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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 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;
# Line 310 | Line 310 | namespace OpenMD {
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 (sd = mol->beginIntegrableObject(ii); sd != NULL;  
324             sd = mol->nextIntegrableObject(ii)) {        
# 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)) {
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 <          
337 >           sd = mol->nextIntegrableObject(ii)) {        
338 >
339            int ioIndex = sd->getGlobalIntegrableObjectIndex();
340            // do one for the IO itself
341            os << prepareSiteLine(sd, ioIndex, 0);
# Line 344 | Line 344 | namespace OpenMD {
344              
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)) {
361  
362 +    const int masterNode = 0;
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,
369 +                           info_->getSnapshotManager()->getCurrentSnapshot());
370 +      os << "    <StuntDoubles>\n";
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);
379 >        buffer += prepareDumpLine(sd);
380        }
381      }
382      
372 –    const int masterNode = 0;
373 –    int nProc;
374 –    MPI_Comm_size(MPI_COMM_WORLD, &nProc);
383      if (worldRank == masterNode) {      
376 –      os << "  <Snapshot>\n";  
377 –      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
378 –      os << "    <StuntDoubles>\n";
379 –        
384        os << buffer;
385 <
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* sd) {
# 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  

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