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Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 75 | Line 76
76   #include "antlr/NoViableAltForCharException.hpp"
77   #include "antlr/NoViableAltException.hpp"
78  
79 + #include "types/DirectionalAdapter.hpp"
80 + #include "types/MultipoleAdapter.hpp"
81 + #include "types/EAMAdapter.hpp"
82 + #include "types/SuttonChenAdapter.hpp"
83 + #include "types/PolarizableAdapter.hpp"
84 + #include "types/FixedChargeAdapter.hpp"
85 + #include "types/FluctuatingChargeAdapter.hpp"
86 +
87   #ifdef IS_MPI
88 + #include "mpi.h"
89   #include "math/ParallelRandNumGen.hpp"
90   #endif
91  
92   namespace OpenMD {
93    
94 <  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
94 >  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95      Globals* simParams = NULL;
96      try {
97  
# Line 92 | Line 102 | namespace OpenMD {
102        const int masterNode = 0;
103        int commStatus;
104        if (worldRank == masterNode) {
105 < #endif
106 <                
105 >        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106 > #endif                
107          SimplePreprocessor preprocessor;
108          preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109                  
# Line 106 | Line 116 | namespace OpenMD {
116              
117                  
118        } else {
119 +
120 +        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121 +
122          //get stream size
123          commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
124  
# Line 229 | Line 242 | namespace OpenMD {
242        simError();
243      }
244  
245 +    simParams->setMDfileVersion(mdFileVersion);
246      return simParams;
247    }
248    
# Line 243 | Line 257 | namespace OpenMD {
257      int metaDataBlockEnd = -1;
258      int i;
259      int mdOffset;
260 +    int mdFileVersion;
261  
262   #ifdef IS_MPI            
263      const int masterNode = 0;
# Line 276 | Line 291 | namespace OpenMD {
291          painCave.isFatal = 1;
292          simError();
293        }
294 +      
295 +      // found the correct opening string, now try to get the file
296 +      // format version number.
297  
298 +      StringTokenizer tokenizer(line, "=<> \t\n\r");
299 +      std::string fileType = tokenizer.nextToken();
300 +      toUpper(fileType);
301 +
302 +      mdFileVersion = 0;
303 +
304 +      if (fileType == "OPENMD") {
305 +        while (tokenizer.hasMoreTokens()) {
306 +          std::string token(tokenizer.nextToken());
307 +          toUpper(token);
308 +          if (token == "VERSION") {
309 +            mdFileVersion = tokenizer.nextTokenAsInt();
310 +            break;
311 +          }
312 +        }
313 +      }
314 +            
315        //scan through the input stream and find MetaData tag        
316        while(mdFile_.getline(buffer, bufferSize)) {
317          ++lineNo;
# Line 332 | Line 367 | namespace OpenMD {
367      std::stringstream rawMetaDataStream(mdRawData);
368  
369      //parse meta-data file
370 <    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
370 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
371 >                                   metaDataBlockStart + 1);
372      
373      //create the force field
374      ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
# Line 386 | Line 422 | namespace OpenMD {
422      //create the molecules
423      createMolecules(info);
424      
425 +    //find the storage layout
426 +
427 +    int storageLayout = computeStorageLayout(info);
428 +
429 +    cerr << "computed Storage Layout = " << storageLayout << "\n";
430 +
431      //allocate memory for DataStorage(circular reference, need to
432      //break it)
433 <    info->setSnapshotManager(new SimSnapshotManager(info));
433 >    info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434      
435      //set the global index of atoms, rigidbodies and cutoffgroups
436      //(only need to be set once, the global index will never change
# Line 589 | Line 631 | namespace OpenMD {
631        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
632      }
633      
592 –    cerr << "molToProcMap:\n";
593 –    for (int i = 0; i < molToProcMap.size(); i++) {
594 –      cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n";
595 –    }
596 –
634      info->setMolToProcMap(molToProcMap);
635      sprintf(checkPointMsg,
636              "Successfully divided the molecules among the processors.\n");
# Line 614 | Line 651 | namespace OpenMD {
651   #endif
652          
653          stampId = info->getMoleculeStampId(i);
654 <        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
655 <                                                   stampId, i, info->getLocalIndexManager());
