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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 682 by tim, Tue Aug 12 17:51:33 2003 UTC

# Line 22 | Line 22
22   #define NPTf_ENS       3
23   #define NPTim_ENS      4
24   #define NPTfm_ENS      5
25 – #define NVEZCONS_ENS   6
26 – #define NVTZCONS_ENS   7
27 – #define NPTiZCONS_ENS  8
28 – #define NPTfZCONS_ENS  9
29 – #define NPTimZCONS_ENS 10
30 – #define NPTfmZCONS_ENS 11
25  
26   #define FF_DUFF 0
27   #define FF_LJ   1
# Line 639 | Line 633 | void SimSetup::gatherInfo( void ){
633    else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634    else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635    else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
642 –
643 –  else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
644 –  else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
645 –  else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646 –    ensembleCase = NPTiZCONS_ENS;
647 –  else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648 –  else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649 –  else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650 –  
636    else{
637      sprintf( painCave.errMsg,
638               "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 1367 | Line 1352 | void SimSetup::makeIntegrator( void ){
1352    NPTf<RealIntegrator>* myNPTf = NULL;
1353    NPTim<RealIntegrator>* myNPTim = NULL;
1354    NPTfm<RealIntegrator>* myNPTfm = NULL;
1370 –  ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1371 –  ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1372 –  ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1373 –  ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1374 –  ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1375 –  ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1355          
1356    for(k=0; k<nInfo; k++){
1357      
1358      switch( ensembleCase ){
1359        
1360      case NVE_ENS:
1361 <      new NVE<RealIntegrator>( &(info[k]), the_ff );
1361 >        if (globals->haveZconstraints()){
1362 >         setupZConstraint(info[k]);
1363 >           new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364 >        }
1365 >
1366 >        else
1367 >        new NVE<RealIntegrator>( &(info[k]), the_ff );
1368        break;
1369        
1370      case NVT_ENS:
1371 <      myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1371 >        if (globals->haveZconstraints()){
1372 >         setupZConstraint(info[k]);
1373 >           myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374 >        }
1375 >        else
1376 >        myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377 >
1378        myNVT->setTargetTemp(globals->getTargetTemp());
1379        
1380        if (globals->haveTauThermostat())
# Line 1399 | Line 1390 | void SimSetup::makeIntegrator( void ){
1390        break;
1391        
1392      case NPTi_ENS:
1393 <      myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1394 <      myNPTi->setTargetTemp( globals->getTargetTemp() );
1393 >        if (globals->haveZconstraints()){
1394 >         setupZConstraint(info[k]);
1395 >           myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396 >        }
1397 >        else
1398 >        myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399 >
1400 >        myNPTi->setTargetTemp( globals->getTargetTemp() );
1401        
1402        if (globals->haveTargetPressure())
1403          myNPTi->setTargetPressure(globals->getTargetPressure());
# Line 1434 | Line 1431 | void SimSetup::makeIntegrator( void ){
1431        break;
1432        
1433      case NPTf_ENS:
1434 <      myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1434 >        if (globals->haveZconstraints()){
1435 >         setupZConstraint(info[k]);
1436 >           myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437 >        }
1438 >        else
1439 >        myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440 >
1441        myNPTf->setTargetTemp( globals->getTargetTemp());
1442        
1443        if (globals->haveTargetPressure())
# Line 1469 | Line 1472 | void SimSetup::makeIntegrator( void ){
1472        break;
1473        
1474      case NPTim_ENS:
1475 <      myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1476 <      myNPTim->setTargetTemp( globals->getTargetTemp());
1475 >        if (globals->haveZconstraints()){
