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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC

# Line 16 | Line 16
16  
17   // some defines for ensemble and Forcefield  cases
18  
19 < #define NVE_ENS   0
20 < #define NVT_ENS   1
21 < #define NPTi_ENS  2
22 < #define NPTf_ENS  3
23 < #define NPTim_ENS 4
24 < #define NPTfm_ENS 5
25 < #define NVEZCONS_ENS 6
26 <
19 > #define NVE_ENS        0
20 > #define NVT_ENS        1
21 > #define NPTi_ENS       2
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
31  
32   #define FF_DUFF 0
33   #define FF_LJ   1
# Line 623 | Line 627 | void SimSetup::gatherInfo( void ){
627    else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
628    else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
629    else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
630 +
631    else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632 +  else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633 +  else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634 +    ensembleCase = NPTiZCONS_ENS;
635 +  else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636 +  else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637 +  else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638 +  
639    else{
640      sprintf( painCave.errMsg,
641               "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 1310 | Line 1322 | void SimSetup::makeIntegrator( void ){
1322    NPTim<RealIntegrator>* myNPTim = NULL;
1323    NPTfm<RealIntegrator>* myNPTfm = NULL;
1324    ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325 +  ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326 +  ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327 +  ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328 +  ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329 +  ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330        
1331    cerr << "setting integrator" <<endl;    
1332    
# Line 1476 | Line 1493 | void SimSetup::makeIntegrator( void ){
1493      break;
1494      
1495    case NVEZCONS_ENS:
1479 –    {
1496  
1481 –      if(globals->haveZConsTime()){  
1482 –
1483 –        //add sample time of z-constraint  into SimInfo's property list                    
1484 –        DoubleData* zconsTimeProp = new DoubleData();
1485 –        zconsTimeProp->setID("zconstime");
1486 –        zconsTimeProp->setData(globals->getZConsTime());
1487 –        info->addProperty(zconsTimeProp);
1488 –      }
1489 –      else{
1490 –        sprintf( painCave.errMsg,
1491 –                 "ZConstraint error: If you use an ZConstraint\n"
1492 –                 " , you must set sample time.\n");
1493 –        painCave.isFatal = 1;
1494 –        simError();      
1495 –      }
1496 –      
1497 –      if(globals->haveIndexOfAllZConsMols()){
1498 –
1499 –        //add index of z-constraint molecules into SimInfo's property list
1500 –        vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1501 –        sort(tempIndex.begin(), tempIndex.end());
1502 –        
1503 –        IndexData* zconsIndex = new IndexData();
1504 –        zconsIndex->setID("zconsindex");
1505 –        zconsIndex->setIndexData(tempIndex);
1506 –        info->addProperty(zconsIndex);
1507 –      }
1508 –      else{
1509 –        sprintf( painCave.errMsg,
1510 –                 "SimSetup error: If you use an ZConstraint\n"
1511 –                 " , you must set index of z-constraint molecules.\n");
1512 –        painCave.isFatal = 1;
1513 –        simError();    
1514 –      
1515 –      }
1497  
1498 <      //Determine the name of ouput file and add it into SimInfo's property list
1499 <      //Be careful, do not use inFileName, since it is a pointer which
1500 <      //point to a string at master node, and slave nodes do not contain that string
1501 <    
1502 <      string zconsOutput(info->finalName);
1503 <            
1504 <      zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1505 <                
1506 <      StringData* zconsFilename = new StringData();
1507 <      zconsFilename->setID("zconsfilename");
1508 <      zconsFilename->setData(zconsOutput);
1498 >    //setup index of z-constraint molecules, z-constraint sampel time
1499 >    //and z-constraint force output name. These parameter should be known
1500 >    //before constructing the z-constraint integrator
1501 >    setupZConstraint();
1502 >      
