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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 952 by tim, Fri Jan 16 21:55:39 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  
31 <    strcpy( outName, entry_plug->sampleName );
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32  
33 <    outFile.open(outName, ios::out | ios::trunc );
33 >    if( !dumpFile ){
34  
33 –    if( !outFile ){
34 –
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
42 –    //outFile.setf( ios::scientific );
43 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 56 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68  
69 + /**
70 + * A hook function to load balancing
71 + */
72 +
73 + void DumpWriter::update(){
74 +  sortByGlobalIndex();          
75 + }
76 +  
77 + /**
78 + * Auxiliary sorting function
79 + */
80 +
81 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 +  return p1.second < p2.second;
83 + }
84 +
85 + /**
86 + * Sorting the local index by global index
87 + */
88 +
89 + void DumpWriter::sortByGlobalIndex(){
90 +  Atom** atoms = entry_plug->atoms;
91 +  
92 +  indexArray.clear();
93 +  
94 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 +  
97 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 +
99 +  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 +  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 +  //}
102 +    
103 + }
104 +
105 + #endif
106 +
107 + void DumpWriter::writeDump(double currentTime){
108 +
109 +  ofstream finalOut;
110 +  vector<ofstream*> fileStreams;
111 +
112 + #ifdef IS_MPI
113 +  if(worldRank == 0 ){
114 + #endif    
115 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 +    if( !finalOut ){
117 +      sprintf( painCave.errMsg,
118 +               "Could not open \"%s\" for final dump output.\n",
119 +               entry_plug->finalName );
120 +      painCave.isFatal = 1;
121 +      simError();
122 +    }
123 + #ifdef IS_MPI
124 +  }
125 + #endif // is_mpi
126 +
127 +  fileStreams.push_back(&finalOut);
128 +  fileStreams.push_back(&dumpFile);
129 +
130 +  writeFrame(fileStreams, currentTime);
131 +
132 + #ifdef IS_MPI
133 +  finalOut.close();
134 + #endif
135 +        
136 + }
137 +
138 + void DumpWriter::writeFinal(double currentTime){
139 +
140 +  ofstream finalOut;
141 +  vector<ofstream*> fileStreams;
142 +
143 + #ifdef IS_MPI
144 +  if(worldRank == 0 ){
145 + #endif // is_mpi
146 +
147 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 +
149 +    if( !finalOut ){
150 +      sprintf( painCave.errMsg,
151 +               "Could not open \"%s\" for final dump output.\n",
152 +               entry_plug->finalName );
153 +      painCave.isFatal = 1;
154 +      simError();
155 +    }
156 +
157 + #ifdef IS_MPI
158 +  }
159 + #endif // is_mpi
160 +  
161 +  fileStreams.push_back(&finalOut);  
162 +  writeFrame(fileStreams, currentTime);
163 +
164 + #ifdef IS_MPI
165 +  finalOut.close();
166 + #endif
167 +  
168 + }
169 +
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171 +
172    const int BUFFERSIZE = 2000;
173    const int MINIBUFFERSIZE = 100;
174  
175 <  char tempBuffer[BUFFERSIZE];
175 >  char tempBuffer[BUFFERSIZE];  
176    char writeLine[BUFFERSIZE];
177  
178 <  int i;
178 >  int i, k;
179  
180   #ifdef IS_MPI
181    
182 +  /*********************************************************************
183 +   * Documentation?  You want DOCUMENTATION?
184 +   *
185 +   * Why all the potatoes below?  
186 +   *
187 +   * To make a long story short, the original version of DumpWriter
188 +   * worked in the most inefficient way possible.  Node 0 would
189 +   * poke each of the node for an individual atom's formatted data
190 +   * as node 0 worked its way down the global index. This was particularly
191 +   * inefficient since the method blocked all processors at every atom
192 +   * (and did it twice!).
193 +   *
194 +   * An intermediate version of DumpWriter could be described from Node
195 +   * zero's perspective as follows:
196 +   *
197 +   *  1) Have 100 of your friends stand in a circle.
198 +   *  2) When you say go, have all of them start tossing potatoes at
199 +   *     you (one at a time).
200 +   *  3) Catch the potatoes.
201 +   *
202 +   * It was an improvement, but MPI has buffers and caches that could
203 +   * best be described in this analogy as "potato nets", so there's no
204 +   * need to block the processors atom-by-atom.
205 +   *
206 +   * This new and improved DumpWriter works in an even more efficient
207 +   * way:
208 +   *
209 +   *  1) Have 100 of your friend stand in a circle.
210 +   *  2) When you say go, have them start tossing 5-pound bags of
211 +   *     potatoes at you.
212 +   *  3) Once you've caught a friend's bag of potatoes,
213 +   *     toss them a spud to let them know they can toss another bag.
214 +   *
215 +   * How's THAT for documentation?
