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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 913 by chuckv, Thu Jan 8 22:25:52 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 72 | Line 154 | void DumpWriter::writeDump( double currentTime ){
154    char writeLine[BUFFERSIZE];
155  
156    int i;
157 +
158   #ifdef IS_MPI
159 <  int j, which_node, done, which_atom, local_index;
160 <  double atomTransData[6];
161 <  double atomOrientData[7];
159 >  
160 >  int *potatoes;
161 >  int myPotato;
162 >
163 >  int nProc;
164 >  int j, which_node, done, which_atom, local_index, currentIndex;
165 >  double atomData6[6];
166 >  double atomData13[13];
167    int isDirectional;
168    char* atomTypeString;
169    char MPIatomTypeString[MINIBUFFERSIZE];
170 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
170 >
171   #else //is_mpi
172    int nAtoms = entry_plug->n_atoms;
173   #endif //is_mpi
# Line 93 | Line 177 | void DumpWriter::writeDump( double currentTime ){
177    Atom** atoms = entry_plug->atoms;
178    double pos[3], vel[3];
179  
96 –  // write current frame to the eor file
97 –
98 –  this->writeFinal( currentTime );
99 –
180   #ifndef IS_MPI
181  
182    outFile << nAtoms << "\n";
# Line 154 | Line 234 | void DumpWriter::writeDump( double currentTime ){
234  
235      outFile << writeLine;
236    }
157 –  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) {
245      MAXTAG = *tagub;
246    } else {
247      MAXTAG = 32767;
248 <  }
248 >  }  
249  
250    int haveError;
251  
# Line 175 | Line 255 | void DumpWriter::writeDump( double currentTime ){
255    // write out header and node 0's coordinates
256  
257    if( worldRank == 0 ){
258 +
259 +    // Node 0 needs a list of the magic potatoes for each processor;
260 +
261 +    nProc = mpiSim->getNumberProcessors();
262 +    potatoes = new int[nProc];
263 +
264 +    for (i = 0; i < nProc; i++)
265 +      potatoes[i] = 0;
266 +    
267      outFile << mpiSim->getTotAtoms() << "\n";
268  
269      outFile << currentTime << ";\t"
# Line 193 | Line 282 | void DumpWriter::writeDump( double currentTime ){
282      outFile << entry_plug->the_integrator->getAdditionalParameters();
283      outFile << endl;
284      outFile.flush();
285 <
286 <    tag = 0;
198 <
285 >    
286 >    currentIndex = 0;
287      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
200 –
201 –      if (tag + 2 >= MAXTAG) {
202 –        // The tag was going to exceed the maximum value, so wrap around to 0:
203 –        tag = 0;
204 –        // Send the newly zeroed tag on to the other nodes:
205 –        MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 –      }
288        
289        // Get the Node number which has this atom;
290        
291        which_node = AtomToProcMap[i];
292        
293        if (which_node != 0) {
294 +
295 +        if (potatoes[which_node] + 3 >= MAXTAG) {
296 +          // The potato was going to exceed the maximum value,
297 +          // so wrap this processor potato back to 0:        
298 +
299 +          potatoes[which_node] = 0;          
300 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
301 +          
302 +        }
303 +
304 +        myPotato = potatoes[which_node];        
305          
306          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
307 >                 myPotato, MPI_COMM_WORLD, &istatus);
308          
309 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
310 <        
311 <        // Null terminate the atomTypeString just in case:
309 >        atomTypeString = MPIatomTypeString;
310 >        
311 >        myPotato++;
312  
221 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
222 –
313          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
314 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
315 <        
316 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
314 >                 myPotato, MPI_COMM_WORLD, &istatus);
315 >              
316 >        myPotato++;
317  
318 <        if (isDirectional) {
319 <
320 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
321 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
322 <
318 >        if (isDirectional) {          
319 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
320 >                   myPotato, MPI_COMM_WORLD, &istatus);
321 >        } else {
