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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 920 by tim, Sat Jan 10 09:46:47 2004 UTC vs.
Revision 929 by tim, Tue Jan 13 15:46:49 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      }
# Line 44 | Line 45 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
45   #ifdef IS_MPI
46    }
47  
48 +  //sort the local atoms by global index
49 +  sortByGlobalIndex();
50 +  
51    sprintf( checkPointMsg,
52             "Sucessfully opened output file for dumping.\n");
53    MPIcheckPoint();
# Line 56 | Line 60 | DumpWriter::~DumpWriter( ){
60    if(worldRank == 0 ){
61   #endif // is_mpi
62  
63 <    outFile.close();
63 >    dumpFile.close();
64  
65   #ifdef IS_MPI
66    }
67   #endif // is_mpi
68   }
69  
70 < void DumpWriter::writeDump( double currentTime ){
70 > #ifdef IS_MPI
71  
72 + /**
73 + * A hook function to load balancing
74 + */
75 +
76 + void DumpWriter::update(){
77 +  sortByGlobalIndex();          
78 + }
79 +  
80 + /**
81 + * Auxiliary sorting function
82 + */
83 +
84 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
85 +  return p1.second < p2.second;
86 + }
87 +
88 + /**
89 + * Sorting the local index by global index
90 + */
91 +
92 + void DumpWriter::sortByGlobalIndex(){
93 +  Atom** atoms = entry_plug->atoms;
94 +  
95 +  indexArray.clear();
96 +  
97 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
98 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
99 +  
100 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
101 + }
102 + #endif
103 +
104 + void DumpWriter::writeDump(double currentTime){
105 +  
106 + // write to eor file
107 +  writeFinal(currentTime);
108 +
109 + //write to dump file
110 +  writeFrame(dumpFile, currentTime);
111 +        
112 + }
113 +
114 + void DumpWriter::writeFinal(double currentTime){
115 +
116 +  ofstream finalOut;    
117 +  
118 +  //Open eor file
119 + #ifdef IS_MPI
120 +  if(worldRank == 0 ){
121 + #endif // is_mpi
122 +
123 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
124 +    if( !finalOut ){
125 +      sprintf( painCave.errMsg,
126 +               "Could not open \"%s\" for final dump output.\n",
127 +               entry_plug->finalName );
128 +      painCave.isFatal = 1;
129 +      simError();
130 +    }
131 +    
132 + #ifdef IS_MPI
133 +  }
134 + #endif
135 +  
136 +  //write to eor file  
137 +  writeFrame(finalOut, currentTime);
138 +  
139 +  //close eor file      
140 + #ifdef IS_MPI
141 +  if(worldRank == 0 ){
142 +    finalOut.close();
143 +  }
144 + #endif // is_mpi
145 +
146 + }
147 +
148 + void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
149 +
150    const int BUFFERSIZE = 2000;
151    const int MINIBUFFERSIZE = 100;
152  
# Line 79 | Line 161 | void DumpWriter::writeDump( double currentTime ){
161    int myPotato;
162  
163    int nProc;
164 <  int j, which_node, done, which_atom, local_index;
164 >  int j, which_node, done, which_atom, local_index, currentIndex;
165    double atomData6[6];
166    double atomData13[13];
167    int isDirectional;
# Line 95 | Line 177 | void DumpWriter::writeDump( double currentTime ){
177    Atom** atoms = entry_plug->atoms;
178    double pos[3], vel[3];
179  
98 –  // write current frame to the eor file
99 –
100 –  this->writeFinal( currentTime );
101 –
180   #ifndef IS_MPI
181  
182    outFile << nAtoms << "\n";
# Line 156 | Line 234 | void DumpWriter::writeDump( double currentTime ){
234  
235      outFile << writeLine;
236    }
159 –  outFile.flush();
237  
238   #else // is_mpi
239  
# Line 205 | Line 282 | void DumpWriter::writeDump( double currentTime ){
282      outFile << entry_plug->the_integrator->getAdditionalParameters();
283      outFile << endl;
284      outFile.flush();
285 <
285 >    
286 >    currentIndex = 0;
287      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
288        
289        // Get the Node number which has this atom;
# Line 228 | Line 306 | void DumpWriter::writeDump( double currentTime ){
306          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307                   myPotato, MPI_COMM_WORLD, &istatus);
308          
231 –        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 –        
233 –        // Null terminate the atomTypeString just in case:
234 –
235 –        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
309          atomTypeString = MPIatomTypeString;
310          
311          myPotato++;
# Line 257 | Line 330 | void DumpWriter::writeDump( double currentTime ){
330          
331          haveError = 0;
332          which_atom = i;
