ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/DumpWriter.cpp
(Generate patch)

Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1878 by gezelter, Thu Jun 13 14:26:09 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 302 | Line 302 | namespace OpenMD {
302    void DumpWriter::writeFrame(std::ostream& os) {
303  
304   #ifdef IS_MPI
305 <    MPI_Status istatus;
305 >    MPI::Status istatus;
306   #endif
307  
308      Molecule* mol;
309 <    StuntDouble* integrableObject;
309 >    StuntDouble* sd;
310      SimInfo::MoleculeIterator mi;
311      Molecule::IntegrableObjectIterator ii;
312      RigidBody::AtomIterator ai;
313 –    Atom* atom;
313  
314   #ifndef IS_MPI
315      os << "  <Snapshot>\n";
# Line 318 | Line 317 | namespace OpenMD {
317      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318  
319      os << "    <StuntDoubles>\n";
320 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
321 <
320 >    for (mol = info_->beginMolecule(mi); mol != NULL;
321 >         mol = info_->nextMolecule(mi)) {
322        
323 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
324 <           integrableObject = mol->nextIntegrableObject(ii)) {  
325 <          os << prepareDumpLine(integrableObject);
323 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
324 >           sd = mol->nextIntegrableObject(ii)) {        
325 >          os << prepareDumpLine(sd);
326            
327        }
328      }    
# Line 331 | Line 330 | namespace OpenMD {
330  
331      if (doSiteData_) {
332        os << "    <SiteData>\n";
333 <      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
334 <              
335 <        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
336 <           integrableObject = mol->nextIntegrableObject(ii)) {  
333 >      for (mol = info_->beginMolecule(mi); mol != NULL;
334 >           mol = info_->nextMolecule(mi)) {
335 >              
336 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
337 >           sd = mol->nextIntegrableObject(ii)) {        
338  
339 <          int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
339 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
340            // do one for the IO itself
341 <          os << prepareSiteLine(integrableObject, ioIndex, 0);
341 >          os << prepareSiteLine(sd, ioIndex, 0);
342  
343 <          if (integrableObject->isRigidBody()) {
343 >          if (sd->isRigidBody()) {
344              
345 <            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
345 >            RigidBody* rb = static_cast<RigidBody*>(sd);
346              int siteIndex = 0;
347 <            for (atom = rb->beginAtom(ai); atom != NULL;  
347 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
348                   atom = rb->nextAtom(ai)) {                                            
349                os << prepareSiteLine(atom, ioIndex, siteIndex);
350                siteIndex++;
# Line 358 | Line 358 | namespace OpenMD {
358  
359      os.flush();
360   #else
361 <    //every node prepares the dump lines for integrable objects belong to itself
362 <    std::string buffer;
363 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
364 <
365 <
366 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
367 <           integrableObject = mol->nextIntegrableObject(ii)) {  
368 <          buffer += prepareDumpLine(integrableObject);
369 <      }
370 <    }
371 <    
361 >
362      const int masterNode = 0;
363 <    int nProc;
364 <    MPI_Comm_size(MPI_COMM_WORLD, &nProc);
363 >    int worldRank = MPI::COMM_WORLD.Get_rank();
364 >    int nProc = MPI::COMM_WORLD.Get_size();
365 >
366      if (worldRank == masterNode) {      
367        os << "  <Snapshot>\n";  
368 <      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
368 >      writeFrameProperties(os,
369 >                           info_->getSnapshotManager()->getCurrentSnapshot());
370        os << "    <StuntDoubles>\n";
371 <        
380 <      os << buffer;
371 >    }
372  
373 +    //every node prepares the dump lines for integrable objects belong to itself
374 +    std::string buffer;
375 +    for (mol = info_->beginMolecule(mi); mol != NULL;
376 +         mol = info_->nextMolecule(mi)) {
377 +      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
378 +           sd = mol->nextIntegrableObject(ii)) {        
379 +        buffer += prepareDumpLine(sd);
380 +      }
381 +    }
382 +    
383 +    if (worldRank == masterNode) {      
384 +      os << buffer;
385 +      
386        for (int i = 1; i < nProc; ++i) {
387 +        // tell processor i to start sending us data:
388 +        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
389  
390          // receive the length of the string buffer that was
391 <        // prepared by processor i
386 <
387 <        MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
391 >        // prepared by processor i:        
392          int recvLength;
393 <        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
393 >        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
394 >                             istatus);
395 >
396 >        // create a buffer to receive the data
397          char* recvBuffer = new char[recvLength];