1503 >    myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1504 >        
1505 >    break;
1506 >    
1507 >    
1508 >  case NVTZCONS_ENS:
1509 >  
1510 >    setupZConstraint();
1511 >    
1512 >    myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513 >    myNVTZCons->setTargetTemp(globals->getTargetTemp());
1514  
1515 <      info->addProperty(zconsFilename);      
1515 >    if (globals->haveTauThermostat())
1516 >      myNVTZCons->setTauThermostat(globals->getTauThermostat());
1517 >
1518 >    else {
1519 >      sprintf( painCave.errMsg,
1520 >               "SimSetup error: If you use the NVT\n"
1521 >               "    ensemble, you must set tauThermostat.\n");
1522 >      painCave.isFatal = 1;
1523 >      simError();
1524 >    }    
1525 >    break;    
1526 >    
1527 >  case NPTiZCONS_ENS:
1528 >  
1529 >    setupZConstraint();
1530 >    
1531 >    myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532 >    myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1533 >
1534 >    if (globals->haveTargetPressure())
1535 >      myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1536 >    else {
1537 >      sprintf( painCave.errMsg,
1538 >               "SimSetup error: If you use a constant pressure\n"
1539 >               "    ensemble, you must set targetPressure in the BASS file.\n");
1540 >      painCave.isFatal = 1;
1541 >      simError();
1542 >    }
1543 >    
1544 >    if( globals->haveTauThermostat() )
1545 >      myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546 >    else{
1547 >      sprintf( painCave.errMsg,
1548 >               "SimSetup error: If you use an NPT\n"
1549 >               "    ensemble, you must set tauThermostat.\n");
1550 >      painCave.isFatal = 1;
1551 >      simError();
1552 >    }
1553 >
1554 >    if( globals->haveTauBarostat() )
1555 >      myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1556 >    else{
1557 >      sprintf( painCave.errMsg,
1558 >               "SimSetup error: If you use an NPT\n"
1559 >               "    ensemble, you must set tauBarostat.\n");
1560 >      painCave.isFatal = 1;
1561 >      simError();
1562 >    }  
1563 >    
1564 >    break;
1565 >    
1566 >  case NPTfZCONS_ENS:
1567 >  
1568 >    setupZConstraint();
1569 >  
1570 >    myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571 >    myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1572 >
1573 >    if (globals->haveTargetPressure())
1574 >      myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1575 >    else {
1576 >      sprintf( painCave.errMsg,
1577 >               "SimSetup error: If you use a constant pressure\n"
1578 >               "    ensemble, you must set targetPressure in the BASS file.\n");
1579 >      painCave.isFatal = 1;
1580 >      simError();
1581 >    }    
1582 >
1583 >    if( globals->haveTauThermostat() )
1584 >      myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585 >    else{
1586 >      sprintf( painCave.errMsg,
1587 >               "SimSetup error: If you use an NPT\n"
1588 >               "    ensemble, you must set tauThermostat.\n");
1589 >      painCave.isFatal = 1;
1590 >      simError();
1591 >    }
1592 >
1593 >    if( globals->haveTauBarostat() )
1594 >      myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1595 >    else{
1596 >      sprintf( painCave.errMsg,
1597 >               "SimSetup error: If you use an NPT\n"
1598 >               "    ensemble, you must set tauBarostat.\n");
1599 >      painCave.isFatal = 1;
1600 >      simError();
1601 >    }  
1602 >    
1603 >    break;  
1604        
1605 <      myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1606 <        
1605 >  case NPTimZCONS_ENS:
1606 >  
1607 >    setupZConstraint();
1608 >  
1609 >    myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1610 >    myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1611 >
1612 >    if (globals->haveTargetPressure())
1613 >      myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1614 >    else {
1615 >      sprintf( painCave.errMsg,
1616 >               "SimSetup error: If you use a constant pressure\n"
1617 >               "    ensemble, you must set targetPressure in the BASS file.\n");
1618 >      painCave.isFatal = 1;
1619 >      simError();
1620 >    }
1621 >    
1622 >    if( globals->haveTauThermostat() )
1623 >      myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624 >    else{
