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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1204 by gezelter, Thu May 27 19:26:42 2004 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC

# Line 10 | Line 10
10   #include "Integrator.hpp"
11   #include "simError.h"
12   #include "RigidBody.hpp"
13 – //#include "ConjugateMinimizer.hpp"
13   #include "OOPSEMinimizer.hpp"
14 + //#include "ConstraintElement.hpp"
15 + //#include "ConstraintPair.hpp"
16  
17   #ifdef IS_MPI
18   #include "mpiBASS.h"
# Line 170 | 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 198 | Line 199 | void SimSetup::makeMolecules(void){
199    char* molName;
200    char rbName[100];
201  
202 +  //ConstraintPair* consPair; //constraint pair
203 +  //ConstraintElement* consElement1;  //first element of constraint pair
204 +  //ConstraintElement* consElement2;  //second element of constraint pair
205 +  //int whichRigidBody;
206 +  //int consAtomIndex;  //index of constraint atom in rigid body's atom array
207 +  //vector<pair<int, int> > jointAtoms;
208    //init the forceField paramters
209  
210    the_ff->readParams();
# Line 209 | Line 216 | void SimSetup::makeMolecules(void){
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;
231  
232      for (i = 0; i < info[k].n_mol; i++){
233        stampID = info[k].molecules[i].getStampID();
# Line 274 | Line 292 | void SimSetup::makeMolecules(void){
292  
293          molInfo.myAtoms[j]->setType(currentAtom->getType());
294   #ifdef IS_MPI
277 –
295          molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279 –
296   #endif // is_mpi
297        }
298  
# Line 499 | Line 515 | void SimSetup::makeMolecules(void){
515  
516          myCutoffGroup = new CutoffGroup();
517          
518 + #ifdef IS_MPI
519 +        myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
520 + #else
521 +        myCutoffGroup->setGlobalIndex(j + groupOffset);
522 + #endif
523 +        
524          for (int cg = 0; cg < nMembers; cg++) {
525  
526            // molI is atom numbering inside this molecule
# Line 506 | Line 528 | void SimSetup::makeMolecules(void){
528  
529            // tempI is atom numbering on local processor
530            tempI = molI + atomOffset;
531 +
532 + #ifdef IS_MPI
533 +          globalID = info[k].atoms[tempI]->getGlobalIndex();
534 +          info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
535 + #else
536 +          globalID = info[k].atoms[tempI]->getIndex();
537 +          info[k].globalGroupMembership[globalID] = j + groupOffset;
538 + #endif
539            
510 –          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
540  
541 +          
542 +          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
543 +          
544            cutoffAtomSet.insert(tempI);
545          }
546 <
546 >        
547          molInfo.myCutoffGroups.push_back(myCutoffGroup);
548 <      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517 <
518 <      //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
548 >        groupOffset++;
549  
550 +      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551 +      
552 +      //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
553 +      
554        for(j = 0; j < molInfo.nAtoms; j++){
555 <
555 >        
556          if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557            myCutoffGroup = new CutoffGroup();
558            myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559 +
560 + #ifdef IS_MPI
561 +          myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562 +          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563 +          info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564 + #else
565 +          myCutoffGroup->setGlobalIndex(j + groupOffset);
566 +          globalID = info[k].atoms[atomOffset + j]->getIndex();
567 +          info[k].globalGroupMembership[globalID] = j+groupOffset;
568 + #endif
569            molInfo.myCutoffGroups.push_back(myCutoffGroup);
570 +          groupOffset++;
571          }
572            
573        }
574  
530 –              
531 –
532 –
575        // After this is all set up, scan through the atoms to
576        // see if they can be added to the integrableObjects:
577  
# Line 560 | Line 602 | void SimSetup::makeMolecules(void){
602          info[k].integrableObjects.push_back(mySD);      
603          molInfo.myIntegrableObjects.push_back(mySD);
604        }
605 <    
605 >
606 >
607 >    /*
608 >
609 >      //creat ConstraintPair.
610 >      molInfo.myConstraintPair.clear();
611        
612 +      for (j = 0; j < molInfo.nBonds; j++){
613 +
614 +        //if both atoms are in the same rigid body, just skip it
615 +        currentBond = comp_stamps[stampID]->getBond(j);
616 +        if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617 +
618 +          tempI = currentBond->getA() + atomOffset;
619 +          if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620 +            consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621 +          else
622 +             consElement1 = new ConstraintAtom(info[k].atoms[tempI]);      
623 +
624 +          tempJ =  currentBond->getB() + atomOffset;
625 +          if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626 +            consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627 +          else
628 +             consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);    
629 +
630 +          consPair = new DistanceConstraintPair(consElement1, consElement2);
631 +          molInfo.myConstraintPairs.push_back(consPair);
632 +        }
633 +      }  
634 +      
635 +      //loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636 +      for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637 +        for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638 +          
639 +          jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640 +
641 +          for(size_t m = 0; m < jointAtoms.size(); m++){          
642 +            consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643 +            consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644 +
645 +            consPair = new JointConstraintPair(consElement1, consElement2);  
646 +            molInfo.myConstraintPairs.push_back(consPair);            
647 +          }
648 +
649 +        }
650 +      }
651 +      
652 + */      
653        // send the arrays off to the forceField for init.
