22 |
|
#define NVT_ENS 1 |
23 |
|
#define NPTi_ENS 2 |
24 |
|
#define NPTf_ENS 3 |
25 |
< |
#define NPTim_ENS 4 |
26 |
< |
#define NPTfm_ENS 5 |
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){ |
95 |
– |
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; |
606 |
|
else if (!strcasecmp(ensemble, "NPTf")){ |
607 |
|
ensembleCase = NPTf_ENS; |
608 |
|
} |
609 |
< |
else if (!strcasecmp(ensemble, "NPTim")){ |
610 |
< |
ensembleCase = NPTim_ENS; |
609 |
< |
} |
610 |
< |
else if (!strcasecmp(ensemble, "NPTfm")){ |
611 |
< |
ensembleCase = NPTfm_ENS; |
609 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
610 |
> |
ensembleCase = NPTxyz_ENS; |
611 |
|
} |
612 |
|
else{ |
613 |
|
sprintf(painCave.errMsg, |
685 |
|
|
686 |
|
if (globals->haveThermalTime()){ |
687 |
|
info[i].thermalTime = globals->getThermalTime(); |
688 |
+ |
} |
689 |
+ |
|
690 |
+ |
info[i].resetIntegrator = 0; |
691 |
+ |
if( globals->haveResetTime() ){ |
692 |
+ |
info[i].resetTime = globals->getResetTime(); |
693 |
+ |
info[i].resetIntegrator = 1; |
694 |
|
} |
695 |
|
|
696 |
|
// check for the temperature set flag |
921 |
|
if (worldRank == 0){ |
922 |
|
#endif //is_mpi |
923 |
|
inName = globals->getInitialConfig(); |
919 |
– |
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<RealIntegrator>* myNPTi = NULL; |
1356 |
< |
NPTf<RealIntegrator>* myNPTf = NULL; |
1357 |
< |
NPTim<RealIntegrator>* myNPTim = NULL; |
1349 |
< |
NPTfm<RealIntegrator>* myNPTfm = 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: |
1397 |
|
if (globals->haveZconstraints()){ |
1398 |
|
setupZConstraint(info[k]); |
1399 |
< |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff); |
1399 |
> |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1400 |
|
} |
1401 |
|
else |
1402 |
< |
myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff); |
1402 |
> |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1403 |
|
|
1404 |
|
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1405 |
|
|
1432 |
|
painCave.isFatal = 1; |
1433 |
|
simError(); |
1434 |
|
} |
1435 |
+ |
|
1436 |
+ |
info->the_integrator = myNPTi; |
1437 |
|
break; |
1438 |
|
|
1439 |
|
case NPTf_ENS: |
1440 |
|
if (globals->haveZconstraints()){ |
1441 |
|
setupZConstraint(info[k]); |
1442 |
< |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1442 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1443 |
|
} |
1444 |
|
else |
1445 |
< |
myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1445 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1446 |
|
|
1447 |
|
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1448 |
|
|
1475 |
|
painCave.isFatal = 1; |
1476 |
|
simError(); |
1477 |
|
} |
1463 |
– |
break; |
1478 |
|
|
1479 |
< |
case NPTim_ENS: |
1466 |
< |
if (globals->haveZconstraints()){ |
1467 |
< |
setupZConstraint(info[k]); |
1468 |
< |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1469 |
< |
} |
1470 |
< |
else |
1471 |
< |
myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1472 |
< |
|
1473 |
< |
myNPTim->setTargetTemp(globals->getTargetTemp()); |
1474 |
< |
|
1475 |
< |
if (globals->haveTargetPressure()) |
1476 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1477 |
< |
else{ |
1478 |
< |
sprintf(painCave.errMsg, |
1479 |
< |
"SimSetup error: If you use a constant pressure\n" |
1480 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1481 |
< |
painCave.isFatal = 1; |
1482 |
< |
simError(); |
1483 |
< |
} |
1484 |
< |
|
1485 |
< |
if (globals->haveTauThermostat()) |
1486 |
< |
myNPTim->setTauThermostat(globals->getTauThermostat()); |
1487 |
< |
else{ |
1488 |
< |
sprintf(painCave.errMsg, |
1489 |
< |
"SimSetup error: If you use an NPT\n" |
1490 |
< |
" ensemble, you must set tauThermostat.\n"); |
1491 |
< |
painCave.isFatal = 1; |
1492 |
< |
simError(); |
1493 |
< |
} |
1494 |
< |
|
1495 |
< |
if (globals->haveTauBarostat()) |
1496 |
< |
myNPTim->setTauBarostat(globals->getTauBarostat()); |
1497 |
< |
else{ |
1498 |
< |
sprintf(painCave.errMsg, |
1499 |
< |
"SimSetup error: If you use an NPT\n" |
1500 |
< |
" ensemble, you must set tauBarostat.\n"); |
1501 |
< |
painCave.isFatal = 1; |
1502 |
< |
simError(); |
1503 |
< |
} |
1479 |
> |
info->the_integrator = myNPTf; |
1480 |
|
break; |
1481 |
|
|
1482 |
< |
case NPTfm_ENS: |
1482 |
> |
case NPTxyz_ENS: |
1483 |
|
if (globals->haveZconstraints()){ |
1484 |
|
setupZConstraint(info[k]); |
1485 |
< |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1485 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1486 |
|
} |
1487 |
|
else |
1488 |
< |
myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1488 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1489 |
|
|
1490 |
< |
myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1490 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1491 |
|
|
1492 |
|
if (globals->haveTargetPressure()) |
1493 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
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 |
< |
} |
1500 |
> |
} |
1501 |
|
|
1502 |
|
if (globals->haveTauThermostat()) |
1503 |
< |
myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1503 |
> |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1504 |
|
else{ |
1505 |
|
sprintf(painCave.errMsg, |
1506 |
|
"SimSetup error: If you use an NPT\n" |
1510 |
|
} |
1511 |
|
|
1512 |
|
if (globals->haveTauBarostat()) |
1513 |
< |
myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1513 |
> |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1514 |
|
else{ |
1515 |
|
sprintf(painCave.errMsg, |
1516 |
|
"SimSetup error: If you use an NPT\n" |
1518 |
|
painCave.isFatal = 1; |
1519 |
|
simError(); |
1520 |
|
} |
1521 |
+ |
|
1522 |
+ |
info->the_integrator = myNPTxyz; |
1523 |
|
break; |
1524 |
|
|
1525 |
|
default: |
1593 |
|
} |
1594 |
|
theInfo.addProperty(zconsTol); |
1595 |
|
|
1596 |
< |
//set Force Substraction Policy |
1596 |
> |
//set Force Subtraction Policy |
1597 |
|
StringData* zconsForcePolicy = new StringData(); |
1598 |
|
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1599 |
|
|
1602 |
|
} |
1603 |
|
else{ |
1604 |
|
sprintf(painCave.errMsg, |
1605 |
< |
"ZConstraint Warning: User does not set force substraction policy, " |
1605 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
1606 |
|
"PolicyByMass is used\n"); |
1607 |
|
painCave.isFatal = 0; |
1608 |
|
simError(); |