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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 949 by chuckv, Thu Jan 15 21:57:10 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
31 <    strcpy( outName, entry_plug->sampleName );
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32  
33 <    outFile.open(outName, ios::out | ios::trunc );
33 >    if( !dumpFile ){
34  
33 –    if( !outFile ){
34 –
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
42 –    //outFile.setf( ios::scientific );
43 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 56 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68  
69 <  const int BUFFERSIZE = 2000;
70 <  const int MINIBUFFERSIZE = 100;
69 > /**
70 > * A hook function to load balancing
71 > */
72  
73 <  char tempBuffer[BUFFERSIZE];
74 <  char writeLine[BUFFERSIZE];
75 <
74 <  int i;
75 <
76 < #ifdef IS_MPI
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 <  int *potatoes;
78 <  int myPotato;
77 > /**
78 > * Auxiliary sorting function
79 > */
80 >
81 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 >  return p1.second < p2.second;
83 > }
84  
85 <  int nProc;
86 <  int j, which_node, done, which_atom, local_index;
87 <  double atomData6[6];
88 <  double atomData13[13];
89 <  int isDirectional;
86 <  char* atomTypeString;
87 <  char MPIatomTypeString[MINIBUFFERSIZE];
88 <
89 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
91 < #endif //is_mpi
92 <
93 <  double q[4];
94 <  DirectionalAtom* dAtom;
85 > /**
86 > * Sorting the local index by global index
87 > */
88 >
89 > void DumpWriter::sortByGlobalIndex(){
90    Atom** atoms = entry_plug->atoms;
91 <  double pos[3], vel[3];
91 >  
92 >  indexArray.clear();
93 >  
94 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98  
99 <  // write current frame to the eor file
99 >  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 >  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 >  //}
102 >    
103 > }
104  
105 <  this->writeFinal( currentTime );
105 > #endif
106  
107 < #ifndef IS_MPI
107 > void DumpWriter::writeDump(double currentTime){
108  
109 <  outFile << nAtoms << "\n";
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111  
112 <  outFile << currentTime << ";\t"
113 <          << entry_plug->Hmat[0][0] << "\t"
114 <          << entry_plug->Hmat[1][0] << "\t"
115 <          << entry_plug->Hmat[2][0] << ";\t"
116 <
117 <          << entry_plug->Hmat[0][1] << "\t"
118 <          << entry_plug->Hmat[1][1] << "\t"
119 <          << entry_plug->Hmat[2][1] << ";\t"
120 <
121 <          << entry_plug->Hmat[0][2] << "\t"
122 <          << entry_plug->Hmat[1][2] << "\t"
123 <          << entry_plug->Hmat[2][2] << ";";
118 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
121 <
122 <  for( i=0; i<nAtoms; i++ ){
123 <
124 <    atoms[i]->getPos(pos);
125 <    atoms[i]->getVel(vel);
126 <
127 <    sprintf( tempBuffer,
128 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
137 <
138 <    if( atoms[i]->isDirectional() ){
139 <
140 <      dAtom = (DirectionalAtom *)atoms[i];
141 <      dAtom->getQ( q );
142 <
143 <      sprintf( tempBuffer,
144 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
145 <               q[0],
146 <               q[1],
147 <               q[2],
148 <               q[3],
149 <               dAtom->getJx(),
150 <               dAtom->getJy(),
151 <               dAtom->getJz());
152 <      strcat( writeLine, tempBuffer );
112 > #ifdef IS_MPI
113 >  printf("Hello from node %d\n", worldRank);
114 >  sortByGlobalIndex();
115 >  if(worldRank == 0 ){
116 >    
117 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 >    if( !finalOut ){
119 >      sprintf( painCave.errMsg,
120 >               "Could not open \"%s\" for final dump output.\n",
121 >               entry_plug->finalName );
122 >      painCave.isFatal = 1;
123 >      simError();
124      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 –
157 –    outFile << writeLine;
125    }
126 <  outFile.flush();
126 > #endif // is_mpi
127  
128 < #else // is_mpi
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130  
131 <  /* 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 <  }  
