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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC vs.
Revision 690 by mmeineke, Tue Aug 12 21:44:06 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 96 | 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    gatherInfo();
102  
103    // creation of complex system objects
# Line 104 | Line 105 | void SimSetup::createSim(void){
105    sysObjectsCreation();
106  
107    // check on the post processing info
108 <  
108 >
109    finalInfoCheck();
110  
111    // initialize the system coordinates
# Line 888 | Line 889 | void SimSetup::initSystemCoords( void ){
889   void SimSetup::initSystemCoords( void ){
890    int i;
891    
892 <  std::cerr << "Setting atom Coords\n";
892 >  char* inName;
893  
894 +
895    (info[0].getConfiguration())->createArrays( info[0].n_atoms );
896    
897    for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
# Line 900 | Line 902 | void SimSetup::initSystemCoords( void ){
902   #ifdef IS_MPI // is_mpi
903      if( worldRank == 0 ){
904   #endif //is_mpi
905 <      fileInit = new InitializeFromFile( globals->getInitialConfig() );
905 >      inName = globals->getInitialConfig();
906 >      fileInit = new InitializeFromFile( inName );
907   #ifdef IS_MPI
908      }else fileInit = new InitializeFromFile( NULL );
909   #endif
# Line 1033 | Line 1036 | void SimSetup::sysObjectsCreation( void ){
1036    int i,k;
1037    
1038    // create the forceField
1039 <  
1039 >
1040    createFF();
1041  
1042    // extract componentList
# Line 1051 | Line 1054 | void SimSetup::sysObjectsCreation( void ){
1054   #endif //is_mpi
1055    
1056    // create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057 <  
1057 >
1058    makeSysArrays();
1059  
1060    // make and initialize the molecules (all but atomic coordinates)
1061 <  
1061 >
1062    makeMolecules();
1063    
1064    for(k=0; k<nInfo; k++){
# Line 1358 | Line 1361 | void SimSetup::makeIntegrator( void ){
1361      switch( ensembleCase ){
1362        
1363      case NVE_ENS:
1364 <        if (haveZConstraint){
1365 <         setupZConstraint();
1364 >        if (globals->haveZconstraints()){
1365 >         setupZConstraint(info[k]);
1366             new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367          }
1368  
# Line 1368 | Line 1371 | void SimSetup::makeIntegrator( void ){
1371        break;
1372        
1373      case NVT_ENS:
1374 <        if (haveZConstraint){
1375 <         setupZConstraint();
1374 >        if (globals->haveZconstraints()){
1375 >         setupZConstraint(info[k]);
1376             myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377          }
1378          else
# Line 1390 | Line 1393 | void SimSetup::makeIntegrator( void ){
1393        break;
1394        
1395      case NPTi_ENS:
1396 <        if (haveZConstraint){
1397 <         setupZConstraint();
1396 >        if (globals->haveZconstraints()){
1397 >         setupZConstraint(info[k]);
1398             myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399          }
1400          else
# Line 1431 | Line 1434 | void SimSetup::makeIntegrator( void ){
1434        break;
1435        
1436      case NPTf_ENS:
1437 <        if (haveZConstraint){
1438 <         setupZConstraint();
1437 >        if (globals->haveZconstraints()){
1438 >         setupZConstraint(info[k]);
1439             myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440          }
1441          else
# Line 1472 | Line 1475 | void SimSetup::makeIntegrator( void ){
1475        break;
1476        
1477      case NPTim_ENS:
1478 <        if (haveZConstraint){
1479 <         setupZConstraint();
1478 >        if (globals->haveZconstraints()){
1479 >         setupZConstraint(info[k]);
1480             myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481          }
1482          else
# Line 1513 | Line 1516 | void SimSetup::makeIntegrator( void ){
1516        break;
1517        
1518      case NPTfm_ENS:
1519 <        if (haveZConstraint){
1520 <         setupZConstraint();
1519 >        if (globals->haveZconstraints()){
1520 >         setupZConstraint(info[k]);
1521             myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522          }
1523          else
# Line 1589 | Line 1592 | void SimSetup::initFortran( void ){
1592  