260 –        local_index=-1;
333          
334 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
335 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
336 <        }
265 <        
266 <        if (local_index != -1) {
334 >        local_index = indexArray[currentIndex].first;        
335 >                
336 >        if (which_atom == indexArray[currentIndex].second) {
337            
338            atomTypeString = atoms[local_index]->getType();
339  
# Line 310 | Line 380 | void DumpWriter::writeDump( double currentTime ){
380          
381          if(haveError) DieDieDie();
382          
383 <        // If we've survived to here, format the line:
314 <        
315 <        if (!isDirectional) {
316 <
317 <          sprintf( tempBuffer,
318 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
319 <                   atomTypeString,
320 <                   atomData6[0],
321 <                   atomData6[1],
322 <                   atomData6[2],
323 <                   atomData6[3],
324 <                   atomData6[4],
325 <                   atomData6[5]);
326 <          
327 <          strcpy( writeLine, tempBuffer );
328 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
329 <
330 <        } else {
331 <          
332 <          sprintf( tempBuffer,
333 <                   "%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",
334 <                   atomTypeString,
335 <                   atomData13[0],
336 <                   atomData13[1],
337 <                   atomData13[2],
338 <                   atomData13[3],
339 <                   atomData13[4],
340 <                   atomData13[5],
341 <                   atomData13[6],
342 <                   atomData13[7],
343 <                   atomData13[8],
344 <                   atomData13[9],
345 <                   atomData13[10],
346 <                   atomData13[11],
347 <                   atomData13[12]);
348 <          
349 <          strcat( writeLine, tempBuffer );
350 <          
351 <        }
352 <        
353 <        outFile << writeLine;
354 <        outFile.flush();
383 >        currentIndex ++;
384        }
385 <    }
385 >      // If we've survived to here, format the line:
386 >      
387 >      if (!isDirectional) {
388 >        
389 >        sprintf( writeLine,
390 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
391 >                 atomTypeString,
392 >                 atomData6[0],
393 >                 atomData6[1],
394 >                 atomData6[2],
395 >                 atomData6[3],
396 >                 atomData6[4],
397 >                 atomData6[5]);
398  
399 <    outFile.flush();
400 <    sprintf( checkPointMsg,
401 <             "Sucessfully took a dump.\n");
402 <    MPIcheckPoint();        
403 <    delete[] potatoes;
404 <  } else {
405 <
406 <    // worldRank != 0, so I'm a remote node.  
407 <
408 <    // Set my magic potato to 0:
409 <
410 <    myPotato = 0;
411 <    
412 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
413 <      
414 <      // Am I the node which has this atom?
415 <      
416 <      if (AtomToProcMap[i] == worldRank) {
417 <
418 <        if (myPotato + 3 >= MAXTAG) {
378 <
379 <          // The potato was going to exceed the maximum value,
380 <          // so wrap this processor potato back to 0 (and block until
381 <          // node 0 says we can go:
382 <
383 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
384 <          
385 <        }
386 <        which_atom = i;
387 <        local_index=-1;
388 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
389 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
390 <        }
391 <        if (local_index != -1) {
392 <        
393 <          atomTypeString = atoms[local_index]->getType();
394 <
395 <          atoms[local_index]->getPos(pos);
396 <          atoms[local_index]->getVel(vel);
397 <
398 <          atomData6[0] = pos[0];
399 <          atomData6[1] = pos[1];
400 <          atomData6[2] = pos[2];
401 <
402 <          atomData6[3] = vel[0];
403 <          atomData6[4] = vel[1];
404 <          atomData6[5] = vel[2];
405 <          
406 <          isDirectional = 0;
407 <
408 <          if( atoms[local_index]->isDirectional() ){
409 <
410 <            isDirectional = 1;
411 <            
412 <            dAtom = (DirectionalAtom *)atoms[local_index];
413 <            dAtom->getQ( q );
414 <            
415 <            for (int j = 0; j < 6 ; j++)
416 <              atomData13[j] = atomData6[j];
417 <            
418 <            atomData13[6] = q[0];
419 <            atomData13[7] = q[1];
