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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 1875 by gezelter, Fri May 17 14:41:42 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   */
# 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 78 | Line 75 | namespace OpenMD {
75      if (worldRank == 0) {
76   #endif
77        
78 <      inFile_ = new std::ifstream(filename_.c_str());
78 >      inFile_ = new std::ifstream(filename_.c_str(),  
79 >                                  ifstream::in | ifstream::binary);
80        
81        if (inFile_->fail()) {
82          sprintf(painCave.errMsg,
# Line 130 | Line 128 | namespace OpenMD {
128    }
129    
130    void DumpReader::scanFile(void) {
131 <    int lineNo = 0;
131 >
132      std::streampos prevPos;
133      std::streampos  currPos;
134      
# Line 143 | Line 141 | namespace OpenMD {
141        prevPos = currPos;
142        bool foundOpenSnapshotTag = false;
143        bool foundClosedSnapshotTag = false;
144 <      bool foundOpenSiteDataTag = false;
144 >
145 >      int lineNo = 0;
146        while(inFile_->getline(buffer, bufferSize)) {
147          ++lineNo;
148          
# Line 204 | Line 203 | namespace OpenMD {
203   #ifdef IS_MPI
204      }
205      
206 <    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 >    MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
207      
208   #endif // is_mpi
209      
# Line 229 | Line 228 | namespace OpenMD {
228        needVel_ = false;
229      }
230      
231 <    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231 >    if (storageLayout & DataStorage::dslAmat ||
232 >        storageLayout & DataStorage::dslDipole ||
233 >        storageLayout & DataStorage::dslQuadrupole) {
234        needQuaternion_ = true;
235      } else {
236        needQuaternion_ = false;
# Line 245 | Line 246 | namespace OpenMD {
246  
247      if (needCOMprops_) {
248        Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
249 +      Thermo thermo(info_);
250        Vector3d com;
251 <      Vector3d comvel;
252 <      Vector3d comw;
253 <      if (needPos_ && needVel_){
254 <        info_->getComAll(com, comvel);
255 <        comw = info_->getAngularMomentum();
256 <      }else{
257 <        com = info_->getCom();
258 <        comvel = 0.0;
259 <        comw   = 0.0;
258 <      }
259 <      s->setCOMprops(com, comvel, comw);      
251 >
252 >      if (needPos_ && needVel_) {
253 >        Vector3d comvel;
254 >        Vector3d comw;
255 >        thermo.getComAll(com, comvel);
256 >        comw = thermo.getAngularMomentum();
257 >      } else {
258 >        com = thermo.getCom();
259 >      }                    
260      }
261 –
261    }
262    
263    void DumpReader::readSet(int whichFrame) {    
# Line 290 | Line 289 | namespace OpenMD {
289        }
290  
291        int sendBufferSize = sendBuffer.size();
292 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
293 <      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
292 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);    
293 >      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294 >                            MPI::CHAR, masterNode);    
295        
296        sstream.str(sendBuffer);
297      } else {
298        int sendBufferSize;
299 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
299 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
300        char * recvBuffer = new char[sendBufferSize+1];
301        assert(recvBuffer);
302        recvBuffer[sendBufferSize] = '\0';
303 <      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
303 >      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
304        sstream.str(recvBuffer);
305        delete [] recvBuffer;
306      }      
# Line 357 | Line 357 | namespace OpenMD {
357  
358      int index = tokenizer.nextTokenAsInt();
359  
360 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
360 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
361  
362 <    if (integrableObject == NULL) {
362 >    if (sd == NULL) {
363        return;
364      }
365      std::string type = tokenizer.nextToken();
# Line 379 | Line 379 | namespace OpenMD {
379        }
380      }
381      
382 <    if (integrableObject->isDirectional()) {
382 >    if (sd->isDirectional()) {
383        if (needQuaternion_) {
384          found = type.find("q");      
385          if (found == std::string::npos) {
# Line 402 | Line 402 | namespace OpenMD {
402              pos[1] = tokenizer.nextTokenAsDouble();
403              pos[2] = tokenizer.nextTokenAsDouble();
404              if (needPos_) {
405 <              integrableObject->setPos(pos);
405 >              sd->setPos(pos);
406              }            
407              break;
408          }
# Line 412 | Line 412 | namespace OpenMD {
412              vel[1] = tokenizer.nextTokenAsDouble();
413              vel[2] = tokenizer.nextTokenAsDouble();
414              if (needVel_) {
415 <              integrableObject->setVel(vel);
415 >              sd->setVel(vel);
416              }
417              break;
418          }
419  
420          case 'q' : {
421             Quat4d q;
422 <           if (integrableObject->isDirectional()) {
422 >           if (sd->isDirectional()) {
423                
424               q[0] = tokenizer.nextTokenAsDouble();
425               q[1] = tokenizer.nextTokenAsDouble();
# Line 438 | Line 438 | namespace OpenMD {
438                
439               q.normalize();
440               if (needQuaternion_) {            
441 <               integrableObject->setQ(q);
441 >               sd->setQ(q);
442               }              
443             }            
444             break;
445          }  
446          case 'j' : {
