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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 919 by tim, Sat Jan 10 02:15:35 2004 UTC vs.
Revision 934 by tim, Tue Jan 13 20:04:28 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
29 –    strcpy( outName, entry_plug->sampleName );
31  
32 <    outFile.open(outName, ios::out | ios::trunc );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    if( !outFile ){
34 >    if( !dumpFile ){
35  
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
43 <    //outFile.setf( ios::scientific );
43 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
44 >    if( !finalOut ){
45 >      sprintf( painCave.errMsg,
46 >               "Could not open \"%s\" for final dump output.\n",
47 >               entry_plug->finalName );
48 >      painCave.isFatal = 1;
49 >      simError();
50 >    }
51  
52   #ifdef IS_MPI
53    }
54  
55 +  //sort the local atoms by global index
56 +  sortByGlobalIndex();
57 +  
58    sprintf( checkPointMsg,
59             "Sucessfully opened output file for dumping.\n");
60    MPIcheckPoint();
# Line 56 | Line 67 | DumpWriter::~DumpWriter( ){
67    if(worldRank == 0 ){
68   #endif // is_mpi
69  
70 <    outFile.close();
70 >    dumpFile.close();
71 >    finalOut.close();
72  
73   #ifdef IS_MPI
74    }
75   #endif // is_mpi
76   }
77  
78 < void DumpWriter::writeDump( double currentTime ){
78 > #ifdef IS_MPI
79  
80 <  const int BUFFERSIZE = 2000;
81 <  const int MINIBUFFERSIZE = 100;
80 > /**
81 > * A hook function to load balancing
82 > */
83  
84 <  char tempBuffer[BUFFERSIZE];
85 <  char writeLine[BUFFERSIZE];
86 <
74 <  int i;
75 <
76 < #ifdef IS_MPI
84 > void DumpWriter::update(){
85 >  sortByGlobalIndex();          
86 > }
87    
88 <  int *potatoes;
89 <  int myPotato;
88 > /**
89 > * Auxiliary sorting function
90 > */
91 >
92 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
93 >  return p1.second < p2.second;
94 > }
95  
96 <  int nProc;
97 <  int j, which_node, done, which_atom, local_index;
98 <  double atomData6[6];
99 <  double atomData13[13];
100 <  int isDirectional;
86 <  char* atomTypeString;
87 <  char MPIatomTypeString[MINIBUFFERSIZE];
88 <
89 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
91 < #endif //is_mpi
92 <
93 <  double q[4];
94 <  DirectionalAtom* dAtom;
96 > /**
97 > * Sorting the local index by global index
98 > */
99 >
100 > void DumpWriter::sortByGlobalIndex(){
101    Atom** atoms = entry_plug->atoms;
102 <  double pos[3], vel[3];
102 >  
103 >  indexArray.clear();
104 >  
105 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
106 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
107 >  
108 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
109 > }
110 > #endif
111  
112 <  // write current frame to the eor file
112 > void DumpWriter::writeDump(double currentTime){
113  
114 <  this->writeFinal( currentTime );
114 >  vector<ofstream*> fileStreams;
115  
116 < #ifndef IS_MPI
116 > #ifdef IS_MPI
117 >  if(worldRank == 0 ){
118 >    finalOut.seekp(0);
119 >  }
120 > #endif // is_mpi
121  
122 <  outFile << nAtoms << "\n";
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  outFile << currentTime << ";\t"
126 <          << entry_plug->Hmat[0][0] << "\t"
127 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\t"
125 >  writeFrame(fileStreams, currentTime);
126 >        
127 > }
128  
129 <          << entry_plug->Hmat[0][1] << "\t"
112 <          << entry_plug->Hmat[1][1] << "\t"
113 <          << entry_plug->Hmat[2][1] << ";\t"
129 > void DumpWriter::writeFinal(double currentTime){
130  
131 <          << 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;
131 >  vector<ofstream*> fileStreams;
132  
133 <  for( i=0; i<nAtoms; i++ ){
134 <
135 <    atoms[i]->getPos(pos);
125 <    atoms[i]->getVel(vel);
126 <
127 <    sprintf( tempBuffer,
