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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 927 by tim, Mon Jan 12 22:54:42 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 +  for(k = 0; k < outFile.size(); k++){
179 +    *outFile[k] << nAtoms << "\n";
180  
181 <  outFile << nAtoms << "\n";
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 <  outFile << currentTime << ";\t"
191 <          << entry_plug->Hmat[0][0] << "\t"
192 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\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][1] << "\t"
195 <          << entry_plug->Hmat[1][1] << "\t"
196 <          << entry_plug->Hmat[2][1] << ";\t"
197 <
115 <          << entry_plug->Hmat[0][2] << "\t"
116 <          << entry_plug->Hmat[1][2] << "\t"
117 <          << entry_plug->Hmat[2][2] << ";";
118 <  //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  
# Line 184 | 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();
206 <    outFile << endl;
207 <    outFile.flush();
286 >    currentIndex = 0;
287  
288      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
289        
# Line 228 | Line 307 | void DumpWriter::writeDump( double currentTime ){
307          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
308                   myPotato, MPI_COMM_WORLD, &istatus);
309          
231 –        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 –        
233 –        // Null terminate the atomTypeString just in case:
234 –
235 –        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
310          atomTypeString = MPIatomTypeString;
311          
312          myPotato++;
# Line 255 | Line 329 | void DumpWriter::writeDump( double currentTime ){
329  
330        } else {
331          
332 <        haveError = 0;
333 <        which_atom = i;
260 <        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 <        }
265 <        
266 <        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 301 | 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 +        currentIndex ++;
385        }
386        // If we've survived to here, format the line:
387        
388        if (!isDirectional) {
389          
390 <        sprintf( tempBuffer,
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]);
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          
328 –        strcpy( writeLine, tempBuffer );
329 –        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
330 –        
402        } else {
403          
404 <        sprintf( tempBuffer,
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]);
349 <        
350 <        strcpy( writeLine, tempBuffer );
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          
421        }
422        
423 <      outFile << writeLine;
424 <      outFile.flush();
423 >      for(k = 0; k < outFile.size(); k++)
424 >        *outFile[k] << writeLine;
425      }
426      
427 <
428 <    outFile.flush();
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 +
435      delete[] potatoes;
436 +
437    } else {
438  
439      // worldRank != 0, so I'm a remote node.  
# Line 368 | Line 441 | void DumpWriter::writeDump( double currentTime ){
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 385 | Line 459 | void DumpWriter::writeDump( double currentTime ){
459            
460          }
461          which_atom = i;
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;
391 <        }
392 <        if (local_index != -1) {
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 415 | Line 487 | void DumpWriter::writeDump( double currentTime ){
487              
488              for (int j = 0; j < 6 ; j++)
489                atomData13[j] = atomData6[j];
418 –            
419 –            atomData13[6] = q[0];
420 –            atomData13[7] = q[1];
421 –            atomData13[8] = q[2];
422 –            atomData13[9] = q[3];
423 –
424 –            atomData13[10] = dAtom->getJx();
425 –            atomData13[11] = dAtom->getJy();
426 –            atomData13[12] = dAtom->getJz();
427 –          }
428 –
429 –        } else {
430 –          sprintf(painCave.errMsg,
431 –                  "Atom %d not found on processor %d\n",
432 –                  i, worldRank );
433 –          haveError= 1;
434 –          simError();
435 –        }
436 –
437 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
438 –
439 –        // null terminate the string before sending (just in case):