447            Vector3d ji;
448 <          if (integrableObject->isDirectional()) {
448 >          if (sd->isDirectional()) {
449               ji[0] = tokenizer.nextTokenAsDouble();
450               ji[1] = tokenizer.nextTokenAsDouble();
451               ji[2] = tokenizer.nextTokenAsDouble();
452               if (needAngMom_) {
453 <               integrableObject->setJ(ji);
453 >               sd->setJ(ji);
454               }
455            }
456            break;
# Line 461 | Line 461 | namespace OpenMD {
461            force[0] = tokenizer.nextTokenAsDouble();
462            force[1] = tokenizer.nextTokenAsDouble();
463            force[2] = tokenizer.nextTokenAsDouble();          
464 <          integrableObject->setFrc(force);
464 >          sd->setFrc(force);
465            break;
466          }
467          case 't' : {
# Line 470 | Line 470 | namespace OpenMD {
470             torque[0] = tokenizer.nextTokenAsDouble();
471             torque[1] = tokenizer.nextTokenAsDouble();
472             torque[2] = tokenizer.nextTokenAsDouble();          
473 <           integrableObject->setTrq(torque);          
473 >           sd->setTrq(torque);          
474             break;
475          }
476          case 'u' : {
477  
478             RealType particlePot;
479             particlePot = tokenizer.nextTokenAsDouble();
480 <           integrableObject->setParticlePot(particlePot);          
480 >           sd->setParticlePot(particlePot);          
481             break;
482          }
483          case 'c' : {
484  
485             RealType flucQPos;
486             flucQPos = tokenizer.nextTokenAsDouble();
487 <           integrableObject->setFlucQPos(flucQPos);          
487 >           sd->setFlucQPos(flucQPos);          
488             break;
489          }
490          case 'w' : {
491  
492             RealType flucQVel;
493             flucQVel = tokenizer.nextTokenAsDouble();
494 <           integrableObject->setFlucQVel(flucQVel);          
494 >           sd->setFlucQVel(flucQVel);          
495             break;
496          }
497          case 'g' : {
498  
499             RealType flucQFrc;
500             flucQFrc = tokenizer.nextTokenAsDouble();
501 <           integrableObject->setFlucQFrc(flucQFrc);          
501 >           sd->setFlucQFrc(flucQFrc);          
502             break;
503          }
504          case 'e' : {
# Line 507 | Line 507 | namespace OpenMD {
507             eField[0] = tokenizer.nextTokenAsDouble();
508             eField[1] = tokenizer.nextTokenAsDouble();
509             eField[2] = tokenizer.nextTokenAsDouble();          
510 <           integrableObject->setElectricField(eField);          
510 >           sd->setElectricField(eField);          
511             break;
512          }
513          default: {
# Line 528 | Line 528 | namespace OpenMD {
528  
529      StringTokenizer tokenizer(line);
530      int nTokens;
531 <    
531 >        
532      nTokens = tokenizer.countTokens();
533      
534      if (nTokens < 2) {  
# Line 543 | Line 543 | namespace OpenMD {
543       */
544  
545      int index = tokenizer.nextTokenAsInt();
546 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
547 <    if (integrableObject == NULL) {
546 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
547 >    if (sd == NULL) {
548        return;
549      }
550 –    StuntDouble* sd = integrableObject;
550  
551      /**
552       * Test to see if the next token is an integer or not.  If not,
# Line 561 | Line 560 | namespace OpenMD {
560      if (i >> siteIndex) {
561        // chew up this token and parse as an int:
562        siteIndex = tokenizer.nextTokenAsInt();
563 <      RigidBody* rb = static_cast<RigidBody*>(integrableObject);
563 >      RigidBody* rb = static_cast<RigidBody*>(sd);
564        sd = rb->getAtoms()[siteIndex];
565      }
566  
# Line 649 | Line 648 | namespace OpenMD {
648  
649    void  DumpReader::readSiteData(std::istream& inputStream) {
650  
652 –    inputStream.getline(buffer, bufferSize);
651      std::string line(buffer);
654 –    
655 –    if (line.find("<SiteData>") == std::string::npos) {
656 –      // site data isn't required for a simulation, so skip
657 –      return;
658 –    }
652  
653 +    // We already found the starting <SiteData> tag or we wouldn't be
654 +    // here, so just start parsing until we get to the ending
655 +    // </SiteData> tag:
656 +    
657      while(inputStream.getline(buffer, bufferSize)) {
658        line = buffer;
659        
# Line 714 | Line 711 | namespace OpenMD {
711          hmat(2, 2) = tokenizer.nextTokenAsDouble();
712          s->setHmat(hmat);      
713        } else if (propertyName == "Thermostat") {
714 <        RealType chi = tokenizer.nextTokenAsDouble();
715 <        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
716 <        s->setChi(chi);
717 <        s->setIntegralOfChiDt(integralOfChiDt);        
714 >        pair<RealType, RealType> thermostat;
715 >        thermostat.first = tokenizer.nextTokenAsDouble();
716 >        thermostat.second = tokenizer.nextTokenAsDouble();
717 >        s->setThermostat(thermostat);
718       } else if (propertyName == "Barostat") {
719          Mat3x3d eta;
720          eta(0, 0) = tokenizer.nextTokenAsDouble();
# Line 729 | Line 726 | namespace OpenMD {
726          eta(2, 0) = tokenizer.nextTokenAsDouble();
727          eta(2, 1) = tokenizer.nextTokenAsDouble();
728          eta(2, 2) = tokenizer.nextTokenAsDouble();
729 <        s->setEta(eta);
729 >        s->setBarostat(eta);
730        } else {
731          sprintf(painCave.errMsg,
732                  "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());

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