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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 947 by gezelter, Thu Jan 15 14:22:16 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
29 –    strcpy( outName, entry_plug->sampleName );
31  
32 <    outFile.open(outName, ios::out | ios::trunc );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    if( !outFile ){
34 >    if( !dumpFile ){
35  
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 100;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
76 <
74 <  int i;
75 <
76 < #ifdef IS_MPI
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77    
78 <  int *potatoes;
79 <  int myPotato;
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 <  int nProc;
87 <  int j, which_node, done, which_atom, local_index;
88 <  double atomData6[6];
89 <  double atomData13[13];
90 <  int isDirectional;
86 <  char* atomTypeString;
87 <  char MPIatomTypeString[MINIBUFFERSIZE];
88 <
89 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
91 < #endif //is_mpi
92 <
93 <  double q[4];
94 <  DirectionalAtom* dAtom;
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91    Atom** atoms = entry_plug->atoms;
92 <  double pos[3], vel[3];
92 >  
93 >  indexArray.clear();
94 >  
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 >  
98 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 > }
100 > #endif
101  
102 <  // write current frame to the eor file
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <  this->writeFinal( currentTime );
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 < #ifndef IS_MPI
108 <
109 <  outFile << nAtoms << "\n";
110 <
111 <  outFile << currentTime << ";\t"
112 <          << entry_plug->Hmat[0][0] << "\t"
113 <          << entry_plug->Hmat[1][0] << "\t"
114 <          << entry_plug->Hmat[2][0] << ";\t"
115 <
116 <          << entry_plug->Hmat[0][1] << "\t"
112 <          << entry_plug->Hmat[1][1] << "\t"
113 <          << entry_plug->Hmat[2][1] << ";\t"
114 <
115 <          << entry_plug->Hmat[0][2] << "\t"
116 <          << entry_plug->Hmat[1][2] << "\t"
117 <          << entry_plug->Hmat[2][2] << ";";
118 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
121 <
122 <  for( i=0; i<nAtoms; i++ ){
123 <
124 <    atoms[i]->getPos(pos);
125 <    atoms[i]->getVel(vel);
126 <
127 <    sprintf( tempBuffer,
128 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
137 <
138 <    if( atoms[i]->isDirectional() ){
139 <
140 <      dAtom = (DirectionalAtom *)atoms[i];
141 <      dAtom->getQ( q );
142 <
143 <      sprintf( tempBuffer,
144 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
145 <               q[0],
146 <               q[1],
147 <               q[2],
148 <               q[3],
149 <               dAtom->getJx(),
150 <               dAtom->getJy(),
151 <               dAtom->getJz());
152 <      strcat( writeLine, tempBuffer );
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 >    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 –
157 –    outFile << writeLine;
118    }
119 <  outFile.flush();
119 > #endif // is_mpi
120  
121 < #else // is_mpi
121 >  fileStreams.push_back(&finalOut);
122 >  fileStreams.push_back(&dumpFile);
123  
124 <  /* 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 <  }  
124 >  writeFrame(fileStreams, currentTime);
125  
126 <  int haveError;
126 > #ifdef IS_MPI
127 >  finalOut.close();
128 > #endif
129 >        
130 > }
131  
132 <  MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
132 > void DumpWriter::writeFinal(double currentTime){
133  
134 <  // write out header and node 0's coordinates
134 >  ofstream finalOut;
135 >  vector<ofstream*> fileStreams;
136  
137 <  if( worldRank == 0 ){
137 > #ifdef IS_MPI
138 >  if(worldRank == 0 ){
139  
140 <    // Node 0 needs a list of the magic potatoes for each processor;
182 <
183 <    nProc = mpiSim->getNumberProcessors();
184 <    potatoes = new int[nProc];
185 <
186 <    for (i = 0; i < nProc; i++)
187 <      potatoes[i] = 0;
188 <    
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:        
140 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141  
142 <          potatoes[which_node] = 0;          
143 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
144 <          
145 <        }
146 <
147 <        myPotato = potatoes[which_node];        
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 <      }
142 >    if( !finalOut ){
143 >      sprintf( painCave.errMsg,
144 >               "Could not open \"%s\" for final dump output.\n",
145 >               entry_plug->finalName );
146 >      painCave.isFatal = 1;
147 >      simError();
148      }
149  
150 <    outFile.flush();
151 <    sprintf( checkPointMsg,
152 <             "Sucessfully took a dump.\n");
153 <    MPIcheckPoint();        
154 <    
361 <  } else {
150 >  }
151 > #endif // is_mpi
152 >  
153 >  fileStreams.push_back(&finalOut);  
154 >  writeFrame(fileStreams, currentTime);
155  
156 <    // worldRank != 0, so I'm a remote node.  
