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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 916 by gezelter, Fri Jan 9 20:29:32 2004 UTC vs.
Revision 934 by tim, Tue Jan 13 20:04:28 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
29 –    strcpy( outName, entry_plug->sampleName );
31  
32 <    outFile.open(outName, ios::out | ios::trunc );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    if( !outFile ){
34 >    if( !dumpFile ){
35  
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
43 <    //outFile.setf( ios::scientific );
43 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
44 >    if( !finalOut ){
45 >      sprintf( painCave.errMsg,
46 >               "Could not open \"%s\" for final dump output.\n",
47 >               entry_plug->finalName );
48 >      painCave.isFatal = 1;
49 >      simError();
50 >    }
51  
52   #ifdef IS_MPI
53    }
54  
55 +  //sort the local atoms by global index
56 +  sortByGlobalIndex();
57 +  
58    sprintf( checkPointMsg,
59             "Sucessfully opened output file for dumping.\n");
60    MPIcheckPoint();
# Line 56 | Line 67 | DumpWriter::~DumpWriter( ){
67    if(worldRank == 0 ){
68   #endif // is_mpi
69  
70 <    outFile.close();
70 >    dumpFile.close();
71 >    finalOut.close();
72  
73   #ifdef IS_MPI
74    }
75   #endif // is_mpi
76   }
77  
78 < void DumpWriter::writeDump( double currentTime ){
78 > #ifdef IS_MPI
79  
80 + /**
81 + * A hook function to load balancing
82 + */
83 +
84 + void DumpWriter::update(){
85 +  sortByGlobalIndex();          
86 + }
87 +  
88 + /**
89 + * Auxiliary sorting function
90 + */
91 +
92 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
93 +  return p1.second < p2.second;
94 + }
95 +
96 + /**
97 + * Sorting the local index by global index
98 + */
99 +
100 + void DumpWriter::sortByGlobalIndex(){
101 +  Atom** atoms = entry_plug->atoms;
102 +  
103 +  indexArray.clear();
104 +  
105 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
106 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
107 +  
108 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
109 + }
110 + #endif
111 +
112 + void DumpWriter::writeDump(double currentTime){
113 +
114 +  vector<ofstream*> fileStreams;
115 +
116 + #ifdef IS_MPI
117 +  if(worldRank == 0 ){
118 +    finalOut.seekp(0);
119 +  }
120 + #endif // is_mpi
121 +
122 +  fileStreams.push_back(&finalOut);
123 +  fileStreams.push_back(&dumpFile);
124 +
125 +  writeFrame(fileStreams, currentTime);
126 +        
127 + }
128 +
129 + void DumpWriter::writeFinal(double currentTime){
130 +
131 +  vector<ofstream*> fileStreams;
132 +
133 + #ifdef IS_MPI
134 +  if(worldRank == 0 ){
135 +    finalOut.seekp(0);
136 +  }
137 + #endif // is_mpi
138 +  
139 +  fileStreams.push_back(&finalOut);  
140 +  writeFrame(fileStreams, currentTime);
141 +  
142 + }
143 +
144 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
145 +
146    const int BUFFERSIZE = 2000;
147    const int MINIBUFFERSIZE = 100;
148  
149    char tempBuffer[BUFFERSIZE];
150    char writeLine[BUFFERSIZE];
151  
152 <  int i;
152 >  int i, k;
153  
154   #ifdef IS_MPI
155    
# Line 79 | Line 157 | void DumpWriter::writeDump( double currentTime ){
157    int myPotato;
158  
159    int nProc;
160 <  int j, which_node, done, which_atom, local_index;
160 >  int j, which_node, done, which_atom, local_index, currentIndex;
161    double atomData6[6];
162    double atomData13[13];
163    int isDirectional;
# Line 95 | Line 173 | void DumpWriter::writeDump( double currentTime ){
173    Atom** atoms = entry_plug->atoms;
174    double pos[3], vel[3];
175  
98 –  // write current frame to the eor file
99 –
100 –  this->writeFinal( currentTime );
101 –
176   #ifndef IS_MPI
177 <
178 <  outFile << nAtoms << "\n";
177 >  
178 >  for(k = 0; k < outFile.size(); k++){
179 >    *outFile[k] << nAtoms << "\n";
180  
181 <  outFile << currentTime << ";\t"
182 <          << entry_plug->Hmat[0][0] << "\t"
183 <          << entry_plug->Hmat[1][0] << "\t"