420 <            atomData13[8] = q[2];
421 <            atomData13[9] = q[3];
422 <
423 <            atomData13[10] = dAtom->getJx();
424 <            atomData13[11] = dAtom->getJy();
425 <            atomData13[12] = dAtom->getJz();
426 <          }
427 <
428 <        } else {
429 <          sprintf(painCave.errMsg,
430 <                  "Atom %d not found on processor %d\n",
431 <                  i, worldRank );
432 <          haveError= 1;
433 <          simError();
434 <        }
435 <
436 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
437 <
438 <        // null terminate the string before sending (just in case):
439 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
440 <
441 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
442 <                 myPotato, MPI_COMM_WORLD);
399 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
400 >        
401 >      } else {
402 >        
403 >        sprintf( writeLine,
404 >                 "%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",
405 >                 atomTypeString,
406 >                 atomData13[0],
407 >                 atomData13[1],
408 >                 atomData13[2],
409 >                 atomData13[3],
410 >                 atomData13[4],
411 >                 atomData13[5],
412 >                 atomData13[6],
413 >                 atomData13[7],
414 >                 atomData13[8],
415 >                 atomData13[9],
416 >                 atomData13[10],
417 >                 atomData13[11],
418 >                 atomData13[12]);
419          
444 –        myPotato++;
445 –
446 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
447 –                 myPotato, MPI_COMM_WORLD);
448 –        
449 –        myPotato++;
450 –        
451 –        if (isDirectional) {
452 –
453 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
454 –                   myPotato, MPI_COMM_WORLD);
455 –          
456 –        } else {
457 –
458 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
459 –                   myPotato, MPI_COMM_WORLD);
460 –        }
461 –
462 –        myPotato++;      
420        }
421 +      
422 +      outFile << writeLine;
423      }
465 –
466 –    sprintf( checkPointMsg,
467 –             "Sucessfully took a dump.\n");
468 –    MPIcheckPoint();        
424      
470 –  }
471 –  
472 – #endif // is_mpi
473 – }
425  
426 < void DumpWriter::writeFinal(double finalTime){
476 <
477 <  char finalName[500];
478 <  ofstream finalOut;
479 <
480 <  const int BUFFERSIZE = 2000;
481 <  const int MINIBUFFERSIZE = 100;
482 <  char tempBuffer[BUFFERSIZE];
483 <  char writeLine[BUFFERSIZE];
484 <
485 <  double q[4];
486 <  DirectionalAtom* dAtom;
487 <  Atom** atoms = entry_plug->atoms;
488 <  int i;
489 < #ifdef IS_MPI
490 <  
491 <  int *potatoes;
492 <  int myPotato;
493 <
494 <  int nProc;
495 <  int j, which_node, done, which_atom, local_index;
496 <  double atomData6[6];
497 <  double atomData13[13];
498 <  int isDirectional;
499 <  char* atomTypeString;
500 <  char MPIatomTypeString[MINIBUFFERSIZE];
501 <
502 < #else //is_mpi
503 <  int nAtoms = entry_plug->n_atoms;
504 < #endif //is_mpi
505 <
506 <  double pos[3], vel[3];
507 <
508 < #ifdef IS_MPI
509 <  if(worldRank == 0 ){
510 < #endif // is_mpi
511 <
512 <    strcpy( finalName, entry_plug->finalName );
513 <
514 <    finalOut.open( finalName, ios::out | ios::trunc );
515 <    if( !finalOut ){
516 <      sprintf( painCave.errMsg,
517 <               "Could not open \"%s\" for final dump output.\n",
518 <               finalName );
519 <      painCave.isFatal = 1;
520 <      simError();
521 <    }
522 <
523 <    // finalOut.setf( ios::scientific );
524 <
525 < #ifdef IS_MPI
526 <  }
527 <
528 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
529 <  MPIcheckPoint();
530 <
531 < #endif //is_mpi
532 <
533 <
534 < #ifndef IS_MPI
535 <
536 <  finalOut << nAtoms << "\n";
537 <
538 <  finalOut << finalTime << ";\t"
539 <           << entry_plug->Hmat[0][0] << "\t"
540 <           << entry_plug->Hmat[1][0] << "\t"
541 <           << entry_plug->Hmat[2][0] << ";\t"
542 <
543 <           << entry_plug->Hmat[0][1] << "\t"
544 <           << entry_plug->Hmat[1][1] << "\t"
545 <           << entry_plug->Hmat[2][1] << ";\t"
546 <
547 <           << entry_plug->Hmat[0][2] << "\t"
548 <           << entry_plug->Hmat[1][2] << "\t"
549 <           << entry_plug->Hmat[2][2] << ";";
550 <
551 <  //write out additional parameters, such as chi and eta
552 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 <  finalOut << endl;
554 <
555 <  for( i=0; i<nAtoms; i++ ){