128 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
137 <
138 <    if( atoms[i]->isDirectional() ){
139 <
140 <      dAtom = (DirectionalAtom *)atoms[i];
141 <      dAtom->getQ( q );
142 <
143 <      sprintf( tempBuffer,
144 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
145 <               q[0],
146 <               q[1],
147 <               q[2],
148 <               q[3],
149 <               dAtom->getJx(),
150 <               dAtom->getJy(),
151 <               dAtom->getJz());
152 <      strcat( writeLine, tempBuffer );
153 <    }
154 <    else
155 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 <
157 <    outFile << writeLine;
133 > #ifdef IS_MPI
134 >  if(worldRank == 0 ){
135 >    finalOut.seekp(0);
136    }
137 <  outFile.flush();
160 <
161 < #else // is_mpi
162 <
163 <  cout << "master" <<endl;
164 <  /* code to find maximum tag value */
137 > #endif // is_mpi
138    
139 <  int tagub, flag, MAXTAG;
140 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
168 <  if (flag) {
169 <    MAXTAG = tagub;
170 <  } else {
171 <    MAXTAG = 32767;
172 <  }  
173 <
174 <  int haveError;
175 <
176 <  MPI_Status istatus;
177 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
178 <
179 <  // write out header and node 0's coordinates
180 <
181 <  if( worldRank == 0 ){
182 <
183 <    // Node 0 needs a list of the magic potatoes for each processor;
184 <
185 <    nProc = mpiSim->getNumberProcessors();
186 <    potatoes = new int[nProc];
187 <
188 <    for (i = 0; i < nProc; i++)
189 <      potatoes[i] = 0;
190 <    
191 <    outFile << mpiSim->getTotAtoms() << "\n";
192 <
193 <    outFile << currentTime << ";\t"
194 <            << entry_plug->Hmat[0][0] << "\t"
195 <            << entry_plug->Hmat[1][0] << "\t"
196 <            << entry_plug->Hmat[2][0] << ";\t"
197 <
198 <            << entry_plug->Hmat[0][1] << "\t"
199 <            << entry_plug->Hmat[1][1] << "\t"
200 <            << entry_plug->Hmat[2][1] << ";\t"
201 <
202 <            << entry_plug->Hmat[0][2] << "\t"
203 <            << entry_plug->Hmat[1][2] << "\t"
204 <            << entry_plug->Hmat[2][2] << ";";
205 <
206 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
207 <    outFile << endl;
208 <    outFile.flush();
209 <
210 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
211 <      
212 <      // Get the Node number which has this atom;
213 <      
214 <      which_node = AtomToProcMap[i];
215 <      
216 <      if (which_node != 0) {
217 <
218 <        if (potatoes[which_node] + 3 >= MAXTAG) {
219 <          // The potato was going to exceed the maximum value,
220 <          // so wrap this processor potato back to 0:        
221 <
222 <          potatoes[which_node] = 0;          
223 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
224 <          
225 <        }
226 <
227 <        myPotato = potatoes[which_node];        
228 <        
229 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
230 <                 myPotato, MPI_COMM_WORLD, &istatus);
231 <        
232 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
233 <        
234 <        // Null terminate the atomTypeString just in case:
235 <
236 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
237 <
238 <        myPotato++;
239 <
240 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
241 <                 myPotato, MPI_COMM_WORLD, &istatus);
242 <              
243 <        myPotato++;
244 <
245 <        if (isDirectional) {          
246 <          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
247 <                   myPotato, MPI_COMM_WORLD, &istatus);
248 <        } else {
249 <          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
250 <                   myPotato, MPI_COMM_WORLD, &istatus);          
251 <        }
252 <        
253 <        myPotato++;
