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Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 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 44 | Line 44
44   #include "primitives/Molecule.hpp"
45   #include "utils/simError.h"
46   #include "io/basic_teebuf.hpp"
47 + #ifdef HAVE_ZLIB
48   #include "io/gzstream.hpp"
49 + #endif
50   #include "io/Globals.hpp"
51  
52 + #ifdef _MSC_VER
53 + #define isnan(x) _isnan((x))
54 + #define isinf(x) (!_finite(x) && !_isnan(x))
55 + #endif
56  
57   #ifdef IS_MPI
58   #include <mpi.h>
# Line 296 | 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;
# Line 315 | Line 321 | namespace OpenMD {
321      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322  
323        
324 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
325 <           integrableObject = mol->nextIntegrableObject(ii)) {  
326 <          os << prepareDumpLine(integrableObject);
324 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
325 >           sd = mol->nextIntegrableObject(ii)) {        
326 >          os << prepareDumpLine(sd);
327            
328        }
329      }    
# Line 325 | Line 331 | namespace OpenMD {
331  
332      if (doSiteData_) {
333        os << "    <SiteData>\n";
334 <      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
334 >      for (mol = info_->beginMolecule(mi); mol != NULL;
335 >           mol = info_->nextMolecule(mi)) {
336                
337 <        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
338 <           integrableObject = mol->nextIntegrableObject(ii)) {  
337 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
338 >           sd = mol->nextIntegrableObject(ii)) {        
339  
340 <          int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
340 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
341            // do one for the IO itself
342 <          os << prepareSiteLine(integrableObject, ioIndex, 0);
342 >          os << prepareSiteLine(sd, ioIndex, 0);
343  
344 <          if (integrableObject->isRigidBody()) {
344 >          if (sd->isRigidBody()) {
345              
346 <            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
346 >            RigidBody* rb = static_cast<RigidBody*>(sd);
347              int siteIndex = 0;
348              for (atom = rb->beginAtom(ai); atom != NULL;  
349                   atom = rb->nextAtom(ai)) {                                            
# Line 352 | Line 359 | namespace OpenMD {
359  
360      os.flush();
361   #else
355 –    //every node prepares the dump lines for integrable objects belong to itself
356 –    std::string buffer;
357 –    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
362  
363 +    const int masterNode = 0;
364 +    int worldRank = MPI::COMM_WORLD.Get_rank();
365 +    int nProc = MPI::COMM_WORLD.Get_size();
366  
367 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
368 <           integrableObject = mol->nextIntegrableObject(ii)) {  
369 <          buffer += prepareDumpLine(integrableObject);
367 >    if (worldRank == masterNode) {      
368 >      os << "  <Snapshot>\n";  
369 >      writeFrameProperties(os,
370 >                           info_->getSnapshotManager()->getCurrentSnapshot());
371 >      os << "    <StuntDoubles>\n";
372 >    }
373 >
374 >    //every node prepares the dump lines for integrable objects belong to itself
375 >    std::string buffer;
376 >    for (mol = info_->beginMolecule(mi); mol != NULL;
377 >         mol = info_->nextMolecule(mi)) {
378 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
379 >           sd = mol->nextIntegrableObject(ii)) {        
380 >        buffer += prepareDumpLine(sd);
381        }
382      }
383      
366 –    const int masterNode = 0;
367 –    int nProc;
368 –    MPI_Comm_size(MPI_COMM_WORLD, &nProc);
384      if (worldRank == masterNode) {      
370 –      os << "  <Snapshot>\n";  
371 –      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
372 –      os << "    <StuntDoubles>\n";
373 –        
385        os << buffer;
386 <
386 >      
387        for (int i = 1; i < nProc; ++i) {
388 +        // tell processor i to start sending us data:
389 +        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
390  
391          // receive the length of the string buffer that was
392 <        // prepared by processor i
380 <
381 <        MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
392 >        // prepared by processor i:        
393          int recvLength;
394 <        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
394 >        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
395 >                             istatus);
396 >
397 >        // create a buffer to receive the data
398          char* recvBuffer = new char[recvLength];
399          if (recvBuffer == NULL) {
400          } else {
401 <          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
401 >          // receive the data:
402 >          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
403 >                               MPI::ANY_TAG, istatus);
404 >          // send it to the file:
405            os << recvBuffer;
406 +          // get rid of the receive buffer:
407            delete [] recvBuffer;
408          }
409        }
392 –      os << "    </StuntDoubles>\n";
393 –      
394 –      os << "  </Snapshot>\n";
395 –      os.flush();
410      } else {
411        int sendBufferLength = buffer.size() + 1;
412        int myturn = 0;
413        for (int i = 1; i < nProc; ++i){
414 <        MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
414 >        // wait for the master node to call our number:
415 >        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
416          if (myturn == worldRank){
417 <          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
418 <          MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
417 >          // send the length of our buffer:
418 >          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
419 >
420 >          // send our buffer:
421 >          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
422 >                               MPI::CHAR, masterNode, 0);
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 = 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 430 | 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 447 | 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 464 | 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 484 | 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 498 | 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 520 | 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 528 | 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 538 | 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 549 | 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 562 | 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 577 | 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 595 | 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 622 | Line 726 | namespace OpenMD {
726   #ifdef IS_MPI
727      if (worldRank == 0) {
728   #endif // is_mpi
729 <
729 >      
730        eorStream = createOStream(eorFilename_);
731 <
731 >      writeFrame(*eorStream);
732 >      
733   #ifdef IS_MPI
734      }
630 – #endif // is_mpi    
631 –
632 –    writeFrame(*eorStream);
633 –
634 – #ifdef IS_MPI
735      if (worldRank == 0) {
736   #endif // is_mpi
737 +
738        writeClosing(*eorStream);
739        delete eorStream;
740 +
741   #ifdef IS_MPI
742      }
743   #endif // is_mpi  
# Line 679 | Line 781 | namespace OpenMD {
781    std::ostream* DumpWriter::createOStream(const std::string& filename) {
782  
783      std::ostream* newOStream;
784 < #ifdef HAVE_LIBZ
784 > #ifdef HAVE_ZLIB
785      if (needCompression_) {
786        newOStream = new ogzstream(filename.c_str());
787      } else {

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