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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1803 by gezelter, Wed Oct 3 14:20:07 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 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;
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) {
# Line 354 | 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 493 | Line 516 | namespace OpenMD {
516      RealType x;
517      RealType y;
518      RealType a;
496 –    int old_atoms;
497 –    int add_atoms;
498 –    int new_atoms;
499 –    int nTarget;
500 –    int done;
501 –    int i;
502 –    int j;
503 –    int loops;
504 –    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      nProcessors = MPI::COMM_WORLD.Get_size();
527      
# Line 516 | 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      
525 –    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 542 | Line 559 | namespace OpenMD {
559        numerator = info->getNGlobalAtoms();
560        denominator = nProcessors;
561        precast = numerator / denominator;
562 <      nTarget = (int)(precast + 0.5);
563 <      
564 <      for(i = 0; i < nGlobalMols; i++) {
562 >      int nTarget = (int)(precast + 0.5);
563 >      
564 >      for(int i = 0; i < nGlobalMols; i++) {
565  
566 <        done = 0;
567 <        loops = 0;
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
# Line 769 | Line 786 | namespace OpenMD {
786        }
787      }
788  
789 <    if (simParams->getOutputElectricField()) {
789 >    if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
790        storageLayout |= DataStorage::dslElectricField;
791      }
792  
# Line 779 | Line 796 | namespace OpenMD {
796        storageLayout |= DataStorage::dslFlucQForce;
797      }
798  
799 +    info->setStorageLayout(storageLayout);
800 +
801      return storageLayout;
802    }
803  
# Line 941 | Line 960 | namespace OpenMD {
960    }
961    
962    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
944 –    Globals* simParams;
945 –
946 –    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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