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root/OpenMD/trunk/src/io/DumpReader.cpp
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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1897 by gezelter, Wed Jul 3 20:21:00 2013 UTC vs.
Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 UTC

# Line 43 | Line 43
43   #define _LARGEFILE_SOURCE64
44   #define _FILE_OFFSET_BITS 64
45  
46 + #ifdef IS_MPI
47 + #include <mpi.h>
48 + #endif
49 +
50   #include <sys/types.h>
51   #include <sys/stat.h>
52  
# Line 60 | Line 64
64   #include "utils/StringTokenizer.hpp"
65   #include "brains/Thermo.hpp"
66  
63 – #ifdef IS_MPI
64 – #include <mpi.h>
65 – #endif
67  
67 –
68   namespace OpenMD {
69    
70    DumpReader::DumpReader(SimInfo* info, const std::string& filename)
# Line 103 | Line 103 | namespace OpenMD {
103   #ifdef IS_MPI
104      
105      if (worldRank == 0) {
106 < #endif
107 <      
106 > #endif
107 >
108        delete inFile_;
109        
110   #ifdef IS_MPI
# Line 203 | Line 203 | namespace OpenMD {
203   #ifdef IS_MPI
204      }
205      
206 <    MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
206 >    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207      
208   #endif // is_mpi
209      
# Line 245 | Line 245 | namespace OpenMD {
245      readSet(whichFrame);
246  
247      if (needCOMprops_) {
248 –      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248        Thermo thermo(info_);
249        Vector3d com;
250  
# Line 289 | Line 288 | namespace OpenMD {
288        }
289  
290        int sendBufferSize = sendBuffer.size();
291 <      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);    
292 <      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293 <                            MPI::CHAR, masterNode);    
291 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
292 >      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293 >                MPI_CHAR, masterNode, MPI_COMM_WORLD);    
294        
295        sstream.str(sendBuffer);
296      } else {
297        int sendBufferSize;
298 <      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
298 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299        char * recvBuffer = new char[sendBufferSize+1];
300        assert(recvBuffer);
301        recvBuffer[sendBufferSize] = '\0';
302 <      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
302 >      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303        sstream.str(recvBuffer);
304        delete [] recvBuffer;
305      }      
# Line 510 | Line 509 | namespace OpenMD {
509             sd->setElectricField(eField);          
510             break;
511          }
512 +        case 's' : {
513 +
514 +           RealType sPot;
515 +           sPot = tokenizer.nextTokenAsDouble();
516 +           sd->setSitePotential(sPot);          
517 +           break;
518 +        }
519          default: {
520                 sprintf(painCave.errMsg,
521                         "DumpReader Error: %s is an unrecognized type\n", type.c_str());
# Line 520 | Line 526 | namespace OpenMD {
526  
527        }
528      }
523 –    
529    }
530    
531  
# Line 613 | Line 618 | namespace OpenMD {
618          sd->setElectricField(eField);          
619          break;
620        }
621 +      case 's' : {
622 +        
623 +        RealType sPot;
624 +        sPot = tokenizer.nextTokenAsDouble();
625 +        sd->setSitePotential(sPot);          
626 +        break;
627 +      }
628        default: {
629          sprintf(painCave.errMsg,
630                  "DumpReader Error: %s is an unrecognized type\n", type.c_str());
# Line 625 | Line 637 | namespace OpenMD {
637    }
638    
639    
640 <  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
640 >    void  DumpReader::readStuntDoubles(std::istream& inputStream) {
641      
642      inputStream.getline(buffer, bufferSize);
643      std::string line(buffer);

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