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root/OpenMD/trunk/src/io/DumpReader.cpp
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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC vs.
Revision 1897 by gezelter, Wed Jul 3 20:21:00 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 128 | Line 128 | namespace OpenMD {
128    }
129    
130    void DumpReader::scanFile(void) {
131 <    int lineNo = 0;
131 >
132      std::streampos prevPos;
133      std::streampos  currPos;
134      
# Line 141 | Line 141 | namespace OpenMD {
141        prevPos = currPos;
142        bool foundOpenSnapshotTag = false;
143        bool foundClosedSnapshotTag = false;
144 <      bool foundOpenSiteDataTag = false;
144 >
145 >      int lineNo = 0;
146        while(inFile_->getline(buffer, bufferSize)) {
147          ++lineNo;
148          
# Line 202 | Line 203 | namespace OpenMD {
203   #ifdef IS_MPI
204      }
205      
206 <    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 >    MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
207      
208   #endif // is_mpi
209      
# Line 227 | Line 228 | namespace OpenMD {
228        needVel_ = false;
229      }
230      
231 <    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231 >    if (storageLayout & DataStorage::dslAmat ||
232 >        storageLayout & DataStorage::dslDipole ||
233 >        storageLayout & DataStorage::dslQuadrupole) {
234        needQuaternion_ = true;
235      } else {
236        needQuaternion_ = false;
# Line 286 | Line 289 | namespace OpenMD {
289        }
290  
291        int sendBufferSize = sendBuffer.size();
292 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
293 <      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
292 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);    
293 >      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294 >                            MPI::CHAR, masterNode);    
295        
296        sstream.str(sendBuffer);
297      } else {
298        int sendBufferSize;
299 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
299 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
300        char * recvBuffer = new char[sendBufferSize+1];
301        assert(recvBuffer);
302        recvBuffer[sendBufferSize] = '\0';
303 <      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
303 >      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
304        sstream.str(recvBuffer);
305        delete [] recvBuffer;
306      }      
# Line 524 | Line 528 | namespace OpenMD {
528  
529      StringTokenizer tokenizer(line);
530      int nTokens;
531 <    
531 >        
532      nTokens = tokenizer.countTokens();
533      
534      if (nTokens < 2) {  
# Line 556 | Line 560 | namespace OpenMD {
560      if (i >> siteIndex) {
561        // chew up this token and parse as an int:
562        siteIndex = tokenizer.nextTokenAsInt();
563 <      RigidBody* rb = static_cast<RigidBody*>(sd);
564 <      sd = rb->getAtoms()[siteIndex];
563 >
564 >      if (sd->isRigidBody()) {
565 >        RigidBody* rb = static_cast<RigidBody*>(sd);
566 >        sd = rb->getAtoms()[siteIndex];
567 >      }
568      }
569  
570      /**
# Line 644 | Line 651 | namespace OpenMD {
651  
652    void  DumpReader::readSiteData(std::istream& inputStream) {
653  
647 –    inputStream.getline(buffer, bufferSize);
654      std::string line(buffer);
649 –    
650 –    if (line.find("<SiteData>") == std::string::npos) {
651 –      // site data isn't required for a simulation, so skip
652 –      return;
653 –    }
655  
656 +    // We already found the starting <SiteData> tag or we wouldn't be
657 +    // here, so just start parsing until we get to the ending
658 +    // </SiteData> tag:
659 +    
660      while(inputStream.getline(buffer, bufferSize)) {
661        line = buffer;
662        

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