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root/group/branches/no-template-branch/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 780 by mmeineke, Mon Sep 22 21:23:25 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  
26   #define FF_DUFF 0
27   #define FF_LJ   1
# Line 603 | Line 601 | void SimSetup::gatherInfo(void){
601    }
602    else if (!strcasecmp(ensemble, "NPTf")){
603      ensembleCase = NPTf_ENS;
606 –  }
607 –  else if (!strcasecmp(ensemble, "NPTim")){
608 –    ensembleCase = NPTim_ENS;
609 –  }
610 –  else if (!strcasecmp(ensemble, "NPTfm")){
611 –    ensembleCase = NPTfm_ENS;
604    }
605    else{
606      sprintf(painCave.errMsg,
# Line 686 | Line 678 | void SimSetup::gatherInfo(void){
678  
679      if (globals->haveThermalTime()){
680        info[i].thermalTime = globals->getThermalTime();
681 +    }
682 +
683 +    info[i].resetIntegrator = 0;
684 +    if( globals->haveResetTime() ){
685 +      info[i].resetTime = globals->getResetTime();
686 +      info[i].resetIntegrator = 1;
687      }
688  
689      // check for the temperature set flag
# Line 1343 | Line 1341 | void SimSetup::makeIntegrator(void){
1341    int k;
1342  
1343    NVT<RealIntegrator>* myNVT = NULL;
1344 <  NPTi<RealIntegrator>* myNPTi = NULL;
1345 <  NPTf<RealIntegrator>* myNPTf = NULL;
1346 <  NPTim<RealIntegrator>* myNPTim = NULL;
1349 <  NPTfm<RealIntegrator>* myNPTfm = NULL;
1350 <
1344 >  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1345 >  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1346 >  
1347    for (k = 0; k < nInfo; k++){
1348      switch (ensembleCase){
1349        case NVE_ENS:
# Line 1383 | Line 1379 | void SimSetup::makeIntegrator(void){
1379        case NPTi_ENS:
1380          if (globals->haveZconstraints()){
1381            setupZConstraint(info[k]);
1382 <          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1382 >          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1383          }
1384          else
1385 <          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1385 >          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1386  
1387          myNPTi->setTargetTemp(globals->getTargetTemp());
1388  
# Line 1424 | Line 1420 | void SimSetup::makeIntegrator(void){
1420        case NPTf_ENS:
1421          if (globals->haveZconstraints()){
1422            setupZConstraint(info[k]);
1423 <          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1423 >          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1424          }
1425          else
1426 <          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1426 >          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1427  
1428          myNPTf->setTargetTemp(globals->getTargetTemp());
1429  
# Line 1453 | Line 1449 | void SimSetup::makeIntegrator(void){
1449  
1450          if (globals->haveTauBarostat())
1451            myNPTf->setTauBarostat(globals->getTauBarostat());
1456 –        else{
1457 –          sprintf(painCave.errMsg,
1458 –                  "SimSetup error: If you use an NPT\n"
1459 –                  "    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");
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());
1452          else{
1453            sprintf(painCave.errMsg,
1454                    "SimSetup error: If you use an NPT\n"
# Line 1503 | Line 1458 | void SimSetup::makeIntegrator(void){
1458          }
1459          break;
1460  
1506 –      case NPTfm_ENS:
1507 –        if (globals->haveZconstraints()){
1508 –          setupZConstraint(info[k]);
1509 –          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510 –        }
1511 –        else
1512 –          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513 –
1514 –        myNPTfm->setTargetTemp(globals->getTargetTemp());
1515 –
1516 –        if (globals->haveTargetPressure())
1517 –          myNPTfm->setTargetPressure(globals->getTargetPressure());
1518 –        else{
1519 –          sprintf(painCave.errMsg,
1520 –                  "SimSetup error: If you use a constant pressure\n"
1521 –                  "    ensemble, you must set targetPressure in the BASS file.\n");
1522 –          painCave.isFatal = 1;
1523 –          simError();
1524 –        }
1525 –
1526 –        if (globals->haveTauThermostat())
1527 –          myNPTfm->setTauThermostat(globals->getTauThermostat());
1528 –        else{
1529 –          sprintf(painCave.errMsg,
1530 –                  "SimSetup error: If you use an NPT\n"
1531 –                  "    ensemble, you must set tauThermostat.\n");
1532 –          painCave.isFatal = 1;
1533 –          simError();
1534 –        }
1535 –
1536 –        if (globals->haveTauBarostat())
1537 –          myNPTfm->setTauBarostat(globals->getTauBarostat());
1538 –        else{
1539 –          sprintf(painCave.errMsg,
1540 –                  "SimSetup error: If you use an NPT\n"
1541 –                  "    ensemble, you must set tauBarostat.\n");
1542 –          painCave.isFatal = 1;
1543 –          simError();
1544 –        }
1545 –        break;
1546 –
1461        default:
1462          sprintf(painCave.errMsg,
1463                  "SimSetup Error. Unrecognized ensemble in case statement.\n");
# Line 1615 | Line 1529 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1529    }
1530    theInfo.addProperty(zconsTol);
1531  
1532 <  //set Force Substraction Policy
1532 >  //set Force Subtraction Policy
1533    StringData* zconsForcePolicy = new StringData();
1534    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1535  
# Line 1624 | Line 1538 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1538    }
1539    else{
1540      sprintf(painCave.errMsg,
1541 <            "ZConstraint Warning: User does not set force substraction policy, "
1542 <            "average force substraction policy is used\n");
1541 >            "ZConstraint Warning: User does not set force Subtraction policy, "
1542 >            "PolicyByMass is used\n");
1543      painCave.isFatal = 0;
1544      simError();
1545 <    zconsForcePolicy->setData("BYNUMBER");
1545 >    zconsForcePolicy->setData("BYMASS");
1546    }
1547  
1548    theInfo.addProperty(zconsForcePolicy);
# Line 1666 | Line 1580 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1580      zconsParaData->addItem(tempParaItem);
1581    }
1582  
1583 +  //check the uniqueness of index  
1584 +  if(!zconsParaData->isIndexUnique()){
1585 +    sprintf(painCave.errMsg,
1586 +            "ZConstraint Error: molIndex is not unique\n");
1587 +    painCave.isFatal = 1;
1588 +    simError();
1589 +  }
1590 +
1591    //sort the parameters by index of molecules
1592    zconsParaData->sortByIndex();
1593 <
1593 >  
1594    //push data into siminfo, therefore, we can retrieve later
1595    theInfo.addProperty(zconsParaData);
1596   }

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