1476 >         setupZConstraint(info[k]);
1477 >           myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478 >        }
1479 >        else
1480 >        myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481 >
1482 >        myNPTim->setTargetTemp( globals->getTargetTemp());
1483        
1484        if (globals->haveTargetPressure())
1485          myNPTim->setTargetPressure(globals->getTargetPressure());
# Line 1504 | Line 1513 | void SimSetup::makeIntegrator( void ){
1513        break;
1514        
1515      case NPTfm_ENS:
1516 <      myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1517 <      myNPTfm->setTargetTemp( globals->getTargetTemp());
1516 >        if (globals->haveZconstraints()){
1517 >         setupZConstraint(info[k]);
1518 >           myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519 >        }
1520 >        else
1521 >        myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522 >
1523 >        myNPTfm->setTargetTemp( globals->getTargetTemp());
1524        
1525        if (globals->haveTargetPressure())
1526          myNPTfm->setTargetPressure(globals->getTargetPressure());
# Line 1529 | Line 1544 | void SimSetup::makeIntegrator( void ){
1544        
1545        if( globals->haveTauBarostat() )
1546          myNPTfm->setTauBarostat( globals->getTauBarostat() );
1532 –      else{
1533 –        sprintf( painCave.errMsg,
1534 –                 "SimSetup error: If you use an NPT\n"
1535 –                 "    ensemble, you must set tauBarostat.\n");
1536 –        painCave.isFatal = 1;
1537 –        simError();
1538 –      }
1539 –      break;
1540 –      
1541 –    case NVEZCONS_ENS:
1542 –      
1543 –      
1544 –      //setup index of z-constraint molecules, z-constraint sampel time
1545 –      //and z-constraint force output name. These parameter should be known
1546 –      //before constructing the z-constraint integrator
1547 –      setupZConstraint();
1548 –      
1549 –      myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550 –      
1551 –      break;
1552 –      
1553 –      
1554 –    case NVTZCONS_ENS:
1555 –      
1556 –      setupZConstraint();
1557 –      
1558 –      myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559 –      myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560 –      
1561 –      if (globals->haveTauThermostat())
1562 –        myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563 –      
1564 –      else {
1565 –        sprintf( painCave.errMsg,
1566 –                 "SimSetup error: If you use the NVT\n"
1567 –                 "    ensemble, you must set tauThermostat.\n");
1568 –        painCave.isFatal = 1;
1569 –        simError();
1570 –      }    
1571 –      break;    
1572 –      
1573 –    case NPTiZCONS_ENS:
1574 –      
1575 –      setupZConstraint();
1576 –      
1577 –      myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578 –      myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579 –      
1580 –      if (globals->haveTargetPressure())
1581 –        myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582 –      else {
1583 –        sprintf( painCave.errMsg,
1584 –                 "SimSetup error: If you use a constant pressure\n"
1585 –                 "    ensemble, you must set targetPressure in the BASS file.\n");
1586 –        painCave.isFatal = 1;
1587 –        simError();
1588 –      }
1589 –      
1590 –      if( globals->haveTauThermostat() )
1591 –        myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592 –      else{
1593 –        sprintf( painCave.errMsg,
1594 –                 "SimSetup error: If you use an NPT\n"
1595 –                 "    ensemble, you must set tauThermostat.\n");
1596 –        painCave.isFatal = 1;
1597 –        simError();
1598 –      }
1599 –      
1600 –      if( globals->haveTauBarostat() )
1601 –        myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602 –      else{
1603 –        sprintf( painCave.errMsg,
1604 –                 "SimSetup error: If you use an NPT\n"
1605 –                 "    ensemble, you must set tauBarostat.\n");
1606 –        painCave.isFatal = 1;
1607 –        simError();
1608 –      }  
1609 –      
1610 –      break;
1611 –      
1612 –    case NPTfZCONS_ENS:
1613 –      
1614 –      setupZConstraint();
1615 –      
1616 –      myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617 –      myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618 –      
