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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 966 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC

# Line 61 | Line 61 | namespace oopse {
61      createDumpFile_ = true;
62   #ifdef HAVE_LIBZ
63      if (needCompression_) {
64 <        filename_ += ".gz";
65 <        eorFilename_ += ".gz";
64 >      filename_ += ".gz";
65 >      eorFilename_ += ".gz";
66      }
67   #endif
68      
69   #ifdef IS_MPI
70  
71 <      if (worldRank == 0) {
71 >    if (worldRank == 0) {
72   #endif // is_mpi
73 –
73          
74 <        dumpFile_ = createOStream(filename_);
74 >      dumpFile_ = createOStream(filename_);
75  
76 <        if (!dumpFile_) {
77 <          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78 <                  filename_.c_str());
79 <          painCave.isFatal = 1;
80 <          simError();
81 <        }
76 >      if (!dumpFile_) {
77 >        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78 >                filename_.c_str());
79 >        painCave.isFatal = 1;
80 >        simError();
81 >      }
82  
83   #ifdef IS_MPI
84  
85 <      }
85 >    }
86  
88 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89 –      MPIcheckPoint();
90 –
87   #endif // is_mpi
88  
89 <    }
89 >  }
90  
91  
92    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
# Line 104 | Line 100 | namespace oopse {
100      createDumpFile_ = true;
101   #ifdef HAVE_LIBZ
102      if (needCompression_) {
103 <        filename_ += ".gz";
104 <        eorFilename_ += ".gz";
103 >      filename_ += ".gz";
104 >      eorFilename_ += ".gz";
105      }
106   #endif
107      
108   #ifdef IS_MPI
109  
110 <      if (worldRank == 0) {
110 >    if (worldRank == 0) {
111   #endif // is_mpi
112  
113        
114 <        dumpFile_ = createOStream(filename_);
114 >      dumpFile_ = createOStream(filename_);
115  
116 <        if (!dumpFile_) {
117 <          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
118 <                  filename_.c_str());
119 <          painCave.isFatal = 1;
120 <          simError();
121 <        }
116 >      if (!dumpFile_) {
117 >        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
118 >                filename_.c_str());
119 >        painCave.isFatal = 1;
120 >        simError();
121 >      }
122  
123   #ifdef IS_MPI
124  
125 <      }
125 >    }
126  
131 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132 –      MPIcheckPoint();
133 –
127   #endif // is_mpi
128  
129 <    }
129 >  }
130    
131    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
132 <  : info_(info), filename_(filename){
132 >    : info_(info), filename_(filename){
133      
134      Globals* simParams = info->getSimParams();
135      eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
# Line 170 | Line 163 | namespace oopse {
163   #ifdef IS_MPI
164        
165      }
166 +
167      
174 –    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175 –    MPIcheckPoint();
176 –    
168   #endif // is_mpi
169      
170    }
180 –  
181 –  
182 –  
183 –  
184 –  
171  
172    DumpWriter::~DumpWriter() {
173  
# Line 190 | Line 176 | namespace oopse {
176      if (worldRank == 0) {
177   #endif // is_mpi
178        if (createDumpFile_){
179 +        writeClosing(*dumpFile_);
180          delete dumpFile_;
181        }
182   #ifdef IS_MPI
# Line 200 | Line 187 | namespace oopse {
187  
188    }
189  
190 <  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
190 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
191  
192 <    RealType currentTime;
192 >    char buffer[1024];
193 >
194 >    os << "    <FrameData>\n";
195 >
196 >    RealType currentTime = s->getTime();
197 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
198 >    os << buffer;
199 >
200      Mat3x3d hmat;
207 –    RealType chi;
208 –    RealType integralOfChiDt;
209 –    Mat3x3d eta;
210 –    
211 –    currentTime = s->getTime();
201      hmat = s->getHmat();
202 <    chi = s->getChi();
203 <    integralOfChiDt = s->getIntegralOfChiDt();
204 <    eta = s->getEta();
205 <    
206 <    os << currentTime << ";\t"
218 <       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
219 <       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
220 <       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
202 >    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
203 >            hmat(0, 0), hmat(1, 0), hmat(2, 0),
204 >            hmat(0, 1), hmat(1, 1), hmat(2, 1),
205 >            hmat(0, 2), hmat(1, 2), hmat(2, 2));
206 >    os << buffer;
207  
208 <    //write out additional parameters, such as chi and eta
