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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 952 by tim, Fri Jan 16 21:55:39 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 <  // write current frame to the eor file
99 >  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 >  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 >  //}
102 >    
103 > }
104  
105 <  this->writeFinal( currentTime );
105 > #endif
106  
107 < #ifndef IS_MPI
107 > void DumpWriter::writeDump(double currentTime){
108  
109 <  outFile << nAtoms << "\n";
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111  
112 <  outFile << currentTime << ";\t"
113 <          << entry_plug->Hmat[0][0] << "\t"
114 <          << entry_plug->Hmat[1][0] << "\t"
115 <          << entry_plug->Hmat[2][0] << ";\t"
116 <
117 <          << entry_plug->Hmat[0][1] << "\t"
118 <          << entry_plug->Hmat[1][1] << "\t"
119 <          << entry_plug->Hmat[2][1] << ";\t"
120 <
121 <          << 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 );
112 > #ifdef IS_MPI
113 >  if(worldRank == 0 ){
114 > #endif    
115 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 >    if( !finalOut ){
117 >      sprintf( painCave.errMsg,
118 >               "Could not open \"%s\" for final dump output.\n",
119 >               entry_plug->finalName );
120 >      painCave.isFatal = 1;
121 >      simError();
122      }
123 <    else
155 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 <
157 <    outFile << writeLine;
123 > #ifdef IS_MPI
124    }
125 <  outFile.flush();
125 > #endif // is_mpi
126  
127 < #else // is_mpi
127 >  fileStreams.push_back(&finalOut);
128 >  fileStreams.push_back(&dumpFile);
129  
130 <  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 <  }  
130 >  writeFrame(fileStreams, currentTime);
131  
132 <  int haveError;
132 > #ifdef IS_MPI
133 >  finalOut.close();
134 > #endif
135 >        
136 > }
137  
138 <  MPI_Status istatus;
177 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
138 > void DumpWriter::writeFinal(double currentTime){
139  
140 <  // write out header and node 0's coordinates
140 >  ofstream finalOut;
141 >  vector<ofstream*> fileStreams;
142  
143 <  if( worldRank == 0 ){
143 > #ifdef IS_MPI
144 >  if(worldRank == 0 ){
145 > #endif // is_mpi
146  
147 <    // 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) {
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148  
149 <        if (potatoes[which_node] + 3 >= MAXTAG) {
150 <          // The potato was going to exceed the maximum value,
151 <          // so wrap this processor potato back to 0:        
152 <
153 <          potatoes[which_node] = 0;          
154 <          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 <      }
149 >    if( !finalOut ){
150 >      sprintf( painCave.errMsg,
151 >               "Could not open \"%s\" for final dump output.\n",
152 >               entry_plug->finalName );
153 >      painCave.isFatal = 1;
154 >      simError();
155      }
156  
157 <    outFile.flush();
158 <    sprintf( checkPointMsg,
159 <             "Sucessfully took a dump.\n");
160 <    MPIcheckPoint();        
161 <    delete[] potatoes;
162 <  } else {
157 > #ifdef IS_MPI
158 >  }
159 > #endif // is_mpi
160 >  
161 >  fileStreams.push_back(&finalOut);  
162 >  writeFrame(fileStreams, currentTime);
163  
164 <    // worldRank != 0, so I'm a remote node.  
165 <
166 <    // 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 <  }
164 > #ifdef IS_MPI
165 >  finalOut.close();
166 > #endif
167    
472 – #endif // is_mpi
168   }
169  
170 < void DumpWriter::writeFinal(double finalTime){
170 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171  
477 –  char finalName[500];
478 –  ofstream finalOut;
479 –
172    const int BUFFERSIZE = 2000;
173    const int MINIBUFFERSIZE = 100;
174 <  char tempBuffer[BUFFERSIZE];
174 >
175 >  char tempBuffer[BUFFERSIZE];  
176    char writeLine[BUFFERSIZE];
177  
178 <  double q[4];
179 <  DirectionalAtom* dAtom;
487 <  Atom** atoms = entry_plug->atoms;
488 <  int i;
178 >  int i, k;
179 >
180   #ifdef IS_MPI
181    
182 +  /*********************************************************************
183 +   * Documentation?  You want DOCUMENTATION?
