90 |
|
#endif // is_mpi |
91 |
|
|
92 |
|
void SimSetup::createSim(void){ |
93 |
– |
int i, j, k, globalAtomIndex; |
93 |
|
|
94 |
|
// gather all of the information from the Bass file |
95 |
|
|
128 |
|
|
129 |
|
|
130 |
|
void SimSetup::makeMolecules(void){ |
131 |
< |
int k, l; |
131 |
> |
int k; |
132 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
133 |
|
molInit molInfo; |
134 |
|
DirectionalAtom* dAtom; |
550 |
|
|
551 |
|
|
552 |
|
void SimSetup::gatherInfo(void){ |
553 |
< |
int i, j, k; |
553 |
> |
int i; |
554 |
|
|
555 |
|
ensembleCase = -1; |
556 |
|
ffCase = -1; |
913 |
|
if (worldRank == 0){ |
914 |
|
#endif //is_mpi |
915 |
|
inName = globals->getInitialConfig(); |
917 |
– |
double* tempDouble = new double[1000000]; |
916 |
|
fileInit = new InitializeFromFile(inName); |
917 |
|
#ifdef IS_MPI |
918 |
|
} |
930 |
|
|
931 |
|
sprintf(painCave.errMsg, |
932 |
|
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
933 |
< |
painCave.isFatal; |
933 |
> |
painCave.isFatal = 1;; |
934 |
|
simError(); |
935 |
|
|
936 |
|
#else |
1156 |
|
} |
1157 |
|
|
1158 |
|
void SimSetup::calcSysValues(void){ |
1159 |
< |
int i, j, k; |
1159 |
> |
int i; |
1160 |
|
|
1161 |
|
int* molMembershipArray; |
1162 |
|
|
1255 |
|
|
1256 |
|
|
1257 |
|
void SimSetup::makeSysArrays(void){ |
1258 |
< |
int i, j, k, l; |
1258 |
> |
|
1259 |
> |
#ifndef IS_MPI |
1260 |
> |
int k, j; |
1261 |
> |
#endif // is_mpi |
1262 |
> |
int i, l; |
1263 |
|
|
1264 |
|
Atom** the_atoms; |
1265 |
|
Molecule* the_molecules; |
1342 |
|
void SimSetup::makeIntegrator(void){ |
1343 |
|
int k; |
1344 |
|
|
1345 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1346 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1347 |
|
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1348 |
|
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1352 |
|
case NVE_ENS: |
1353 |
|
if (globals->haveZconstraints()){ |
1354 |
|
setupZConstraint(info[k]); |
1355 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1355 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1356 |
|
} |
1357 |
< |
else |
1358 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1357 |
> |
else{ |
1358 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1359 |
> |
} |
1360 |
> |
|
1361 |
> |
info->the_integrator = myNVE; |
1362 |
|
break; |
1363 |
|
|
1364 |
|
case NVT_ENS: |
1380 |
|
painCave.isFatal = 1; |
1381 |
|
simError(); |
1382 |
|
} |
1383 |
+ |
|
1384 |
+ |
info->the_integrator = myNVT; |
1385 |
|
break; |
1386 |
|
|
1387 |
|
case NPTi_ENS: |
1423 |
|
painCave.isFatal = 1; |
1424 |
|
simError(); |
1425 |
|
} |
1426 |
+ |
|
1427 |
+ |
info->the_integrator = myNPTi; |
1428 |
|
break; |
1429 |
|
|
1430 |
|
case NPTf_ENS: |
1466 |
|
painCave.isFatal = 1; |
1467 |
|
simError(); |
1468 |
|
} |
1469 |
+ |
|
1470 |
+ |
info->the_integrator = myNPTf; |
1471 |
|
break; |
1472 |
|
|
1473 |
|
default: |