209 <
210 <    os << chi << "\t" << integralOfChiDt << ";\t";
208 >    RealType chi = s->getChi();
209 >    RealType integralOfChiDt = s->getIntegralOfChiDt();
210 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
211 >    os << buffer;
212  
213 <    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
214 <       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
215 <       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
216 <        
217 <    os << "\n";
213 >    Mat3x3d eta;
214 >    eta = s->getEta();
215 >    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
216 >            eta(0, 0), eta(1, 0), eta(2, 0),
217 >            eta(0, 1), eta(1, 1), eta(2, 1),
218 >            eta(0, 2), eta(1, 2), eta(2, 2));
219 >    os << buffer;
220 >
221 >    os << "    </FrameData>\n";
222    }
223  
224    void DumpWriter::writeFrame(std::ostream& os) {
234 –    const int BUFFERSIZE = 2000;
235 –    const int MINIBUFFERSIZE = 100;
225  
226 <    char tempBuffer[BUFFERSIZE];
227 <    char writeLine[BUFFERSIZE];
226 > #ifdef IS_MPI
227 >    MPI_Status istatus;
228 > #endif
229  
240 –    Quat4d q;
241 –    Vector3d ji;
242 –    Vector3d pos;
243 –    Vector3d vel;
244 –    Vector3d frc;
245 –    Vector3d trq;
246 –
230      Molecule* mol;
231      StuntDouble* integrableObject;
232      SimInfo::MoleculeIterator mi;
233      Molecule::IntegrableObjectIterator ii;
251 –  
252 –    int nTotObjects;    
253 –    nTotObjects = info_->getNGlobalIntegrableObjects();
234  
235   #ifndef IS_MPI
236 +    os << "  <Snapshot>\n";
237 +
238 +    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
239  
240 <
258 <    os << nTotObjects << "\n";
259 <        
260 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
261 <
240 >    os << "    <StuntDoubles>\n";
241      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
242  
243        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
244 <           integrableObject = mol->nextIntegrableObject(ii)) {
245 <                
244 >           integrableObject = mol->nextIntegrableObject(ii)) {  
245 >        os << prepareDumpLine(integrableObject);
246  
247 <        pos = integrableObject->getPos();
248 <        vel = integrableObject->getVel();
247 >      }
248 >    }    
249 >    os << "    </StuntDoubles>\n";
250  
251 <        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
272 <                integrableObject->getType().c_str(),
273 <                pos[0], pos[1], pos[2],
274 <                vel[0], vel[1], vel[2]);
251 >    os << "  </Snapshot>\n";
252  
253 <        strcpy(writeLine, tempBuffer);
254 <
255 <        if (integrableObject->isDirectional()) {
256 <          q = integrableObject->getQ();
257 <          ji = integrableObject->getJ();
258 <
259 <          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
260 <                  q[0], q[1], q[2], q[3],
261 <                  ji[0], ji[1], ji[2]);
285 <          strcat(writeLine, tempBuffer);
286 <        } else {
287 <          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
288 <        }
289 <
290 <        if (needForceVector_) {
291 <          frc = integrableObject->getFrc();
292 <          trq = integrableObject->getTrq();
293 <          
294 <          sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
295 <                  frc[0], frc[1], frc[2],
296 <                  trq[0], trq[1], trq[2]);
297 <          strcat(writeLine, tempBuffer);
298 <        }
299 <        
300 <        strcat(writeLine, "\n");
301 <        os << writeLine;
302 <
253 >    os.flush();
254 > #else
255 >    //every node prepares the dump lines for integrable objects belong to itself
256 >    std::string buffer;
257 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
258 >      
259 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
260 >           integrableObject = mol->nextIntegrableObject(ii)) {  
261 >        buffer += prepareDumpLine(integrableObject);
262        }
263      }
264 <
306 <    os.flush();
307 < #else // is_mpi
308 <    /*********************************************************************
309 <     * Documentation?  You want DOCUMENTATION?
310 <     *
311 <     * Why all the potatoes below?  
312 <     *
313 <     * To make a long story short, the original version of DumpWriter
314 <     * worked in the most inefficient way possible.  Node 0 would
315 <     * poke each of the node for an individual atom's formatted data
316 <     * as node 0 worked its way down the global index. This was particularly
317 <     * inefficient since the method blocked all processors at every atom
318 <     * (and did it twice!).
319 <     *
320 <     * An intermediate version of DumpWriter could be described from Node
321 <     * zero's perspective as follows:
322 <     *
323 <     *  1) Have 100 of your friends stand in a circle.
324 <     *  2) When you say go, have all of them start tossing potatoes at
325 <     *     you (one at a time).
326 <     *  3) Catch the potatoes.
327 <     *
328 <     * It was an improvement, but MPI has buffers and caches that could
329 <     * best be described in this analogy as "potato nets", so there's no
330 <     * need to block the processors atom-by-atom.
331 <     *
332 <     * This new and improved DumpWriter works in an even more efficient
333 <     * way:
334 <     *
335 <     *  1) Have 100 of your friend stand in a circle.
336 <     *  2) When you say go, have them start tossing 5-pound bags of
337 <     *     potatoes at you.
338 <     *  3) Once you've caught a friend's bag of potatoes,
339 <     *     toss them a spud to let them know they can toss another bag.
340 <     *
341 <     * How's THAT for documentation?
342 <     *
343 <     *********************************************************************/
264 >    
265      const int masterNode = 0;
266  
267 <    int * potatoes;
268 <    int myPotato;
269 <    int nProc;
270 <    int which_node;
271 <    RealType atomData[19];
272 <    int isDirectional;
352 <    char MPIatomTypeString[MINIBUFFERSIZE];
353 <    int msgLen; // the length of message actually recieved at master nodes
354 <    int haveError;
355 <    MPI_Status istatus;
356 <    int nCurObj;
357 <    
358 <    // code to find maximum tag value
359 <    int * tagub;
360 <    int flag;
361 <    int MAXTAG;
362 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
267 >    if (worldRank == masterNode) {      
268 >      os << "  <Snapshot>\n";  
269 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270 >      os << "    <StuntDoubles>\n";
271 >        
272 >      os << buffer;
273  
274 <    if (flag) {
365 <      MAXTAG = *tagub;
366 <    } else {
367 <      MAXTAG = 32767;
368 <    }
369 <
370 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
371 <
372 <      // Node 0 needs a list of the magic potatoes for each processor;
373 <
274 >      int nProc;
275        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
276 <      potatoes = new int[nProc];
276 >      for (int i = 1; i < nProc; ++i) {
277  
278 <      //write out the comment lines
279 <      for(int i = 0; i < nProc; i++) {
379 <        potatoes[i] = 0;
380 <      }
278 >        // receive the length of the string buffer that was
279 >        // prepared by processor i
280  
281 +        int recvLength;
282 +        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
283 +        char* recvBuffer = new char[recvLength];
284 +        if (recvBuffer == NULL) {
285 +        } else {
286 +          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
287 +          os << recvBuffer;
288 +          delete recvBuffer;
289 +        }
290 +      }
291 +      os << "    </StuntDoubles>\n";
292 +      
293 +      os << "  </Snapshot>\n";
294 +      os.flush();
295 +    } else {
296 +      int sendBufferLength = buffer.size() + 1;
297 +      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
298 +      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
299 +    }
300  
301 <      os << nTotObjects << "\n";
384 <      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
301 > #endif // is_mpi
302  
303 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
303 >  }
304  
305 <        // Get the Node number which has this atom;
305 >  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
306 >        
307 >    int index = integrableObject->getGlobalIntegrableObjectIndex();
308 >    std::string type("pv");
309 >    std::string line;
310 >    char tempBuffer[4096];
311  
312 <        which_node = info_->getMolToProc(i);
312 >    Vector3d pos;
313 >    Vector3d vel;
314 >    pos = integrableObject->getPos();
315 >    vel = integrableObject->getVel();          
316 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
317 >            pos[0], pos[1], pos[2],
318 >            vel[0], vel[1], vel[2]);                    
319 >    line += tempBuffer;
320  
321 <        if (which_node != masterNode) { //current molecule is in slave node
322 <          if (potatoes[which_node] + 1 >= MAXTAG) {
323 <            // The potato was going to exceed the maximum value,
324 <            // so wrap this processor potato back to 0:        
325 <
326 <            potatoes[which_node] = 0;
327 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
328 <                     MPI_COMM_WORLD);
329 <          }
330 <
402 <          myPotato = potatoes[which_node];
403 <
404 <          //recieve the number of integrableObject in current molecule
405 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
406 <                   MPI_COMM_WORLD, &istatus);
407 <          myPotato++;
408 <
409 <          for(int l = 0; l < nCurObj; l++) {
410 <            if (potatoes[which_node] + 2 >= MAXTAG) {
411 <              // The potato was going to exceed the maximum value,
412 <              // so wrap this processor potato back to 0:        
413 <
414 <              potatoes[which_node] = 0;
415 <              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416 <                       0, MPI_COMM_WORLD);
417 <            }
418 <
419 <            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
420 <                     which_node, myPotato, MPI_COMM_WORLD,
421 <                     &istatus);
422 <
423 <            myPotato++;
424 <
425 <            MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
426 <                     MPI_COMM_WORLD, &istatus);
427 <            myPotato++;
428 <
429 <            MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
430 <
431 <            if (msgLen == 13 || msgLen == 19)
432 <              isDirectional = 1;
433 <            else
434 <              isDirectional = 0;
435 <
436 <            // If we've survived to here, format the line:
437 <
438 <            if (!isDirectional) {
439 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
440 <                      MPIatomTypeString, atomData[0],
441 <                      atomData[1], atomData[2],
442 <                      atomData[3], atomData[4],
443 <                      atomData[5]);
444 <
445 <              strcat(writeLine,
446 <                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
447 <            } else {
448 <              sprintf(writeLine,
449 <                      "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
450 <                      MPIatomTypeString,
451 <                      atomData[0],
452 <                      atomData[1],
453 <                      atomData[2],
454 <                      atomData[3],
455 <                      atomData[4],
456 <                      atomData[5],
457 <                      atomData[6],
458 <                      atomData[7],
459 <                      atomData[8],
460 <                      atomData[9],
461 <                      atomData[10],
462 <                      atomData[11],
463 <                      atomData[12]);
464 <            }
465 <            
466 <            if (needForceVector_) {
467 <              if (!isDirectional) {
468 <                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
469 <                        atomData[6],
470 <                        atomData[7],
471 <                        atomData[8],
472 <                        atomData[9],
473 <                        atomData[10],
474 <                        atomData[11]);
475 <              } else {
476 <                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
477 <                        atomData[13],
478 <                        atomData[14],
479 <                        atomData[15],
480 <                        atomData[16],
481 <                        atomData[17],
482 <                        atomData[18]);
483 <              }
484 <            }
485 <
486 <            os << writeLine << "\n";
487 <
488 <          } // end for(int l =0)
489 <
490 <          potatoes[which_node] = myPotato;
491 <        } else { //master node has current molecule
492 <
493 <          mol = info_->getMoleculeByGlobalIndex(i);
494 <
495 <          if (mol == NULL) {
496 <            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
497 <            painCave.isFatal = 1;
498 <            simError();
499 <          }
500 <                
501 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
502 <               integrableObject = mol->nextIntegrableObject(ii)) {      
503 <
504 <            pos = integrableObject->getPos();
505 <            vel = integrableObject->getVel();
506 <
507 <            atomData[0] = pos[0];
508 <            atomData[1] = pos[1];
509 <            atomData[2] = pos[2];
510 <
511 <            atomData[3] = vel[0];
512 <            atomData[4] = vel[1];
513 <            atomData[5] = vel[2];
514 <
515 <            isDirectional = 0;
516 <
517 <            if (integrableObject->isDirectional()) {
518 <              isDirectional = 1;
519 <
520 <              q = integrableObject->getQ();
521 <              ji = integrableObject->getJ();
522 <
523 <              for(int j = 0; j < 6; j++) {
524 <                atomData[j] = atomData[j];
525 <              }
526 <
527 <              atomData[6] = q[0];
528 <              atomData[7] = q[1];
529 <              atomData[8] = q[2];
530 <              atomData[9] = q[3];
531 <
532 <              atomData[10] = ji[0];
533 <              atomData[11] = ji[1];
534 <              atomData[12] = ji[2];
535 <            }
536 <
537 <            if (needForceVector_) {
538 <              frc = integrableObject->getFrc();
539 <              trq = integrableObject->getTrq();
540 <
541 <              if (!isDirectional) {
542 <                atomData[6] = frc[0];
543 <                atomData[7] = frc[1];
544 <                atomData[8] = frc[2];
545 <                atomData[9] = trq[0];