322 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
323 >                   myPotato, MPI_COMM_WORLD, &istatus);          
324          }
325 +        
326 +        myPotato++;
327 +        potatoes[which_node] = myPotato;
328  
329        } else {
330          
331          haveError = 0;
332          which_atom = i;
333 <        local_index=-1;
334 <
335 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
336 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
337 <        }
245 <
246 <        if (local_index != -1) {
247 <
333 >        
334 >        local_index = indexArray[currentIndex].first;        
335 >                
336 >        if (which_atom == indexArray[currentIndex].second) {
337 >          
338            atomTypeString = atoms[local_index]->getType();
339  
340            atoms[local_index]->getPos(pos);
341 <          atoms[local_index]->getVel(vel);
341 >          atoms[local_index]->getVel(vel);          
342  
343 <          atomTransData[0] = pos[0];
344 <          atomTransData[1] = pos[1];
345 <          atomTransData[2] = pos[2];
343 >          atomData6[0] = pos[0];
344 >          atomData6[1] = pos[1];
345 >          atomData6[2] = pos[2];
346  
347 <          atomTransData[3] = vel[0];
348 <          atomTransData[4] = vel[1];
349 <          atomTransData[5] = vel[2];
347 >          atomData6[3] = vel[0];
348 >          atomData6[4] = vel[1];
349 >          atomData6[5] = vel[2];
350            
351            isDirectional = 0;
352  
# Line 266 | Line 356 | void DumpWriter::writeDump( double currentTime ){
356              
357              dAtom = (DirectionalAtom *)atoms[local_index];
358              dAtom->getQ( q );
269 –            
270 –            atomOrientData[0] = q[0];
271 –            atomOrientData[1] = q[1];
272 –            atomOrientData[2] = q[2];
273 –            atomOrientData[3] = q[3];
359  
360 <            atomOrientData[4] = dAtom->getJx();
361 <            atomOrientData[5] = dAtom->getJy();
362 <            atomOrientData[6] = dAtom->getJz();
360 >            for (int j = 0; j < 6 ; j++)
361 >              atomData13[j] = atomData6[j];            
362 >            
363 >            atomData13[6] = q[0];
364 >            atomData13[7] = q[1];
365 >            atomData13[8] = q[2];
366 >            atomData13[9] = q[3];
367 >            
368 >            atomData13[10] = dAtom->getJx();
369 >            atomData13[11] = dAtom->getJy();
370 >            atomData13[12] = dAtom->getJz();
371            }
372 <
372 >          
373          } else {
374            sprintf(painCave.errMsg,
375                    "Atom %d not found on processor %d\n",
# Line 284 | Line 377 | void DumpWriter::writeDump( double currentTime ){
377            haveError= 1;
378            simError();
379          }
380 <
380 >        
381          if(haveError) DieDieDie();
289 –                              
290 –        // If we've survived to here, format the line:
382          
383 <        sprintf( tempBuffer,
384 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
385 <                 atomTypeString,
386 <                 atomTransData[0],
387 <                 atomTransData[1],
388 <                 atomTransData[2],
389 <                 atomTransData[3],
390 <                 atomTransData[4],
391 <                 atomTransData[5]);
383 >        currentIndex ++;
384 >      }
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 <        strcpy( writeLine, tempBuffer );
400 <
401 <        if (isDirectional) {
402 <
403 <          sprintf( tempBuffer,
404 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
405 <                   atomOrientData[0],
406 <                   atomOrientData[1],
407 <                   atomOrientData[2],
408 <                   atomOrientData[3],
409 <                   atomOrientData[4],
410 <                   atomOrientData[5],
411 <                   atomOrientData[6]);
412 <          strcat( writeLine, tempBuffer );
413 <
414 <        } else {
415 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
416 <        }
417 <
418 <        outFile << writeLine;
419 <        outFile.flush();
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 >        
420        }
421 +      
422 +      outFile << writeLine;
423      }
424 +    
425  
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.  
434 +
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 338 | Line 443 | void DumpWriter::writeDump( double currentTime ){
443        
444        if (AtomToProcMap[i] == worldRank) {
445  
446 <        local_index=-1;
447 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
448 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
446 >        if (myPotato + 3 >= MAXTAG) {
447 >
448 >          // The potato was going to exceed the maximum value,
449 >          // so wrap this processor potato back to 0 (and block until
450 >          // node 0 says we can go:
451 >
452 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
453 >          
454          }
455 <        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  
462            atoms[local_index]->getPos(pos);
463            atoms[local_index]->getVel(vel);
464  
465 <          atomTransData[0] = pos[0];
466 <          atomTransData[1] = pos[1];
467 <          atomTransData[2] = pos[2];
465 >          atomData6[0] = pos[0];
466 >          atomData6[1] = pos[1];
467 >          atomData6[2] = pos[2];
468  
469 <          atomTransData[3] = vel[0];
470 <          atomTransData[4] = vel[1];
471 <          atomTransData[5] = vel[2];
469 >          atomData6[3] = vel[0];
470 >          atomData6[4] = vel[1];
471 >          atomData6[5] = vel[2];
472            
473            isDirectional = 0;
474  
# Line 366 | Line 479 | void DumpWriter::writeDump( double currentTime ){
479              dAtom = (DirectionalAtom *)atoms[local_index];
480              dAtom->getQ( q );
481              
482 <            atomOrientData[0] = q[0];
483 <            atomOrientData[1] = q[1];
484 <            atomOrientData[2] = q[2];
485 <            atomOrientData[3] = q[3];
482 >            for (int j = 0; j < 6 ; j++)
483 >              atomData13[j] = atomData6[j];
484 >            
485 >            atomData13[6] = q[0];
486 >            atomData13[7] = q[1];
487 >            atomData13[8] = q[2];
488 >            atomData13[9] = q[3];
489  
490 <            atomOrientData[4] = dAtom->getJx();
491 <            atomOrientData[5] = dAtom->getJy();
492 <            atomOrientData[6] = dAtom->getJz();
490 >            atomData13[10] = dAtom->getJx();
491 >            atomData13[11] = dAtom->getJy();
492 >            atomData13[12] = dAtom->getJz();
493            }
494  
495          } else {
# Line 384 | Line 500 | void DumpWriter::writeDump( double currentTime ){
500            simError();
501          }
502  
387 –        // I've survived this far, so send off the data!
388 –
389 –        atomTypeTag          = 4*i;
390 –        atomIsDirectionalTag = 4*i + 1;
391 –        atomTransDataTag     = 4*i + 2;
392 –        atomOrientDataTag    = 4*i + 3;
393 –
394 –
503          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
504  
505          // null terminate the string before sending (just in case):
506          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
507  
508          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
509 <                 atomTypeTag, MPI_COMM_WORLD);
509 >                 myPotato, MPI_COMM_WORLD);
510          
511 +        myPotato++;
512 +
513          MPI_Send(&isDirectional, 1, MPI_INT, 0,
514 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
514 >                 myPotato, MPI_COMM_WORLD);
515          
516 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
517 <                 atomTransDataTag, MPI_COMM_WORLD);
408 <
516 >        myPotato++;
517 >        
518          if (isDirectional) {
519  
520 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
521 <                   atomOrientDataTag, MPI_COMM_WORLD);
520 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
521 >                   myPotato, MPI_COMM_WORLD);
522            
523 <        }
415 <      
416 <      }
417 <    }
523 >        } else {
524  
525 <    sprintf( checkPointMsg,
526 <             "Sucessfully took a dump.\n");
421 <    MPIcheckPoint();        
422 <    
423 <  }
424 <  
425 <  painCave.isEventLoop = 0;
426 <
427 < #endif // is_mpi
428 < }
429 <
430 < void DumpWriter::writeFinal(double finalTime){
431 <
432 <  char finalName[500];
433 <  ofstream finalOut;
434 <
435 <  const int BUFFERSIZE = 2000;
436 <  const int MINIBUFFERSIZE = 100;
437 <  char tempBuffer[BUFFERSIZE];
438 <  char writeLine[BUFFERSIZE];
439 <
440 <  double q[4];
441 <  DirectionalAtom* dAtom;
442 <  Atom** atoms = entry_plug->atoms;
443 <  int i;
444 < #ifdef IS_MPI
445 <  int j, which_node, done, which_atom, local_index;
446 <  double atomTransData[6];
447 <  double atomOrientData[7];
448 <  int isDirectional;
449 <  char* atomTypeString;
450 <  char MPIatomTypeString[MINIBUFFERSIZE];
451 <  int atomTypeTag;
452 <  int atomIsDirectionalTag;
453 <  int atomTransDataTag;
454 <  int atomOrientDataTag;
455 < #else //is_mpi
456 <  int nAtoms = entry_plug->n_atoms;
457 < #endif //is_mpi
458 <
459 <  double pos[3], vel[3];
460 <
461 < #ifdef IS_MPI
462 <  if(worldRank == 0 ){
463 < #endif // is_mpi
464 <
465 <    strcpy( finalName, entry_plug->finalName );
466 <
467 <    finalOut.open( finalName, ios::out | ios::trunc );
468 <    if( !finalOut ){
469 <      sprintf( painCave.errMsg,
470 <               "Could not open \"%s\" for final dump output.\n",
471 <               finalName );
472 <      painCave.isFatal = 1;
473 <      simError();
474 <    }
475 <
476 <    // finalOut.setf( ios::scientific );
477 <
478 < #ifdef IS_MPI
479 <  }
480 <
481 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
482 <  MPIcheckPoint();
483 <
484 < #endif //is_mpi
485 <
486 <
487 < #ifndef IS_MPI
488 <
489 <  finalOut << nAtoms << "\n";
490 <
491 <  finalOut << finalTime << ";\t"
492 <           << entry_plug->Hmat[0][0] << "\t"
493 <           << entry_plug->Hmat[1][0] << "\t"
494 <           << entry_plug->Hmat[2][0] << ";\t"
495 <
496 <           << entry_plug->Hmat[0][1] << "\t"
497 <           << entry_plug->Hmat[1][1] << "\t"
498 <           << entry_plug->Hmat[2][1] << ";\t"
499 <
500 <           << entry_plug->Hmat[0][2] << "\t"
501 <           << entry_plug->Hmat[1][2] << "\t"
502 <           << entry_plug->Hmat[2][2] << ";";
503 <
504 <  //write out additional parameters, such as chi and eta
505 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
506 <  finalOut << endl;
507 <
508 <  for( i=0; i<nAtoms; i++ ){
509 <
510 <    atoms[i]->getPos(pos);
511 <    atoms[i]->getVel(vel);
512 <
513 <    sprintf( tempBuffer,
514 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <             atoms[i]->getType(),
516 <             pos[0],
517 <             pos[1],
518 <             pos[2],
519 <             vel[0],
520 <             vel[1],
521 <             vel[2]);
522 <    strcpy( writeLine, tempBuffer );
523 <
524 <    if( atoms[i]->isDirectional() ){
525 <
526 <      dAtom = (DirectionalAtom *)atoms[i];
527 <      dAtom->getQ( q );
528 <
529 <      sprintf( tempBuffer,
530 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <               q[0],
532 <               q[1],
533 <               q[2],
534 <               q[3],
535 <               dAtom->getJx(),
536 <               dAtom->getJy(),
537 <               dAtom->getJz());
538 <      strcat( writeLine, tempBuffer );
539 <    }
540 <    else
541 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
542 <
543 <    finalOut << writeLine;
544 <  }
545 <  finalOut.flush();
546 <  finalOut.close();
547 <
548 < #else // is_mpi
549 <
550 <  // first thing first, suspend fatalities.
