ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 916 by gezelter, Fri Jan 9 20:29:32 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  
240    /* code to find maximum tag value */
241 +  
242    int *tagub, flag, MAXTAG;
243    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
244    if (flag) {
# Line 204 | 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 227 | Line 306 | void DumpWriter::writeDump( double currentTime ){
306          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307                   myPotato, MPI_COMM_WORLD, &istatus);
308          
309 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
310 <        
232 <        // Null terminate the atomTypeString just in case:
233 <
234 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
235 <
309 >        atomTypeString = MPIatomTypeString;
310 >        
311          myPotato++;
312  
313          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 255 | Line 330 | void DumpWriter::writeDump( double currentTime ){
330          
331          haveError = 0;
332          which_atom = i;
258 –        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 <        }
263 <        
264 <        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 308 | Line 380 | void DumpWriter::writeDump( double currentTime ){
380          
381          if(haveError) DieDieDie();
382          
383 <        // If we've survived to here, format the line:
384 <        
385 <        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();
353 <      }
354 <    }
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++ ) {
383 >        currentIndex ++;
384 >      }
385 >      // If we've survived to here, format the line:
386        
387 <      // Am I the node which has this atom?
388 <      
389 <      if (AtomToProcMap[i] == worldRank) {
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 <        if (myPotato + 3 >= MAXTAG) {
400 <
401 <          // The potato was going to exceed the maximum value,
402 <          // so wrap this processor potato back to 0 (and block until
403 <          // node 0 says we can go:
404 <
405 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
406 <          
407 <        }
408 <
409 <        local_index=-1;
410 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
411 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
412 <        }
413 <        if (local_index != -1) {
414 <        
415 <          atomTypeString = atoms[local_index]->getType();
416 <
417 <          atoms[local_index]->getPos(pos);
418 <          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);
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          
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++;      
420        }
421 +      
422 +      outFile << writeLine;
423      }
463 –
464 –    sprintf( checkPointMsg,
465 –             "Sucessfully took a dump.\n");
466 –    MPIcheckPoint();        
424      
468 –  }
469 –  
470 – #endif // is_mpi
471 – }
425  
426 < 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;
685 <
686 <      } else {
687 <        
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();
785 <      }
786 <    }
787 <
788 <    finalOut.flush();
426 >    outFile.flush();
427      sprintf( checkPointMsg,
428               "Sucessfully took a dump.\n");
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 <
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

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines