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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1714 by gezelter, Sat May 19 18:12:46 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    
249    SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250                                    bool loadInitCoords) {
251 <
251 >    
252      const int bufferSize = 65535;
253      char buffer[bufferSize];
254      int lineNo = 0;
# 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 369 | Line 405 | namespace OpenMD {
405      }
406      
407      ff->parse(forcefieldFileName);
372 –    ff->setFortranForceOptions();
408      //create SimInfo
409      SimInfo * info = new SimInfo(ff, simParams);
410  
# Line 387 | Line 422 | namespace OpenMD {
422      //create the molecules
423      createMolecules(info);
424      
425 <    
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 413 | Line 453 | namespace OpenMD {
453      
454      if (loadInitCoords)
455        loadCoordinates(info, mdFileName);    
416 –    
456      return info;
457    }
458    
# Line 612 | 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 625 | Line 666 | namespace OpenMD {
666        
667      } //end for(int i=0)  
668    }
669 +    
670 +  int SimCreator::computeStorageLayout(SimInfo* info) {
671 +
672 +    Globals* simParams = info->getSimParams();
673 +    int nRigidBodies = info->getNGlobalRigidBodies();
674 +    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
675 +    set<AtomType*>::iterator i;
676 +    bool hasDirectionalAtoms = false;
677 +    bool hasFixedCharge = false;
678 +    bool hasMultipoles = false;    
679 +    bool hasPolarizable = false;    
680 +    bool hasFluctuatingCharge = false;    
681 +    bool hasMetallic = false;
682 +    int storageLayout = 0;
683 +    storageLayout |= DataStorage::dslPosition;
684 +    storageLayout |= DataStorage::dslVelocity;
685 +    storageLayout |= DataStorage::dslForce;
686 +
687 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
688 +
689 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
690 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
691 +      EAMAdapter ea = EAMAdapter( (*i) );
692 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
693 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
694 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
695 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
696 +
697 +      if (da.isDirectional()){
698 +        hasDirectionalAtoms = true;
699 +      }
700 +      if (ma.isMultipole()){
701 +        hasMultipoles = true;
702 +      }
703 +      if (ea.isEAM() || sca.isSuttonChen()){
704 +        hasMetallic = true;
705 +      }
706 +      if ( fca.isFixedCharge() ){
707 +        hasFixedCharge = true;
708 +      }
709 +      if ( fqa.isFluctuatingCharge() ){
710 +        hasFluctuatingCharge = true;
711 +      }
712 +      if ( pa.isPolarizable() ){
713 +        hasPolarizable = true;
714 +      }
715 +    }
716 +    
717 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
718 +      storageLayout |= DataStorage::dslAmat;
719 +      if(storageLayout & DataStorage::dslVelocity) {
720 +        storageLayout |= DataStorage::dslAngularMomentum;
721 +      }
722 +      if (storageLayout & DataStorage::dslForce) {
723 +        storageLayout |= DataStorage::dslTorque;
724 +      }
725 +    }
726 +    if (hasMultipoles) {
727 +      storageLayout |= DataStorage::dslElectroFrame;
728 +    }
729 +    if (hasFixedCharge || hasFluctuatingCharge) {
730 +      storageLayout |= DataStorage::dslSkippedCharge;
731 +    }
732 +    if (hasMetallic) {
733 +      storageLayout |= DataStorage::dslDensity;
734 +      storageLayout |= DataStorage::dslFunctional;
735 +      storageLayout |= DataStorage::dslFunctionalDerivative;
736 +    }
737 +    if (hasPolarizable) {
738 +      storageLayout |= DataStorage::dslElectricField;
739 +    }
740 +    if (hasFluctuatingCharge){
741 +      storageLayout |= DataStorage::dslFlucQPosition;
742 +      if(storageLayout & DataStorage::dslVelocity) {
743 +        storageLayout |= DataStorage::dslFlucQVelocity;
744 +      }
745 +      if (storageLayout & DataStorage::dslForce) {
746 +        storageLayout |= DataStorage::dslFlucQForce;
747 +      }
748 +    }
749      
750 +    // if the user has asked for them, make sure we've got the memory for the
751 +    // objects defined.
