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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 682 by tim, Tue Aug 12 17:51:33 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 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 >      double* tempDouble = new double[1000000];
907 >      fileInit = new InitializeFromFile( inName );
908   #ifdef IS_MPI
909      }else fileInit = new InitializeFromFile( NULL );
910   #endif
# Line 1033 | Line 1037 | void SimSetup::sysObjectsCreation( void ){
1037    int i,k;
1038    
1039    // create the forceField
1040 <  
1040 >
1041    createFF();
1042  
1043    // extract componentList
# Line 1051 | Line 1055 | void SimSetup::sysObjectsCreation( void ){
1055   #endif //is_mpi
1056    
1057    // create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058 <  
1058 >
1059    makeSysArrays();
1060  
1061    // make and initialize the molecules (all but atomic coordinates)
1062 <  
1062 >
1063    makeMolecules();
1064    
1065    for(k=0; k<nInfo; k++){
# Line 1608 | Line 1612 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1612                 " , you must set sample time.\n");
1613        painCave.isFatal = 1;
1614        simError();      
1611 –    }
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);
1615      }
1616  
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 –
1617      //push zconsTol into siminfo, if user does not specify
1618      //value for zconsTol, a default value will be used
1619      DoubleData* zconsTol = new DoubleData();
# Line 1641 | Line 1622 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1622        zconsTol->setData(globals->getZconsTol());
1623      }
1624           else{
1625 <                double defaultZConsTol = 1E-6;
1625 >                double defaultZConsTol = 0.01;
1626        sprintf( painCave.errMsg,
1627                 "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628                 " , default value %f is used.\n", defaultZConsTol);
# Line 1651 | Line 1632 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1632        zconsTol->setData(defaultZConsTol);
1633           }
1634      theInfo.addProperty(zconsTol);
1635 +
1636 +    //set Force Substraction Policy
1637 +    StringData* zconsForcePolicy =  new StringData();
1638 +    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639 +                
1640 +         if(globals->haveZconsForcePolicy()){
1641 +      zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642 +         }      
1643 +         else{
1644 +       sprintf( painCave.errMsg,
1645 +               "ZConstraint Warning: User does not set force substraction policy, "
1646 +               "average force substraction policy is used\n");
1647 +       painCave.isFatal = 0;
1648 +       simError();
1649 +                 zconsForcePolicy->setData("BYNUMBER");
1650 +         }
1651          
1652 +         theInfo.addProperty(zconsForcePolicy);
1653 +        
1654      //Determine the name of ouput file and add it into SimInfo's property list
1655      //Be careful, do not use inFileName, since it is a pointer which
1656      //point to a string at master node, and slave nodes do not contain that string
# Line 1664 | Line 1663 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1663      zconsFilename->setID(ZCONSFILENAME_ID);
1664      zconsFilename->setData(zconsOutput);
1665      
1666 <    theInfo.addProperty(zconsFilename);      
1666 >    theInfo.addProperty(zconsFilename);
1667 >                
1668 >    //setup index, pos and other parameters of z-constraint molecules
1669 >    nZConstraints = globals->getNzConstraints();
1670 >    theInfo.nZconstraints = nZConstraints;
1671 >        
1672 >    zconStamp = globals->getZconStamp();
1673 >    ZConsParaItem tempParaItem;
1674 >
1675 >    ZConsParaData* zconsParaData = new ZConsParaData();
1676 >    zconsParaData->setID(ZCONSPARADATA_ID);
1677 >  
1678 >    for(int i = 0; i < nZConstraints; i++){
1679 >    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680 >    tempParaItem.zPos = zconStamp[i]->getZpos();
1681 >    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682 >    tempParaItem.kRatio = zconStamp[i]->getKratio();
1683 >
1684 >    zconsParaData->addItem(tempParaItem);
1685 >    }
1686 >
1687 >    //sort the parameters by index of molecules
1688 >    zconsParaData->sortByIndex();
1689 >        
1690 >    //push data into siminfo, therefore, we can retrieve later
1691 >    theInfo.addProperty(zconsParaData);
1692 >      
1693   }

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