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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC vs.
Revision 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 10;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77 >  
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 i;
87 < #ifdef IS_MPI
88 <  int j, which_node, done, which_atom, local_index;
89 <  double atomTransData[6];
90 <  double atomOrientData[7];
79 <  int isDirectional;
80 <  char* atomTypeString;
81 <  char MPIatomTypeString[MINIBUFFERSIZE];
82 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
87 < #else //is_mpi
88 <  int nAtoms = entry_plug->n_atoms;
89 < #endif //is_mpi
90 <
91 <  double q[4];
92 <  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";
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 > #ifdef IS_MPI
120 >  }
121 > #endif // is_mpi
122  
123 <  outFile << currentTime << ";\t"
124 <          << entry_plug->Hmat[0][0] << "\t"
106 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125  
126 <          << entry_plug->Hmat[0][1] << "\t"
110 <          << entry_plug->Hmat[1][1] << "\t"
111 <          << entry_plug->Hmat[2][1] << ";\t"
126 >  writeFrame(fileStreams, currentTime);
127  
128 <          << entry_plug->Hmat[0][2] << "\t"
129 <          << entry_plug->Hmat[1][2] << "\t"
130 <          << entry_plug->Hmat[2][2] << ";";
131 <  //write out additional parameters, such as chi and eta
132 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
118 <  outFile << endl;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  for( i=0; i<nAtoms; i++ ){
134 > void DumpWriter::writeFinal(double currentTime){
135  
136 <    atoms[i]->getPos(pos);
137 <    atoms[i]->getVel(vel);
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
139 <    sprintf( tempBuffer,
140 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
141 <             atoms[i]->getType(),
128 <             pos[0],
129 <             pos[1],
130 <             pos[2],
131 <             vel[0],
132 <             vel[1],
133 <             vel[2]);
134 <    strcpy( writeLine, tempBuffer );
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <    if( atoms[i]->isDirectional() ){
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <      dAtom = (DirectionalAtom *)atoms[i];
146 <      dAtom->getQ( q );
147 <
148 <      sprintf( tempBuffer,
149 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
150 <               q[0],
144 <               q[1],
145 <               q[2],
146 <               q[3],
147 <               dAtom->getJx(),
148 <               dAtom->getJy(),
149 <               dAtom->getJz());
150 <      strcat( writeLine, tempBuffer );
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 –    else
153 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
152  
153 <    outFile << writeLine;
153 > #ifdef IS_MPI
154    }
155 <  outFile.flush();
155 > #endif // is_mpi
156 >  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159  
160 < #else // is_mpi
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163 >  
164 > }
165  
166 <  // first thing first, suspend fatalities.
162 <  painCave.isEventLoop = 1;
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
168 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
169 <  int haveError;
168 >  const int BUFFERSIZE = 2000;
169 >  const int MINIBUFFERSIZE = 100;
170  
171 <  MPI_Status istatus;
172 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
171 >  char tempBuffer[BUFFERSIZE];  
172 >  char writeLine[BUFFERSIZE];
173  
174 <  // write out header and node 0's coordinates
174 >  int i, k;
175  
176 <  if( worldRank == 0 ){
177 <    outFile << mpiSim->getTotAtoms() << "\n";
178 <
179 <    outFile << currentTime << ";\t"
180 <            << entry_plug->Hmat[0][0] << "\t"
181 <            << entry_plug->Hmat[1][0] << "\t"
182 <            << entry_plug->Hmat[2][0] << ";\t"
183 <
184 <            << entry_plug->Hmat[0][1] << "\t"
185 <            << entry_plug->Hmat[1][1] << "\t"
186 <            << entry_plug->Hmat[2][1] << ";\t"
187 <
188 <            << entry_plug->Hmat[0][2] << "\t"
189 <            << entry_plug->Hmat[1][2] << "\t"
190 <            << entry_plug->Hmat[2][2] << ";";
191 <
192 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
193 <    outFile << endl;
194 <    outFile.flush();
195 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
196 <      // Get the Node number which has this atom;
197 <
198 <      which_node = AtomToProcMap[i];
199 <
200 <      if (which_node != 0) {
201 <        
202 <        atomTypeTag          = 4*i;
203 <        atomIsDirectionalTag = 4*i + 1;
204 <        atomTransDataTag     = 4*i + 2;
205 <        atomOrientDataTag    = 4*i + 3;
206 <
207 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
208 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
209 <        
210 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
211 <
212 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
213 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
210 <        
211 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
212 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
