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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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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 1234 by tim, Fri Jun 4 03:15:31 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 + #include "ConstraintManager.hpp"
17  
18   #ifdef IS_MPI
19   #include "mpiBASS.h"
# Line 156 | Line 158 | void SimSetup::createSim(void){
158  
159    initFortran();
160  
161 +  //creat constraint manager
162 +  for(int i = 0; i < nInfo; i++)
163 +    info[i].consMan = new ConstraintManager(&info[i]);
164 +
165    if (globals->haveMinimizer())
166      // make minimizer
167      makeMinimizer();
# Line 170 | Line 176 | void SimSetup::makeMolecules(void){
176    int i, j, k;
177    int exI, exJ, exK, exL, slI, slJ;
178    int tempI, tempJ, tempK, tempL;
179 <  int molI;
180 <  int stampID, atomOffset, rbOffset;
179 >  int molI, globalID;
180 >  int stampID, atomOffset, rbOffset, groupOffset;
181    molInit molInfo;
182    DirectionalAtom* dAtom;
183    RigidBody* myRB;
# Line 198 | Line 204 | void SimSetup::makeMolecules(void){
204    char* molName;
205    char rbName[100];
206  
207 +  ConstraintPair* consPair; //constraint pair
208 +  ConstraintElement* consElement1;  //first element of constraint pair
209 +  ConstraintElement* consElement2;  //second element of constraint pair
210 +  int whichRigidBody;
211 +  int consAtomIndex;  //index of constraint atom in rigid body's atom array
212 +  vector<pair<int, int> > jointAtoms;
213 +  double bondLength2;
214    //init the forceField paramters
215  
216    the_ff->readParams();
# Line 208 | Line 221 | void SimSetup::makeMolecules(void){
221  
222    for (k = 0; k < nInfo; k++){
223      the_ff->setSimInfo(&(info[k]));
224 +
225 + #ifdef IS_MPI
226 +    info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227 +    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228 +      info[k].globalGroupMembership[i] = 0;
229 + #else
230 +    info[k].globalGroupMembership = new int[info[k].n_atoms];
231 +    for (i = 0; i < info[k].n_atoms; i++)
232 +      info[k].globalGroupMembership[i] = 0;
233 + #endif
234  
235      atomOffset = 0;
236 +    groupOffset = 0;
237  
238      for (i = 0; i < info[k].n_mol; i++){
239        stampID = info[k].molecules[i].getStampID();
# Line 274 | Line 298 | void SimSetup::makeMolecules(void){
298  
299          molInfo.myAtoms[j]->setType(currentAtom->getType());
300   #ifdef IS_MPI
277 –
301          molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279 –
302   #endif // is_mpi
303        }
304  
# Line 499 | Line 521 | void SimSetup::makeMolecules(void){
521  
522          myCutoffGroup = new CutoffGroup();
523          
524 + #ifdef IS_MPI
525 +        myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526 + #else
527 +        myCutoffGroup->setGlobalIndex(groupOffset);
528 + #endif
529 +        
530          for (int cg = 0; cg < nMembers; cg++) {
531  
532            // molI is atom numbering inside this molecule
# Line 506 | Line 534 | void SimSetup::makeMolecules(void){
534  
535            // tempI is atom numbering on local processor
536            tempI = molI + atomOffset;
509 –          
510 –          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
537  
538 + #ifdef IS_MPI
539 +          globalID = info[k].atoms[tempI]->getGlobalIndex();
540 +          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541 + #else
542 +          globalID = info[k].atoms[tempI]->getIndex();
543 +          info[k].globalGroupMembership[globalID] = groupOffset;
544 + #endif                    
545 +          myCutoffGroup->addAtom(info[k].atoms[tempI]);
546            cutoffAtomSet.insert(tempI);
547          }
548 <
548 >        
549          molInfo.myCutoffGroups.push_back(myCutoffGroup);
550 <      }//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
550 >        groupOffset++;
551  
552 +      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553 +      
554 +      
555 +      // create a cutoff group for every atom in current molecule which
556 +      // does not belong to cutoffgroup defined at mdl file
557 +      
558        for(j = 0; j < molInfo.nAtoms; j++){
559 <
559 >        
560          if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561            myCutoffGroup = new CutoffGroup();
