– |
Vector3d getAtomPosByIindex(int iIndex) { |
| 208 |
– |
#ifdef IS_MPI |
| 209 |
– |
return atomIData.position[iIndex]; |
| 210 |
– |
#else |
| 211 |
– |
return atomData.position[iIndex]; |
| 212 |
– |
#endif |
| 213 |
– |
} |
| 214 |
– |
Vector3d getAtomPosByJindex(int jIndex) { |
| 215 |
– |
#ifdef IS_MPI |
| 216 |
– |
return atomJData.position[jIndex]; |
| 217 |
– |
#else |
| 218 |
– |
return atomData.position[jIndex]; |
| 219 |
– |
#endif |
| 213 |
|
} |
| 214 |
|
|
| 222 |
– |
Vector3d getCutoffGroupPosByIindex(int iIndex) { |
| 223 |
– |
#ifdef IS_MPI |
| 224 |
– |
return cgIData.position[iIndex]; |
| 225 |
– |
#else |
| 226 |
– |
return cgData.position[iIndex]; |
| 227 |
– |
#endif |
| 228 |
– |
} |
| 229 |
– |
Vector3d getCutoffGroupPosByJindex(int jIndex) { |
| 230 |
– |
#ifdef IS_MPI |
| 231 |
– |
return cgJData.position[jIndex]; |
| 232 |
– |
#else |
| 233 |
– |
return cgData.position[jIndex]; |
| 234 |
– |
#endif |
| 235 |
– |
} |
| 236 |
– |
|
| 215 |
|
DataStorage atomData; |
| 216 |
|
DataStorage rigidbodyData; |
| 217 |
|
DataStorage cgData; |
| 218 |
|
Stats statData; |
| 219 |
|
|
| 242 |
– |
#ifdef IS_MPI |
| 243 |
– |
DataStorage atomIData; |
| 244 |
– |
DataStorage atomJData; |
| 245 |
– |
DataStorage cgIData; |
| 246 |
– |
DataStorage cgJData; |
| 247 |
– |
#endif |
| 248 |
– |
|
| 249 |
– |
|
| 220 |
|
private: |
| 221 |
|
RealType currentTime_; |
| 222 |
|
|