184 <          << entry_plug->Hmat[2][0] << ";\t"
181 >    *outFile[k] << currentTime << ";\t"
182 >               << entry_plug->Hmat[0][0] << "\t"
183 >                     << entry_plug->Hmat[1][0] << "\t"
184 >                     << entry_plug->Hmat[2][0] << ";\t"
185 >              
186 >               << entry_plug->Hmat[0][1] << "\t"
187 >                     << entry_plug->Hmat[1][1] << "\t"
188 >                     << entry_plug->Hmat[2][1] << ";\t"
189  
190 <          << entry_plug->Hmat[0][1] << "\t"
191 <          << entry_plug->Hmat[1][1] << "\t"
192 <          << entry_plug->Hmat[2][1] << ";\t"
190 >                     << entry_plug->Hmat[0][2] << "\t"
191 >                     << entry_plug->Hmat[1][2] << "\t"
192 >                     << entry_plug->Hmat[2][2] << ";";
193  
194 <          << entry_plug->Hmat[0][2] << "\t"
195 <          << entry_plug->Hmat[1][2] << "\t"
196 <          << entry_plug->Hmat[2][2] << ";";
197 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
121 <
194 >    //write out additional parameters, such as chi and eta
195 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
196 >  }
197 >  
198    for( i=0; i<nAtoms; i++ ){
199  
200      atoms[i]->getPos(pos);
# Line 154 | Line 230 | void DumpWriter::writeDump( double currentTime ){
230      else
231        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232  
233 <    outFile << writeLine;
233 >    for(k = 0; k < outFile.size(); k++)
234 >      *outFile[k] << writeLine;
235    }
159 –  outFile.flush();
236  
237   #else // is_mpi
238  
239    /* code to find maximum tag value */
240 +  
241    int *tagub, flag, MAXTAG;
242    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
243    if (flag) {
# Line 183 | Line 260 | void DumpWriter::writeDump( double currentTime ){
260      nProc = mpiSim->getNumberProcessors();
261      potatoes = new int[nProc];
262  
263 +    //write out the comment lines
264      for (i = 0; i < nProc; i++)
265        potatoes[i] = 0;
266      
267 <    outFile << mpiSim->getTotAtoms() << "\n";
267 >      for(k = 0; k < outFile.size(); k++){
268 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
269  
270 <    outFile << currentTime << ";\t"
271 <            << entry_plug->Hmat[0][0] << "\t"
272 <            << entry_plug->Hmat[1][0] << "\t"
273 <            << entry_plug->Hmat[2][0] << ";\t"
270 >        *outFile[k] << currentTime << ";\t"
271 >                         << entry_plug->Hmat[0][0] << "\t"
272 >                         << entry_plug->Hmat[1][0] << "\t"
273 >                         << entry_plug->Hmat[2][0] << ";\t"
274  
275 <            << entry_plug->Hmat[0][1] << "\t"
276 <            << entry_plug->Hmat[1][1] << "\t"
277 <            << entry_plug->Hmat[2][1] << ";\t"
275 >                         << entry_plug->Hmat[0][1] << "\t"
276 >                         << entry_plug->Hmat[1][1] << "\t"
277 >                         << entry_plug->Hmat[2][1] << ";\t"
278  
279 <            << entry_plug->Hmat[0][2] << "\t"
280 <            << entry_plug->Hmat[1][2] << "\t"
281 <            << entry_plug->Hmat[2][2] << ";";
279 >                         << entry_plug->Hmat[0][2] << "\t"
280 >                         << entry_plug->Hmat[1][2] << "\t"
281 >                         << entry_plug->Hmat[2][2] << ";";
282 >  
283 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
284 >    }
285  
286 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
205 <    outFile << endl;
206 <    outFile.flush();
286 >    currentIndex = 0;
287  
288      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
289        
# Line 227 | Line 307 | void DumpWriter::writeDump( double currentTime ){
307          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
308                   myPotato, MPI_COMM_WORLD, &istatus);
309          
310 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
311 <        
232 <        // Null terminate the atomTypeString just in case:
