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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1211 by tim, Tue Jun 1 15:57:30 2004 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 2004 UTC

# Line 171 | Line 171 | void SimSetup::makeMolecules(void){
171    int i, j, k;
172    int exI, exJ, exK, exL, slI, slJ;
173    int tempI, tempJ, tempK, tempL;
174 <  int molI;
175 <  int stampID, atomOffset, rbOffset;
174 >  int molI, globalID;
175 >  int stampID, atomOffset, rbOffset, groupOffset;
176    molInit molInfo;
177    DirectionalAtom* dAtom;
178    RigidBody* myRB;
# Line 215 | Line 215 | void SimSetup::makeMolecules(void){
215  
216    for (k = 0; k < nInfo; k++){
217      the_ff->setSimInfo(&(info[k]));
218 +
219 + #ifdef IS_MPI
220 +    info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221 +    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222 +      info[k].globalGroupMembership[i] = 0;
223 + #else
224 +    info[k].globalGroupMembership = new int[info[k].n_atoms];
225 +    for (i = 0; i < info[k].n_atoms; i++)
226 +      info[k].globalGroupMembership[i] = 0;
227 + #endif
228  
229      atomOffset = 0;
230      groupOffset = 0;
# Line 282 | Line 292 | void SimSetup::makeMolecules(void){
292  
293          molInfo.myAtoms[j]->setType(currentAtom->getType());
294   #ifdef IS_MPI
285 –
295          molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287 –
296   #endif // is_mpi
297        }
298  
# Line 506 | Line 514 | void SimSetup::makeMolecules(void){
514          nMembers = currentCutoffGroup->getNMembers();
515  
516          myCutoffGroup = new CutoffGroup();
509 –        myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
517          
518 + #ifdef IS_MPI
519 +        myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520 + #else
521 +        myCutoffGroup->setGlobalIndex(groupOffset);
522 + #endif
523 +        
524          for (int cg = 0; cg < nMembers; cg++) {
525  
526            // molI is atom numbering inside this molecule
# Line 517 | Line 530 | void SimSetup::makeMolecules(void){
530            tempI = molI + atomOffset;
531  
532   #ifdef IS_MPI
533 <          globalID = info[k].atoms[tempI]->getGlobalIndex()
533 >          globalID = info[k].atoms[tempI]->getGlobalIndex();
534 >          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535   #else
536            globalID = info[k].atoms[tempI]->getIndex();
537 < #endif
538 <
539 <          globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526 <
527 <          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
528 <
537 >          info[k].globalGroupMembership[globalID] = groupOffset;
538 > #endif                    
539 >          myCutoffGroup->addAtom(info[k].atoms[tempI]);
540            cutoffAtomSet.insert(tempI);
541          }
542 <      
542 >        
543          molInfo.myCutoffGroups.push_back(myCutoffGroup);
544          groupOffset++;
545  
546        }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547 <
548 <      //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
549 <
547 >      
548 >      
549 >      // create a cutoff group for every atom in current molecule which
550 >      // does not belong to cutoffgroup defined at mdl file
551 >      
552        for(j = 0; j < molInfo.nAtoms; j++){
553 <
553 >        
554          if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555            myCutoffGroup = new CutoffGroup();
556            myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557 <          myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
557 >          
558   #ifdef IS_MPI
559 <          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
560 < #else
559 >          myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560 >          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561 >          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562 > #else
563 >          myCutoffGroup->setGlobalIndex(groupOffset);
564            globalID = info[k].atoms[atomOffset + j]->getIndex();
565 +          info[k].globalGroupMembership[globalID] = groupOffset;
566   #endif
550 –          globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
567            molInfo.myCutoffGroups.push_back(myCutoffGroup);
568            groupOffset++;
569 <        }
554 <          
569 >        }          
570        }
571  
572        // After this is all set up, scan through the atoms to
# Line 641 | Line 656 | void SimSetup::makeMolecules(void){
656                                   theTorsions);
657  
658        info[k].molecules[i].initialize(molInfo);
659 <
660 <
659 >      
660 >      
661        atomOffset += molInfo.nAtoms;
662        delete[] theBonds;
663        delete[] theBends;
664        delete[] theTorsions;
665 <    }    
665 >    }
666 >
667 >
668 >
669 > #ifdef IS_MPI    
670 >    // Since the globalGroupMembership has been zero filled and we've only
671 >    // poked values into the atoms we know, we can do an Allreduce
672 >    // to get the full globalGroupMembership array (We think).
