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root/OpenMD/branches/development/src/io/DumpReader.cpp
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trunk/src/io/DumpReader.cpp (file contents), Revision 1450 by gezelter, Thu Jun 17 19:11:37 2010 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

# Line 36 | Line 36
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).                        
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   #define _LARGEFILE_SOURCE64
# Line 57 | 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
62 –
64   #include <mpi.h>
65 < #define TAKE_THIS_TAG_CHAR 0
65 < #define TAKE_THIS_TAG_INT 1
65 > #endif
66  
67 – #endif // is_mpi
67  
69 –
68   namespace OpenMD {
69    
70    DumpReader::DumpReader(SimInfo* info, const std::string& filename)
# Line 142 | Line 140 | namespace OpenMD {
140        prevPos = currPos;
141        bool foundOpenSnapshotTag = false;
142        bool foundClosedSnapshotTag = false;
143 +      bool foundOpenSiteDataTag = false;
144        while(inFile_->getline(buffer, bufferSize)) {
145          ++lineNo;
146          
# Line 243 | Line 242 | namespace OpenMD {
242  
243      if (needCOMprops_) {
244        Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
245 +      Thermo thermo(info_);
246        Vector3d com;
247 –      Vector3d comvel;
248 –      Vector3d comw;
249 –      if (needPos_ && needVel_){
250 –        info_->getComAll(com, comvel);
251 –        comw = info_->getAngularMomentum();
252 –      }else{
253 –        com = info_->getCom();
254 –        comvel = 0.0;
255 –        comw   = 0.0;
256 –      }
257 –      s->setCOMprops(com, comvel, comw);      
258 –    }
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 324 | Line 321 | namespace OpenMD {
321  
322      inputStream.getline(buffer, bufferSize);
323      line = buffer;
324 <    if (line.find("</Snapshot>") == std::string::npos) {
325 <      sprintf(painCave.errMsg,
326 <              "DumpReader Error: can not find </Snapshot>\n");
327 <      painCave.isFatal = 1;
328 <      simError();
329 <    }        
330 <  
324 >
325 >    if (line.find("<SiteData>") != std::string::npos) {
326 >      //read SiteData
327 >      readSiteData(inputStream);        
328 >    } else {
329 >      if (line.find("</Snapshot>") == std::string::npos) {
330 >        sprintf(painCave.errMsg,
331 >                "DumpReader Error: can not find </Snapshot>\n");
332 >        painCave.isFatal = 1;
333 >        simError();
334 >      }        
335 >    }
336    }
337    
338    void DumpReader::parseDumpLine(const std::string& line) {
# Line 466 | Line 468 | namespace OpenMD {
468             integrableObject->setTrq(torque);          
469             break;
470          }
471 +        case 'u' : {
472 +
473 +           RealType particlePot;
474 +           particlePot = tokenizer.nextTokenAsDouble();
475 +           integrableObject->setParticlePot(particlePot);          
476 +           break;
477 +        }
478 +        case 'c' : {
479 +
480 +           RealType flucQPos;
481 +           flucQPos = tokenizer.nextTokenAsDouble();
482 +           integrableObject->setFlucQPos(flucQPos);          
483 +           break;
484 +        }
485 +        case 'w' : {
486 +
487 +           RealType flucQVel;
488 +           flucQVel = tokenizer.nextTokenAsDouble();
489 +           integrableObject->setFlucQVel(flucQVel);          
490 +           break;
491 +        }
492 +        case 'g' : {
493 +
494 +           RealType flucQFrc;
495 +           flucQFrc = tokenizer.nextTokenAsDouble();
496 +           integrableObject->setFlucQFrc(flucQFrc);          
497 +           break;
498 +        }
499 +        case 'e' : {
500 +
501 +           Vector3d eField;
502 +           eField[0] = tokenizer.nextTokenAsDouble();
503 +           eField[1] = tokenizer.nextTokenAsDouble();
504 +           eField[2] = tokenizer.nextTokenAsDouble();          
505 +           integrableObject->setElectricField(eField);          
506 +           break;
507 +        }
508          default: {
509                 sprintf(painCave.errMsg,
510                         "DumpReader Error: %s is an unrecognized type\n", type.c_str());
# Line 480 | Line 519 | namespace OpenMD {
519    }
520    
521  
522 <  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
522 >  void DumpReader::parseSiteLine(const std::string& line) {
523 >
524 >    StringTokenizer tokenizer(line);
525 >    int nTokens;
526 >    
527 >    nTokens = tokenizer.countTokens();
528 >    
529 >    if (nTokens < 2) {  
530 >      sprintf(painCave.errMsg,
531 >              "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
532 >      painCave.isFatal = 1;
533 >      simError();
534 >    }
535 >
536 >    /**
537 >     * The first token is the global integrable object index.