546 <                atomData[10] = trq[1];
547 <                atomData[11] = trq[2];
548 <              } else {
549 <                atomData[13] = frc[0];
550 <                atomData[14] = frc[1];
551 <                atomData[15] = frc[2];
552 <                atomData[16] = trq[0];
553 <                atomData[17] = trq[1];
554 <                atomData[18] = trq[2];
555 <              }
556 <            }
557 <
558 <            // If we've survived to here, format the line:
559 <
560 <            if (!isDirectional) {
561 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
562 <                      integrableObject->getType().c_str(), atomData[0],
563 <                      atomData[1], atomData[2],
564 <                      atomData[3], atomData[4],
565 <                      atomData[5]);
566 <
567 <              strcat(writeLine,
568 <                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
569 <            } else {
570 <              sprintf(writeLine,
571 <                      "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
572 <                      integrableObject->getType().c_str(),
573 <                      atomData[0],
574 <                      atomData[1],
575 <                      atomData[2],
576 <                      atomData[3],
577 <                      atomData[4],
578 <                      atomData[5],
579 <                      atomData[6],
580 <                      atomData[7],
581 <                      atomData[8],
582 <                      atomData[9],
583 <                      atomData[10],
584 <                      atomData[11],
585 <                      atomData[12]);
586 <            }
587 <
588 <            if (needForceVector_) {
589 <              if (!isDirectional) {
590 <              sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
591 <                      atomData[6],
592 <                      atomData[7],
593 <                      atomData[8],
594 <                      atomData[9],
595 <                      atomData[10],
596 <                      atomData[11]);
597 <              } else {
598 <                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
599 <                        atomData[13],
600 <                        atomData[14],
601 <                        atomData[15],
602 <                        atomData[16],
603 <                        atomData[17],
604 <                        atomData[18]);
605 <              }
606 <            }
607 <
608 <            os << writeLine << "\n";
609 <
610 <          } //end for(iter = integrableObject.begin())
611 <        }
612 <      } //end for(i = 0; i < mpiSim->getNmol())
613 <
614 <      os.flush();
615 <        
616 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
617 <      MPIcheckPoint();
618 <
619 <      delete [] potatoes;
620 <    } else {
621 <
622 <      // worldRank != 0, so I'm a remote node.  
623 <
624 <      // Set my magic potato to 0:
625 <
626 <      myPotato = 0;
627 <
628 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
629 <
630 <        // Am I the node which has this integrableObject?
631 <        int whichNode = info_->getMolToProc(i);
632 <        if (whichNode == worldRank) {
633 <          if (myPotato + 1 >= MAXTAG) {
634 <
635 <            // The potato was going to exceed the maximum value,
636 <            // so wrap this processor potato back to 0 (and block until
637 <            // node 0 says we can go:
638 <
639 <            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
640 <                     &istatus);
641 <          }
642 <
643 <          mol = info_->getMoleculeByGlobalIndex(i);
644 <
645 <                
646 <          nCurObj = mol->getNIntegrableObjects();
647 <
648 <          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
649 <          myPotato++;
650 <
651 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
652 <               integrableObject = mol->nextIntegrableObject(ii)) {
653 <
654 <            if (myPotato + 2 >= MAXTAG) {
655 <
656 <              // The potato was going to exceed the maximum value,
657 <              // so wrap this processor potato back to 0 (and block until
658 <              // node 0 says we can go:
659 <
660 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
661 <                       &istatus);
662 <            }
663 <
664 <            pos = integrableObject->getPos();
665 <            vel = integrableObject->getVel();
666 <
667 <            atomData[0] = pos[0];
668 <            atomData[1] = pos[1];
669 <            atomData[2] = pos[2];
670 <
671 <            atomData[3] = vel[0];
672 <            atomData[4] = vel[1];
673 <            atomData[5] = vel[2];
674 <
675 <            isDirectional = 0;
676 <
677 <            if (integrableObject->isDirectional()) {
678 <              isDirectional = 1;
679 <
680 <              q = integrableObject->getQ();
681 <              ji = integrableObject->getJ();
682 <
683 <              atomData[6] = q[0];
