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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 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 = 10;
69 > /**
70 > * A hook function to load balancing
71 > */
72  
73 <  char tempBuffer[BUFFERSIZE];
74 <  char writeLine[BUFFERSIZE];
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76 >  
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 i;
86 < #ifdef IS_MPI
87 <  int j, which_node, done, which_atom, local_index;
88 <  double atomTransData[6];
89 <  double atomOrientData[7];
79 <  int isDirectional;
80 <  char* atomTypeString;
81 <  int me;
82 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
86 < #else //is_mpi
87 <  int nAtoms = entry_plug->n_atoms;
88 < #endif //is_mpi
89 <
90 <  double q[4];
91 <  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"
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 >    }
125 >  }
126 > #endif // is_mpi
127  
128 <          << entry_plug->Hmat[0][1] << "\t"
129 <          << entry_plug->Hmat[1][1] << "\t"
110 <          << entry_plug->Hmat[2][1] << ";\t"
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130  
131 <          << entry_plug->Hmat[0][2] << "\t"
113 <          << entry_plug->Hmat[1][2] << "\t"
114 <          << entry_plug->Hmat[2][2] << ";";
115 <  //write out additional parameters, such as chi and eta
116 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
117 <  outFile << endl;
131 >  writeFrame(fileStreams, currentTime);
132  
133 <  for( i=0; i<nAtoms; i++ ){
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137 > }
138  
139 <    atoms[i]->getPos(pos);
122 <    atoms[i]->getVel(vel);
139 > void DumpWriter::writeFinal(double currentTime){
140  
141 <    sprintf( tempBuffer,
142 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
126 <             atoms[i]->getType(),
127 <             pos[0],
128 <             pos[1],
129 <             pos[2],
130 <             vel[0],
131 <             vel[1],
132 <             vel[2]);
133 <    strcpy( writeLine, tempBuffer );
141 >  ofstream finalOut;
142 >  vector<ofstream*> fileStreams;
143  
144 <    if( atoms[i]->isDirectional() ){
144 > #ifdef IS_MPI
145 >  if(worldRank == 0 ){
146  
147 <      dAtom = (DirectionalAtom *)atoms[i];
138 <      dAtom->getQ( q );
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148  
149 <      sprintf( tempBuffer,
150 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
151 <               q[0],
152 <               q[1],
153 <               q[2],
154 <               q[3],
146 <               dAtom->getJx(),
147 <               dAtom->getJy(),
148 <               dAtom->getJz());
149 <      strcat( writeLine, tempBuffer );
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      }
151 –    else
152 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156  
154 –    outFile << writeLine;
157    }
158 <  outFile.flush();
158 > #endif // is_mpi
159 >  
160 >  fileStreams.push_back(&finalOut);  
161 >  writeFrame(fileStreams, currentTime);
162  
163 < #else // is_mpi
163 > #ifdef IS_MPI
164 >  finalOut.close();
165 > #endif
166 >  
167 > }
168  
169 <  // first thing first, suspend fatalities.
161 <  painCave.isEventLoop = 1;
169 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
170  
171 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172 <  int haveError;
171 >  const int BUFFERSIZE = 2000;
172 >  const int MINIBUFFERSIZE = 100;
173  
174 <  MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
174 >  char tempBuffer[BUFFERSIZE];  
175 >  char writeLine[BUFFERSIZE];
176  
177 <  // write out header and node 0's coordinates
177 >  int i, k;
178  
179 <  if( worldRank == 0 ){
180 <    outFile << mpiSim->getTotAtoms() << "\n";
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 <    outFile << currentTime << ";\t"
219 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << entry_plug->Hmat[2][0] << ";\t"
178 <
179 <            << entry_plug->Hmat[0][1] << "\t"
180 <            << entry_plug->Hmat[1][1] << "\t"
181 <            << entry_plug->Hmat[2][1] << ";\t"
182 <
183 <            << entry_plug->Hmat[0][2] << "\t"
184 <            << entry_plug->Hmat[1][2] << "\t"
185 <            << entry_plug->Hmat[2][2] << ";";
186 <
187 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
188 <    outFile << endl;
189 <    outFile.flush();
190 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
191 <      // Get the Node number which has this atom;
218 >  int *potatoes;
219 >  int myPotato;
220  
221 <      which_node = AtomToProcMap[i];
222 <
223 <      if (which_node != 0) {
224 <        
197 <        atomTypeTag          = 4*i;
198 <        atomIsDirectionalTag = 4*i + 1;
199 <        atomTransDataTag     = 4*i + 2;
200 <        atomOrientDataTag    = 4*i + 3;
201 <
202 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
203 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
204 <        
205 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
206 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
207 <        
