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root/OpenMD/branches/development/src/io/DumpReader.cpp
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Comparing branches/development/src/io/DumpReader.cpp (file contents):
Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

# Line 58 | Line 58
58   #include "utils/simError.h"
59   #include "utils/MemoryUtils.hpp"
60   #include "utils/StringTokenizer.hpp"
61 + #include "brains/Thermo.hpp"
62  
63   #ifdef IS_MPI
63 –
64   #include <mpi.h>
65 < #define TAKE_THIS_TAG_CHAR 0
66 < #define TAKE_THIS_TAG_INT 1
65 > #endif
66  
68 – #endif // is_mpi
67  
70 –
68   namespace OpenMD {
69    
70    DumpReader::DumpReader(SimInfo* info, const std::string& filename)
# Line 229 | Line 226 | namespace OpenMD {
226        needVel_ = false;
227      }
228      
229 <    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
229 >    if (storageLayout & DataStorage::dslAmat ||
230 >        storageLayout & DataStorage::dslDipole ||
231 >        storageLayout & DataStorage::dslQuadrupole) {
232        needQuaternion_ = true;
233      } else {
234        needQuaternion_ = false;
# Line 245 | Line 244 | namespace OpenMD {
244  
245      if (needCOMprops_) {
246        Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247 +      Thermo thermo(info_);
248        Vector3d com;
249 –      Vector3d comvel;
250 –      Vector3d comw;
251 –      if (needPos_ && needVel_){
252 –        info_->getComAll(com, comvel);
253 –        comw = info_->getAngularMomentum();
254 –      }else{
255 –        com = info_->getCom();
256 –        comvel = 0.0;
257 –        comw   = 0.0;
258 –      }
259 –      s->setCOMprops(com, comvel, comw);      
260 –    }
249  
250 +      if (needPos_ && needVel_) {
251 +        Vector3d comvel;
252 +        Vector3d comw;
253 +        thermo.getComAll(com, comvel);
254 +        comw = thermo.getAngularMomentum();
255 +      } else {
256 +        com = thermo.getCom();
257 +      }                    
258 +    }
259    }
260    
261    void DumpReader::readSet(int whichFrame) {    
# Line 357 | Line 354 | namespace OpenMD {
354  
355      int index = tokenizer.nextTokenAsInt();
356  
357 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
357 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358  
359 <    if (integrableObject == NULL) {
359 >    if (sd == NULL) {
360        return;
361      }
362      std::string type = tokenizer.nextToken();
# Line 379 | Line 376 | namespace OpenMD {
376        }
377      }
378      
379 <    if (integrableObject->isDirectional()) {
379 >    if (sd->isDirectional()) {
380        if (needQuaternion_) {
381          found = type.find("q");      
382          if (found == std::string::npos) {
# Line 402 | Line 399 | namespace OpenMD {
399              pos[1] = tokenizer.nextTokenAsDouble();
400              pos[2] = tokenizer.nextTokenAsDouble();
401              if (needPos_) {
402 <              integrableObject->setPos(pos);
402 >              sd->setPos(pos);
403              }            
404              break;
405          }
# Line 412 | Line 409 | namespace OpenMD {
409              vel[1] = tokenizer.nextTokenAsDouble();
410              vel[2] = tokenizer.nextTokenAsDouble();
411              if (needVel_) {
412 <              integrableObject->setVel(vel);
412 >              sd->setVel(vel);
413              }
414              break;
415          }
416  
417          case 'q' : {
418             Quat4d q;
419 <           if (integrableObject->isDirectional()) {
419 >           if (sd->isDirectional()) {
420                
421               q[0] = tokenizer.nextTokenAsDouble();
422               q[1] = tokenizer.nextTokenAsDouble();
# Line 438 | Line 435 | namespace OpenMD {
435                
436               q.normalize();
437               if (needQuaternion_) {            
438 <               integrableObject->setQ(q);
438 >               sd->setQ(q);
439               }              
440             }            
441             break;
442          }  
443          case 'j' : {
444            Vector3d ji;
445 <          if (integrableObject->isDirectional()) {
445 >          if (sd->isDirectional()) {
446               ji[0] = tokenizer.nextTokenAsDouble();
447               ji[1] = tokenizer.nextTokenAsDouble();
448               ji[2] = tokenizer.nextTokenAsDouble();
449               if (needAngMom_) {
450 <               integrableObject->setJ(ji);
450 >               sd->setJ(ji);