233 <
234 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
235 <
310 >        atomTypeString = MPIatomTypeString;
311 >        
312          myPotato++;
313  
314          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 253 | Line 329 | void DumpWriter::writeDump( double currentTime ){
329  
330        } else {
331          
332 <        haveError = 0;
333 <        which_atom = i;
258 <        local_index=-1;
332 >        haveError = 0;
333 >              which_atom = i;
334          
335 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
336 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
337 <        }
263 <        
264 <        if (local_index != -1) {
335 >        local_index = indexArray[currentIndex].first;        
336 >                
337 >        if (which_atom == indexArray[currentIndex].second) {
338            
339            atomTypeString = atoms[local_index]->getType();
340  
341 <          atoms[local_index]->getPos(pos);
342 <          atoms[local_index]->getVel(vel);          
341 >                atoms[local_index]->getPos(pos);
342 >                atoms[local_index]->getVel(vel);          
343  
344            atomData6[0] = pos[0];
345            atomData6[1] = pos[1];
# Line 299 | Line 372 | void DumpWriter::writeDump( double currentTime ){
372            }
373            
374          } else {
375 <          sprintf(painCave.errMsg,
376 <                  "Atom %d not found on processor %d\n",
377 <                  i, worldRank );
378 <          haveError= 1;
379 <          simError();
380 <        }
375 >          sprintf(painCave.errMsg,
376 >                              "Atom %d not found on processor %d\n",
377 >                              i, worldRank );
378 >                haveError= 1;
379 >                simError();
380 >              }
381          
382 <        if(haveError) DieDieDie();
382 >        if(haveError) DieDieDie();
383          
384 <        // If we've survived to here, format the line:
312 <        
313 <        if (!isDirectional) {
314 <
315 <          sprintf( tempBuffer,
316 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
317 <                   atomTypeString,
318 <                   atomData6[0],
319 <                   atomData6[1],
320 <                   atomData6[2],
321 <                   atomData6[3],
322 <                   atomData6[4],
323 <                   atomData6[5]);
324 <          
325 <          strcpy( writeLine, tempBuffer );
326 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
327 <
328 <        } else {
329 <          
330 <          sprintf( tempBuffer,
331 <                   "%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\n",
332 <                   atomTypeString,
333 <                   atomData13[0],
334 <                   atomData13[1],
335 <                   atomData13[2],
336 <                   atomData13[3],
337 <                   atomData13[4],
338 <                   atomData13[5],
339 <                   atomData13[6],
340 <                   atomData13[7],
341 <                   atomData13[8],
342 <                   atomData13[9],
343 <                   atomData13[10],
344 <                   atomData13[11],
345 <                   atomData13[12]);
346 <          
347 <          strcat( writeLine, tempBuffer );
348 <          
349 <        }
350 <        
351 <        outFile << writeLine;
352 <        outFile.flush();
384 >        currentIndex ++;
385        }
386 <    }
355 <
356 <    outFile.flush();
357 <    sprintf( checkPointMsg,
358 <             "Sucessfully took a dump.\n");
359 <    MPIcheckPoint();        
360 <    
361 <  } else {
362 <
363 <    // worldRank != 0, so I'm a remote node.  
364 <
365 <    // Set my magic potato to 0:
366 <
367 <    myPotato = 0;
368 <    
369 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
386 >      // If we've survived to here, format the line:
387        
388 <      // Am I the node which has this atom?