254 <        potatoes[which_node] = myPotato;
255 <
256 <      } else {
257 <        
258 <        haveError = 0;
259 <        which_atom = i;
260 <        local_index=-1;
261 <        
262 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
263 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
264 <        }
265 <        
266 <        if (local_index != -1) {
267 <          
268 <          atomTypeString = atoms[local_index]->getType();
269 <
270 <          atoms[local_index]->getPos(pos);
271 <          atoms[local_index]->getVel(vel);          
272 <
273 <          atomData6[0] = pos[0];
274 <          atomData6[1] = pos[1];
275 <          atomData6[2] = pos[2];
276 <
277 <          atomData6[3] = vel[0];
278 <          atomData6[4] = vel[1];
279 <          atomData6[5] = vel[2];
280 <          
281 <          isDirectional = 0;
282 <
283 <          if( atoms[local_index]->isDirectional() ){
284 <
285 <            isDirectional = 1;
286 <            
287 <            dAtom = (DirectionalAtom *)atoms[local_index];
288 <            dAtom->getQ( q );
289 <
290 <            for (int j = 0; j < 6 ; j++)
291 <              atomData13[j] = atomData6[j];            
292 <            
293 <            atomData13[6] = q[0];
294 <            atomData13[7] = q[1];
295 <            atomData13[8] = q[2];
296 <            atomData13[9] = q[3];
297 <            
298 <            atomData13[10] = dAtom->getJx();
299 <            atomData13[11] = dAtom->getJy();
300 <            atomData13[12] = dAtom->getJz();
301 <          }
302 <          
303 <        } else {
304 <          sprintf(painCave.errMsg,
305 <                  "Atom %d not found on processor %d\n",
306 <                  i, worldRank );
307 <          haveError= 1;
308 <          simError();
309 <        }
310 <        
311 <        if(haveError) DieDieDie();
312 <        
313 <        // If we've survived to here, format the line:
314 <        
315 <        if (!isDirectional) {
316 <
317 <          sprintf( tempBuffer,
318 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
319 <                   atomTypeString,
320 <                   atomData6[0],
321 <                   atomData6[1],
322 <                   atomData6[2],
323 <                   atomData6[3],
324 <                   atomData6[4],
325 <                   atomData6[5]);
326 <          
327 <          strcpy( writeLine, tempBuffer );
328 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
329 <
330 <        } else {
331 <          
332 <          sprintf( tempBuffer,
333 <                   "%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",
334 <                   atomTypeString,
335 <                   atomData13[0],
336 <                   atomData13[1],
337 <                   atomData13[2],
338 <                   atomData13[3],
339 <                   atomData13[4],
340 <                   atomData13[5],
341 <                   atomData13[6],
342 <                   atomData13[7],
343 <                   atomData13[8],
344 <                   atomData13[9],
345 <                   atomData13[10],
346 <                   atomData13[11],
347 <                   atomData13[12]);
348 <          
349 <          strcat( writeLine, tempBuffer );
350 <          
351 <        }
352 <        
353 <        outFile << writeLine;
354 <        outFile.flush();
355 <      }
356 <    }
357 <
358 <    outFile.flush();
359 <    sprintf( checkPointMsg,
360 <             "Sucessfully took a dump.\n");
361 <    MPIcheckPoint();        
362 <    delete[] potatoes;
363 <  } else {
364 <
365 <    // worldRank != 0, so I'm a remote node.  
366 <
367 <    // Set my magic potato to 0:
368 <
369 <    myPotato = 0;
370 <    
371 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
372 <      
373 <      // Am I the node which has this atom?