208 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
209 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
210 <
211 <        if (isDirectional) {
212 <
213 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
214 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
215 <
216 <        }
217 <
218 <      } else {
219 <        
220 <        haveError = 0;
221 <        which_atom = i;
222 <        local_index=-1;
223 <
224 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
225 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
226 <        }
227 <
228 <        if (local_index != -1) {
229 <
230 <          atomTypeString = atoms[local_index]->getType();
231 <
232 <          atoms[local_index]->getPos(pos);
233 <          atoms[local_index]->getVel(vel);
234 <
235 <          atomTransData[0] = pos[0];
236 <          atomTransData[1] = pos[1];
237 <          atomTransData[2] = pos[2];
238 <
239 <          atomTransData[3] = vel[0];
240 <          atomTransData[4] = vel[1];
241 <          atomTransData[5] = vel[2];
242 <          
243 <          isDirectional = 0;
244 <
245 <          if( atoms[local_index]->isDirectional() ){
246 <
247 <            isDirectional = 1;
248 <            
249 <            dAtom = (DirectionalAtom *)atoms[local_index];
250 <            dAtom->getQ( q );
251 <            
252 <            atomOrientData[0] = q[0];
253 <            atomOrientData[1] = q[1];
254 <            atomOrientData[2] = q[2];
255 <            atomOrientData[3] = q[3];
256 <
257 <            atomOrientData[4] = dAtom->getJx();
258 <            atomOrientData[5] = dAtom->getJy();
259 <            atomOrientData[6] = dAtom->getJz();
260 <          }
261 <
262 <        } else {
263 <          sprintf(painCave.errMsg,
264 <                  "Atom %d not found on processor %d\n",
265 <                  i, worldRank );
266 <          haveError= 1;
267 <          simError();
268 <        }
269 <
270 <        if(haveError) DieDieDie();
271 <                              
272 <        // If we've survived to here, format the line:
273 <        
274 <        sprintf( tempBuffer,
275 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
276 <                 atomTypeString,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 atomTransData[5]);
283 <
284 <        strcpy( writeLine, tempBuffer );
285 <
286 <        if (isDirectional) {
287 <
288 <          sprintf( tempBuffer,
289 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
290 <                   atomOrientData[0],
291 <                   atomOrientData[1],
292 <                   atomOrientData[2],
293 <                   atomOrientData[3],
294 <                   atomOrientData[4],
295 <                   atomOrientData[5],
296 <                   atomOrientData[6]);
297 <          strcat( writeLine, tempBuffer );
298 <
299 <        } else {
300 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
301 <        }
302 <
303 <        outFile << writeLine;
304 <        outFile.flush();
305 <      }
306 <    }
307 <
308 <    outFile.flush();
309 <    sprintf( checkPointMsg,
310 <             "Sucessfully took a dump.\n");
311 <    MPIcheckPoint();        
312 <    
313 <  } else {
314 <
315 <    // worldRank != 0, so I'm a remote node.  
316 <    
317 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
318 <      
319 <      // Am I the node which has this atom?
320 <      
321 <      if (AtomToProcMap[i] == worldRank) {
322 <
323 <        local_index=-1;
324 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
325 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
326 <        }
327 <        if (local_index != -1) {
328 <        
329 <          atomTypeString = atoms[local_index]->getType();
330 <
331 <          atoms[local_index]->getPos(pos);
332 <          atoms[local_index]->getVel(vel);
333 <
334 <          atomTransData[0] = pos[0];
335 <          atomTransData[1] = pos[1];
336 <          atomTransData[2] = pos[2];
337 <
338 <          atomTransData[3] = vel[0];
339 <          atomTransData[4] = vel[1];
340 <          atomTransData[5] = vel[2];
341 <          
342 <          isDirectional = 0;
343 <
344 <          if( atoms[local_index]->isDirectional() ){
345 <
346 <            isDirectional = 1;
347 <            
348 <            dAtom = (DirectionalAtom *)atoms[local_index];
349 <            dAtom->getQ( q );
350 <            
351 <            atomOrientData[0] = q[0];
352 <            atomOrientData[1] = q[1];
353 <            atomOrientData[2] = q[2];
354 <            atomOrientData[3] = q[3];
355 <
356 <            atomOrientData[4] = dAtom->getJx();
357 <            atomOrientData[5] = dAtom->getJy();
358 <            atomOrientData[6] = dAtom->getJz();
359 <          }
360 <
361 <        } else {
362 <          sprintf(painCave.errMsg,
363 <                  "Atom %d not found on processor %d\n",
364 <                  i, worldRank );
365 <          haveError= 1;
366 <          simError();
367 <        }
368 <
369 <        // I've survived this far, so send off the data!
