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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 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   */
42 +
43 + #include "config.h"
44 +
45 + #ifdef IS_MPI
46 + #include <mpi.h>
47 + #endif
48  
49   #include "io/DumpWriter.hpp"
50   #include "primitives/Molecule.hpp"
# Line 54 | Line 60
60   #define isinf(x) (!_finite(x) && !_isnan(x))
61   #endif
62  
57 – #ifdef IS_MPI
58 – #include <mpi.h>
59 – #endif
60 –
63   using namespace std;
64   namespace OpenMD {
65  
# Line 310 | Line 312 | namespace OpenMD {
312      SimInfo::MoleculeIterator mi;
313      Molecule::IntegrableObjectIterator ii;
314      RigidBody::AtomIterator ai;
313 –    Atom* atom;
315  
316   #ifndef IS_MPI
317      os << "  <Snapshot>\n";
# Line 318 | Line 319 | namespace OpenMD {
319      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320  
321      os << "    <StuntDoubles>\n";
322 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
323 <
322 >    for (mol = info_->beginMolecule(mi); mol != NULL;
323 >         mol = info_->nextMolecule(mi)) {
324        
325        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
326             sd = mol->nextIntegrableObject(ii)) {        
# Line 335 | Line 336 | namespace OpenMD {
336             mol = info_->nextMolecule(mi)) {
337                
338          for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
339 <             sd = mol->nextIntegrableObject(ii)) {      
340 <          
339 >           sd = mol->nextIntegrableObject(ii)) {        
340 >
341            int ioIndex = sd->getGlobalIntegrableObjectIndex();
342            // do one for the IO itself
343            os << prepareSiteLine(sd, ioIndex, 0);
# Line 345 | Line 346 | namespace OpenMD {
346              
347              RigidBody* rb = static_cast<RigidBody*>(sd);
348              int siteIndex = 0;
349 <            for (atom = rb->beginAtom(ai); atom != NULL;  
349 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
350                   atom = rb->nextAtom(ai)) {                                            
351                os << prepareSiteLine(atom, ioIndex, siteIndex);
352                siteIndex++;
# Line 420 | Line 421 | namespace OpenMD {
421            // send our buffer:
422            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
423                                 MPI::CHAR, masterNode, 0);
424 +
425          }
426        }
427      }
# Line 447 | Line 449 | namespace OpenMD {
449              
450              RigidBody* rb = static_cast<RigidBody*>(sd);
451              int siteIndex = 0;
452 <            for (atom = rb->beginAtom(ai); atom != NULL;  
452 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
453                   atom = rb->nextAtom(ai)) {                                            
454                buffer += prepareSiteLine(atom, ioIndex, siteIndex);
455                siteIndex++;
# Line 625 | Line 627 | namespace OpenMD {
627    }
628  
629    std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
630 <        
630 >    int storageLayout = info_->getSnapshotManager()->getStorageLayout();
631  
632      std::string id;
633      std::string type;
# Line 641 | Line 643 | namespace OpenMD {
643      }
644                
645      if (needFlucQ_) {
646 <      type += "cw";
647 <      RealType fqPos = sd->getFlucQPos();
648 <      if (isinf(fqPos) || isnan(fqPos) ) {      
649 <        sprintf( painCave.errMsg,
650 <                 "DumpWriter detected a numerical error writing the"
651 <                 " fluctuating charge for object %s", id.c_str());      
652 <        painCave.isFatal = 1;
653 <        simError();
654 <      }
655 <      sprintf(tempBuffer, " %13e ", fqPos);
656 <      line += tempBuffer;
657 <    
658 <      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;
646 >      if (storageLayout & DataStorage::dslFlucQPosition) {
647 >        type += "c";
648 >        RealType fqPos = sd->getFlucQPos();
649 >        if (isinf(fqPos) || isnan(fqPos) ) {      
650 >          sprintf( painCave.errMsg,
651 >                   "DumpWriter detected a numerical error writing the"
652 >                   " fluctuating charge for object %s", id.c_str());      
653 >          painCave.isFatal = 1;
654 >          simError();
655 >        }
656 >        sprintf(tempBuffer, " %13e ", fqPos);
657 >        line += tempBuffer;
658 >      }
659  
660 <      if (needForceVector_) {
661 <        type += "g";
662 <        RealType fqFrc = sd->getFlucQFrc();        
663 <        if (isinf(fqFrc) || isnan(fqFrc) ) {      
660 >      if (storageLayout & DataStorage::dslFlucQVelocity) {
