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#include <cmath> |
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#include <string> |
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#include <sprng.h> |
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTxyz_ENS 4 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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#endif // is_mpi |
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|
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void SimSetup::createSim(void){ |
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int i, j, k, globalAtomIndex; |
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|
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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){ |
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initSystemCoords(); |
111 |
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|
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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|
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// make the output filenames |
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|
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|
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void SimSetup::makeMolecules(void){ |
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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){ |
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int i, j, k; |
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int i; |
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|
559 |
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ensembleCase = -1; |
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ffCase = -1; |
604 |
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} |
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else if (!strcasecmp(ensemble, "NPTf")){ |
606 |
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ensembleCase = NPTf_ENS; |
607 |
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} |
608 |
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else if (!strcasecmp(ensemble, "NPTxyz")){ |
609 |
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ensembleCase = NPTxyz_ENS; |
610 |
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} |
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else{ |
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sprintf(painCave.errMsg, |
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if (worldRank == 0){ |
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#endif //is_mpi |
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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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|
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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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|
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#else |
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} |
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|
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void SimSetup::calcSysValues(void){ |
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int i, j, k; |
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int i; |
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|
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int* molMembershipArray; |
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|
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|
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void SimSetup::makeSysArrays(void){ |
1265 |
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int i, j, k, l; |
1265 |
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|
1266 |
> |
#ifndef IS_MPI |
1267 |
> |
int k, j; |
1268 |
> |
#endif // is_mpi |
1269 |
> |
int i, l; |
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|
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Atom** the_atoms; |
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Molecule* the_molecules; |
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NVT<RealIntegrator>* myNVT = NULL; |
1354 |
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NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1355 |
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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){ |
1478 |
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info->the_integrator = myNPTf; |
1479 |
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break; |
1480 |
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|
1481 |
+ |
case NPTxyz_ENS: |
1482 |
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if (globals->haveZconstraints()){ |
1483 |
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setupZConstraint(info[k]); |
1484 |
+ |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1485 |
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} |
1486 |
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else |
1487 |
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myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1488 |
+ |
|
1489 |
+ |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1490 |
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|
1491 |
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if (globals->haveTargetPressure()) |
1492 |
+ |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1493 |
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else{ |
1494 |
+ |
sprintf(painCave.errMsg, |
1495 |
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"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 |
+ |
} |
1500 |
+ |
|
1501 |
+ |
if (globals->haveTauThermostat()) |
1502 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1503 |
+ |
else{ |
1504 |
+ |
sprintf(painCave.errMsg, |
1505 |
+ |
"SimSetup error: If you use an NPT\n" |
1506 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1507 |
+ |
painCave.isFatal = 1; |
1508 |
+ |
simError(); |
1509 |
+ |
} |
1510 |
+ |
|
1511 |
+ |
if (globals->haveTauBarostat()) |
1512 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1513 |
+ |
else{ |
1514 |
+ |
sprintf(painCave.errMsg, |
1515 |
+ |
"SimSetup error: If you use an NPT\n" |
1516 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1517 |
+ |
painCave.isFatal = 1; |
1518 |
+ |
simError(); |
1519 |
+ |
} |
1520 |
+ |
|
1521 |
+ |
info->the_integrator = myNPTxyz; |
1522 |
+ |
break; |
1523 |
+ |
|
1524 |
|
default: |
1525 |
|
sprintf(painCave.errMsg, |
1526 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |