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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 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 = 10;
151 >  const int MINIBUFFERSIZE = 100;
152  
153    char tempBuffer[BUFFERSIZE];
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 <  int me;
170 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
169 >  char MPIatomTypeString[MINIBUFFERSIZE];
170 >
171   #else //is_mpi
172    int nAtoms = entry_plug->n_atoms;
173   #endif //is_mpi
# Line 92 | Line 177 | void DumpWriter::writeDump( double currentTime ){
177    Atom** atoms = entry_plug->atoms;
178    double pos[3], vel[3];
179  
95 –  // write current frame to the eor file
96 –
97 –  this->writeFinal( currentTime );
98 –
180   #ifndef IS_MPI
181  
182    outFile << nAtoms << "\n";
# Line 153 | Line 234 | void DumpWriter::writeDump( double currentTime ){
234  
235      outFile << writeLine;
236    }
156 –  outFile.flush();
237  
238   #else // is_mpi
239  
240 <  // first thing first, suspend fatalities.
241 <  painCave.isEventLoop = 1;
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 >  }  
249  
163 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
250    int haveError;
251  
252    MPI_Status istatus;
# Line 169 | 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 187 | Line 282 | void DumpWriter::writeDump( double currentTime ){
282      outFile << entry_plug->the_integrator->getAdditionalParameters();
283      outFile << endl;
284      outFile.flush();
285 +    
286 +    currentIndex = 0;
287      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
288 +      
289        // Get the Node number which has this atom;
290 <
290 >      
291        which_node = AtomToProcMap[i];
292 <
292 >      
293        if (which_node != 0) {
196 –        
197 –        atomTypeTag          = 4*i;
198 –        atomIsDirectionalTag = 4*i + 1;
199 –        atomTransDataTag     = 4*i + 2;
200 –        atomOrientDataTag    = 4*i + 3;
294  
295 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
296 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
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(&isDirectional, 1, MPI_INT, which_node,
307 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
306 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307 >                 myPotato, MPI_COMM_WORLD, &istatus);
308          
309 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
310 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
309 >        atomTypeString = MPIatomTypeString;
310 >        
311 >        myPotato++;
312  
313 <        if (isDirectional) {
313 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
314 >                 myPotato, MPI_COMM_WORLD, &istatus);
315 >              
316 >        myPotato++;
317  
318 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
319 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
320 <
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 <        }
227 <
228 <        if (local_index != -1) {
229 <
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 248 | Line 356 | void DumpWriter::writeDump( double currentTime ){
356              
357              dAtom = (DirectionalAtom *)atoms[local_index];
358              dAtom->getQ( q );
251 –            
252 –            atomOrientData[0] = q[0];
253 –            atomOrientData[1] = q[1];
254 –            atomOrientData[2] = q[2];
255 –            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 266 | Line 377 | void DumpWriter::writeDump( double currentTime ){
377            haveError= 1;
378            simError();
379          }
380 <
380 >        
381          if(haveError) DieDieDie();
271 –                              
272 –        // 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 320 | 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 348 | 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 366 | Line 500 | void DumpWriter::writeDump( double currentTime ){
500            simError();
501          }
502  
503 <        // I've survived this far, so send off the data!
503 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
504  
505 <        atomTypeTag          = 4*i;
506 <        atomIsDirectionalTag = 4*i + 1;
373 <        atomTransDataTag     = 4*i + 2;
374 <        atomOrientDataTag    = 4*i + 3;
505 >        // null terminate the string before sending (just in case):
506 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
507  
508 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
509 <                 atomTypeTag, MPI_COMM_WORLD);
508 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
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);
384 <
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            
390 –        }
391 –      
392 –      }
393 –    }
394 –
395 –    sprintf( checkPointMsg,
396 –             "Sucessfully took a dump.\n");
397 –    MPIcheckPoint();        
398 –    
399 –  }
400 –  
401 –  painCave.isEventLoop = 0;
402 –
403 – #endif // is_mpi
404 – }
405 –
406 – void DumpWriter::writeFinal(double finalTime){
407 –
408 –  char finalName[500];
409 –  ofstream finalOut;
410 –
411 –  const int BUFFERSIZE = 2000;
412 –  const int MINIBUFFERSIZE = 10;
413 –  char tempBuffer[BUFFERSIZE];
414 –  char writeLine[BUFFERSIZE];
415 –
416 –  double q[4];
417 –  DirectionalAtom* dAtom;
418 –  Atom** atoms = entry_plug->atoms;
419 –  int i;
420 – #ifdef IS_MPI
421 –  int j, which_node, done, which_atom, local_index;
422 –  double atomTransData[6];
423 –  double atomOrientData[7];
424 –  int isDirectional;
425 –  char* atomTypeString;
426 –  int atomTypeTag;
427 –  int atomIsDirectionalTag;
428 –  int atomTransDataTag;
429 –  int atomOrientDataTag;
430 – #else //is_mpi
431 –  int nAtoms = entry_plug->n_atoms;
432 – #endif //is_mpi
433 –
434 –  double pos[3], vel[3];
435 –
436 – #ifdef IS_MPI
437 –  if(worldRank == 0 ){
438 – #endif // is_mpi
439 –
440 –    strcpy( finalName, entry_plug->finalName );
441 –
442 –    finalOut.open( finalName, ios::out | ios::trunc );
443 –    if( !finalOut ){
444 –      sprintf( painCave.errMsg,
445 –               "Could not open \"%s\" for final dump output.\n",
446 –               finalName );
447 –      painCave.isFatal = 1;
448 –      simError();
449 –    }
450 –
451 –    // finalOut.setf( ios::scientific );
452 –
453 – #ifdef IS_MPI
454 –  }
455 –
456 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 –  MPIcheckPoint();
458 –
459 – #endif //is_mpi
460 –
461 –
462 – #ifndef IS_MPI
463 –
464 –  finalOut << nAtoms << "\n";
465 –
466 –  finalOut << finalTime << ";\t"
467 –           << entry_plug->Hmat[0][0] << "\t"
468 –           << entry_plug->Hmat[1][0] << "\t"
469 –           << entry_plug->Hmat[2][0] << ";\t"
470 –
471 –           << entry_plug->Hmat[0][1] << "\t"
472 –           << entry_plug->Hmat[1][1] << "\t"
473 –           << entry_plug->Hmat[2][1] << ";\t"
474 –
475 –           << entry_plug->Hmat[0][2] << "\t"
476 –           << entry_plug->Hmat[1][2] << "\t"
477 –           << entry_plug->Hmat[2][2] << ";";
478 –
479 –  //write out additional parameters, such as chi and eta
480 –  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 –  finalOut << endl;
482 –
483 –  for( i=0; i<nAtoms; i++ ){
484 –
485 –    atoms[i]->getPos(pos);
486 –    atoms[i]->getVel(vel);
487 –
488 –    sprintf( tempBuffer,
489 –             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 –             atoms[i]->getType(),
491 –             pos[0],
492 –             pos[1],
493 –             pos[2],
494 –             vel[0],
495 –             vel[1],
496 –             vel[2]);
497 –    strcpy( writeLine, tempBuffer );
498 –
499 –    if( atoms[i]->isDirectional() ){
500 –
501 –      dAtom = (DirectionalAtom *)atoms[i];
502 –      dAtom->getQ( q );
503 –
504 –      sprintf( tempBuffer,
505 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 –               q[0],
507 –               q[1],
508 –               q[2],
509 –               q[3],
510 –               dAtom->getJx(),
511 –               dAtom->getJy(),
512 –               dAtom->getJz());
513 –      strcat( writeLine, tempBuffer );
514 –    }
515 –    else
516 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
517 –
518 –    finalOut << writeLine;
519 –  }
520 –  finalOut.flush();
521 –  finalOut.close();
522 –
523 – #else // is_mpi
524 –
525 –  // first thing first, suspend fatalities.
526 –  painCave.isEventLoop = 1;
527 –
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
529 –  int haveError;
530 –
531 –  MPI_Status istatus;
532 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
533 –
534 –  // write out header and node 0's coordinates
535 –
536 –  if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\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 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 –    finalOut << endl;
554 –    finalOut.flush();
555 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
556 –      // Get the Node number which has this atom;
557 –
558 –      which_node = AtomToProcMap[i];
559 –
560 –      if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
566 –
567 –        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
568 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
569 –        
570 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
571 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
572 –        
573 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
574 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
575 –
576 –        if (isDirectional) {
577 –
578 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
579 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
580 –
581 –        }
582 –
583 –      } else {
584 –        
585 –        haveError = 0;
586 –        which_atom = i;
587 –        local_index=-1;
588 –
589 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
590 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
591 –        }
592 –
593 –        if (local_index != -1) {
594 –
595 –          atomTypeString = atoms[local_index]->getType();
596 –
597 –          atoms[local_index]->getPos(pos);
598 –          atoms[local_index]->getVel(vel);
599 –
600 –          atomTransData[0] = pos[0];
601 –          atomTransData[1] = pos[1];
602 –          atomTransData[2] = pos[2];
603 –
604 –          atomTransData[3] = vel[0];
605 –          atomTransData[4] = vel[1];
606 –          atomTransData[5] = vel[2];
607 –          
608 –          isDirectional = 0;
609 –
610 –          if( atoms[local_index]->isDirectional() ){
611 –
612 –            isDirectional = 1;
613 –            
614 –            dAtom = (DirectionalAtom *)atoms[local_index];
615 –            dAtom->getQ( q );
616 –            
617 –            atomOrientData[0] = q[0];
618 –            atomOrientData[1] = q[1];
619 –            atomOrientData[2] = q[2];
620 –            atomOrientData[3] = q[3];
621 –
622 –            atomOrientData[4] = dAtom->getJx();
623 –            atomOrientData[5] = dAtom->getJy();
624 –            atomOrientData[6] = dAtom->getJz();
625 –          }
626 –
523          } else {
628 –          sprintf(painCave.errMsg,
629 –                  "Atom %d not found on processor %d\n",
630 –                  i, worldRank );
631 –          haveError= 1;
632 –          simError();
633 –        }
524  
525 <        if(haveError) DieDieDie();
526 <                              
637 <        // If we've survived to here, format the line:
638 <        
639 <        sprintf( tempBuffer,
640 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
641 <                 atomTypeString,
642 <                 atomTransData[0],
643 <                 atomTransData[1],
644 <                 atomTransData[2],
645 <                 atomTransData[3],
646 <                 atomTransData[4],
647 <                 atomTransData[5]);
648 <
649 <        strcpy( writeLine, tempBuffer );
650 <
651 <        if (isDirectional) {
652 <
653 <          sprintf( tempBuffer,
654 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 <                   atomOrientData[0],
656 <                   atomOrientData[1],
657 <                   atomOrientData[2],
658 <                   atomOrientData[3],
659 <                   atomOrientData[4],
660 <                   atomOrientData[5],
661 <                   atomOrientData[6]);
662 <          strcat( writeLine, tempBuffer );
663 <
664 <        } else {
665 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
525 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
526 >                   myPotato, MPI_COMM_WORLD);
527          }
528  
529 <        finalOut << writeLine;
530 <        finalOut.flush();
529 >        myPotato++;  
530 >        currentIndex++;    
531        }
532      }
533  
673 –    finalOut.flush();
534      sprintf( checkPointMsg,
535               "Sucessfully took a dump.\n");
536      MPIcheckPoint();        
537      
538 <  } else {
679 <
680 <    // worldRank != 0, so I'm a remote node.  
681 <    
682 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
683 <      
684 <      // Am I the node which has this atom?
685 <      
686 <      if (AtomToProcMap[i] == worldRank) {
687 <
688 <        local_index=-1;
689 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
690 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
691 <        }
692 <        if (local_index != -1) {
693 <        
694 <          atomTypeString = atoms[local_index]->getType();
695 <
696 <          atoms[local_index]->getPos(pos);
697 <          atoms[local_index]->getVel(vel);
698 <
699 <          atomTransData[0] = pos[0];
700 <          atomTransData[1] = pos[1];
701 <          atomTransData[2] = pos[2];
702 <
703 <          atomTransData[3] = vel[0];
704 <          atomTransData[4] = vel[1];
705 <          atomTransData[5] = vel[2];
706 <          
707 <          isDirectional = 0;
708 <
709 <          if( atoms[local_index]->isDirectional() ){
710 <
711 <            isDirectional = 1;
712 <            
713 <            dAtom = (DirectionalAtom *)atoms[local_index];
714 <            dAtom->getQ( q );
715 <            
716 <            atomOrientData[0] = q[0];
717 <            atomOrientData[1] = q[1];
718 <            atomOrientData[2] = q[2];
719 <            atomOrientData[3] = q[3];
720 <
721 <            atomOrientData[4] = dAtom->getJx();
722 <            atomOrientData[5] = dAtom->getJy();
723 <            atomOrientData[6] = dAtom->getJz();
724 <          }
725 <
726 <        } else {
727 <          sprintf(painCave.errMsg,
728 <                  "Atom %d not found on processor %d\n",
729 <                  i, worldRank );
730 <          haveError= 1;
731 <          simError();
732 <        }
733 <
734 <        // I've survived this far, so send off the data!
735 <
736 <        atomTypeTag          = 4*i;
737 <        atomIsDirectionalTag = 4*i + 1;
738 <        atomTransDataTag     = 4*i + 2;
739 <        atomOrientDataTag    = 4*i + 3;
740 <
741 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
742 <                 atomTypeTag, MPI_COMM_WORLD);
743 <        
744 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
745 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
746 <        
747 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
748 <                 atomTransDataTag, MPI_COMM_WORLD);
749 <
750 <        if (isDirectional) {
751 <
752 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
753 <                   atomOrientDataTag, MPI_COMM_WORLD);
754 <          
755 <        }
756 <      
757 <      }
758 <    }
759 <
760 <    sprintf( checkPointMsg,
761 <             "Sucessfully wrote final file.\n");
762 <    MPIcheckPoint();        
763 <    
764 <  }
538 >  }
539    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
540   #endif // is_mpi
541   }
542  
772 –
773 –
543   #ifdef IS_MPI
544  
545   // a couple of functions to let us escape the write loop

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