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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 1000 by tim, Fri Jan 30 21:47:22 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
31 <    strcpy( outName, entry_plug->sampleName );
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32  
33 <    outFile.open(outName, ios::out | ios::trunc );
33 >    if( !dumpFile ){
34  
33 –    if( !outFile ){
34 –
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
42 –    //outFile.setf( ios::scientific );
43 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 56 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68  
69 <  const int BUFFERSIZE = 2000;
70 <  const int MINIBUFFERSIZE = 100;
69 > /**
70 > * A hook function to load balancing
71 > */
72  
73 <  char tempBuffer[BUFFERSIZE];
74 <  char writeLine[BUFFERSIZE];
75 <
74 <  int i;
75 <
76 < #ifdef IS_MPI
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 <  int *potatoes;
78 <  int myPotato;
77 > /**
78 > * Auxiliary sorting function
79 > */
80 >
81 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 >  return p1.second < p2.second;
83 > }
84  
85 <  int nProc;
86 <  int j, which_node, done, which_atom, local_index;
87 <  double atomData6[6];
88 <  double atomData13[13];
89 <  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;
85 > /**
86 > * Sorting the local index by global index
87 > */
88 >
89 > void DumpWriter::sortByGlobalIndex(){
90    Atom** atoms = entry_plug->atoms;
91 <  double pos[3], vel[3];
91 >  
92 >  indexArray.clear();
93 >  
94 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 > }
99  
100 <  // write current frame to the eor file
100 > #endif
101  
102 <  this->writeFinal( currentTime );
102 > void DumpWriter::writeDump(double currentTime){
103  
104 < #ifndef IS_MPI
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <  outFile << nAtoms << "\n";
108 <
109 <  outFile << currentTime << ";\t"
110 <          << entry_plug->Hmat[0][0] << "\t"
111 <          << entry_plug->Hmat[1][0] << "\t"
112 <          << entry_plug->Hmat[2][0] << ";\t"
113 <
114 <          << entry_plug->Hmat[0][1] << "\t"
115 <          << entry_plug->Hmat[1][1] << "\t"
116 <          << 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 > #endif    
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      }
118 <    else
155 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 <
157 <    outFile << writeLine;
118 > #ifdef IS_MPI
119    }
120 <  outFile.flush();
120 > #endif // is_mpi
121  
122 < #else // is_mpi
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  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 <  }  
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  int haveError;
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  MPI_Status istatus;
177 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <  // write out header and node 0's coordinates
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <  if( worldRank == 0 ){
139 <
140 <    // 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) {
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <        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:        
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
144 <          potatoes[which_node] = 0;          
145 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
146 <          
147 <        }
148 <
149 <        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 <      }
144 >    if( !finalOut ){
145 >      sprintf( painCave.errMsg,
146 >               "Could not open \"%s\" for final dump output.\n",
147 >               entry_plug->finalName );
148 >      painCave.isFatal = 1;
149 >      simError();
150      }
151  
152 <    outFile.flush();
153 <    sprintf( checkPointMsg,
154 <             "Sucessfully took a dump.\n");
155 <    MPIcheckPoint();        
156 <    delete[] potatoes;
157 <  } 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() ){
152 > #ifdef IS_MPI
153 >  }
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 <            isDirectional = 1;
160 <            
161 <            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 <  }
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162    
472 – #endif // is_mpi
163   }
164  
165 < void DumpWriter::writeFinal(double finalTime){
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
477 –  char finalName[500];
478 –  ofstream finalOut;
479 –
167    const int BUFFERSIZE = 2000;
168    const int MINIBUFFERSIZE = 100;
169 <  char tempBuffer[BUFFERSIZE];
169 >
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  double q[4];
174 <  DirectionalAtom* dAtom;
487 <  Atom** atoms = entry_plug->atoms;
488 <  int i;
173 >  int i, k;
174 >
175   #ifdef IS_MPI
176    
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214    int *potatoes;
215    int myPotato;
216  
217    int nProc;
218 <  int j, which_node, done, which_atom, local_index;
218 >  int j, which_node, done, which_atom, local_index, currentIndex;
219    double atomData6[6];
220    double atomData13[13];
221    int isDirectional;
# Line 503 | Line 226 | void DumpWriter::writeFinal(double finalTime){
226    int nAtoms = entry_plug->n_atoms;
227   #endif //is_mpi
228  
229 +  double q[4];
230 +  DirectionalAtom* dAtom;
231 +  Atom** atoms = entry_plug->atoms;
232    double pos[3], vel[3];
233  
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 –
234   #ifndef IS_MPI
235 +  
236 +  for(k = 0; k < outFile.size(); k++){
237 +    *outFile[k] << nAtoms << "\n";
238  
239 <  finalOut << nAtoms << "\n";
239 >    *outFile[k] << currentTime << ";\t"
240 >               << entry_plug->Hmat[0][0] << "\t"