654        
655        the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
# Line 571 | Line 659 | void SimSetup::makeMolecules(void){
659                                   theTorsions);
660  
661        info[k].molecules[i].initialize(molInfo);
662 <
663 <
662 >      
663 >      
664        atomOffset += molInfo.nAtoms;
665        delete[] theBonds;
666        delete[] theBends;
667        delete[] theTorsions;
668 <    }    
668 >    }
669 >
670 >
671 >
672 > #ifdef IS_MPI    
673 >    // Since the globalGroupMembership has been zero filled and we've only
674 >    // poked values into the atoms we know, we can do an Allreduce
675 >    // to get the full globalGroupMembership array (We think).
676 >    // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677 >    // docs said we could.
678 >
679 >    int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];    
680 >
681 >    MPI_Allreduce(info[k].globalGroupMembership,
682 >                  ggMjunk,
683 >                  mpiSim->getNAtomsGlobal(),
684 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685 >
686 >    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687 >      info[k].globalGroupMembership[i] = ggMjunk[i];
688 >
689 >    delete[] ggMjunk;
690 >    
691 > #endif
692 >
693 >
694 >
695    }
696  
697   #ifdef IS_MPI
# Line 950 | Line 1064 | void SimSetup::gatherInfo(void){
1064      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065  
1066      // check for thermodynamic integration
1067 <    if (globals->getUseThermInt()) {
1067 >    if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069 <        info[i].useThermInt = globals->getUseThermInt();
1069 >        info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070          info[i].thermIntLambda = globals->getThermIntLambda();
1071          info[i].thermIntK = globals->getThermIntK();
1072          
# Line 962 | Line 1076 | void SimSetup::gatherInfo(void){
1076        else {
1077          sprintf(painCave.errMsg,
1078                  "SimSetup Error:\n"
1079 <                "\tKeyword useThermInt was set to 'true' but\n"
1079 >                "\tKeyword useSolidThermInt was set to 'true' but\n"
1080                  "\tthermodynamicIntegrationLambda (and/or\n"
1081                  "\tthermodynamicIntegrationK) was not specified.\n"
1082                  "\tPlease provide a lambda value and k value in your .bass file.\n");
# Line 970 | Line 1084 | void SimSetup::gatherInfo(void){
1084          simError();    
1085        }
1086      }
1087 +    else if(globals->getUseLiquidThermInt()) {
1088 +      if (globals->getUseSolidThermInt()) {
1089 +        sprintf( painCave.errMsg,
1090 +                 "SimSetup Warning: It appears that you have both solid and\n"
1091 +                 "\tliquid thermodynamic integration activated in your .bass\n"
1092 +                 "\tfile. To avoid confusion, specify only one technique in\n"
1093 +                 "\tyour .bass file. Liquid-state thermodynamic integration\n"
1094 +                 "\twill be assumed for the current simulation. If this is not\n"
1095 +                 "\twhat you desire, set useSolidThermInt to 'true' and\n"
1096 +                 "\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097 +        painCave.isFatal = 0;
1098 +        simError();
1099 +      }
1100 +      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101 +        info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102 +        info[i].thermIntLambda = globals->getThermIntLambda();
1103 +        info[i].thermIntK = globals->getThermIntK();
1104 +      }
1105 +      else {
1106 +        sprintf(painCave.errMsg,
1107 +                "SimSetup Error:\n"
1108 +                "\tKeyword useLiquidThermInt was set to 'true' but\n"
1109 +                "\tthermodynamicIntegrationLambda (and/or\n"
1110 +                "\tthermodynamicIntegrationK) was not specified.\n"
1111 +                "\tPlease provide a lambda value and k value in your .bass file.\n");
1112 +        painCave.isFatal = 1;
1113 +        simError();    
1114 +      }
1115 +    }
1116      else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1117          sprintf(painCave.errMsg,
1118                  "SimSetup Warning: If you want to use Thermodynamic\n"
1119 <                "\tIntegration, set useThermInt to 'true' in your .bass file.\n"
1120 <                "\tThe useThermInt keyword is 'false' by default, so your\n"
1121 <                "\tlambda and/or k values are being ignored.\n");
1119 >                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120 >                "\t'true' in your .bass file.  These keywords are set to\n"
1121 >                "\t'false' by default, so your lambda and/or k values are\n"
1122 >                "\tbeing ignored.\n");
1123          painCave.isFatal = 0;
1124          simError();  
1125      }
# Line 1509 | Line 1653 | void SimSetup::mpiMolDivide(void){
1653  
1654    mpiSim->divideLabor();
1655    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656 +  globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657    //globalMolIndex = mpiSim->getGlobalMolIndex();
1658  
1659    // set up the local variables

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