562            myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525 –          molInfo.myCutoffGroups.push_back(myCutoffGroup);
526 –        }
563            
564 + #ifdef IS_MPI
565 +          myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566 +          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567 +          info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568 + #else
569 +          myCutoffGroup->setGlobalIndex(groupOffset);
570 +          globalID = info[k].atoms[atomOffset + j]->getIndex();
571 +          info[k].globalGroupMembership[globalID] = groupOffset;
572 + #endif
573 +          molInfo.myCutoffGroups.push_back(myCutoffGroup);
574 +          groupOffset++;
575 +        }          
576        }
577  
530 –              
531 –
532 –
578        // After this is all set up, scan through the atoms to
579        // see if they can be added to the integrableObjects:
580  
# Line 560 | Line 605 | void SimSetup::makeMolecules(void){
605          info[k].integrableObjects.push_back(mySD);      
606          molInfo.myIntegrableObjects.push_back(mySD);
607        }
608 <    
564 <      
608 >        
609        // send the arrays off to the forceField for init.
610        
611        the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
# Line 570 | Line 614 | void SimSetup::makeMolecules(void){
614        the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615                                   theTorsions);
616  
573 –      info[k].molecules[i].initialize(molInfo);
617  
618 +      //creat ConstraintPair.
619 +      molInfo.myConstraintPairs.clear();
620 +      
621 +      for (j = 0; j < molInfo.nBonds; j++){
622  
623 +        //if bond is constrained bond, add it into constraint pair
624 +        if(molInfo.myBonds[j]->is_constrained()){
625 +
626 +          //if both atoms are in the same rigid body, just skip it
627 +          currentBond = comp_stamps[stampID]->getBond(j);
628 +          
629 +          if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630 +
631 +            tempI = currentBond->getA() + atomOffset;
632 +            if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633 +              consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634 +            else
635 +               consElement1 = new ConstraintAtom(info[k].atoms[tempI]);      
636 +
637 +            tempJ =  currentBond->getB() + atomOffset;
638 +            if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639 +              consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640 +            else
641 +               consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);    
642 +
643 +            bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();            
644 +            consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645 +
646 +            molInfo.myConstraintPairs.push_back(consPair);
647 +          }
648 +        }//end if(molInfo.myBonds[j]->is_constrained())
649 +      }  
650 +      
651 +      //loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652 +      for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653 +        for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654 +          
655 +          jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656 +
657 +          for(size_t m = 0; m < jointAtoms.size(); m++){          
658 +            consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659 +            consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660 +
661 +            consPair = new JointConstraintPair(consElement1, consElement2);  
662 +            molInfo.myConstraintPairs.push_back(consPair);            
663 +          }
664 +
665 +        }
666 +      }
667 +      
668 +
669 +      info[k].molecules[i].initialize(molInfo);
670 +      
671 +      
672        atomOffset += molInfo.nAtoms;
673        delete[] theBonds;
674        delete[] theBends;
675        delete[] theTorsions;
676 <    }    
676 >    }
677 >
678 >
679 >
680 > #ifdef IS_MPI    
681 >    // Since the globalGroupMembership has been zero filled and we've only
682 >    // poked values into the atoms we know, we can do an Allreduce
683 >    // to get the full globalGroupMembership array (We think).
684 >    // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685 >    // docs said we could.