538 >     */
539 >
540 >    int index = tokenizer.nextTokenAsInt();
541 >    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
542 >    if (integrableObject == NULL) {
543 >      return;
544 >    }
545 >    StuntDouble* sd = integrableObject;
546  
547 +    /**
548 +     * Test to see if the next token is an integer or not.  If not,
549 +     * we've got data on the integrable object itself.  If there is an
550 +     * integer, we're parsing data for a site on a rigid body.
551 +     */
552 +
553 +    std::string indexTest = tokenizer.peekNextToken();
554 +    std::istringstream i(indexTest);
555 +    int siteIndex;
556 +    if (i >> siteIndex) {
557 +      // chew up this token and parse as an int:
558 +      siteIndex = tokenizer.nextTokenAsInt();
559 +      RigidBody* rb = static_cast<RigidBody*>(integrableObject);
560 +      sd = rb->getAtoms()[siteIndex];
561 +    }
562 +
563 +    /**
564 +     * The next token contains information on what follows.
565 +     */
566 +    std::string type = tokenizer.nextToken();
567 +    int size = type.size();
568 +    
569 +    for(int i = 0; i < size; ++i) {
570 +      switch(type[i]) {
571 +        
572 +      case 'u' : {
573 +        
574 +        RealType particlePot;
575 +        particlePot = tokenizer.nextTokenAsDouble();
576 +        sd->setParticlePot(particlePot);
577 +        break;
578 +      }
579 +      case 'c' : {
580 +        
581 +        RealType flucQPos;
582 +        flucQPos = tokenizer.nextTokenAsDouble();
583 +        sd->setFlucQPos(flucQPos);
584 +        break;
585 +      }
586 +      case 'w' : {
587 +        
588 +        RealType flucQVel;
589 +        flucQVel = tokenizer.nextTokenAsDouble();
590 +        sd->setFlucQVel(flucQVel);
591 +        break;
592 +      }
593 +      case 'g' : {
594 +        
595 +        RealType flucQFrc;
596 +        flucQFrc = tokenizer.nextTokenAsDouble();
597 +        sd->setFlucQFrc(flucQFrc);
598 +        break;
599 +      }
600 +      case 'e' : {
601 +        
602 +        Vector3d eField;
603 +        eField[0] = tokenizer.nextTokenAsDouble();
604 +        eField[1] = tokenizer.nextTokenAsDouble();
605 +        eField[2] = tokenizer.nextTokenAsDouble();  
606 +        sd->setElectricField(eField);          
607 +        break;
608 +      }
609 +      default: {
610 +        sprintf(painCave.errMsg,
611 +                "DumpReader Error: %s is an unrecognized type\n", type.c_str());
612 +        painCave.isFatal = 1;
613 +        simError();
614 +        break;  
615 +      }
616 +      }
617 +    }    
618 +  }
619 +  
620 +  
621 +  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
622 +    
623      inputStream.getline(buffer, bufferSize);
624      std::string line(buffer);
625      
# Line 504 | Line 642 | namespace OpenMD {
642    
643    }
644  
645 +  void  DumpReader::readSiteData(std::istream& inputStream) {
646 +
647 +    inputStream.getline(buffer, bufferSize);
648 +    std::string line(buffer);
649 +    
650 +    if (line.find("<SiteData>") == std::string::npos) {
651 +      // site data isn't required for a simulation, so skip
652 +      return;
653 +    }
654 +
655 +    while(inputStream.getline(buffer, bufferSize)) {
656 +      line = buffer;
657 +      
658 +      if(line.find("</SiteData>") != std::string::npos) {
659 +        break;
660 +      }
661 +
662 +      parseSiteLine(line);
663 +    }
664 +  
665 +  }
666 +
667    void DumpReader::readFrameProperties(std::istream& inputStream) {
668  
669      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 549 | Line 709 | namespace OpenMD {
709          hmat(2, 2) = tokenizer.nextTokenAsDouble();
710          s->setHmat(hmat);      
711        } else if (propertyName == "Thermostat") {
712 <        RealType chi = tokenizer.nextTokenAsDouble();
713 <        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
714 <        s->setChi(chi);
715 <        s->setIntegralOfChiDt(integralOfChiDt);        
712 >        pair<RealType, RealType> thermostat;
713 >        thermostat.first = tokenizer.nextTokenAsDouble();
714 >        thermostat.second = tokenizer.nextTokenAsDouble();
715 >        s->setThermostat(thermostat);
716       } else if (propertyName == "Barostat") {
717          Mat3x3d eta;
718          eta(0, 0) = tokenizer.nextTokenAsDouble();
# Line 564 | Line 724 | namespace OpenMD {
724          eta(2, 0) = tokenizer.nextTokenAsDouble();
725          eta(2, 1) = tokenizer.nextTokenAsDouble();
726          eta(2, 2) = tokenizer.nextTokenAsDouble();
727 <        s->setEta(eta);
727 >        s->setBarostat(eta);
728        } else {
729          sprintf(painCave.errMsg,
730                  "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());

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