389 <      
390 <      if (AtomToProcMap[i] == worldRank) {
391 <
392 <        if (myPotato + 3 >= MAXTAG) {
393 <
394 <          // The potato was going to exceed the maximum value,
395 <          // so wrap this processor potato back to 0 (and block until
396 <          // node 0 says we can go:
397 <
398 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
382 <          
383 <        }
384 <
385 <        local_index=-1;
386 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
387 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
388 <        }
389 <        if (local_index != -1) {
390 <        
391 <          atomTypeString = atoms[local_index]->getType();
392 <
393 <          atoms[local_index]->getPos(pos);
394 <          atoms[local_index]->getVel(vel);
395 <
396 <          atomData6[0] = pos[0];
397 <          atomData6[1] = pos[1];
398 <          atomData6[2] = pos[2];
399 <
400 <          atomData6[3] = vel[0];
401 <          atomData6[4] = vel[1];
402 <          atomData6[5] = vel[2];
403 <          
404 <          isDirectional = 0;
405 <
406 <          if( atoms[local_index]->isDirectional() ){
407 <
408 <            isDirectional = 1;
409 <            
410 <            dAtom = (DirectionalAtom *)atoms[local_index];
411 <            dAtom->getQ( q );
412 <            
413 <            for (int j = 0; j < 6 ; j++)
414 <              atomData13[j] = atomData6[j];
415 <            
416 <            atomData13[6] = q[0];
417 <            atomData13[7] = q[1];
418 <            atomData13[8] = q[2];
419 <            atomData13[9] = q[3];
420 <
421 <            atomData13[10] = dAtom->getJx();
422 <            atomData13[11] = dAtom->getJy();
423 <            atomData13[12] = dAtom->getJz();
424 <          }
425 <
426 <        } else {
427 <          sprintf(painCave.errMsg,
428 <                  "Atom %d not found on processor %d\n",
429 <                  i, worldRank );
430 <          haveError= 1;
431 <          simError();
432 <        }
433 <
434 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
435 <
436 <        // null terminate the string before sending (just in case):
437 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
438 <
439 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
440 <                 myPotato, MPI_COMM_WORLD);
441 <        
442 <        myPotato++;
443 <
444 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
445 <                 myPotato, MPI_COMM_WORLD);
446 <        
447 <        myPotato++;
448 <        
449 <        if (isDirectional) {
450 <
451 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
452 <                   myPotato, MPI_COMM_WORLD);
453 <          
454 <        } else {
455 <
456 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
457 <                   myPotato, MPI_COMM_WORLD);
458 <        }
459 <
460 <        myPotato++;      
461 <      }
462 <    }
463 <
464 <    sprintf( checkPointMsg,
465 <             "Sucessfully took a dump.\n");
466 <    MPIcheckPoint();        
467 <    
468 <  }
469 <  
470 < #endif // is_mpi
471 < }
472 <
473 < void DumpWriter::writeFinal(double finalTime){
474 <
475 <  char finalName[500];
476 <  ofstream finalOut;
477 <
478 <  const int BUFFERSIZE = 2000;
479 <  const int MINIBUFFERSIZE = 100;
480 <  char tempBuffer[BUFFERSIZE];
481 <  char writeLine[BUFFERSIZE];
482 <
483 <  double q[4];
484 <  DirectionalAtom* dAtom;
485 <  Atom** atoms = entry_plug->atoms;
486 <  int i;
487 < #ifdef IS_MPI
488 <  
489 <  int *potatoes;
490 <  int myPotato;
491 <
492 <  int nProc;
493 <  int j, which_node, done, which_atom, local_index;
494 <  double atomData6[6];
495 <  double atomData13[13];
496 <  int isDirectional;
497 <  char* atomTypeString;
498 <  char MPIatomTypeString[MINIBUFFERSIZE];
499 <
500 < #else //is_mpi
501 <  int nAtoms = entry_plug->n_atoms;
502 < #endif //is_mpi
503 <
504 <  double pos[3], vel[3];
505 <
506 < #ifdef IS_MPI
507 <  if(worldRank == 0 ){
508 < #endif // is_mpi
509 <
510 <    strcpy( finalName, entry_plug->finalName );
511 <
512 <    finalOut.open( finalName, ios::out | ios::trunc );
513 <    if( !finalOut ){
514 <      sprintf( painCave.errMsg,
515 <               "Could not open \"%s\" for final dump output.\n",
516 <               finalName );
517 <      painCave.isFatal = 1;
518 <      simError();
519 <    }
520 <
521 <    // finalOut.setf( ios::scientific );
522 <
523 < #ifdef IS_MPI
524 <  }
525 <
526 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
527 <  MPIcheckPoint();
528 <
529 < #endif //is_mpi
530 <
531 <
532 < #ifndef IS_MPI
533 <
534 <  finalOut << nAtoms << "\n";
535 <
536 <  finalOut << finalTime << ";\t"
537 <           << entry_plug->Hmat[0][0] << "\t"
538 <           << entry_plug->Hmat[1][0] << "\t"
539 <           << entry_plug->Hmat[2][0] << ";\t"
540 <
541 <           << entry_plug->Hmat[0][1] << "\t"