1625 >      sprintf( painCave.errMsg,
1626 >               "SimSetup error: If you use an NPT\n"
1627 >               "    ensemble, you must set tauThermostat.\n");
1628 >      painCave.isFatal = 1;
1629 >      simError();
1630 >    }
1631 >
1632 >    if( globals->haveTauBarostat() )
1633 >      myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634 >    else{
1635 >      sprintf( painCave.errMsg,
1636 >               "SimSetup error: If you use an NPT\n"
1637 >               "    ensemble, you must set tauBarostat.\n");
1638 >      painCave.isFatal = 1;
1639 >      simError();
1640 >    }  
1641 >    
1642      break;
1643 +    
1644 +  case NPTfmZCONS_ENS:
1645 +  
1646 +    setupZConstraint();
1647 +    
1648 +    myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649 +    myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650 +
1651 +    if (globals->haveTargetPressure())
1652 +      myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653 +    else {
1654 +      sprintf( painCave.errMsg,
1655 +               "SimSetup error: If you use a constant pressure\n"
1656 +               "    ensemble, you must set targetPressure in the BASS file.\n");
1657 +      painCave.isFatal = 1;
1658 +      simError();
1659      }
1660      
1661 +    if( globals->haveTauThermostat() )
1662 +      myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663 +    else{
1664 +      sprintf( painCave.errMsg,
1665 +               "SimSetup error: If you use an NPT\n"
1666 +               "    ensemble, you must set tauThermostat.\n");
1667 +      painCave.isFatal = 1;
1668 +      simError();
1669 +    }
1670 +
1671 +    if( globals->haveTauBarostat() )
1672 +      myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673 +    else{
1674 +      sprintf( painCave.errMsg,
1675 +               "SimSetup error: If you use an NPT\n"
1676 +               "    ensemble, you must set tauBarostat.\n");
1677 +      painCave.isFatal = 1;
1678 +      simError();
1679 +    }    
1680 +    break;      
1681 +      
1682 +  
1683 +    
1684    default:
1685      sprintf( painCave.errMsg,
1686               "SimSetup Error. Unrecognized ensemble in case statement.\n");
# Line 1568 | Line 1716 | void SimSetup::initFortran( void ){
1716   #endif // is_mpi
1717  
1718   }
1719 +
1720 + void SimSetup::setupZConstraint()
1721 + {
1722 +  if(globals->haveZConsTime()){  
1723 +
1724 +  //add sample time of z-constraint  into SimInfo's property list                    
1725 +  DoubleData* zconsTimeProp = new DoubleData();
1726 +  zconsTimeProp->setID("zconstime");
1727 +  zconsTimeProp->setData(globals->getZConsTime());
1728 +  info->addProperty(zconsTimeProp);
1729 +  }
1730 +  else{
1731 +    sprintf( painCave.errMsg,
1732 +             "ZConstraint error: If you use an ZConstraint\n"
1733 +             " , you must set sample time.\n");
1734 +    painCave.isFatal = 1;
1735 +    simError();      
1736 +  }
1737 +      
1738 +  if(globals->haveIndexOfAllZConsMols()){
1739 +
1740 +        //add index of z-constraint molecules into SimInfo's property list
1741 +        vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1742 +        
1743 +        //sort the index
1744 +        sort(tempIndex.begin(), tempIndex.end());
1745 +        
1746 +        IndexData* zconsIndex = new IndexData();
1747 +        zconsIndex->setID("zconsindex");
1748 +        zconsIndex->setIndexData(tempIndex);
1749 +        info->addProperty(zconsIndex);
1750 +  }
1751 +  else{
1752 +    sprintf( painCave.errMsg,
1753 +             "SimSetup error: If you use an ZConstraint\n"
1754 +             " , you must set index of z-constraint molecules.\n");
1755 +    painCave.isFatal = 1;
1756 +    simError();    
1757 +      
1758 +  }
1759 +
1760 +  //Determine the name of ouput file and add it into SimInfo's property list
1761 +  //Be careful, do not use inFileName, since it is a pointer which
1762 +  //point to a string at master node, and slave nodes do not contain that string
1763 +    
1764 +  string zconsOutput(info->finalName);
1765 +            
1766 +  zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1767 +                
1768 +  StringData* zconsFilename = new StringData();
1769 +  zconsFilename->setID("zconsfilename");
1770 +  zconsFilename->setData(zconsOutput);
1771 +
1772 +  info->addProperty(zconsFilename);      
1773 +
1774 + }

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