370 <
371 <        atomTypeTag          = 4*i;
372 <        atomIsDirectionalTag = 4*i + 1;
373 <        atomTransDataTag     = 4*i + 2;
374 <        atomOrientDataTag    = 4*i + 3;
375 <
376 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
377 <                 atomTypeTag, MPI_COMM_WORLD);
378 <        
379 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
380 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
381 <        
382 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
383 <                 atomTransDataTag, MPI_COMM_WORLD);
384 <
385 <        if (isDirectional) {
386 <
387 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
388 <                   atomOrientDataTag, MPI_COMM_WORLD);
389 <          
390 <        }
391 <      
392 <      }
393 <    }
394 <
395 <    sprintf( checkPointMsg,
396 <             "Sucessfully took a dump.\n");
397 <    MPIcheckPoint();        
398 <    
399 <  }
400 <  
401 <  painCave.isEventLoop = 0;
402 <
403 < #endif // is_mpi
404 < }
405 <
406 < void DumpWriter::writeFinal(double finalTime){
407 <
408 <  char finalName[500];
409 <  ofstream finalOut;
410 <
411 <  const int BUFFERSIZE = 2000;
412 <  const int MINIBUFFERSIZE = 10;
413 <  char tempBuffer[BUFFERSIZE];
414 <  char writeLine[BUFFERSIZE];
415 <
416 <  double q[4];
417 <  DirectionalAtom* dAtom;
418 <  Atom** atoms = entry_plug->atoms;
419 <  int i;
420 < #ifdef IS_MPI
421 <  int j, which_node, done, which_atom, local_index;
422 <  double atomTransData[6];
423 <  double atomOrientData[7];
221 >  int nProc;
222 >  int j, which_node, done, which_atom, local_index, currentIndex;
223 >  double atomData6[6];
224 >  double atomData13[13];
225    int isDirectional;
226    char* atomTypeString;
227 <  int atomTypeTag;
228 <  int atomIsDirectionalTag;
428 <  int atomTransDataTag;
429 <  int atomOrientDataTag;
227 >  char MPIatomTypeString[MINIBUFFERSIZE];
228 >
229   #else //is_mpi
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  
436 – #ifdef IS_MPI
437 –  if(worldRank == 0 ){
438 – #endif // is_mpi
439 –
440 –    strcpy( finalName, entry_plug->finalName );
441 –
442 –    finalOut.open( finalName, ios::out | ios::trunc );
443 –    if( !finalOut ){
444 –      sprintf( painCave.errMsg,
445 –               "Could not open \"%s\" for final dump output.\n",
446 –               finalName );
447 –      painCave.isFatal = 1;
448 –      simError();
449 –    }
450 –
451 –    // finalOut.setf( ios::scientific );
452 –
453 – #ifdef IS_MPI
454 –  }
455 –
456 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 –  MPIcheckPoint();
458 –
459 – #endif //is_mpi
460 –
461 –
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"
469 <           << 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 <
475 <           << entry_plug->Hmat[0][2] << "\t"
476 <           << entry_plug->Hmat[1][2] << "\t"
477 <           << entry_plug->Hmat[2][2] << ";";
478 <
479 <  //write out additional parameters, such as chi and eta
480 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 <  finalOut << endl;
482 <
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 515 | 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    }
520 –  finalOut.flush();
521 –  finalOut.close();
298  
299   #else // is_mpi
300  
301 <  // first thing first, suspend fatalities.