542 <           << entry_plug->Hmat[1][1] << "\t"
543 <           << entry_plug->Hmat[2][1] << ";\t"
544 <
545 <           << entry_plug->Hmat[0][2] << "\t"
546 <           << entry_plug->Hmat[1][2] << "\t"
547 <           << entry_plug->Hmat[2][2] << ";";
548 <
549 <  //write out additional parameters, such as chi and eta
550 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
551 <  finalOut << endl;
552 <
553 <  for( i=0; i<nAtoms; i++ ){
554 <
555 <    atoms[i]->getPos(pos);
556 <    atoms[i]->getVel(vel);
557 <
558 <    sprintf( tempBuffer,
559 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
560 <             atoms[i]->getType(),
561 <             pos[0],
562 <             pos[1],
563 <             pos[2],
564 <             vel[0],
565 <             vel[1],
566 <             vel[2]);
567 <    strcpy( writeLine, tempBuffer );
568 <
569 <    if( atoms[i]->isDirectional() ){
570 <
571 <      dAtom = (DirectionalAtom *)atoms[i];
572 <      dAtom->getQ( q );
573 <
574 <      sprintf( tempBuffer,
575 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
576 <               q[0],
577 <               q[1],
578 <               q[2],
579 <               q[3],
580 <               dAtom->getJx(),
581 <               dAtom->getJy(),
582 <               dAtom->getJz());
583 <      strcat( writeLine, tempBuffer );
584 <    }
585 <    else
586 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
587 <
588 <    finalOut << writeLine;
589 <  }
590 <  finalOut.flush();
591 <  finalOut.close();
592 <
593 < #else // is_mpi
594 <
595 <  /* code to find maximum tag value */
596 <  int *tagub, flag, MAXTAG;
597 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
598 <  if (flag) {
599 <    MAXTAG = *tagub;
600 <  } else {
601 <    MAXTAG = 32767;
602 <  }  
603 <
604 <  int haveError;
605 <
606 <  MPI_Status istatus;
607 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
608 <
609 <  // write out header and node 0's coordinates
610 <
611 <  if( worldRank == 0 ){
612 <
613 <    // Node 0 needs a list of the magic potatoes for each processor;
614 <
615 <    nProc = mpiSim->getNumberProcessors();
616 <    potatoes = new int[nProc];
617 <
618 <    for (i = 0; i < nProc; i++)
619 <      potatoes[i] = 0;
620 <    
621 <    finalOut << mpiSim->getTotAtoms() << "\n";
622 <
623 <    finalOut << finalTime << ";\t"
624 <            << entry_plug->Hmat[0][0] << "\t"
625 <            << entry_plug->Hmat[1][0] << "\t"
626 <            << entry_plug->Hmat[2][0] << ";\t"
627 <
628 <            << entry_plug->Hmat[0][1] << "\t"
629 <            << entry_plug->Hmat[1][1] << "\t"
630 <            << entry_plug->Hmat[2][1] << ";\t"
631 <
632 <            << entry_plug->Hmat[0][2] << "\t"
633 <            << entry_plug->Hmat[1][2] << "\t"
634 <            << entry_plug->Hmat[2][2] << ";";
635 <
636 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
637 <    finalOut << endl;
638 <    finalOut.flush();
639 <
640 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
641 <      
642 <      // Get the Node number which has this atom;
643 <      
644 <      which_node = AtomToProcMap[i];
645 <      
646 <      if (which_node != 0) {
647 <
648 <        if (potatoes[which_node] + 3 >= MAXTAG) {
649 <          // The potato was going to exceed the maximum value,
650 <          // so wrap this processor potato back to 0:        
651 <
652 <          potatoes[which_node] = 0;          
653 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
654 <          
655 <        }
656 <
657 <        myPotato = potatoes[which_node];        
658 <        
659 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
660 <                 myPotato, MPI_COMM_WORLD, &istatus);
661 <        
662 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
663 <        
664 <        // Null terminate the atomTypeString just in case:
665 <
666 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
667 <
668 <        myPotato++;
669 <
670 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
671 <                 myPotato, MPI_COMM_WORLD, &istatus);
672 <              
673 <        myPotato++;
674 <
675 <        if (isDirectional) {          
676 <          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
677 <                   myPotato, MPI_COMM_WORLD, &istatus);
678 <        } else {
679 <          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
680 <                   myPotato, MPI_COMM_WORLD, &istatus);          
681 <        }
682 <        
683 <        myPotato++;
684 <        potatoes[which_node] = myPotato;
388 >      if (!isDirectional) {
389 >        
390 >        sprintf( writeLine,
391 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392 >                             atomTypeString,
393 >                             atomData6[0],
394 >                             atomData6[1],
395 >                             atomData6[2],
396 >                             atomData6[3],
397 >                             atomData6[4],
398 >                             atomData6[5]);
399  
400 +              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
401 +        
402        } else {
403 +        
404 +              sprintf( writeLine,
405 +                             "%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\n",
406 +                             atomTypeString,
407 +                             atomData13[0],
408 +                             atomData13[1],
409 +                             atomData13[2],
410 +                             atomData13[3],
411 +                             atomData13[4],
412 +                             atomData13[5],
413 +                             atomData13[6],
414 +                             atomData13[7],
415 +                             atomData13[8],
416 +                             atomData13[9],
417 +                             atomData13[10],
418 +                             atomData13[11],
419 +                             atomData13[12]);
420          
688 –        haveError = 0;
689 –        which_atom = i;
690 –        local_index=-1;
691 –        
692 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
693 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
694 –        }
695 –        
696 –        if (local_index != -1) {
697 –          
698 –          atomTypeString = atoms[local_index]->getType();
699 –
700 –          atoms[local_index]->getPos(pos);
701 –          atoms[local_index]->getVel(vel);          
702 –
703 –          atomData6[0] = pos[0];
704 –          atomData6[1] = pos[1];
705 –          atomData6[2] = pos[2];
706 –
707 –          atomData6[3] = vel[0];
708 –          atomData6[4] = vel[1];
709 –          atomData6[5] = vel[2];
710 –          
711 –          isDirectional = 0;
712 –
713 –          if( atoms[local_index]->isDirectional() ){
714 –
715 –            isDirectional = 1;
716 –            
717 –            dAtom = (DirectionalAtom *)atoms[local_index];
718 –            dAtom->getQ( q );
719 –
720 –            for (int j = 0; j < 6 ; j++)
721 –              atomData13[j] = atomData6[j];            
722 –            
723 –            atomData13[6] = q[0];
724 –            atomData13[7] = q[1];
725 –            atomData13[8] = q[2];
726 –            atomData13[9] = q[3];
727 –            
728 –            atomData13[10] = dAtom->getJx();
729 –            atomData13[11] = dAtom->getJy();
730 –            atomData13[12] = dAtom->getJz();
731 –          }
732 –          
733 –        } else {
734 –          sprintf(painCave.errMsg,
735 –                  "Atom %d not found on processor %d\n",
736 –                  i, worldRank );
737 –          haveError= 1;
738 –          simError();
739 –        }
740 –        
741 –        if(haveError) DieDieDie();
742 –        
743 –        // If we've survived to here, format the line:
744 –        
745 –        if (!isDirectional) {
746 –
747 –          sprintf( tempBuffer,
748 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
749 –                   atomTypeString,
750 –                   atomData6[0],
751 –                   atomData6[1],
752 –                   atomData6[2],
753 –                   atomData6[3],
754 –                   atomData6[4],
755 –                   atomData6[5]);
756 –          
757 –          strcpy( writeLine, tempBuffer );
758 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
759 –
760 –        } else {
761 –          
762 –          sprintf( tempBuffer,
763 –                   "%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\n",
764 –                   atomTypeString,
765 –                   atomData13[0],
766 –                   atomData13[1],
767 –                   atomData13[2],
768 –                   atomData13[3],
769 –                   atomData13[4],
770 –                   atomData13[5],
771 –                   atomData13[6],
772 –                   atomData13[7],
773 –                   atomData13[8],
774 –                   atomData13[9],
775 –                   atomData13[10],
776 –                   atomData13[11],
777 –                   atomData13[12]);
778 –          
779 –          strcat( writeLine, tempBuffer );
780 –          
781 –        }
782 –        
783 –        finalOut << writeLine;
784 –        finalOut.flush();
421        }
422 +      
423 +      for(k = 0; k < outFile.size(); k++)
424 +        *outFile[k] << writeLine;
425      }
426 <
427 <    finalOut.flush();
426 >    
427 >    for(k = 0; k < outFile.size(); k++)
428 >      outFile[k]->flush();
429 >    
430      sprintf( checkPointMsg,
431               "Sucessfully took a dump.\n");
432 +
433      MPIcheckPoint();        
434 <    
434 >
435 >    delete[] potatoes;
436 >
437    } else {
438  
439      // worldRank != 0, so I'm a remote node.  