374 <      
375 <      if (AtomToProcMap[i] == worldRank) {
376 <
377 <        if (myPotato + 3 >= MAXTAG) {
378 <
379 <          // The potato was going to exceed the maximum value,
380 <          // so wrap this processor potato back to 0 (and block until
381 <          // node 0 says we can go:
382 <
383 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
384 <          
385 <        }
386 <        which_atom = i;
387 <        local_index=-1;
388 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
389 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
390 <        }
391 <        if (local_index != -1) {
392 <        
393 <          atomTypeString = atoms[local_index]->getType();
394 <
395 <          atoms[local_index]->getPos(pos);
396 <          atoms[local_index]->getVel(vel);
397 <
398 <          atomData6[0] = pos[0];
399 <          atomData6[1] = pos[1];
400 <          atomData6[2] = pos[2];
401 <
402 <          atomData6[3] = vel[0];
403 <          atomData6[4] = vel[1];
404 <          atomData6[5] = vel[2];
405 <          
406 <          isDirectional = 0;
407 <
408 <          if( atoms[local_index]->isDirectional() ){
409 <
410 <            isDirectional = 1;
411 <            
412 <            dAtom = (DirectionalAtom *)atoms[local_index];
413 <            dAtom->getQ( q );
414 <            
415 <            for (int j = 0; j < 6 ; j++)
416 <              atomData13[j] = atomData6[j];
417 <            
418 <            atomData13[6] = q[0];
419 <            atomData13[7] = q[1];
420 <            atomData13[8] = q[2];
421 <            atomData13[9] = q[3];
422 <
423 <            atomData13[10] = dAtom->getJx();
424 <            atomData13[11] = dAtom->getJy();
425 <            atomData13[12] = dAtom->getJz();
426 <          }
427 <
428 <        } else {
429 <          sprintf(painCave.errMsg,
430 <                  "Atom %d not found on processor %d\n",
431 <                  i, worldRank );
432 <          haveError= 1;
433 <          simError();
434 <        }
435 <
436 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
437 <
438 <        // null terminate the string before sending (just in case):
439 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
440 <
441 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
442 <                 myPotato, MPI_COMM_WORLD);
443 <        
444 <        myPotato++;
445 <
446 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
447 <                 myPotato, MPI_COMM_WORLD);
448 <        
449 <        myPotato++;
450 <        
451 <        if (isDirectional) {
452 <
453 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
454 <                   myPotato, MPI_COMM_WORLD);
455 <          
456 <        } else {
457 <
458 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
459 <                   myPotato, MPI_COMM_WORLD);
460 <        }
461 <
462 <        myPotato++;      
463 <      }
464 <    }
465 <
466 <    sprintf( checkPointMsg,
467 <             "Sucessfully took a dump.\n");
468 <    MPIcheckPoint();        
469 <    
470 <  }
139 >  fileStreams.push_back(&finalOut);  
140 >  writeFrame(fileStreams, currentTime);
141    
472 – #endif // is_mpi
142   }
143  
144 < void DumpWriter::writeFinal(double finalTime){
144 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
145  
477 –  char finalName[500];
478 –  ofstream finalOut;
479 –
146    const int BUFFERSIZE = 2000;
147    const int MINIBUFFERSIZE = 100;
148 +
149    char tempBuffer[BUFFERSIZE];
150    char writeLine[BUFFERSIZE];
151  
152 <  double q[4];
153 <  DirectionalAtom* dAtom;
487 <  Atom** atoms = entry_plug->atoms;
488 <  int i;
152 >  int i, k;
153 >
154   #ifdef IS_MPI
155    
156    int *potatoes;
157    int myPotato;
158  
159    int nProc;
160 <  int j, which_node, done, which_atom, local_index;
160 >  int j, which_node, done, which_atom, local_index, currentIndex;
161    double atomData6[6];
162    double atomData13[13];
163    int isDirectional;
# Line 503 | Line 168 | void DumpWriter::writeFinal(double finalTime){
168    int nAtoms = entry_plug->n_atoms;
169   #endif //is_mpi
170  
171 +  double q[4];
172 +  DirectionalAtom* dAtom;
173 +  Atom** atoms = entry_plug->atoms;
174    double pos[3], vel[3];
175  
508 – #ifdef IS_MPI
509 –  if(worldRank == 0 ){
510 – #endif // is_mpi
511 –
512 –    strcpy( finalName, entry_plug->finalName );
513 –
514 –    finalOut.open( finalName, ios::out | ios::trunc );
515 –    if( !finalOut ){
516 –      sprintf( painCave.errMsg,
517 –               "Could not open \"%s\" for final dump output.\n",
518 –               finalName );
519 –      painCave.isFatal = 1;
520 –      simError();
521 –    }
522 –
523 –    // finalOut.setf( ios::scientific );
524 –
525 – #ifdef IS_MPI
526 –  }
527 –
