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Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC vs.
Revision 1875 by gezelter, Fri May 17 14:41:42 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>
59 < #endif //is_mpi
59 > #endif
60  
61   using namespace std;
62   namespace OpenMD {
# Line 257 | Line 263 | namespace OpenMD {
263              hmat(0, 2), hmat(1, 2), hmat(2, 2));
264      os << buffer;
265  
266 <    RealType chi = s->getChi();
267 <    RealType integralOfChiDt = s->getIntegralOfChiDt();
268 <    if (isinf(chi) || isnan(chi) ||
269 <        isinf(integralOfChiDt) || isnan(integralOfChiDt)) {      
266 >    pair<RealType, RealType> thermostat = s->getThermostat();
267 >
268 >    if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269 >        isinf(thermostat.second) || isnan(thermostat.second)) {      
270        sprintf( painCave.errMsg,
271                 "DumpWriter detected a numerical error writing the thermostat");
272        painCave.isFatal = 1;
273        simError();
274      }
275 <    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
275 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276 >            thermostat.second);
277      os << buffer;
278  
279      Mat3x3d eta;
280 <    eta = s->getEta();
280 >    eta = s->getBarostat();
281  
282      for (unsigned int i = 0; i < 3; i++) {
283        for (unsigned int j = 0; j < 3; j++) {
# Line 295 | 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;
306 –    Atom* atom;
313  
314   #ifndef IS_MPI
315      os << "  <Snapshot>\n";
# Line 311 | 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 324 | 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 (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
337 <           integrableObject = mol->nextIntegrableObject(ii)) {  
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 351 | Line 358 | namespace OpenMD {
358  
359      os.flush();
360   #else
354 –    //every node prepares the dump lines for integrable objects belong to itself
355 –    std::string buffer;
356 –    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
361  
358 –
359 –      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
360 –           integrableObject = mol->nextIntegrableObject(ii)) {  
361 –          buffer += prepareDumpLine(integrableObject);
362 –      }
363 –    }
364 –    
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 <        
373 <      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
379 <
380 <        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        }
391 –      os << "    </StuntDoubles>\n";
392 –      
393 –      os << "  </Snapshot>\n";
394 –      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 +    if (worldRank == masterNode) {      
427 +      os << "    </StuntDoubles>\n";
428 +    }
429  
430 < #endif // is_mpi
430 >    if (doSiteData_) {
431 >      if (worldRank == masterNode) {
432 >        os << "    <SiteData>\n";
433 >      }
434 >      buffer.clear();
435 >      for (mol = info_->beginMolecule(mi); mol != NULL;
436 >           mol = info_->nextMolecule(mi)) {
437 >              
438 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
439 >             sd = mol->nextIntegrableObject(ii)) {      
440 >          
441 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
442 >          // do one for the IO itself
443 >          buffer += prepareSiteLine(sd, ioIndex, 0);
444  
445 <  }
445 >          if (sd->isRigidBody()) {
446 >            
447 >            RigidBody* rb = static_cast<RigidBody*>(sd);
448 >            int siteIndex = 0;
449 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
450 >                 atom = rb->nextAtom(ai)) {                                            
451 >              buffer += prepareSiteLine(atom, ioIndex, siteIndex);
452 >              siteIndex++;
453 >            }
454 >          }
455 >        }
456 >      }
457  
458 <  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
458 >      if (worldRank == masterNode) {    
459 >        os << buffer;
460 >        
461 >        for (int i = 1; i < nProc; ++i) {
462 >          
463 >          // tell processor i to start sending us data:
464 >          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
465 >          
466 >          // receive the length of the string buffer that was
467 >          // prepared by processor i:        
468 >          int recvLength;
469 >          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
470 >                               istatus);
471 >          
472 >          // create a buffer to receive the data
473 >          char* recvBuffer = new char[recvLength];
474 >          if (recvBuffer == NULL) {
475 >          } else {
476 >            // receive the data:
477 >            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
478 >                                 MPI::ANY_TAG, istatus);
479 >            // send it to the file:
480 >            os << recvBuffer;
481 >            // get rid of the receive buffer:
482 >            delete [] recvBuffer;
483 >          }
484 >        }      
485 >      } else {
486 >        int sendBufferLength = buffer.size() + 1;
487 >        int myturn = 0;
488 >        for (int i = 1; i < nProc; ++i){
489 >          // wait for the master node to call our number:
490 >          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
491 >          if (myturn == worldRank){
492 >            // send the length of our buffer:
493 >            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
494 >            // send our buffer:
495 >            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
496 >                                 MPI::CHAR, masterNode, 0);
497 >          }
498 >        }
499 >      }
500 >      
501 >      if (worldRank == masterNode) {    
502 >        os << "    </SiteData>\n";
503 >      }
504 >    }
505 >    
506 >    if (worldRank == masterNode) {
507 >      os << "  </Snapshot>\n";
508 >      os.flush();
