4 |
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#include <cmath> |
5 |
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#include <string> |
6 |
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#include <sprng.h> |
7 |
– |
|
7 |
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#include "SimSetup.hpp" |
8 |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#define NVT_ENS 1 |
22 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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< |
#define NPTim_ENS 4 |
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< |
#define NPTfm_ENS 5 |
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> |
#define NPTxyz_ENS 4 |
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|
26 |
+ |
|
27 |
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
91 |
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#endif // is_mpi |
92 |
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|
93 |
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void SimSetup::createSim(void){ |
95 |
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int i, j, k, globalAtomIndex; |
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|
95 |
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// gather all of the information from the Bass file |
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|
108 |
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|
109 |
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if (!isInfoArray){ |
110 |
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initSystemCoords(); |
111 |
+ |
|
112 |
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if( !(globals->getUseInitTime()) ) |
113 |
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info[0].currentTime = 0.0; |
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} |
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|
116 |
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// make the output filenames |
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|
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|
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void SimSetup::makeMolecules(void){ |
135 |
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int k, l; |
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> |
int k; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
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|
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|
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void SimSetup::gatherInfo(void){ |
557 |
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int i, j, k; |
557 |
> |
int i; |
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|
559 |
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ensembleCase = -1; |
560 |
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ffCase = -1; |
605 |
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else if (!strcasecmp(ensemble, "NPTf")){ |
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ensembleCase = NPTf_ENS; |
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} |
608 |
< |
else if (!strcasecmp(ensemble, "NPTim")){ |
609 |
< |
ensembleCase = NPTim_ENS; |
609 |
< |
} |
610 |
< |
else if (!strcasecmp(ensemble, "NPTfm")){ |
611 |
< |
ensembleCase = NPTfm_ENS; |
608 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
609 |
> |
ensembleCase = NPTxyz_ENS; |
610 |
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} |
611 |
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else{ |
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sprintf(painCave.errMsg, |
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if (worldRank == 0){ |
921 |
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#endif //is_mpi |
922 |
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inName = globals->getInitialConfig(); |
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double* tempDouble = new double[1000000]; |
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fileInit = new InitializeFromFile(inName); |
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#ifdef IS_MPI |
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} |
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|
938 |
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sprintf(painCave.errMsg, |
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"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
940 |
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painCave.isFatal; |
940 |
> |
painCave.isFatal = 1;; |
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simError(); |
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|
943 |
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#else |
1163 |
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} |
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|
1165 |
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void SimSetup::calcSysValues(void){ |
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int i, j, k; |
1166 |
> |
int i; |
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|
1168 |
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int* molMembershipArray; |
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|
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|
1263 |
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|
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void SimSetup::makeSysArrays(void){ |
1265 |
< |
int i, j, k, l; |
1265 |
> |
|
1266 |
> |
#ifndef IS_MPI |
1267 |
> |
int k, j; |
1268 |
> |
#endif // is_mpi |
1269 |
> |
int i, l; |
1270 |
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|
1271 |
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Atom** the_atoms; |
1272 |
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Molecule* the_molecules; |
1349 |