157 <
158 <    // 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() ){
407 <
408 <            isDirectional = 1;
409 <            
410 <            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 <  }
156 > #ifdef IS_MPI
157 >  finalOut.close();
158 > #endif
159    
470 – #endif // is_mpi
160   }
161  
162 < void DumpWriter::writeFinal(double finalTime){
162 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163  
475 –  char finalName[500];
476 –  ofstream finalOut;
477 –
164    const int BUFFERSIZE = 2000;
165    const int MINIBUFFERSIZE = 100;
166 <  char tempBuffer[BUFFERSIZE];
166 >
167 >  char tempBuffer[BUFFERSIZE];  
168    char writeLine[BUFFERSIZE];
169  
170 <  double q[4];
171 <  DirectionalAtom* dAtom;
485 <  Atom** atoms = entry_plug->atoms;
486 <  int i;
170 >  int i, k;
171 >
172   #ifdef IS_MPI
173    
174 +  /*********************************************************************
175 +   * Documentation?  You want DOCUMENTATION?
176 +   *
177 +   * Why all the potatoes below?  
178 +   *
179 +   * To make a long story short, the original version of DumpWriter
180 +   * worked in the most inefficient way possible.  Node 0 would
181 +   * poke each of the node for an individual atom's formatted data
182 +   * as node 0 worked its way down the global index. This was particularly
183 +   * inefficient since the method blocked all processors at every atom
184 +   * (and did it twice!).
185 +   *
186 +   * An intermediate version of DumpWriter could be described from Node
187 +   * zero's perspective as follows:
188 +   *
189 +   *  1) Have 100 of your friends stand in a circle.
190 +   *  2) When you say go, have all of them start tossing potatoes at
191 +   *     you (one at a time).
192 +   *  3) Catch the potatoes.
193 +   *
194 +   * It was an improvement, but MPI has buffers and caches that could
195 +   * best be described in this analogy as "potato nets", so there's no
196 +   * need to block the processors atom-by-atom.
197 +   *
198 +   * This new and improved DumpWriter works in an even more efficient
199 +   * way:
200 +   *
201 +   *  1) Have 100 of your friend stand in a circle.
202 +   *  2) When you say go, have them start tossing 5-pound bags of
203 +   *     potatoes at you.
204 +   *  3) Once you've caught a friend's bag of potatoes,
205 +   *     toss them a spud to let them know they can toss another bag.
206 +   *
207 +   * How's THAT for documentation?
208 +   *
209 +   *********************************************************************/
210 +
211    int *potatoes;
212    int myPotato;
213  
214    int nProc;
215 <  int j, which_node, done, which_atom, local_index;
215 >  int j, which_node, done, which_atom, local_index, currentIndex;
216    double atomData6[6];
217    double atomData13[13];
218    int isDirectional;
# Line 501 | Line 223 | void DumpWriter::writeFinal(double finalTime){
223    int nAtoms = entry_plug->n_atoms;
224   #endif //is_mpi
225  
226 +  double q[4];
227 +  DirectionalAtom* dAtom;
228 +  Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230  
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 –
231   #ifndef IS_MPI
232 +  
233 +  for(k = 0; k < outFile.size(); k++){
234 +    *outFile[k] << nAtoms << "\n";
235  
236 <  finalOut << nAtoms << "\n";
236 >    *outFile[k] << currentTime << ";\t"
237 >               << entry_plug->Hmat[0][0] << "\t"
238 >                     << entry_plug->Hmat[1][0] << "\t"
239 >                     << entry_plug->Hmat[2][0] << ";\t"
240 >              
241 >               << entry_plug->Hmat[0][1] << "\t"
242 >                     << entry_plug->Hmat[1][1] << "\t"
243 >                     << entry_plug->Hmat[2][1] << ";\t"
244  
245 <  finalOut << finalTime << ";\t"
246 <           << entry_plug->Hmat[0][0] << "\t"
247 <           << entry_plug->Hmat[1][0] << "\t"
539 <           << entry_plug->Hmat[2][0] << ";\t"
245 >                     << entry_plug->Hmat[0][2] << "\t"
246 >                     << entry_plug->Hmat[1][2] << "\t"
247 >                     << entry_plug->Hmat[2][2] << ";";
248  
249 <           << entry_plug->Hmat[0][1] << "\t"
250 <           << entry_plug->Hmat[1][1] << "\t"
251 <           << entry_plug->Hmat[2][1] << ";\t"
252 <
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 <
249 >    //write out additional parameters, such as chi and eta
250 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251 >  }
252 >  
253    for( i=0; i<nAtoms; i++ ){
254  
255      atoms[i]->getPos(pos);
# Line 585 | Line 285 | void DumpWriter::writeFinal(double finalTime){
285      else
286        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287  
288 <    finalOut << writeLine;
288 >    for(k = 0; k < outFile.size(); k++)
289 >      *outFile[k] << writeLine;
290    }
590 –  finalOut.flush();
591 –  finalOut.close();
291  
292   #else // is_mpi
293  
294    /* code to find maximum tag value */
295 +  
296    int *tagub, flag, MAXTAG;
297    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
298    if (flag) {
# Line 615 | Line 315 | void DumpWriter::writeFinal(double finalTime){
315      nProc = mpiSim->getNumberProcessors();
316      potatoes = new int[nProc];
317  