528 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
529 –  MPIcheckPoint();
530 –
531 – #endif //is_mpi
532 –
533 –
176   #ifndef IS_MPI
177 +  
178 +  for(k = 0; k < outFile.size(); k++){
179 +    *outFile[k] << nAtoms << "\n";
180  
181 <  finalOut << nAtoms << "\n";
181 >    *outFile[k] << currentTime << ";\t"
182 >               << entry_plug->Hmat[0][0] << "\t"
183 >                     << entry_plug->Hmat[1][0] << "\t"
184 >                     << entry_plug->Hmat[2][0] << ";\t"
185 >              
186 >               << entry_plug->Hmat[0][1] << "\t"
187 >                     << entry_plug->Hmat[1][1] << "\t"
188 >                     << entry_plug->Hmat[2][1] << ";\t"
189  
190 <  finalOut << finalTime << ";\t"
191 <           << entry_plug->Hmat[0][0] << "\t"
192 <           << entry_plug->Hmat[1][0] << "\t"
541 <           << entry_plug->Hmat[2][0] << ";\t"
190 >                     << entry_plug->Hmat[0][2] << "\t"
191 >                     << entry_plug->Hmat[1][2] << "\t"
192 >                     << entry_plug->Hmat[2][2] << ";";
193  
194 <           << entry_plug->Hmat[0][1] << "\t"
195 <           << entry_plug->Hmat[1][1] << "\t"
196 <           << entry_plug->Hmat[2][1] << ";\t"
197 <
547 <           << entry_plug->Hmat[0][2] << "\t"
548 <           << entry_plug->Hmat[1][2] << "\t"
549 <           << entry_plug->Hmat[2][2] << ";";
550 <
551 <  //write out additional parameters, such as chi and eta
552 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 <  finalOut << endl;
554 <
194 >    //write out additional parameters, such as chi and eta
195 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
196 >  }
197 >  
198    for( i=0; i<nAtoms; i++ ){
199  
200      atoms[i]->getPos(pos);
# Line 587 | Line 230 | void DumpWriter::writeFinal(double finalTime){
230      else
231        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232  
233 <    finalOut << writeLine;
233 >    for(k = 0; k < outFile.size(); k++)
234 >      *outFile[k] << writeLine;
235    }
592 –  finalOut.flush();
593 –  finalOut.close();
236  
237   #else // is_mpi
238  
239    /* code to find maximum tag value */
240 +  
241    int *tagub, flag, MAXTAG;
242    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
243    if (flag) {
# Line 617 | Line 260 | void DumpWriter::writeFinal(double finalTime){
260      nProc = mpiSim->getNumberProcessors();
261      potatoes = new int[nProc];
262  
263 +    //write out the comment lines
264      for (i = 0; i < nProc; i++)
265        potatoes[i] = 0;
266      
267 <    finalOut << mpiSim->getTotAtoms() << "\n";
267 >      for(k = 0; k < outFile.size(); k++){
268 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
269  
270 <    finalOut << finalTime << ";\t"
271 <            << entry_plug->Hmat[0][0] << "\t"
272 <            << entry_plug->Hmat[1][0] << "\t"
273 <            << entry_plug->Hmat[2][0] << ";\t"
270 >        *outFile[k] << currentTime << ";\t"
271 >                         << entry_plug->Hmat[0][0] << "\t"
272 >                         << entry_plug->Hmat[1][0] << "\t"
273 >                         << entry_plug->Hmat[2][0] << ";\t"
274  
275 <            << entry_plug->Hmat[0][1] << "\t"
276 <            << entry_plug->Hmat[1][1] << "\t"
277 <            << entry_plug->Hmat[2][1] << ";\t"
275 >                         << entry_plug->Hmat[0][1] << "\t"
276 >                         << entry_plug->Hmat[1][1] << "\t"
277 >                         << entry_plug->Hmat[2][1] << ";\t"
278  
279 <            << entry_plug->Hmat[0][2] << "\t"
280 <            << entry_plug->Hmat[1][2] << "\t"
281 <            << entry_plug->Hmat[2][2] << ";";
279 >                         << entry_plug->Hmat[0][2] << "\t"
280 >                         << entry_plug->Hmat[1][2] << "\t"
281 >                         << entry_plug->Hmat[2][2] << ";";
282 >  
283 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
284 >    }
285  
286 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
639 <    finalOut << endl;
640 <    finalOut.flush();
286 >    currentIndex = 0;
287  
288      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
289        
# Line 661 | Line 307 | void DumpWriter::writeFinal(double finalTime){
307          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
308                   myPotato, MPI_COMM_WORLD, &istatus);
309          
310 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
311 <        
666 <        // Null terminate the atomTypeString just in case:
667 <
668 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
669 <
310 >        atomTypeString = MPIatomTypeString;
311 >        
312          myPotato++;
313  
314          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 687 | Line 329 | void DumpWriter::writeFinal(double finalTime){
