| 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 |
|
|
| 488 |
|
|
| 489 |
|
|
| 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++) |
| 517 |
< |
|
| 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 |
| 948 |
|
|
| 949 |
|
info[i].useInitXSstate = globals->getUseInitXSstate(); |
| 950 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 951 |
< |
|
| 951 |
> |
|
| 952 |
> |
// check for thermodynamic integration |
| 953 |
> |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 954 |
> |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 955 |
> |
info[i].thermIntK = globals->getThermIntK(); |
| 956 |
> |
info[i].useThermInt = 1; |
| 957 |
> |
|
| 958 |
> |
Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
| 959 |
> |
info[i].restraint = myRestraint; |
| 960 |
> |
} |
| 961 |
|
} |
| 962 |
|
|
| 963 |
|
//setup seed for random number generator |
| 1267 |
|
} |
| 1268 |
|
else{ |
| 1269 |
|
strcat(info[k].statusName, ".stat"); |
| 1270 |
+ |
} |
| 1271 |
+ |
} |
| 1272 |
+ |
|
| 1273 |
+ |
strcpy(info[k].rawPotName, inFileName); |
| 1274 |
+ |
nameLength = strlen(info[k].rawPotName); |
| 1275 |
+ |
endTest = &(info[k].rawPotName[nameLength - 5]); |
| 1276 |
+ |
if (!strcmp(endTest, ".bass")){ |
| 1277 |
+ |
strcpy(endTest, ".raw"); |
| 1278 |
+ |
} |
| 1279 |
+ |
else if (!strcmp(endTest, ".BASS")){ |
| 1280 |
+ |
strcpy(endTest, ".raw"); |
| 1281 |
+ |
} |
| 1282 |
+ |
else{ |
| 1283 |
+ |
endTest = &(info[k].rawPotName[nameLength - 4]); |
| 1284 |
+ |
if (!strcmp(endTest, ".bss")){ |
| 1285 |
+ |
strcpy(endTest, ".raw"); |
| 1286 |
|
} |
| 1287 |
+ |
else if (!strcmp(endTest, ".mdl")){ |
| 1288 |
+ |
strcpy(endTest, ".raw"); |
| 1289 |
+ |
} |
| 1290 |
+ |
else{ |
| 1291 |
+ |
strcat(info[k].rawPotName, ".raw"); |
| 1292 |
+ |
} |
| 1293 |
|
} |
| 1294 |
|
|
| 1295 |
|
#ifdef IS_MPI |
