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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 916 by gezelter, Fri Jan 9 20:29:32 2004 UTC vs.
Revision 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
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  
101 <  // write current frame to the eor file
101 > #endif
102  
103 <  this->writeFinal( currentTime );
103 > void DumpWriter::writeDump(double currentTime){
104  
105 < #ifndef IS_MPI
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107  
108 <  outFile << nAtoms << "\n";
109 <
110 <  outFile << currentTime << ";\t"
111 <          << entry_plug->Hmat[0][0] << "\t"
112 <          << entry_plug->Hmat[1][0] << "\t"
113 <          << entry_plug->Hmat[2][0] << ";\t"
114 <
115 <          << entry_plug->Hmat[0][1] << "\t"
116 <          << entry_plug->Hmat[1][1] << "\t"
117 <          << 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 );
108 > #ifdef IS_MPI
109 >  if(worldRank == 0 ){
110 > #endif    
111 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 >    if( !finalOut ){
113 >      sprintf( painCave.errMsg,
114 >               "Could not open \"%s\" for final dump output.\n",
115 >               entry_plug->finalName );
116 >      painCave.isFatal = 1;
117 >      simError();
118      }
119 <    else
155 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 <
157 <    outFile << writeLine;
119 > #ifdef IS_MPI
120    }
121 <  outFile.flush();
121 > #endif // is_mpi
122  
123 < #else // is_mpi
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125  
126 <  /* code to find maximum tag value */
164 <  int *tagub, flag, MAXTAG;
165 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
166 <  if (flag) {
167 <    MAXTAG = *tagub;
168 <  } else {
169 <    MAXTAG = 32767;
170 <  }  
126 >  writeFrame(fileStreams, currentTime);
127  
128 <  int haveError;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
134 > void DumpWriter::writeFinal(double currentTime){
135  
136 <  // write out header and node 0's coordinates
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
139 <  if( worldRank == 0 ){
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <    // Node 0 needs a list of the magic potatoes for each processor;
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <    nProc = mpiSim->getNumberProcessors();
146 <    potatoes = new int[nProc];
147 <
148 <    for (i = 0; i < nProc; i++)
149 <      potatoes[i] = 0;
150 <    
189 <    outFile << mpiSim->getTotAtoms() << "\n";
190 <
191 <    outFile << currentTime << ";\t"
192 <            << entry_plug->Hmat[0][0] << "\t"
193 <            << entry_plug->Hmat[1][0] << "\t"
194 <            << entry_plug->Hmat[2][0] << ";\t"
195 <
196 <            << entry_plug->Hmat[0][1] << "\t"
197 <            << entry_plug->Hmat[1][1] << "\t"
198 <            << entry_plug->Hmat[2][1] << ";\t"
199 <
200 <            << entry_plug->Hmat[0][2] << "\t"
201 <            << entry_plug->Hmat[1][2] << "\t"
202 <            << entry_plug->Hmat[2][2] << ";";
203 <
204 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
205 <    outFile << endl;
206 <    outFile.flush();
207 <
208 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
209 <      
210 <      // Get the Node number which has this atom;
211 <      
212 <      which_node = AtomToProcMap[i];
213 <      
214 <      if (which_node != 0) {
215 <
216 <        if (potatoes[which_node] + 3 >= MAXTAG) {
217 <          // The potato was going to exceed the maximum value,
218 <          // so wrap this processor potato back to 0:        
219 <
220 <          potatoes[which_node] = 0;          
221 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
222 <          
223 <        }
224 <
225 <        myPotato = potatoes[which_node];        
226 <        
227 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
228 <                 myPotato, MPI_COMM_WORLD, &istatus);
229 <        
230 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
231 <        
232 <        // Null terminate the atomTypeString just in case:
233 <
234 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
235 <
236 <        myPotato++;
237 <
238 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
239 <                 myPotato, MPI_COMM_WORLD, &istatus);
240 <              
241 <        myPotato++;
242 <
243 <        if (isDirectional) {          
244 <          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
245 <                   myPotato, MPI_COMM_WORLD, &istatus);
246 <        } else {
247 <          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
248 <                   myPotato, MPI_COMM_WORLD, &istatus);          
249 <        }
250 <        
251 <        myPotato++;
252 <        potatoes[which_node] = myPotato;
253 <
254 <      } else {
255 <        
256 <        haveError = 0;
257 <        which_atom = i;
258 <        local_index=-1;
259 <        
260 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
261 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
262 <        }
263 <        
264 <        if (local_index != -1) {
265 <          
266 <          atomTypeString = atoms[local_index]->getType();
267 <
268 <          atoms[local_index]->getPos(pos);
269 <          atoms[local_index]->getVel(vel);          
270 <
271 <          atomData6[0] = pos[0];
272 <          atomData6[1] = pos[1];
273 <          atomData6[2] = pos[2];
274 <
275 <          atomData6[3] = vel[0];
276 <          atomData6[4] = vel[1];
277 <          atomData6[5] = vel[2];
278 <          
279 <          isDirectional = 0;
280 <
281 <          if( atoms[local_index]->isDirectional() ){
282 <
283 <            isDirectional = 1;
284 <            
285 <            dAtom = (DirectionalAtom *)atoms[local_index];
286 <            dAtom->getQ( q );
287 <
288 <            for (int j = 0; j < 6 ; j++)
289 <              atomData13[j] = atomData6[j];            
290 <            
291 <            atomData13[6] = q[0];
292 <            atomData13[7] = q[1];
293 <            atomData13[8] = q[2];
294 <            atomData13[9] = q[3];
295 <            
296 <            atomData13[10] = dAtom->getJx();
297 <            atomData13[11] = dAtom->getJy();
298 <            atomData13[12] = dAtom->getJz();
299 <          }
300 <          
301 <        } else {
302 <          sprintf(painCave.errMsg,
303 <                  "Atom %d not found on processor %d\n",
304 <                  i, worldRank );
305 <          haveError= 1;
306 <          simError();
307 <        }
308 <        
309 <        if(haveError) DieDieDie();
310 <        
311 <        // If we've survived to here, format the line:
312 <        
313 <        if (!isDirectional) {
314 <
315 <          sprintf( tempBuffer,
316 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
317 <                   atomTypeString,
318 <                   atomData6[0],
319 <                   atomData6[1],
320 <                   atomData6[2],
321 <                   atomData6[3],
322 <                   atomData6[4],
323 <                   atomData6[5]);
324 <          
325 <          strcpy( writeLine, tempBuffer );
326 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
327 <
328 <        } else {
329 <          
330 <          sprintf( tempBuffer,
331 <                   "%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",
332 <                   atomTypeString,
333 <                   atomData13[0],
334 <                   atomData13[1],
335 <                   atomData13[2],
336 <                   atomData13[3],
337 <                   atomData13[4],
338 <                   atomData13[5],
339 <                   atomData13[6],
340 <                   atomData13[7],
341 <                   atomData13[8],
342 <                   atomData13[9],
343 <                   atomData13[10],
344 <                   atomData13[11],
345 <                   atomData13[12]);
346 <          
347 <          strcat( writeLine, tempBuffer );
348 <          
349 <        }
350 <        
351 <        outFile << writeLine;
352 <        outFile.flush();
353 <      }
145 >    if( !finalOut ){
146 >      sprintf( painCave.errMsg,
147 >               "Could not open \"%s\" for final dump output.\n",
148 >               entry_plug->finalName );
149 >      painCave.isFatal = 1;
150 >      simError();
151      }
152  
153 <    outFile.flush();
154 <    sprintf( checkPointMsg,
155 <             "Sucessfully took a dump.\n");
156 <    MPIcheckPoint();        
157 <    
158 <  } else {
362 <
363 <    // worldRank != 0, so I'm a remote node.  
364 <
365 <    // Set my magic potato to 0:
366 <
367 <    myPotato = 0;
368 <    
369 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
370 <      
371 <      // Am I the node which has this atom?
372 <      
373 <      if (AtomToProcMap[i] == worldRank) {
374 <
375 <        if (myPotato + 3 >= MAXTAG) {
376 <
377 <          // The potato was going to exceed the maximum value,
378 <          // so wrap this processor potato back to 0 (and block until
379 <          // node 0 says we can go:
380 <
381 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
382 <          
383 <        }
384 <
385 <        local_index=-1;
386 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
387 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
388 <        }
389 <        if (local_index != -1) {
390 <        
391 <          atomTypeString = atoms[local_index]->getType();
392 <
393 <          atoms[local_index]->getPos(pos);
394 <          atoms[local_index]->getVel(vel);
395 <
396 <          atomData6[0] = pos[0];
397 <          atomData6[1] = pos[1];
398 <          atomData6[2] = pos[2];
399 <
400 <          atomData6[3] = vel[0];
401 <          atomData6[4] = vel[1];
402 <          atomData6[5] = vel[2];
403 <          
404 <          isDirectional = 0;
405 <
406 <          if( atoms[local_index]->isDirectional() ){
153 > #ifdef IS_MPI
154 >  }
155 > #endif // is_mpi
156 >  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159  
160 <            isDirectional = 1;
161 <            
162 <            dAtom = (DirectionalAtom *)atoms[local_index];
411 <            dAtom->getQ( q );
412 <            
413 <            for (int j = 0; j < 6 ; j++)
414 <              atomData13[j] = atomData6[j];
415 <            
416 <            atomData13[6] = q[0];
417 <            atomData13[7] = q[1];
418 <            atomData13[8] = q[2];
419 <            atomData13[9] = q[3];
420 <
421 <            atomData13[10] = dAtom->getJx();
422 <            atomData13[11] = dAtom->getJy();
423 <            atomData13[12] = dAtom->getJz();
424 <          }
425 <
426 <        } else {
427 <          sprintf(painCave.errMsg,
428 <                  "Atom %d not found on processor %d\n",
429 <                  i, worldRank );
430 <          haveError= 1;
431 <          simError();
432 <        }
433 <
434 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
435 <
436 <        // null terminate the string before sending (just in case):
437 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
438 <
439 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
440 <                 myPotato, MPI_COMM_WORLD);
441 <        
442 <        myPotato++;
443 <
444 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
445 <                 myPotato, MPI_COMM_WORLD);
446 <        
447 <        myPotato++;
448 <        
449 <        if (isDirectional) {
450 <
451 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
452 <                   myPotato, MPI_COMM_WORLD);
453 <          
454 <        } else {
455 <
456 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
457 <                   myPotato, MPI_COMM_WORLD);
458 <        }
459 <
460 <        myPotato++;      
461 <      }
462 <    }
463 <
464 <    sprintf( checkPointMsg,
465 <             "Sucessfully took a dump.\n");
466 <    MPIcheckPoint();        
467 <    
468 <  }
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163    
470 – #endif // is_mpi
164   }
165  
166 < void DumpWriter::writeFinal(double finalTime){
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
475 –  char finalName[500];
476 –  ofstream finalOut;
477 –
168    const int BUFFERSIZE = 2000;
169    const int MINIBUFFERSIZE = 100;
170 <  char tempBuffer[BUFFERSIZE];
170 >
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174 <  double q[4];
175 <  DirectionalAtom* dAtom;
485 <  Atom** atoms = entry_plug->atoms;
486 <  int i;
174 >  int i, k;
175 >
176   #ifdef IS_MPI
177    
178 +  /*********************************************************************
179 +   * Documentation?  You want DOCUMENTATION?
180 +   *
181 +   * Why all the potatoes below?  
182 +   *
183 +   * To make a long story short, the original version of DumpWriter
184 +   * worked in the most inefficient way possible.  Node 0 would
185 +   * poke each of the node for an individual atom's formatted data
186 +   * as node 0 worked its way down the global index. This was particularly
187 +   * inefficient since the method blocked all processors at every atom
188 +   * (and did it twice!).
189 +   *
190 +   * An intermediate version of DumpWriter could be described from Node
191 +   * zero's perspective as follows:
192 +   *
193 +   *  1) Have 100 of your friends stand in a circle.
194 +   *  2) When you say go, have all of them start tossing potatoes at
195 +   *     you (one at a time).
196 +   *  3) Catch the potatoes.
197 +   *
198 +   * It was an improvement, but MPI has buffers and caches that could
199 +   * best be described in this analogy as "potato nets", so there's no
200 +   * need to block the processors atom-by-atom.
201 +   *
202 +   * This new and improved DumpWriter works in an even more efficient
203 +   * way:
204 +   *
205 +   *  1) Have 100 of your friend stand in a circle.
206 +   *  2) When you say go, have them start tossing 5-pound bags of
207 +   *     potatoes at you.
208 +   *  3) Once you've caught a friend's bag of potatoes,
209 +   *     toss them a spud to let them know they can toss another bag.
210 +   *
211 +   * How's THAT for documentation?
212 +   *
213 +   *********************************************************************/
214 +
215    int *potatoes;
216    int myPotato;
217  
218    int nProc;
219 <  int j, which_node, done, which_atom, local_index;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220    double atomData6[6];
221    double atomData13[13];
222    int isDirectional;
# Line 501 | Line 227 | void DumpWriter::writeFinal(double finalTime){
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 +  double q[4];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
506 – #ifdef IS_MPI
507 –  if(worldRank == 0 ){
508 – #endif // is_mpi
509 –
510 –    strcpy( finalName, entry_plug->finalName );
511 –
512 –    finalOut.open( finalName, ios::out | ios::trunc );
513 –    if( !finalOut ){
514 –      sprintf( painCave.errMsg,
515 –               "Could not open \"%s\" for final dump output.\n",
516 –               finalName );
517 –      painCave.isFatal = 1;
518 –      simError();
519 –    }
520 –
521 –    // finalOut.setf( ios::scientific );
522 –
523 – #ifdef IS_MPI
524 –  }
525 –
526 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
527 –  MPIcheckPoint();
528 –
529 – #endif //is_mpi
530 –
531 –
235   #ifndef IS_MPI
236 +  
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239  
240 <  finalOut << nAtoms << "\n";
240 >    *outFile[k] << currentTime << ";\t"
241 >               << entry_plug->Hmat[0][0] << "\t"
242 >                     << entry_plug->Hmat[1][0] << "\t"
243 >                     << entry_plug->Hmat[2][0] << ";\t"
244 >              
245 >               << entry_plug->Hmat[0][1] << "\t"
246 >                     << entry_plug->Hmat[1][1] << "\t"
247 >                     << entry_plug->Hmat[2][1] << ";\t"
248  
249 <  finalOut << finalTime << ";\t"
250 <           << entry_plug->Hmat[0][0] << "\t"
251 <           << entry_plug->Hmat[1][0] << "\t"
539 <           << entry_plug->Hmat[2][0] << ";\t"
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252  
253 <           << entry_plug->Hmat[0][1] << "\t"
254 <           << entry_plug->Hmat[1][1] << "\t"
255 <           << entry_plug->Hmat[2][1] << ";\t"
256 <
545 <           << entry_plug->Hmat[0][2] << "\t"
546 <           << entry_plug->Hmat[1][2] << "\t"
547 <           << entry_plug->Hmat[2][2] << ";";
548 <
549 <  //write out additional parameters, such as chi and eta
550 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
551 <  finalOut << endl;
552 <
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 >  }
256 >  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 585 | Line 289 | void DumpWriter::writeFinal(double finalTime){
289      else
290        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291  
292 <    finalOut << writeLine;
292 >    for(k = 0; k < outFile.size(); k++)
293 >      *outFile[k] << writeLine;
294    }
590 –  finalOut.flush();
591 –  finalOut.close();
295  
296   #else // is_mpi
297  
298    /* code to find maximum tag value */
299 +  
300    int *tagub, flag, MAXTAG;
301    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302    if (flag) {
# Line 615 | Line 319 | void DumpWriter::writeFinal(double finalTime){
319      nProc = mpiSim->getNumberProcessors();
320      potatoes = new int[nProc];
321  
322 +    //write out the comment lines
323      for (i = 0; i < nProc; i++)
324        potatoes[i] = 0;
325      
326 <    finalOut << mpiSim->getTotAtoms() << "\n";
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328  
329 <    finalOut << finalTime << ";\t"
330 <            << entry_plug->Hmat[0][0] << "\t"
331 <            << entry_plug->Hmat[1][0] << "\t"
332 <            << entry_plug->Hmat[2][0] << ";\t"
329 >        *outFile[k] << currentTime << ";\t"
330 >                         << entry_plug->Hmat[0][0] << "\t"
331 >                         << entry_plug->Hmat[1][0] << "\t"
332 >                         << entry_plug->Hmat[2][0] << ";\t"
333  
334 <            << entry_plug->Hmat[0][1] << "\t"
335 <            << entry_plug->Hmat[1][1] << "\t"
336 <            << entry_plug->Hmat[2][1] << ";\t"
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337  
338 <            << entry_plug->Hmat[0][2] << "\t"
339 <            << entry_plug->Hmat[1][2] << "\t"
340 <            << entry_plug->Hmat[2][2] << ";";
338 >                         << entry_plug->Hmat[0][2] << "\t"
339 >                         << entry_plug->Hmat[1][2] << "\t"
340 >                         << entry_plug->Hmat[2][2] << ";";
341 >  
342 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343 >    }
344  
345 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
637 <    finalOut << endl;
638 <    finalOut.flush();
345 >    currentIndex = 0;
346  
347      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
348        
# Line 659 | Line 366 | void DumpWriter::writeFinal(double finalTime){
366          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367                   myPotato, MPI_COMM_WORLD, &istatus);
368          
369 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
370 <        
664 <        // Null terminate the atomTypeString just in case:
665 <
666 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
667 <
369 >        atomTypeString = MPIatomTypeString;
370 >        
371          myPotato++;
372  
373          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 685 | Line 388 | void DumpWriter::writeFinal(double finalTime){
388  
389        } else {
390          
391 <        haveError = 0;
391 >        haveError = 0;
392          which_atom = i;
690 –        local_index=-1;
393          
394 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
693 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
694 <        }
695 <        
696 <        if (local_index != -1) {
394 >          local_index = indexArray[currentIndex].first;        
395            
396 <          atomTypeString = atoms[local_index]->getType();
397 <
396 >          if (which_atom == indexArray[currentIndex].second) {
397 >            
398 >            atomTypeString = atoms[local_index]->getType();
399 >            
400            atoms[local_index]->getPos(pos);
401            atoms[local_index]->getVel(vel);          
402 <
402 >          
403            atomData6[0] = pos[0];
404            atomData6[1] = pos[1];
405            atomData6[2] = pos[2];
# Line 732 | Line 432 | void DumpWriter::writeFinal(double finalTime){
432            
433          } else {
434            sprintf(painCave.errMsg,
435 <                  "Atom %d not found on processor %d\n",
436 <                  i, worldRank );
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437            haveError= 1;
438            simError();
439          }
440          
441 <        if(haveError) DieDieDie();
441 >        if(haveError) DieDieDie();
442          
443 <        // If we've survived to here, format the line:
444 <        
445 <        if (!isDirectional) {
446 <
447 <          sprintf( tempBuffer,
448 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
449 <                   atomTypeString,
450 <                   atomData6[0],
451 <                   atomData6[1],
452 <                   atomData6[2],
453 <                   atomData6[3],
454 <                   atomData6[4],
455 <                   atomData6[5]);
456 <          
457 <          strcpy( writeLine, tempBuffer );
458 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 <
460 <        } else {
461 <          
462 <          sprintf( tempBuffer,
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 <          
779 <          strcat( writeLine, tempBuffer );
780 <          
781 <        }
443 >        currentIndex++;
444 >      }
445 >      // If we've survived to here, format the line:
446 >      
447 >      if (!isDirectional) {
448 >        
449 >        sprintf( writeLine,
450 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 >                 atomTypeString,
452 >                 atomData6[0],
453 >                 atomData6[1],
454 >                 atomData6[2],
455 >                 atomData6[3],
456 >                 atomData6[4],
457 >                 atomData6[5]);
458 >        
459 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460 >        
461 >      } else {
462 >        
463 >        sprintf( writeLine,
464 >                 "%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",
465 >                 atomTypeString,
466 >                 atomData13[0],
467 >                 atomData13[1],
468 >                 atomData13[2],
469 >                 atomData13[3],
470 >                 atomData13[4],
471 >                 atomData13[5],
472 >                 atomData13[6],
473 >                 atomData13[7],
474 >                 atomData13[8],
475 >                 atomData13[9],
476 >                 atomData13[10],
477 >                 atomData13[11],
478 >                 atomData13[12]);
479          
783 –        finalOut << writeLine;
784 –        finalOut.flush();
480        }
481 +      
482 +      for(k = 0; k < outFile.size(); k++)
483 +        *outFile[k] << writeLine;
484      }
485 <
486 <    finalOut.flush();
485 >    
486 >    for(k = 0; k < outFile.size(); k++)
487 >      outFile[k]->flush();
488 >    
489      sprintf( checkPointMsg,
490               "Sucessfully took a dump.\n");
491 +    
492      MPIcheckPoint();        
493      
494 +    delete[] potatoes;
495 +    
496    } else {
497  
498      // worldRank != 0, so I'm a remote node.  
