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root/OpenMD/branches/development/src/io/DumpWriter.cpp
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Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC vs.
Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

# Line 65 | Line 65 | namespace OpenMD {
65      needFlucQ_         = simParams->getOutputFluctuatingCharges();
66      needElectricField_ = simParams->getOutputElectricField();
67  
68 +    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
69 +      doSiteData_ = true;
70 +    } else {
71 +      doSiteData_ = false;
72 +    }
73 +
74      createDumpFile_ = true;
75   #ifdef HAVE_LIBZ
76      if (needCompression_) {
# Line 108 | Line 114 | namespace OpenMD {
114      needFlucQ_         = simParams->getOutputFluctuatingCharges();
115      needElectricField_ = simParams->getOutputElectricField();
116  
117 +    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
118 +      doSiteData_ = true;
119 +    } else {
120 +      doSiteData_ = false;
121 +    }
122 +
123      createDumpFile_ = true;
124   #ifdef HAVE_LIBZ
125      if (needCompression_) {
# Line 151 | Line 163 | namespace OpenMD {
163      needFlucQ_         = simParams->getOutputFluctuatingCharges();
164      needElectricField_ = simParams->getOutputElectricField();
165  
166 +    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
167 +      doSiteData_ = true;
168 +    } else {
169 +      doSiteData_ = false;
170 +    }
171 +
172   #ifdef HAVE_LIBZ
173      if (needCompression_) {
174        filename_ += ".gz";
# Line 284 | Line 302 | namespace OpenMD {
302      StuntDouble* integrableObject;
303      SimInfo::MoleculeIterator mi;
304      Molecule::IntegrableObjectIterator ii;
305 +    RigidBody::AtomIterator ai;
306 +    Atom* atom;
307  
308   #ifndef IS_MPI
309      os << "  <Snapshot>\n";
# Line 301 | Line 321 | namespace OpenMD {
321        }
322      }    
323      os << "    </StuntDoubles>\n";
324 <    
324 >
325 >    if (doSiteData_) {
326 >      os << "    <SiteData>\n";
327 >      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
328 >              
329 >        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
330 >           integrableObject = mol->nextIntegrableObject(ii)) {  
331 >
332 >          int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
333 >          // do one for the IO itself
334 >          os << prepareSiteLine(integrableObject, ioIndex, 0);
335 >
336 >          if (integrableObject->isRigidBody()) {
337 >            
338 >            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
339 >            int siteIndex = 0;
340 >            for (atom = rb->beginAtom(ai); atom != NULL;  
341 >                 atom = rb->nextAtom(ai)) {                                            
342 >              os << prepareSiteLine(atom, ioIndex, siteIndex);
343 >              siteIndex++;
344 >            }
345 >          }
346 >        }
347 >      }    
348 >      os << "    </SiteData>\n";
349 >    }
350      os << "  </Snapshot>\n";
351  
352      os.flush();
# Line 470 | Line 515 | namespace OpenMD {
515        }      
516      }
517  
518 <    if (needParticlePot_) {
519 <      type += "u";
520 <      RealType particlePot = integrableObject->getParticlePot();
521 <      if (isinf(particlePot) || isnan(particlePot)) {      
522 <        sprintf( painCave.errMsg,
523 <                 "DumpWriter detected a numerical error writing the particle "
524 <                 " potential for object %d", index);      
525 <        painCave.isFatal = 1;
526 <        simError();
527 <      }
528 <      sprintf(tempBuffer, " %13e", particlePot);
529 <      line += tempBuffer;
518 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
519 >    return std::string(tempBuffer);
520 >  }
521 >
522 >  std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
523 >        
524 >
525 >    std::string id;
526 >    std::string type;
527 >    std::string line;
528 >    char tempBuffer[4096];
529 >
530 >    if (integrableObject->isRigidBody()) {
531 >      sprintf(tempBuffer, "%10d           ", ioIndex);
532 >      id = std::string(tempBuffer);
533 >    } else {
534 >      sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
535 >      id = std::string(tempBuffer);
536      }
537 <    
537 >              
538      if (needFlucQ_) {
539        type += "cw";
540        RealType fqPos = integrableObject->getFlucQPos();
541        if (isinf(fqPos) || isnan(fqPos) ) {      
542          sprintf( painCave.errMsg,
543                   "DumpWriter detected a numerical error writing the"
544 <                 " fluctuating charge for object %d", index);      
544 >                 " fluctuating charge for object %s", id.c_str());      
545          painCave.isFatal = 1;
546          simError();
547        }
# Line 501 | Line 552 | namespace OpenMD {
552        if (isinf(fqVel) || isnan(fqVel) ) {      
553          sprintf( painCave.errMsg,
554                   "DumpWriter detected a numerical error writing the"
555 <                 " fluctuating charge velocity for object %d", index);      
555 >                 " fluctuating charge velocity for object %s", id.c_str());      
556          painCave.isFatal = 1;
557          simError();
558        }
# Line 514 | Line 565 | namespace OpenMD {
565          if (isinf(fqFrc) || isnan(fqFrc) ) {      
566            sprintf( painCave.errMsg,
567                     "DumpWriter detected a numerical error writing the"
568 <                   " fluctuating charge force for object %d", index);      
568 >                   " fluctuating charge force for object %s", id.c_str());      
569            painCave.isFatal = 1;
570            simError();
571          }
# Line 531 | Line 582 | namespace OpenMD {
582            isinf(eField[2]) || isnan(eField[2]) ) {      
583          sprintf( painCave.errMsg,
584                   "DumpWriter detected a numerical error writing the electric"
585 <                 " field for object %d", index);      
585 >                 " field for object %s", id.c_str());      
586          painCave.isFatal = 1;
587          simError();
588        }
# Line 540 | Line 591 | namespace OpenMD {
591        line += tempBuffer;
592      }
593  
594 <    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
594 >
595 >    if (needParticlePot_) {
596 >      type += "u";
597 >      RealType particlePot = integrableObject->getParticlePot();
598 >      if (isinf(particlePot) || isnan(particlePot)) {      
599 >        sprintf( painCave.errMsg,
600 >                 "DumpWriter detected a numerical error writing the particle "
601 >                 " potential for object %s", id.c_str());      
602 >        painCave.isFatal = 1;
603 >        simError();
604 >      }
605 >      sprintf(tempBuffer, " %13e", particlePot);
606 >      line += tempBuffer;
607 >    }
608 >    
609 >
610 >    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
611      return std::string(tempBuffer);
612    }
613  
# Line 621 | Line 688 | namespace OpenMD {
688      newOStream = new std::ofstream(filename.c_str());
689   #endif
690      //write out MetaData first
691 <    (*newOStream) << "<OpenMD version=1>" << std::endl;
691 >    (*newOStream) << "<OpenMD version=2>" << std::endl;
692      (*newOStream) << "  <MetaData>" << std::endl;
693      (*newOStream) << info_->getRawMetaData();
694      (*newOStream) << "  </MetaData>" << std::endl;

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