22 |
|
#define NVT_ENS 1 |
23 |
|
#define NPTi_ENS 2 |
24 |
|
#define NPTf_ENS 3 |
25 |
+ |
#define NPTxyz_ENS 4 |
26 |
|
|
27 |
+ |
|
28 |
|
#define FF_DUFF 0 |
29 |
|
#define FF_LJ 1 |
30 |
|
#define FF_EAM 2 |
92 |
|
#endif // is_mpi |
93 |
|
|
94 |
|
void SimSetup::createSim(void){ |
93 |
– |
int i, j, k, globalAtomIndex; |
95 |
|
|
96 |
|
// gather all of the information from the Bass file |
97 |
|
|
109 |
|
|
110 |
|
if (!isInfoArray){ |
111 |
|
initSystemCoords(); |
112 |
+ |
|
113 |
+ |
if( !(globals->getUseInitTime()) ) |
114 |
+ |
info[0].currentTime = 0.0; |
115 |
|
} |
116 |
|
|
117 |
|
// make the output filenames |
133 |
|
|
134 |
|
|
135 |
|
void SimSetup::makeMolecules(void){ |
136 |
< |
int k, l; |
136 |
> |
int k; |
137 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
138 |
|
molInit molInfo; |
139 |
|
DirectionalAtom* dAtom; |
555 |
|
|
556 |
|
|
557 |
|
void SimSetup::gatherInfo(void){ |
558 |
< |
int i, j, k; |
558 |
> |
int i; |
559 |
|
|
560 |
|
ensembleCase = -1; |
561 |
|
ffCase = -1; |
605 |
|
} |
606 |
|
else if (!strcasecmp(ensemble, "NPTf")){ |
607 |
|
ensembleCase = NPTf_ENS; |
608 |
+ |
} |
609 |
+ |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
610 |
+ |
ensembleCase = NPTxyz_ENS; |
611 |
|
} |
612 |
|
else{ |
613 |
|
sprintf(painCave.errMsg, |
921 |
|
if (worldRank == 0){ |
922 |
|
#endif //is_mpi |
923 |
|
inName = globals->getInitialConfig(); |
917 |
– |
double* tempDouble = new double[1000000]; |
924 |
|
fileInit = new InitializeFromFile(inName); |
925 |
|
#ifdef IS_MPI |
926 |
|
} |
938 |
|
|
939 |
|
sprintf(painCave.errMsg, |
940 |
|
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
941 |
< |
painCave.isFatal; |
941 |
> |
painCave.isFatal = 1;; |
942 |
|
simError(); |
943 |
|
|
944 |
|
#else |
1164 |
|
} |
1165 |
|
|
1166 |
|
void SimSetup::calcSysValues(void){ |
1167 |
< |
int i, j, k; |
1167 |
> |
int i; |
1168 |
|
|
1169 |
|
int* molMembershipArray; |
1170 |
|
|
1263 |
|
|
1264 |
|
|
1265 |
|
void SimSetup::makeSysArrays(void){ |
1266 |
< |
int i, j, k, l; |
1266 |
> |
|
1267 |
> |
#ifndef IS_MPI |
1268 |
> |
int k, j; |
1269 |
> |
#endif // is_mpi |
1270 |
> |
int i, l; |
1271 |
|
|
1272 |
|
Atom** the_atoms; |
1273 |
|
Molecule* the_molecules; |
1350 |
|
void SimSetup::makeIntegrator(void){ |
1351 |
|
int k; |
1352 |
|
|
1353 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1354 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1355 |
|
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1356 |
|
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1357 |
+ |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1358 |
|
|
1359 |
|
for (k = 0; k < nInfo; k++){ |
1360 |
|
switch (ensembleCase){ |
1361 |
|
case NVE_ENS: |
1362 |
|
if (globals->haveZconstraints()){ |
1363 |
|
setupZConstraint(info[k]); |
1364 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1364 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1365 |
|
} |
1366 |
< |
else |
1367 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1366 |
> |
else{ |
1367 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1368 |
> |
} |
1369 |
> |
|
1370 |
> |
info->the_integrator = myNVE; |
1371 |
|
break; |
1372 |
|
|
1373 |
|
case NVT_ENS: |
1389 |
|
painCave.isFatal = 1; |
1390 |
|
simError(); |
1391 |
|
} |
1392 |
+ |
|
1393 |
+ |
info->the_integrator = myNVT; |
1394 |
|
break; |
1395 |
|
|
1396 |
|
case NPTi_ENS: |
1432 |
|
painCave.isFatal = 1; |
1433 |
|
simError(); |
1434 |
|
} |
1435 |
+ |
|
1436 |
+ |
info->the_integrator = myNPTi; |
1437 |
|
break; |
1438 |
|
|
1439 |
|
case NPTf_ENS: |
1468 |
|
|
1469 |
|
if (globals->haveTauBarostat()) |
1470 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1471 |
+ |
else{ |
1472 |
+ |
sprintf(painCave.errMsg, |
1473 |
+ |
"SimSetup error: If you use an NPT\n" |
1474 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1475 |
+ |
painCave.isFatal = 1; |
1476 |
+ |
simError(); |
1477 |
+ |
} |
1478 |
+ |
|
1479 |
+ |
info->the_integrator = myNPTf; |
1480 |
+ |
break; |
1481 |
+ |
|
1482 |
+ |
case NPTxyz_ENS: |
1483 |
+ |
if (globals->haveZconstraints()){ |
1484 |
+ |
setupZConstraint(info[k]); |
1485 |
+ |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1486 |
+ |
} |
1487 |
+ |
else |
1488 |
+ |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1489 |
+ |
|
1490 |
+ |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1491 |
+ |
|
1492 |
+ |
if (globals->haveTargetPressure()) |
1493 |
+ |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1494 |
|
else{ |
1495 |
|
sprintf(painCave.errMsg, |
1496 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1497 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1498 |
+ |
painCave.isFatal = 1; |
1499 |
+ |
simError(); |
1500 |
+ |
} |
1501 |
+ |
|
1502 |
+ |
if (globals->haveTauThermostat()) |
1503 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1504 |
+ |
else{ |
1505 |
+ |
sprintf(painCave.errMsg, |
1506 |
|
"SimSetup error: If you use an NPT\n" |
1507 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1508 |
+ |
painCave.isFatal = 1; |
1509 |
+ |
simError(); |
1510 |
+ |
} |
1511 |
+ |
|
1512 |
+ |
if (globals->haveTauBarostat()) |
1513 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1514 |
+ |
else{ |
1515 |
+ |
sprintf(painCave.errMsg, |
1516 |
+ |
"SimSetup error: If you use an NPT\n" |
1517 |
|
" ensemble, you must set tauBarostat.\n"); |
1518 |
|
painCave.isFatal = 1; |
1519 |
|
simError(); |
1520 |
|
} |
1521 |
+ |
|
1522 |
+ |
info->the_integrator = myNPTxyz; |
1523 |
|
break; |
1524 |
|
|
1525 |
|
default: |