213 <
214 <        if (isDirectional) {
215 <
216 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
217 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
218 <
219 <        }
220 <
221 <      } else {
222 <        
223 <        haveError = 0;
224 <        which_atom = i;
225 <        local_index=-1;
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 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
216 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
217 <        }
218 <
219 <        if (local_index != -1) {
220 <
221 <          atomTypeString = atoms[local_index]->getType();
234 <
235 <          atoms[local_index]->getPos(pos);
236 <          atoms[local_index]->getVel(vel);
237 <
238 <          atomTransData[0] = pos[0];
239 <          atomTransData[1] = pos[1];
240 <          atomTransData[2] = pos[2];
241 <
242 <          atomTransData[3] = vel[0];
243 <          atomTransData[4] = vel[1];
244 <          atomTransData[5] = vel[2];
245 <          
246 <          isDirectional = 0;
247 <
248 <          if( atoms[local_index]->isDirectional() ){
249 <
250 <            isDirectional = 1;
251 <            
252 <            dAtom = (DirectionalAtom *)atoms[local_index];
253 <            dAtom->getQ( q );
254 <            
255 <            atomOrientData[0] = q[0];
256 <            atomOrientData[1] = q[1];
257 <            atomOrientData[2] = q[2];
258 <            atomOrientData[3] = q[3];
259 <
260 <            atomOrientData[4] = dAtom->getJx();
261 <            atomOrientData[5] = dAtom->getJy();
262 <            atomOrientData[6] = dAtom->getJz();
263 <          }
264 <
265 <        } else {
266 <          sprintf(painCave.errMsg,
267 <                  "Atom %d not found on processor %d\n",
268 <                  i, worldRank );
269 <          haveError= 1;
270 <          simError();
271 <        }
272 <
273 <        if(haveError) DieDieDie();
274 <                              
275 <        // If we've survived to here, format the line:
276 <        
277 <        sprintf( tempBuffer,
278 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
279 <                 atomTypeString,
280 <                 atomTransData[0],
281 <                 atomTransData[1],
282 <                 atomTransData[2],
283 <                 atomTransData[3],
284 <                 atomTransData[4],
285 <                 atomTransData[5]);
286 <
287 <        strcpy( writeLine, tempBuffer );
288 <
289 <        if (isDirectional) {
290 <
291 <          sprintf( tempBuffer,
292 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
293 <                   atomOrientData[0],
294 <                   atomOrientData[1],
295 <                   atomOrientData[2],
296 <                   atomOrientData[3],
297 <                   atomOrientData[4],
298 <                   atomOrientData[5],
299 <                   atomOrientData[6]);
300 <          strcat( writeLine, tempBuffer );
301 <
302 <        } else {
303 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
304 <        }
305 <
306 <        outFile << writeLine;
307 <        outFile.flush();
308 <      }
309 <    }
310 <
311 <    outFile.flush();
312 <    sprintf( checkPointMsg,
313 <             "Sucessfully took a dump.\n");
314 <    MPIcheckPoint();        
315 <    
316 <  } else {
317 <
318 <    // worldRank != 0, so I'm a remote node.  
319 <    
320 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
321 <      
322 <      // Am I the node which has this atom?
323 <      
324 <      if (AtomToProcMap[i] == worldRank) {
325 <
326 <        local_index=-1;
327 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
328 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
329 <        }
330 <        if (local_index != -1) {
331 <        
332 <          atomTypeString = atoms[local_index]->getType();
333 <
334 <          atoms[local_index]->getPos(pos);
335 <          atoms[local_index]->getVel(vel);
336 <
337 <          atomTransData[0] = pos[0];
338 <          atomTransData[1] = pos[1];
339 <          atomTransData[2] = pos[2];
340 <
341 <          atomTransData[3] = vel[0];
342 <          atomTransData[4] = vel[1];
343 <          atomTransData[5] = vel[2];
344 <          
345 <          isDirectional = 0;
346 <
347 <          if( atoms[local_index]->isDirectional() ){
348 <
349 <            isDirectional = 1;
350 <            
351 <            dAtom = (DirectionalAtom *)atoms[local_index];
352 <            dAtom->getQ( q );
353 <            
354 <            atomOrientData[0] = q[0];
355 <            atomOrientData[1] = q[1];
356 <            atomOrientData[2] = q[2];
357 <            atomOrientData[3] = q[3];
358 <
359 <            atomOrientData[4] = dAtom->getJx();
360 <            atomOrientData[5] = dAtom->getJy();
361 <            atomOrientData[6] = dAtom->getJz();
362 <          }
363 <
364 <        } else {
365 <          sprintf(painCave.errMsg,
366 <                  "Atom %d not found on processor %d\n",
367 <                  i, worldRank );
368 <          haveError= 1;
369 <          simError();
370 <        }
371 <
372 <        // I've survived this far, so send off the data!
