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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1469 by gezelter, Mon Jul 19 14:07:59 2010 UTC vs.
Revision 1794 by gezelter, Thu Sep 6 19:44:06 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 55 | Line 56
56   #include "brains/SimCreator.hpp"
57   #include "brains/SimSnapshotManager.hpp"
58   #include "io/DumpReader.hpp"
59 < #include "UseTheForce/ForceFieldFactory.hpp"
59 > #include "brains/ForceField.hpp"
60   #include "utils/simError.h"
61   #include "utils/StringUtils.hpp"
62   #include "math/SeqRandNumGen.hpp"
# 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 242 | Line 256 | namespace OpenMD {
256      int metaDataBlockStart = -1;
257      int metaDataBlockEnd = -1;
258      int i;
259 <    int mdOffset;
259 >    streamoff mdOffset;
260 >    int mdFileVersion;
261  
262 +
263   #ifdef IS_MPI            
264      const int masterNode = 0;
265      if (worldRank == masterNode) {
266   #endif
267  
268 <      std::ifstream mdFile_(mdFileName.c_str());
268 >      std::ifstream mdFile_;
269 >      mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270        
271        if (mdFile_.fail()) {
272          sprintf(painCave.errMsg,
# Line 276 | Line 293 | namespace OpenMD {
293          painCave.isFatal = 1;
294          simError();
295        }
296 +      
297 +      // found the correct opening string, now try to get the file
298 +      // format version number.
299 +
300 +      StringTokenizer tokenizer(line, "=<> \t\n\r");
301 +      std::string fileType = tokenizer.nextToken();
302 +      toUpper(fileType);
303 +
304 +      mdFileVersion = 0;
305  
306 +      if (fileType == "OPENMD") {
307 +        while (tokenizer.hasMoreTokens()) {
308 +          std::string token(tokenizer.nextToken());
309 +          toUpper(token);
310 +          if (token == "VERSION") {
311 +            mdFileVersion = tokenizer.nextTokenAsInt();
312 +            break;
313 +          }
314 +        }
315 +      }
316 +            
317        //scan through the input stream and find MetaData tag        
318        while(mdFile_.getline(buffer, bufferSize)) {
319          ++lineNo;
# Line 332 | Line 369 | namespace OpenMD {
369      std::stringstream rawMetaDataStream(mdRawData);
370  
371      //parse meta-data file
372 <    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
372 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373 >                                   metaDataBlockStart + 1);
374      
375      //create the force field
376 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
376 >    ForceField * ff = new ForceField(simParams->getForceField());
377  
378      if (ff == NULL) {
379        sprintf(painCave.errMsg,
# Line 369 | Line 407 | namespace OpenMD {
407      }
408      
409      ff->parse(forcefieldFileName);
372 –    ff->setFortranForceOptions();
410      //create SimInfo
411      SimInfo * info = new SimInfo(ff, simParams);
412  
# Line 387 | Line 424 | namespace OpenMD {
424      //create the molecules
425      createMolecules(info);
426      
427 <    
427 >    //find the storage layout
428 >
429 >    int storageLayout = computeStorageLayout(info);
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 hasDipoles = false;    
679 +    bool hasQuadrupoles = false;    
680 +    bool hasPolarizable = false;    
681 +    bool hasFluctuatingCharge = false;    
682 +    bool hasMetallic = false;
683 +    int storageLayout = 0;
684 +    storageLayout |= DataStorage::dslPosition;
685 +    storageLayout |= DataStorage::dslVelocity;
686 +    storageLayout |= DataStorage::dslForce;
687 +
688 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
689 +
690 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
691 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
692 +      EAMAdapter ea = EAMAdapter( (*i) );
693 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
694 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
695 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
696 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
697 +
698 +      if (da.isDirectional()){
699 +        hasDirectionalAtoms = true;
700 +      }
701 +      if (ma.isDipole()){
702 +        hasDipoles = true;
703 +      }
704 +      if (ma.isQuadrupole()){
705 +        hasQuadrupoles = true;
706 +      }
707 +      if (ea.isEAM() || sca.isSuttonChen()){
708 +        hasMetallic = true;
709 +      }
710 +      if ( fca.isFixedCharge() ){
711 +        hasFixedCharge = true;
712 +      }
713 +      if ( fqa.isFluctuatingCharge() ){
714 +        hasFluctuatingCharge = true;
715 +      }
716 +      if ( pa.isPolarizable() ){
717 +        hasPolarizable = true;
718 +      }
719 +    }
720 +    
721 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
722 +      storageLayout |= DataStorage::dslAmat;
723 +      if(storageLayout & DataStorage::dslVelocity) {
724 +        storageLayout |= DataStorage::dslAngularMomentum;
725 +      }
726 +      if (storageLayout & DataStorage::dslForce) {
727 +        storageLayout |= DataStorage::dslTorque;
728 +      }
729 +    }
730 +    if (hasDipoles) {
731 +      storageLayout |= DataStorage::dslDipole;
732 +    }
733 +    if (hasQuadrupoles) {
734 +      storageLayout |= DataStorage::dslQuadrupole;
735 +    }
736 +    if (hasFixedCharge || hasFluctuatingCharge) {
737 +      storageLayout |= DataStorage::dslSkippedCharge;
738 +    }
739 +    if (hasMetallic) {
740 +      storageLayout |= DataStorage::dslDensity;
741 +      storageLayout |= DataStorage::dslFunctional;
742 +      storageLayout |= DataStorage::dslFunctionalDerivative;
743 +    }
744 +    if (hasPolarizable) {
745 +      storageLayout |= DataStorage::dslElectricField;
746 +    }
747 +    if (hasFluctuatingCharge){
748 +      storageLayout |= DataStorage::dslFlucQPosition;
749 +      if(storageLayout & DataStorage::dslVelocity) {
750 +        storageLayout |= DataStorage::dslFlucQVelocity;
751 +      }
752 +      if (storageLayout & DataStorage::dslForce) {
753 +        storageLayout |= DataStorage::dslFlucQForce;
754 +      }
755 +    }
756      
757 +    // if the user has asked for them, make sure we've got the memory for the
758 +    // objects defined.
759 +
760 +    if (simParams->getOutputParticlePotential()) {
761 +      storageLayout |= DataStorage::dslParticlePot;
762 +    }
763 +
764 +    if (simParams->havePrintHeatFlux()) {
765 +      if (simParams->getPrintHeatFlux()) {
766 +        storageLayout |= DataStorage::dslParticlePot;
767 +      }
768 +    }
769 +
770 +    if (simParams->getOutputElectricField()) {
771 +      storageLayout |= DataStorage::dslElectricField;
772 +    }
773 +
774 +    if (simParams->getOutputFluctuatingCharges()) {
775 +      storageLayout |= DataStorage::dslFlucQPosition;
776 +      storageLayout |= DataStorage::dslFlucQVelocity;
777 +      storageLayout |= DataStorage::dslFlucQForce;
778 +    }
779 +
780 +    return storageLayout;
781 +  }
782 +
783    void SimCreator::setGlobalIndex(SimInfo *info) {
784      SimInfo::MoleculeIterator mi;
785      Molecule::AtomIterator ai;
# Line 640 | Line 794 | namespace OpenMD {
794      int beginRigidBodyIndex;
795      int beginCutoffGroupIndex;
796      int nGlobalAtoms = info->getNGlobalAtoms();
643 –
644 –    /**@todo fixme */
645 – #ifndef IS_MPI
797      
798      beginAtomIndex = 0;
648 –    beginRigidBodyIndex = 0;
649 –    beginCutoffGroupIndex = 0;
650 –    
651 – #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 –    
799      //rigidbody's index begins right after atom's
800 <    beginRigidBodyIndex += info->getNGlobalAtoms();
801 <    
802 <    for(mol = info->beginMolecule(mi); mol != NULL;
803 <        mol = info->nextMolecule(mi)) {
800 >    beginRigidBodyIndex = info->getNGlobalAtoms();
801 >    beginCutoffGroupIndex = 0;
802 >
803 >    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
804        
805 <      //local index(index in DataStorge) of atom is important
806 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
807 <        atom->setGlobalIndex(beginAtomIndex++);
805 > #ifdef IS_MPI      
806 >      if (info->getMolToProc(i) == worldRank) {
807 > #endif        
808 >        // stuff to do if I own this molecule
809 >        mol = info->getMoleculeByGlobalIndex(i);
810 >
811 >        //local index(index in DataStorge) of atom is important
812 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
813 >          atom->setGlobalIndex(beginAtomIndex++);
814 >        }
815 >        
816 >        for(rb = mol->beginRigidBody(ri); rb != NULL;
817 >            rb = mol->nextRigidBody(ri)) {
818 >          rb->setGlobalIndex(beginRigidBodyIndex++);
819 >        }
820 >        
821 >        //local index of cutoff group is trivial, it only depends on
822 >        //the order of travesing
823 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
824 >            cg = mol->nextCutoffGroup(ci)) {
825 >          cg->setGlobalIndex(beginCutoffGroupIndex++);
826 >        }        
827 >        
828 > #ifdef IS_MPI        
829 >      }  else {
830 >
831 >        // stuff to do if I don't own this molecule
832 >        
833 >        int stampId = info->getMoleculeStampId(i);
834 >        MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
835 >
836 >        beginAtomIndex += stamp->getNAtoms();
837 >        beginRigidBodyIndex += stamp->getNRigidBodies();
838 >        beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
839        }
840 <      
841 <      for(rb = mol->beginRigidBody(ri); rb != NULL;
842 <          rb = mol->nextRigidBody(ri)) {
843 <        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 <    
840 > #endif          
841 >
842 >    } //end for(int i=0)  
843 >
844      //fill globalGroupMembership
845      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
846      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
# Line 721 | Line 852 | namespace OpenMD {
852          
853        }      
854      }
855 <    
855 >  
856   #ifdef IS_MPI    
857      // Since the globalGroupMembership has been zero filled and we've only
858      // poked values into the atoms we know, we can do an Allreduce
# Line 784 | Line 915 | namespace OpenMD {
915      for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
916        int myGlobalIndex = mol->getGlobalIndex();
917        int globalIO = startingIOIndexForMol[myGlobalIndex];
918 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
919 <           integrableObject = mol->nextIntegrableObject(ioi)) {
920 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
921 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
918 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
919 >           sd = mol->nextIntegrableObject(ioi)) {
920 >        sd->setGlobalIntegrableObjectIndex(globalIO);
921 >        IOIndexToIntegrableObject[globalIO] = sd;
922          globalIO++;
923        }
924      }
925 <    
925 >      
926      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
927      
928    }
929    
930    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
931      Globals* simParams;
932 +
933      simParams = info->getSimParams();
934      
803 –    
935      DumpReader reader(info, mdFileName);
936      int nframes = reader.getNFrames();
937 <    
937 >
938      if (nframes > 0) {
939        reader.readFrame(nframes - 1);
940      } else {
# Line 814 | Line 945 | namespace OpenMD {
945        painCave.isFatal = 1;
946        simError();
947      }
817 –    
948      //copy the current snapshot to previous snapshot
949      info->getSnapshotManager()->advance();
950    }

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