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 |
|
|
107 |
|
|
108 |
|
if (!isInfoArray){ |
109 |
|
initSystemCoords(); |
110 |
+ |
|
111 |
+ |
if( !(globals->getUseInitTime()) ) |
112 |
+ |
info[0].currentTime = 0.0; |
113 |
|
} |
114 |
|
|
115 |
|
// make the output filenames |
131 |
|
|
132 |
|
|
133 |
|
void SimSetup::makeMolecules(void){ |
134 |
< |
int k, l; |
134 |
> |
int k; |
135 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
136 |
|
molInit molInfo; |
137 |
|
DirectionalAtom* dAtom; |
553 |
|
|
554 |
|
|
555 |
|
void SimSetup::gatherInfo(void){ |
556 |
< |
int i, j, k; |
556 |
> |
int i; |
557 |
|
|
558 |
|
ensembleCase = -1; |
559 |
|
ffCase = -1; |
916 |
|
if (worldRank == 0){ |
917 |
|
#endif //is_mpi |
918 |
|
inName = globals->getInitialConfig(); |
917 |
– |
double* tempDouble = new double[1000000]; |
919 |
|
fileInit = new InitializeFromFile(inName); |
920 |
|
#ifdef IS_MPI |
921 |
|
} |
933 |
|
|
934 |
|
sprintf(painCave.errMsg, |
935 |
|
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
936 |
< |
painCave.isFatal; |
936 |
> |
painCave.isFatal = 1;; |
937 |
|
simError(); |
938 |
|
|
939 |
|
#else |
1159 |
|
} |
1160 |
|
|
1161 |
|
void SimSetup::calcSysValues(void){ |
1162 |
< |
int i, j, k; |
1162 |
> |
int i; |
1163 |
|
|
1164 |
|
int* molMembershipArray; |
1165 |
|
|
1258 |
|
|
1259 |
|
|
1260 |
|
void SimSetup::makeSysArrays(void){ |
1261 |
< |
int i, j, k, l; |
1261 |
> |
|
1262 |
> |
#ifndef IS_MPI |
1263 |
> |
int k, j; |
1264 |
> |
#endif // is_mpi |
1265 |
> |
int i, l; |
1266 |
|
|
1267 |
|
Atom** the_atoms; |
1268 |
|
Molecule* the_molecules; |
1345 |
|
void SimSetup::makeIntegrator(void){ |
1346 |
|
int k; |
1347 |
|
|
1348 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1349 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1350 |
|
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1351 |
|
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1355 |
|
case NVE_ENS: |
1356 |
|
if (globals->haveZconstraints()){ |
1357 |
|
setupZConstraint(info[k]); |
1358 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1358 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1359 |
|
} |
1360 |
< |
else |
1361 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1360 |
> |
else{ |
1361 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1362 |
> |
} |
1363 |
> |
|
1364 |
> |
info->the_integrator = myNVE; |
1365 |
|
break; |
1366 |
|
|
1367 |
|
case NVT_ENS: |
1383 |
|
painCave.isFatal = 1; |
1384 |
|
simError(); |
1385 |
|
} |
1386 |
+ |
|
1387 |
+ |
info->the_integrator = myNVT; |
1388 |
|
break; |
1389 |
|
|
1390 |
|
case NPTi_ENS: |
1426 |
|
painCave.isFatal = 1; |
1427 |
|
simError(); |
1428 |
|
} |
1429 |
+ |
|
1430 |
+ |
info->the_integrator = myNPTi; |
1431 |
|
break; |
1432 |
|
|
1433 |
|
case NPTf_ENS: |
1469 |
|
painCave.isFatal = 1; |
1470 |
|
simError(); |
1471 |
|
} |
1472 |
+ |
|
1473 |
+ |
info->the_integrator = myNPTf; |
1474 |
|
break; |
1475 |
|
|
1476 |
|
default: |