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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 936 by tim, Tue Jan 13 20:35:25 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  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 100;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
76 <
74 <  int i;
75 <
76 < #ifdef IS_MPI
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77    
78 <  int *potatoes;
79 <  int myPotato;
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 <  int nProc;
87 <  int j, which_node, done, which_atom, local_index;
88 <  double atomData6[6];
89 <  double atomData13[13];
90 <  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;
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91    Atom** atoms = entry_plug->atoms;
92 <  double pos[3], vel[3];
92 >  
93 >  indexArray.clear();
94 >  
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 >  
98 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 > }
100 > #endif
101  
102 <  // write current frame to the eor file
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <  this->writeFinal( currentTime );
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 < #ifndef IS_MPI
108 <
109 <  outFile << nAtoms << "\n";
110 <
111 <  outFile << currentTime << ";\t"
112 <          << entry_plug->Hmat[0][0] << "\t"
113 <          << entry_plug->Hmat[1][0] << "\t"
114 <          << entry_plug->Hmat[2][0] << ";\t"
115 <
116 <          << entry_plug->Hmat[0][1] << "\t"
112 <          << entry_plug->Hmat[1][1] << "\t"
113 <          << entry_plug->Hmat[2][1] << ";\t"
114 <
115 <          << entry_plug->Hmat[0][2] << "\t"
116 <          << entry_plug->Hmat[1][2] << "\t"
117 <          << entry_plug->Hmat[2][2] << ";";
118 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
121 <
122 <  for( i=0; i<nAtoms; i++ ){
123 <
124 <    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 );
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 >    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 –
157 –    outFile << writeLine;
118    }
119 <  outFile.flush();
119 > #endif // is_mpi
120  
121 < #else // is_mpi
121 >  fileStreams.push_back(&finalOut);
122 >  fileStreams.push_back(&dumpFile);
123  
124 <  cout << "master" <<endl;
164 <  /* code to find maximum tag value */
165 <  
166 <  int tagub, flag, MAXTAG;
167 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
168 <  if (flag) {
169 <    MAXTAG = tagub;
170 <  } else {
171 <    MAXTAG = 32767;
172 <  }  
124 >  writeFrame(fileStreams, currentTime);
125  
126 <  int haveError;
126 > #ifdef IS_MPI
127 >  finalOut.close();
128 > #endif
129 >        
130 > }
131  
132 <  MPI_Status istatus;
177 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
132 > void DumpWriter::writeFinal(double currentTime){
133  
134 <  // write out header and node 0's coordinates
135 <
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();
134 >  ofstream finalOut;
135 >  vector<ofstream*> fileStreams;
136  
137 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
138 <      
212 <      // Get the Node number which has this atom;
213 <      
214 <      which_node = AtomToProcMap[i];
215 <      
216 <      if (which_node != 0) {
137 > #ifdef IS_MPI
138 >  if(worldRank == 0 ){
139  
140 <        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:        
140 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141  
142 <          potatoes[which_node] = 0;          
143 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
144 <          
145 <        }
146 <
147 <        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 <      }
142 >    if( !finalOut ){
143 >      sprintf( painCave.errMsg,
144 >               "Could not open \"%s\" for final dump output.\n",
145 >               entry_plug->finalName );
146 >      painCave.isFatal = 1;
147 >      simError();
148      }
149  
150 <    outFile.flush();
151 <    sprintf( checkPointMsg,
152 <             "Sucessfully took a dump.\n");
153 <    MPIcheckPoint();        
154 <    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);
150 >  }
151 > #endif // is_mpi
152 >  
153 >  fileStreams.push_back(&finalOut);  
154 >  writeFrame(fileStreams, currentTime);
155  
156 <          atomData6[0] = pos[0];
157 <          atomData6[1] = pos[1];
158 <          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 <  }
156 > #ifdef IS_MPI
157 >  finalOut.close();
158 > #endif
159    
472 – #endif // is_mpi
160   }
161  
162 < void DumpWriter::writeFinal(double finalTime){
162 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163  
477 –  char finalName[500];
478 –  ofstream finalOut;
479 –
164    const int BUFFERSIZE = 2000;
165    const int MINIBUFFERSIZE = 100;
166 <  char tempBuffer[BUFFERSIZE];
166 >
167 >  char tempBuffer[BUFFERSIZE];  
168    char writeLine[BUFFERSIZE];
169  
170 <  double q[4];
171 <  DirectionalAtom* dAtom;