398          if (recvBuffer == NULL) {
399          } else {
400 <          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
400 >          // receive the data:
401 >          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
402 >                               MPI::ANY_TAG, istatus);
403 >          // send it to the file:
404            os << recvBuffer;
405 +          // get rid of the receive buffer:
406            delete [] recvBuffer;
407          }
408        }
398 –      os << "    </StuntDoubles>\n";
399 –      
400 –      os << "  </Snapshot>\n";
401 –      os.flush();
409      } else {
410        int sendBufferLength = buffer.size() + 1;
411        int myturn = 0;
412        for (int i = 1; i < nProc; ++i){
413 <        MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
413 >        // wait for the master node to call our number:
414 >        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
415          if (myturn == worldRank){
416 <          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
417 <          MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
416 >          // send the length of our buffer:
417 >          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
418 >
419 >          // send our buffer:
420 >          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
421 >                               MPI::CHAR, masterNode, 0);
422 >
423          }
424        }
425      }
426 +    
427 +    if (worldRank == masterNode) {      
428 +      os << "    </StuntDoubles>\n";
429 +    }
430  
431 < #endif // is_mpi
431 >    if (doSiteData_) {
432 >      if (worldRank == masterNode) {
433 >        os << "    <SiteData>\n";
434 >      }
435 >      buffer.clear();
436 >      for (mol = info_->beginMolecule(mi); mol != NULL;
437 >           mol = info_->nextMolecule(mi)) {
438 >              
439 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
440 >             sd = mol->nextIntegrableObject(ii)) {      
441 >          
442 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
443 >          // do one for the IO itself
444 >          buffer += prepareSiteLine(sd, ioIndex, 0);
445 >
446 >          if (sd->isRigidBody()) {
447 >            
448 >            RigidBody* rb = static_cast<RigidBody*>(sd);
449 >            int siteIndex = 0;
450 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
451 >                 atom = rb->nextAtom(ai)) {                                            
452 >              buffer += prepareSiteLine(atom, ioIndex, siteIndex);
453 >              siteIndex++;
454 >            }
455 >          }
456 >        }
457 >      }
458  
459 +      if (worldRank == masterNode) {    
460 +        os << buffer;
461 +        
462 +        for (int i = 1; i < nProc; ++i) {
463 +          
464 +          // tell processor i to start sending us data:
465 +          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
466 +          
467 +          // receive the length of the string buffer that was
468 +          // prepared by processor i:        
469 +          int recvLength;
470 +          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
471 +                               istatus);
472 +          
473 +          // create a buffer to receive the data
474 +          char* recvBuffer = new char[recvLength];
475 +          if (recvBuffer == NULL) {
476 +          } else {
477 +            // receive the data:
478 +            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
479 +                                 MPI::ANY_TAG, istatus);
480 +            // send it to the file:
481 +            os << recvBuffer;
482 +            // get rid of the receive buffer:
483 +            delete [] recvBuffer;
484 +          }
485 +        }      
486 +      } else {
487 +        int sendBufferLength = buffer.size() + 1;
488 +        int myturn = 0;
489 +        for (int i = 1; i < nProc; ++i){
490 +          // wait for the master node to call our number:
491 +          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
492 +          if (myturn == worldRank){
493 +            // send the length of our buffer:
494 +            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
495 +            // send our buffer:
496 +            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
497 +                                 MPI::CHAR, masterNode, 0);
498 +          }
499 +        }
500 +      }
501 +      
502 +      if (worldRank == masterNode) {    
503 +        os << "    </SiteData>\n";
504 +      }
505 +    }
506 +    
507 +    if (worldRank == masterNode) {
508 +      os << "  </Snapshot>\n";
509 +      os.flush();
510 +    }
511 +    
512 + #endif // is_mpi
513 +    
514    }
515  
516 <  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
516 >  std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
517          
518 <    int index = integrableObject->getGlobalIntegrableObjectIndex();
518 >    int index = sd->getGlobalIntegrableObjectIndex();
519      std::string type("pv");
520      std::string line;
521      char tempBuffer[4096];
522  
523      Vector3d pos;
524      Vector3d vel;
525 <    pos = integrableObject->getPos();
