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Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 44 | Line 44
44   * @file SimCreator.cpp
45   * @author tlin
46   * @date 11/03/2004
47 – * @time 13:51am
47   * @version 1.0
48   */
49   #include <exception>
# Line 56 | 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 100 | Line 99 | namespace OpenMD {
99   #ifdef IS_MPI            
100        int streamSize;
101        const int masterNode = 0;
102 <      int commStatus;
102 >
103        if (worldRank == masterNode) {
104 <        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
104 >        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105   #endif                
106          SimplePreprocessor preprocessor;
107          preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
# Line 110 | Line 109 | namespace OpenMD {
109   #ifdef IS_MPI            
110          //brocasting the stream size
111          streamSize = ppStream.str().size() +1;
112 <        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                  
113 <
114 <        commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
116 <            
117 <                
112 >        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
113 >        MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
114 >                          
115        } else {
116 +        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
117  
120 –        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121 –
118          //get stream size
119 <        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
119 >        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
120  
121          char* buf = new char[streamSize];
122          assert(buf);
123                  
124          //receive file content
125 <        commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
125 >        MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
126                  
127          ppStream.str(buf);
128          delete [] buf;
133 –
129        }
130   #endif            
131        // Create a scanner that reads from the input stream
# Line 255 | Line 250 | namespace OpenMD {
250      std::string mdRawData;
251      int metaDataBlockStart = -1;
252      int metaDataBlockEnd = -1;
253 <    int i;
254 <    int mdOffset;
253 >    int i, j;
254 >    streamoff mdOffset;
255      int mdFileVersion;
256  
257 +    // Create a string for embedding the version information in the MetaData
258 +    std::string version;
259 +    version.assign("## Last run using OpenMD Version: ");
260 +    version.append(OPENMD_VERSION_MAJOR);
261 +    version.append(".");
262 +    version.append(OPENMD_VERSION_MINOR);
263 +
264 +    std::string svnrev;
265 +    //convert a macro from compiler to a string in c++
266 +    STR_DEFINE(svnrev, SVN_REV );
267 +    version.append(" Revision: ");
268 +    // If there's no SVN revision, just call this the RELEASE revision.
269 +    if (!svnrev.empty()) {
270 +      version.append(svnrev);
271 +    } else {
272 +      version.append("RELEASE");
273 +    }
274 +  
275   #ifdef IS_MPI            
276      const int masterNode = 0;
277      if (worldRank == masterNode) {
278   #endif
279  
280 <      std::ifstream mdFile_(mdFileName.c_str());
280 >      std::ifstream mdFile_;
281 >      mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
282        
283        if (mdFile_.fail()) {
284          sprintf(painCave.errMsg,
# Line 352 | Line 366 | namespace OpenMD {
366  
367        mdRawData.clear();
368  
369 +      bool foundVersion = false;
370 +
371        for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
372          mdFile_.getline(buffer, bufferSize);
373 <        mdRawData += buffer;
373 >        std::string line = trimLeftCopy(buffer);
374 >        j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
375 >        if (static_cast<size_t>(j) != string::npos) {
376 >          foundVersion = true;
377 >          mdRawData += version;
378 >        } else {
379 >          mdRawData += buffer;
380 >        }
381          mdRawData += "\n";
382        }
383 <
383 >      
384 >      if (!foundVersion) mdRawData += version + "\n";
385 >      
386        mdFile_.close();
387  
388   #ifdef IS_MPI
# Line 371 | Line 396 | namespace OpenMD {
396                                     metaDataBlockStart + 1);
397      
398      //create the force field
399 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
399 >    ForceField * ff = new ForceField(simParams->getForceField());
400  
401      if (ff == NULL) {
402        sprintf(painCave.errMsg,
# Line 491 | Line 516 | namespace OpenMD {
516      RealType x;
517      RealType y;
518      RealType a;
494 –    int old_atoms;
495 –    int add_atoms;
496 –    int new_atoms;
497 –    int nTarget;
498 –    int done;
499 –    int i;
500 –    int j;
501 –    int loops;
502 –    int which_proc;
519      int nProcessors;
520      std::vector<int> atomsPerProc;
521      int nGlobalMols = info->getNGlobalMolecules();
522 <    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
522 >    std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
523 >                                                    // error
524 >                                                    // condition:
525      
526 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
526 >    nProcessors = MPI::COMM_WORLD.Get_size();
527      
528      if (nProcessors > nGlobalMols) {
529        sprintf(painCave.errMsg,