487 <  Atom** atoms = entry_plug->atoms;
488 <  int i;
170 >  int i, k;
171 >
172   #ifdef IS_MPI
173    
174    int *potatoes;
175    int myPotato;
176  
177    int nProc;
178 <  int j, which_node, done, which_atom, local_index;
178 >  int j, which_node, done, which_atom, local_index, currentIndex;
179    double atomData6[6];
180    double atomData13[13];
181    int isDirectional;
# Line 503 | Line 186 | void DumpWriter::writeFinal(double finalTime){
186    int nAtoms = entry_plug->n_atoms;
187   #endif //is_mpi
188  
189 +  double q[4];
190 +  DirectionalAtom* dAtom;
191 +  Atom** atoms = entry_plug->atoms;
192    double pos[3], vel[3];
193  
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 –
194   #ifndef IS_MPI
195 +  
196 +  for(k = 0; k < outFile.size(); k++){
197 +    *outFile[k] << nAtoms << "\n";
198  
199 <  finalOut << nAtoms << "\n";
199 >    *outFile[k] << currentTime << ";\t"
200 >               << entry_plug->Hmat[0][0] << "\t"
201 >                     << entry_plug->Hmat[1][0] << "\t"
202 >                     << entry_plug->Hmat[2][0] << ";\t"
203 >              
204 >               << entry_plug->Hmat[0][1] << "\t"
205 >                     << entry_plug->Hmat[1][1] << "\t"
206 >                     << entry_plug->Hmat[2][1] << ";\t"
207  
208 <  finalOut << finalTime << ";\t"
209 <           << entry_plug->Hmat[0][0] << "\t"
210 <           << entry_plug->Hmat[1][0] << "\t"
541 <           << entry_plug->Hmat[2][0] << ";\t"
208 >                     << entry_plug->Hmat[0][2] << "\t"
209 >                     << entry_plug->Hmat[1][2] << "\t"
210 >                     << entry_plug->Hmat[2][2] << ";";
211  
212 <           << entry_plug->Hmat[0][1] << "\t"
213 <           << entry_plug->Hmat[1][1] << "\t"
214 <           << entry_plug->Hmat[2][1] << ";\t"
215 <
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 <
212 >    //write out additional parameters, such as chi and eta
213 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
214 >  }
215 >  
216    for( i=0; i<nAtoms; i++ ){
217  
218      atoms[i]->getPos(pos);
# Line 587 | Line 248 | void DumpWriter::writeFinal(double finalTime){
248      else
249        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
250  
251 <    finalOut << writeLine;
251 >    for(k = 0; k < outFile.size(); k++)
252 >      *outFile[k] << writeLine;
253    }
592 –  finalOut.flush();
593 –  finalOut.close();
254  
255   #else // is_mpi
256  
257    /* code to find maximum tag value */
258 +  
259    int *tagub, flag, MAXTAG;
260    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
261    if (flag) {
# Line 617 | Line 278 | void DumpWriter::writeFinal(double finalTime){
278      nProc = mpiSim->getNumberProcessors();
279      potatoes = new int[nProc];
280  
281 +    //write out the comment lines
282      for (i = 0; i < nProc; i++)
283        potatoes[i] = 0;
284      
285 <    finalOut << mpiSim->getTotAtoms() << "\n";
285 >      for(k = 0; k < outFile.size(); k++){
286 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
287  
288 <    finalOut << finalTime << ";\t"
289 <            << entry_plug->Hmat[0][0] << "\t"
290 <            << entry_plug->Hmat[1][0] << "\t"
291 <            << entry_plug->Hmat[2][0] << ";\t"
288 >        *outFile[k] << currentTime << ";\t"
289 >                         << entry_plug->Hmat[0][0] << "\t"
290 >                         << entry_plug->Hmat[1][0] << "\t"
291 >                         << entry_plug->Hmat[2][0] << ";\t"
292  
293 <            << entry_plug->Hmat[0][1] << "\t"
294 <            << entry_plug->Hmat[1][1] << "\t"
295 <            << entry_plug->Hmat[2][1] << ";\t"
293 >                         << entry_plug->Hmat[0][1] << "\t"
294 >                         << entry_plug->Hmat[1][1] << "\t"
295 >                         << entry_plug->Hmat[2][1] << ";\t"
296  
297 <            << entry_plug->Hmat[0][2] << "\t"
298 <            << entry_plug->Hmat[1][2] << "\t"
299 <            << entry_plug->Hmat[2][2] << ";";
297 >                         << entry_plug->Hmat[0][2] << "\t"
298 >                         << entry_plug->Hmat[1][2] << "\t"
299 >                         << entry_plug->Hmat[2][2] << ";";
300 >  
301 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
302 >    }
303  
304 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
639 <    finalOut << endl;
640 <    finalOut.flush();
304 >    currentIndex = 0;
305  
306      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
307        
# Line 661 | Line 325 | void DumpWriter::writeFinal(double finalTime){
325          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
326                   myPotato, MPI_COMM_WORLD, &istatus);
327          
328 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
329 <        
666 <        // Null terminate the atomTypeString just in case:
667 <
668 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
669 <