318 +    //write out the comment lines
319      for (i = 0; i < nProc; i++)
320        potatoes[i] = 0;
321      
322 <    finalOut << mpiSim->getTotAtoms() << "\n";
322 >      for(k = 0; k < outFile.size(); k++){
323 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
324  
325 <    finalOut << finalTime << ";\t"
326 <            << entry_plug->Hmat[0][0] << "\t"
327 <            << entry_plug->Hmat[1][0] << "\t"
328 <            << entry_plug->Hmat[2][0] << ";\t"
627 <
628 <            << entry_plug->Hmat[0][1] << "\t"
629 <            << entry_plug->Hmat[1][1] << "\t"
630 <            << entry_plug->Hmat[2][1] << ";\t"
325 >        *outFile[k] << currentTime << ";\t"
326 >                         << entry_plug->Hmat[0][0] << "\t"
327 >                         << entry_plug->Hmat[1][0] << "\t"
328 >                         << entry_plug->Hmat[2][0] << ";\t"
329  
330 <            << entry_plug->Hmat[0][2] << "\t"
331 <            << entry_plug->Hmat[1][2] << "\t"
332 <            << entry_plug->Hmat[2][2] << ";";
330 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333  
334 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
335 <    finalOut << endl;
336 <    finalOut.flush();
334 >                         << entry_plug->Hmat[0][2] << "\t"
335 >                         << entry_plug->Hmat[1][2] << "\t"
336 >                         << entry_plug->Hmat[2][2] << ";";
337 >  
338 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339 >    }
340  
341 +    currentIndex = 0;
342 +
343      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344        
345        // Get the Node number which has this atom;
# Line 659 | Line 362 | void DumpWriter::writeFinal(double finalTime){
362          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363                   myPotato, MPI_COMM_WORLD, &istatus);
364          
365 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
366 <        
664 <        // Null terminate the atomTypeString just in case:
665 <
666 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
667 <
365 >        atomTypeString = MPIatomTypeString;
366 >        
367          myPotato++;
368  
369          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 685 | Line 384 | void DumpWriter::writeFinal(double finalTime){
384  
385        } else {
386          
387 <        haveError = 0;
388 <        which_atom = i;
690 <        local_index=-1;
387 >        haveError = 0;
388 >              which_atom = i;
389          
390 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
391 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
392 <        }
695 <        
696 <        if (local_index != -1) {
390 >        local_index = indexArray[currentIndex].first;        
391 >                
392 >        if (which_atom == indexArray[currentIndex].second) {
393            
394            atomTypeString = atoms[local_index]->getType();
395  
396 <          atoms[local_index]->getPos(pos);
397 <          atoms[local_index]->getVel(vel);          
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398  
399            atomData6[0] = pos[0];
400            atomData6[1] = pos[1];
# Line 731 | Line 427 | void DumpWriter::writeFinal(double finalTime){
427            }
428            
429          } else {
430 <          sprintf(painCave.errMsg,
431 <                  "Atom %d not found on processor %d\n",
432 <                  i, worldRank );
433 <          haveError= 1;
434 <          simError();
435 <        }
430 >          sprintf(painCave.errMsg,
431 >                              "Atom %d not found on processor %d\n",
432 >                              i, worldRank );
433 >                haveError= 1;
434 >                simError();
435 >              }
436          
437 <        if(haveError) DieDieDie();
437 >        if(haveError) DieDieDie();
438          
439 <        // If we've survived to here, format the line:
440 <        
441 <        if (!isDirectional) {
439 >        currentIndex ++;
440 >      }
441 >      // If we've survived to here, format the line:
442 >      
443 >      if (!isDirectional) {
444 >        
445 >        sprintf( writeLine,
446 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 >                             atomTypeString,
448 >                             atomData6[0],
449 >                             atomData6[1],
450 >                             atomData6[2],
451 >                             atomData6[3],
452 >                             atomData6[4],
453 >                             atomData6[5]);
454  
455 <          sprintf( tempBuffer,
456 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
457 <                   atomTypeString,
458 <                   atomData6[0],
459 <                   atomData6[1],
460 <                   atomData6[2],
461 <                   atomData6[3],
462 <                   atomData6[4],
463 <                   atomData6[5]);
464 <          
465 <          strcpy( writeLine, tempBuffer );
466 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
467 <
468 <        } else {
469 <          
470 <          sprintf( tempBuffer,
471 <                   "%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",
