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Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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 "io/DumpWriter.hpp"
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 58 | Line 65 | namespace OpenMD {
65      : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
66  
67      Globals* simParams = info->getSimParams();
68 <    needCompression_ = simParams->getCompressDumpFile();
69 <    needForceVector_ = simParams->getOutputForceVector();
68 >    needCompression_   = simParams->getCompressDumpFile();
69 >    needForceVector_   = simParams->getOutputForceVector();
70 >    needParticlePot_   = simParams->getOutputParticlePotential();
71 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
72 >    needElectricField_ = simParams->getOutputElectricField();
73 >
74 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75 >      doSiteData_ = true;
76 >    } else {
77 >      doSiteData_ = false;
78 >    }
79 >
80      createDumpFile_ = true;
81   #ifdef HAVE_LIBZ
82      if (needCompression_) {
# Line 97 | Line 114 | namespace OpenMD {
114      Globals* simParams = info->getSimParams();
115      eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
116  
117 <    needCompression_ = simParams->getCompressDumpFile();
118 <    needForceVector_ = simParams->getOutputForceVector();
117 >    needCompression_   = simParams->getCompressDumpFile();
118 >    needForceVector_   = simParams->getOutputForceVector();
119 >    needParticlePot_   = simParams->getOutputParticlePotential();
120 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
121 >    needElectricField_ = simParams->getOutputElectricField();
122 >
123 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124 >      doSiteData_ = true;
125 >    } else {
126 >      doSiteData_ = false;
127 >    }
128 >
129      createDumpFile_ = true;
130   #ifdef HAVE_LIBZ
131      if (needCompression_) {
# Line 136 | Line 163 | namespace OpenMD {
163      Globals* simParams = info->getSimParams();
164      eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
165      
166 <    needCompression_ = simParams->getCompressDumpFile();
167 <    needForceVector_ = simParams->getOutputForceVector();
168 <    
166 >    needCompression_   = simParams->getCompressDumpFile();
167 >    needForceVector_   = simParams->getOutputForceVector();
168 >    needParticlePot_   = simParams->getOutputParticlePotential();
169 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
170 >    needElectricField_ = simParams->getOutputElectricField();
171 >
172 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173 >      doSiteData_ = true;
174 >    } else {
175 >      doSiteData_ = false;
176 >    }
177 >
178   #ifdef HAVE_LIBZ
179      if (needCompression_) {
180        filename_ += ".gz";
# Line 227 | 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 265 | 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;
314  
315   #ifndef IS_MPI
316      os << "  <Snapshot>\n";
# Line 282 | 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      }    
330      os << "    </StuntDoubles>\n";
331 <    
331 >
332 >    if (doSiteData_) {
333 >      os << "    <SiteData>\n";
334 >      for (mol = info_->beginMolecule(mi); mol != NULL;
335 >           mol = info_->nextMolecule(mi)) {
336 >              
337 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
338 >           sd = mol->nextIntegrableObject(ii)) {        
339 >
340 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
341 >          // do one for the IO itself
342 >          os << prepareSiteLine(sd, ioIndex, 0);
343 >
344 >          if (sd->isRigidBody()) {
345 >            
346 >            RigidBody* rb = static_cast<RigidBody*>(sd);
347 >            int siteIndex = 0;
348 >            for (atom = rb->beginAtom(ai); atom != NULL;  
349 >                 atom = rb->nextAtom(ai)) {                                            
350 >              os << prepareSiteLine(atom, ioIndex, siteIndex);
351 >              siteIndex++;
352 >            }
353 >          }
354 >        }
355 >      }    
356 >      os << "    </SiteData>\n";
357 >    }
358      os << "  </Snapshot>\n";
359  
360      os.flush();
361   #else
297 –    //every node prepares the dump lines for integrable objects belong to itself
298 –    std::string buffer;
299 –    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
362  
301 –
302 –      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303 –           integrableObject = mol->nextIntegrableObject(ii)) {  
304 –          buffer += prepareDumpLine(integrableObject);
305 –      }
306 –    }
307 –    
363      const int masterNode = 0;
364 +    int worldRank = MPI::COMM_WORLD.Get_rank();
365 +    int nProc = MPI::COMM_WORLD.Get_size();
366  
367      if (worldRank == masterNode) {      
368        os << "  <Snapshot>\n";  
369 <      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
369 >      writeFrameProperties(os,
370 >                           info_->getSnapshotManager()->getCurrentSnapshot());
371        os << "    <StuntDoubles>\n";
372 <        
315 <      os << buffer;
372 >    }
373  
374 <      int nProc;
375 <      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
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 >    
384 >    if (worldRank == masterNode) {      
385 >      os << buffer;
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
