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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 920 by tim, Sat Jan 10 09:46:47 2004 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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 <  
165 <  int *tagub, flag, MAXTAG;
166 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
167 <  if (flag) {
168 <    MAXTAG = *tagub;
169 <  } else {
170 <    MAXTAG = 32767;
171 <  }  
126 >  writeFrame(fileStreams, currentTime);
127  
128 <  int haveError;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  MPI_Status istatus;
176 <  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 ){
140 <
141 <    // Node 0 needs a list of the magic potatoes for each processor;
183 <
184 <    nProc = mpiSim->getNumberProcessors();
185 <    potatoes = new int[nProc];
186 <
187 <    for (i = 0; i < nProc; i++)
188 <      potatoes[i] = 0;
189 <    
190 <    outFile << mpiSim->getTotAtoms() << "\n";
191 <
192 <    outFile << currentTime << ";\t"
193 <            << entry_plug->Hmat[0][0] << "\t"
194 <            << entry_plug->Hmat[1][0] << "\t"
195 <            << entry_plug->Hmat[2][0] << ";\t"
196 <
197 <            << entry_plug->Hmat[0][1] << "\t"
198 <            << entry_plug->Hmat[1][1] << "\t"
199 <            << entry_plug->Hmat[2][1] << ";\t"
200 <
201 <            << entry_plug->Hmat[0][2] << "\t"
202 <            << entry_plug->Hmat[1][2] << "\t"
203 <            << entry_plug->Hmat[2][2] << ";";
204 <
205 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
206 <    outFile << endl;
207 <    outFile.flush();
208 <
209 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
210 <      
211 <      // Get the Node number which has this atom;
212 <      
213 <      which_node = AtomToProcMap[i];
214 <      
215 <      if (which_node != 0) {
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <        if (potatoes[which_node] + 3 >= MAXTAG) {
218 <          // The potato was going to exceed the maximum value,
219 <          // so wrap this processor potato back to 0:        
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <          potatoes[which_node] = 0;          
146 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
147 <          
148 <        }
149 <
150 <        myPotato = potatoes[which_node];        
227 <        
228 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
229 <                 myPotato, MPI_COMM_WORLD, &istatus);
230 <        
231 <        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 <        
233 <        // Null terminate the atomTypeString just in case:
234 <
235 <        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
236 <        atomTypeString = MPIatomTypeString;
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 <      }
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 <    delete[] potatoes;
158 <  } else {
153 > #ifdef IS_MPI
154 >  }
155 > #endif // is_mpi
156 >  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159  
160 <    // worldRank != 0, so I'm a remote node.  
161 <
162 <    // 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 <  }
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163    
472 – #endif // is_mpi
164   }
165  
166 < void DumpWriter::writeFinal(double finalTime){
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
477 –  char finalName[500];
478 –  ofstream finalOut;
479 –
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;
487 <  Atom** atoms = entry_plug->atoms;
488 <  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 503 | Line 227 | void DumpWriter::writeFinal(double finalTime){
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 +  double q[4], ji[3];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
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 –
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"
541 <           << 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 <
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 <
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 572 | Line 274 | void DumpWriter::writeFinal(double finalTime){
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 579 | Line 282 | void DumpWriter::writeFinal(double finalTime){
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292  
293 <    finalOut << writeLine;
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
592 –  finalOut.flush();
593 –  finalOut.close();
296  
297   #else // is_mpi
298  
299    /* code to find maximum tag value */
300 +  
301    int *tagub, flag, MAXTAG;
302    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303    if (flag) {
# Line 617 | Line 320 | void DumpWriter::writeFinal(double finalTime){
320      nProc = mpiSim->getNumberProcessors();
321      potatoes = new int[nProc];
322  
323 +    //write out the comment lines
324      for (i = 0; i < nProc; i++)
325        potatoes[i] = 0;
326      
327 <    finalOut << mpiSim->getTotAtoms() << "\n";
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <    finalOut << finalTime << ";\t"
331 <            << entry_plug->Hmat[0][0] << "\t"
332 <            << entry_plug->Hmat[1][0] << "\t"
333 <            << entry_plug->Hmat[2][0] << ";\t"
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334  
335 <            << entry_plug->Hmat[0][1] << "\t"
336 <            << entry_plug->Hmat[1][1] << "\t"
337 <            << entry_plug->Hmat[2][1] << ";\t"
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338  