241 >                     << entry_plug->Hmat[1][0] << "\t"
242 >                     << entry_plug->Hmat[2][0] << ";\t"
243 >              
244 >               << entry_plug->Hmat[0][1] << "\t"
245 >                     << entry_plug->Hmat[1][1] << "\t"
246 >                     << entry_plug->Hmat[2][1] << ";\t"
247  
248 <  finalOut << finalTime << ";\t"
249 <           << entry_plug->Hmat[0][0] << "\t"
250 <           << entry_plug->Hmat[1][0] << "\t"
541 <           << entry_plug->Hmat[2][0] << ";\t"
248 >                     << entry_plug->Hmat[0][2] << "\t"
249 >                     << entry_plug->Hmat[1][2] << "\t"
250 >                     << entry_plug->Hmat[2][2] << ";";
251  
252 <           << entry_plug->Hmat[0][1] << "\t"
253 <           << entry_plug->Hmat[1][1] << "\t"
254 <           << entry_plug->Hmat[2][1] << ";\t"
255 <
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 <
252 >    //write out additional parameters, such as chi and eta
253 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 >  }
255 >  
256    for( i=0; i<nAtoms; i++ ){
257  
258      atoms[i]->getPos(pos);
# Line 587 | Line 288 | void DumpWriter::writeFinal(double finalTime){
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290  
291 <    finalOut << writeLine;
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
592 –  finalOut.flush();
593 –  finalOut.close();
294  
295   #else // is_mpi
296  
297    /* code to find maximum tag value */
298 +  
299    int *tagub, flag, MAXTAG;
300    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301    if (flag) {
# Line 617 | Line 318 | void DumpWriter::writeFinal(double finalTime){
318      nProc = mpiSim->getNumberProcessors();
319      potatoes = new int[nProc];
320  
321 +    //write out the comment lines
322      for (i = 0; i < nProc; i++)
323        potatoes[i] = 0;
324      
325 <    finalOut << mpiSim->getTotAtoms() << "\n";
326 <
625 <    finalOut << finalTime << ";\t"
626 <            << entry_plug->Hmat[0][0] << "\t"
627 <            << entry_plug->Hmat[1][0] << "\t"
628 <            << entry_plug->Hmat[2][0] << ";\t"
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327  
328 <            << entry_plug->Hmat[0][1] << "\t"
329 <            << entry_plug->Hmat[1][1] << "\t"
330 <            << entry_plug->Hmat[2][1] << ";\t"
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332  
333 <            << entry_plug->Hmat[0][2] << "\t"
334 <            << entry_plug->Hmat[1][2] << "\t"
335 <            << entry_plug->Hmat[2][2] << ";";
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336  
337 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
338 <    finalOut << endl;
339 <    finalOut.flush();
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343  
344 +    currentIndex = 0;
345 +
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
347        
348        // Get the Node number which has this atom;
# Line 661 | Line 365 | void DumpWriter::writeFinal(double finalTime){
365          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366                   myPotato, MPI_COMM_WORLD, &istatus);
367          
368 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
369 <        
666 <        // Null terminate the atomTypeString just in case:
667 <
668 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
669 <
368 >        atomTypeString = MPIatomTypeString;
369 >        
370          myPotato++;
371  
372          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 687 | Line 387 | void DumpWriter::writeFinal(double finalTime){
387  
388        } else {
389          
390 <        haveError = 0;
390 >        haveError = 0;
391          which_atom = i;
692 –        local_index=-1;
392          
393 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
695 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
696 <        }
697 <        
698 <        if (local_index != -1) {
393 >          local_index = indexArray[currentIndex].first;        
394            
395 <          atomTypeString = atoms[local_index]->getType();
396 <
395 >          if (which_atom == indexArray[currentIndex].second) {
396 >            
397 >            atomTypeString = atoms[local_index]->getType();
398 >            
399            atoms[local_index]->getPos(pos);
400            atoms[local_index]->getVel(vel);          
401 <
401 >          
402            atomData6[0] = pos[0];
403            atomData6[1] = pos[1];
404            atomData6[2] = pos[2];
# Line 734 | Line 431 | void DumpWriter::writeFinal(double finalTime){
431            
432          } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438          }
439          
440 <        if(haveError) DieDieDie();
440 >        if(haveError) DieDieDie();
441          
442 <        // If we've survived to here, format the line:
443 <        
444 <        if (!isDirectional) {
445 <
446 <          sprintf( tempBuffer,
447 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
448 <                   atomTypeString,
449 <                   atomData6[0],
450 <                   atomData6[1],
451 <                   atomData6[2],
452 <                   atomData6[3],
453 <                   atomData6[4],
454 <                   atomData6[5]);
455 <          
456 <          strcpy( writeLine, tempBuffer );
457 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
458 <
459 <        } else {
460 <          
461 <          sprintf( tempBuffer,
462 <                   "%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",
463 <                   atomTypeString,
464 <                   atomData13[0],
465 <                   atomData13[1],