184 +   *
185 +   * Why all the potatoes below?  
186 +   *
187 +   * To make a long story short, the original version of DumpWriter
188 +   * worked in the most inefficient way possible.  Node 0 would
189 +   * poke each of the node for an individual atom's formatted data
190 +   * as node 0 worked its way down the global index. This was particularly
191 +   * inefficient since the method blocked all processors at every atom
192 +   * (and did it twice!).
193 +   *
194 +   * An intermediate version of DumpWriter could be described from Node
195 +   * zero's perspective as follows:
196 +   *
197 +   *  1) Have 100 of your friends stand in a circle.
198 +   *  2) When you say go, have all of them start tossing potatoes at
199 +   *     you (one at a time).
200 +   *  3) Catch the potatoes.
201 +   *
202 +   * It was an improvement, but MPI has buffers and caches that could
203 +   * best be described in this analogy as "potato nets", so there's no
204 +   * need to block the processors atom-by-atom.
205 +   *
206 +   * This new and improved DumpWriter works in an even more efficient
207 +   * way:
208 +   *
209 +   *  1) Have 100 of your friend stand in a circle.
210 +   *  2) When you say go, have them start tossing 5-pound bags of
211 +   *     potatoes at you.
212 +   *  3) Once you've caught a friend's bag of potatoes,
213 +   *     toss them a spud to let them know they can toss another bag.
214 +   *
215 +   * How's THAT for documentation?
216 +   *
217 +   *********************************************************************/
218 +
219    int *potatoes;
220    int myPotato;
221  
222    int nProc;
223 <  int j, which_node, done, which_atom, local_index;
223 >  int j, which_node, done, which_atom, local_index, currentIndex;
224    double atomData6[6];
225    double atomData13[13];
226    int isDirectional;
# Line 503 | Line 231 | void DumpWriter::writeFinal(double finalTime){
231    int nAtoms = entry_plug->n_atoms;
232   #endif //is_mpi
233  
234 +  double q[4];
235 +  DirectionalAtom* dAtom;
236 +  Atom** atoms = entry_plug->atoms;
237    double pos[3], vel[3];
238  
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 –
239   #ifndef IS_MPI
240 +  
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243  
244 <  finalOut << nAtoms << "\n";
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252  
253 <  finalOut << finalTime << ";\t"
254 <           << entry_plug->Hmat[0][0] << "\t"
255 <           << entry_plug->Hmat[1][0] << "\t"
541 <           << entry_plug->Hmat[2][0] << ";\t"
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256  
257 <           << entry_plug->Hmat[0][1] << "\t"
258 <           << entry_plug->Hmat[1][1] << "\t"
259 <           << entry_plug->Hmat[2][1] << ";\t"
260 <
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 <
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 >  }
260 >  
261    for( i=0; i<nAtoms; i++ ){
262  
263      atoms[i]->getPos(pos);
# Line 587 | Line 293 | void DumpWriter::writeFinal(double finalTime){
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295  
296 <    finalOut << writeLine;
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
592 –  finalOut.flush();
593 –  finalOut.close();
299  
300   #else // is_mpi
301  
302    /* code to find maximum tag value */
303 +  
304    int *tagub, flag, MAXTAG;
305    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306    if (flag) {
# Line 617 | Line 323 | void DumpWriter::writeFinal(double finalTime){
323      nProc = mpiSim->getNumberProcessors();
324      potatoes = new int[nProc];
325  
326 +    //write out the comment lines
327      for (i = 0; i < nProc; i++)
328        potatoes[i] = 0;
329      
330 <    finalOut << mpiSim->getTotAtoms() << "\n";
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332  
333 <    finalOut << finalTime << ";\t"
334 <            << entry_plug->Hmat[0][0] << "\t"
335 <            << entry_plug->Hmat[1][0] << "\t"
336 <            << entry_plug->Hmat[2][0] << ";\t"
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337  
338 <            << entry_plug->Hmat[0][1] << "\t"
339 <            << entry_plug->Hmat[1][1] << "\t"
340 <            << entry_plug->Hmat[2][1] << ";\t"
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341  
342 <            << entry_plug->Hmat[0][2] << "\t"
343 <            << entry_plug->Hmat[1][2] << "\t"
344 <            << entry_plug->Hmat[2][2] << ";";
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348  
349 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
639 <    finalOut << endl;
640 <    finalOut.flush();
349 >    currentIndex = 0;
350  
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352        
# Line 661 | Line 370 | void DumpWriter::writeFinal(double finalTime){
370          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371                   myPotato, MPI_COMM_WORLD, &istatus);