302 <  painCave.isEventLoop = 1;
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) {
306 >    MAXTAG = *tagub;
307 >  } else {
308 >    MAXTAG = 32767;
309 >  }  
310  
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
311    int haveError;
312  
313    MPI_Status istatus;
# Line 534 | Line 316 | void DumpWriter::writeFinal(double finalTime){
316    // write out header and node 0's coordinates
317  
318    if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\n";
319  
320 <    finalOut << finalTime << ";\t"
540 <            << entry_plug->Hmat[0][0] << "\t"
541 <            << entry_plug->Hmat[1][0] << "\t"
542 <            << entry_plug->Hmat[2][0] << ";\t"
320 >    // Node 0 needs a list of the magic potatoes for each processor;
321  
322 <            << entry_plug->Hmat[0][1] << "\t"
323 <            << entry_plug->Hmat[1][1] << "\t"
546 <            << entry_plug->Hmat[2][1] << ";\t"
322 >    nProc = mpiSim->getNumberProcessors();
323 >    potatoes = new int[nProc];
324  
325 <            << entry_plug->Hmat[0][2] << "\t"
326 <            << entry_plug->Hmat[1][2] << "\t"
327 <            << entry_plug->Hmat[2][2] << ";";
325 >    //write out the comment lines
326 >    for (i = 0; i < nProc; i++)
327 >      potatoes[i] = 0;
328 >    
329 >      for(k = 0; k < outFile.size(); k++){
330 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
331  
332 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
333 <    finalOut << endl;
334 <    finalOut.flush();
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"
340 >
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 >    currentIndex = 0;
349 >
350      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
351 +      
352        // Get the Node number which has this atom;
353 <
353 >      
354        which_node = AtomToProcMap[i];
355 <
355 >      
356        if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
357  
358 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
359 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
358 >        if (potatoes[which_node] + 3 >= MAXTAG) {
359 >          // The potato was going to exceed the maximum value,
360 >          // so wrap this processor potato back to 0:        
361 >
362 >          potatoes[which_node] = 0;          
363 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
364 >          
365 >        }
366 >
367 >        myPotato = potatoes[which_node];        
368          
369 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
369 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371          
372 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
373 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
372 >        atomTypeString = MPIatomTypeString;
373 >        
374 >        myPotato++;
375  
376 <        if (isDirectional) {
376 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >              
379 >        myPotato++;
380  
381 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
382 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
383 <
381 >        if (isDirectional) {          
382 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);
384 >        } else {
385 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
386 >                   myPotato, MPI_COMM_WORLD, &istatus);          
387          }
388 +        
389 +        myPotato++;
390 +        potatoes[which_node] = myPotato;
391  
392        } else {
393          
394 <        haveError = 0;
394 >        haveError = 0;
395          which_atom = i;
396 <        local_index=-1;
396 >        
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) {
404 <
405 <          atomTypeString = atoms[local_index]->getType();
406 <
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) {
404 >          
405 >          local_index = indexArray[currentIndex].first;        
406 >          
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);
412 >          atoms[local_index]->getVel(vel);          
413 >          
414 >          atomData6[0] = pos[0];
415 >          atomData6[1] = pos[1];
416 >          atomData6[2] = pos[2];
417  
418 <          atomTransData[0] = pos[0];
419 <          atomTransData[1] = pos[1];
420 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
418 >          atomData6[3] = vel[0];
419 >          atomData6[4] = vel[1];
420 >          atomData6[5] = vel[2];
421            
422            isDirectional = 0;
423  
# Line 613 | Line 427 | void DumpWriter::writeFinal(double finalTime){
427              
428              dAtom = (DirectionalAtom *)atoms[local_index];
429              dAtom->getQ( q );
616 –            
617 –            atomOrientData[0] = q[0];
618 –            atomOrientData[1] = q[1];
619 –            atomOrientData[2] = q[2];
620 –            atomOrientData[3] = q[3];
430  
431 <            atomOrientData[4] = dAtom->getJx();
432 <            atomOrientData[5] = dAtom->getJy();
433 <            atomOrientData[6] = dAtom->getJz();
431 >            for (int j = 0; j < 6 ; j++)
432 >              atomData13[j] = atomData6[j];            
433 >            
434 >            atomData13[6] = q[0];
435 >            atomData13[7] = q[1];
436 >            atomData13[8] = q[2];
437 >            atomData13[9] = q[3];
438 >            
439 >            atomData13[10] = dAtom->getJx();
440 >            atomData13[11] = dAtom->getJy();
441 >            atomData13[12] = dAtom->getJz();
442            }
443 <
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          }
634 –
635 –        if(haveError) DieDieDie();
636 –                              
637 –        // If we've survived to here, format the line:
451          
452 <        sprintf( tempBuffer,
453 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
454 <                 atomTypeString,
642 <                 atomTransData[0],
643 <                 atomTransData[1],
644 <                 atomTransData[2],
645 <                 atomTransData[3],
646 <                 atomTransData[4],
647 <                 atomTransData[5]);
648 <
649 <        strcpy( writeLine, tempBuffer );
650 <
651 <        if (isDirectional) {
652 <
653 <          sprintf( tempBuffer,
654 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 <                   atomOrientData[0],
656 <                   atomOrientData[1],
657 <                   atomOrientData[2],
658 <                   atomOrientData[3],
659 <                   atomOrientData[4],
660 <                   atomOrientData[5],
661 <                   atomOrientData[6]);
662 <          strcat( writeLine, tempBuffer );
663 <
664 <        } else {
665 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
666 <        }
667 <
668 <        finalOut << writeLine;
669 <        finalOut.flush();
452 >        if(haveError) DieDieDie();
453 >        
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 +        
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.  
