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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC vs.
Revision 1723 by gezelter, Thu May 24 20:59:54 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      //allocate memory for DataStorage(circular reference, need to
430      //break it)
431 <    info->setSnapshotManager(new SimSnapshotManager(info));
431 >    info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
432      
433      //set the global index of atoms, rigidbodies and cutoffgroups
434      //(only need to be set once, the global index will never change
# Line 609 | Line 649 | namespace OpenMD {
649   #endif
650          
651          stampId = info->getMoleculeStampId(i);
652 <        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
653 <                                                   stampId, i, info->getLocalIndexManager());
652 >        Molecule * mol = molCreator.createMolecule(info->getForceField(),
653 >                                                   info->getMoleculeStamp(stampId),
654 >                                                   stampId, i,
655 >                                                   info->getLocalIndexManager());
656          
657          info->addMolecule(mol);
658          
# Line 623 | Line 665 | namespace OpenMD {
665      } //end for(int i=0)  
666    }
667      
668 +  int SimCreator::computeStorageLayout(SimInfo* info) {
669 +
670 +    Globals* simParams = info->getSimParams();
671 +    int nRigidBodies = info->getNGlobalRigidBodies();
672 +    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
673 +    set<AtomType*>::iterator i;
674 +    bool hasDirectionalAtoms = false;
675 +    bool hasFixedCharge = false;
676 +    bool hasMultipoles = false;    
677 +    bool hasPolarizable = false;    
678 +    bool hasFluctuatingCharge = false;    
679 +    bool hasMetallic = false;
680 +    int storageLayout = 0;
681 +    storageLayout |= DataStorage::dslPosition;
682 +    storageLayout |= DataStorage::dslVelocity;
683 +    storageLayout |= DataStorage::dslForce;
684 +
685 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
686 +
687 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
688 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
689 +      EAMAdapter ea = EAMAdapter( (*i) );
690 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
691 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
692 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
693 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
694 +
695 +      if (da.isDirectional()){
696 +        hasDirectionalAtoms = true;
697 +      }
698 +      if (ma.isMultipole()){
699 +        hasMultipoles = true;
700 +      }
701 +      if (ea.isEAM() || sca.isSuttonChen()){
702 +        hasMetallic = true;
703 +      }
704 +      if ( fca.isFixedCharge() ){
705 +        hasFixedCharge = true;
706 +      }
707 +      if ( fqa.isFluctuatingCharge() ){
708 +        hasFluctuatingCharge = true;
709 +      }
710 +      if ( pa.isPolarizable() ){
711 +        hasPolarizable = true;
712 +      }
713 +    }
714 +    
715 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
716 +      storageLayout |= DataStorage::dslAmat;
717 +      if(storageLayout & DataStorage::dslVelocity) {
718 +        storageLayout |= DataStorage::dslAngularMomentum;
719 +      }
720 +      if (storageLayout & DataStorage::dslForce) {
721 +        storageLayout |= DataStorage::dslTorque;
722 +      }
723 +    }
724 +    if (hasMultipoles) {
725 +      storageLayout |= DataStorage::dslElectroFrame;
726 +    }
727 +    if (hasFixedCharge || hasFluctuatingCharge) {
728 +      storageLayout |= DataStorage::dslSkippedCharge;
729 +    }
730 +    if (hasMetallic) {
731 +      storageLayout |= DataStorage::dslDensity;
732 +      storageLayout |= DataStorage::dslFunctional;
733 +      storageLayout |= DataStorage::dslFunctionalDerivative;
734 +    }
735 +    if (hasPolarizable) {
736 +      storageLayout |= DataStorage::dslElectricField;
737 +    }
738 +    if (hasFluctuatingCharge){
739 +      storageLayout |= DataStorage::dslFlucQPosition;
740 +      if(storageLayout & DataStorage::dslVelocity) {
741 +        storageLayout |= DataStorage::dslFlucQVelocity;
742 +      }
743 +      if (storageLayout & DataStorage::dslForce) {
744 +        storageLayout |= DataStorage::dslFlucQForce;
745 +      }
746 +    }
747 +    
748 +    // if the user has asked for them, make sure we've got the memory for the
749 +    // objects defined.