372          
373 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
374 <        
666 <        // Null terminate the atomTypeString just in case:
667 <
668 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
669 <
373 >        atomTypeString = MPIatomTypeString;
374 >        
375          myPotato++;
376  
377          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 687 | Line 392 | void DumpWriter::writeFinal(double finalTime){
392  
393        } else {
394          
395 <        haveError = 0;
395 >        haveError = 0;
396          which_atom = i;
692 –        local_index=-1;
397          
398 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
399 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
400 <        }
398 >        //local_index = -1;
399 >
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403          
404 <        if (local_index != -1) {
404 >        //if (local_index != -1) {
405 >          
406 >          local_index = indexArray[currentIndex].first;        
407            
408 <          atomTypeString = atoms[local_index]->getType();
409 <
408 >          if (which_atom == indexArray[currentIndex].second) {
409 >            
410 >            atomTypeString = atoms[local_index]->getType();
411 >            
412            atoms[local_index]->getPos(pos);
413            atoms[local_index]->getVel(vel);          
414 <
414 >          
415            atomData6[0] = pos[0];
416            atomData6[1] = pos[1];
417            atomData6[2] = pos[2];
# Line 734 | Line 444 | void DumpWriter::writeFinal(double finalTime){
444            
445          } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451          }
452          
453 <        if(haveError) DieDieDie();
453 >        if(haveError) DieDieDie();
454          
455 <        // If we've survived to here, format the line:
456 <        
457 <        if (!isDirectional) {
458 <
459 <          sprintf( tempBuffer,
460 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
461 <                   atomTypeString,
462 <                   atomData6[0],
463 <                   atomData6[1],
464 <                   atomData6[2],
465 <                   atomData6[3],
466 <                   atomData6[4],
467 <                   atomData6[5]);
468 <          
469 <          strcpy( writeLine, tempBuffer );
470 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
471 <
472 <        } else {
473 <          
474 <          sprintf( tempBuffer,
475 <                   "%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",
476 <                   atomTypeString,
477 <                   atomData13[0],
478 <                   atomData13[1],
479 <                   atomData13[2],
480 <                   atomData13[3],
481 <                   atomData13[4],
482 <                   atomData13[5],
483 <                   atomData13[6],
484 <                   atomData13[7],
485 <                   atomData13[8],
486 <                   atomData13[9],
487 <                   atomData13[10],
488 <                   atomData13[11],
489 <                   atomData13[12]);
490 <          
781 <          strcat( writeLine, tempBuffer );
782 <          
783 <        }
455 >        currentIndex++;
456 >      }
457 >      // If we've survived to here, format the line:
458 >      
459 >      if (!isDirectional) {
460 >        
461 >        sprintf( writeLine,
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470 >        
471 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 >        
473 >      } else {
474 >        
475 >        sprintf( writeLine,
476 >                 "%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",
477 >                 atomTypeString,
478 >                 atomData13[0],
479 >                 atomData13[1],
480 >                 atomData13[2],
481 >                 atomData13[3],
482 >                 atomData13[4],
483 >                 atomData13[5],
484 >                 atomData13[6],
485 >                 atomData13[7],
486 >                 atomData13[8],
487 >                 atomData13[9],
488 >                 atomData13[10],
489 >                 atomData13[11],
490 >                 atomData13[12]);
491          
785 –        finalOut << writeLine;
786 –        finalOut.flush();
492        }
493 +      
494 +      for(k = 0; k < outFile.size(); k++)
495 +        *outFile[k] << writeLine;
496      }
497 <
498 <    finalOut.flush();
497 >    
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501      sprintf( checkPointMsg,
502               "Sucessfully took a dump.\n");
503 <    delete[] potatoes;
794 <      
503 >    
504      MPIcheckPoint();        
505      
506 +    delete[] potatoes;
507 +    
508    } else {
509  
510      // worldRank != 0, so I'm a remote node.  