373 <
374 <        atomTypeTag          = 4*i;
375 <        atomIsDirectionalTag = 4*i + 1;
376 <        atomTransDataTag     = 4*i + 2;
377 <        atomOrientDataTag    = 4*i + 3;
378 <
379 <
380 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
381 <
382 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
383 <                 atomTypeTag, MPI_COMM_WORLD);
384 <        
385 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
386 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
387 <        
388 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
389 <                 atomTransDataTag, MPI_COMM_WORLD);
390 <
391 <        if (isDirectional) {
392 <
393 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
394 <                   atomOrientDataTag, MPI_COMM_WORLD);
395 <          
396 <        }
397 <      
398 <      }
399 <    }
400 <
401 <    sprintf( checkPointMsg,
402 <             "Sucessfully took a dump.\n");
403 <    MPIcheckPoint();        
404 <    
405 <  }
406 <  
407 <  painCave.isEventLoop = 0;
408 <
409 < #endif // is_mpi
410 < }
411 <
412 < void DumpWriter::writeFinal(double finalTime){
413 <
414 <  char finalName[500];
415 <  ofstream finalOut;
416 <
417 <  const int BUFFERSIZE = 2000;
418 <  const int MINIBUFFERSIZE = 10;
419 <  char tempBuffer[BUFFERSIZE];
420 <  char writeLine[BUFFERSIZE];
421 <
422 <  double q[4];
423 <  DirectionalAtom* dAtom;
424 <  Atom** atoms = entry_plug->atoms;
425 <  int i;
426 < #ifdef IS_MPI
427 <  int j, which_node, done, which_atom, local_index;
428 <  double atomTransData[6];
429 <  double atomOrientData[7];
215 >  int *potatoes;
216 >  int myPotato;
217 >
218 >  int nProc;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220 >  double atomData6[6];
221 >  double atomData13[13];
222    int isDirectional;
223    char* atomTypeString;
224    char MPIatomTypeString[MINIBUFFERSIZE];
225 <  int atomTypeTag;
434 <  int atomIsDirectionalTag;
435 <  int atomTransDataTag;
436 <  int atomOrientDataTag;
225 >
226   #else //is_mpi
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 +  double q[4];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
443 – #ifdef IS_MPI
444 –  if(worldRank == 0 ){
445 – #endif // is_mpi
446 –
447 –    strcpy( finalName, entry_plug->finalName );
448 –
449 –    finalOut.open( finalName, ios::out | ios::trunc );
450 –    if( !finalOut ){
451 –      sprintf( painCave.errMsg,
452 –               "Could not open \"%s\" for final dump output.\n",
453 –               finalName );
454 –      painCave.isFatal = 1;
455 –      simError();
456 –    }
457 –
458 –    // finalOut.setf( ios::scientific );
459 –
460 – #ifdef IS_MPI
461 –  }
462 –
463 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
464 –  MPIcheckPoint();
465 –
466 – #endif //is_mpi
467 –
468 –
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"
476 <           << 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 <
482 <           << entry_plug->Hmat[0][2] << "\t"
483 <           << entry_plug->Hmat[1][2] << "\t"
484 <           << entry_plug->Hmat[2][2] << ";";
485 <
486 <  //write out additional parameters, such as chi and eta
487 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
488 <  finalOut << endl;
489 <
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 522 | Line 289 | void DumpWriter::writeFinal(double finalTime){
289      else
290        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291  
292 <    finalOut << writeLine;
292 >    for(k = 0; k < outFile.size(); k++)
293 >      *outFile[k] << writeLine;
294    }
527 –  finalOut.flush();
528 –  finalOut.close();
295  
296   #else // is_mpi
297  
298 <  // first thing first, suspend fatalities.
