| 183 |
|
BendStamp* currentBend; |
| 184 |
|
TorsionStamp* currentTorsion; |
| 185 |
|
RigidBodyStamp* currentRigidBody; |
| 186 |
< |
|
| 186 |
> |
CutoffGroupStamp* currentCutoffGroup; |
| 187 |
> |
CutoffGroup* myCutoffGroup; |
| 188 |
> |
|
| 189 |
|
bond_pair* theBonds; |
| 190 |
|
bend_set* theBends; |
| 191 |
|
torsion_set* theTorsions; |
| 218 |
|
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
| 219 |
|
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 220 |
|
molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
| 221 |
+ |
molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
| 222 |
|
|
| 223 |
|
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
| 224 |
|
|
| 483 |
|
info[k].rigidBodies.push_back(myRB); |
| 484 |
|
} |
| 485 |
|
|
| 486 |
+ |
|
| 487 |
+ |
//creat cutoff group for molecule |
| 488 |
+ |
molInfo.myCutoffGroups.clear(); |
| 489 |
+ |
for (j = 0; j < molInfo.nCutoffGroups; j++){ |
| 490 |
+ |
|
| 491 |
+ |
currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
| 492 |
+ |
nMembers = currentCutoffGroup->getNMembers(); |
| 493 |
|
|
| 494 |
+ |
myCutoffGroup = new CutoffGroup(); |
| 495 |
+ |
|
| 496 |
+ |
for (int cg = 0; cg < nMembers; cg++) { |
| 497 |
+ |
|
| 498 |
+ |
// molI is atom numbering inside this molecule |
| 499 |
+ |
molI = currentCutoffGroup->getMember(cg); |
| 500 |
+ |
|
| 501 |
+ |
// tempI is atom numbering on local processor |
| 502 |
+ |
tempI = molI + atomOffset; |
| 503 |
+ |
|
| 504 |
+ |
myCutoffGroup->addAtom(info[k].atoms[tempI]); |
| 505 |
+ |
} |
| 506 |
+ |
|
| 507 |
+ |
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 508 |
+ |
}//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
| 509 |
+ |
|
| 510 |
+ |
|
| 511 |
+ |
|
| 512 |
|
// After this is all set up, scan through the atoms to |
| 513 |
|
// see if they can be added to the integrableObjects: |
| 514 |
|
|
| 1310 |
|
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
| 1311 |
|
LinkedMolStamp* currentStamp = NULL; |
| 1312 |
|
comp_stamps = new MoleculeStamp * [n_components]; |
| 1313 |
+ |
bool haveCutoffGroups; |
| 1314 |
|
|
| 1315 |
+ |
haveCutoffGroups = false; |
| 1316 |
+ |
|
| 1317 |
|
// make an array of molecule stamps that match the components used. |
| 1318 |
|
// also extract the used stamps out into a separate linked list |
| 1319 |
|
|
| 1348 |
|
headStamp->add(currentStamp); |
| 1349 |
|
comp_stamps[i] = headStamp->match(id); |
| 1350 |
|
} |
| 1351 |
+ |
|
| 1352 |
+ |
if(comp_stamps[i]->getNCutoffGroups() > 0) |
| 1353 |
+ |
haveCutoffGroups = true; |
| 1354 |
|
} |
| 1355 |
+ |
|
| 1356 |
+ |
for (i = 0; i < nInfo; i++) |
| 1357 |
+ |
info[i].haveCutoffGroups = haveCutoffGroups; |
| 1358 |
|
|
| 1359 |
|
#ifdef IS_MPI |
| 1360 |
|
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
| 1529 |
|
info[l].atoms = the_atoms; |
| 1530 |
|
info[l].molecules = the_molecules; |
| 1531 |
|
info[l].nGlobalExcludes = 0; |
| 1532 |
< |
|
| 1532 |
> |
|
| 1533 |
|
the_ff->setSimInfo(info); |
| 1534 |
|
} |
| 1535 |
|
} |
