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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 1871 by gezelter, Fri May 10 14:59:13 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 143 | Line 141 | namespace OpenMD {
141        prevPos = currPos;
142        bool foundOpenSnapshotTag = false;
143        bool foundClosedSnapshotTag = false;
144 <      bool foundOpenSiteDataTag = false;
144 >
145        while(inFile_->getline(buffer, bufferSize)) {
146          ++lineNo;
147          
# Line 204 | Line 202 | namespace OpenMD {
202   #ifdef IS_MPI
203      }
204      
205 <    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
205 >    MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
206      
207   #endif // is_mpi
208      
# Line 229 | Line 227 | namespace OpenMD {
227        needVel_ = false;
228      }
229      
230 <    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
230 >    if (storageLayout & DataStorage::dslAmat ||
231 >        storageLayout & DataStorage::dslDipole ||
232 >        storageLayout & DataStorage::dslQuadrupole) {
233        needQuaternion_ = true;
234      } else {
235        needQuaternion_ = false;
# Line 245 | Line 245 | namespace OpenMD {
245  
246      if (needCOMprops_) {
247        Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248 +      Thermo thermo(info_);
249        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 –    }
250  
251 +      if (needPos_ && needVel_) {
252 +        Vector3d comvel;
253 +        Vector3d comw;
254 +        thermo.getComAll(com, comvel);
255 +        comw = thermo.getAngularMomentum();
256 +      } else {
257 +        com = thermo.getCom();
258 +      }                    
259 +    }
260    }
261    
262    void DumpReader::readSet(int whichFrame) {    
# Line 290 | Line 288 | namespace OpenMD {
288        }
289  
290        int sendBufferSize = sendBuffer.size();
291 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
292 <      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
291 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);    
292 >      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293 >                            MPI::CHAR, masterNode);    
294        
295        sstream.str(sendBuffer);
296      } else {
297        int sendBufferSize;
298 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
298 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
299        char * recvBuffer = new char[sendBufferSize+1];
300        assert(recvBuffer);
301        recvBuffer[sendBufferSize] = '\0';
302 <      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
302 >      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
303        sstream.str(recvBuffer);
304        delete [] recvBuffer;
305      }      
# Line 357 | Line 356 | namespace OpenMD {
356  
357      int index = tokenizer.nextTokenAsInt();
358  
359 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
359 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
360  
361 <    if (integrableObject == NULL) {
361 >    if (sd == NULL) {
362        return;
363      }
364      std::string type = tokenizer.nextToken();
# Line 379 | Line 378 | namespace OpenMD {
378        }
379      }
380      
381 <    if (integrableObject->isDirectional()) {
381 >    if (sd->isDirectional()) {
382        if (needQuaternion_) {
383          found = type.find("q");      
384          if (found == std::string::npos) {
# Line 402 | Line 401 | namespace OpenMD {
401              pos[1] = tokenizer.nextTokenAsDouble();
402              pos[2] = tokenizer.nextTokenAsDouble();
403              if (needPos_) {
404 <              integrableObject->setPos(pos);
404 >              sd->setPos(pos);
405              }            
406              break;
407          }
# Line 412 | Line 411 | namespace OpenMD {
411              vel[1] = tokenizer.nextTokenAsDouble();
412              vel[2] = tokenizer.nextTokenAsDouble();
413              if (needVel_) {
414 <              integrableObject->setVel(vel);
414 >              sd->setVel(vel);
415              }
416              break;
417          }
418  
419          case 'q' : {
420             Quat4d q;
421 <           if (integrableObject->isDirectional()) {
421 >           if (sd->isDirectional()) {
422                
423               q[0] = tokenizer.nextTokenAsDouble();
424               q[1] = tokenizer.nextTokenAsDouble();
# Line 438 | Line 437 | namespace OpenMD {
437                
438               q.normalize();
439               if (needQuaternion_) {            
440 <               integrableObject->setQ(q);
440 >               sd->setQ(q);