323 <
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        }
334 –      os << "    </StuntDoubles>\n";
335 –      
336 –      os << "  </Snapshot>\n";
337 –      os.flush();
410      } else {
411        int sendBufferLength = buffer.size() + 1;
412 <      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
413 <      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
412 >      int myturn = 0;
413 >      for (int i = 1; i < nProc; ++i){
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 >          // 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 366 | 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 383 | 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 400 | 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 420 | Line 588 | namespace OpenMD {
588  
589      if (needForceVector_) {
590        type += "f";
591 <      Vector3d frc;
424 <
425 <      frc = integrableObject->getFrc();
426 <
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 437 | 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;
443 <        
444 <        trq = integrableObject->getTrq();
445 <        
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 451 | Line 613 | namespace OpenMD {
613                     " for object %d", index);      
614            painCave.isFatal = 1;
615            simError();
616 <        }
455 <        
616 >        }        
617          sprintf(tempBuffer, " %13e %13e %13e",
618                  trq[0], trq[1], trq[2]);
619          line += tempBuffer;
620        }      
621      }
622 <    
622 >
623      sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
624      return std::string(tempBuffer);
625    }
626  
627 +  std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628 +        
629 +
630 +    std::string id;
631 +    std::string type;
632 +    std::string line;
633 +    char tempBuffer[4096];
634 +
635 +    if (sd->isRigidBody()) {
636 +      sprintf(tempBuffer, "%10d           ", ioIndex);
637 +      id = std::string(tempBuffer);
638 +    } else {
639 +      sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
640 +      id = std::string(tempBuffer);
641 +    }
642 +              
643 +    if (needFlucQ_) {
644 +      type += "cw";
645 +      RealType fqPos = sd->getFlucQPos();
646 +      if (isinf(fqPos) || isnan(fqPos) ) {      
647 +        sprintf( painCave.errMsg,
648 +                 "DumpWriter detected a numerical error writing the"
649 +                 " fluctuating charge for object %s", id.c_str());      
650 +        painCave.isFatal = 1;
651 +        simError();
652 +      }
653 +      sprintf(tempBuffer, " %13e ", fqPos);
654 +      line += tempBuffer;
655 +    
656 +      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;
666 +
667 +      if (needForceVector_) {
668 +        type += "g";
669 +        RealType fqFrc = sd->getFlucQFrc();        
670 +        if (isinf(fqFrc) || isnan(fqFrc) ) {      
671 +          sprintf( painCave.errMsg,
672 +                   "DumpWriter detected a numerical error writing the"
673 +                   " fluctuating charge force for object %s", id.c_str());      
674 +          painCave.isFatal = 1;
675 +          simError();
676 +        }
677 +        sprintf(tempBuffer, " %13e ", fqFrc);        
678 +        line += tempBuffer;
679 +      }
680 +    }
681 +
682 +    if (needElectricField_) {
683 +      type += "e";
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]) ) {      
688 +        sprintf( painCave.errMsg,
689 +                 "DumpWriter detected a numerical error writing the electric"
690 +                 " field for object %s", id.c_str());      
691 +        painCave.isFatal = 1;
692 +        simError();
693 +      }
694 +      sprintf(tempBuffer, " %13e %13e %13e",
695 +              eField[0], eField[1], eField[2]);
696 +      line += tempBuffer;
697 +    }
698 +
699 +
700 +    if (needParticlePot_) {
701 +      type += "u";
702 +      RealType particlePot = sd->getParticlePot();
703 +      if (isinf(particlePot) || isnan(particlePot)) {      
704 +        sprintf( painCave.errMsg,
705 +                 "DumpWriter detected a numerical error writing the particle "
706 +                 " potential for object %s", id.c_str());      
707 +        painCave.isFatal = 1;
708 +        simError();
709 +      }
710 +      sprintf(tempBuffer, " %13e", particlePot);
711 +      line += tempBuffer;
712 +    }
713 +    
714 +
715 +    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
716 +    return std::string(tempBuffer);
717 +  }
718 +
719    void DumpWriter::writeDump() {
720      writeFrame(*dumpFile_);
721    }
# Line 473 | 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      }
481 – #endif // is_mpi    
482 –
483 –    writeFrame(*eorStream);
484 –
485 – #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 530 | 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 {
# Line 540 | Line 791 | namespace OpenMD {
791      newOStream = new std::ofstream(filename.c_str());
792   #endif
793      //write out MetaData first
794 <    (*newOStream) << "<OpenMD version=1>" << std::endl;
794 >    (*newOStream) << "<OpenMD version=2>" << std::endl;
795      (*newOStream) << "  <MetaData>" << std::endl;
796      (*newOStream) << info_->getRawMetaData();
797      (*newOStream) << "  </MetaData>" << std::endl;

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