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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 689 by tim, Tue Aug 12 19:56:49 2003 UTC

# Line 5 | Line 5
5   #include <string>
6  
7   #include "SimSetup.hpp"
8 + #include "ReadWrite.hpp"
9   #include "parse_me.h"
10   #include "Integrator.hpp"
11   #include "simError.h"
# Line 22 | Line 23
23   #define NPTf_ENS       3
24   #define NPTim_ENS      4
25   #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
26  
27   #define FF_DUFF 0
28   #define FF_LJ   1
# Line 102 | Line 97 | void SimSetup::createSim(void){
97    int i, j, k, globalAtomIndex;
98    
99    // gather all of the information from the Bass file
100 <  
100 >
101 >  std::cerr << "gathering info\n";
102 >
103    gatherInfo();
104  
105    // creation of complex system objects
106  
107 +  std::cerr << "creating system objects\n";
108 +
109    sysObjectsCreation();
110  
111    // check on the post processing info
112    
113 +  std::cerr << "performing final info check.\n";
114 +
115    finalInfoCheck();
116  
117    // initialize the system coordinates
118  
119 +  std::cerr << "about to init coords\n";
120 +
121    if( !isInfoArray ) initSystemCoords();  
122  
123    // make the output filenames
# Line 639 | Line 642 | void SimSetup::gatherInfo( void ){
642    else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
643    else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
644    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 –  
645    else{
646      sprintf( painCave.errMsg,
647               "SimSetup Warning. Unrecognized Ensemble -> %s, "
# Line 903 | Line 897 | void SimSetup::initSystemCoords( void ){
897   void SimSetup::initSystemCoords( void ){
898    int i;
899    
900 +  char* inName;
901 +
902    std::cerr << "Setting atom Coords\n";
903  
904    (info[0].getConfiguration())->createArrays( info[0].n_atoms );
# Line 915 | Line 911 | void SimSetup::initSystemCoords( void ){
911   #ifdef IS_MPI // is_mpi
912      if( worldRank == 0 ){
913   #endif //is_mpi
914 <      fileInit = new InitializeFromFile( globals->getInitialConfig() );
914 >      inName = globals->getInitialConfig();
915 >      fileInit = new InitializeFromFile( inName );
916   #ifdef IS_MPI
917      }else fileInit = new InitializeFromFile( NULL );
918   #endif
# Line 1048 | Line 1045 | void SimSetup::sysObjectsCreation( void ){
1045    int i,k;
1046    
1047    // create the forceField
1048 <  
1048 >
1049    createFF();
1050  
1051    // extract componentList
# Line 1066 | Line 1063 | void SimSetup::sysObjectsCreation( void ){
1063   #endif //is_mpi
1064    
1065    // create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066 <  
1066 >
1067    makeSysArrays();
1068  
1069    // make and initialize the molecules (all but atomic coordinates)
1070 <  
1070 >
1071    makeMolecules();
1072    
1073    for(k=0; k<nInfo; k++){
# Line 1367 | Line 1364 | void SimSetup::makeIntegrator( void ){
1364    NPTf<RealIntegrator>* myNPTf = NULL;
1365    NPTim<RealIntegrator>* myNPTim = NULL;
1366    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;
1367          
1368    for(k=0; k<nInfo; k++){
1369      
1370      switch( ensembleCase ){
1371        
1372      case NVE_ENS:
1373 <      new NVE<RealIntegrator>( &(info[k]), the_ff );
1373 >        if (globals->haveZconstraints()){
1374 >         setupZConstraint(info[k]);
1375 >           new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376 >        }
1377 >
1378 >        else
1379 >        new NVE<RealIntegrator>( &(info[k]), the_ff );
1380        break;
1381        
1382      case NVT_ENS:
1383 <      myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1383 >        if (globals->haveZconstraints()){
1384 >         setupZConstraint(info[k]);
1385 >           myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386 >        }
1387 >        else
1388 >        myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389 >
1390        myNVT->setTargetTemp(globals->getTargetTemp());
1391        