440 –        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
441 –
442 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
443 –                 myPotato, MPI_COMM_WORLD);
444 –        
445 –        myPotato++;
446 –
447 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
448 –                 myPotato, MPI_COMM_WORLD);
449 –        
450 –        myPotato++;
451 –        
452 –        if (isDirectional) {
453 –
454 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
455 –                   myPotato, MPI_COMM_WORLD);
456 –          
457 –        } else {
458 –
459 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
460 –                   myPotato, MPI_COMM_WORLD);
461 –        }
462 –
463 –        myPotato++;      
464 –      }
465 –    }
466 –
467 –    sprintf( checkPointMsg,
468 –             "Sucessfully took a dump.\n");
469 –    MPIcheckPoint();        
470 –    
471 –  }
472 –  
473 – #endif // is_mpi
474 – }
475 –
476 – void DumpWriter::writeFinal(double finalTime){
477 –
478 –  char finalName[500];
479 –  ofstream finalOut;
480 –
481 –  const int BUFFERSIZE = 2000;
482 –  const int MINIBUFFERSIZE = 100;
483 –  char tempBuffer[BUFFERSIZE];
484 –  char writeLine[BUFFERSIZE];
485 –
486 –  double q[4];
487 –  DirectionalAtom* dAtom;
488 –  Atom** atoms = entry_plug->atoms;
489 –  int i;
490 – #ifdef IS_MPI
491 –  
492 –  int *potatoes;
493 –  int myPotato;
494 –
495 –  int nProc;
496 –  int j, which_node, done, which_atom, local_index;
497 –  double atomData6[6];
498 –  double atomData13[13];
499 –  int isDirectional;
500 –  char* atomTypeString;
501 –  char MPIatomTypeString[MINIBUFFERSIZE];
502 –
503 – #else //is_mpi
504 –  int nAtoms = entry_plug->n_atoms;
505 – #endif //is_mpi
506 –
507 –  double pos[3], vel[3];
508 –
509 – #ifdef IS_MPI
510 –  if(worldRank == 0 ){
511 – #endif // is_mpi
512 –
513 –    strcpy( finalName, entry_plug->finalName );
514 –
515 –    finalOut.open( finalName, ios::out | ios::trunc );
516 –    if( !finalOut ){
517 –      sprintf( painCave.errMsg,
518 –               "Could not open \"%s\" for final dump output.\n",
519 –               finalName );
520 –      painCave.isFatal = 1;
521 –      simError();
522 –    }
523 –
524 –    // finalOut.setf( ios::scientific );
525 –
526 – #ifdef IS_MPI
527 –  }
528 –
529 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
530 –  MPIcheckPoint();
531 –
532 – #endif //is_mpi
533 –
534 –
535 – #ifndef IS_MPI
536 –
537 –  finalOut << nAtoms << "\n";
538 –
539 –  finalOut << finalTime << ";\t"
540 –           << entry_plug->Hmat[0][0] << "\t"
541 –           << entry_plug->Hmat[1][0] << "\t"
542 –           << entry_plug->Hmat[2][0] << ";\t"
543 –
544 –           << entry_plug->Hmat[0][1] << "\t"
545 –           << entry_plug->Hmat[1][1] << "\t"
546 –           << entry_plug->Hmat[2][1] << ";\t"
547 –
548 –           << entry_plug->Hmat[0][2] << "\t"
549 –           << entry_plug->Hmat[1][2] << "\t"
550 –           << entry_plug->Hmat[2][2] << ";";
551 –
552 –  //write out additional parameters, such as chi and eta
553 –  finalOut << entry_plug->the_integrator->getAdditionalParameters();
554 –  finalOut << endl;
555 –
556 –  for( i=0; i<nAtoms; i++ ){
557 –
558 –    atoms[i]->getPos(pos);
559 –    atoms[i]->getVel(vel);
560 –
561 –    sprintf( tempBuffer,
562 –             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563 –             atoms[i]->getType(),
564 –             pos[0],
565 –             pos[1],
566 –             pos[2],
567 –             vel[0],
568 –             vel[1],
569 –             vel[2]);
570 –    strcpy( writeLine, tempBuffer );
571 –
572 –    if( atoms[i]->isDirectional() ){
573 –
574 –      dAtom = (DirectionalAtom *)atoms[i];
575 –      dAtom->getQ( q );
576 –
577 –      sprintf( tempBuffer,
578 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
579 –               q[0],
580 –               q[1],
581 –               q[2],
582 –               q[3],
583 –               dAtom->getJx(),
584 –               dAtom->getJy(),
585 –               dAtom->getJz());
586 –      strcat( writeLine, tempBuffer );
587 –    }
588 –    else
589 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
590 –
591 –    finalOut << writeLine;
592 –  }
593 –  finalOut.flush();
594 –  finalOut.close();
595 –
596 – #else // is_mpi
597 –
598 –  /* code to find maximum tag value */
599 –  int *tagub, flag, MAXTAG;
600 –  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