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void SimSetup::makeIntegrator(void){ |
1350 |
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int k; |
1351 |
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|
1352 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1353 |
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NVT<RealIntegrator>* myNVT = NULL; |
1354 |
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NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1355 |
< |
NPTf<RealIntegrator>* myNPTf = NULL; |
1356 |
< |
NPTim<RealIntegrator>* myNPTim = NULL; |
1355 |
< |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1355 |
> |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1356 |
> |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1357 |
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|
1358 |
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for (k = 0; k < nInfo; k++){ |
1359 |
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switch (ensembleCase){ |
1360 |
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case NVE_ENS: |
1361 |
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if (globals->haveZconstraints()){ |
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setupZConstraint(info[k]); |
1363 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1363 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1364 |
|
} |
1365 |
< |
else |
1366 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1365 |
> |
else{ |
1366 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1367 |
> |
} |
1368 |
> |
|
1369 |
> |
info->the_integrator = myNVE; |
1370 |
|
break; |
1371 |
|
|
1372 |
|
case NVT_ENS: |
1388 |
|
painCave.isFatal = 1; |
1389 |
|
simError(); |
1390 |
|
} |
1391 |
+ |
|
1392 |
+ |
info->the_integrator = myNVT; |
1393 |
|
break; |
1394 |
|
|
1395 |
|
case NPTi_ENS: |
1431 |
|
painCave.isFatal = 1; |
1432 |
|
simError(); |
1433 |
|
} |
1434 |
+ |
|
1435 |
+ |
info->the_integrator = myNPTi; |
1436 |
|
break; |
1437 |
|
|
1438 |
|
case NPTf_ENS: |
1439 |
|
if (globals->haveZconstraints()){ |
1440 |
|
setupZConstraint(info[k]); |
1441 |
< |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1441 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1442 |
|
} |
1443 |
|
else |
1444 |
< |
myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1444 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1445 |
|
|
1446 |
|
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1447 |
|
|
1474 |
|
painCave.isFatal = 1; |
1475 |
|
simError(); |
1476 |
|
} |
1469 |
– |
break; |
1477 |
|
|
1478 |
< |
case NPTim_ENS: |
1472 |
< |
if (globals->haveZconstraints()){ |
1473 |
< |
setupZConstraint(info[k]); |
1474 |
< |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1475 |
< |
} |
1476 |
< |
else |
1477 |
< |
myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1478 |
< |
|
1479 |
< |
myNPTim->setTargetTemp(globals->getTargetTemp()); |
1480 |
< |
|
1481 |
< |
if (globals->haveTargetPressure()) |
1482 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1483 |
< |
else{ |
1484 |
< |
sprintf(painCave.errMsg, |
1485 |
< |
"SimSetup error: If you use a constant pressure\n" |
1486 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1487 |
< |
painCave.isFatal = 1; |
1488 |
< |
simError(); |
1489 |
< |
} |
1490 |
< |
|
1491 |
< |
if (globals->haveTauThermostat()) |
1492 |
< |
myNPTim->setTauThermostat(globals->getTauThermostat()); |
1493 |
< |
else{ |
1494 |
< |
sprintf(painCave.errMsg, |
1495 |
< |
"SimSetup error: If you use an NPT\n" |
1496 |
< |
" ensemble, you must set tauThermostat.\n"); |
1497 |
< |
painCave.isFatal = 1; |
1498 |
< |
simError(); |
1499 |
< |
} |
1500 |
< |
|
1501 |
< |
if (globals->haveTauBarostat()) |
1502 |
< |
myNPTim->setTauBarostat(globals->getTauBarostat()); |
1503 |
< |
else{ |
1504 |
< |
sprintf(painCave.errMsg, |
1505 |
< |
"SimSetup error: If you use an NPT\n" |
1506 |
< |
" ensemble, you must set tauBarostat.\n"); |
1507 |
< |
painCave.isFatal = 1; |
1508 |
< |
simError(); |
1509 |
< |
} |
1478 |
> |
info->the_integrator = myNPTf; |
1479 |
|
break; |
1480 |
|
|
1481 |
< |
case NPTfm_ENS: |
1481 |
> |
case NPTxyz_ENS: |
1482 |
|
if (globals->haveZconstraints()){ |
1483 |
|
setupZConstraint(info[k]); |
1484 |
< |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1484 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1485 |
|
} |
1486 |
|
else |
1487 |
< |
myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1487 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1488 |
|
|
1489 |
< |
myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1489 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1490 |
|
|
1491 |
|
if (globals->haveTargetPressure()) |
1492 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1492 |
> |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1493 |
|
else{ |
1494 |
|
sprintf(painCave.errMsg, |
1495 |
|
"SimSetup error: If you use a constant pressure\n" |
1496 |
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
1497 |
|
painCave.isFatal = 1; |
1498 |
|
simError(); |
1499 |
< |
} |
1499 |
> |
} |
1500 |
|
|
1501 |
|
if (globals->haveTauThermostat()) |
1502 |
< |
myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1502 |
> |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1503 |
|
else{ |
1504 |
|
sprintf(painCave.errMsg, |
1505 |
|
"SimSetup error: If you use an NPT\n" |
1509 |
|
} |
1510 |
|
|
1511 |
|
if (globals->haveTauBarostat()) |
1512 |
< |
myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1512 |
> |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1513 |
|
else{ |
1514 |
|
sprintf(painCave.errMsg, |
1515 |
|
"SimSetup error: If you use an NPT\n" |
1517 |
|
painCave.isFatal = 1; |
1518 |
|
simError(); |
1519 |
|
} |
1520 |
+ |
|
1521 |
+ |
info->the_integrator = myNPTxyz; |
1522 |
|
break; |
1523 |
|
|
1524 |
|
default: |