# Line 514 | Line 532 | namespace OpenMD {
532                "\tthe number of molecules.  This will not result in a \n"
533                "\tusable division of atoms for force decomposition.\n"
534                "\tEither try a smaller number of processors, or run the\n"
535 <              "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
535 >              "\tsingle-processor version of OpenMD.\n", nProcessors,
536 >              nGlobalMols);
537        
538        painCave.isFatal = 1;
539        simError();
540      }
541      
523 –    int seedValue;
542      Globals * simParams = info->getSimParams();
543 <    SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
543 >    SeqRandNumGen* myRandom; //divide labor does not need Parallel
544 >                             //random number generator
545      if (simParams->haveSeed()) {
546 <      seedValue = simParams->getSeed();
546 >      int seedValue = simParams->getSeed();
547        myRandom = new SeqRandNumGen(seedValue);
548      }else {
549        myRandom = new SeqRandNumGen();
# Line 540 | Line 559 | namespace OpenMD {
559        numerator = info->getNGlobalAtoms();
560        denominator = nProcessors;
561        precast = numerator / denominator;
562 <      nTarget = (int)(precast + 0.5);
562 >      int nTarget = (int)(precast + 0.5);
563        
564 <      for(i = 0; i < nGlobalMols; i++) {
565 <        done = 0;
566 <        loops = 0;
564 >      for(int i = 0; i < nGlobalMols; i++) {
565 >
566 >        int done = 0;
567 >        int loops = 0;
568          
569          while (!done) {
570            loops++;
571            
572            // Pick a processor at random
573            
574 <          which_proc = (int) (myRandom->rand() * nProcessors);
574 >          int which_proc = (int) (myRandom->rand() * nProcessors);
575            
576            //get the molecule stamp first
577            int stampId = info->getMoleculeStampId(i);
578            MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
579            
580            // How many atoms does this processor have so far?
581 <          old_atoms = atomsPerProc[which_proc];
582 <          add_atoms = moleculeStamp->getNAtoms();
583 <          new_atoms = old_atoms + add_atoms;
581 >          int old_atoms = atomsPerProc[which_proc];
582 >          int add_atoms = moleculeStamp->getNAtoms();
583 >          int new_atoms = old_atoms + add_atoms;
584            
585            // If we've been through this loop too many times, we need
586            // to just give up and assign the molecule to this processor
587            // and be done with it.
588            
589            if (loops > 100) {
590 +
591              sprintf(painCave.errMsg,
592 <                    "I've tried 100 times to assign molecule %d to a "
593 <                    " processor, but can't find a good spot.\n"
594 <                    "I'm assigning it at random to processor %d.\n",
592 >                    "There have been 100 attempts to assign molecule %d to an\n"
593 >                    "\tunderworked processor, but there's no good place to\n"
594 >                    "\tleave it.  OpenMD is assigning it at random to processor %d.\n",
595                      i, which_proc);
596 <            
596 >          
597              painCave.isFatal = 0;
598 +            painCave.severity = OPENMD_INFO;
599              simError();
600              
601              molToProcMap[i] = which_proc;
# Line 618 | Line 640 | namespace OpenMD {
640        }
641        
642        delete myRandom;
643 <      
643 >
644        // Spray out this nonsense to all other processors:
645 <      
624 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646      } else {
647        
648        // Listen to your marching orders from processor 0:
649 <      
650 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
649 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
650 >
651      }
652      
653      info->setMolToProcMap(molToProcMap);
# Line 673 | Line 694 | namespace OpenMD {
694      set<AtomType*>::iterator i;
695      bool hasDirectionalAtoms = false;
696      bool hasFixedCharge = false;
697 <    bool hasMultipoles = false;    
697 >    bool hasDipoles = false;    
698 >    bool hasQuadrupoles = false;    
699      bool hasPolarizable = false;    
700      bool hasFluctuatingCharge = false;    
701      bool hasMetallic = false;
# Line 695 | Line 717 | namespace OpenMD {
717        if (da.isDirectional()){
718          hasDirectionalAtoms = true;
719        }
720 <      if (ma.isMultipole()){
721 <        hasMultipoles = true;
720 >      if (ma.isDipole()){
721 >        hasDipoles = true;
722        }
723 +      if (ma.isQuadrupole()){
724 +        hasQuadrupoles = true;
725 +      }
726        if (ea.isEAM() || sca.isSuttonChen()){
727          hasMetallic = true;
728        }
# Line 721 | Line 746 | namespace OpenMD {
746          storageLayout |= DataStorage::dslTorque;
747        }
748      }
749 <    if (hasMultipoles) {
750 <      storageLayout |= DataStorage::dslElectroFrame;
749 >    if (hasDipoles) {
750 >      storageLayout |= DataStorage::dslDipole;
751      }
752 +    if (hasQuadrupoles) {
753 +      storageLayout |= DataStorage::dslQuadrupole;
754 +    }
755      if (hasFixedCharge || hasFluctuatingCharge) {
756        storageLayout |= DataStorage::dslSkippedCharge;
757      }
# Line 751 | Line 779 | namespace OpenMD {
779      if (simParams->getOutputParticlePotential()) {
780        storageLayout |= DataStorage::dslParticlePot;
