| 70 |
|
frameData.torsionPotential = 0.0; |
| 71 |
|
frameData.inversionPotential = 0.0; |
| 72 |
|
frameData.lrPotentials = potVec(0.0); |
| 73 |
+ |
frameData.reciprocalPotential = 0.0; |
| 74 |
|
frameData.excludedPotentials = potVec(0.0); |
| 75 |
|
frameData.restraintPotential = 0.0; |
| 76 |
|
frameData.rawPotential = 0.0; |
| 104 |
|
frameData.torsionPotential = 0.0; |
| 105 |
|
frameData.inversionPotential = 0.0; |
| 106 |
|
frameData.lrPotentials = potVec(0.0); |
| 107 |
+ |
frameData.reciprocalPotential = 0.0; |
| 108 |
|
frameData.excludedPotentials = potVec(0.0); |
| 109 |
|
frameData.restraintPotential = 0.0; |
| 110 |
|
frameData.rawPotential = 0.0; |
| 189 |
|
/** Returns the number of rigid bodies */ |
| 190 |
|
int Snapshot::getNumberOfCutoffGroups() { |
| 191 |
|
return cgData.getSize(); |
| 192 |
+ |
} |
| 193 |
+ |
|
| 194 |
+ |
/** Returns the number of bytes in a FrameData structure */ |
| 195 |
+ |
int Snapshot::getFrameDataSize() { |
| 196 |
+ |
return sizeof(FrameData); |
| 197 |
|
} |
| 198 |
|
|
| 199 |
|
/** Returns the H-Matrix */ |
| 304 |
|
frameData.volume = vol; |
| 305 |
|
} |
| 306 |
|
|
| 307 |
+ |
|
| 308 |
|
/** Wrap a vector according to periodic boundary conditions */ |
| 309 |
|
void Snapshot::wrapVector(Vector3d& pos) { |
| 310 |
|
|
| 311 |
< |
Vector3d scaled = scaleVector(pos); |
| 312 |
< |
|
| 313 |
< |
for (int i = 0; i < 3; i++) |
| 314 |
< |
scaled[i] -= roundMe(scaled[i]); |
| 315 |
< |
|
| 308 |
< |
if( !frameData.orthoRhombic ) |
| 309 |
< |
pos = frameData.hmat * scaled; |
| 310 |
< |
else { |
| 311 |
< |
|
| 311 |
> |
if( !frameData.orthoRhombic ) { |
| 312 |
> |
Vector3d scaled = frameData.invHmat * pos; |
| 313 |
> |
for (int i = 0; i < 3; i++) { |
| 314 |
> |
scaled[i] -= roundMe( scaled[i] ); |
| 315 |
> |
} |
| 316 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 317 |
< |
for (int i=0; i<3; i++) { |
| 318 |
< |
pos[i] = scaled[i] * frameData.hmat(i, i); |
| 319 |
< |
} |
| 317 |
> |
pos = frameData.hmat * scaled; |
| 318 |
> |
} else { |
| 319 |
> |
RealType scaled; |
| 320 |
> |
for (int i=0; i<3; i++) { |
| 321 |
> |
scaled = pos[i] * frameData.invHmat(i,i); |
| 322 |
> |
scaled -= roundMe( scaled ); |
| 323 |
> |
pos[i] = scaled * frameData.hmat(i,i); |
| 324 |
> |
} |
| 325 |
|
} |
| 326 |
|
} |
| 327 |
|
|
| 421 |
|
return frameData.shortRangePotential; |
| 422 |
|
} |
| 423 |
|
|
| 424 |
+ |
void Snapshot::setReciprocalPotential(RealType rp){ |
| 425 |
+ |
frameData.reciprocalPotential = rp; |
| 426 |
+ |
} |
| 427 |
+ |
|
| 428 |
+ |
RealType Snapshot::getReciprocalPotential() { |
| 429 |
+ |
return frameData.reciprocalPotential; |
| 430 |
+ |
} |
| 431 |
+ |
|
| 432 |
|
void Snapshot::setLongRangePotential(potVec lrPot) { |
| 433 |
|
frameData.lrPotentials = lrPot; |
| 434 |
|
} |
| 438 |
|
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 439 |
|
frameData.longRangePotential += frameData.lrPotentials[i]; |
| 440 |
|
} |
| 441 |
+ |
frameData.longRangePotential += frameData.reciprocalPotential; |
| 442 |
|
hasLongRangePotential = true; |
| 443 |
|
} |
| 444 |
|
return frameData.longRangePotential; |
