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root/OpenMD/branches/development/src/brains/SimCreator.cpp
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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1600 by gezelter, Wed Aug 3 20:20:37 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

# Line 81 | Line 81 | namespace OpenMD {
81  
82   namespace OpenMD {
83    
84 <  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
84 >  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
85      Globals* simParams = NULL;
86      try {
87  
# Line 92 | Line 92 | namespace OpenMD {
92        const int masterNode = 0;
93        int commStatus;
94        if (worldRank == masterNode) {
95 < #endif
96 <                
95 >        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
96 > #endif                
97          SimplePreprocessor preprocessor;
98          preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
99                  
# Line 106 | Line 106 | namespace OpenMD {
106              
107                  
108        } else {
109 +
110 +        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
111 +
112          //get stream size
113          commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
114  
# Line 229 | Line 232 | namespace OpenMD {
232        simError();
233      }
234  
235 +    simParams->setMDfileVersion(mdFileVersion);
236      return simParams;
237    }
238    
# Line 243 | Line 247 | namespace OpenMD {
247      int metaDataBlockEnd = -1;
248      int i;
249      int mdOffset;
250 +    int mdFileVersion;
251  
252   #ifdef IS_MPI            
253      const int masterNode = 0;
# Line 276 | Line 281 | namespace OpenMD {
281          painCave.isFatal = 1;
282          simError();
283        }
284 +      
285 +      // found the correct opening string, now try to get the file
286 +      // format version number.
287  
288 +      StringTokenizer tokenizer(line, "=<> \t\n\r");
289 +      std::string fileType = tokenizer.nextToken();
290 +      toUpper(fileType);
291 +
292 +      mdFileVersion = 0;
293 +
294 +      if (fileType == "OPENMD") {
295 +        while (tokenizer.hasMoreTokens()) {
296 +          std::string token(tokenizer.nextToken());
297 +          toUpper(token);
298 +          if (token == "VERSION") {
299 +            mdFileVersion = tokenizer.nextTokenAsInt();
300 +            break;
301 +          }
302 +        }
303 +      }
304 +            
305        //scan through the input stream and find MetaData tag        
306        while(mdFile_.getline(buffer, bufferSize)) {
307          ++lineNo;
# Line 332 | Line 357 | namespace OpenMD {
357      std::stringstream rawMetaDataStream(mdRawData);
358  
359      //parse meta-data file
360 <    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
360 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
361 >                                   metaDataBlockStart + 1);
362      
363      //create the force field
364      ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
# Line 589 | Line 615 | namespace OpenMD {
615        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
616      }
617      
592 –    cerr << "molToProcMap:\n";
593 –    for (int i = 0; i < molToProcMap.size(); i++) {
594 –      cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n";
595 –    }
596 –
618      info->setMolToProcMap(molToProcMap);
619      sprintf(checkPointMsg,
620              "Successfully divided the molecules among the processors.\n");
# Line 712 | Line 733 | namespace OpenMD {
733      MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
734                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
735      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 –
736   #else
737      info->setGlobalGroupMembership(globalGroupMembership);
738   #endif
# Line 776 | Line 792 | namespace OpenMD {
792          globalIO++;
793        }
794      }
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 –    }
795        
796      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
797      

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