654 >        Molecule * mol = molCreator.createMolecule(info->getForceField(),
655 >                                                   info->getMoleculeStamp(stampId),
656 >                                                   stampId, i,
657 >                                                   info->getLocalIndexManager());
658          
659          info->addMolecule(mol);
660          
# Line 628 | Line 667 | namespace OpenMD {
667      } //end for(int i=0)  
668    }
669      
670 +  int SimCreator::computeStorageLayout(SimInfo* info) {
671 +
672 +    int nRigidBodies = info->getNGlobalRigidBodies();
673 +    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
674 +    set<AtomType*>::iterator i;
675 +    bool hasDirectionalAtoms = false;
676 +    bool hasFixedCharge = false;
677 +    bool hasMultipoles = false;    
678 +    bool hasPolarizable = false;    
679 +    bool hasFluctuatingCharge = false;    
680 +    bool hasMetallic = false;
681 +    int storageLayout = 0;
682 +    storageLayout |= DataStorage::dslPosition;
683 +    storageLayout |= DataStorage::dslVelocity;
684 +    storageLayout |= DataStorage::dslForce;
685 +
686 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
687 +
688 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
689 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
690 +      EAMAdapter ea = EAMAdapter( (*i) );
691 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
692 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
693 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
694 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
695 +
696 +      if (da.isDirectional()){
697 +        hasDirectionalAtoms = true;
698 +      }
699 +      if (ma.isMultipole()){
700 +        hasMultipoles = true;
701 +      }
702 +      if (ea.isEAM() || sca.isSuttonChen()){
703 +        hasMetallic = true;
704 +      }
705 +      if ( fca.isFixedCharge() ){
706 +        hasFixedCharge = true;
707 +      }
708 +      if ( fqa.isFluctuatingCharge() ){
709 +        hasFluctuatingCharge = true;
710 +      }
711 +      if ( pa.isPolarizable() ){
712 +        hasPolarizable = true;
713 +      }
714 +    }
715 +    
716 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
717 +      storageLayout |= DataStorage::dslAmat;
718 +      if(storageLayout & DataStorage::dslVelocity) {
719 +        storageLayout |= DataStorage::dslAngularMomentum;
720 +      }
721 +      if (storageLayout & DataStorage::dslForce) {
722 +        storageLayout |= DataStorage::dslTorque;
723 +      }
724 +    }
725 +    if (hasMultipoles) {
726 +      storageLayout |= DataStorage::dslElectroFrame;
727 +    }
728 +    if (hasFixedCharge || hasFluctuatingCharge) {
729 +      storageLayout |= DataStorage::dslSkippedCharge;
730 +    }
731 +    if (hasMetallic) {
732 +      storageLayout |= DataStorage::dslDensity;
733 +      storageLayout |= DataStorage::dslFunctional;
734 +      storageLayout |= DataStorage::dslFunctionalDerivative;
735 +    }
736 +    if (hasPolarizable) {
737 +      storageLayout |= DataStorage::dslElectricField;
738 +    }
739 +    if (hasFluctuatingCharge){
740 +      storageLayout |= DataStorage::dslFlucQPosition;
741 +      if(storageLayout & DataStorage::dslVelocity) {
742 +        storageLayout |= DataStorage::dslFlucQVelocity;
743 +      }
744 +      if (storageLayout & DataStorage::dslForce) {
745 +        storageLayout |= DataStorage::dslFlucQForce;
746 +      }
747 +    }
748 +    return storageLayout;
749 +  }
750 +
751    void SimCreator::setGlobalIndex(SimInfo *info) {
752      SimInfo::MoleculeIterator mi;
753      Molecule::AtomIterator ai;
# Line 642 | Line 762 | namespace OpenMD {
762      int beginRigidBodyIndex;
763      int beginCutoffGroupIndex;
764      int nGlobalAtoms = info->getNGlobalAtoms();
645 –
646 –    /**@todo fixme */
647 – #ifndef IS_MPI
765      
766      beginAtomIndex = 0;
767      beginRigidBodyIndex = 0;
768      beginCutoffGroupIndex = 0;
769 <    
770 < #else
654 <    
655 <    int nproc;
656 <    int myNode;
657 <    
658 <    myNode = worldRank;
659 <    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
660 <    
661 <    std::vector < int > tmpAtomsInProc(nproc, 0);
662 <    std::vector < int > tmpRigidBodiesInProc(nproc, 0);
663 <    std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
664 <    std::vector < int > NumAtomsInProc(nproc, 0);
665 <    std::vector < int > NumRigidBodiesInProc(nproc, 0);
666 <    std::vector < int > NumCutoffGroupsInProc(nproc, 0);
667 <    
668 <    tmpAtomsInProc[myNode] = info->getNAtoms();
669 <    tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
670 <    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
671 <    