525 >    pos = sd->getPos();
526  
527      if (isinf(pos[0]) || isnan(pos[0]) ||
528          isinf(pos[1]) || isnan(pos[1]) ||
# Line 436 | Line 534 | namespace OpenMD {
534        simError();
535      }
536  
537 <    vel = integrableObject->getVel();          
537 >    vel = sd->getVel();        
538  
539      if (isinf(vel[0]) || isnan(vel[0]) ||
540          isinf(vel[1]) || isnan(vel[1]) ||
# Line 453 | Line 551 | namespace OpenMD {
551              vel[0], vel[1], vel[2]);                    
552      line += tempBuffer;
553  
554 <    if (integrableObject->isDirectional()) {
554 >    if (sd->isDirectional()) {
555        type += "qj";
556        Quat4d q;
557        Vector3d ji;
558 <      q = integrableObject->getQ();
558 >      q = sd->getQ();
559  
560        if (isinf(q[0]) || isnan(q[0]) ||
561            isinf(q[1]) || isnan(q[1]) ||
# Line 470 | Line 568 | namespace OpenMD {
568          simError();
569        }
570  
571 <      ji = integrableObject->getJ();
571 >      ji = sd->getJ();
572  
573        if (isinf(ji[0]) || isnan(ji[0]) ||
574            isinf(ji[1]) || isnan(ji[1]) ||
# Line 490 | Line 588 | namespace OpenMD {
588  
589      if (needForceVector_) {
590        type += "f";
591 <      Vector3d frc = integrableObject->getFrc();
591 >      Vector3d frc = sd->getFrc();
592        if (isinf(frc[0]) || isnan(frc[0]) ||
593            isinf(frc[1]) || isnan(frc[1]) ||
594            isinf(frc[2]) || isnan(frc[2]) ) {      
# Line 504 | Line 602 | namespace OpenMD {
602                frc[0], frc[1], frc[2]);
603        line += tempBuffer;
604        
605 <      if (integrableObject->isDirectional()) {
605 >      if (sd->isDirectional()) {
606          type += "t";
607 <        Vector3d trq = integrableObject->getTrq();        
607 >        Vector3d trq = sd->getTrq();        
608          if (isinf(trq[0]) || isnan(trq[0]) ||
609              isinf(trq[1]) || isnan(trq[1]) ||
610              isinf(trq[2]) || isnan(trq[2]) ) {      
# Line 526 | Line 624 | namespace OpenMD {
624      return std::string(tempBuffer);
625    }
626  
627 <  std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
627 >  std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628          
629  
630      std::string id;
# Line 534 | Line 632 | namespace OpenMD {
632      std::string line;
633      char tempBuffer[4096];
634  
635 <    if (integrableObject->isRigidBody()) {
635 >    if (sd->isRigidBody()) {
636        sprintf(tempBuffer, "%10d           ", ioIndex);
637        id = std::string(tempBuffer);
638      } else {
# Line 544 | Line 642 | namespace OpenMD {
642                
643      if (needFlucQ_) {
644        type += "cw";
645 <      RealType fqPos = integrableObject->getFlucQPos();
645 >      RealType fqPos = sd->getFlucQPos();
646        if (isinf(fqPos) || isnan(fqPos) ) {      
647          sprintf( painCave.errMsg,
648                   "DumpWriter detected a numerical error writing the"
# Line 555 | Line 653 | namespace OpenMD {
653        sprintf(tempBuffer, " %13e ", fqPos);
654        line += tempBuffer;
655      
656 <      RealType fqVel = integrableObject->getFlucQVel();
656 >      RealType fqVel = sd->getFlucQVel();
657        if (isinf(fqVel) || isnan(fqVel) ) {      
658          sprintf( painCave.errMsg,
659                   "DumpWriter detected a numerical error writing the"
# Line 568 | Line 666 | namespace OpenMD {
666  
667        if (needForceVector_) {
668          type += "g";
669 <        RealType fqFrc = integrableObject->getFlucQFrc();        
669 >        RealType fqFrc = sd->getFlucQFrc();        
670          if (isinf(fqFrc) || isnan(fqFrc) ) {      
671            sprintf( painCave.errMsg,
672                     "DumpWriter detected a numerical error writing the"
# Line 583 | Line 681 | namespace OpenMD {
681  
682      if (needElectricField_) {
683        type += "e";
684 <      Vector3d eField= integrableObject->getElectricField();
684 >      Vector3d eField= sd->getElectricField();
685        if (isinf(eField[0]) || isnan(eField[0]) ||
686            isinf(eField[1]) || isnan(eField[1]) ||
687            isinf(eField[2]) || isnan(eField[2]) ) {      
# Line 601 | Line 699 | namespace OpenMD {
699  
700      if (needParticlePot_) {
701        type += "u";
702 <      RealType particlePot = integrableObject->getParticlePot();
702 >      RealType particlePot = sd->getParticlePot();
703        if (isinf(particlePot) || isnan(particlePot)) {      
704          sprintf( painCave.errMsg,
705                   "DumpWriter detected a numerical error writing the particle "
# Line 628 | Line 726 | namespace OpenMD {
726   #ifdef IS_MPI
727      if (worldRank == 0) {
728   #endif // is_mpi
729 <
729 >      
730        eorStream = createOStream(eorFilename_);
731  
732   #ifdef IS_MPI
733      }
734 < #endif // is_mpi    
735 <
734 > #endif
735 >    
736      writeFrame(*eorStream);
737 <
737 >      
738   #ifdef IS_MPI
739      if (worldRank == 0) {
740 < #endif // is_mpi
740 > #endif
741 >      
742        writeClosing(*eorStream);
743        delete eorStream;
744 +      
745   #ifdef IS_MPI
746      }
747   #endif // is_mpi  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines