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Revision 1600 by gezelter, Wed Aug 3 20:20:37 2011 UTC vs.
Revision 1812 by gezelter, Fri Nov 16 21:18:42 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   /**
44   * @file SimCreator.cpp
45   * @author tlin
46   * @date 11/03/2004
46 – * @time 13:51am
47   * @version 1.0
48   */
49   #include <exception>
# Line 55 | Line 55
55   #include "brains/SimCreator.hpp"
56   #include "brains/SimSnapshotManager.hpp"
57   #include "io/DumpReader.hpp"
58 < #include "UseTheForce/ForceFieldFactory.hpp"
58 > #include "brains/ForceField.hpp"
59   #include "utils/simError.h"
60   #include "utils/StringUtils.hpp"
61   #include "math/SeqRandNumGen.hpp"
# Line 75 | Line 75
75   #include "antlr/NoViableAltForCharException.hpp"
76   #include "antlr/NoViableAltException.hpp"
77  
78 + #include "types/DirectionalAdapter.hpp"
79 + #include "types/MultipoleAdapter.hpp"
80 + #include "types/EAMAdapter.hpp"
81 + #include "types/SuttonChenAdapter.hpp"
82 + #include "types/PolarizableAdapter.hpp"
83 + #include "types/FixedChargeAdapter.hpp"
84 + #include "types/FluctuatingChargeAdapter.hpp"
85 +
86   #ifdef IS_MPI
87 + #include "mpi.h"
88   #include "math/ParallelRandNumGen.hpp"
89   #endif
90  
91   namespace OpenMD {
92    
93 <  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
93 >  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94      Globals* simParams = NULL;
95      try {
96  
# Line 92 | Line 101 | namespace OpenMD {
101        const int masterNode = 0;
102        int commStatus;
103        if (worldRank == masterNode) {
104 < #endif
105 <                
104 >        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
105 > #endif                
106          SimplePreprocessor preprocessor;
107          preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108                  
# Line 106 | Line 115 | namespace OpenMD {
115              
116                  
117        } else {
118 +
119 +        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120 +
121          //get stream size
122          commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
123  
# Line 229 | Line 241 | namespace OpenMD {
241        simError();
242      }
243  
244 +    simParams->setMDfileVersion(mdFileVersion);
245      return simParams;
246    }
247    
# Line 241 | Line 254 | namespace OpenMD {
254      std::string mdRawData;
255      int metaDataBlockStart = -1;
256      int metaDataBlockEnd = -1;
257 <    int i;
258 <    int mdOffset;
257 >    int i, j;
258 >    streamoff mdOffset;
259 >    int mdFileVersion;
260  
261 +    // Create a string for embedding the version information in the MetaData
262 +    std::string version;
263 +    version.assign("## Last run using OpenMD Version: ");
264 +    version.append(OPENMD_VERSION_MAJOR);
265 +    version.append(".");
266 +    version.append(OPENMD_VERSION_MINOR);
267 +
268 +    std::string svnrev;
269 +    //convert a macro from compiler to a string in c++
270 +    STR_DEFINE(svnrev, SVN_REV );
271 +    version.append(" Revision: ");
272 +    // If there's no SVN revision, just call this the RELEASE revision.
273 +    if (!svnrev.empty()) {
274 +      version.append(svnrev);
275 +    } else {
276 +      version.append("RELEASE");
277 +    }
278 +  
279   #ifdef IS_MPI            
280      const int masterNode = 0;
281      if (worldRank == masterNode) {
282   #endif
283  
284 <      std::ifstream mdFile_(mdFileName.c_str());
284 >      std::ifstream mdFile_;
285 >      mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286        
287        if (mdFile_.fail()) {
288          sprintf(painCave.errMsg,
# Line 276 | Line 309 | namespace OpenMD {
309          painCave.isFatal = 1;
310          simError();
311        }
312 +      
313 +      // found the correct opening string, now try to get the file
314 +      // format version number.