1392        if (globals->haveTauThermostat())
# Line 1399 | Line 1402 | void SimSetup::makeIntegrator( void ){
1402        break;
1403        
1404      case NPTi_ENS:
1405 <      myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1406 <      myNPTi->setTargetTemp( globals->getTargetTemp() );
1405 >        if (globals->haveZconstraints()){
1406 >         setupZConstraint(info[k]);
1407 >           myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408 >        }
1409 >        else
1410 >        myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411 >
1412 >        myNPTi->setTargetTemp( globals->getTargetTemp() );
1413        
1414        if (globals->haveTargetPressure())
1415          myNPTi->setTargetPressure(globals->getTargetPressure());
# Line 1434 | Line 1443 | void SimSetup::makeIntegrator( void ){
1443        break;
1444        
1445      case NPTf_ENS:
1446 <      myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1446 >        if (globals->haveZconstraints()){
1447 >         setupZConstraint(info[k]);
1448 >           myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449 >        }
1450 >        else
1451 >        myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452 >
1453        myNPTf->setTargetTemp( globals->getTargetTemp());
1454        
1455        if (globals->haveTargetPressure())
# Line 1469 | Line 1484 | void SimSetup::makeIntegrator( void ){
1484        break;
1485        
1486      case NPTim_ENS:
1487 <      myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1488 <      myNPTim->setTargetTemp( globals->getTargetTemp());
1487 >        if (globals->haveZconstraints()){
1488 >         setupZConstraint(info[k]);
1489 >           myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490 >        }
1491 >        else
1492 >        myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493 >
1494 >        myNPTim->setTargetTemp( globals->getTargetTemp());
1495        
1496        if (globals->haveTargetPressure())
1497          myNPTim->setTargetPressure(globals->getTargetPressure());
# Line 1504 | Line 1525 | void SimSetup::makeIntegrator( void ){
1525        break;
1526        
1527      case NPTfm_ENS:
1528 <      myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1529 <      myNPTfm->setTargetTemp( globals->getTargetTemp());
1528 >        if (globals->haveZconstraints()){
1529 >         setupZConstraint(info[k]);
1530 >           myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531 >        }
1532 >        else
1533 >        myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534 >
1535 >        myNPTfm->setTargetTemp( globals->getTargetTemp());
1536        
1537        if (globals->haveTargetPressure())
1538          myNPTfm->setTargetPressure(globals->getTargetPressure());
# Line 1529 | Line 1556 | void SimSetup::makeIntegrator( void ){
1556        
1557        if( globals->haveTauBarostat() )
1558          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() );
1559        else{
1560          sprintf( painCave.errMsg,
1561                   "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() );
1641 –      else{
1642 –        sprintf( painCave.errMsg,
1643 –                 "SimSetup error: If you use an NPT\n"
1562                   "    ensemble, you must set tauBarostat.\n");
1563          painCave.isFatal = 1;
1564          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();
1565        }
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 –      
1566        break;
1567        
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 –      
1568      default:
1569        sprintf( painCave.errMsg,
1570                 "SimSetup Error. Unrecognized ensemble in case statement.\n");
# Line 1763 | Line 1601 | void SimSetup::setupZConstraint()
1601  
1602   }
1603  
1604 < void SimSetup::setupZConstraint()
1604 > void SimSetup::setupZConstraint(SimInfo& theInfo)
1605   {
1606 <  int k;
1607 <
1608 <  for(k=0; k<nInfo; k++){
1609 <    
1772 <    if(globals->haveZConsTime()){  
1606 >    int nZConstraints;