673 >    // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674 >    // docs said we could.
675 >
676 >    int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];    
677 >
678 >    MPI_Allreduce(info[k].globalGroupMembership,
679 >                  ggMjunk,
680 >                  mpiSim->getNAtomsGlobal(),
681 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682 >
683 >    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684 >      info[k].globalGroupMembership[i] = ggMjunk[i];
685 >
686 >    delete[] ggMjunk;
687 >    
688 > #endif
689 >
690 >
691 >
692    }
693  
694   #ifdef IS_MPI
# Line 1020 | Line 1061 | void SimSetup::gatherInfo(void){
1061      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062  
1063      // check for thermodynamic integration
1064 <    if (globals->getUseThermInt()) {
1064 >    if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066 <        info[i].useThermInt = globals->getUseThermInt();
1066 >        info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067          info[i].thermIntLambda = globals->getThermIntLambda();
1068          info[i].thermIntK = globals->getThermIntK();
1069          
# Line 1032 | Line 1073 | void SimSetup::gatherInfo(void){
1073        else {
1074          sprintf(painCave.errMsg,
1075                  "SimSetup Error:\n"
1076 <                "\tKeyword useThermInt was set to 'true' but\n"
1076 >                "\tKeyword useSolidThermInt was set to 'true' but\n"
1077 >                "\tthermodynamicIntegrationLambda (and/or\n"
1078 >                "\tthermodynamicIntegrationK) was not specified.\n"
1079 >                "\tPlease provide a lambda value and k value in your .bass file.\n");
1080 >        painCave.isFatal = 1;
1081 >        simError();    
1082 >      }
1083 >    }
1084 >    else if(globals->getUseLiquidThermInt()) {
1085 >      if (globals->getUseSolidThermInt()) {
1086 >        sprintf( painCave.errMsg,
1087 >                 "SimSetup Warning: It appears that you have both solid and\n"
1088 >                 "\tliquid thermodynamic integration activated in your .bass\n"
1089 >                 "\tfile. To avoid confusion, specify only one technique in\n"
1090 >                 "\tyour .bass file. Liquid-state thermodynamic integration\n"
1091 >                 "\twill be assumed for the current simulation. If this is not\n"
1092 >                 "\twhat you desire, set useSolidThermInt to 'true' and\n"
1093 >                 "\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094 >        painCave.isFatal = 0;
1095 >        simError();
1096 >      }
1097 >      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098 >        info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099 >        info[i].thermIntLambda = globals->getThermIntLambda();
1100 >        info[i].thermIntK = globals->getThermIntK();
1101 >      }
1102 >      else {
1103 >        sprintf(painCave.errMsg,
1104 >                "SimSetup Error:\n"
1105 >                "\tKeyword useLiquidThermInt was set to 'true' but\n"
1106                  "\tthermodynamicIntegrationLambda (and/or\n"
1107                  "\tthermodynamicIntegrationK) was not specified.\n"
1108                  "\tPlease provide a lambda value and k value in your .bass file.\n");
# Line 1043 | Line 1113 | void SimSetup::gatherInfo(void){
1113      else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1114          sprintf(painCave.errMsg,
1115                  "SimSetup Warning: If you want to use Thermodynamic\n"
1116 <                "\tIntegration, set useThermInt to 'true' in your .bass file.\n"
1117 <                "\tThe useThermInt keyword is 'false' by default, so your\n"
1118 <                "\tlambda and/or k values are being ignored.\n");
1116 >                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117 >                "\t'true' in your .bass file.  These keywords are set to\n"
1118 >                "\t'false' by default, so your lambda and/or k values are\n"
1119 >                "\tbeing ignored.\n");
1120          painCave.isFatal = 0;
1121          simError();  
1122      }
# Line 1579 | Line 1650 | void SimSetup::mpiMolDivide(void){
1650  
1651    mpiSim->divideLabor();
1652    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653 +  globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654    //globalMolIndex = mpiSim->getGlobalMolIndex();
1655  
1656    // set up the local variables

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