556 <
557 <    atoms[i]->getPos(pos);
558 <    atoms[i]->getVel(vel);
559 <
560 <    sprintf( tempBuffer,
561 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
562 <             atoms[i]->getType(),
563 <             pos[0],
564 <             pos[1],
565 <             pos[2],
566 <             vel[0],
567 <             vel[1],
568 <             vel[2]);
569 <    strcpy( writeLine, tempBuffer );
570 <
571 <    if( atoms[i]->isDirectional() ){
572 <
573 <      dAtom = (DirectionalAtom *)atoms[i];
574 <      dAtom->getQ( q );
575 <
576 <      sprintf( tempBuffer,
577 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
578 <               q[0],
579 <               q[1],
580 <               q[2],
581 <               q[3],
582 <               dAtom->getJx(),
583 <               dAtom->getJy(),
584 <               dAtom->getJz());
585 <      strcat( writeLine, tempBuffer );
586 <    }
587 <    else
588 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
589 <
590 <    finalOut << writeLine;
591 <  }
592 <  finalOut.flush();
593 <  finalOut.close();
594 <
595 < #else // is_mpi
596 <
597 <  /* code to find maximum tag value */
598 <  int *tagub, flag, MAXTAG;
599 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
600 <  if (flag) {
601 <    MAXTAG = *tagub;
602 <  } else {
603 <    MAXTAG = 32767;
604 <  }  
605 <
606 <  int haveError;
607 <
608 <  MPI_Status istatus;
609 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
610 <
611 <  // write out header and node 0's coordinates
612 <
613 <  if( worldRank == 0 ){
614 <
615 <    // Node 0 needs a list of the magic potatoes for each processor;
616 <
617 <    nProc = mpiSim->getNumberProcessors();
618 <    potatoes = new int[nProc];
619 <
620 <    for (i = 0; i < nProc; i++)
621 <      potatoes[i] = 0;
622 <    
623 <    finalOut << mpiSim->getTotAtoms() << "\n";
624 <
625 <    finalOut << finalTime << ";\t"
626 <            << entry_plug->Hmat[0][0] << "\t"
627 <            << entry_plug->Hmat[1][0] << "\t"
628 <            << entry_plug->Hmat[2][0] << ";\t"
629 <
630 <            << entry_plug->Hmat[0][1] << "\t"
631 <            << entry_plug->Hmat[1][1] << "\t"
632 <            << entry_plug->Hmat[2][1] << ";\t"
633 <
634 <            << entry_plug->Hmat[0][2] << "\t"
635 <            << entry_plug->Hmat[1][2] << "\t"
636 <            << entry_plug->Hmat[2][2] << ";";
637 <
638 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
639 <    finalOut << endl;
640 <    finalOut.flush();
641 <
642 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
643 <      
644 <      // Get the Node number which has this atom;
645 <      
646 <      which_node = AtomToProcMap[i];
647 <      
648 <      if (which_node != 0) {
649 <
650 <        if (potatoes[which_node] + 3 >= MAXTAG) {
651 <          // The potato was going to exceed the maximum value,
652 <          // so wrap this processor potato back to 0:        
653 <
654 <          potatoes[which_node] = 0;          
655 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
656 <          
657 <        }
658 <
659 <        myPotato = potatoes[which_node];        
660 <        
661 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
662 <                 myPotato, MPI_COMM_WORLD, &istatus);
663 <        
664 <        atomTypeString = MPIatomTypeString;
665 <                
666 <        myPotato++;
667 <
668 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
669 <                 myPotato, MPI_COMM_WORLD, &istatus);
670 <              
671 <        myPotato++;
672 <
673 <        if (isDirectional) {          
674 <          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
675 <                   myPotato, MPI_COMM_WORLD, &istatus);
676 <        } else {
677 <          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
678 <                   myPotato, MPI_COMM_WORLD, &istatus);          
679 <        }
680 <        
681 <        myPotato++;
682 <        potatoes[which_node] = myPotato;
683 <
684 <      } else {
685 <        
686 <        haveError = 0;
687 <        which_atom = i;
688 <        local_index=-1;
689 <        
690 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
691 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
692 <        }
693 <        
694 <        if (local_index != -1) {
695 <          
696 <          atomTypeString = atoms[local_index]->getType();
697 <
698 <          atoms[local_index]->getPos(pos);
699 <          atoms[local_index]->getVel(vel);          
700 <
701 <          atomData6[0] = pos[0];
702 <          atomData6[1] = pos[1];