1607 >    ZconStamp** zconStamp;
1608 >        
1609 >    if(globals->haveZconstraintTime()){  
1610        
1611        //add sample time of z-constraint  into SimInfo's property list                    
1612        DoubleData* zconsTimeProp = new DoubleData();
1613 <      zconsTimeProp->setID("zconstime");
1614 <      zconsTimeProp->setData(globals->getZConsTime());
1615 <      info[k].addProperty(zconsTimeProp);
1613 >      zconsTimeProp->setID(ZCONSTIME_ID);
1614 >      zconsTimeProp->setData(globals->getZconsTime());
1615 >      theInfo.addProperty(zconsTimeProp);
1616      }
1617      else{
1618        sprintf( painCave.errMsg,
# Line 1784 | Line 1621 | void SimSetup::setupZConstraint()
1621        painCave.isFatal = 1;
1622        simError();      
1623      }
1624 <    
1625 <    if(globals->haveIndexOfAllZConsMols()){
1626 <
1627 <      //add index of z-constraint molecules into SimInfo's property list
1628 <      vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1629 <      
1630 <      //sort the index
1631 <      sort(tempIndex.begin(), tempIndex.end());
1632 <      
1633 <      IndexData* zconsIndex = new IndexData();
1634 <      zconsIndex->setID("zconsindex");
1635 <      zconsIndex->setIndexData(tempIndex);
1636 <      info[k].addProperty(zconsIndex);
1624 >
1625 >    //
1626 >    nZConstraints = globals->getNzConstraints();
1627 >    zconStamp = globals->getZconStamp();
1628 >    ZConsParaItem tempParaItem;
1629 >
1630 >    ZConsParaData* zconsParaData = new ZConsParaData();
1631 >    zconsParaData->setID(ZCONSPARADATA_ID);
1632 >  
1633 >    for(int i = 0; i < nZConstraints; i++){
1634 >    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635 >    tempParaItem.zPos = zconStamp[i]->getZpos();
1636 >    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637 >    tempParaItem.kRatio = zconStamp[i]->getKratio();
1638 >
1639 >    zconsParaData->addItem(tempParaItem);
1640      }
1641 <    else{
1642 <      sprintf( painCave.errMsg,
1643 <               "SimSetup error: If you use an ZConstraint\n"
1644 <               " , you must set index of z-constraint molecules.\n");
1645 <      painCave.isFatal = 1;
1646 <      simError();    
1647 <      
1641 >
1642 >    //sort the parameters by index of molecules
1643 >    zconsParaData->sortByIndex();
1644 >        
1645 >    //push data into siminfo, therefore, we can retrieve later
1646 >    theInfo.addProperty(zconsParaData);
1647 >
1648 >    //push zconsTol into siminfo, if user does not specify
1649 >    //value for zconsTol, a default value will be used
1650 >    DoubleData* zconsTol = new DoubleData();
1651 >    zconsTol->setID(ZCONSTOL_ID);
1652 >    if(globals->haveZconsTol()){
1653 >      zconsTol->setData(globals->getZconsTol());
1654      }
1655 <    
1655 >         else{
1656 >                double defaultZConsTol = 1E-6;
1657 >      sprintf( painCave.errMsg,
1658 >               "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659 >               " , default value %f is used.\n", defaultZConsTol);
1660 >      painCave.isFatal = 0;
1661 >      simError();      
1662 >
1663 >      zconsTol->setData(defaultZConsTol);
1664 >         }
1665 >    theInfo.addProperty(zconsTol);
1666 >        
1667      //Determine the name of ouput file and add it into SimInfo's property list
1668      //Be careful, do not use inFileName, since it is a pointer which
1669      //point to a string at master node, and slave nodes do not contain that string
1670      
1671 <    string zconsOutput(info[k].finalName);
1671 >    string zconsOutput(theInfo.finalName);
1672      
1673      zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674      
1675      StringData* zconsFilename = new StringData();
1676 <    zconsFilename->setID("zconsfilename");
1676 >    zconsFilename->setID(ZCONSFILENAME_ID);
1677      zconsFilename->setData(zconsOutput);
1678      
1679 <    info[k].addProperty(zconsFilename);      
1823 <  }
1679 >    theInfo.addProperty(zconsFilename);      
1680   }

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