672 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
673 <    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
674 <                  MPI_SUM, MPI_COMM_WORLD);
675 <    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
676 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
677 <    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
678 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
679 <    
680 <    beginAtomIndex = 0;
681 <    beginRigidBodyIndex = 0;
682 <    beginCutoffGroupIndex = 0;
683 <    
684 <    for(int i = 0; i < myNode; i++) {
685 <      beginAtomIndex += NumAtomsInProc[i];
686 <      beginRigidBodyIndex += NumRigidBodiesInProc[i];
687 <      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
688 <    }
689 <    
690 < #endif
691 <    
692 <    //rigidbody's index begins right after atom's
693 <    beginRigidBodyIndex += info->getNGlobalAtoms();
694 <    
695 <    for(mol = info->beginMolecule(mi); mol != NULL;
696 <        mol = info->nextMolecule(mi)) {
769 >
770 >    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
771        
772 <      //local index(index in DataStorge) of atom is important
773 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
774 <        atom->setGlobalIndex(beginAtomIndex++);
772 > #ifdef IS_MPI      
773 >      if (info->getMolToProc(i) == worldRank) {
774 > #endif        
775 >        // stuff to do if I own this molecule
776 >        mol = info->getMoleculeByGlobalIndex(i);
777 >
778 >        //local index(index in DataStorge) of atom is important
779 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
780 >          atom->setGlobalIndex(beginAtomIndex++);
781 >        }
782 >        
783 >        for(rb = mol->beginRigidBody(ri); rb != NULL;
784 >            rb = mol->nextRigidBody(ri)) {
785 >          rb->setGlobalIndex(beginRigidBodyIndex++);
786 >        }
787 >        
788 >        //local index of cutoff group is trivial, it only depends on
789 >        //the order of travesing
790 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
791 >            cg = mol->nextCutoffGroup(ci)) {
792 >          cg->setGlobalIndex(beginCutoffGroupIndex++);
793 >        }        
794 >        
795 > #ifdef IS_MPI        
796 >      }  else {
797 >
798 >        // stuff to do if I don't own this molecule
799 >        
800 >        int stampId = info->getMoleculeStampId(i);
801 >        MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
802 >
803 >        beginAtomIndex += stamp->getNAtoms();
804 >        beginRigidBodyIndex += stamp->getNRigidBodies();
805 >        beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
806        }
807 <      
808 <      for(rb = mol->beginRigidBody(ri); rb != NULL;
809 <          rb = mol->nextRigidBody(ri)) {
810 <        rb->setGlobalIndex(beginRigidBodyIndex++);
706 <      }
707 <      
708 <      //local index of cutoff group is trivial, it only depends on the order of travesing
709 <      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
710 <          cg = mol->nextCutoffGroup(ci)) {
711 <        cg->setGlobalIndex(beginCutoffGroupIndex++);
712 <      }
713 <    }
714 <    
807 > #endif          
808 >
809 >    } //end for(int i=0)  
810 >
811      //fill globalGroupMembership
812 <    std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), -1);
812 >    std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
813      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
814        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
815          
# Line 732 | Line 828 | namespace OpenMD {
828      // docs said we could.
829      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
830      MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
831 <                  MPI_INT, MPI_MAX, MPI_COMM_WORLD);
831 >                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
832      info->setGlobalGroupMembership(tmpGroupMembership);
737 –
738 –    cerr << "ggm:\n";
739 –    for (int i = 0; i < tmpGroupMembership.size(); i++)
740 –      cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n";
741 –
833   #else
834      info->setGlobalGroupMembership(globalGroupMembership);
835   #endif
# Line 798 | Line 889 | namespace OpenMD {
889          globalIO++;
890        }
891      }
801 –    cerr << "ioi2io:\n";
802 –    for (int i = 0; i < IOIndexToIntegrableObject.size(); i++) {
803 –      if (IOIndexToIntegrableObject[i] != NULL) {
804 –        cerr << "i = " << i << "globalIOindex = " << IOIndexToIntegrableObject[i]->getGlobalIntegrableObjectIndex() << "\n";
805 –      }
806 –    }
892        
893      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
894      

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