# Line 801 | Line 512 | void DumpWriter::writeFinal(double finalTime){
512      // Set my magic potato to 0:
513  
514      myPotato = 0;
515 +    currentIndex = 0;
516      
517      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518        
# Line 809 | Line 521 | void DumpWriter::writeFinal(double finalTime){
521        if (AtomToProcMap[i] == worldRank) {
522  
523          if (myPotato + 3 >= MAXTAG) {
524 <
524 >          
525            // The potato was going to exceed the maximum value,
526            // so wrap this processor potato back to 0 (and block until
527            // node 0 says we can go:
528 <
528 >          
529            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530            
531          }
532 <        which_atom = i;  
533 <        local_index=-1;
534 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
535 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
536 <        }
537 <        if (local_index != -1) {
532 >        which_atom = i;
533 >
534 >        //local_index = -1;
535 >
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541 >
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545          
546            atomTypeString = atoms[local_index]->getType();
547 <
547 >          
548            atoms[local_index]->getPos(pos);
549            atoms[local_index]->getVel(vel);
550 <
550 >          
551            atomData6[0] = pos[0];
552            atomData6[1] = pos[1];
553            atomData6[2] = pos[2];
# Line 853 | Line 572 | void DumpWriter::writeFinal(double finalTime){
572              atomData13[7] = q[1];
573              atomData13[8] = q[2];
574              atomData13[9] = q[3];
575 <
575 >  
576              atomData13[10] = dAtom->getJx();
577              atomData13[11] = dAtom->getJy();
578              atomData13[12] = dAtom->getJz();
# Line 861 | Line 580 | void DumpWriter::writeFinal(double finalTime){
580  
581          } else {
582            sprintf(painCave.errMsg,
583 <                  "Atom %d not found on processor %d\n",
584 <                  i, worldRank );
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585            haveError= 1;
586            simError();
587          }
588 <
588 >        
589          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591          // null terminate the string before sending (just in case):
592          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593  
594          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 <                 myPotato, MPI_COMM_WORLD);
595 >                             myPotato, MPI_COMM_WORLD);
596          
597          myPotato++;
598  
599          MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 <                 myPotato, MPI_COMM_WORLD);
600 >                             myPotato, MPI_COMM_WORLD);
601          
602          myPotato++;
603          
# Line 893 | Line 612 | void DumpWriter::writeFinal(double finalTime){
612                     myPotato, MPI_COMM_WORLD);
613          }
614  
615 <        myPotato++;      
615 >        myPotato++;  
616 >        currentIndex++;    
617        }
618      }
619  
# Line 903 | Line 623 | void DumpWriter::writeFinal(double finalTime){
623      
624    }
625    
906 –  if( worldRank == 0 ) finalOut.close();
626   #endif // is_mpi
627   }
628  
910 –
911 –
629   #ifdef IS_MPI
630  
631   // a couple of functions to let us escape the write loop

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