131 >  writeFrame(fileStreams, currentTime);
132  
133 <  int haveError;
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137 > }
138  
139 <  MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
139 > void DumpWriter::writeFinal(double currentTime){
140  
141 <  // write out header and node 0's coordinates
142 <
179 <  if( worldRank == 0 ){
180 <
181 <    // 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) {
141 >  ofstream finalOut;
142 >  vector<ofstream*> fileStreams;
143  
144 <        if (potatoes[which_node] + 3 >= MAXTAG) {
145 <          // The potato was going to exceed the maximum value,
218 <          // so wrap this processor potato back to 0:        
144 > #ifdef IS_MPI
145 >  if(worldRank == 0 ){
146  
147 <          potatoes[which_node] = 0;          
221 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
222 <          
223 <        }
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148  
149 <        myPotato = potatoes[which_node];        
150 <        
151 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
152 <                 myPotato, MPI_COMM_WORLD, &istatus);
153 <        
154 <        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 <      }
149 >    if( !finalOut ){
150 >      sprintf( painCave.errMsg,
151 >               "Could not open \"%s\" for final dump output.\n",
152 >               entry_plug->finalName );
153 >      painCave.isFatal = 1;
154 >      simError();
155      }
156  
157 <    outFile.flush();
158 <    sprintf( checkPointMsg,
159 <             "Sucessfully took a dump.\n");
160 <    MPIcheckPoint();        
161 <    
361 <  } else {
157 >  }
158 > #endif // is_mpi
159 >  
160 >  fileStreams.push_back(&finalOut);  
161 >  writeFrame(fileStreams, currentTime);
162  
163 <    // worldRank != 0, so I'm a remote node.  
164 <
165 <    // 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 <  }
163 > #ifdef IS_MPI
164 >  finalOut.close();
165 > #endif
166    
470 – #endif // is_mpi
167   }
168  
169 < void DumpWriter::writeFinal(double finalTime){
169 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
170  
475 –  char finalName[500];
476 –  ofstream finalOut;
477 –
171    const int BUFFERSIZE = 2000;
172    const int MINIBUFFERSIZE = 100;
173 <  char tempBuffer[BUFFERSIZE];
173 >
174 >  char tempBuffer[BUFFERSIZE];  
175    char writeLine[BUFFERSIZE];
176  
177 <  double q[4];
178 <  DirectionalAtom* dAtom;
485 <  Atom** atoms = entry_plug->atoms;
486 <  int i;
177 >  int i, k;
178 >
179   #ifdef IS_MPI
180    
181 +  /*********************************************************************
182 +   * Documentation?  You want DOCUMENTATION?
183 +   *
184 +   * Why all the potatoes below?  
185 +   *
186 +   * To make a long story short, the original version of DumpWriter
187 +   * worked in the most inefficient way possible.  Node 0 would
188 +   * poke each of the node for an individual atom's formatted data
189 +   * as node 0 worked its way down the global index. This was particularly
190 +   * inefficient since the method blocked all processors at every atom
191 +   * (and did it twice!).
192 +   *
193 +   * An intermediate version of DumpWriter could be described from Node
194 +   * zero's perspective as follows:
195 +   *
196 +   *  1) Have 100 of your friends stand in a circle.
197 +   *  2) When you say go, have all of them start tossing potatoes at
198 +   *     you (one at a time).
199 +   *  3) Catch the potatoes.
200 +   *
201 +   * It was an improvement, but MPI has buffers and caches that could
202 +   * best be described in this analogy as "potato nets", so there's no
203 +   * need to block the processors atom-by-atom.
204 +   *
205 +   * This new and improved DumpWriter works in an even more efficient
206 +   * way:
207 +   *
208 +   *  1) Have 100 of your friend stand in a circle.
209 +   *  2) When you say go, have them start tossing 5-pound bags of
210 +   *     potatoes at you.
211 +   *  3) Once you've caught a friend's bag of potatoes,
212 +   *     toss them a spud to let them know they can toss another bag.
213 +   *
214 +   * How's THAT for documentation?