299 <  painCave.isEventLoop = 1;
298 >  /* code to find maximum tag value */
299 >  
300 >  int *tagub, flag, MAXTAG;
301 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302 >  if (flag) {
303 >    MAXTAG = *tagub;
304 >  } else {
305 >    MAXTAG = 32767;
306 >  }  
307  
535 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
308    int haveError;
309  
310    MPI_Status istatus;
# Line 541 | Line 313 | void DumpWriter::writeFinal(double finalTime){
313    // write out header and node 0's coordinates
314  
315    if( worldRank == 0 ){
544 –    finalOut << mpiSim->getTotAtoms() << "\n";
316  
317 <    finalOut << finalTime << ";\t"
547 <            << entry_plug->Hmat[0][0] << "\t"
548 <            << entry_plug->Hmat[1][0] << "\t"
549 <            << entry_plug->Hmat[2][0] << ";\t"
317 >    // Node 0 needs a list of the magic potatoes for each processor;
318  
319 <            << entry_plug->Hmat[0][1] << "\t"
320 <            << entry_plug->Hmat[1][1] << "\t"
553 <            << entry_plug->Hmat[2][1] << ";\t"
319 >    nProc = mpiSim->getNumberProcessors();
320 >    potatoes = new int[nProc];
321  
322 <            << entry_plug->Hmat[0][2] << "\t"
323 <            << entry_plug->Hmat[1][2] << "\t"
324 <            << entry_plug->Hmat[2][2] << ";";
322 >    //write out the comment lines
323 >    for (i = 0; i < nProc; i++)
324 >      potatoes[i] = 0;
325 >    
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328  
329 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
330 <    finalOut << endl;
331 <    finalOut.flush();
329 >        *outFile[k] << currentTime << ";\t"
330 >                         << entry_plug->Hmat[0][0] << "\t"
331 >                         << entry_plug->Hmat[1][0] << "\t"
332 >                         << entry_plug->Hmat[2][0] << ";\t"
333 >
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][2] << "\t"
339 >                         << entry_plug->Hmat[1][2] << "\t"
340 >                         << entry_plug->Hmat[2][2] << ";";
341 >  
342 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343 >    }
344 >
345 >    currentIndex = 0;
346 >
347      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
348 +      
349        // Get the Node number which has this atom;
350 <
350 >      
351        which_node = AtomToProcMap[i];
352 <
352 >      
353        if (which_node != 0) {
568 –        
569 –        atomTypeTag          = 4*i;
570 –        atomIsDirectionalTag = 4*i + 1;
571 –        atomTransDataTag     = 4*i + 2;
572 –        atomOrientDataTag    = 4*i + 3;
354  
355 +        if (potatoes[which_node] + 3 >= MAXTAG) {
356 +          // The potato was going to exceed the maximum value,
357 +          // so wrap this processor potato back to 0:        
358 +
359 +          potatoes[which_node] = 0;          
360 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
361 +          
362 +        }
363 +
364 +        myPotato = potatoes[which_node];        
365 +        
366          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
367 >                 myPotato, MPI_COMM_WORLD, &istatus);
368          
369 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
369 >        atomTypeString = MPIatomTypeString;
370 >        
371 >        myPotato++;
372  
373          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
374 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
375 <        
376 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
583 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
374 >                 myPotato, MPI_COMM_WORLD, &istatus);
375 >              
376 >        myPotato++;
377  
378 <        if (isDirectional) {
379 <
380 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
381 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
382 <
378 >        if (isDirectional) {          
379 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
380 >                   myPotato, MPI_COMM_WORLD, &istatus);
381 >        } else {
382 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);          
384          }
385 +        
386 +        myPotato++;
387 +        potatoes[which_node] = myPotato;
388  
389        } else {
390          
391 <        haveError = 0;
391 >        haveError = 0;
392          which_atom = i;
393 <        local_index=-1;
394 <
395 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
396 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
397 <        }
398 <
399 <        if (local_index != -1) {
603 <
604 <          atomTypeString = atoms[local_index]->getType();
605 <
393 >        
394 >          local_index = indexArray[currentIndex].first;        
395 >          
396 >          if (which_atom == indexArray[currentIndex].second) {
397 >            
398 >            atomTypeString = atoms[local_index]->getType();
399 >            
400            atoms[local_index]->getPos(pos);
401 <          atoms[local_index]->getVel(vel);
401 >          atoms[local_index]->getVel(vel);          
