| 167 |
|
|
| 168 |
|
void SimSetup::makeMolecules(void){ |
| 169 |
|
int i, j, k; |
| 170 |
< |
int exI, exJ, exK, exL, slI; |
| 170 |
> |
int exI, exJ, exK, exL, slI, slJ; |
| 171 |
|
int tempI, tempJ, tempK, tempL; |
| 172 |
|
int molI; |
| 173 |
|
int stampID, atomOffset, rbOffset; |
| 465 |
|
|
| 466 |
|
} |
| 467 |
|
} |
| 468 |
+ |
|
| 469 |
+ |
molInfo.myRigidBodies.push_back(myRB); |
| 470 |
+ |
info[k].rigidBodies.push_back(myRB); |
| 471 |
+ |
} |
| 472 |
+ |
|
| 473 |
+ |
|
| 474 |
+ |
// After this is all set up, scan through the atoms to |
| 475 |
+ |
// see if they can be added to the integrableObjects: |
| 476 |
+ |
|
| 477 |
+ |
for (j = 0; j < molInfo.nAtoms; j++){ |
| 478 |
+ |
|
| 479 |
+ |
#ifdef IS_MPI |
| 480 |
+ |
slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
| 481 |
+ |
#else |
| 482 |
+ |
slJ = j+atomOffset; |
| 483 |
+ |
#endif |
| 484 |
+ |
|
| 485 |
+ |
// if they aren't on the skip list, then they can be integrated |
| 486 |
+ |
|
| 487 |
+ |
if (skipList.find(slJ) == skipList.end()) { |
| 488 |
+ |
mySD = (StuntDouble *) molInfo.myAtoms[j]; |
| 489 |
+ |
info[k].integrableObjects.push_back(mySD); |
| 490 |
+ |
molInfo.myIntegrableObjects.push_back(mySD); |
| 491 |
+ |
} |
| 492 |
+ |
} |
| 493 |
+ |
|
| 494 |
+ |
// all rigid bodies are integrated: |
| 495 |
+ |
|
| 496 |
+ |
for (j = 0; j < molInfo.nRigidBodies; j++) { |
| 497 |
+ |
mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
| 498 |
+ |
info[k].integrableObjects.push_back(mySD); |
| 499 |
+ |
molInfo.myIntegrableObjects.push_back(mySD); |
| 500 |
|
} |
| 501 |
+ |
|
| 502 |
|
|
| 503 |
|
// send the arrays off to the forceField for init. |
| 504 |
|
|
| 515 |
|
delete[] theBonds; |
| 516 |
|
delete[] theBends; |
| 517 |
|
delete[] theTorsions; |
| 518 |
< |
} |
| 486 |
< |
|
| 487 |
< |
// build up the integrableObjects vector: |
| 488 |
< |
|
| 489 |
< |
for (i = 0; i < info[k].n_atoms; i++) { |
| 490 |
< |
|
| 491 |
< |
#ifdef IS_MPI |
| 492 |
< |
slI = info[k].atoms[i]->getGlobalIndex(); |
| 493 |
< |
#else |
| 494 |
< |
slI = i; |
| 495 |
< |
#endif |
| 496 |
< |
|
| 497 |
< |
if (skipList.find(slI) == skipList.end()) { |
| 498 |
< |
mySD = (StuntDouble *) info[k].atoms[i]; |
| 499 |
< |
info[k].integrableObjects.push_back(mySD); |
| 500 |
< |
} |
| 501 |
< |
} |
| 502 |
< |
for (i = 0; i < info[k].rigidBodies.size(); i++) { |
| 503 |
< |
mySD = (StuntDouble *) info[k].rigidBodies[i]; |
| 504 |
< |
info[k].integrableObjects.push_back(mySD); |
| 505 |
< |
} |
| 506 |
< |
|
| 518 |
> |
} |
| 519 |
|
} |
| 520 |
|
|
| 521 |
|
#ifdef IS_MPI |