315  
316 +      StringTokenizer tokenizer(line, "=<> \t\n\r");
317 +      std::string fileType = tokenizer.nextToken();
318 +      toUpper(fileType);
319 +
320 +      mdFileVersion = 0;
321 +
322 +      if (fileType == "OPENMD") {
323 +        while (tokenizer.hasMoreTokens()) {
324 +          std::string token(tokenizer.nextToken());
325 +          toUpper(token);
326 +          if (token == "VERSION") {
327 +            mdFileVersion = tokenizer.nextTokenAsInt();
328 +            break;
329 +          }
330 +        }
331 +      }
332 +            
333        //scan through the input stream and find MetaData tag        
334        while(mdFile_.getline(buffer, bufferSize)) {
335          ++lineNo;
# Line 317 | Line 370 | namespace OpenMD {
370  
371        mdRawData.clear();
372  
373 +      bool foundVersion = false;
374 +
375        for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376          mdFile_.getline(buffer, bufferSize);
377 <        mdRawData += buffer;
377 >        std::string line = trimLeftCopy(buffer);
378 >        j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379 >        if (static_cast<size_t>(j) != string::npos) {
380 >          foundVersion = true;
381 >          mdRawData += version;
382 >        } else {
383 >          mdRawData += buffer;
384 >        }
385          mdRawData += "\n";
386        }
387 <
387 >      
388 >      if (!foundVersion) mdRawData += version + "\n";
389 >      
390        mdFile_.close();
391  
392   #ifdef IS_MPI
# Line 332 | Line 396 | namespace OpenMD {
396      std::stringstream rawMetaDataStream(mdRawData);
397  
398      //parse meta-data file
399 <    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
399 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
400 >                                   metaDataBlockStart + 1);
401      
402      //create the force field
403 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
403 >    ForceField * ff = new ForceField(simParams->getForceField());
404  
405      if (ff == NULL) {
406        sprintf(painCave.errMsg,
# Line 386 | Line 451 | namespace OpenMD {
451      //create the molecules
452      createMolecules(info);
453      
454 +    //find the storage layout
455 +
456 +    int storageLayout = computeStorageLayout(info);
457 +
458      //allocate memory for DataStorage(circular reference, need to
459      //break it)
460 <    info->setSnapshotManager(new SimSnapshotManager(info));
460 >    info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
461      
462      //set the global index of atoms, rigidbodies and cutoffgroups
463      //(only need to be set once, the global index will never change
# Line 465 | Line 534 | namespace OpenMD {
534      int nGlobalMols = info->getNGlobalMolecules();
535      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
536      
537 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
537 >    nProcessors = MPI::COMM_WORLD.Get_size();
538      
539      if (nProcessors > nGlobalMols) {
540        sprintf(painCave.errMsg,
# Line 503 | Line 572 | namespace OpenMD {
572        nTarget = (int)(precast + 0.5);
573        
574        for(i = 0; i < nGlobalMols; i++) {
575 +
576          done = 0;
577          loops = 0;
578          
# Line 527 | Line 597 | namespace OpenMD {
597            // and be done with it.
598            
599            if (loops > 100) {
600 +
601              sprintf(painCave.errMsg,
602 <                    "I've tried 100 times to assign molecule %d to a "
603 <                    " processor, but can't find a good spot.\n"
604 <                    "I'm assigning it at random to processor %d.\n",
602 >                    "There have been 100 attempts to assign molecule %d to an\n"
603 >                    "\tunderworked processor, but there's no good place to\n"
604 >                    "\tleave it.  OpenMD is assigning it at random to processor %d.\n",
605                      i, which_proc);
606 <            
606 >          
607              painCave.isFatal = 0;
608 +            painCave.severity = OPENMD_INFO;
609              simError();
610              
611              molToProcMap[i] = which_proc;
# Line 578 | Line 650 | namespace OpenMD {
650        }
651        
652        delete myRandom;