402 >          
403 >          atomData6[0] = pos[0];
404 >          atomData6[1] = pos[1];
405 >          atomData6[2] = pos[2];
406  
407 <          atomTransData[0] = pos[0];
408 <          atomTransData[1] = pos[1];
409 <          atomTransData[2] = pos[2];
612 <
613 <          atomTransData[3] = vel[0];
614 <          atomTransData[4] = vel[1];
615 <          atomTransData[5] = vel[2];
407 >          atomData6[3] = vel[0];
408 >          atomData6[4] = vel[1];
409 >          atomData6[5] = vel[2];
410            
411            isDirectional = 0;
412  
# Line 622 | Line 416 | void DumpWriter::writeFinal(double finalTime){
416              
417              dAtom = (DirectionalAtom *)atoms[local_index];
418              dAtom->getQ( q );
625 –            
626 –            atomOrientData[0] = q[0];
627 –            atomOrientData[1] = q[1];
628 –            atomOrientData[2] = q[2];
629 –            atomOrientData[3] = q[3];
419  
420 <            atomOrientData[4] = dAtom->getJx();
421 <            atomOrientData[5] = dAtom->getJy();
422 <            atomOrientData[6] = dAtom->getJz();
420 >            for (int j = 0; j < 6 ; j++)
421 >              atomData13[j] = atomData6[j];            
422 >            
423 >            atomData13[6] = q[0];
424 >            atomData13[7] = q[1];
425 >            atomData13[8] = q[2];
426 >            atomData13[9] = q[3];
427 >            
428 >            atomData13[10] = dAtom->getJx();
429 >            atomData13[11] = dAtom->getJy();
430 >            atomData13[12] = dAtom->getJz();
431            }
432 <
432 >          
433          } else {
434            sprintf(painCave.errMsg,
435 <                  "Atom %d not found on processor %d\n",
436 <                  i, worldRank );
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437            haveError= 1;
438            simError();
439          }
643 –
644 –        if(haveError) DieDieDie();
645 –                              
646 –        // If we've survived to here, format the line:
440          
441 <        sprintf( tempBuffer,
442 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
443 <                 atomTypeString,
651 <                 atomTransData[0],
652 <                 atomTransData[1],
653 <                 atomTransData[2],
654 <                 atomTransData[3],
655 <                 atomTransData[4],
656 <                 atomTransData[5]);
657 <
658 <        strcpy( writeLine, tempBuffer );
659 <
660 <        if (isDirectional) {
661 <
662 <          sprintf( tempBuffer,
663 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
664 <                   atomOrientData[0],
665 <                   atomOrientData[1],
666 <                   atomOrientData[2],
667 <                   atomOrientData[3],
668 <                   atomOrientData[4],
669 <                   atomOrientData[5],
670 <                   atomOrientData[6]);
671 <          strcat( writeLine, tempBuffer );
672 <
673 <        } else {
674 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
675 <        }
676 <
677 <        finalOut << writeLine;
678 <        finalOut.flush();
441 >        if(haveError) DieDieDie();
442 >        
443 >        currentIndex++;
444        }
445 +      // If we've survived to here, format the line:
446 +      
447 +      if (!isDirectional) {
448 +        
449 +        sprintf( writeLine,
450 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 +                 atomTypeString,
452 +                 atomData6[0],
453 +                 atomData6[1],
454 +                 atomData6[2],
455 +                 atomData6[3],
456 +                 atomData6[4],
457 +                 atomData6[5]);
458 +        
459 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460 +        
461 +      } else {
462 +        
463 +        sprintf( writeLine,
464 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
465 +                 atomTypeString,
466 +                 atomData13[0],
467 +                 atomData13[1],
468 +                 atomData13[2],
469 +                 atomData13[3],
470 +                 atomData13[4],
471 +                 atomData13[5],
472 +                 atomData13[6],
473 +                 atomData13[7],
474 +                 atomData13[8],
475 +                 atomData13[9],
476 +                 atomData13[10],
477 +                 atomData13[11],
478 +                 atomData13[12]);
479 +        
480 +      }
481 +      
482 +      for(k = 0; k < outFile.size(); k++)
483 +        *outFile[k] << writeLine;
484      }
485 <
486 <    finalOut.flush();
485 >    
486 >    for(k = 0; k < outFile.size(); k++)
487 >      outFile[k]->flush();
488 >    
489      sprintf( checkPointMsg,
490               "Sucessfully took a dump.\n");
491 +    
492      MPIcheckPoint();        
493      
494 +    delete[] potatoes;
495 +    
496    } else {
497  
498      // worldRank != 0, so I'm a remote node.  