509 >    }
510 >    
511 > #endif // is_mpi
512 >    
513 >  }
514 >
515 >  std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
516          
517 <    int index = integrableObject->getGlobalIntegrableObjectIndex();
517 >    int index = sd->getGlobalIntegrableObjectIndex();
518      std::string type("pv");
519      std::string line;
520      char tempBuffer[4096];
521  
522      Vector3d pos;
523      Vector3d vel;
524 <    pos = integrableObject->getPos();
524 >    pos = sd->getPos();
525  
526      if (isinf(pos[0]) || isnan(pos[0]) ||
527          isinf(pos[1]) || isnan(pos[1]) ||
# Line 429 | Line 533 | namespace OpenMD {
533        simError();
534      }
535  
536 <    vel = integrableObject->getVel();          
536 >    vel = sd->getVel();        
537  
538      if (isinf(vel[0]) || isnan(vel[0]) ||
539          isinf(vel[1]) || isnan(vel[1]) ||
# Line 446 | Line 550 | namespace OpenMD {
550              vel[0], vel[1], vel[2]);                    
551      line += tempBuffer;
552  
553 <    if (integrableObject->isDirectional()) {
553 >    if (sd->isDirectional()) {
554        type += "qj";
555        Quat4d q;
556        Vector3d ji;
557 <      q = integrableObject->getQ();
557 >      q = sd->getQ();
558  
559        if (isinf(q[0]) || isnan(q[0]) ||
560            isinf(q[1]) || isnan(q[1]) ||
# Line 463 | Line 567 | namespace OpenMD {
567          simError();
568        }
569  
570 <      ji = integrableObject->getJ();
570 >      ji = sd->getJ();
571  
572        if (isinf(ji[0]) || isnan(ji[0]) ||
573            isinf(ji[1]) || isnan(ji[1]) ||
# Line 483 | Line 587 | namespace OpenMD {
587  
588      if (needForceVector_) {
589        type += "f";
590 <      Vector3d frc = integrableObject->getFrc();
590 >      Vector3d frc = sd->getFrc();
591        if (isinf(frc[0]) || isnan(frc[0]) ||
592            isinf(frc[1]) || isnan(frc[1]) ||
593            isinf(frc[2]) || isnan(frc[2]) ) {      
# Line 497 | Line 601 | namespace OpenMD {
601                frc[0], frc[1], frc[2]);
602        line += tempBuffer;
603        
604 <      if (integrableObject->isDirectional()) {
604 >      if (sd->isDirectional()) {
605          type += "t";
606 <        Vector3d trq = integrableObject->getTrq();        
606 >        Vector3d trq = sd->getTrq();        
607          if (isinf(trq[0]) || isnan(trq[0]) ||
608              isinf(trq[1]) || isnan(trq[1]) ||
609              isinf(trq[2]) || isnan(trq[2]) ) {      
# Line 519 | Line 623 | namespace OpenMD {
623      return std::string(tempBuffer);
624    }
625  
626 <  std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
626 >  std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
627          
628  
629      std::string id;
# Line 527 | Line 631 | namespace OpenMD {
631      std::string line;
632      char tempBuffer[4096];
633  
634 <    if (integrableObject->isRigidBody()) {
634 >    if (sd->isRigidBody()) {
635        sprintf(tempBuffer, "%10d           ", ioIndex);
636        id = std::string(tempBuffer);
637      } else {
# Line 537 | Line 641 | namespace OpenMD {
641                
642      if (needFlucQ_) {
643        type += "cw";
644 <      RealType fqPos = integrableObject->getFlucQPos();
644 >      RealType fqPos = sd->getFlucQPos();
645        if (isinf(fqPos) || isnan(fqPos) ) {      
646          sprintf( painCave.errMsg,
647                   "DumpWriter detected a numerical error writing the"
# Line 548 | Line 652 | namespace OpenMD {
652        sprintf(tempBuffer, " %13e ", fqPos);
653        line += tempBuffer;
654      
655 <      RealType fqVel = integrableObject->getFlucQVel();
655 >      RealType fqVel = sd->getFlucQVel();
656        if (isinf(fqVel) || isnan(fqVel) ) {      
657          sprintf( painCave.errMsg,
658                   "DumpWriter detected a numerical error writing the"
# Line 561 | Line 665 | namespace OpenMD {
665  
666        if (needForceVector_) {
667          type += "g";
668 <        RealType fqFrc = integrableObject->getFlucQFrc();        
668 >        RealType fqFrc = sd->getFlucQFrc();        
669          if (isinf(fqFrc) || isnan(fqFrc) ) {      
670            sprintf( painCave.errMsg,
671                     "DumpWriter detected a numerical error writing the"
# Line 576 | Line 680 | namespace OpenMD {
680  
681      if (needElectricField_) {
682        type += "e";
683 <      Vector3d eField= integrableObject->getElectricField();
683 >      Vector3d eField= sd->getElectricField();
684        if (isinf(eField[0]) || isnan(eField[0]) ||
685            isinf(eField[1]) || isnan(eField[1]) ||
686            isinf(eField[2]) || isnan(eField[2]) ) {      
# Line 594 | Line 698 | namespace OpenMD {
698  
699      if (needParticlePot_) {
700        type += "u";
701 <      RealType particlePot = integrableObject->getParticlePot();
701 >      RealType particlePot = sd->getParticlePot();
702        if (isinf(particlePot) || isnan(particlePot)) {      
703          sprintf( painCave.errMsg,
704                   "DumpWriter detected a numerical error writing the particle "
# Line 621 | Line 725 | namespace OpenMD {
725   #ifdef IS_MPI
726      if (worldRank == 0) {
727   #endif // is_mpi
728 <
728 >      
729        eorStream = createOStream(eorFilename_);
730 <
730 >      writeFrame(*eorStream);
731 >      
732   #ifdef IS_MPI
733      }
629 – #endif // is_mpi    
630 –
631 –    writeFrame(*eorStream);
632 –
633 – #ifdef IS_MPI
734      if (worldRank == 0) {
735   #endif // is_mpi
736 +
737        writeClosing(*eorStream);
738        delete eorStream;
739 +
740   #ifdef IS_MPI
741      }
742   #endif // is_mpi  
# Line 678 | Line 780 | namespace OpenMD {
780    std::ostream* DumpWriter::createOStream(const std::string& filename) {
781  
782      std::ostream* newOStream;
783 < #ifdef HAVE_LIBZ
783 > #ifdef HAVE_ZLIB
784      if (needCompression_) {
785        newOStream = new ogzstream(filename.c_str());
786      } else {

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