# Line 797 | Line 441 | void DumpWriter::writeFinal(double finalTime){
441      // Set my magic potato to 0:
442  
443      myPotato = 0;
444 +    currentIndex = 0;
445      
446      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
447        
# Line 813 | Line 458 | void DumpWriter::writeFinal(double finalTime){
458            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
459            
460          }
461 <
462 <        local_index=-1;
463 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
464 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
820 <        }
821 <        if (local_index != -1) {
461 >        which_atom = i;
462 >        local_index = indexArray[currentIndex].first;        
463 >                
464 >        if (which_atom == indexArray[currentIndex].second) {
465          
466            atomTypeString = atoms[local_index]->getType();
467  
468 <          atoms[local_index]->getPos(pos);
469 <          atoms[local_index]->getVel(vel);
468 >                atoms[local_index]->getPos(pos);
469 >                atoms[local_index]->getVel(vel);
470  
471            atomData6[0] = pos[0];
472            atomData6[1] = pos[1];
# Line 849 | Line 492 | void DumpWriter::writeFinal(double finalTime){
492              atomData13[7] = q[1];
493              atomData13[8] = q[2];
494              atomData13[9] = q[3];
495 <
495 >  
496              atomData13[10] = dAtom->getJx();
497              atomData13[11] = dAtom->getJy();
498              atomData13[12] = dAtom->getJz();
499            }
500  
501          } else {
502 <          sprintf(painCave.errMsg,
503 <                  "Atom %d not found on processor %d\n",
504 <                  i, worldRank );
505 <          haveError= 1;
506 <          simError();
507 <        }
502 >                sprintf(painCave.errMsg,
503 >                              "Atom %d not found on processor %d\n",
504 >                              i, worldRank );
505 >                haveError= 1;
506 >                simError();
507 >              }
508  
509          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
510  
# Line 869 | Line 512 | void DumpWriter::writeFinal(double finalTime){
512          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
513  
514          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
515 <                 myPotato, MPI_COMM_WORLD);
515 >                             myPotato, MPI_COMM_WORLD);
516          
517          myPotato++;
518  
519          MPI_Send(&isDirectional, 1, MPI_INT, 0,
520 <                 myPotato, MPI_COMM_WORLD);
520 >                             myPotato, MPI_COMM_WORLD);
521          
522          myPotato++;
523          
# Line 889 | Line 532 | void DumpWriter::writeFinal(double finalTime){
532                     myPotato, MPI_COMM_WORLD);
533          }
534  
535 <        myPotato++;      
535 >        myPotato++;  
536 >        currentIndex++;    
537        }
538      }
539  
# Line 899 | Line 543 | void DumpWriter::writeFinal(double finalTime){
543      
544    }
545    
902 –  if( worldRank == 0 ) finalOut.close();
546   #endif // is_mpi
547   }
548  
906 –
907 –
549   #ifdef IS_MPI
550  
551   // a couple of functions to let us escape the write loop

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