1593   }
1594  
1595 < void SimSetup::setupZConstraint()
1595 > void SimSetup::setupZConstraint(SimInfo& theInfo)
1596   {
1597 <  int k;
1598 <
1599 <  for(k=0; k<nInfo; k++){
1600 <    
1598 <    if(globals->haveZConsTime()){  
1597 >    int nZConstraints;
1598 >    ZconStamp** zconStamp;
1599 >        
1600 >    if(globals->haveZconstraintTime()){  
1601        
1602        //add sample time of z-constraint  into SimInfo's property list                    
1603        DoubleData* zconsTimeProp = new DoubleData();
1604 <      zconsTimeProp->setID("zconstime");
1605 <      zconsTimeProp->setData(globals->getZConsTime());
1606 <      info[k].addProperty(zconsTimeProp);
1604 >      zconsTimeProp->setID(ZCONSTIME_ID);
1605 >      zconsTimeProp->setData(globals->getZconsTime());
1606 >      theInfo.addProperty(zconsTimeProp);
1607      }
1608      else{
1609        sprintf( painCave.errMsg,
# Line 1610 | Line 1612 | void SimSetup::setupZConstraint()
1612        painCave.isFatal = 1;
1613        simError();      
1614      }
1615 <    
1616 <    if(globals->haveIndexOfAllZConsMols()){
1617 <
1618 <      //add index of z-constraint molecules into SimInfo's property list
1619 <      vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1620 <      
1621 <      //sort the index
1622 <      sort(tempIndex.begin(), tempIndex.end());
1623 <      
1624 <      IndexData* zconsIndex = new IndexData();
1625 <      zconsIndex->setID("zconsindex");
1626 <      zconsIndex->setIndexData(tempIndex);
1627 <      info[k].addProperty(zconsIndex);
1615 >
1616 >    //
1617 >    nZConstraints = globals->getNzConstraints();
1618 >    zconStamp = globals->getZconStamp();
1619 >    ZConsParaItem tempParaItem;
1620 >
1621 >    ZConsParaData* zconsParaData = new ZConsParaData();
1622 >    zconsParaData->setID(ZCONSPARADATA_ID);
1623 >  
1624 >    for(int i = 0; i < nZConstraints; i++){
1625 >    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1626 >    tempParaItem.zPos = zconStamp[i]->getZpos();
1627 >    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1628 >    tempParaItem.kRatio = zconStamp[i]->getKratio();
1629 >
1630 >    zconsParaData->addItem(tempParaItem);
1631      }
1632 <    else{
1633 <      sprintf( painCave.errMsg,
1634 <               "SimSetup error: If you use an ZConstraint\n"
1635 <               " , you must set index of z-constraint molecules.\n");
1636 <      painCave.isFatal = 1;
1637 <      simError();    
1638 <      
1632 >
1633 >    //sort the parameters by index of molecules
1634 >    zconsParaData->sortByIndex();
1635 >        
1636 >    //push data into siminfo, therefore, we can retrieve later
1637 >    theInfo.addProperty(zconsParaData);
1638 >
1639 >    //push zconsTol into siminfo, if user does not specify
1640 >    //value for zconsTol, a default value will be used
1641 >    DoubleData* zconsTol = new DoubleData();
1642 >    zconsTol->setID(ZCONSTOL_ID);
1643 >    if(globals->haveZconsTol()){
1644 >      zconsTol->setData(globals->getZconsTol());
1645      }
1646 <    
1646 >         else{
1647 >                double defaultZConsTol = 1E-6;
1648 >      sprintf( painCave.errMsg,
1649 >               "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650 >               " , default value %f is used.\n", defaultZConsTol);
1651 >      painCave.isFatal = 0;
1652 >      simError();      
1653 >
1654 >      zconsTol->setData(defaultZConsTol);
1655 >         }
1656 >    theInfo.addProperty(zconsTol);
1657 >        
1658      //Determine the name of ouput file and add it into SimInfo's property list
1659      //Be careful, do not use inFileName, since it is a pointer which
1660      //point to a string at master node, and slave nodes do not contain that string
1661      
1662 <    string zconsOutput(info[k].finalName);
1662 >    string zconsOutput(theInfo.finalName);
1663      
1664      zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1665      
1666      StringData* zconsFilename = new StringData();
1667 <    zconsFilename->setID("zconsfilename");
1667 >    zconsFilename->setID(ZCONSFILENAME_ID);
1668      zconsFilename->setData(zconsOutput);
1669      
1670 <    info[k].addProperty(zconsFilename);      
1649 <  }
1670 >    theInfo.addProperty(zconsFilename);      
1671   }

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