329  
330        } else {
331          
332 <        haveError = 0;
333 <        which_atom = i;
692 <        local_index=-1;
332 >        haveError = 0;
333 >              which_atom = i;
334          
335 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
336 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
337 <        }
697 <        
698 <        if (local_index != -1) {
335 >        local_index = indexArray[currentIndex].first;        
336 >                
337 >        if (which_atom == indexArray[currentIndex].second) {
338            
339            atomTypeString = atoms[local_index]->getType();
340  
341 <          atoms[local_index]->getPos(pos);
342 <          atoms[local_index]->getVel(vel);          
341 >                atoms[local_index]->getPos(pos);
342 >                atoms[local_index]->getVel(vel);          
343  
344            atomData6[0] = pos[0];
345            atomData6[1] = pos[1];
# Line 733 | Line 372 | void DumpWriter::writeFinal(double finalTime){
372            }
373            
374          } else {
375 <          sprintf(painCave.errMsg,
376 <                  "Atom %d not found on processor %d\n",
377 <                  i, worldRank );
378 <          haveError= 1;
379 <          simError();
380 <        }
375 >          sprintf(painCave.errMsg,
376 >                              "Atom %d not found on processor %d\n",
377 >                              i, worldRank );
378 >                haveError= 1;
379 >                simError();
380 >              }
381          
382 <        if(haveError) DieDieDie();
382 >        if(haveError) DieDieDie();
383          
384 <        // If we've survived to here, format the line:
385 <        
386 <        if (!isDirectional) {
384 >        currentIndex ++;
385 >      }
386 >      // If we've survived to here, format the line:
387 >      
388 >      if (!isDirectional) {
389 >        
390 >        sprintf( writeLine,
391 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392 >                             atomTypeString,
393 >                             atomData6[0],
394 >                             atomData6[1],
395 >                             atomData6[2],
396 >                             atomData6[3],
397 >                             atomData6[4],
398 >                             atomData6[5]);
399  
400 <          sprintf( tempBuffer,
401 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
402 <                   atomTypeString,
403 <                   atomData6[0],
404 <                   atomData6[1],
405 <                   atomData6[2],
406 <                   atomData6[3],
407 <                   atomData6[4],
408 <                   atomData6[5]);
409 <          
410 <          strcpy( writeLine, tempBuffer );
411 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
412 <
413 <        } else {
414 <          
415 <          sprintf( tempBuffer,
416 <                   "%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",
417 <                   atomTypeString,
418 <                   atomData13[0],
419 <                   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 <          strcat( writeLine, tempBuffer );
782 <          
783 <        }
400 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
401 >        
402 >      } else {
403 >        
404 >              sprintf( writeLine,
405 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
406 >                             atomTypeString,
407 >                             atomData13[0],
408 >                             atomData13[1],
409 >                             atomData13[2],
410 >                             atomData13[3],
411 >                             atomData13[4],
412 >                             atomData13[5],
413 >                             atomData13[6],
414 >                             atomData13[7],
415 >                             atomData13[8],
416 >                             atomData13[9],
417 >                             atomData13[10],
418 >                             atomData13[11],
419 >                             atomData13[12]);
420          
785 –        finalOut << writeLine;
786 –        finalOut.flush();
421        }
422 +      
423 +      for(k = 0; k < outFile.size(); k++)
424 +        *outFile[k] << writeLine;
425      }
426 <
427 <    finalOut.flush();
426 >    
427 >    for(k = 0; k < outFile.size(); k++)
428 >      outFile[k]->flush();
429 >    
430      sprintf( checkPointMsg,
431               "Sucessfully took a dump.\n");
432 <    delete[] potatoes;
794 <      
432 >
433      MPIcheckPoint();        
434 <    
434 >
435 >    delete[] potatoes;
436 >
437    } else {
438  
439      // worldRank != 0, so I'm a remote node.  