215 +   *
216 +   *********************************************************************/
217 +
218    int *potatoes;
219    int myPotato;
220  
221    int nProc;
222 <  int j, which_node, done, which_atom, local_index;
222 >  int j, which_node, done, which_atom, local_index, currentIndex;
223    double atomData6[6];
224    double atomData13[13];
225    int isDirectional;
# Line 501 | Line 230 | void DumpWriter::writeFinal(double finalTime){
230    int nAtoms = entry_plug->n_atoms;
231   #endif //is_mpi
232  
233 +  double q[4];
234 +  DirectionalAtom* dAtom;
235 +  Atom** atoms = entry_plug->atoms;
236    double pos[3], vel[3];
237  
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 –
238   #ifndef IS_MPI
239 +  
240 +  for(k = 0; k < outFile.size(); k++){
241 +    *outFile[k] << nAtoms << "\n";
242  
243 <  finalOut << nAtoms << "\n";
243 >    *outFile[k] << currentTime << ";\t"
244 >               << entry_plug->Hmat[0][0] << "\t"
245 >                     << entry_plug->Hmat[1][0] << "\t"
246 >                     << entry_plug->Hmat[2][0] << ";\t"
247 >              
248 >               << entry_plug->Hmat[0][1] << "\t"
249 >                     << entry_plug->Hmat[1][1] << "\t"
250 >                     << entry_plug->Hmat[2][1] << ";\t"
251  
252 <  finalOut << finalTime << ";\t"
253 <           << entry_plug->Hmat[0][0] << "\t"
254 <           << entry_plug->Hmat[1][0] << "\t"
539 <           << entry_plug->Hmat[2][0] << ";\t"
252 >                     << entry_plug->Hmat[0][2] << "\t"
253 >                     << entry_plug->Hmat[1][2] << "\t"
254 >                     << entry_plug->Hmat[2][2] << ";";
255  
256 <           << entry_plug->Hmat[0][1] << "\t"
257 <           << entry_plug->Hmat[1][1] << "\t"
258 <           << entry_plug->Hmat[2][1] << ";\t"
259 <
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 <
256 >    //write out additional parameters, such as chi and eta
257 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
258 >  }
259 >  
260    for( i=0; i<nAtoms; i++ ){
261  
262      atoms[i]->getPos(pos);
# Line 585 | Line 292 | void DumpWriter::writeFinal(double finalTime){
292      else
293        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
294  
295 <    finalOut << writeLine;
295 >    for(k = 0; k < outFile.size(); k++)
296 >      *outFile[k] << writeLine;
297    }
590 –  finalOut.flush();
591 –  finalOut.close();
298  
299   #else // is_mpi
300  
301    /* code to find maximum tag value */
302 +  
303    int *tagub, flag, MAXTAG;
304    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
305    if (flag) {
# Line 615 | Line 322 | void DumpWriter::writeFinal(double finalTime){
322      nProc = mpiSim->getNumberProcessors();
323      potatoes = new int[nProc];
324  
325 +    //write out the comment lines
326      for (i = 0; i < nProc; i++)
327        potatoes[i] = 0;
328      
329 <    finalOut << mpiSim->getTotAtoms() << "\n";
329 >      for(k = 0; k < outFile.size(); k++){
330 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
331  
332 <    finalOut << finalTime << ";\t"
333 <            << entry_plug->Hmat[0][0] << "\t"
334 <            << entry_plug->Hmat[1][0] << "\t"
335 <            << entry_plug->Hmat[2][0] << ";\t"
332 >        *outFile[k] << currentTime << ";\t"
333 >                         << entry_plug->Hmat[0][0] << "\t"
334 >                         << entry_plug->Hmat[1][0] << "\t"
335 >                         << entry_plug->Hmat[2][0] << ";\t"
336  
337 <            << entry_plug->Hmat[0][1] << "\t"
338 <            << entry_plug->Hmat[1][1] << "\t"
339 <            << entry_plug->Hmat[2][1] << ";\t"
337 >                         << entry_plug->Hmat[0][1] << "\t"
338 >                         << entry_plug->Hmat[1][1] << "\t"
339 >                         << entry_plug->Hmat[2][1] << ";\t"
340  
341 <            << entry_plug->Hmat[0][2] << "\t"
342 <            << entry_plug->Hmat[1][2] << "\t"
343 <            << entry_plug->Hmat[2][2] << ";";
341 >                         << entry_plug->Hmat[0][2] << "\t"
342 >                         << entry_plug->Hmat[1][2] << "\t"
343 >                         << entry_plug->Hmat[2][2] << ";";
344 >  
345 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
346 >    }
347  
348 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
637 <    finalOut << endl;
638 <    finalOut.flush();
348 >    currentIndex = 0;
349  
350      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
351        
# Line 659 | Line 369 | void DumpWriter::writeFinal(double finalTime){
369          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
370                   myPotato, MPI_COMM_WORLD, &istatus);
371          
372 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
373 <        
664 <        // Null terminate the atomTypeString just in case:
665 <
666 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
667 <
372 >        atomTypeString = MPIatomTypeString;
373 >        
374          myPotato++;
375  