686 >
687 >    int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];    
688 >
689 >    MPI_Allreduce(info[k].globalGroupMembership,
690 >                  ggMjunk,
691 >                  mpiSim->getNAtomsGlobal(),
692 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693 >
694 >    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695 >      info[k].globalGroupMembership[i] = ggMjunk[i];
696 >
697 >    delete[] ggMjunk;
698 >    
699 > #endif
700 >
701 >
702 >
703    }
704  
705   #ifdef IS_MPI
# Line 950 | Line 1072 | void SimSetup::gatherInfo(void){
1072      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1073  
1074      // check for thermodynamic integration
1075 <    if (globals->getUseThermInt()) {
1075 >    if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1076        if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1077 <        info[i].useThermInt = globals->getUseThermInt();
1077 >        info[i].useSolidThermInt = globals->getUseSolidThermInt();
1078          info[i].thermIntLambda = globals->getThermIntLambda();
1079          info[i].thermIntK = globals->getThermIntK();
1080          
# Line 962 | Line 1084 | void SimSetup::gatherInfo(void){
1084        else {
1085          sprintf(painCave.errMsg,
1086                  "SimSetup Error:\n"
1087 <                "\tKeyword useThermInt was set to 'true' but\n"
1087 >                "\tKeyword useSolidThermInt was set to 'true' but\n"
1088                  "\tthermodynamicIntegrationLambda (and/or\n"
1089                  "\tthermodynamicIntegrationK) was not specified.\n"
1090                  "\tPlease provide a lambda value and k value in your .bass file.\n");
# Line 970 | Line 1092 | void SimSetup::gatherInfo(void){
1092          simError();    
1093        }
1094      }
1095 +    else if(globals->getUseLiquidThermInt()) {
1096 +      if (globals->getUseSolidThermInt()) {
1097 +        sprintf( painCave.errMsg,
1098 +                 "SimSetup Warning: It appears that you have both solid and\n"
1099 +                 "\tliquid thermodynamic integration activated in your .bass\n"
1100 +                 "\tfile. To avoid confusion, specify only one technique in\n"
1101 +                 "\tyour .bass file. Liquid-state thermodynamic integration\n"
1102 +                 "\twill be assumed for the current simulation. If this is not\n"
1103 +                 "\twhat you desire, set useSolidThermInt to 'true' and\n"
1104 +                 "\tuseLiquidThermInt to 'false' in your .bass file.\n");
1105 +        painCave.isFatal = 0;
1106 +        simError();
1107 +      }
1108 +      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1109 +        info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1110 +        info[i].thermIntLambda = globals->getThermIntLambda();
1111 +        info[i].thermIntK = globals->getThermIntK();
1112 +      }
1113 +      else {
1114 +        sprintf(painCave.errMsg,
1115 +                "SimSetup Error:\n"
1116 +                "\tKeyword useLiquidThermInt was set to 'true' but\n"
1117 +                "\tthermodynamicIntegrationLambda (and/or\n"
1118 +                "\tthermodynamicIntegrationK) was not specified.\n"
1119 +                "\tPlease provide a lambda value and k value in your .bass file.\n");
1120 +        painCave.isFatal = 1;
1121 +        simError();    
1122 +      }
1123 +    }
1124      else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1125          sprintf(painCave.errMsg,
1126                  "SimSetup Warning: If you want to use Thermodynamic\n"
1127 <                "\tIntegration, set useThermInt to 'true' in your .bass file.\n"
1128 <                "\tThe useThermInt keyword is 'false' by default, so your\n"
1129 <                "\tlambda and/or k values are being ignored.\n");
1127 >                "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1128 >                "\t'true' in your .bass file.  These keywords are set to\n"
1129 >                "\t'false' by default, so your lambda and/or k values are\n"
1130 >                "\tbeing ignored.\n");
1131          painCave.isFatal = 0;
1132          simError();  
1133      }
# Line 1509 | Line 1661 | void SimSetup::mpiMolDivide(void){
1661  
1662    mpiSim->divideLabor();
1663    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1664 +  globalGroupIndex = mpiSim->getGlobalGroupIndex();
1665    //globalMolIndex = mpiSim->getGlobalMolIndex();
1666  
1667    // set up the local variables

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