499 +
500 +    // Set my magic potato to 0:
501 +
502 +    myPotato = 0;
503 +    currentIndex = 0;
504      
505      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
506        
# Line 694 | Line 508 | void DumpWriter::writeFinal(double finalTime){
508        
509        if (AtomToProcMap[i] == worldRank) {
510  
511 <        local_index=-1;
512 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
513 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
511 >        if (myPotato + 3 >= MAXTAG) {
512 >          
513 >          // The potato was going to exceed the maximum value,
514 >          // so wrap this processor potato back to 0 (and block until
515 >          // node 0 says we can go:
516 >          
517 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518 >          
519          }
520 <        if (local_index != -1) {
520 >        which_atom = i;
521 >
522 >        local_index = indexArray[currentIndex].first;        
523 >                
524 >        if (which_atom == indexArray[currentIndex].second) {
525          
526            atomTypeString = atoms[local_index]->getType();
527 <
527 >          
528            atoms[local_index]->getPos(pos);
529            atoms[local_index]->getVel(vel);
530 +          
531 +          atomData6[0] = pos[0];
532 +          atomData6[1] = pos[1];
533 +          atomData6[2] = pos[2];
534  
535 <          atomTransData[0] = pos[0];
536 <          atomTransData[1] = pos[1];
537 <          atomTransData[2] = pos[2];
711 <
712 <          atomTransData[3] = vel[0];
713 <          atomTransData[4] = vel[1];
714 <          atomTransData[5] = vel[2];
535 >          atomData6[3] = vel[0];
536 >          atomData6[4] = vel[1];
537 >          atomData6[5] = vel[2];
538            
539            isDirectional = 0;
540  
# Line 722 | Line 545 | void DumpWriter::writeFinal(double finalTime){
545              dAtom = (DirectionalAtom *)atoms[local_index];
546              dAtom->getQ( q );
547              
548 <            atomOrientData[0] = q[0];
549 <            atomOrientData[1] = q[1];
550 <            atomOrientData[2] = q[2];
551 <            atomOrientData[3] = q[3];
552 <
553 <            atomOrientData[4] = dAtom->getJx();
554 <            atomOrientData[5] = dAtom->getJy();
555 <            atomOrientData[6] = dAtom->getJz();
548 >            for (int j = 0; j < 6 ; j++)
549 >              atomData13[j] = atomData6[j];
550 >            
551 >            atomData13[6] = q[0];
552 >            atomData13[7] = q[1];
553 >            atomData13[8] = q[2];
554 >            atomData13[9] = q[3];
555 >  
556 >            atomData13[10] = dAtom->getJx();
557 >            atomData13[11] = dAtom->getJy();
558 >            atomData13[12] = dAtom->getJz();
559            }
560  
561          } else {
562            sprintf(painCave.errMsg,
563 <                  "Atom %d not found on processor %d\n",
564 <                  i, worldRank );
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565            haveError= 1;
566            simError();
567          }
568 <
743 <        // I've survived this far, so send off the data!
744 <
745 <        atomTypeTag          = 4*i;
746 <        atomIsDirectionalTag = 4*i + 1;
747 <        atomTransDataTag     = 4*i + 2;
748 <        atomOrientDataTag    = 4*i + 3;
749 <
568 >        
569          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570  
571 +        // null terminate the string before sending (just in case):
572 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573 +
574          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575 <                 atomTypeTag, MPI_COMM_WORLD);
575 >                             myPotato, MPI_COMM_WORLD);
576          
577 +        myPotato++;
578 +
579          MPI_Send(&isDirectional, 1, MPI_INT, 0,
580 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
580 >                             myPotato, MPI_COMM_WORLD);
581          
582 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
583 <                 atomTransDataTag, MPI_COMM_WORLD);
760 <
582 >        myPotato++;
583 >        
584          if (isDirectional) {
585  
586 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
587 <                   atomOrientDataTag, MPI_COMM_WORLD);
586 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588            
589 +        } else {
590 +
591 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
592 +                   myPotato, MPI_COMM_WORLD);
593          }
594 <      
594 >
595 >        myPotato++;  
596 >        currentIndex++;    
597        }
598      }
599  
600      sprintf( checkPointMsg,
601 <             "Sucessfully wrote final file.\n");
601 >             "Sucessfully took a dump.\n");
602      MPIcheckPoint();        
603      
604 <  }
604 >  }
605    
777 –  painCave.isEventLoop = 0;
778 –
779 –  if( worldRank == 0 ) finalOut.close();
606   #endif // is_mpi
607   }
608  
783 –
784 –
609   #ifdef IS_MPI
610  
611   // a couple of functions to let us escape the write loop

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