| 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 |
|
|
| 263 |
|
else{ |
| 264 |
|
|
| 265 |
|
molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
| 266 |
+ |
|
| 267 |
|
} |
| 268 |
|
|
| 269 |
|
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
| 268 |
– |
|
| 270 |
|
#ifdef IS_MPI |
| 271 |
|
|
| 272 |
|
molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
| 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); |
| 422 |
|
|
| 423 |
|
myRB = new RigidBody(); |
| 424 |
|
|
| 425 |
< |
sprintf(rbName,"%s_RB_%s", molName, j); |
| 425 |
> |
sprintf(rbName,"%s_RB_%d", molName, j); |
| 426 |
|
myRB->setType(rbName); |
| 427 |
|
|
| 428 |
|
for (rb1 = 0; rb1 < nMembers; rb1++) { |
| 464 |
|
// used for the exclude list: |
| 465 |
|
|
| 466 |
|
#ifdef IS_MPI |
| 467 |
< |
exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
| 468 |
< |
exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
| 467 |
> |
exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
| 468 |
> |
exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
| 469 |
|
#else |
| 470 |
< |
exI = tempI + 1; |
| 471 |
< |
exJ = tempJ + 1; |
| 470 |
> |
exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
| 471 |
> |
exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
| 472 |
|
#endif |
| 473 |
|
|
| 474 |
|
info[k].excludes->addPair(exI, exJ); |
| 483 |
|
|
| 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 |
|
|
| 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" |