376          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 685 | Line 391 | void DumpWriter::writeFinal(double finalTime){
391  
392        } else {
393          
394 <        haveError = 0;
394 >        haveError = 0;
395          which_atom = i;
690 –        local_index=-1;
396          
397 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
398 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
399 <        }
397 >        //local_index = -1;
398 >
399 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
400 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
401 >        //}
402          
403 <        if (local_index != -1) {
403 >        //if (local_index != -1) {
404 >          
405 >          local_index = indexArray[currentIndex].first;        
406            
407 <          atomTypeString = atoms[local_index]->getType();
408 <
407 >          if (which_atom == indexArray[currentIndex].second) {
408 >            
409 >            atomTypeString = atoms[local_index]->getType();
410 >            
411            atoms[local_index]->getPos(pos);
412            atoms[local_index]->getVel(vel);          
413 <
413 >          
414            atomData6[0] = pos[0];
415            atomData6[1] = pos[1];
416            atomData6[2] = pos[2];
# Line 732 | Line 443 | void DumpWriter::writeFinal(double finalTime){
443            
444          } else {
445            sprintf(painCave.errMsg,
446 <                  "Atom %d not found on processor %d\n",
447 <                  i, worldRank );
446 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
447 >                  which_atom, worldRank, currentIndex, local_index );
448            haveError= 1;
449            simError();
450          }
451          
452 <        if(haveError) DieDieDie();
452 >        if(haveError) DieDieDie();
453          
454 <        // If we've survived to here, format the line:
455 <        
456 <        if (!isDirectional) {
457 <
458 <          sprintf( tempBuffer,
459 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
460 <                   atomTypeString,
461 <                   atomData6[0],
462 <                   atomData6[1],
463 <                   atomData6[2],
464 <                   atomData6[3],
465 <                   atomData6[4],
466 <                   atomData6[5]);
467 <          
468 <          strcpy( writeLine, tempBuffer );
469 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
470 <
471 <        } else {
472 <          
473 <          sprintf( tempBuffer,
474 <                   "%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",
475 <                   atomTypeString,
476 <                   atomData13[0],
477 <                   atomData13[1],
478 <                   atomData13[2],
479 <                   atomData13[3],
480 <                   atomData13[4],
481 <                   atomData13[5],
482 <                   atomData13[6],
483 <                   atomData13[7],
484 <                   atomData13[8],
485 <                   atomData13[9],
486 <                   atomData13[10],
487 <                   atomData13[11],
488 <                   atomData13[12]);
489 <          
779 <          strcat( writeLine, tempBuffer );
780 <          
781 <        }
454 >        currentIndex++;
455 >      }
456 >      // If we've survived to here, format the line:
457 >      
458 >      if (!isDirectional) {
459 >        
460 >        sprintf( writeLine,
461 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
462 >                 atomTypeString,
463 >                 atomData6[0],
464 >                 atomData6[1],
465 >                 atomData6[2],
466 >                 atomData6[3],
467 >                 atomData6[4],
468 >                 atomData6[5]);
469 >        
470 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
471 >        
472 >      } else {
473 >        
474 >        sprintf( writeLine,
475 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
476 >                 atomTypeString,
477 >                 atomData13[0],
478 >                 atomData13[1],
479 >                 atomData13[2],
480 >                 atomData13[3],
481 >                 atomData13[4],
482 >                 atomData13[5],
483 >                 atomData13[6],
484 >                 atomData13[7],
485 >                 atomData13[8],
486 >                 atomData13[9],
487 >                 atomData13[10],
488 >                 atomData13[11],
489 >                 atomData13[12]);
490          
783 –        finalOut << writeLine;
784 –        finalOut.flush();
491        }
492 +      
493 +      for(k = 0; k < outFile.size(); k++)
494 +        *outFile[k] << writeLine;
495      }
496 <
497 <    finalOut.flush();
496 >    
497 >    for(k = 0; k < outFile.size(); k++)
498 >      outFile[k]->flush();
499 >    
500      sprintf( checkPointMsg,
501               "Sucessfully took a dump.\n");
502 +    
503      MPIcheckPoint();        
504      
505 +    delete[] potatoes;
506 +    
507    } else {
508  
509      // worldRank != 0, so I'm a remote node.  