472 <                   atomTypeString,
473 <                   atomData13[0],
474 <                   atomData13[1],
767 <                   atomData13[2],
768 <                   atomData13[3],
769 <                   atomData13[4],
770 <                   atomData13[5],
771 <                   atomData13[6],
772 <                   atomData13[7],
773 <                   atomData13[8],
774 <                   atomData13[9],
775 <                   atomData13[10],
776 <                   atomData13[11],
777 <                   atomData13[12]);
778 <          
779 <          strcat( writeLine, tempBuffer );
780 <          
781 <        }
455 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 >        
457 >      } else {
458 >        
459 >              sprintf( writeLine,
460 >                             "%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",
461 >                             atomTypeString,
462 >                             atomData13[0],
463 >                             atomData13[1],
464 >                             atomData13[2],
465 >                             atomData13[3],
466 >                             atomData13[4],
467 >                             atomData13[5],
468 >                             atomData13[6],
469 >                             atomData13[7],
470 >                             atomData13[8],
471 >                             atomData13[9],
472 >                             atomData13[10],
473 >                             atomData13[11],
474 >                             atomData13[12]);
475          
783 –        finalOut << writeLine;
784 –        finalOut.flush();
476        }
477 +      
478 +      for(k = 0; k < outFile.size(); k++)
479 +        *outFile[k] << writeLine;
480      }
481 <
482 <    finalOut.flush();
481 >    
482 >    for(k = 0; k < outFile.size(); k++)
483 >      outFile[k]->flush();
484 >    
485      sprintf( checkPointMsg,
486               "Sucessfully took a dump.\n");
487 +
488      MPIcheckPoint();        
489 <    
489 >
490 >    delete[] potatoes;
491 >
492    } else {
493  
494      // worldRank != 0, so I'm a remote node.  
# Line 797 | Line 496 | void DumpWriter::writeFinal(double finalTime){
496      // Set my magic potato to 0:
497  
498      myPotato = 0;
499 +    currentIndex = 0;
500      
501      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
502        
# Line 813 | Line 513 | void DumpWriter::writeFinal(double finalTime){
513            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514            
515          }
516 <
517 <        local_index=-1;
518 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
519 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
820 <        }
821 <        if (local_index != -1) {
516 >        which_atom = i;
517 >        local_index = indexArray[currentIndex].first;        
518 >                
519 >        if (which_atom == indexArray[currentIndex].second) {
520          
521            atomTypeString = atoms[local_index]->getType();
522  
523 <          atoms[local_index]->getPos(pos);
524 <          atoms[local_index]->getVel(vel);
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525  
526            atomData6[0] = pos[0];
527            atomData6[1] = pos[1];
# Line 849 | Line 547 | void DumpWriter::writeFinal(double finalTime){
547              atomData13[7] = q[1];
548              atomData13[8] = q[2];
549              atomData13[9] = q[3];
550 <
550 >  
551              atomData13[10] = dAtom->getJx();
552              atomData13[11] = dAtom->getJy();
553              atomData13[12] = dAtom->getJz();
554            }
555  
556          } else {
557 <          sprintf(painCave.errMsg,
558 <                  "Atom %d not found on processor %d\n",
559 <                  i, worldRank );
560 <          haveError= 1;
561 <          simError();
562 <        }
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563  
564          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565  
# Line 869 | Line 567 | void DumpWriter::writeFinal(double finalTime){
567          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568  
569          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 <                 myPotato, MPI_COMM_WORLD);
570 >                             myPotato, MPI_COMM_WORLD);
571          
572          myPotato++;
573  
574          MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 <                 myPotato, MPI_COMM_WORLD);
575 >                             myPotato, MPI_COMM_WORLD);
576          
577          myPotato++;
578          
# Line 889 | Line 587 | void DumpWriter::writeFinal(double finalTime){
587                     myPotato, MPI_COMM_WORLD);
588          }
589  
590 <        myPotato++;      
590 >        myPotato++;  
591 >        currentIndex++;    
592        }
593      }
594  
# Line 899 | Line 598 | void DumpWriter::writeFinal(double finalTime){
598      
599    }
600    
902 –  if( worldRank == 0 ) finalOut.close();
601   #endif // is_mpi
602   }
603  
906 –
907 –
604   #ifdef IS_MPI
605  
606   // a couple of functions to let us escape the write loop

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