| 185 |
|
RigidBodyStamp* currentRigidBody; |
| 186 |
|
CutoffGroupStamp* currentCutoffGroup; |
| 187 |
|
CutoffGroup* myCutoffGroup; |
| 188 |
< |
|
| 188 |
> |
int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file |
| 189 |
> |
set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file |
| 190 |
> |
|
| 191 |
|
bond_pair* theBonds; |
| 192 |
|
bend_set* theBends; |
| 193 |
|
torsion_set* theTorsions; |
| 220 |
|
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
| 221 |
|
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 222 |
|
molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
| 223 |
< |
molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
| 223 |
> |
|
| 224 |
> |
nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
| 225 |
|
|
| 226 |
|
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
| 227 |
|
|
| 228 |
|
if (molInfo.nBonds > 0) |
| 229 |
< |
molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
| 229 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
| 230 |
|
else |
| 231 |
|
molInfo.myBonds = NULL; |
| 232 |
|
|
| 233 |
|
if (molInfo.nBends > 0) |
| 234 |
< |
molInfo.myBends = new (Bend *) [molInfo.nBends]; |
| 234 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
| 235 |
|
else |
| 236 |
|
molInfo.myBends = NULL; |
| 237 |
|
|
| 238 |
|
if (molInfo.nTorsions > 0) |
| 239 |
< |
molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
| 239 |
> |
molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
| 240 |
|
else |
| 241 |
|
molInfo.myTorsions = NULL; |
| 242 |
|
|
| 487 |
|
} |
| 488 |
|
|
| 489 |
|
|
| 490 |
< |
//creat cutoff group for molecule |
| 490 |
> |
//create cutoff group for molecule |
| 491 |
> |
|
| 492 |
> |
cutoffAtomSet.clear(); |
| 493 |
|
molInfo.myCutoffGroups.clear(); |
| 494 |
< |
for (j = 0; j < molInfo.nCutoffGroups; j++){ |
| 494 |
> |
|
| 495 |
> |
for (j = 0; j < nCutoffGroups; j++){ |
| 496 |
|
|
| 497 |
|
currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
| 498 |
|
nMembers = currentCutoffGroup->getNMembers(); |
| 506 |
|
|
| 507 |
|
// tempI is atom numbering on local processor |
| 508 |
|
tempI = molI + atomOffset; |
| 509 |
< |
|
| 509 |
> |
|
| 510 |
|
myCutoffGroup->addAtom(info[k].atoms[tempI]); |
| 511 |
+ |
|
| 512 |
+ |
cutoffAtomSet.insert(tempI); |
| 513 |
|
} |
| 514 |
|
|
| 515 |
|
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 516 |
|
}//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
| 509 |
– |
|
| 517 |
|
|
| 518 |
+ |
//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
| 519 |
|
|
| 520 |
+ |
for(j = 0; j < molInfo.nAtoms; j++){ |
| 521 |
+ |
|
| 522 |
+ |
if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
| 523 |
+ |
myCutoffGroup = new CutoffGroup(); |
| 524 |
+ |
myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
| 525 |
+ |
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 526 |
+ |
} |
| 527 |
+ |
|
| 528 |
+ |
} |
| 529 |
+ |
|
| 530 |
+ |
|
| 531 |
+ |
|
| 532 |
+ |
|
| 533 |
|
// After this is all set up, scan through the atoms to |
| 534 |
|
// see if they can be added to the integrableObjects: |
| 535 |
|
|
| 585 |
|
MPIcheckPoint(); |
| 586 |
|
#endif // is_mpi |
| 587 |
|
|
| 567 |
– |
// clean up the forcefield |
| 568 |
– |
|
| 569 |
– |
if (!globals->haveRcut()){ |
| 570 |
– |
|
| 571 |
– |
the_ff->calcRcut(); |
| 572 |
– |
|
| 573 |
– |
} else { |
| 574 |
– |
|
| 575 |
– |
the_ff->setRcut( globals->getRcut() ); |
| 576 |
– |
} |
| 577 |
– |
|
| 578 |
– |
the_ff->cleanMe(); |
| 588 |
|
} |
| 589 |
|
|
| 590 |
|
void SimSetup::initFromBass(void){ |
| 1025 |
|
#endif //is_mpi |
| 1026 |
|
|
| 1027 |
|
double theRcut, theRsw; |
| 1028 |
+ |
|
| 1029 |
+ |
if (globals->haveRcut()) { |
| 1030 |
+ |
theRcut = globals->getRcut(); |
| 1031 |
|
|
| 1032 |
+ |
if (globals->haveRsw()) |
| 1033 |
+ |
theRsw = globals->getRsw(); |
| 1034 |
+ |
else |
| 1035 |
+ |
theRsw = theRcut; |
| 1036 |
+ |
|
| 1037 |
+ |
info[i].setDefaultRcut(theRcut, theRsw); |
| 1038 |
+ |
|
| 1039 |
+ |
} else { |
| 1040 |
+ |
|
| 1041 |
+ |
the_ff->calcRcut(); |
| 1042 |
+ |
theRcut = info[i].getRcut(); |
| 1043 |
+ |
|
| 1044 |
+ |
if (globals->haveRsw()) |
| 1045 |
+ |
theRsw = globals->getRsw(); |
| 1046 |
+ |
else |
| 1047 |
+ |
theRsw = theRcut; |
| 1048 |
+ |
|
| 1049 |
+ |
info[i].setDefaultRcut(theRcut, theRsw); |
| 1050 |
+ |
} |
| 1051 |
+ |
|
| 1052 |
|
if (globals->getUseRF()){ |
| 1053 |
|
info[i].useReactionField = 1; |
| 1054 |
< |
|
| 1054 |
> |
|
| 1055 |
|
if (!globals->haveRcut()){ |
| 1056 |
|
sprintf(painCave.errMsg, |
| 1057 |
|
"SimSetup Warning: No value was set for the cutoffRadius.\n" |
| 1128 |
|
strcpy(checkPointMsg, "post processing checks out"); |
| 1129 |
|
MPIcheckPoint(); |
| 1130 |
|
#endif // is_mpi |
| 1131 |
+ |
|
| 1132 |
+ |
// clean up the forcefield |
| 1133 |
+ |
the_ff->cleanMe(); |
| 1134 |
|
} |
| 1135 |
|
|
| 1136 |
|
void SimSetup::initSystemCoords(void){ |
