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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 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   */
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 310 | Line 319 | namespace OpenMD {
319      SimInfo::MoleculeIterator mi;
320      Molecule::IntegrableObjectIterator ii;
321      RigidBody::AtomIterator ai;
313 –    Atom* atom;
322  
323   #ifndef IS_MPI
324      os << "  <Snapshot>\n";
# Line 318 | Line 326 | namespace OpenMD {
326      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327  
328      os << "    <StuntDoubles>\n";
329 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
330 <
329 >    for (mol = info_->beginMolecule(mi); mol != NULL;
330 >         mol = info_->nextMolecule(mi)) {
331        
332        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
333             sd = mol->nextIntegrableObject(ii)) {        
# Line 335 | Line 343 | namespace OpenMD {
343             mol = info_->nextMolecule(mi)) {
344                
345          for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
346 <             sd = mol->nextIntegrableObject(ii)) {      
347 <          
346 >           sd = mol->nextIntegrableObject(ii)) {        
347 >
348            int ioIndex = sd->getGlobalIntegrableObjectIndex();
349            // do one for the IO itself
350            os << prepareSiteLine(sd, ioIndex, 0);
# Line 345 | Line 353 | namespace OpenMD {
353              
354              RigidBody* rb = static_cast<RigidBody*>(sd);
355              int siteIndex = 0;
356 <            for (atom = rb->beginAtom(ai); atom != NULL;  
356 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
357                   atom = rb->nextAtom(ai)) {                                            
358                os << prepareSiteLine(atom, ioIndex, siteIndex);
359                siteIndex++;
# Line 361 | 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 386 | 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 412 | 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        }
438      }
# Line 447 | Line 460 | namespace OpenMD {
460              
461              RigidBody* rb = static_cast<RigidBody*>(sd);
462              int siteIndex = 0;
463 <            for (atom = rb->beginAtom(ai); atom != NULL;  
463 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
464                   atom = rb->nextAtom(ai)) {                                            
465                buffer += prepareSiteLine(atom, ioIndex, siteIndex);
466                siteIndex++;
# 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 625 | Line 638 | namespace OpenMD {
638    }
639  
640    std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
641 <        
641 >    int storageLayout = info_->getSnapshotManager()->getStorageLayout();
642  
643      std::string id;
644      std::string type;
# Line 641 | Line 654 | namespace OpenMD {
654      }
655                
656      if (needFlucQ_) {
657 <      type += "cw";
658 <      RealType fqPos = sd->getFlucQPos();
659 <      if (isinf(fqPos) || isnan(fqPos) ) {      
660 <        sprintf( painCave.errMsg,
661 <                 "DumpWriter detected a numerical error writing the"
662 <                 " fluctuating charge for object %s", id.c_str());      
663 <        painCave.isFatal = 1;
664 <        simError();
665 <      }
666 <      sprintf(tempBuffer, " %13e ", fqPos);
667 <      line += tempBuffer;
668 <    
669 <      RealType fqVel = sd->getFlucQVel();
657 <      if (isinf(fqVel) || isnan(fqVel) ) {      
658 <        sprintf( painCave.errMsg,
659 <                 "DumpWriter detected a numerical error writing the"
660 <                 " fluctuating charge velocity for object %s", id.c_str());      
661 <        painCave.isFatal = 1;
662 <        simError();
663 <      }
664 <      sprintf(tempBuffer, " %13e ", fqVel);
665 <      line += tempBuffer;
657 >      if (storageLayout & DataStorage::dslFlucQPosition) {
658 >        type += "c";
659 >        RealType fqPos = sd->getFlucQPos();
660 >        if (isinf(fqPos) || isnan(fqPos) ) {      
661 >          sprintf( painCave.errMsg,
662 >                   "DumpWriter detected a numerical error writing the"
663 >                   " fluctuating charge for object %s", id.c_str());      
664 >          painCave.isFatal = 1;
665 >          simError();
666 >        }
667 >        sprintf(tempBuffer, " %13e ", fqPos);
668 >        line += tempBuffer;
669 >      }
670  
671 <      if (needForceVector_) {
672 <        type += "g";
673 <        RealType fqFrc = sd->getFlucQFrc();        
674 <        if (isinf(fqFrc) || isnan(fqFrc) ) {      
671 >      if (storageLayout & DataStorage::dslFlucQVelocity) {
672 >        type += "w";    
673 >        RealType fqVel = sd->getFlucQVel();
674 >        if (isinf(fqVel) || isnan(fqVel) ) {      
675            sprintf( painCave.errMsg,
676                     "DumpWriter detected a numerical error writing the"
677 <                   " fluctuating charge force for object %s", id.c_str());      