510 +
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 685 | Line 519 | void DumpWriter::writeFinal(double finalTime){
519        
520        if (AtomToProcMap[i] == worldRank) {
521  
522 <        local_index=-1;
523 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
524 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
522 >        if (myPotato + 3 >= MAXTAG) {
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 >          
528 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
529 >          
530          }
531 <        if (local_index != -1) {
531 >        which_atom = i;
532 >
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 +          
550 +          atomData6[0] = pos[0];
551 +          atomData6[1] = pos[1];
552 +          atomData6[2] = pos[2];
553  
554 <          atomTransData[0] = pos[0];
555 <          atomTransData[1] = pos[1];
556 <          atomTransData[2] = pos[2];
702 <
703 <          atomTransData[3] = vel[0];
704 <          atomTransData[4] = vel[1];
705 <          atomTransData[5] = vel[2];
554 >          atomData6[3] = vel[0];
555 >          atomData6[4] = vel[1];
556 >          atomData6[5] = vel[2];
557            
558            isDirectional = 0;
559  
# Line 713 | Line 564 | void DumpWriter::writeFinal(double finalTime){
564              dAtom = (DirectionalAtom *)atoms[local_index];
565              dAtom->getQ( q );
566              
567 <            atomOrientData[0] = q[0];
568 <            atomOrientData[1] = q[1];
569 <            atomOrientData[2] = q[2];
570 <            atomOrientData[3] = q[3];
571 <
572 <            atomOrientData[4] = dAtom->getJx();
573 <            atomOrientData[5] = dAtom->getJy();
574 <            atomOrientData[6] = dAtom->getJz();
567 >            for (int j = 0; j < 6 ; j++)
568 >              atomData13[j] = atomData6[j];
569 >            
570 >            atomData13[6] = q[0];
571 >            atomData13[7] = q[1];
572 >            atomData13[8] = q[2];
573 >            atomData13[9] = q[3];
574 >  
575 >            atomData13[10] = dAtom->getJx();
576 >            atomData13[11] = dAtom->getJy();
577 >            atomData13[12] = dAtom->getJz();
578            }
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 +        
588 +        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
589  
590 <        // I've survived this far, so send off the data!
590 >        // null terminate the string before sending (just in case):
591 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
592  
593 <        atomTypeTag          = 4*i;
594 <        atomIsDirectionalTag = 4*i + 1;
738 <        atomTransDataTag     = 4*i + 2;
739 <        atomOrientDataTag    = 4*i + 3;
740 <
741 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
742 <                 atomTypeTag, MPI_COMM_WORLD);
593 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
594 >                             myPotato, MPI_COMM_WORLD);
595          
596 +        myPotato++;
597 +
598          MPI_Send(&isDirectional, 1, MPI_INT, 0,
599 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
599 >                             myPotato, MPI_COMM_WORLD);
600          
601 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
602 <                 atomTransDataTag, MPI_COMM_WORLD);
749 <
601 >        myPotato++;
602 >        
603          if (isDirectional) {
604  
605 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
606 <                   atomOrientDataTag, MPI_COMM_WORLD);
605 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
606 >                   myPotato, MPI_COMM_WORLD);
607            
608 +        } else {
609 +
610 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
611 +                   myPotato, MPI_COMM_WORLD);
612          }
613 <      
613 >
614 >        myPotato++;  
615 >        currentIndex++;    
616        }
617      }
618  
619      sprintf( checkPointMsg,
620 <             "Sucessfully wrote final file.\n");
620 >             "Sucessfully took a dump.\n");
621      MPIcheckPoint();        
622      
623 <  }
623 >  }
624    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
625   #endif // is_mpi
626   }
627  
772 –
773 –
628   #ifdef IS_MPI
629  
630   // a couple of functions to let us escape the write loop

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