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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 951 by mmeineke, Fri Jan 16 21:51:51 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"
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] << ";";
115 <  //write out additional parameters, such as chi and eta
116 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
117 <  outFile << endl;
118 <
119 <  for( i=0; i<nAtoms; i++ ){
120 <
121 <    atoms[i]->getPos(pos);
122 <    atoms[i]->getVel(vel);
123 <
124 <    sprintf( tempBuffer,
125 <             "%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 );
134 <
135 <    if( atoms[i]->isDirectional() ){
136 <
137 <      dAtom = (DirectionalAtom *)atoms[i];
138 <      dAtom->getQ( q );
139 <
140 <      sprintf( tempBuffer,
141 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
142 <               q[0],
143 <               q[1],
144 <               q[2],
145 <               q[3],
146 <               dAtom->getJx(),
147 <               dAtom->getJy(),
148 <               dAtom->getJz());
149 <      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      }
151 –    else
152 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
153 –
154 –    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 <  // first thing first, suspend fatalities.
161 <  painCave.isEventLoop = 1;
131 >  writeFrame(fileStreams, currentTime);
132  
133 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
134 <  int haveError;
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137 > }
138  
139 <  MPI_Status istatus;
167 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
139 > void DumpWriter::writeFinal(double currentTime){
140  
169 –  // write out header and node 0's coordinates
170 –
171 –  if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
173 –
174 –    outFile << currentTime << ";\t"
175 –            << 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;
192 –
193 –      which_node = AtomToProcMap[i];
194 –
195 –      if (which_node != 0) {
196 –        
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];
141    ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143  
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;
144   #ifdef IS_MPI
421 –  int j, which_node, done, which_atom, local_index;
422 –  double atomTransData[6];
423 –  double atomOrientData[7];
424 –  int isDirectional;
425 –  char* atomTypeString;
426 –  int atomTypeTag;
427 –  int atomIsDirectionalTag;
428 –  int atomTransDataTag;
429 –  int atomOrientDataTag;
430 – #else //is_mpi
431 –  int nAtoms = entry_plug->n_atoms;
432 – #endif //is_mpi
433 –
434 –  double pos[3], vel[3];
435 –
436 – #ifdef IS_MPI
145    if(worldRank == 0 ){
146   #endif // is_mpi
147  
148 <    strcpy( finalName, entry_plug->finalName );
148 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149  
442 –    finalOut.open( finalName, ios::out | ios::trunc );
150      if( !finalOut ){
151        sprintf( painCave.errMsg,
152                 "Could not open \"%s\" for final dump output.\n",
153 <               finalName );
153 >               entry_plug->finalName );
154        painCave.isFatal = 1;
155        simError();
156      }
157  
451 –    // finalOut.setf( ios::scientific );
452 –
158   #ifdef IS_MPI
159    }
160 + #endif // is_mpi
161 +  
162 +  fileStreams.push_back(&finalOut);  
163 +  writeFrame(fileStreams, currentTime);
164  
165 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
166 <  MPIcheckPoint();
165 > #ifdef IS_MPI
166 >  finalOut.close();
167 > #endif
168 >  
169 > }
170  
171 < #endif //is_mpi
171 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172  
173 +  const int BUFFERSIZE = 2000;
174 +  const int MINIBUFFERSIZE = 100;
175  
176 < #ifndef IS_MPI
176 >  char tempBuffer[BUFFERSIZE];  
177 >  char writeLine[BUFFERSIZE];
178  
179 <  finalOut << nAtoms << "\n";
179 >  int i, k;
180  
181 <  finalOut << finalTime << ";\t"
182 <           << entry_plug->Hmat[0][0] << "\t"
183 <           << entry_plug->Hmat[1][0] << "\t"
184 <           << entry_plug->Hmat[2][0] << ";\t"
185 <
186 <           << entry_plug->Hmat[0][1] << "\t"
187 <           << entry_plug->Hmat[1][1] << "\t"
188 <           << entry_plug->Hmat[2][1] << ";\t"
189 <
190 <           << entry_plug->Hmat[0][2] << "\t"
191 <           << entry_plug->Hmat[1][2] << "\t"
192 <           << entry_plug->Hmat[2][2] << ";";
193 <
194 <  //write out additional parameters, such as chi and eta
195 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
196 <  finalOut << endl;
181 > #ifdef IS_MPI
182 >  
183 >  /*********************************************************************
184 >   * Documentation?  You want DOCUMENTATION?
185 >   *
186 >   * Why all the potatoes below?  
187 >   *
188 >   * To make a long story short, the original version of DumpWriter
189 >   * worked in the most inefficient way possible.  Node 0 would
190 >   * poke each of the node for an individual atom's formatted data
191 >   * as node 0 worked its way down the global index. This was particularly
192 >   * inefficient since the method blocked all processors at every atom
193 >   * (and did it twice!).
194 >   *
195 >   * An intermediate version of DumpWriter could be described from Node
196 >   * zero's perspective as follows:
197 >   *
198 >   *  1) Have 100 of your friends stand in a circle.