1619 –      if (globals->haveTargetPressure())
1620 –        myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621 –      else {
1622 –        sprintf( painCave.errMsg,
1623 –                 "SimSetup error: If you use a constant pressure\n"
1624 –                 "    ensemble, you must set targetPressure in the BASS file.\n");
1625 –        painCave.isFatal = 1;
1626 –        simError();
1627 –      }    
1628 –      
1629 –      if( globals->haveTauThermostat() )
1630 –        myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631 –      else{
1632 –        sprintf( painCave.errMsg,
1633 –                 "SimSetup error: If you use an NPT\n"
1634 –                 "    ensemble, you must set tauThermostat.\n");
1635 –        painCave.isFatal = 1;
1636 –        simError();
1637 –      }
1638 –      
1639 –      if( globals->haveTauBarostat() )
1640 –        myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1547        else{
1548          sprintf( painCave.errMsg,
1549                   "SimSetup error: If you use an NPT\n"
1550                   "    ensemble, you must set tauBarostat.\n");
1551          painCave.isFatal = 1;
1552          simError();
1647 –      }  
1648 –      
1649 –      break;  
1650 –      
1651 –    case NPTimZCONS_ENS:
1652 –      
1653 –      setupZConstraint();
1654 –      
1655 –      myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656 –      myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657 –      
1658 –      if (globals->haveTargetPressure())
1659 –        myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660 –      else {
1661 –        sprintf( painCave.errMsg,
1662 –                 "SimSetup error: If you use a constant pressure\n"
1663 –                 "    ensemble, you must set targetPressure in the BASS file.\n");
1664 –        painCave.isFatal = 1;
1665 –        simError();
1553        }
1667 –      
1668 –      if( globals->haveTauThermostat() )
1669 –        myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670 –      else{
1671 –        sprintf( painCave.errMsg,
1672 –                 "SimSetup error: If you use an NPT\n"
1673 –                 "    ensemble, you must set tauThermostat.\n");
1674 –        painCave.isFatal = 1;
1675 –        simError();
1676 –      }
1677 –      
1678 –      if( globals->haveTauBarostat() )
1679 –        myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680 –      else{
1681 –        sprintf( painCave.errMsg,
1682 –                 "SimSetup error: If you use an NPT\n"
1683 –                 "    ensemble, you must set tauBarostat.\n");
1684 –        painCave.isFatal = 1;
1685 –        simError();
1686 –      }  
1687 –      
1554        break;
1555        
1690 –    case NPTfmZCONS_ENS:
1691 –      
1692 –      setupZConstraint();
1693 –      
1694 –      myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695 –      myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696 –      
1697 –      if (globals->haveTargetPressure())
1698 –        myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699 –      else {
1700 –        sprintf( painCave.errMsg,
1701 –                 "SimSetup error: If you use a constant pressure\n"
1702 –                 "    ensemble, you must set targetPressure in the BASS file.\n");
1703 –        painCave.isFatal = 1;
1704 –        simError();
1705 –      }
1706 –      
1707 –      if( globals->haveTauThermostat() )
1708 –        myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709 –      else{
1710 –        sprintf( painCave.errMsg,
1711 –                 "SimSetup error: If you use an NPT\n"
1712 –                 "    ensemble, you must set tauThermostat.\n");
1713 –        painCave.isFatal = 1;
1714 –        simError();
1715 –      }
1716 –      
1717 –      if( globals->haveTauBarostat() )
1718 –        myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719 –      else{
1720 –        sprintf( painCave.errMsg,
1721 –                 "SimSetup error: If you use an NPT\n"
1722 –                 "    ensemble, you must set tauBarostat.\n");
1723 –        painCave.isFatal = 1;
1724 –        simError();
1725 –      }    
1726 –      break;      
1727 –      
1728 –      
1729 –      
1556      default:
1557        sprintf( painCave.errMsg,
1558                 "SimSetup Error. Unrecognized ensemble in case statement.\n");