216 +   *
217 +   *********************************************************************/
218 +
219    int *potatoes;
220    int myPotato;
221  
222    int nProc;
223 <  int j, which_node, done, which_atom, local_index;
223 >  int j, which_node, done, which_atom, local_index, currentIndex;
224    double atomData6[6];
225    double atomData13[13];
226    int isDirectional;
# Line 95 | Line 236 | void DumpWriter::writeDump( double currentTime ){
236    Atom** atoms = entry_plug->atoms;
237    double pos[3], vel[3];
238  
98 –  // write current frame to the eor file
99 –
100 –  this->writeFinal( currentTime );
101 –
239   #ifndef IS_MPI
240 +  
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243  
244 <  outFile << nAtoms << "\n";
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252  
253 <  outFile << currentTime << ";\t"
254 <          << entry_plug->Hmat[0][0] << "\t"
255 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\t"
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256  
257 <          << entry_plug->Hmat[0][1] << "\t"
258 <          << entry_plug->Hmat[1][1] << "\t"
259 <          << entry_plug->Hmat[2][1] << ";\t"
260 <
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 <
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 >  }
260 >  
261    for( i=0; i<nAtoms; i++ ){
262  
263      atoms[i]->getPos(pos);
# Line 154 | Line 293 | void DumpWriter::writeDump( double currentTime ){
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295  
296 <    outFile << writeLine;
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
159 –  outFile.flush();
299  
300   #else // is_mpi
301  
# Line 184 | Line 323 | void DumpWriter::writeDump( double currentTime ){
323      nProc = mpiSim->getNumberProcessors();
324      potatoes = new int[nProc];
325  
326 +    //write out the comment lines
327      for (i = 0; i < nProc; i++)
328        potatoes[i] = 0;
329      
330 <    outFile << mpiSim->getTotAtoms() << "\n";
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332  
333 <    outFile << currentTime << ";\t"
334 <            << entry_plug->Hmat[0][0] << "\t"
335 <            << entry_plug->Hmat[1][0] << "\t"
336 <            << entry_plug->Hmat[2][0] << ";\t"
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337  
338 <            << entry_plug->Hmat[0][1] << "\t"
339 <            << entry_plug->Hmat[1][1] << "\t"
340 <            << entry_plug->Hmat[2][1] << ";\t"
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341  
342 <            << entry_plug->Hmat[0][2] << "\t"
343 <            << entry_plug->Hmat[1][2] << "\t"
344 <            << entry_plug->Hmat[2][2] << ";";
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348  
349 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
206 <    outFile << endl;
207 <    outFile.flush();
349 >    currentIndex = 0;
350  
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352        
# Line 228 | Line 370 | void DumpWriter::writeDump( double currentTime ){
370          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371                   myPotato, MPI_COMM_WORLD, &istatus);
372          
231 –        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 –        
233 –        // Null terminate the atomTypeString just in case:
234 –
235 –        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
373          atomTypeString = MPIatomTypeString;
374          
375          myPotato++;
# Line 255 | Line 392 | void DumpWriter::writeDump( double currentTime ){
392  
393        } else {
394          
395 <        haveError = 0;
395 >        haveError = 0;
396          which_atom = i;
260 –        local_index=-1;
397          
398 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
399 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
400 <        }
398 >        //local_index = -1;
399 >
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403          
404 <        if (local_index != -1) {
404 >        //if (local_index != -1) {
405 >          
406 >          local_index = indexArray[currentIndex].first;        
407            
408 <          atomTypeString = atoms[local_index]->getType();
409 <
408 >          if (which_atom == indexArray[currentIndex].second) {
409 >            
410 >            atomTypeString = atoms[local_index]->getType();
411 >            
412            atoms[local_index]->getPos(pos);
413            atoms[local_index]->getVel(vel);          
414 <
414 >          
415            atomData6[0] = pos[0];
416            atomData6[1] = pos[1];
417            atomData6[2] = pos[2];
# Line 302 | Line 444 | void DumpWriter::writeDump( double currentTime ){
444            
445          } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451          }
452          
453 <        if(haveError) DieDieDie();
453 >        if(haveError) DieDieDie();
454          
455 +        currentIndex++;
456        }
457        // If we've survived to here, format the line:
458        
459        if (!isDirectional) {
460          
461 <        sprintf( tempBuffer,
461 >        sprintf( writeLine,
462                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463                   atomTypeString,
464                   atomData6[0],
# Line 325 | Line 468 | void DumpWriter::writeDump( double currentTime ){
468                   atomData6[4],
469                   atomData6[5]);
470          
328 –        strcpy( writeLine, tempBuffer );
471          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472          
473        } else {
474          
475 <        sprintf( tempBuffer,
475 >        sprintf( writeLine,
476                   "%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",
477                   atomTypeString,
478                   atomData13[0],
# Line 346 | Line 488 | void DumpWriter::writeDump( double currentTime ){
488                   atomData13[10],
489                   atomData13[11],
490                   atomData13[12]);
349 –        
350 –        strcpy( writeLine, tempBuffer );
491          
492        }
493        
494 <      outFile << writeLine;
495 <      outFile.flush();
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
497      
498 <
499 <    outFile.flush();
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501      sprintf( checkPointMsg,
502               "Sucessfully took a dump.\n");
503 +    
504      MPIcheckPoint();        
505 +    
506      delete[] potatoes;
507 +    
508    } else {
509  
510      // worldRank != 0, so I'm a remote node.  