466 <                   atomData13[2],
467 <                   atomData13[3],
468 <                   atomData13[4],
469 <                   atomData13[5],
470 <                   atomData13[6],
471 <                   atomData13[7],
472 <                   atomData13[8],
473 <                   atomData13[9],
474 <                   atomData13[10],
475 <                   atomData13[11],
476 <                   atomData13[12]);
477 <          
781 <          strcat( writeLine, tempBuffer );
782 <          
783 <        }
442 >        currentIndex++;
443 >      }
444 >      // If we've survived to here, format the line:
445 >      
446 >      if (!isDirectional) {
447 >        
448 >        sprintf( writeLine,
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457 >        
458 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 >        
460 >      } else {
461 >        
462 >        sprintf( writeLine,
463 >                 "%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",
464 >                 atomTypeString,
465 >                 atomData13[0],
466 >                 atomData13[1],
467 >                 atomData13[2],
468 >                 atomData13[3],
469 >                 atomData13[4],
470 >                 atomData13[5],
471 >                 atomData13[6],
472 >                 atomData13[7],
473 >                 atomData13[8],
474 >                 atomData13[9],
475 >                 atomData13[10],
476 >                 atomData13[11],
477 >                 atomData13[12]);
478          
785 –        finalOut << writeLine;
786 –        finalOut.flush();
479        }
480 +      
481 +      for(k = 0; k < outFile.size(); k++)
482 +        *outFile[k] << writeLine;
483      }
484 <
485 <    finalOut.flush();
484 >    
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487 >    
488      sprintf( checkPointMsg,
489               "Sucessfully took a dump.\n");
490 <    delete[] potatoes;
794 <      
490 >    
491      MPIcheckPoint();        
492      
493 +    delete[] potatoes;
494 +    
495    } else {
496  
497      // worldRank != 0, so I'm a remote node.  
# Line 801 | Line 499 | void DumpWriter::writeFinal(double finalTime){
499      // Set my magic potato to 0:
500  
501      myPotato = 0;
502 +    currentIndex = 0;
503      
504      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
505        
# Line 809 | Line 508 | void DumpWriter::writeFinal(double finalTime){
508        if (AtomToProcMap[i] == worldRank) {
509  
510          if (myPotato + 3 >= MAXTAG) {
511 <
511 >          
512            // The potato was going to exceed the maximum value,
513            // so wrap this processor potato back to 0 (and block until
514            // node 0 says we can go:
515 <
515 >          
516            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517            
518          }
519 <        which_atom = i;  
520 <        local_index=-1;
521 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
522 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
523 <        }
825 <        if (local_index != -1) {
519 >        which_atom = i;
520 >
521 >        local_index = indexArray[currentIndex].first;        
522 >                
523 >        if (which_atom == indexArray[currentIndex].second) {
524          
525            atomTypeString = atoms[local_index]->getType();
526 <
526 >          
527            atoms[local_index]->getPos(pos);
528            atoms[local_index]->getVel(vel);
529 <
529 >          
530            atomData6[0] = pos[0];
531            atomData6[1] = pos[1];
532            atomData6[2] = pos[2];
# Line 853 | Line 551 | void DumpWriter::writeFinal(double finalTime){
551              atomData13[7] = q[1];
552              atomData13[8] = q[2];
553              atomData13[9] = q[3];
554 <
554 >  
555              atomData13[10] = dAtom->getJx();
556              atomData13[11] = dAtom->getJy();
557              atomData13[12] = dAtom->getJz();
# Line 861 | Line 559 | void DumpWriter::writeFinal(double finalTime){
559  
560          } else {
561            sprintf(painCave.errMsg,
562 <                  "Atom %d not found on processor %d\n",
563 <                  i, worldRank );
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564            haveError= 1;
565            simError();
566          }
567 <
567 >        
568          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570          // null terminate the string before sending (just in case):
571          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572  
573          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 <                 myPotato, MPI_COMM_WORLD);
574 >                             myPotato, MPI_COMM_WORLD);
575          
576          myPotato++;
577  
578          MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 <                 myPotato, MPI_COMM_WORLD);
579 >                             myPotato, MPI_COMM_WORLD);
580          
581          myPotato++;
582          
# Line 893 | Line 591 | void DumpWriter::writeFinal(double finalTime){
591                     myPotato, MPI_COMM_WORLD);
592          }
593  
594 <        myPotato++;      
594 >        myPotato++;  
595 >        currentIndex++;    
596        }
597      }
598  
# Line 903 | Line 602 | void DumpWriter::writeFinal(double finalTime){
602      
603    }
604    
906 –  if( worldRank == 0 ) finalOut.close();
605   #endif // is_mpi
606   }
607  
910 –
911 –
608   #ifdef IS_MPI
609  
610   // a couple of functions to let us escape the write loop

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