781      }
782 <    if (simParams->getOutputElectricField()) {
782 >
783 >    if (simParams->havePrintHeatFlux()) {
784 >      if (simParams->getPrintHeatFlux()) {
785 >        storageLayout |= DataStorage::dslParticlePot;
786 >      }
787 >    }
788 >
789 >    if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
790        storageLayout |= DataStorage::dslElectricField;
791      }
792 +
793      if (simParams->getOutputFluctuatingCharges()) {
794        storageLayout |= DataStorage::dslFlucQPosition;
795        storageLayout |= DataStorage::dslFlucQVelocity;
796        storageLayout |= DataStorage::dslFlucQForce;
797      }
798  
799 +    info->setStorageLayout(storageLayout);
800 +
801      return storageLayout;
802    }
803  
# Line 777 | Line 815 | namespace OpenMD {
815      int beginRigidBodyIndex;
816      int beginCutoffGroupIndex;
817      int nGlobalAtoms = info->getNGlobalAtoms();
818 +    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
819      
820      beginAtomIndex = 0;
821 <    beginRigidBodyIndex = 0;
821 >    //rigidbody's index begins right after atom's
822 >    beginRigidBodyIndex = info->getNGlobalAtoms();
823      beginCutoffGroupIndex = 0;
824  
825      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
# Line 842 | Line 882 | namespace OpenMD {
882      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
883      // docs said we could.
884      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
885 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
886 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
885 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
886 >                              &tmpGroupMembership[0], nGlobalAtoms,
887 >                              MPI::INT, MPI::SUM);
888      info->setGlobalGroupMembership(tmpGroupMembership);
889   #else
890      info->setGlobalGroupMembership(globalGroupMembership);
891   #endif
892      
893      //fill molMembership
894 <    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
894 >    std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
895 >                                         info->getNGlobalRigidBodies(), 0);
896      
897 <    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
897 >    for(mol = info->beginMolecule(mi); mol != NULL;
898 >        mol = info->nextMolecule(mi)) {
899        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
900          globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
901        }
902 +      for (rb = mol->beginRigidBody(ri); rb != NULL;
903 +           rb = mol->nextRigidBody(ri)) {
904 +        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
905 +      }
906      }
907      
908   #ifdef IS_MPI
909 <    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
909 >    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
910 >                                      info->getNGlobalRigidBodies(), 0);
911 >    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
912 >                              nGlobalAtoms + nGlobalRigidBodies,
913 >                              MPI::INT, MPI::SUM);
914      
864 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
865 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
866 –    
915      info->setGlobalMolMembership(tmpMolMembership);
916   #else
917      info->setGlobalMolMembership(globalMolMembership);
# Line 873 | Line 921 | namespace OpenMD {
921      // here the molecules are listed by their global indices.
922  
923      std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
924 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
924 >    for (mol = info->beginMolecule(mi); mol != NULL;
925 >         mol = info->nextMolecule(mi)) {
926        nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();      
927      }
928      
929   #ifdef IS_MPI
930      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
931 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
931 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
933   #else
934      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
935   #endif    
# Line 894 | Line 943 | namespace OpenMD {
943      }
944      
945      std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
946 <    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
946 >    for (mol = info->beginMolecule(mi); mol != NULL;
947 >         mol = info->nextMolecule(mi)) {
948        int myGlobalIndex = mol->getGlobalIndex();
949        int globalIO = startingIOIndexForMol[myGlobalIndex];
950 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
951 <           integrableObject = mol->nextIntegrableObject(ioi)) {
952 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
953 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
950 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
951 >           sd = mol->nextIntegrableObject(ioi)) {
952 >        sd->setGlobalIntegrableObjectIndex(globalIO);
953 >        IOIndexToIntegrableObject[globalIO] = sd;
954          globalIO++;
955        }
956      }
# Line 910 | Line 960 | namespace OpenMD {
960    }
961    
962    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
913 –    Globals* simParams;
914 –
915 –    simParams = info->getSimParams();
963      
964      DumpReader reader(info, mdFileName);
965      int nframes = reader.getNFrames();
966 <
966 >    
967      if (nframes > 0) {
968        reader.readFrame(nframes - 1);
969      } else {

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