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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 722 by tim, Tue Aug 26 20:02:29 2003 UTC vs.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

# Line 22 | Line 22
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
# Line 92 | Line 92 | void SimSetup::createSim(void){
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  
# Line 110 | Line 109 | void SimSetup::createSim(void){
109  
110    if (!isInfoArray){
111      initSystemCoords();
112 +
113 +    if( !(globals->getUseInitTime()) )
114 +      info[0].currentTime = 0.0;
115    }  
116  
117    // make the output filenames
# Line 131 | Line 133 | void SimSetup::makeMolecules(void){
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;
# Line 553 | Line 555 | void SimSetup::gatherInfo(void){
555  
556  
557   void SimSetup::gatherInfo(void){
558 <  int i, j, k;
558 >  int i;
559  
560    ensembleCase = -1;
561    ffCase = -1;
# Line 604 | Line 606 | void SimSetup::gatherInfo(void){
606    else if (!strcasecmp(ensemble, "NPTf")){
607      ensembleCase = NPTf_ENS;
608    }
609 <  else if (!strcasecmp(ensemble, "NPTim")){
610 <    ensembleCase = NPTim_ENS;
609 >  else if (!strcasecmp(ensemble, "NPTxyz")){
610 >    ensembleCase = NPTxyz_ENS;
611    }
610 –  else if (!strcasecmp(ensemble, "NPTfm")){
611 –    ensembleCase = NPTfm_ENS;
612 –  }
612    else{
613      sprintf(painCave.errMsg,
614              "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 688 | Line 687 | void SimSetup::gatherInfo(void){
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
697  
698      if (globals->haveTempSet())
# Line 916 | Line 921 | void SimSetup::initSystemCoords(void){
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      }
# Line 934 | Line 938 | void SimSetup::initSystemCoords(void){
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
# Line 1160 | Line 1164 | void SimSetup::calcSysValues(void){
1164   }
1165  
1166   void SimSetup::calcSysValues(void){
1167 <  int i, j, k;
1167 >  int i;
1168  
1169    int* molMembershipArray;
1170  
# Line 1259 | Line 1263 | void SimSetup::makeSysArrays(void){
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;
# Line 1342 | Line 1350 | void SimSetup::makeIntegrator(void){
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;
1358 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1350 <
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:
# Line 1378 | Line 1389 | void SimSetup::makeIntegrator(void){
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  
# Line 1419 | Line 1432 | void SimSetup::makeIntegrator(void){
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  
# Line 1457 | Line 1472 | void SimSetup::makeIntegrator(void){
1472            sprintf(painCave.errMsg,
1473                    "SimSetup error: If you use an NPT\n"
1474                    "    ensemble, you must set tauBarostat.\n");
1460 –          painCave.isFatal = 1;
1461 –          simError();
1462 –        }
1463 –        break;
1464 –
1465 –      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");
1475            painCave.isFatal = 1;
1476            simError();
1477          }
1478  
1479 <        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"
# Line 1534 | Line 1510 | void SimSetup::makeIntegrator(void){
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"
# Line 1542 | Line 1518 | void SimSetup::makeIntegrator(void){
1518            painCave.isFatal = 1;
1519            simError();
1520          }
1521 +
1522 +        info->the_integrator = myNPTxyz;
1523          break;
1524  
1525        default:
# Line 1615 | Line 1593 | void SimSetup::setupZConstraint(SimInfo& theInfo){
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  
# Line 1624 | Line 1602 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1602    }
1603    else{
1604      sprintf(painCave.errMsg,
1605 <            "ZConstraint Warning: User does not set force substraction policy, "
1606 <            "average force substraction policy is used\n");
1605 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1606 >            "PolicyByMass is used\n");
1607      painCave.isFatal = 0;
1608      simError();
1609 <    zconsForcePolicy->setData("BYNUMBER");
1609 >    zconsForcePolicy->setData("BYMASS");
1610    }
1611  
1612    theInfo.addProperty(zconsForcePolicy);
# Line 1666 | Line 1644 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1644      zconsParaData->addItem(tempParaItem);
1645    }
1646  
1647 +  //check the uniqueness of index  
1648 +  if(!zconsParaData->isIndexUnique()){
1649 +    sprintf(painCave.errMsg,
1650 +            "ZConstraint Error: molIndex is not unique\n");
1651 +    painCave.isFatal = 1;
1652 +    simError();
1653 +  }
1654 +
1655    //sort the parameters by index of molecules
1656    zconsParaData->sortByIndex();
1657 <
1657 >  
1658    //push data into siminfo, therefore, we can retrieve later
1659    theInfo.addProperty(zconsParaData);
1660   }

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