199 >   *  2) When you say go, have all of them start tossing potatoes at
200 >   *     you (one at a time).
201 >   *  3) Catch the potatoes.
202 >   *
203 >   * It was an improvement, but MPI has buffers and caches that could
204 >   * best be described in this analogy as "potato nets", so there's no
205 >   * need to block the processors atom-by-atom.
206 >   *
207 >   * This new and improved DumpWriter works in an even more efficient
208 >   * way:
209 >   *
210 >   *  1) Have 100 of your friend stand in a circle.
211 >   *  2) When you say go, have them start tossing 5-pound bags of
212 >   *     potatoes at you.
213 >   *  3) Once you've caught a friend's bag of potatoes,
214 >   *     toss them a spud to let them know they can toss another bag.
215 >   *
216 >   * How's THAT for documentation?
217 >   *
218 >   *********************************************************************/
219  
220 +  int *potatoes;
221 +  int myPotato;
222 +
223 +  int nProc;
224 +  int j, which_node, done, which_atom, local_index, currentIndex;
225 +  double atomData6[6];
226 +  double atomData13[13];
227 +  int isDirectional;
228 +  char* atomTypeString;
229 +  char MPIatomTypeString[MINIBUFFERSIZE];
230 +
231 + #else //is_mpi
232 +  int nAtoms = entry_plug->n_atoms;
233 + #endif //is_mpi
234 +
235 +  double q[4];
236 +  DirectionalAtom* dAtom;
237 +  Atom** atoms = entry_plug->atoms;
238 +  double pos[3], vel[3];
239 +
240 + #ifndef IS_MPI
241 +  
242 +  for(k = 0; k < outFile.size(); k++){
243 +    *outFile[k] << nAtoms << "\n";
244 +
245 +    *outFile[k] << currentTime << ";\t"
246 +               << entry_plug->Hmat[0][0] << "\t"
247 +                     << entry_plug->Hmat[1][0] << "\t"
248 +                     << entry_plug->Hmat[2][0] << ";\t"
249 +              
250 +               << entry_plug->Hmat[0][1] << "\t"
251 +                     << entry_plug->Hmat[1][1] << "\t"
252 +                     << entry_plug->Hmat[2][1] << ";\t"
253 +
254 +                     << entry_plug->Hmat[0][2] << "\t"
255 +                     << entry_plug->Hmat[1][2] << "\t"
256 +                     << entry_plug->Hmat[2][2] << ";";
257 +
258 +    //write out additional parameters, such as chi and eta
259 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
260 +  }
261 +  
262    for( i=0; i<nAtoms; i++ ){
263  
264      atoms[i]->getPos(pos);
# Line 515 | Line 294 | void DumpWriter::writeFinal(double finalTime){
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296  
297 <    finalOut << writeLine;
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
520 –  finalOut.flush();
521 –  finalOut.close();
300  
301   #else // is_mpi
302  
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  /* code to find maximum tag value */
304 >  
305 >  int *tagub, flag, MAXTAG;
306 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
307 >  if (flag) {
308 >    MAXTAG = *tagub;
309 >  } else {
310 >    MAXTAG = 32767;
311 >  }  
312  
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313    int haveError;
314  
315    MPI_Status istatus;
# Line 534 | Line 318 | void DumpWriter::writeFinal(double finalTime){
318    // write out header and node 0's coordinates
319  
320    if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\n";
321  
322 <    finalOut << finalTime << ";\t"
540 <            << entry_plug->Hmat[0][0] << "\t"
541 <            << entry_plug->Hmat[1][0] << "\t"
542 <            << entry_plug->Hmat[2][0] << ";\t"
322 >    // Node 0 needs a list of the magic potatoes for each processor;
323  
324 <            << entry_plug->Hmat[0][1] << "\t"
325 <            << entry_plug->Hmat[1][1] << "\t"
546 <            << entry_plug->Hmat[2][1] << ";\t"
324 >    nProc = mpiSim->getNumberProcessors();
325 >    potatoes = new int[nProc];
326  
327 <            << entry_plug->Hmat[0][2] << "\t"
328 <            << entry_plug->Hmat[1][2] << "\t"
329 <            << entry_plug->Hmat[2][2] << ";";
327 >    //write out the comment lines
328 >    for (i = 0; i < nProc; i++)
329 >      potatoes[i] = 0;
330 >    
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333  
334 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
335 <    finalOut << endl;
336 <    finalOut.flush();
334 >        *outFile[k] << currentTime << ";\t"
335 >                         << entry_plug->Hmat[0][0] << "\t"
336 >                         << entry_plug->Hmat[1][0] << "\t"
337 >                         << entry_plug->Hmat[2][0] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][1] << "\t"
340 >                         << entry_plug->Hmat[1][1] << "\t"
341 >                         << entry_plug->Hmat[2][1] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][2] << "\t"
344 >                         << entry_plug->Hmat[1][2] << "\t"
345 >                         << entry_plug->Hmat[2][2] << ";";
346 >  
347 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
348 >    }
349 >
350 >    currentIndex = 0;
351 >
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
353 +      
354        // Get the Node number which has this atom;
355 <
355 >      
356        which_node = AtomToProcMap[i];
357 <
357 >      
358        if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
359  
360 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
361 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
360 >        if (potatoes[which_node] + 3 >= MAXTAG) {
361 >          // The potato was going to exceed the maximum value,
362 >          // so wrap this processor potato back to 0:        
363 >
364 >          potatoes[which_node] = 0;          