653 <      
653 >
654        // Spray out this nonsense to all other processors:
655 <      
584 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
655 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
656      } else {
657        
658        // Listen to your marching orders from processor 0:
659 <      
660 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
659 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
660 >
661      }
662      
592 –    cerr << "molToProcMap:\n";
593 –    for (int i = 0; i < molToProcMap.size(); i++) {
594 –      cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n";
595 –    }
596 –
663      info->setMolToProcMap(molToProcMap);
664      sprintf(checkPointMsg,
665              "Successfully divided the molecules among the processors.\n");
# Line 629 | Line 695 | namespace OpenMD {
695        
696      } //end for(int i=0)  
697    }
698 +    
699 +  int SimCreator::computeStorageLayout(SimInfo* info) {
700 +
701 +    Globals* simParams = info->getSimParams();
702 +    int nRigidBodies = info->getNGlobalRigidBodies();
703 +    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
704 +    set<AtomType*>::iterator i;
705 +    bool hasDirectionalAtoms = false;
706 +    bool hasFixedCharge = false;
707 +    bool hasDipoles = false;    
708 +    bool hasQuadrupoles = false;    
709 +    bool hasPolarizable = false;    
710 +    bool hasFluctuatingCharge = false;    
711 +    bool hasMetallic = false;
712 +    int storageLayout = 0;
713 +    storageLayout |= DataStorage::dslPosition;
714 +    storageLayout |= DataStorage::dslVelocity;
715 +    storageLayout |= DataStorage::dslForce;
716 +
717 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
718 +
719 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
720 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
721 +      EAMAdapter ea = EAMAdapter( (*i) );
722 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
723 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
724 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
725 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
726 +
727 +      if (da.isDirectional()){
728 +        hasDirectionalAtoms = true;
729 +      }
730 +      if (ma.isDipole()){
731 +        hasDipoles = true;
732 +      }
733 +      if (ma.isQuadrupole()){
734 +        hasQuadrupoles = true;
735 +      }
736 +      if (ea.isEAM() || sca.isSuttonChen()){
737 +        hasMetallic = true;
738 +      }
739 +      if ( fca.isFixedCharge() ){
740 +        hasFixedCharge = true;
741 +      }
742 +      if ( fqa.isFluctuatingCharge() ){
743 +        hasFluctuatingCharge = true;
744 +      }
745 +      if ( pa.isPolarizable() ){
746 +        hasPolarizable = true;
747 +      }
748 +    }
749      
750 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
751 +      storageLayout |= DataStorage::dslAmat;
752 +      if(storageLayout & DataStorage::dslVelocity) {
753 +        storageLayout |= DataStorage::dslAngularMomentum;
754 +      }
755 +      if (storageLayout & DataStorage::dslForce) {
756 +        storageLayout |= DataStorage::dslTorque;
757 +      }
758 +    }
759 +    if (hasDipoles) {
760 +      storageLayout |= DataStorage::dslDipole;
761 +    }
762 +    if (hasQuadrupoles) {
763 +      storageLayout |= DataStorage::dslQuadrupole;
764 +    }
765 +    if (hasFixedCharge || hasFluctuatingCharge) {
766 +      storageLayout |= DataStorage::dslSkippedCharge;
767 +    }
768 +    if (hasMetallic) {
769 +      storageLayout |= DataStorage::dslDensity;
770 +      storageLayout |= DataStorage::dslFunctional;
771 +      storageLayout |= DataStorage::dslFunctionalDerivative;
772 +    }
773 +    if (hasPolarizable) {
774 +      storageLayout |= DataStorage::dslElectricField;
775 +    }
776 +    if (hasFluctuatingCharge){
777 +      storageLayout |= DataStorage::dslFlucQPosition;
778 +      if(storageLayout & DataStorage::dslVelocity) {
779 +        storageLayout |= DataStorage::dslFlucQVelocity;
780 +      }
781 +      if (storageLayout & DataStorage::dslForce) {
782 +        storageLayout |= DataStorage::dslFlucQForce;
783 +      }
784 +    }
785 +    
786 +    // if the user has asked for them, make sure we've got the memory for the
787 +    // objects defined.