441               }              
442             }            
443             break;
444          }  
445          case 'j' : {
446            Vector3d ji;
447 <          if (integrableObject->isDirectional()) {
447 >          if (sd->isDirectional()) {
448               ji[0] = tokenizer.nextTokenAsDouble();
449               ji[1] = tokenizer.nextTokenAsDouble();
450               ji[2] = tokenizer.nextTokenAsDouble();
451               if (needAngMom_) {
452 <               integrableObject->setJ(ji);
452 >               sd->setJ(ji);
453               }
454            }
455            break;
# Line 461 | Line 460 | namespace OpenMD {
460            force[0] = tokenizer.nextTokenAsDouble();
461            force[1] = tokenizer.nextTokenAsDouble();
462            force[2] = tokenizer.nextTokenAsDouble();          
463 <          integrableObject->setFrc(force);
463 >          sd->setFrc(force);
464            break;
465          }
466          case 't' : {
# Line 470 | Line 469 | namespace OpenMD {
469             torque[0] = tokenizer.nextTokenAsDouble();
470             torque[1] = tokenizer.nextTokenAsDouble();
471             torque[2] = tokenizer.nextTokenAsDouble();          
472 <           integrableObject->setTrq(torque);          
472 >           sd->setTrq(torque);          
473             break;
474          }
475          case 'u' : {
476  
477             RealType particlePot;
478             particlePot = tokenizer.nextTokenAsDouble();
479 <           integrableObject->setParticlePot(particlePot);          
479 >           sd->setParticlePot(particlePot);          
480             break;
481          }
482          case 'c' : {
483  
484             RealType flucQPos;
485             flucQPos = tokenizer.nextTokenAsDouble();
486 <           integrableObject->setFlucQPos(flucQPos);          
486 >           sd->setFlucQPos(flucQPos);          
487             break;
488          }
489          case 'w' : {
490  
491             RealType flucQVel;
492             flucQVel = tokenizer.nextTokenAsDouble();
493 <           integrableObject->setFlucQVel(flucQVel);          
493 >           sd->setFlucQVel(flucQVel);          
494             break;
495          }
496          case 'g' : {
497  
498             RealType flucQFrc;
499             flucQFrc = tokenizer.nextTokenAsDouble();
500 <           integrableObject->setFlucQFrc(flucQFrc);          
500 >           sd->setFlucQFrc(flucQFrc);          
501             break;
502          }
503          case 'e' : {
# Line 507 | Line 506 | namespace OpenMD {
506             eField[0] = tokenizer.nextTokenAsDouble();
507             eField[1] = tokenizer.nextTokenAsDouble();
508             eField[2] = tokenizer.nextTokenAsDouble();          
509 <           integrableObject->setElectricField(eField);          
509 >           sd->setElectricField(eField);          
510             break;
511          }
512          default: {
# Line 528 | Line 527 | namespace OpenMD {
527  
528      StringTokenizer tokenizer(line);
529      int nTokens;
530 <    
530 >        
531      nTokens = tokenizer.countTokens();
532      
533      if (nTokens < 2) {  
# Line 543 | Line 542 | namespace OpenMD {
542       */
543  
544      int index = tokenizer.nextTokenAsInt();
545 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
546 <    if (integrableObject == NULL) {
545 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
546 >    if (sd == NULL) {
547        return;
548      }
550 –    StuntDouble* sd = integrableObject;
549  
550      /**
551       * Test to see if the next token is an integer or not.  If not,
# Line 561 | Line 559 | namespace OpenMD {
559      if (i >> siteIndex) {
560        // chew up this token and parse as an int:
561        siteIndex = tokenizer.nextTokenAsInt();
562 <      RigidBody* rb = static_cast<RigidBody*>(integrableObject);
562 >      RigidBody* rb = static_cast<RigidBody*>(sd);
563        sd = rb->getAtoms()[siteIndex];
564      }
565  
# Line 649 | Line 647 | namespace OpenMD {
647  
648    void  DumpReader::readSiteData(std::istream& inputStream) {
649  
652 –    inputStream.getline(buffer, bufferSize);
650      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 –    }
651  
652 +    // We already found the starting <SiteData> tag or we wouldn't be
653 +    // here, so just start parsing until we get to the ending
654 +    // </SiteData> tag:
655 +    
656      while(inputStream.getline(buffer, bufferSize)) {
657        line = buffer;
658        
# 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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