# Line 368 | Line 512 | void DumpWriter::writeDump( double currentTime ){
512      // Set my magic potato to 0:
513  
514      myPotato = 0;
515 +    currentIndex = 0;
516      
517      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518        
# Line 376 | Line 521 | void DumpWriter::writeDump( double currentTime ){
521        if (AtomToProcMap[i] == worldRank) {
522  
523          if (myPotato + 3 >= MAXTAG) {
524 <
524 >          
525            // The potato was going to exceed the maximum value,
526            // so wrap this processor potato back to 0 (and block until
527            // node 0 says we can go:
528 <
528 >          
529            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530            
531          }
532          which_atom = i;
388 –        local_index=-1;
389 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
390 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
391 –        }
392 –        if (local_index != -1) {
393 –        
394 –          atomTypeString = atoms[local_index]->getType();
533  
534 <          atoms[local_index]->getPos(pos);
397 <          atoms[local_index]->getVel(vel);
534 >        //local_index = -1;
535  
536 <          atomData6[0] = pos[0];
537 <          atomData6[1] = pos[1];
538 <          atomData6[2] = pos[2];
402 <
403 <          atomData6[3] = vel[0];
404 <          atomData6[4] = vel[1];
405 <          atomData6[5] = vel[2];
406 <          
407 <          isDirectional = 0;
408 <
409 <          if( atoms[local_index]->isDirectional() ){
410 <
411 <            isDirectional = 1;
412 <            
413 <            dAtom = (DirectionalAtom *)atoms[local_index];
414 <            dAtom->getQ( q );
415 <            
416 <            for (int j = 0; j < 6 ; j++)
417 <              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);
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539          
540 <        myPotato++;
540 >        //if (local_index != -1) {
541  
542 <        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;
542 >        local_index = indexArray[currentIndex].first;        
543                  
544 <        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;
715 <            
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 <            
722 <            atomData13[6] = q[0];
723 <            atomData13[7] = q[1];
724 <            atomData13[8] = q[2];
725 <            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 <    }
788 <  
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) {
544 >        if (which_atom == indexArray[currentIndex].second) {
545          
546            atomTypeString = atoms[local_index]->getType();
547 <
547 >          
548            atoms[local_index]->getPos(pos);
549            atoms[local_index]->getVel(vel);
550 <
550 >          
551            atomData6[0] = pos[0];
552            atomData6[1] = pos[1];
553            atomData6[2] = pos[2];
# Line 852 | Line 572 | void DumpWriter::writeFinal(double finalTime){
572              atomData13[7] = q[1];
573              atomData13[8] = q[2];
574              atomData13[9] = q[3];
575 <
575 >  
576              atomData13[10] = dAtom->getJx();
577              atomData13[11] = dAtom->getJy();
578              atomData13[12] = dAtom->getJz();
# Line 860 | Line 580 | void DumpWriter::writeFinal(double finalTime){
580  
581          } else {
582            sprintf(painCave.errMsg,
583 <                  "Atom %d not found on processor %d\n",
584 <                  i, worldRank );
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585            haveError= 1;
586            simError();
587          }
588 <
588 >        
589          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591          // null terminate the string before sending (just in case):
592          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593  
594          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 <                 myPotato, MPI_COMM_WORLD);
595 >                             myPotato, MPI_COMM_WORLD);
596          
597          myPotato++;
598  
599          MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 <                 myPotato, MPI_COMM_WORLD);
600 >                             myPotato, MPI_COMM_WORLD);
601          
602          myPotato++;
603          
# Line 892 | Line 612 | void DumpWriter::writeFinal(double finalTime){
612                     myPotato, MPI_COMM_WORLD);
613          }
614  
615 <        myPotato++;      
615 >        myPotato++;  
616 >        currentIndex++;    
617        }
618      }
619  
# Line 902 | Line 623 | void DumpWriter::writeFinal(double finalTime){
623      
624    }
625    
905 –  if( worldRank == 0 ) finalOut.close();
626   #endif // is_mpi
627   }
628  
909 –
910 –
629   #ifdef IS_MPI
630  
631   // a couple of functions to let us escape the write loop

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