677 >                   " fluctuating charge velocity for object %s", id.c_str());      
678            painCave.isFatal = 1;
679            simError();
680          }
681 <        sprintf(tempBuffer, " %13e ", fqFrc);        
681 >        sprintf(tempBuffer, " %13e ", fqVel);
682          line += tempBuffer;
683        }
680 –    }
684  
685 +      if (needForceVector_) {
686 +        if (storageLayout & DataStorage::dslFlucQForce) {          
687 +          type += "g";
688 +          RealType fqFrc = sd->getFlucQFrc();        
689 +          if (isinf(fqFrc) || isnan(fqFrc) ) {      
690 +            sprintf( painCave.errMsg,
691 +                     "DumpWriter detected a numerical error writing the"
692 +                     " fluctuating charge force for object %s", id.c_str());      
693 +            painCave.isFatal = 1;
694 +            simError();
695 +          }
696 +          sprintf(tempBuffer, " %13e ", fqFrc);        
697 +          line += tempBuffer;
698 +        }
699 +      }
700 +    }
701 +    
702      if (needElectricField_) {
703 <      type += "e";
704 <      Vector3d eField= sd->getElectricField();
705 <      if (isinf(eField[0]) || isnan(eField[0]) ||
706 <          isinf(eField[1]) || isnan(eField[1]) ||
707 <          isinf(eField[2]) || isnan(eField[2]) ) {      
708 <        sprintf( painCave.errMsg,
709 <                 "DumpWriter detected a numerical error writing the electric"
710 <                 " field for object %s", id.c_str());      
711 <        painCave.isFatal = 1;
712 <        simError();
703 >      if (storageLayout & DataStorage::dslElectricField) {
704 >        type += "e";
705 >        Vector3d eField= sd->getElectricField();
706 >        if (isinf(eField[0]) || isnan(eField[0]) ||
707 >            isinf(eField[1]) || isnan(eField[1]) ||
708 >            isinf(eField[2]) || isnan(eField[2]) ) {      
709 >          sprintf( painCave.errMsg,
710 >                   "DumpWriter detected a numerical error writing the electric"
711 >                   " field for object %s", id.c_str());      
712 >          painCave.isFatal = 1;
713 >          simError();
714 >        }
715 >        sprintf(tempBuffer, " %13e %13e %13e",
716 >                eField[0], eField[1], eField[2]);
717 >        line += tempBuffer;
718        }
694 –      sprintf(tempBuffer, " %13e %13e %13e",
695 –              eField[0], eField[1], eField[2]);
696 –      line += tempBuffer;
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 <      type += "u";
739 <      RealType particlePot = sd->getParticlePot();
740 <      if (isinf(particlePot) || isnan(particlePot)) {      
741 <        sprintf( painCave.errMsg,
742 <                 "DumpWriter detected a numerical error writing the particle "
743 <                 " potential for object %s", id.c_str());      
744 <        painCave.isFatal = 1;
745 <        simError();
738 >      if (storageLayout & DataStorage::dslParticlePot) {
739 >        type += "u";
740 >        RealType particlePot = sd->getParticlePot();
741 >        if (isinf(particlePot) || isnan(particlePot)) {      
742 >          sprintf( painCave.errMsg,
743 >                   "DumpWriter detected a numerical error writing the particle "
744 >                   " potential for object %s", id.c_str());      
745 >          painCave.isFatal = 1;
746 >          simError();
747 >        }
748 >        sprintf(tempBuffer, " %13e", particlePot);
749 >        line += tempBuffer;
750        }
710 –      sprintf(tempBuffer, " %13e", particlePot);
711 –      line += tempBuffer;
751      }
752 <    
714 <
752 >  
753      sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
754      return std::string(tempBuffer);
755    }
# Line 721 | 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
768 <
768 >      
769        eorStream = createOStream(eorFilename_);
770  
771   #ifdef IS_MPI
772      }
773 < #endif // is_mpi    
774 <
773 > #endif
774 >    
775      writeFrame(*eorStream);
776 <
776 >      
777   #ifdef IS_MPI
778      if (worldRank == 0) {
779 < #endif // is_mpi
779 > #endif
780 >      
781        writeClosing(*eorStream);
782        delete eorStream;
783 +      
784   #ifdef IS_MPI
785      }
786   #endif // is_mpi  
# Line 753 | Line 794 | namespace OpenMD {
794   #ifdef IS_MPI
795      if (worldRank == 0) {
796   #endif // is_mpi
756 –
797        buffers.push_back(dumpFile_->rdbuf());
758 –
798        eorStream = createOStream(eorFilename_);
760 –
799        buffers.push_back(eorStream->rdbuf());
762 –        
800   #ifdef IS_MPI
801      }
802   #endif // is_mpi    
803  
804      TeeBuf tbuf(buffers.begin(), buffers.end());
805      std::ostream os(&tbuf);
769 –
806      writeFrame(os);
807  
808   #ifdef IS_MPI
# Line 776 | Line 812 | namespace OpenMD {
812        delete eorStream;
813   #ifdef IS_MPI
814      }
815 < #endif // is_mpi  
780 <    
815 > #endif // is_mpi      
816    }
817  
818    std::ostream* DumpWriter::createOStream(const std::string& filename) {

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