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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 1769 by gezelter, Mon Jul 9 14:15:52 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 245 | Line 242 | namespace OpenMD {
242  
243      if (needCOMprops_) {
244        Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
245 +      Thermo thermo(info_);
246        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 –    }
247  
248 +      if (needPos_ && needVel_) {
249 +        Vector3d comvel;
250 +        Vector3d comw;
251 +        thermo.getComAll(com, comvel);
252 +        comw = thermo.getAngularMomentum();
253 +      } else {
254 +        com = thermo.getCom();
255 +      }                    
256 +    }
257    }
258    
259    void DumpReader::readSet(int whichFrame) {    
# Line 357 | Line 352 | namespace OpenMD {
352  
353      int index = tokenizer.nextTokenAsInt();
354  
355 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
356  
357 <    if (integrableObject == NULL) {
357 >    if (sd == NULL) {
358        return;
359      }
360      std::string type = tokenizer.nextToken();
# Line 379 | Line 374 | namespace OpenMD {
374        }
375      }
376      
377 <    if (integrableObject->isDirectional()) {
377 >    if (sd->isDirectional()) {
378        if (needQuaternion_) {
379          found = type.find("q");      
380          if (found == std::string::npos) {
# Line 402 | Line 397 | namespace OpenMD {
397              pos[1] = tokenizer.nextTokenAsDouble();
398              pos[2] = tokenizer.nextTokenAsDouble();
399              if (needPos_) {
400 <              integrableObject->setPos(pos);
400 >              sd->setPos(pos);
401              }            
402              break;
403          }
# Line 412 | Line 407 | namespace OpenMD {
407              vel[1] = tokenizer.nextTokenAsDouble();
408              vel[2] = tokenizer.nextTokenAsDouble();
409              if (needVel_) {
410 <              integrableObject->setVel(vel);
410 >              sd->setVel(vel);
411              }
412              break;
413          }
414  
415          case 'q' : {
416             Quat4d q;
417 <           if (integrableObject->isDirectional()) {
417 >           if (sd->isDirectional()) {
418                
419               q[0] = tokenizer.nextTokenAsDouble();
420               q[1] = tokenizer.nextTokenAsDouble();
# Line 438 | Line 433 | namespace OpenMD {
433                
434               q.normalize();
435               if (needQuaternion_) {            
436 <               integrableObject->setQ(q);
436 >               sd->setQ(q);
437               }              
438             }            
439             break;
440          }  
441          case 'j' : {
442            Vector3d ji;
443 <          if (integrableObject->isDirectional()) {
443 >          if (sd->isDirectional()) {
444               ji[0] = tokenizer.nextTokenAsDouble();
445               ji[1] = tokenizer.nextTokenAsDouble();
446               ji[2] = tokenizer.nextTokenAsDouble();
447               if (needAngMom_) {
448 <               integrableObject->setJ(ji);
448 >               sd->setJ(ji);
449               }
450            }
451            break;
# Line 461 | Line 456 | namespace OpenMD {
456            force[0] = tokenizer.nextTokenAsDouble();
457            force[1] = tokenizer.nextTokenAsDouble();
458            force[2] = tokenizer.nextTokenAsDouble();          
459 <          integrableObject->setFrc(force);
459 >          sd->setFrc(force);
460            break;
461          }
462          case 't' : {
# Line 470 | Line 465 | namespace OpenMD {
465             torque[0] = tokenizer.nextTokenAsDouble();
466             torque[1] = tokenizer.nextTokenAsDouble();
467             torque[2] = tokenizer.nextTokenAsDouble();          
468 <           integrableObject->setTrq(torque);          
468 >           sd->setTrq(torque);          
469             break;
470          }
471          case 'u' : {
472  
473             RealType particlePot;
474             particlePot = tokenizer.nextTokenAsDouble();
475 <           integrableObject->setParticlePot(particlePot);          
475 >           sd->setParticlePot(particlePot);          
476             break;
477          }
478          case 'c' : {
479  
480             RealType flucQPos;
481             flucQPos = tokenizer.nextTokenAsDouble();
482 <           integrableObject->setFlucQPos(flucQPos);          
482 >           sd->setFlucQPos(flucQPos);          
483             break;
484          }
485          case 'w' : {
486  
487             RealType flucQVel;
488             flucQVel = tokenizer.nextTokenAsDouble();
489 <           integrableObject->setFlucQVel(flucQVel);          
489 >           sd->setFlucQVel(flucQVel);          
490             break;
491          }
492          case 'g' : {
493  
494             RealType flucQFrc;
495             flucQFrc = tokenizer.nextTokenAsDouble();
496 <           integrableObject->setFlucQFrc(flucQFrc);          
496 >           sd->setFlucQFrc(flucQFrc);          
497             break;
498          }
499          case 'e' : {
# Line 507 | Line 502 | namespace OpenMD {
502             eField[0] = tokenizer.nextTokenAsDouble();
503             eField[1] = tokenizer.nextTokenAsDouble();
504             eField[2] = tokenizer.nextTokenAsDouble();          
505 <           integrableObject->setElectricField(eField);          
505 >           sd->setElectricField(eField);          
506             break;
507          }
508          default: {
# Line 543 | Line 538 | namespace OpenMD {
538       */
539  
540      int index = tokenizer.nextTokenAsInt();
541 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
542 <    if (integrableObject == NULL) {
541 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
542 >    if (sd == NULL) {
543        return;
544      }
550 –    StuntDouble* sd = integrableObject;
545  
546      /**
547       * Test to see if the next token is an integer or not.  If not,
# Line 561 | Line 555 | namespace OpenMD {
555      if (i >> siteIndex) {
556        // chew up this token and parse as an int:
557        siteIndex = tokenizer.nextTokenAsInt();
558 <      RigidBody* rb = static_cast<RigidBody*>(integrableObject);
558 >      RigidBody* rb = static_cast<RigidBody*>(sd);
559        sd = rb->getAtoms()[siteIndex];
560      }
561  
# Line 714 | Line 708 | namespace OpenMD {
708          hmat(2, 2) = tokenizer.nextTokenAsDouble();
709          s->setHmat(hmat);      
710        } else if (propertyName == "Thermostat") {
711 <        RealType chi = tokenizer.nextTokenAsDouble();
712 <        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
713 <        s->setChi(chi);
714 <        s->setIntegralOfChiDt(integralOfChiDt);        
711 >        pair<RealType, RealType> thermostat;
712 >        thermostat.first = tokenizer.nextTokenAsDouble();
713 >        thermostat.second = tokenizer.nextTokenAsDouble();
714 >        s->setThermostat(thermostat);
715       } else if (propertyName == "Barostat") {
716          Mat3x3d eta;
717          eta(0, 0) = tokenizer.nextTokenAsDouble();
# Line 729 | Line 723 | namespace OpenMD {
723          eta(2, 0) = tokenizer.nextTokenAsDouble();
724          eta(2, 1) = tokenizer.nextTokenAsDouble();
725          eta(2, 2) = tokenizer.nextTokenAsDouble();
726 <        s->setEta(eta);
726 >        s->setBarostat(eta);
727        } else {
728          sprintf(painCave.errMsg,
729                  "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());

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