684 <              atomData[7] = q[1];
685 <              atomData[8] = q[2];
686 <              atomData[9] = q[3];
687 <
688 <              atomData[10] = ji[0];
689 <              atomData[11] = ji[1];
690 <              atomData[12] = ji[2];
691 <            }
692 <
693 <            if (needForceVector_) {
694 <              frc = integrableObject->getFrc();
695 <              trq = integrableObject->getTrq();
696 <              
697 <              if (!isDirectional) {
698 <                atomData[6] = frc[0];
699 <                atomData[7] = frc[1];
700 <                atomData[8] = frc[2];
701 <                
702 <                atomData[9] = trq[0];
703 <                atomData[10] = trq[1];
704 <                atomData[11] = trq[2];
705 <              } else {
706 <                atomData[13] = frc[0];
707 <                atomData[14] = frc[1];
708 <                atomData[15] = frc[2];
709 <                
710 <                atomData[16] = trq[0];
711 <                atomData[17] = trq[1];
712 <                atomData[18] = trq[2];
713 <              }
714 <            }
715 <
716 <            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
717 <
718 <            // null terminate the  std::string before sending (just in case):
719 <            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
720 <
721 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
722 <                     myPotato, MPI_COMM_WORLD);
723 <
724 <            myPotato++;
725 <
726 <            if (isDirectional && needForceVector_) {
727 <              MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
728 <                       MPI_COMM_WORLD);
729 <            } else if (isDirectional) {
730 <              MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
731 <                       MPI_COMM_WORLD);
732 <            } else if (needForceVector_) {
733 <              MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
734 <                       MPI_COMM_WORLD);
735 <            } else {
736 <              MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
737 <                       MPI_COMM_WORLD);
738 <            }
739 <
740 <            myPotato++;
741 <          }
742 <                    
743 <        }
744 <            
745 <      }
746 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
747 <      MPIcheckPoint();
321 >    if (integrableObject->isDirectional()) {
322 >      type += "qj";
323 >      Quat4d q;
324 >      Vector3d ji;
325 >      q = integrableObject->getQ();
326 >      ji = integrableObject->getJ();
327 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
328 >              q[0], q[1], q[2], q[3],
329 >              ji[0], ji[1], ji[2]);
330 >      line += tempBuffer;
331      }
332  
333 < #endif // is_mpi
334 <
333 >    if (needForceVector_) {
334 >      type += "ft";
335 >      Vector3d frc;
336 >      Vector3d trq;
337 >      frc = integrableObject->getFrc();
338 >      trq = integrableObject->getTrq();
339 >              
340 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
341 >              frc[0], frc[1], frc[2],
342 >              trq[0], trq[1], trq[2]);
343 >      line += tempBuffer;
344 >    }
345 >        
346 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
347 >    return std::string(tempBuffer);
348    }
349  
350    void DumpWriter::writeDump() {
# Line 773 | Line 369 | namespace oopse {
369   #ifdef IS_MPI
370      if (worldRank == 0) {
371   #endif // is_mpi
372 <    delete eorStream;
373 <
372 >      writeClosing(*eorStream);
373 >      delete eorStream;
374   #ifdef IS_MPI
375      }
376   #endif // is_mpi  
# Line 807 | Line 403 | namespace oopse {
403   #ifdef IS_MPI
404      if (worldRank == 0) {
405   #endif // is_mpi
406 <    delete eorStream;
407 <
406 >      writeClosing(*eorStream);
407 >      delete eorStream;
408   #ifdef IS_MPI
409      }
410   #endif // is_mpi  
411      
412    }
413  
414 < std::ostream* DumpWriter::createOStream(const std::string& filename) {
414 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
415  
416      std::ostream* newOStream;
417   #ifdef HAVE_LIBZ
418      if (needCompression_) {
419 <        newOStream = new ogzstream(filename.c_str());
419 >      newOStream = new ogzstream(filename.c_str());
420      } else {
421 <        newOStream = new std::ofstream(filename.c_str());
421 >      newOStream = new std::ofstream(filename.c_str());
422      }
423   #else
424      newOStream = new std::ofstream(filename.c_str());
425   #endif
426 +    //write out MetaData first
427 +    (*newOStream) << "<OOPSE version=4>" << std::endl;
428 +    (*newOStream) << "  <MetaData>" << std::endl;
429 +    (*newOStream) << info_->getRawMetaData();
430 +    (*newOStream) << "  </MetaData>" << std::endl;
431      return newOStream;
432 < }
432 >  }
433  
434 +  void DumpWriter::writeClosing(std::ostream& os) {
435 +
436 +    os << "</OOPSE>\n";
437 +    os.flush();
438 +  }
439 +
440   }//end namespace oopse

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