703 <          atomData6[2] = pos[2];
704 <
705 <          atomData6[3] = vel[0];
706 <          atomData6[4] = vel[1];
707 <          atomData6[5] = vel[2];
708 <          
709 <          isDirectional = 0;
710 <
711 <          if( atoms[local_index]->isDirectional() ){
712 <
713 <            isDirectional = 1;
714 <            
715 <            dAtom = (DirectionalAtom *)atoms[local_index];
716 <            dAtom->getQ( q );
717 <
718 <            for (int j = 0; j < 6 ; j++)
719 <              atomData13[j] = atomData6[j];            
720 <            
721 <            atomData13[6] = q[0];
722 <            atomData13[7] = q[1];
723 <            atomData13[8] = q[2];
724 <            atomData13[9] = q[3];
725 <            
726 <            atomData13[10] = dAtom->getJx();
727 <            atomData13[11] = dAtom->getJy();
728 <            atomData13[12] = dAtom->getJz();
729 <          }
730 <          
731 <        } else {
732 <          sprintf(painCave.errMsg,
733 <                  "Atom %d not found on processor %d\n",
734 <                  i, worldRank );
735 <          haveError= 1;
736 <          simError();
737 <        }
738 <        
739 <        if(haveError) DieDieDie();
740 <        
741 <        // If we've survived to here, format the line:
742 <        
743 <        if (!isDirectional) {
744 <
745 <          sprintf( tempBuffer,
746 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
747 <                   atomTypeString,
748 <                   atomData6[0],
749 <                   atomData6[1],
750 <                   atomData6[2],
751 <                   atomData6[3],
752 <                   atomData6[4],
753 <                   atomData6[5]);
754 <          
755 <          strcpy( writeLine, tempBuffer );
756 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
757 <
758 <        } else {
759 <          
760 <          sprintf( tempBuffer,
761 <                   "%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",
762 <                   atomTypeString,
763 <                   atomData13[0],
764 <                   atomData13[1],
765 <                   atomData13[2],
766 <                   atomData13[3],
767 <                   atomData13[4],
768 <                   atomData13[5],
769 <                   atomData13[6],
770 <                   atomData13[7],
771 <                   atomData13[8],
772 <                   atomData13[9],
773 <                   atomData13[10],
774 <                   atomData13[11],
775 <                   atomData13[12]);
776 <          
777 <          strcat( writeLine, tempBuffer );
778 <          
779 <        }
780 <        
781 <        finalOut << writeLine;
782 <        finalOut.flush();
783 <      }
784 <    }
785 <
786 <    finalOut.flush();
426 >    outFile.flush();
427      sprintf( checkPointMsg,
428               "Sucessfully took a dump.\n");
789 –    delete[] potatoes;
790 –      
429      MPIcheckPoint();        
430 <    
430 >    delete[] potatoes;
431    } else {
432  
433      // worldRank != 0, so I'm a remote node.  
# Line 797 | Line 435 | void DumpWriter::writeFinal(double finalTime){
435      // Set my magic potato to 0:
436  
437      myPotato = 0;
438 +    currentIndex = 0;
439      
440      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
441        
# Line 813 | Line 452 | void DumpWriter::writeFinal(double finalTime){
452            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
453            
454          }
455 <        which_atom = i;  
456 <        local_index=-1;
457 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
458 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
820 <        }
821 <        if (local_index != -1) {
455 >        which_atom = i;
456 >        local_index = indexArray[currentIndex].first;        
457 >                
458 >        if (which_atom == indexArray[currentIndex].second) {
459          
460            atomTypeString = atoms[local_index]->getType();
461  
# Line 889 | Line 526 | void DumpWriter::writeFinal(double finalTime){
526                     myPotato, MPI_COMM_WORLD);
527          }
528  
529 <        myPotato++;      
529 >        myPotato++;  
530 >        currentIndex++;    
531        }
532      }
533  
# Line 899 | Line 537 | void DumpWriter::writeFinal(double finalTime){
537      
538    }
539    
902 –  if( worldRank == 0 ) finalOut.close();
540   #endif // is_mpi
541   }
542  
906 –
907 –
543   #ifdef IS_MPI
544  
545   // a couple of functions to let us escape the write loop

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