339 <            << entry_plug->Hmat[0][2] << "\t"
340 <            << entry_plug->Hmat[1][2] << "\t"
341 <            << entry_plug->Hmat[2][2] << ";";
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345  
346 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
639 <    finalOut << endl;
640 <    finalOut.flush();
346 >    currentIndex = 0;
347  
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349        
# Line 662 | Line 368 | void DumpWriter::writeFinal(double finalTime){
368                   myPotato, MPI_COMM_WORLD, &istatus);
369          
370          atomTypeString = MPIatomTypeString;
371 <                
371 >        
372          myPotato++;
373  
374          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 683 | Line 389 | void DumpWriter::writeFinal(double finalTime){
389  
390        } else {
391          
392 <        haveError = 0;
392 >        haveError = 0;
393          which_atom = i;
688 –        local_index=-1;
394          
395 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
691 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
692 <        }
693 <        
694 <        if (local_index != -1) {
395 >          local_index = indexArray[currentIndex].first;        
396            
397 <          atomTypeString = atoms[local_index]->getType();
398 <
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401            atoms[local_index]->getPos(pos);
402            atoms[local_index]->getVel(vel);          
403 <
403 >          
404            atomData6[0] = pos[0];
405            atomData6[1] = pos[1];
406            atomData6[2] = pos[2];
# Line 714 | Line 417 | void DumpWriter::writeFinal(double finalTime){
417              
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 +            dAtom->getJ( ji );
421  
422              for (int j = 0; j < 6 ; j++)
423                atomData13[j] = atomData6[j];            
# Line 723 | Line 427 | void DumpWriter::writeFinal(double finalTime){
427              atomData13[8] = q[2];
428              atomData13[9] = q[3];
429              
430 <            atomData13[10] = dAtom->getJx();
431 <            atomData13[11] = dAtom->getJy();
432 <            atomData13[12] = dAtom->getJz();
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433            }
434            
435          } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441          }
442          
443 <        if(haveError) DieDieDie();
443 >        if(haveError) DieDieDie();
444          
445 <        // If we've survived to here, format the line:
446 <        
447 <        if (!isDirectional) {
448 <
449 <          sprintf( tempBuffer,
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 <          strcpy( writeLine, tempBuffer );
460 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
461 <
462 <        } else {
463 <          
464 <          sprintf( tempBuffer,
465 <                   "%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",
466 <                   atomTypeString,
467 <                   atomData13[0],
468 <                   atomData13[1],
469 <                   atomData13[2],
470 <                   atomData13[3],
471 <                   atomData13[4],
472 <                   atomData13[5],
473 <                   atomData13[6],
474 <                   atomData13[7],
475 <                   atomData13[8],
476 <                   atomData13[9],
477 <                   atomData13[10],
478 <                   atomData13[11],
479 <                   atomData13[12]);
480 <          
777 <          strcat( writeLine, tempBuffer );
778 <          
779 <        }
445 >        currentIndex++;
446 >      }
447 >      // If we've survived to here, format the line:
448 >      
449 >      if (!isDirectional) {
450 >        
451 >        sprintf( writeLine,
452 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                 atomTypeString,
454 >                 atomData6[0],
455 >                 atomData6[1],
456 >                 atomData6[2],
457 >                 atomData6[3],
458 >                 atomData6[4],
459 >                 atomData6[5]);
460 >        
461 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 >        
463 >      } else {
464 >        
465 >        sprintf( writeLine,
466 >                 "%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",
467 >                 atomTypeString,
468 >                 atomData13[0],
469 >                 atomData13[1],
470 >                 atomData13[2],
471 >                 atomData13[3],
472 >                 atomData13[4],
473 >                 atomData13[5],
474 >                 atomData13[6],
475 >                 atomData13[7],
476 >                 atomData13[8],
477 >                 atomData13[9],
478 >                 atomData13[10],
479 >                 atomData13[11],
480 >                 atomData13[12]);
481          
781 –        finalOut << writeLine;
782 –        finalOut.flush();
482        }
483 +      
484 +      for(k = 0; k < outFile.size(); k++)
485 +        *outFile[k] << writeLine;
486      }
487 <
488 <    finalOut.flush();
487 >    
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491      sprintf( checkPointMsg,
492               "Sucessfully took a dump.\n");
493 <    delete[] potatoes;
790 <      
493 >    
494      MPIcheckPoint();        
495      
496 +    delete[] potatoes;
497 +    
498    } else {
499  
500      // worldRank != 0, so I'm a remote node.  