601 –  if (flag) {
602 –    MAXTAG = *tagub;
603 –  } else {
604 –    MAXTAG = 32767;
605 –  }  
606 –
607 –  int haveError;
608 –
609 –  MPI_Status istatus;
610 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
611 –
612 –  // write out header and node 0's coordinates
613 –
614 –  if( worldRank == 0 ){
615 –
616 –    // Node 0 needs a list of the magic potatoes for each processor;
617 –
618 –    nProc = mpiSim->getNumberProcessors();
619 –    potatoes = new int[nProc];
620 –
621 –    for (i = 0; i < nProc; i++)
622 –      potatoes[i] = 0;
623 –    
624 –    finalOut << mpiSim->getTotAtoms() << "\n";
625 –
626 –    finalOut << finalTime << ";\t"
627 –            << entry_plug->Hmat[0][0] << "\t"
628 –            << entry_plug->Hmat[1][0] << "\t"
629 –            << entry_plug->Hmat[2][0] << ";\t"
630 –
631 –            << entry_plug->Hmat[0][1] << "\t"
632 –            << entry_plug->Hmat[1][1] << "\t"
633 –            << entry_plug->Hmat[2][1] << ";\t"
634 –
635 –            << entry_plug->Hmat[0][2] << "\t"
636 –            << entry_plug->Hmat[1][2] << "\t"
637 –            << entry_plug->Hmat[2][2] << ";";
638 –
639 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
640 –    finalOut << endl;
641 –    finalOut.flush();
642 –
643 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
644 –      
645 –      // Get the Node number which has this atom;
646 –      
647 –      which_node = AtomToProcMap[i];
648 –      
649 –      if (which_node != 0) {
650 –
651 –        if (potatoes[which_node] + 3 >= MAXTAG) {
652 –          // The potato was going to exceed the maximum value,
653 –          // so wrap this processor potato back to 0:        
654 –
655 –          potatoes[which_node] = 0;          
656 –          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
657 –          
658 –        }
659 –
660 –        myPotato = potatoes[which_node];        
661 –        
662 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
663 –                 myPotato, MPI_COMM_WORLD, &istatus);
664 –        
665 –        atomTypeString = MPIatomTypeString;
666 –                
667 –        myPotato++;
668 –
669 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
670 –                 myPotato, MPI_COMM_WORLD, &istatus);
671 –              
672 –        myPotato++;
673 –
674 –        if (isDirectional) {          
675 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
676 –                   myPotato, MPI_COMM_WORLD, &istatus);
677 –        } else {
678 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
679 –                   myPotato, MPI_COMM_WORLD, &istatus);          
680 –        }
681 –        
682 –        myPotato++;
683 –        potatoes[which_node] = myPotato;
684 –
685 –      } else {
686 –        
687 –        haveError = 0;
688 –        which_atom = i;
689 –        local_index=-1;
690 –        
691 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
692 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
693 –        }
694 –        
695 –        if (local_index != -1) {
696 –          
697 –          atomTypeString = atoms[local_index]->getType();
698 –
699 –          atoms[local_index]->getPos(pos);
700 –          atoms[local_index]->getVel(vel);          
701 –
702 –          atomData6[0] = pos[0];
703 –          atomData6[1] = pos[1];
704 –          atomData6[2] = pos[2];
705 –
706 –          atomData6[3] = vel[0];
707 –          atomData6[4] = vel[1];
708 –          atomData6[5] = vel[2];
709 –          
710 –          isDirectional = 0;
711 –
712 –          if( atoms[local_index]->isDirectional() ){
713 –
714 –            isDirectional = 1;
490              
716 –            dAtom = (DirectionalAtom *)atoms[local_index];
717 –            dAtom->getQ( q );
718 –
719 –            for (int j = 0; j < 6 ; j++)
720 –              atomData13[j] = atomData6[j];            
721 –            
491              atomData13[6] = q[0];
492              atomData13[7] = q[1];
493              atomData13[8] = q[2];
494              atomData13[9] = q[3];
726 –            
727 –            atomData13[10] = dAtom->getJx();
728 –            atomData13[11] = dAtom->getJy();
729 –            atomData13[12] = dAtom->getJz();
730 –          }
731 –          
732 –        } else {
733 –          sprintf(painCave.errMsg,
734 –                  "Atom %d not found on processor %d\n",
735 –                  i, worldRank );