551 <  painCave.isEventLoop = 1;
552 <
553 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
554 <  int haveError;
555 <
556 <  MPI_Status istatus;
557 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
558 <
559 <  // write out header and node 0's coordinates
560 <
561 <  if( worldRank == 0 ){
562 <    finalOut << mpiSim->getTotAtoms() << "\n";
563 <
564 <    finalOut << finalTime << ";\t"
565 <            << entry_plug->Hmat[0][0] << "\t"
566 <            << entry_plug->Hmat[1][0] << "\t"
567 <            << entry_plug->Hmat[2][0] << ";\t"
568 <
569 <            << entry_plug->Hmat[0][1] << "\t"
570 <            << entry_plug->Hmat[1][1] << "\t"
571 <            << entry_plug->Hmat[2][1] << ";\t"
572 <
573 <            << entry_plug->Hmat[0][2] << "\t"
574 <            << entry_plug->Hmat[1][2] << "\t"
575 <            << entry_plug->Hmat[2][2] << ";";
576 <
577 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
578 <    finalOut << endl;
579 <    finalOut.flush();
580 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
581 <      // Get the Node number which has this atom;
582 <
583 <      which_node = AtomToProcMap[i];
584 <
585 <      if (which_node != 0) {
586 <        
587 <        atomTypeTag          = 4*i;
588 <        atomIsDirectionalTag = 4*i + 1;
589 <        atomTransDataTag     = 4*i + 2;
590 <        atomOrientDataTag    = 4*i + 3;
591 <
592 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
593 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
594 <        
595 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
596 <
597 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
598 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
599 <        
600 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
601 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
602 <
603 <        if (isDirectional) {
604 <
605 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
606 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
607 <
525 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
526 >                   myPotato, MPI_COMM_WORLD);
527          }
528  
529 <      } else {
530 <        
612 <        haveError = 0;
613 <        which_atom = i;
614 <        local_index=-1;
615 <
616 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
617 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
618 <        }
619 <
620 <        if (local_index != -1) {
621 <
622 <          atomTypeString = atoms[local_index]->getType();
623 <
624 <          atoms[local_index]->getPos(pos);
625 <          atoms[local_index]->getVel(vel);
626 <
627 <          atomTransData[0] = pos[0];
628 <          atomTransData[1] = pos[1];
629 <          atomTransData[2] = pos[2];
630 <
631 <          atomTransData[3] = vel[0];
632 <          atomTransData[4] = vel[1];
633 <          atomTransData[5] = vel[2];
634 <          
635 <          isDirectional = 0;
636 <
637 <          if( atoms[local_index]->isDirectional() ){
638 <
639 <            isDirectional = 1;
640 <            
641 <            dAtom = (DirectionalAtom *)atoms[local_index];
642 <            dAtom->getQ( q );
643 <            
644 <            atomOrientData[0] = q[0];
645 <            atomOrientData[1] = q[1];
646 <            atomOrientData[2] = q[2];
647 <            atomOrientData[3] = q[3];
648 <
649 <            atomOrientData[4] = dAtom->getJx();
650 <            atomOrientData[5] = dAtom->getJy();
651 <            atomOrientData[6] = dAtom->getJz();
652 <          }
653 <
654 <        } else {
655 <          sprintf(painCave.errMsg,
656 <                  "Atom %d not found on processor %d\n",
657 <                  i, worldRank );
658 <          haveError= 1;
659 <          simError();
660 <        }
661 <
662 <        if(haveError) DieDieDie();
663 <                              
664 <        // If we've survived to here, format the line:
665 <        
666 <        sprintf( tempBuffer,
667 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
668 <                 atomTypeString,
669 <                 atomTransData[0],
670 <                 atomTransData[1],
671 <                 atomTransData[2],
672 <                 atomTransData[3],
673 <                 atomTransData[4],
674 <                 atomTransData[5]);
675 <
676 <        strcpy( writeLine, tempBuffer );
677 <
678 <        if (isDirectional) {
679 <
680 <          sprintf( tempBuffer,
681 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
682 <                   atomOrientData[0],
683 <                   atomOrientData[1],
684 <                   atomOrientData[2],
685 <                   atomOrientData[3],
686 <                   atomOrientData[4],
687 <                   atomOrientData[5],
688 <                   atomOrientData[6]);
689 <          strcat( writeLine, tempBuffer );
690 <
691 <        } else {
692 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
693 <        }
694 <
695 <        finalOut << writeLine;
696 <        finalOut.flush();
529 >        myPotato++;  
530 >        currentIndex++;    
531        }
532      }
533  
700 –    finalOut.flush();
534      sprintf( checkPointMsg,
535               "Sucessfully took a dump.\n");
536      MPIcheckPoint();        
537      
538 <  } else {
706 <
707 <    // worldRank != 0, so I'm a remote node.  