# Line 801 | Line 441 | void DumpWriter::writeFinal(double finalTime){
441      // Set my magic potato to 0:
442  
443      myPotato = 0;
444 +    currentIndex = 0;
445      
446      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
447        
# Line 817 | Line 458 | void DumpWriter::writeFinal(double finalTime){
458            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
459            
460          }
461 <        which_atom = i;  
462 <        local_index=-1;
463 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
464 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
824 <        }
825 <        if (local_index != -1) {
461 >        which_atom = i;
462 >        local_index = indexArray[currentIndex].first;        
463 >                
464 >        if (which_atom == indexArray[currentIndex].second) {
465          
466            atomTypeString = atoms[local_index]->getType();
467  
468 <          atoms[local_index]->getPos(pos);
469 <          atoms[local_index]->getVel(vel);
468 >                atoms[local_index]->getPos(pos);
469 >                atoms[local_index]->getVel(vel);
470  
471            atomData6[0] = pos[0];
472            atomData6[1] = pos[1];
# Line 853 | Line 492 | void DumpWriter::writeFinal(double finalTime){
492              atomData13[7] = q[1];
493              atomData13[8] = q[2];
494              atomData13[9] = q[3];
495 <
495 >  
496              atomData13[10] = dAtom->getJx();
497              atomData13[11] = dAtom->getJy();
498              atomData13[12] = dAtom->getJz();
499            }
500  
501          } else {
502 <          sprintf(painCave.errMsg,
503 <                  "Atom %d not found on processor %d\n",
504 <                  i, worldRank );
505 <          haveError= 1;
506 <          simError();
507 <        }
502 >                sprintf(painCave.errMsg,
503 >                              "Atom %d not found on processor %d\n",
504 >                              i, worldRank );
505 >                haveError= 1;
506 >                simError();
507 >              }
508  
509          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
510  
# Line 873 | Line 512 | void DumpWriter::writeFinal(double finalTime){
512          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
513  
514          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
515 <                 myPotato, MPI_COMM_WORLD);
515 >                             myPotato, MPI_COMM_WORLD);
516          
517          myPotato++;
518  
519          MPI_Send(&isDirectional, 1, MPI_INT, 0,
520 <                 myPotato, MPI_COMM_WORLD);
520 >                             myPotato, MPI_COMM_WORLD);
521          
522          myPotato++;
523          
# Line 893 | Line 532 | void DumpWriter::writeFinal(double finalTime){
532                     myPotato, MPI_COMM_WORLD);
533          }
534  
535 <        myPotato++;      
535 >        myPotato++;  
536 >        currentIndex++;    
537        }
538      }
539  
# Line 903 | Line 543 | void DumpWriter::writeFinal(double finalTime){
543      
544    }
545    
906 –  if( worldRank == 0 ) finalOut.close();
546   #endif // is_mpi
547   }
548  
910 –
911 –
549   #ifdef IS_MPI
550  
551   // a couple of functions to let us escape the write loop

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