661 >        type += "w";    
662 >        RealType fqVel = sd->getFlucQVel();
663 >        if (isinf(fqVel) || isnan(fqVel) ) {      
664            sprintf( painCave.errMsg,
665                     "DumpWriter detected a numerical error writing the"
666 <                   " fluctuating charge force for object %s", id.c_str());      
666 >                   " fluctuating charge velocity for object %s", id.c_str());      
667            painCave.isFatal = 1;
668            simError();
669          }
670 <        sprintf(tempBuffer, " %13e ", fqFrc);        
670 >        sprintf(tempBuffer, " %13e ", fqVel);
671          line += tempBuffer;
672        }
680 –    }
673  
674 +      if (needForceVector_) {
675 +        if (storageLayout & DataStorage::dslFlucQForce) {          
676 +          type += "g";
677 +          RealType fqFrc = sd->getFlucQFrc();        
678 +          if (isinf(fqFrc) || isnan(fqFrc) ) {      
679 +            sprintf( painCave.errMsg,
680 +                     "DumpWriter detected a numerical error writing the"
681 +                     " fluctuating charge force for object %s", id.c_str());      
682 +            painCave.isFatal = 1;
683 +            simError();
684 +          }
685 +          sprintf(tempBuffer, " %13e ", fqFrc);        
686 +          line += tempBuffer;
687 +        }
688 +      }
689 +    }
690 +    
691      if (needElectricField_) {
692 <      type += "e";
693 <      Vector3d eField= sd->getElectricField();
694 <      if (isinf(eField[0]) || isnan(eField[0]) ||
695 <          isinf(eField[1]) || isnan(eField[1]) ||
696 <          isinf(eField[2]) || isnan(eField[2]) ) {      
697 <        sprintf( painCave.errMsg,
698 <                 "DumpWriter detected a numerical error writing the electric"
699 <                 " field for object %s", id.c_str());      
700 <        painCave.isFatal = 1;
701 <        simError();
692 >      if (storageLayout & DataStorage::dslElectricField) {
693 >        type += "e";
694 >        Vector3d eField= sd->getElectricField();
695 >        if (isinf(eField[0]) || isnan(eField[0]) ||
696 >            isinf(eField[1]) || isnan(eField[1]) ||
697 >            isinf(eField[2]) || isnan(eField[2]) ) {      
698 >          sprintf( painCave.errMsg,
699 >                   "DumpWriter detected a numerical error writing the electric"
700 >                   " field for object %s", id.c_str());      
701 >          painCave.isFatal = 1;
702 >          simError();
703 >        }
704 >        sprintf(tempBuffer, " %13e %13e %13e",
705 >                eField[0], eField[1], eField[2]);
706 >        line += tempBuffer;
707        }
694 –      sprintf(tempBuffer, " %13e %13e %13e",
695 –              eField[0], eField[1], eField[2]);
696 –      line += tempBuffer;
708      }
709  
710  
711      if (needParticlePot_) {
712 <      type += "u";
713 <      RealType particlePot = sd->getParticlePot();
714 <      if (isinf(particlePot) || isnan(particlePot)) {      
715 <        sprintf( painCave.errMsg,
716 <                 "DumpWriter detected a numerical error writing the particle "
717 <                 " potential for object %s", id.c_str());      
718 <        painCave.isFatal = 1;
719 <        simError();
712 >      if (storageLayout & DataStorage::dslParticlePot) {
713 >        type += "u";
714 >        RealType particlePot = sd->getParticlePot();
715 >        if (isinf(particlePot) || isnan(particlePot)) {      
716 >          sprintf( painCave.errMsg,
717 >                   "DumpWriter detected a numerical error writing the particle "
718 >                   " potential for object %s", id.c_str());      
719 >          painCave.isFatal = 1;
720 >          simError();
721 >        }
722 >        sprintf(tempBuffer, " %13e", particlePot);
723 >        line += tempBuffer;
724        }
710 –      sprintf(tempBuffer, " %13e", particlePot);
711 –      line += tempBuffer;
725      }
726 <    
714 <
726 >  
727      sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
728      return std::string(tempBuffer);
729    }
# Line 726 | Line 738 | namespace OpenMD {
738   #ifdef IS_MPI
739      if (worldRank == 0) {
740   #endif // is_mpi
741 <
741 >      
742        eorStream = createOStream(eorFilename_);
743  
744   #ifdef IS_MPI
745      }
746 < #endif // is_mpi    
747 <
746 > #endif
747 >    
748      writeFrame(*eorStream);
749 <
749 >      
750   #ifdef IS_MPI
751      if (worldRank == 0) {
752 < #endif // is_mpi
752 > #endif
753 >      
754        writeClosing(*eorStream);
755        delete eorStream;
756 +      
757   #ifdef IS_MPI
758      }
759   #endif // is_mpi  

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