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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 64 | Line 64 | namespace OpenMD {
64   namespace OpenMD {
65  
66    DumpWriter::DumpWriter(SimInfo* info)
67 <    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
67 >    : info_(info), filename_(info->getDumpFileName()),
68 >      eorFilename_(info->getFinalConfigFileName()){
69  
70      Globals* simParams = info->getSimParams();
71      needCompression_   = simParams->getCompressDumpFile();
# Line 72 | Line 73 | namespace OpenMD {
73      needParticlePot_   = simParams->getOutputParticlePotential();
74      needFlucQ_         = simParams->getOutputFluctuatingCharges();
75      needElectricField_ = simParams->getOutputElectricField();
76 +    needSitePotential_ = simParams->getOutputSitePotential();
77  
78 <    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
78 >    if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
79 >        needSitePotential_) {
80        doSiteData_ = true;
81      } else {
82        doSiteData_ = false;
# Line 121 | Line 124 | namespace OpenMD {
124      needParticlePot_   = simParams->getOutputParticlePotential();
125      needFlucQ_         = simParams->getOutputFluctuatingCharges();
126      needElectricField_ = simParams->getOutputElectricField();
127 +    needSitePotential_ = simParams->getOutputSitePotential();
128  
129 <    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
129 >    if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
130 >        needSitePotential_) {
131        doSiteData_ = true;
132      } else {
133        doSiteData_ = false;
# Line 170 | Line 175 | namespace OpenMD {
175      needParticlePot_   = simParams->getOutputParticlePotential();
176      needFlucQ_         = simParams->getOutputFluctuatingCharges();
177      needElectricField_ = simParams->getOutputElectricField();
178 +    needSitePotential_ = simParams->getOutputSitePotential();
179  
180 <    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
180 >    if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
181 >        needSitePotential_) {
182        doSiteData_ = true;
183      } else {
184        doSiteData_ = false;
# Line 304 | Line 311 | namespace OpenMD {
311    void DumpWriter::writeFrame(std::ostream& os) {
312  
313   #ifdef IS_MPI
314 <    MPI::Status istatus;
314 >    MPI_Status istatus;
315   #endif
316  
317      Molecule* mol;
# Line 362 | Line 369 | namespace OpenMD {
369   #else
370  
371      const int masterNode = 0;
372 <    int worldRank = MPI::COMM_WORLD.Get_rank();
373 <    int nProc = MPI::COMM_WORLD.Get_size();
372 >    int worldRank;
373 >    int nProc;
374 >
375 >    MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376 >    MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377 >
378  
379      if (worldRank == masterNode) {      
380        os << "  <Snapshot>\n";  
# Line 387 | Line 398 | namespace OpenMD {
398        
399        for (int i = 1; i < nProc; ++i) {
400          // tell processor i to start sending us data:
390 –        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
401  
402 +        MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
403 +
404          // receive the length of the string buffer that was
405          // prepared by processor i:        
406          int recvLength;
407 <        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
408 <                             istatus);
407 >        MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
408 >                 &istatus);
409  
410          // create a buffer to receive the data
411          char* recvBuffer = new char[recvLength];
412          if (recvBuffer == NULL) {
413          } else {
414            // receive the data:
415 <          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
416 <                               MPI::ANY_TAG, istatus);
415 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
416 >                               MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
417            // send it to the file:
418            os << recvBuffer;
419            // get rid of the receive buffer:
# Line 413 | Line 425 | namespace OpenMD {
425        int myturn = 0;
426        for (int i = 1; i < nProc; ++i){
427          // wait for the master node to call our number:
428 <        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
428 >        MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
429          if (myturn == worldRank){
430            // send the length of our buffer:
419 –          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
431  
432 +          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
433 +
434            // send our buffer:
435 <          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
436 <                               MPI::CHAR, masterNode, 0);
435 >          MPI_Send((void *)buffer.c_str(), sendBufferLength,
436 >                   MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
437  
438          }
439        }
# Line 464 | Line 477 | namespace OpenMD {
477          for (int i = 1; i < nProc; ++i) {
478            
479            // tell processor i to start sending us data:
480 <          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
480 >          MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
481            
482            // receive the length of the string buffer that was
483            // prepared by processor i:        
484            int recvLength;
485 <          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
486 <                               istatus);
485 >          MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
486 >                   &istatus);
487            
488            // create a buffer to receive the data
489            char* recvBuffer = new char[recvLength];
490            if (recvBuffer == NULL) {
491            } else {
492              // receive the data:
493 <            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
494 <                                 MPI::ANY_TAG, istatus);
493 >            MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
494 >                     MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
495              // send it to the file:
496              os << recvBuffer;
497              // get rid of the receive buffer:
# Line 490 | Line 503 | namespace OpenMD {
503          int myturn = 0;
504          for (int i = 1; i < nProc; ++i){
505            // wait for the master node to call our number:
506 <          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
506 >          MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
507            if (myturn == worldRank){
508              // send the length of our buffer:
509 <            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
509 >            MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
510              // send our buffer:
511 <            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
512 <                                 MPI::CHAR, masterNode, 0);
511 >            MPI_Send((void *)buffer.c_str(), sendBufferLength,
512 >                     MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
513            }
514          }
515        }
# Line 707 | Line 720 | namespace OpenMD {
720        }
721      }
722  
723 <
723 >    if (needSitePotential_) {
724 >      if (storageLayout & DataStorage::dslSitePotential) {          
725 >        type += "s";
726 >        RealType sPot = sd->getSitePotential();        
727 >        if (isinf(sPot) || isnan(sPot) ) {      
728 >          sprintf( painCave.errMsg,
729 >                   "DumpWriter detected a numerical error writing the"
730 >                   " site potential for object %s", id.c_str());      
731 >          painCave.isFatal = 1;
732 >          simError();
733 >        }
734 >        sprintf(tempBuffer, " %13e ", sPot);        
735 >        line += tempBuffer;
736 >      }
737 >    }    
738 >    
739      if (needParticlePot_) {
740        if (storageLayout & DataStorage::dslParticlePot) {
741          type += "u";
# Line 733 | Line 761 | namespace OpenMD {
761    }
762  
763    void DumpWriter::writeEor() {
764 <    std::ostream* eorStream;
765 <    
764 >
765 >    std::ostream* eorStream = NULL;
766 >
767   #ifdef IS_MPI
768      if (worldRank == 0) {
769   #endif // is_mpi
# Line 763 | Line 792 | namespace OpenMD {
792  
793    void DumpWriter::writeDumpAndEor() {
794      std::vector<std::streambuf*> buffers;
795 <    std::ostream* eorStream;
795 >    std::ostream* eorStream = NULL;
796   #ifdef IS_MPI
797      if (worldRank == 0) {
798   #endif // is_mpi
770 –
799        buffers.push_back(dumpFile_->rdbuf());
772 –
800        eorStream = createOStream(eorFilename_);
774 –
801        buffers.push_back(eorStream->rdbuf());
776 –        
802   #ifdef IS_MPI
803      }
804   #endif // is_mpi    
805  
806      TeeBuf tbuf(buffers.begin(), buffers.end());
807      std::ostream os(&tbuf);
783 –
808      writeFrame(os);
809  
810   #ifdef IS_MPI
# Line 790 | Line 814 | namespace OpenMD {
814        delete eorStream;
815   #ifdef IS_MPI
816      }
817 < #endif // is_mpi  
794 <    
817 > #endif // is_mpi      
818    }
819  
820    std::ostream* DumpWriter::createOStream(const std::string& filename) {

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