328 >        atomTypeString = MPIatomTypeString;
329 >        
330          myPotato++;
331  
332          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 687 | Line 347 | void DumpWriter::writeFinal(double finalTime){
347  
348        } else {
349          
350 <        haveError = 0;
351 <        which_atom = i;
692 <        local_index=-1;
350 >        haveError = 0;
351 >              which_atom = i;
352          
353 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
354 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
355 <        }
697 <        
698 <        if (local_index != -1) {
353 >        local_index = indexArray[currentIndex].first;        
354 >                
355 >        if (which_atom == indexArray[currentIndex].second) {
356            
357            atomTypeString = atoms[local_index]->getType();
358  
359 <          atoms[local_index]->getPos(pos);
360 <          atoms[local_index]->getVel(vel);          
359 >                atoms[local_index]->getPos(pos);
360 >                atoms[local_index]->getVel(vel);          
361  
362            atomData6[0] = pos[0];
363            atomData6[1] = pos[1];
# Line 733 | Line 390 | void DumpWriter::writeFinal(double finalTime){
390            }
391            
392          } else {
393 <          sprintf(painCave.errMsg,
394 <                  "Atom %d not found on processor %d\n",
395 <                  i, worldRank );
396 <          haveError= 1;
397 <          simError();
398 <        }
393 >          sprintf(painCave.errMsg,
394 >                              "Atom %d not found on processor %d\n",
395 >                              i, worldRank );
396 >                haveError= 1;
397 >                simError();
398 >              }
399          
400 <        if(haveError) DieDieDie();
400 >        if(haveError) DieDieDie();
401          
402 <        // If we've survived to here, format the line:
403 <        
404 <        if (!isDirectional) {
402 >        currentIndex ++;
403 >      }
404 >      // If we've survived to here, format the line:
405 >      
406 >      if (!isDirectional) {
407 >        
408 >        sprintf( writeLine,
409 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
410 >                             atomTypeString,
411 >                             atomData6[0],
412 >                             atomData6[1],
413 >                             atomData6[2],
414 >                             atomData6[3],
415 >                             atomData6[4],
416 >                             atomData6[5]);
417  
418 <          sprintf( tempBuffer,
419 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
420 <                   atomTypeString,
421 <                   atomData6[0],
422 <                   atomData6[1],
423 <                   atomData6[2],
424 <                   atomData6[3],
425 <                   atomData6[4],
426 <                   atomData6[5]);
427 <          
428 <          strcpy( writeLine, tempBuffer );
429 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
430 <
431 <        } else {
432 <          
433 <          sprintf( tempBuffer,
434 <                   "%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",
435 <                   atomTypeString,
436 <                   atomData13[0],
437 <                   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 <        }
418 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
419 >        
420 >      } else {
421 >        
422 >              sprintf( writeLine,
423 >                             "%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",
424 >                             atomTypeString,
425 >                             atomData13[0],
426 >                             atomData13[1],
427 >                             atomData13[2],
428 >                             atomData13[3],
429 >                             atomData13[4],
430 >                             atomData13[5],
431 >                             atomData13[6],
432 >                             atomData13[7],
433 >                             atomData13[8],
434 >                             atomData13[9],
435 >                             atomData13[10],
436 >                             atomData13[11],
437 >                             atomData13[12]);
438          
785 –        finalOut << writeLine;
786 –        finalOut.flush();
439        }
440 +      
441 +      for(k = 0; k < outFile.size(); k++)
442 +        *outFile[k] << writeLine;
443      }
444 <
445 <    finalOut.flush();
444 >    
445 >    for(k = 0; k < outFile.size(); k++)
446 >      outFile[k]->flush();
447 >    
448      sprintf( checkPointMsg,
449               "Sucessfully took a dump.\n");
450 <    delete[] potatoes;
794 <      
450 >
451      MPIcheckPoint();        
452 <    
452 >
453 >    delete[] potatoes;
454 >
455    } else {
456  
457      // worldRank != 0, so I'm a remote node.  
