| 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); |
| 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 |
| 834 |
|
} |
| 835 |
|
|
| 836 |
|
//check whether sample time, status time, thermal time and reset time are divisble by dt |
| 837 |
< |
if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
| 837 |
> |
if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
| 838 |
|
sprintf(painCave.errMsg, |
| 839 |
|
"Sample time is not divisible by dt.\n" |
| 840 |
|
"\tThis will result in samples that are not uniformly\n" |
| 844 |
|
simError(); |
| 845 |
|
} |
| 846 |
|
|
| 847 |
< |
if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
| 847 |
> |
if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
| 848 |
|
sprintf(painCave.errMsg, |
| 849 |
|
"Status time is not divisible by dt.\n" |
| 850 |
|
"\tThis will result in status reports that are not uniformly\n" |
| 880 |
|
if (globals->haveSampleTime()){ |
| 881 |
|
info[i].sampleTime = globals->getSampleTime(); |
| 882 |
|
info[i].statusTime = info[i].sampleTime; |
| 876 |
– |
info[i].thermalTime = info[i].sampleTime; |
| 883 |
|
} |
| 884 |
|
else{ |
| 885 |
|
info[i].sampleTime = globals->getRunTime(); |
| 886 |
|
info[i].statusTime = info[i].sampleTime; |
| 881 |
– |
info[i].thermalTime = info[i].sampleTime; |
| 887 |
|
} |
| 888 |
|
|
| 889 |
|
if (globals->haveStatusTime()){ |
| 892 |
|
|
| 893 |
|
if (globals->haveThermalTime()){ |
| 894 |
|
info[i].thermalTime = globals->getThermalTime(); |
| 895 |
+ |
} else { |
| 896 |
+ |
info[i].thermalTime = globals->getRunTime(); |
| 897 |
|
} |
| 898 |
|
|
| 899 |
|
info[i].resetIntegrator = 0; |
| 911 |
|
|
| 912 |
|
info[i].useInitXSstate = globals->getUseInitXSstate(); |
| 913 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 914 |
+ |
info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs(); |
| 915 |
+ |
|
| 916 |
|
|
| 917 |
|
} |
| 918 |
|
|
| 966 |
|
void SimSetup::finalInfoCheck(void){ |
| 967 |
|
int index; |
| 968 |
|
int usesDipoles; |
| 969 |
+ |
int usesCharges; |
| 970 |
|
int i; |
| 971 |
|
|
| 972 |
|
for (i = 0; i < nInfo; i++){ |
| 978 |
|
usesDipoles = (info[i].atoms[index])->hasDipole(); |
| 979 |
|
index++; |
| 980 |
|
} |
| 981 |
< |
|
| 981 |
> |
index = 0; |
| 982 |
> |
usesCharges = 0; |
| 983 |
> |
while ((index < info[i].n_atoms) && !usesCharges){ |
| 984 |
> |
usesCharges= (info[i].atoms[index])->hasCharge(); |
| 985 |
> |
index++; |
| 986 |
> |
} |
| 987 |
|
#ifdef IS_MPI |
| 988 |
|
int myUse = usesDipoles; |
| 989 |
|
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 1034 |
|
info[i].dielectric = globals->getDielectric(); |
| 1035 |
|
} |
| 1036 |
|
else{ |
| 1037 |
< |
if (usesDipoles){ |
| 1037 |
> |
if (usesDipoles || usesCharges){ |
| 1038 |
|
if (!globals->haveECR()){ |
| 1039 |
|
sprintf(painCave.errMsg, |
| 1040 |
|
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
| 1367 |
|
int localMol, allMol; |
| 1368 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 1369 |
|
int local_rigid; |
| 1355 |
– |
vector<int> globalAtomIndex; |
| 1370 |
|
vector<int> globalMolIndex; |
| 1371 |
|
|
| 1372 |
|
mpiSim = new mpiSimulation(info); |
| 1373 |
|
|
| 1374 |
|
mpiSim->divideLabor(); |
| 1375 |
|
globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
| 1376 |
< |
globalMolIndex = mpiSim->getGlobalMolIndex(); |
| 1376 |
> |
//globalMolIndex = mpiSim->getGlobalMolIndex(); |
| 1377 |
|
|
| 1378 |
|
// set up the local variables |
| 1379 |
|
|