# Line 797 | Line 500 | void DumpWriter::writeFinal(double finalTime){
500      // Set my magic potato to 0:
501  
502      myPotato = 0;
503 +    currentIndex = 0;
504      
505      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
506        
# Line 805 | Line 509 | void DumpWriter::writeFinal(double finalTime){
509        if (AtomToProcMap[i] == worldRank) {
510  
511          if (myPotato + 3 >= MAXTAG) {
512 <
512 >          
513            // The potato was going to exceed the maximum value,
514            // so wrap this processor potato back to 0 (and block until
515            // node 0 says we can go:
516 <
516 >          
517            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518            
519          }
520 +        which_atom = i;
521  
522 <        local_index=-1;
523 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
524 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
820 <        }
821 <        if (local_index != -1) {
522 >        local_index = indexArray[currentIndex].first;        
523 >                
524 >        if (which_atom == indexArray[currentIndex].second) {
525          
526            atomTypeString = atoms[local_index]->getType();
527 <
527 >          
528            atoms[local_index]->getPos(pos);
529            atoms[local_index]->getVel(vel);
530 <
530 >          
531            atomData6[0] = pos[0];
532            atomData6[1] = pos[1];
533            atomData6[2] = pos[2];
# Line 849 | Line 552 | void DumpWriter::writeFinal(double finalTime){
552              atomData13[7] = q[1];
553              atomData13[8] = q[2];
554              atomData13[9] = q[3];
555 <
555 >  
556              atomData13[10] = dAtom->getJx();
557              atomData13[11] = dAtom->getJy();
558              atomData13[12] = dAtom->getJz();
# Line 857 | Line 560 | void DumpWriter::writeFinal(double finalTime){
560  
561          } else {
562            sprintf(painCave.errMsg,
563 <                  "Atom %d not found on processor %d\n",
564 <                  i, worldRank );
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565            haveError= 1;
566            simError();
567          }
568 <
568 >        
569          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570  
571          // null terminate the string before sending (just in case):
572          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573  
574          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575 <                 myPotato, MPI_COMM_WORLD);
575 >                             myPotato, MPI_COMM_WORLD);
576          
577          myPotato++;
578  
579          MPI_Send(&isDirectional, 1, MPI_INT, 0,
580 <                 myPotato, MPI_COMM_WORLD);
580 >                             myPotato, MPI_COMM_WORLD);
581          
582          myPotato++;
583          
# Line 889 | Line 592 | void DumpWriter::writeFinal(double finalTime){
592                     myPotato, MPI_COMM_WORLD);
593          }
594  
595 <        myPotato++;      
595 >        myPotato++;  
596 >        currentIndex++;    
597        }
598      }
599  
# Line 899 | Line 603 | void DumpWriter::writeFinal(double finalTime){
603      
604    }
605    
902 –  if( worldRank == 0 ) finalOut.close();
606   #endif // is_mpi
607   }
608  
906 –
907 –
609   #ifdef IS_MPI
610  
611   // a couple of functions to let us escape the write loop

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