736 –          haveError= 1;
737 –          simError();
738 –        }
739 –        
740 –        if(haveError) DieDieDie();
741 –        
742 –      }
743 –
744 –
745 –      // If we've survived to here, format the line:
746 –      
747 –      if (!isDirectional) {
748 –        
749 –        sprintf( tempBuffer,
750 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
751 –                 atomTypeString,
752 –                 atomData6[0],
753 –                 atomData6[1],
754 –                 atomData6[2],
755 –                 atomData6[3],
756 –                 atomData6[4],
757 –                 atomData6[5]);
758 –        
759 –        strcpy( writeLine, tempBuffer );
760 –        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
761 –        
762 –      } else {
763 –        
764 –        sprintf( tempBuffer,
765 –                 "%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",
766 –                 atomTypeString,
767 –                 atomData13[0],
768 –                 atomData13[1],
769 –                 atomData13[2],
770 –                 atomData13[3],
771 –                 atomData13[4],
772 –                 atomData13[5],
773 –                 atomData13[6],
774 –                 atomData13[7],
775 –                 atomData13[8],
776 –                 atomData13[9],
777 –                 atomData13[10],
778 –                 atomData13[11],
779 –                 atomData13[12]);
780 –        
781 –        strcpy( writeLine, tempBuffer );
782 –        
783 –      }
784 –        
785 –      finalOut << writeLine;
786 –      finalOut.flush();
787 –    }
495    
789 –    finalOut.flush();
790 –    sprintf( checkPointMsg,
791 –             "Sucessfully took a dump.\n");
792 –    delete[] potatoes;
793 –    
794 –    MPIcheckPoint();        
795 –    
796 –  } else {
797 –
798 –    // worldRank != 0, so I'm a remote node.  
799 –
800 –    // Set my magic potato to 0:
801 –
802 –    myPotato = 0;
803 –    
804 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
805 –      
806 –      // Am I the node which has this atom?
807 –      
808 –      if (AtomToProcMap[i] == worldRank) {
809 –
810 –        if (myPotato + 3 >= MAXTAG) {
811 –
812 –          // The potato was going to exceed the maximum value,
813 –          // so wrap this processor potato back to 0 (and block until
814 –          // node 0 says we can go:
815 –
816 –          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
817 –          
818 –        }
819 –        which_atom = i;  
820 –        local_index=-1;
821 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
822 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
823 –        }
824 –        if (local_index != -1) {
825 –        
826 –          atomTypeString = atoms[local_index]->getType();
827 –
828 –          atoms[local_index]->getPos(pos);
829 –          atoms[local_index]->getVel(vel);
830 –
831 –          atomData6[0] = pos[0];
832 –          atomData6[1] = pos[1];
833 –          atomData6[2] = pos[2];
834 –
835 –          atomData6[3] = vel[0];
836 –          atomData6[4] = vel[1];
837 –          atomData6[5] = vel[2];
838 –          
839 –          isDirectional = 0;
840 –
841 –          if( atoms[local_index]->isDirectional() ){
842 –
843 –            isDirectional = 1;
844 –            
845 –            dAtom = (DirectionalAtom *)atoms[local_index];
846 –            dAtom->getQ( q );
847 –            
848 –            for (int j = 0; j < 6 ; j++)
849 –              atomData13[j] = atomData6[j];
850 –            
851 –            atomData13[6] = q[0];
852 –            atomData13[7] = q[1];
853 –            atomData13[8] = q[2];
854 –            atomData13[9] = q[3];
855 –
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 872 | 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 892 | Line 532 | void DumpWriter::writeFinal(double finalTime){
532                     myPotato, MPI_COMM_WORLD);
533          }
534  
535 <        myPotato++;      
535 >        myPotato++;  
536 >        currentIndex++;    
537        }
538      }
539  
# Line 902 | Line 543 | void DumpWriter::writeFinal(double finalTime){
543      
544    }
545    
905 –  if( worldRank == 0 ) finalOut.close();
546   #endif // is_mpi
547   }
548  
909 –
910 –
549   #ifdef IS_MPI
550  
551   // a couple of functions to let us escape the write loop

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