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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1921 by gezelter, Thu Aug 1 18:23:07 2013 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

# Line 39 | Line 39
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42 +
43 + #include "config.h"
44 +
45 + #ifdef IS_MPI
46 + #include <mpi.h>
47 + #endif
48  
49   #include "io/DumpWriter.hpp"
50   #include "primitives/Molecule.hpp"
# Line 54 | Line 60
60   #define isinf(x) (!_finite(x) && !_isnan(x))
61   #endif
62  
57 – #ifdef IS_MPI
58 – #include <mpi.h>
59 – #endif
60 –
63   using namespace std;
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 70 | 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 119 | 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 168 | 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 302 | 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 360 | 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";  
381        writeFrameProperties(os,
# Line 385 | Line 398 | namespace OpenMD {
398        
399        for (int i = 1; i < nProc; ++i) {
400          // tell processor i to start sending us data:
401 <        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
401 >        MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
402  
403          // receive the length of the string buffer that was
404          // prepared by processor i:        
405          int recvLength;
406 <        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
407 <                             istatus);
406 >        MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
407 >                 &istatus);
408  
409          // create a buffer to receive the data
410          char* recvBuffer = new char[recvLength];
411          if (recvBuffer == NULL) {
412          } else {
413            // receive the data:
414 <          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
415 <                               MPI::ANY_TAG, istatus);
414 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
415 >                               MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
416            // send it to the file:
417            os << recvBuffer;
418            // get rid of the receive buffer:
# Line 411 | Line 424 | namespace OpenMD {
424        int myturn = 0;
425        for (int i = 1; i < nProc; ++i){
426          // wait for the master node to call our number:
427 <        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
427 >        MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
428          if (myturn == worldRank){
429            // send the length of our buffer:
430 <          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
430 >          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
431  
432            // send our buffer:
433 <          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
434 <                               MPI::CHAR, masterNode, 0);
433 >          MPI_Send((void *)buffer.c_str(), sendBufferLength,
434 >                   MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
435  
436          }
437        }
# Line 462 | Line 475 | namespace OpenMD {
475          for (int i = 1; i < nProc; ++i) {
476            
477            // tell processor i to start sending us data:
478 <          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
478 >          MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
479            
480            // receive the length of the string buffer that was
481            // prepared by processor i:        
482            int recvLength;
483 <          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
484 <                               istatus);
483 >          MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
484 >                   &istatus);
485            
486            // create a buffer to receive the data
487            char* recvBuffer = new char[recvLength];
488            if (recvBuffer == NULL) {
489            } else {
490              // receive the data:
491 <            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
492 <                                 MPI::ANY_TAG, istatus);
491 >            MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
492 >                     MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
493              // send it to the file:
494              os << recvBuffer;
495              // get rid of the receive buffer:
# Line 488 | Line 501 | namespace OpenMD {
501          int myturn = 0;
502          for (int i = 1; i < nProc; ++i){
503            // wait for the master node to call our number:
504 <          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
504 >          MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
505            if (myturn == worldRank){
506              // send the length of our buffer:
507 <            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
507 >            MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
508              // send our buffer:
509 <            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
510 <                                 MPI::CHAR, masterNode, 0);
509 >            MPI_Send((void *)buffer.c_str(), sendBufferLength,
510 >                     MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
511            }
512          }
513        }
# Line 705 | Line 718 | namespace OpenMD {
718        }
719      }
720  
721 <
721 >    if (needSitePotential_) {
722 >      if (storageLayout & DataStorage::dslSitePotential) {          
723 >        type += "s";
724 >        RealType sPot = sd->getSitePotential();        
725 >        if (isinf(sPot) || isnan(sPot) ) {      
726 >          sprintf( painCave.errMsg,
727 >                   "DumpWriter detected a numerical error writing the"
728 >                   " site potential for object %s", id.c_str());      
729 >          painCave.isFatal = 1;
730 >          simError();
731 >        }
732 >        sprintf(tempBuffer, " %13e ", sPot);        
733 >        line += tempBuffer;
734 >      }
735 >    }    
736 >    
737      if (needParticlePot_) {
738        if (storageLayout & DataStorage::dslParticlePot) {
739          type += "u";
# Line 731 | Line 759 | namespace OpenMD {
759    }
760  
761    void DumpWriter::writeEor() {
762 <    std::ostream* eorStream;
763 <    
762 >
763 >    std::ostream* eorStream = NULL;
764 >
765   #ifdef IS_MPI
766      if (worldRank == 0) {
767   #endif // is_mpi
# Line 765 | Line 794 | namespace OpenMD {
794   #ifdef IS_MPI
795      if (worldRank == 0) {
796   #endif // is_mpi
768 –
797        buffers.push_back(dumpFile_->rdbuf());
770 –
798        eorStream = createOStream(eorFilename_);
772 –
799        buffers.push_back(eorStream->rdbuf());
774 –        
800   #ifdef IS_MPI
801      }
802   #endif // is_mpi    
803  
804      TeeBuf tbuf(buffers.begin(), buffers.end());
805      std::ostream os(&tbuf);
781 –
806      writeFrame(os);
807  
808   #ifdef IS_MPI
# Line 788 | Line 812 | namespace OpenMD {
812        delete eorStream;
813   #ifdef IS_MPI
814      }
815 < #endif // is_mpi  
792 <    
815 > #endif // is_mpi      
816    }
817  
818    std::ostream* DumpWriter::createOStream(const std::string& filename) {

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