# Line 797 | Line 502 | void DumpWriter::writeFinal(double finalTime){
502      // Set my magic potato to 0:
503  
504      myPotato = 0;
505 +    currentIndex = 0;
506      
507      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
# Line 805 | Line 511 | void DumpWriter::writeFinal(double finalTime){
511        if (AtomToProcMap[i] == worldRank) {
512  
513          if (myPotato + 3 >= MAXTAG) {
514 <
514 >          
515            // The potato was going to exceed the maximum value,
516            // so wrap this processor potato back to 0 (and block until
517            // node 0 says we can go:
518 <
518 >          
519            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520            
521          }
522 <        which_atom = i;  
523 <        local_index=-1;
524 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
525 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
526 <        }
821 <        if (local_index != -1) {
522 >        which_atom = i;
523 >
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527          
528            atomTypeString = atoms[local_index]->getType();
529 <
529 >          
530            atoms[local_index]->getPos(pos);
531            atoms[local_index]->getVel(vel);
532 <
532 >          
533            atomData6[0] = pos[0];
534            atomData6[1] = pos[1];
535            atomData6[2] = pos[2];
# Line 841 | Line 546 | void DumpWriter::writeFinal(double finalTime){
546              
547              dAtom = (DirectionalAtom *)atoms[local_index];
548              dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550              
551              for (int j = 0; j < 6 ; j++)
552                atomData13[j] = atomData6[j];
# Line 849 | Line 555 | void DumpWriter::writeFinal(double finalTime){
555              atomData13[7] = q[1];
556              atomData13[8] = q[2];
557              atomData13[9] = q[3];
558 <
559 <            atomData13[10] = dAtom->getJx();
560 <            atomData13[11] = dAtom->getJy();
561 <            atomData13[12] = dAtom->getJz();
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562            }
563  
564          } else {
565            sprintf(painCave.errMsg,
566 <                  "Atom %d not found on processor %d\n",
567 <                  i, worldRank );
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568            haveError= 1;
569            simError();
570          }
571 <
571 >        
572          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574          // null terminate the string before sending (just in case):
575          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576  
577          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 <                 myPotato, MPI_COMM_WORLD);
578 >                             myPotato, MPI_COMM_WORLD);
579          
580          myPotato++;
581  
582          MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 <                 myPotato, MPI_COMM_WORLD);
583 >                             myPotato, MPI_COMM_WORLD);
584          
585          myPotato++;
586          
# Line 889 | Line 595 | void DumpWriter::writeFinal(double finalTime){
595                     myPotato, MPI_COMM_WORLD);
596          }
597  
598 <        myPotato++;      
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
601      }
602  
# Line 899 | Line 606 | void DumpWriter::writeFinal(double finalTime){
606      
607    }
608    
902 –  if( worldRank == 0 ) finalOut.close();
609   #endif // is_mpi
610   }
611  
906 –
907 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop

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