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root/OpenMD/trunk/src/io/DumpReader.cpp
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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC vs.
Revision 2000 by gezelter, Sat May 31 22:35:05 2014 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 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
106 > #endif
107 >
108 >      inFile_->~istream();
109        
108 –      delete inFile_;
109 –      
110   #ifdef IS_MPI
111        
112      }
# 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 142 | Line 142 | namespace OpenMD {
142        bool foundOpenSnapshotTag = false;
143        bool foundClosedSnapshotTag = 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::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 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::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);    
293 <      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294 <                            MPI::CHAR, masterNode);    
292 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
293 >      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294 >                MPI_CHAR, masterNode, MPI_COMM_WORLD);    
295        
296        sstream.str(sendBuffer);
297      } else {
298        int sendBufferSize;
299 <      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
299 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300        char * recvBuffer = new char[sendBufferSize+1];
301        assert(recvBuffer);
302        recvBuffer[sendBufferSize] = '\0';
303 <      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
303 >      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304        sstream.str(recvBuffer);
305        delete [] recvBuffer;
306      }      
# Line 507 | Line 510 | namespace OpenMD {
510             sd->setElectricField(eField);          
511             break;
512          }
513 +        case 's' : {
514 +
515 +           RealType sPot;
516 +           sPot = tokenizer.nextTokenAsDouble();
517 +           sd->setSitePotential(sPot);          
518 +           break;
519 +        }
520          default: {
521                 sprintf(painCave.errMsg,
522                         "DumpReader Error: %s is an unrecognized type\n", type.c_str());
# Line 517 | Line 527 | namespace OpenMD {
527  
528        }
529      }
520 –    
530    }
531    
532  
# Line 525 | Line 534 | namespace OpenMD {
534  
535      StringTokenizer tokenizer(line);
536      int nTokens;
537 <    
537 >        
538      nTokens = tokenizer.countTokens();
539      
540      if (nTokens < 2) {  
# Line 557 | Line 566 | namespace OpenMD {
566      if (i >> siteIndex) {
567        // chew up this token and parse as an int:
568        siteIndex = tokenizer.nextTokenAsInt();
569 <      RigidBody* rb = static_cast<RigidBody*>(sd);
570 <      sd = rb->getAtoms()[siteIndex];
569 >
570 >      if (sd->isRigidBody()) {
571 >        RigidBody* rb = static_cast<RigidBody*>(sd);
572 >        sd = rb->getAtoms()[siteIndex];
573 >      }
574      }
575  
576      /**
# Line 607 | Line 619 | namespace OpenMD {
619          sd->setElectricField(eField);          
620          break;
621        }
622 +      case 's' : {
623 +        
624 +        RealType sPot;
625 +        sPot = tokenizer.nextTokenAsDouble();
626 +        sd->setSitePotential(sPot);          
627 +        break;
628 +      }
629        default: {
630          sprintf(painCave.errMsg,
631                  "DumpReader Error: %s is an unrecognized type\n", type.c_str());
# Line 619 | Line 638 | namespace OpenMD {
638    }
639    
640    
641 <  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
641 >    void  DumpReader::readStuntDoubles(std::istream& inputStream) {
642      
643      inputStream.getline(buffer, bufferSize);
644      std::string line(buffer);
# Line 645 | Line 664 | namespace OpenMD {
664  
665    void  DumpReader::readSiteData(std::istream& inputStream) {
666  
648 –    inputStream.getline(buffer, bufferSize);
667      std::string line(buffer);
650 –    
651 –    if (line.find("<SiteData>") == std::string::npos) {
652 –      // site data isn't required for a simulation, so skip
653 –      return;
654 –    }
668  
669 +    // We already found the starting <SiteData> tag or we wouldn't be
670 +    // here, so just start parsing until we get to the ending
671 +    // </SiteData> tag:
672 +    
673      while(inputStream.getline(buffer, bufferSize)) {
674        line = buffer;
675        

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