750 +
751 +    if (simParams->getOutputParticlePotential()) {
752 +      storageLayout |= DataStorage::dslParticlePot;
753 +    }
754 +
755 +    if (simParams->havePrintHeatFlux()) {
756 +      if (simParams->getPrintHeatFlux()) {
757 +        storageLayout |= DataStorage::dslParticlePot;
758 +      }
759 +    }
760 +
761 +    if (simParams->getOutputElectricField()) {
762 +      storageLayout |= DataStorage::dslElectricField;
763 +    }
764 +    if (simParams->getOutputFluctuatingCharges()) {
765 +      storageLayout |= DataStorage::dslFlucQPosition;
766 +      storageLayout |= DataStorage::dslFlucQVelocity;
767 +      storageLayout |= DataStorage::dslFlucQForce;
768 +    }
769 +
770 +    return storageLayout;
771 +  }
772 +
773    void SimCreator::setGlobalIndex(SimInfo *info) {
774      SimInfo::MoleculeIterator mi;
775      Molecule::AtomIterator ai;
# Line 637 | Line 784 | namespace OpenMD {
784      int beginRigidBodyIndex;
785      int beginCutoffGroupIndex;
786      int nGlobalAtoms = info->getNGlobalAtoms();
640 –
641 –    /**@todo fixme */
642 – #ifndef IS_MPI
787      
788      beginAtomIndex = 0;
789      beginRigidBodyIndex = 0;
790      beginCutoffGroupIndex = 0;
791 <    
792 < #else
649 <    
650 <    int nproc;
651 <    int myNode;
652 <    
653 <    myNode = worldRank;
654 <    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
655 <    
656 <    std::vector < int > tmpAtomsInProc(nproc, 0);
657 <    std::vector < int > tmpRigidBodiesInProc(nproc, 0);
658 <    std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
659 <    std::vector < int > NumAtomsInProc(nproc, 0);
660 <    std::vector < int > NumRigidBodiesInProc(nproc, 0);
661 <    std::vector < int > NumCutoffGroupsInProc(nproc, 0);
662 <    
663 <    tmpAtomsInProc[myNode] = info->getNAtoms();
664 <    tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
665 <    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
666 <    
667 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
668 <    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
669 <                  MPI_SUM, MPI_COMM_WORLD);
670 <    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
671 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
672 <    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
673 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
674 <    
675 <    beginAtomIndex = 0;
676 <    beginRigidBodyIndex = 0;
677 <    beginCutoffGroupIndex = 0;
678 <    
679 <    for(int i = 0; i < myNode; i++) {
680 <      beginAtomIndex += NumAtomsInProc[i];
681 <      beginRigidBodyIndex += NumRigidBodiesInProc[i];
682 <      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
683 <    }
684 <    
685 < #endif
686 <    
687 <    //rigidbody's index begins right after atom's
688 <    beginRigidBodyIndex += info->getNGlobalAtoms();
689 <    
690 <    for(mol = info->beginMolecule(mi); mol != NULL;
691 <        mol = info->nextMolecule(mi)) {
791 >
792 >    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
793        
794 <      //local index(index in DataStorge) of atom is important
795 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
796 <        atom->setGlobalIndex(beginAtomIndex++);
794 > #ifdef IS_MPI      
795 >      if (info->getMolToProc(i) == worldRank) {
796 > #endif        
797 >        // stuff to do if I own this molecule
798 >        mol = info->getMoleculeByGlobalIndex(i);
799 >
800 >        //local index(index in DataStorge) of atom is important
801 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
802 >          atom->setGlobalIndex(beginAtomIndex++);
803 >        }
804 >        
805 >        for(rb = mol->beginRigidBody(ri); rb != NULL;
806 >            rb = mol->nextRigidBody(ri)) {
807 >          rb->setGlobalIndex(beginRigidBodyIndex++);
808 >        }
809 >        
810 >        //local index of cutoff group is trivial, it only depends on
811 >        //the order of travesing
812 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
813 >            cg = mol->nextCutoffGroup(ci)) {
814 >          cg->setGlobalIndex(beginCutoffGroupIndex++);
815 >        }        
816 >        
817 > #ifdef IS_MPI        
818 >      }  else {
819 >
820 >        // stuff to do if I don't own this molecule
821 >        
822 >        int stampId = info->getMoleculeStampId(i);
823 >        MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
824 >
825 >        beginAtomIndex += stamp->getNAtoms();
826 >        beginRigidBodyIndex += stamp->getNRigidBodies();
827 >        beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
828        }
829 <      
830 <      for(rb = mol->beginRigidBody(ri); rb != NULL;
831 <          rb = mol->nextRigidBody(ri)) {
832 <        rb->setGlobalIndex(beginRigidBodyIndex++);
701 <      }
702 <      
703 <      //local index of cutoff group is trivial, it only depends on the order of travesing
704 <      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
705 <          cg = mol->nextCutoffGroup(ci)) {
706 <        cg->setGlobalIndex(beginCutoffGroupIndex++);
707 <      }
708 <    }
709 <    
829 > #endif          
830 >
831 >    } //end for(int i=0)  
832 >
833      //fill globalGroupMembership
834      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
835      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
# Line 718 | Line 841 | namespace OpenMD {
841          
842        }      
843      }
844 <    
844 >  
845   #ifdef IS_MPI    
846      // Since the globalGroupMembership has been zero filled and we've only
847      // poked values into the atoms we know, we can do an Allreduce
# Line 788 | Line 911 | namespace OpenMD {
911          globalIO++;
912        }
913      }
914 <    
914 >      
915      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
916      
917    }

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