# Line 1763 | Line 1589 | void SimSetup::setupZConstraint()
1589  
1590   }
1591  
1592 < void SimSetup::setupZConstraint()
1592 > void SimSetup::setupZConstraint(SimInfo& theInfo)
1593   {
1594 <  int k;
1595 <
1596 <  for(k=0; k<nInfo; k++){
1597 <    
1772 <    if(globals->haveZConsTime()){  
1594 >    int nZConstraints;
1595 >    ZconStamp** zconStamp;
1596 >        
1597 >    if(globals->haveZconstraintTime()){  
1598        
1599        //add sample time of z-constraint  into SimInfo's property list                    
1600        DoubleData* zconsTimeProp = new DoubleData();
1601 <      zconsTimeProp->setID("zconstime");
1602 <      zconsTimeProp->setData(globals->getZConsTime());
1603 <      info[k].addProperty(zconsTimeProp);
1601 >      zconsTimeProp->setID(ZCONSTIME_ID);
1602 >      zconsTimeProp->setData(globals->getZconsTime());
1603 >      theInfo.addProperty(zconsTimeProp);
1604      }
1605      else{
1606        sprintf( painCave.errMsg,
# Line 1784 | Line 1609 | void SimSetup::setupZConstraint()
1609        painCave.isFatal = 1;
1610        simError();      
1611      }
1612 <    
1613 <    if(globals->haveIndexOfAllZConsMols()){
1614 <
1615 <      //add index of z-constraint molecules into SimInfo's property list
1616 <      vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1617 <      
1618 <      //sort the index
1619 <      sort(tempIndex.begin(), tempIndex.end());
1620 <      
1621 <      IndexData* zconsIndex = new IndexData();
1622 <      zconsIndex->setID("zconsindex");
1623 <      zconsIndex->setIndexData(tempIndex);
1624 <      info[k].addProperty(zconsIndex);
1612 >
1613 >    //
1614 >    nZConstraints = globals->getNzConstraints();
1615 >    zconStamp = globals->getZconStamp();
1616 >    ZConsParaItem tempParaItem;
1617 >
1618 >    ZConsParaData* zconsParaData = new ZConsParaData();
1619 >    zconsParaData->setID(ZCONSPARADATA_ID);
1620 >  
1621 >    for(int i = 0; i < nZConstraints; i++){
1622 >    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1623 >    tempParaItem.zPos = zconStamp[i]->getZpos();
1624 >    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1625 >    tempParaItem.kRatio = zconStamp[i]->getKratio();
1626 >
1627 >    zconsParaData->addItem(tempParaItem);
1628      }
1629 <    else{
1630 <      sprintf( painCave.errMsg,
1631 <               "SimSetup error: If you use an ZConstraint\n"
1632 <               " , you must set index of z-constraint molecules.\n");
1633 <      painCave.isFatal = 1;
1634 <      simError();    
1635 <      
1629 >
1630 >    //sort the parameters by index of molecules
1631 >    zconsParaData->sortByIndex();
1632 >        
1633 >    //push data into siminfo, therefore, we can retrieve later
1634 >    theInfo.addProperty(zconsParaData);
1635 >
1636 >    //push zconsTol into siminfo, if user does not specify
1637 >    //value for zconsTol, a default value will be used
1638 >    DoubleData* zconsTol = new DoubleData();
1639 >    zconsTol->setID(ZCONSTOL_ID);
1640 >    if(globals->haveZconsTol()){
1641 >      zconsTol->setData(globals->getZconsTol());
1642      }
1643 <    
1643 >         else{
1644 >                double defaultZConsTol = 1E-6;
1645 >      sprintf( painCave.errMsg,
1646 >               "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1647 >               " , default value %f is used.\n", defaultZConsTol);
1648 >      painCave.isFatal = 0;
1649 >      simError();      
1650 >
1651 >      zconsTol->setData(defaultZConsTol);
1652 >         }
1653 >    theInfo.addProperty(zconsTol);
1654 >        
1655      //Determine the name of ouput file and add it into SimInfo's property list
1656      //Be careful, do not use inFileName, since it is a pointer which
1657      //point to a string at master node, and slave nodes do not contain that string
1658      
1659 <    string zconsOutput(info[k].finalName);
1659 >    string zconsOutput(theInfo.finalName);
1660      
1661      zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1662      
1663      StringData* zconsFilename = new StringData();
1664 <    zconsFilename->setID("zconsfilename");
1664 >    zconsFilename->setID(ZCONSFILENAME_ID);
1665      zconsFilename->setData(zconsOutput);
1666      
1667 <    info[k].addProperty(zconsFilename);      
1823 <  }
1667 >    theInfo.addProperty(zconsFilename);      
1668   }

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