# Line 797 | Line 511 | void DumpWriter::writeFinal(double finalTime){
511      // Set my magic potato to 0:
512  
513      myPotato = 0;
514 +    currentIndex = 0;
515      
516      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
517        
# Line 805 | Line 520 | void DumpWriter::writeFinal(double finalTime){
520        if (AtomToProcMap[i] == worldRank) {
521  
522          if (myPotato + 3 >= MAXTAG) {
523 <
523 >          
524            // The potato was going to exceed the maximum value,
525            // so wrap this processor potato back to 0 (and block until
526            // node 0 says we can go:
527 <
527 >          
528            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
529            
530          }
531 +        which_atom = i;
532  
533 <        local_index=-1;
534 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
535 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
536 <        }
537 <        if (local_index != -1) {
533 >        //local_index = -1;
534 >
535 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
536 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
537 >        //}
538 >        
539 >        //if (local_index != -1) {
540 >
541 >        local_index = indexArray[currentIndex].first;        
542 >                
543 >        if (which_atom == indexArray[currentIndex].second) {
544          
545            atomTypeString = atoms[local_index]->getType();
546 <
546 >          
547            atoms[local_index]->getPos(pos);
548            atoms[local_index]->getVel(vel);
549 <
549 >          
550            atomData6[0] = pos[0];
551            atomData6[1] = pos[1];
552            atomData6[2] = pos[2];
# Line 849 | Line 571 | void DumpWriter::writeFinal(double finalTime){
571              atomData13[7] = q[1];
572              atomData13[8] = q[2];
573              atomData13[9] = q[3];
574 <
574 >  
575              atomData13[10] = dAtom->getJx();
576              atomData13[11] = dAtom->getJy();
577              atomData13[12] = dAtom->getJz();
# Line 857 | Line 579 | void DumpWriter::writeFinal(double finalTime){
579  
580          } else {
581            sprintf(painCave.errMsg,
582 <                  "Atom %d not found on processor %d\n",
583 <                  i, worldRank );
582 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
583 >                  which_atom, worldRank, currentIndex, local_index );
584            haveError= 1;
585            simError();
586          }
587 <
587 >        
588          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
589  
590          // null terminate the string before sending (just in case):
591          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
592  
593          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
594 <                 myPotato, MPI_COMM_WORLD);
594 >                             myPotato, MPI_COMM_WORLD);
595          
596          myPotato++;
597  
598          MPI_Send(&isDirectional, 1, MPI_INT, 0,
599 <                 myPotato, MPI_COMM_WORLD);
599 >                             myPotato, MPI_COMM_WORLD);
600          
601          myPotato++;
602          
# Line 889 | Line 611 | void DumpWriter::writeFinal(double finalTime){
611                     myPotato, MPI_COMM_WORLD);
612          }
613  
614 <        myPotato++;      
614 >        myPotato++;  
615 >        currentIndex++;    
616        }
617      }
618  
# Line 899 | Line 622 | void DumpWriter::writeFinal(double finalTime){
622      
623    }
624    
902 –  if( worldRank == 0 ) finalOut.close();
625   #endif // is_mpi
626   }
627  
906 –
907 –
628   #ifdef IS_MPI
629  
630   // a couple of functions to let us escape the write loop

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