| 147 |
|
// make the output filenames |
| 148 |
|
|
| 149 |
|
makeOutNames(); |
| 150 |
– |
|
| 151 |
– |
if (globals->haveMinimizer()) |
| 152 |
– |
// make minimizer |
| 153 |
– |
makeMinimizer(); |
| 154 |
– |
else |
| 155 |
– |
// make the integrator |
| 156 |
– |
makeIntegrator(); |
| 150 |
|
|
| 151 |
|
#ifdef IS_MPI |
| 152 |
|
mpiSim->mpiRefresh(); |
| 155 |
|
// initialize the Fortran |
| 156 |
|
|
| 157 |
|
initFortran(); |
| 158 |
+ |
|
| 159 |
+ |
if (globals->haveMinimizer()) |
| 160 |
+ |
// make minimizer |
| 161 |
+ |
makeMinimizer(); |
| 162 |
+ |
else |
| 163 |
+ |
// make the integrator |
| 164 |
+ |
makeIntegrator(); |
| 165 |
+ |
|
| 166 |
|
} |
| 167 |
|
|
| 168 |
|
|
| 191 |
|
set<int> skipList; |
| 192 |
|
|
| 193 |
|
double phi, theta, psi; |
| 194 |
+ |
char* molName; |
| 195 |
+ |
char rbName[100]; |
| 196 |
|
|
| 197 |
|
//init the forceField paramters |
| 198 |
|
|
| 209 |
|
|
| 210 |
|
for (i = 0; i < info[k].n_mol; i++){ |
| 211 |
|
stampID = info[k].molecules[i].getStampID(); |
| 212 |
+ |
molName = comp_stamps[stampID]->getID(); |
| 213 |
|
|
| 214 |
|
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 215 |
|
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
| 263 |
|
else{ |
| 264 |
|
|
| 265 |
|
molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
| 266 |
+ |
|
| 267 |
|
} |
| 268 |
|
|
| 269 |
|
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
| 265 |
– |
|
| 270 |
|
#ifdef IS_MPI |
| 271 |
|
|
| 272 |
< |
molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
| 272 |
> |
molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
| 273 |
|
|
| 274 |
|
#endif // is_mpi |
| 275 |
|
} |
| 410 |
|
info[k].excludes->addPair(exK, exL); |
| 411 |
|
} |
| 412 |
|
|
| 413 |
+ |
|
| 414 |
+ |
molInfo.myRigidBodies.clear(); |
| 415 |
+ |
|
| 416 |
|
for (j = 0; j < molInfo.nRigidBodies; j++){ |
| 417 |
|
|
| 418 |
|
currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
| 421 |
|
// Create the Rigid Body: |
| 422 |
|
|
| 423 |
|
myRB = new RigidBody(); |
| 424 |
+ |
|
| 425 |
+ |
sprintf(rbName,"%s_RB_%d", molName, j); |
| 426 |
+ |
myRB->setType(rbName); |
| 427 |
|
|
| 428 |
|
for (rb1 = 0; rb1 < nMembers; rb1++) { |
| 429 |
|
|
| 484 |
|
// After this is all set up, scan through the atoms to |
| 485 |
|
// see if they can be added to the integrableObjects: |
| 486 |
|
|
| 487 |
+ |
molInfo.myIntegrableObjects.clear(); |
| 488 |
+ |
|
| 489 |
+ |
|
| 490 |
|
for (j = 0; j < molInfo.nAtoms; j++){ |
| 491 |
|
|
| 492 |
|
#ifdef IS_MPI |
| 964 |
|
void SimSetup::finalInfoCheck(void){ |
| 965 |
|
int index; |
| 966 |
|
int usesDipoles; |
| 967 |
+ |
int usesCharges; |
| 968 |
|
int i; |
| 969 |
|
|
| 970 |
|
for (i = 0; i < nInfo; i++){ |
| 976 |
|
usesDipoles = (info[i].atoms[index])->hasDipole(); |
| 977 |
|
index++; |
| 978 |
|
} |
| 979 |
< |
|
| 979 |
> |
index = 0; |
| 980 |
> |
usesCharges = 0; |
| 981 |
> |
while ((index < info[i].n_atoms) && !usesCharges){ |
| 982 |
> |
usesCharges= (info[i].atoms[index])->hasCharge(); |
| 983 |
> |
index++; |
| 984 |
> |
} |
| 985 |
|
#ifdef IS_MPI |
| 986 |
|
int myUse = usesDipoles; |
| 987 |
|
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 1032 |
|
info[i].dielectric = globals->getDielectric(); |
| 1033 |
|
} |
| 1034 |
|
else{ |
| 1035 |
< |
if (usesDipoles){ |
| 1035 |
> |
if (usesDipoles || usesCharges){ |
| 1036 |
|
if (!globals->haveECR()){ |
| 1037 |
|
sprintf(painCave.errMsg, |
| 1038 |
|
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
| 1365 |
|
int localMol, allMol; |
| 1366 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 1367 |
|
int local_rigid; |
| 1368 |
+ |
vector<int> globalAtomIndex; |
| 1369 |
+ |
vector<int> globalMolIndex; |
| 1370 |
|
|
| 1371 |
|
mpiSim = new mpiSimulation(info); |
| 1372 |
|
|
| 1373 |
< |
globalIndex = mpiSim->divideLabor(); |
| 1373 |
> |
mpiSim->divideLabor(); |
| 1374 |
> |
globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
| 1375 |
> |
globalMolIndex = mpiSim->getGlobalMolIndex(); |
| 1376 |
|
|
| 1377 |
|
// set up the local variables |
| 1378 |
|
|
| 1386 |
|
local_bends = 0; |
| 1387 |
|
local_torsions = 0; |
| 1388 |
|
local_rigid = 0; |
| 1389 |
< |
globalAtomIndex = 0; |
| 1389 |
> |
globalAtomCounter = 0; |
| 1390 |
|
|
| 1391 |
|
for (i = 0; i < n_components; i++){ |
| 1392 |
|
for (j = 0; j < components_nmol[i]; j++){ |
| 1399 |
|
localMol++; |
| 1400 |
|
} |
| 1401 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
| 1402 |
< |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
| 1403 |
< |
globalAtomIndex++; |
| 1402 |
> |
info[0].molMembershipArray[globalAtomCounter] = allMol; |
| 1403 |
> |
globalAtomCounter++; |
| 1404 |
|
} |
| 1405 |
|
|
| 1406 |
|
allMol++; |
| 1468 |
|
#else // is_mpi |
| 1469 |
|
|
| 1470 |
|
molIndex = 0; |
| 1471 |
< |
globalAtomIndex = 0; |
| 1471 |
> |
globalAtomCounter = 0; |
| 1472 |
|
for (i = 0; i < n_components; i++){ |
| 1473 |
|
for (j = 0; j < components_nmol[i]; j++){ |
| 1474 |
|
the_molecules[molIndex].setStampID(i); |
| 1475 |
|
the_molecules[molIndex].setMyIndex(molIndex); |
| 1476 |
|
the_molecules[molIndex].setGlobalIndex(molIndex); |
| 1477 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
| 1478 |
< |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
| 1479 |
< |
globalAtomIndex++; |
| 1478 |
> |
info[l].molMembershipArray[globalAtomCounter] = molIndex; |
| 1479 |
> |
globalAtomCounter++; |
| 1480 |
|
} |
| 1481 |
|
molIndex++; |
| 1482 |
|
} |