708 <    
709 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
710 <      
711 <      // Am I the node which has this atom?
712 <      
713 <      if (AtomToProcMap[i] == worldRank) {
714 <
715 <        local_index=-1;
716 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
717 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
718 <        }
719 <        if (local_index != -1) {
720 <        
721 <          atomTypeString = atoms[local_index]->getType();
722 <
723 <          atoms[local_index]->getPos(pos);
724 <          atoms[local_index]->getVel(vel);
725 <
726 <          atomTransData[0] = pos[0];
727 <          atomTransData[1] = pos[1];
728 <          atomTransData[2] = pos[2];
729 <
730 <          atomTransData[3] = vel[0];
731 <          atomTransData[4] = vel[1];
732 <          atomTransData[5] = vel[2];
733 <          
734 <          isDirectional = 0;
735 <
736 <          if( atoms[local_index]->isDirectional() ){
737 <
738 <            isDirectional = 1;
739 <            
740 <            dAtom = (DirectionalAtom *)atoms[local_index];
741 <            dAtom->getQ( q );
742 <            
743 <            atomOrientData[0] = q[0];
744 <            atomOrientData[1] = q[1];
745 <            atomOrientData[2] = q[2];
746 <            atomOrientData[3] = q[3];
747 <
748 <            atomOrientData[4] = dAtom->getJx();
749 <            atomOrientData[5] = dAtom->getJy();
750 <            atomOrientData[6] = dAtom->getJz();
751 <          }
752 <
753 <        } else {
754 <          sprintf(painCave.errMsg,
755 <                  "Atom %d not found on processor %d\n",
756 <                  i, worldRank );
757 <          haveError= 1;
758 <          simError();
759 <        }
760 <
761 <        // I've survived this far, so send off the data!
762 <
763 <        atomTypeTag          = 4*i;
764 <        atomIsDirectionalTag = 4*i + 1;
765 <        atomTransDataTag     = 4*i + 2;
766 <        atomOrientDataTag    = 4*i + 3;
767 <
768 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
769 <
770 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
771 <                 atomTypeTag, MPI_COMM_WORLD);
772 <        
773 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
774 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
775 <        
776 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
777 <                 atomTransDataTag, MPI_COMM_WORLD);
778 <
779 <        if (isDirectional) {
780 <
781 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
782 <                   atomOrientDataTag, MPI_COMM_WORLD);
783 <          
784 <        }
785 <      
786 <      }
787 <    }
788 <
789 <    sprintf( checkPointMsg,
790 <             "Sucessfully wrote final file.\n");
791 <    MPIcheckPoint();        
792 <    
793 <  }
538 >  }
539    
795 –  painCave.isEventLoop = 0;
796 –
797 –  if( worldRank == 0 ) finalOut.close();
540   #endif // is_mpi
541   }
542  
801 –
802 –
543   #ifdef IS_MPI
544  
545   // a couple of functions to let us escape the write loop

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