788 +
789 +    if (simParams->getOutputParticlePotential()) {
790 +      storageLayout |= DataStorage::dslParticlePot;
791 +    }
792 +
793 +    if (simParams->havePrintHeatFlux()) {
794 +      if (simParams->getPrintHeatFlux()) {
795 +        storageLayout |= DataStorage::dslParticlePot;
796 +      }
797 +    }
798 +
799 +    if (simParams->getOutputElectricField()) {
800 +      storageLayout |= DataStorage::dslElectricField;
801 +    }
802 +
803 +    if (simParams->getOutputFluctuatingCharges()) {
804 +      storageLayout |= DataStorage::dslFlucQPosition;
805 +      storageLayout |= DataStorage::dslFlucQVelocity;
806 +      storageLayout |= DataStorage::dslFlucQForce;
807 +    }
808 +
809 +    return storageLayout;
810 +  }
811 +
812    void SimCreator::setGlobalIndex(SimInfo *info) {
813      SimInfo::MoleculeIterator mi;
814      Molecule::AtomIterator ai;
# Line 644 | Line 823 | namespace OpenMD {
823      int beginRigidBodyIndex;
824      int beginCutoffGroupIndex;
825      int nGlobalAtoms = info->getNGlobalAtoms();
826 +    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
827      
828      beginAtomIndex = 0;
829 <    beginRigidBodyIndex = 0;
829 >    //rigidbody's index begins right after atom's
830 >    beginRigidBodyIndex = info->getNGlobalAtoms();
831      beginCutoffGroupIndex = 0;
832  
833      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 709 | Line 890 | namespace OpenMD {
890      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
891      // docs said we could.
892      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
893 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
894 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
893 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
894 >                              &tmpGroupMembership[0], nGlobalAtoms,
895 >                              MPI::INT, MPI::SUM);
896      info->setGlobalGroupMembership(tmpGroupMembership);
715 –
716 –    cerr << "ggm:\n";
717 –    for (int i = 0; i < tmpGroupMembership.size(); i++)
718 –      cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n";
719 –
897   #else
898      info->setGlobalGroupMembership(globalGroupMembership);
899   #endif
900      
901      //fill molMembership
902 <    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
902 >    std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
903 >                                         info->getNGlobalRigidBodies(), 0);
904      
905 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
905 >    for(mol = info->beginMolecule(mi); mol != NULL;
906 >        mol = info->nextMolecule(mi)) {
907        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
908          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
909        }
910 +      for (rb = mol->beginRigidBody(ri); rb != NULL;
911 +           rb = mol->nextRigidBody(ri)) {
912 +        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
913 +      }
914      }
915      
916   #ifdef IS_MPI
917 <    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
917 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
918 >                                      info->getNGlobalRigidBodies(), 0);
919 >    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
920 >                              nGlobalAtoms + nGlobalRigidBodies,
921 >                              MPI::INT, MPI::SUM);
922      
736 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
737 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
738 –    
923      info->setGlobalMolMembership(tmpMolMembership);
924   #else
925      info->setGlobalMolMembership(globalMolMembership);
# Line 745 | Line 929 | namespace OpenMD {
929      // here the molecules are listed by their global indices.
930  
931      std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
932 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
932 >    for (mol = info->beginMolecule(mi); mol != NULL;
933 >         mol = info->nextMolecule(mi)) {
934        nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
935      }
936      
937   #ifdef IS_MPI
938      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
939 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
939 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
941   #else
942      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
943   #endif    
# Line 766 | Line 951 | namespace OpenMD {
951      }
952      
953      std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
954 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
954 >    for (mol = info->beginMolecule(mi); mol != NULL;
955 >         mol = info->nextMolecule(mi)) {
956        int myGlobalIndex = mol->getGlobalIndex();
957        int globalIO = startingIOIndexForMol[myGlobalIndex];
958 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
959 <           integrableObject = mol->nextIntegrableObject(ioi)) {
960 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
961 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
958 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
959 >           sd = mol->nextIntegrableObject(ioi)) {
960 >        sd->setGlobalIntegrableObjectIndex(globalIO);
961 >        IOIndexToIntegrableObject[globalIO] = sd;
962          globalIO++;
963        }
964      }
779 –    cerr << "ioi2io:\n";
780 –    for (int i = 0; i < IOIndexToIntegrableObject.size(); i++) {
781 –      if (IOIndexToIntegrableObject[i] != NULL) {
782 –        cerr << "i = " << i << "globalIOindex = " << IOIndexToIntegrableObject[i]->getGlobalIntegrableObjectIndex() << "\n";
783 –      }
784 –    }
965        
966      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
967      

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