451               }
452            }
453            break;
# Line 461 | Line 458 | namespace OpenMD {
458            force[0] = tokenizer.nextTokenAsDouble();
459            force[1] = tokenizer.nextTokenAsDouble();
460            force[2] = tokenizer.nextTokenAsDouble();          
461 <          integrableObject->setFrc(force);
461 >          sd->setFrc(force);
462            break;
463          }
464          case 't' : {
# Line 470 | Line 467 | namespace OpenMD {
467             torque[0] = tokenizer.nextTokenAsDouble();
468             torque[1] = tokenizer.nextTokenAsDouble();
469             torque[2] = tokenizer.nextTokenAsDouble();          
470 <           integrableObject->setTrq(torque);          
470 >           sd->setTrq(torque);          
471             break;
472          }
473          case 'u' : {
474  
475             RealType particlePot;
476             particlePot = tokenizer.nextTokenAsDouble();
477 <           integrableObject->setParticlePot(particlePot);          
477 >           sd->setParticlePot(particlePot);          
478             break;
479          }
480          case 'c' : {
481  
482             RealType flucQPos;
483             flucQPos = tokenizer.nextTokenAsDouble();
484 <           integrableObject->setFlucQPos(flucQPos);          
484 >           sd->setFlucQPos(flucQPos);          
485             break;
486          }
487          case 'w' : {
488  
489             RealType flucQVel;
490             flucQVel = tokenizer.nextTokenAsDouble();
491 <           integrableObject->setFlucQVel(flucQVel);          
491 >           sd->setFlucQVel(flucQVel);          
492             break;
493          }
494          case 'g' : {
495  
496             RealType flucQFrc;
497             flucQFrc = tokenizer.nextTokenAsDouble();
498 <           integrableObject->setFlucQFrc(flucQFrc);          
498 >           sd->setFlucQFrc(flucQFrc);          
499             break;
500          }
501          case 'e' : {
# Line 507 | Line 504 | namespace OpenMD {
504             eField[0] = tokenizer.nextTokenAsDouble();
505             eField[1] = tokenizer.nextTokenAsDouble();
506             eField[2] = tokenizer.nextTokenAsDouble();          
507 <           integrableObject->setElectricField(eField);          
507 >           sd->setElectricField(eField);          
508             break;
509          }
510          default: {
# Line 543 | Line 540 | namespace OpenMD {
540       */
541  
542      int index = tokenizer.nextTokenAsInt();
543 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
544 <    if (integrableObject == NULL) {
543 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
544 >    if (sd == NULL) {
545        return;
546      }
550 –    StuntDouble* sd = integrableObject;
547  
548      /**
549       * Test to see if the next token is an integer or not.  If not,
# Line 561 | Line 557 | namespace OpenMD {
557      if (i >> siteIndex) {
558        // chew up this token and parse as an int:
559        siteIndex = tokenizer.nextTokenAsInt();
560 <      RigidBody* rb = static_cast<RigidBody*>(integrableObject);
560 >      RigidBody* rb = static_cast<RigidBody*>(sd);
561        sd = rb->getAtoms()[siteIndex];
562      }
563  
# Line 714 | Line 710 | namespace OpenMD {
710          hmat(2, 2) = tokenizer.nextTokenAsDouble();
711          s->setHmat(hmat);      
712        } else if (propertyName == "Thermostat") {
713 <        RealType chi = tokenizer.nextTokenAsDouble();
714 <        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
715 <        s->setChi(chi);
716 <        s->setIntegralOfChiDt(integralOfChiDt);        
713 >        pair<RealType, RealType> thermostat;
714 >        thermostat.first = tokenizer.nextTokenAsDouble();
715 >        thermostat.second = tokenizer.nextTokenAsDouble();
716 >        s->setThermostat(thermostat);
717       } else if (propertyName == "Barostat") {
718          Mat3x3d eta;
719          eta(0, 0) = tokenizer.nextTokenAsDouble();
# Line 729 | Line 725 | namespace OpenMD {
725          eta(2, 0) = tokenizer.nextTokenAsDouble();
726          eta(2, 1) = tokenizer.nextTokenAsDouble();
727          eta(2, 2) = tokenizer.nextTokenAsDouble();
728 <        s->setEta(eta);
728 >        s->setBarostat(eta);
729        } else {
730          sprintf(painCave.errMsg,
731                  "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());

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