752 +
753 +    if (simParams->getOutputParticlePotential()) {
754 +      storageLayout |= DataStorage::dslParticlePot;
755 +    }
756 +    if (simParams->getOutputElectricField()) {
757 +      storageLayout |= DataStorage::dslElectricField;
758 +    }
759 +    if (simParams->getOutputFluctuatingCharges()) {
760 +      storageLayout |= DataStorage::dslFlucQPosition;
761 +      storageLayout |= DataStorage::dslFlucQVelocity;
762 +      storageLayout |= DataStorage::dslFlucQForce;
763 +    }
764 +
765 +    return storageLayout;
766 +  }
767 +
768    void SimCreator::setGlobalIndex(SimInfo *info) {
769      SimInfo::MoleculeIterator mi;
770      Molecule::AtomIterator ai;
# Line 640 | Line 779 | namespace OpenMD {
779      int beginRigidBodyIndex;
780      int beginCutoffGroupIndex;
781      int nGlobalAtoms = info->getNGlobalAtoms();
643 –
644 –    /**@todo fixme */
645 – #ifndef IS_MPI
782      
783      beginAtomIndex = 0;
784      beginRigidBodyIndex = 0;
785      beginCutoffGroupIndex = 0;
786 <    
787 < #else
652 <    
653 <    int nproc;
654 <    int myNode;
655 <    
656 <    myNode = worldRank;
657 <    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
658 <    
659 <    std::vector < int > tmpAtomsInProc(nproc, 0);
660 <    std::vector < int > tmpRigidBodiesInProc(nproc, 0);
661 <    std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
662 <    std::vector < int > NumAtomsInProc(nproc, 0);
663 <    std::vector < int > NumRigidBodiesInProc(nproc, 0);
664 <    std::vector < int > NumCutoffGroupsInProc(nproc, 0);
665 <    
666 <    tmpAtomsInProc[myNode] = info->getNAtoms();
667 <    tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
668 <    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
669 <    
670 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
671 <    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
672 <                  MPI_SUM, MPI_COMM_WORLD);
673 <    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
674 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
675 <    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
676 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
677 <    
678 <    beginAtomIndex = 0;
679 <    beginRigidBodyIndex = 0;
680 <    beginCutoffGroupIndex = 0;
681 <    
682 <    for(int i = 0; i < myNode; i++) {
683 <      beginAtomIndex += NumAtomsInProc[i];
684 <      beginRigidBodyIndex += NumRigidBodiesInProc[i];
685 <      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
686 <    }
687 <    
688 < #endif
689 <    
690 <    //rigidbody's index begins right after atom's
691 <    beginRigidBodyIndex += info->getNGlobalAtoms();
692 <    
693 <    for(mol = info->beginMolecule(mi); mol != NULL;
694 <        mol = info->nextMolecule(mi)) {
786 >
787 >    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
788        
789 <      //local index(index in DataStorge) of atom is important
790 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
791 <        atom->setGlobalIndex(beginAtomIndex++);
789 > #ifdef IS_MPI      
790 >      if (info->getMolToProc(i) == worldRank) {
791 > #endif        
792 >        // stuff to do if I own this molecule
793 >        mol = info->getMoleculeByGlobalIndex(i);
794 >
795 >        //local index(index in DataStorge) of atom is important
796 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
797 >          atom->setGlobalIndex(beginAtomIndex++);
798 >        }
799 >        
800 >        for(rb = mol->beginRigidBody(ri); rb != NULL;
801 >            rb = mol->nextRigidBody(ri)) {
802 >          rb->setGlobalIndex(beginRigidBodyIndex++);
803 >        }
804 >        
805 >        //local index of cutoff group is trivial, it only depends on
806 >        //the order of travesing
807 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
808 >            cg = mol->nextCutoffGroup(ci)) {
809 >          cg->setGlobalIndex(beginCutoffGroupIndex++);
810 >        }        
811 >        
812 > #ifdef IS_MPI        
813 >      }  else {
814 >
815 >        // stuff to do if I don't own this molecule
816 >        
817 >        int stampId = info->getMoleculeStampId(i);
818 >        MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
819 >
820 >        beginAtomIndex += stamp->getNAtoms();
821 >        beginRigidBodyIndex += stamp->getNRigidBodies();
822 >        beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
823        }
824 <      
825 <      for(rb = mol->beginRigidBody(ri); rb != NULL;
826 <          rb = mol->nextRigidBody(ri)) {
827 <        rb->setGlobalIndex(beginRigidBodyIndex++);
704 <      }
705 <      
706 <      //local index of cutoff group is trivial, it only depends on the order of travesing
707 <      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
708 <          cg = mol->nextCutoffGroup(ci)) {
709 <        cg->setGlobalIndex(beginCutoffGroupIndex++);
710 <      }
711 <    }
712 <    
824 > #endif          
825 >
826 >    } //end for(int i=0)  
827 >
828      //fill globalGroupMembership
829      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
830      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
# Line 721 | Line 836 | namespace OpenMD {
836          
837        }      
838      }
839 <    
839 >  
840   #ifdef IS_MPI    
841      // Since the globalGroupMembership has been zero filled and we've only
842      // poked values into the atoms we know, we can do an Allreduce
# Line 791 | Line 906 | namespace OpenMD {
906          globalIO++;
907        }
908      }
909 <    
909 >      
910      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
911      
912    }
913    
914    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
915      Globals* simParams;
916 +
917      simParams = info->getSimParams();
918      
803 –    
919      DumpReader reader(info, mdFileName);
920      int nframes = reader.getNFrames();
921 <    
921 >
922      if (nframes > 0) {
923        reader.readFrame(nframes - 1);
924      } else {
# Line 814 | Line 929 | namespace OpenMD {
929        painCave.isFatal = 1;
930        simError();
931      }
817 –    
932      //copy the current snapshot to previous snapshot
933      info->getSnapshotManager()->advance();
934    }

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