# Line 801 | Line 459 | void DumpWriter::writeFinal(double finalTime){
459      // Set my magic potato to 0:
460  
461      myPotato = 0;
462 +    currentIndex = 0;
463      
464      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
465        
# Line 817 | Line 476 | void DumpWriter::writeFinal(double finalTime){
476            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
477            
478          }
479 <        which_atom = i;  
480 <        local_index=-1;
481 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
482 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
824 <        }
825 <        if (local_index != -1) {
479 >        which_atom = i;
480 >        local_index = indexArray[currentIndex].first;        
481 >                
482 >        if (which_atom == indexArray[currentIndex].second) {
483          
484            atomTypeString = atoms[local_index]->getType();
485  
486 <          atoms[local_index]->getPos(pos);
487 <          atoms[local_index]->getVel(vel);
486 >                atoms[local_index]->getPos(pos);
487 >                atoms[local_index]->getVel(vel);
488  
489            atomData6[0] = pos[0];
490            atomData6[1] = pos[1];
# Line 853 | Line 510 | void DumpWriter::writeFinal(double finalTime){
510              atomData13[7] = q[1];
511              atomData13[8] = q[2];
512              atomData13[9] = q[3];
513 <
513 >  
514              atomData13[10] = dAtom->getJx();
515              atomData13[11] = dAtom->getJy();
516              atomData13[12] = dAtom->getJz();
517            }
518  
519          } else {
520 <          sprintf(painCave.errMsg,
521 <                  "Atom %d not found on processor %d\n",
522 <                  i, worldRank );
523 <          haveError= 1;
524 <          simError();
525 <        }
520 >                sprintf(painCave.errMsg,
521 >                              "Atom %d not found on processor %d\n",
522 >                              i, worldRank );
523 >                haveError= 1;
524 >                simError();
525 >              }
526  
527          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
528  
# Line 873 | Line 530 | void DumpWriter::writeFinal(double finalTime){
530          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
531  
532          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
533 <                 myPotato, MPI_COMM_WORLD);
533 >                             myPotato, MPI_COMM_WORLD);
534          
535          myPotato++;
536  
537          MPI_Send(&isDirectional, 1, MPI_INT, 0,
538 <                 myPotato, MPI_COMM_WORLD);
538 >                             myPotato, MPI_COMM_WORLD);
539          
540          myPotato++;
541          
# Line 893 | Line 550 | void DumpWriter::writeFinal(double finalTime){
550                     myPotato, MPI_COMM_WORLD);
551          }
552  
553 <        myPotato++;      
553 >        myPotato++;  
554 >        currentIndex++;    
555        }
556      }
557  
# Line 903 | Line 561 | void DumpWriter::writeFinal(double finalTime){
561      
562    }
563    
906 –  if( worldRank == 0 ) finalOut.close();
564   #endif // is_mpi
565   }
566  
910 –
911 –
567   #ifdef IS_MPI
568  
569   // a couple of functions to let us escape the write loop

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