365 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
366 >          
367 >        }
368 >
369 >        myPotato = potatoes[which_node];        
370          
371 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
372 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
371 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
372 >                 myPotato, MPI_COMM_WORLD, &istatus);
373          
374 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
375 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
374 >        atomTypeString = MPIatomTypeString;
375 >        
376 >        myPotato++;
377  
378 <        if (isDirectional) {
378 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
379 >                 myPotato, MPI_COMM_WORLD, &istatus);
380 >              
381 >        myPotato++;
382  
383 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
384 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
385 <
383 >        if (isDirectional) {          
384 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
385 >                   myPotato, MPI_COMM_WORLD, &istatus);
386 >        } else {
387 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
388 >                   myPotato, MPI_COMM_WORLD, &istatus);          
389          }
390 +        
391 +        myPotato++;
392 +        potatoes[which_node] = myPotato;
393  
394        } else {
395          
396 <        haveError = 0;
396 >        haveError = 0;
397          which_atom = i;
398 <        local_index=-1;
398 >        
399 >        //local_index = -1;
400  
401 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 <        }
404 <
405 <        if (local_index != -1) {
406 <
407 <          atomTypeString = atoms[local_index]->getType();
408 <
401 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 >        //}
404 >        
405 >        //if (local_index != -1) {
406 >          
407 >          local_index = indexArray[currentIndex].first;        
408 >          
409 >          if (which_atom == indexArray[currentIndex].second) {
410 >            
411 >            atomTypeString = atoms[local_index]->getType();
412 >            
413            atoms[local_index]->getPos(pos);
414 <          atoms[local_index]->getVel(vel);
414 >          atoms[local_index]->getVel(vel);          
415 >          
416 >          atomData6[0] = pos[0];
417 >          atomData6[1] = pos[1];
418 >          atomData6[2] = pos[2];
419  
420 <          atomTransData[0] = pos[0];
421 <          atomTransData[1] = pos[1];
422 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
420 >          atomData6[3] = vel[0];
421 >          atomData6[4] = vel[1];
422 >          atomData6[5] = vel[2];
423            
424            isDirectional = 0;
425  
# Line 613 | Line 429 | void DumpWriter::writeFinal(double finalTime){
429              
430              dAtom = (DirectionalAtom *)atoms[local_index];
431              dAtom->getQ( q );
616 –            
617 –            atomOrientData[0] = q[0];
618 –            atomOrientData[1] = q[1];
619 –            atomOrientData[2] = q[2];
620 –            atomOrientData[3] = q[3];
432  
433 <            atomOrientData[4] = dAtom->getJx();
434 <            atomOrientData[5] = dAtom->getJy();
435 <            atomOrientData[6] = dAtom->getJz();
433 >            for (int j = 0; j < 6 ; j++)
434 >              atomData13[j] = atomData6[j];            
435 >            
436 >            atomData13[6] = q[0];
437 >            atomData13[7] = q[1];
438 >            atomData13[8] = q[2];
439 >            atomData13[9] = q[3];
440 >            
441 >            atomData13[10] = dAtom->getJx();
442 >            atomData13[11] = dAtom->getJy();
443 >            atomData13[12] = dAtom->getJz();
444            }
445 <
445 >          
446          } else {
447            sprintf(painCave.errMsg,
448 <                  "Atom %d not found on processor %d\n",
449 <                  i, worldRank );
448 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
449 >                  which_atom, worldRank, currentIndex, local_index );
450            haveError= 1;
451            simError();
452          }
634 –
635 –        if(haveError) DieDieDie();
636 –                              
637 –        // If we've survived to here, format the line:
453          
454 <        sprintf( tempBuffer,
455 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
456 <                 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();
454 >        if(haveError) DieDieDie();
455 >        
456 >        currentIndex++;
457        }
458 +      // If we've survived to here, format the line:
459 +      
460 +      if (!isDirectional) {
461 +        
462 +        sprintf( writeLine,
463 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 +                 atomTypeString,
465 +                 atomData6[0],
466 +                 atomData6[1],
467 +                 atomData6[2],
468 +                 atomData6[3],
469 +                 atomData6[4],
470 +                 atomData6[5]);
471 +        
472 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 +        
474 +      } else {
475 +        
476 +        sprintf( writeLine,
477 +                 "%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",
478 +                 atomTypeString,
479 +                 atomData13[0],
480 +                 atomData13[1],
481 +                 atomData13[2],
482 +                 atomData13[3],
483 +                 atomData13[4],
484 +                 atomData13[5],
485 +                 atomData13[6],
486 +                 atomData13[7],
487 +                 atomData13[8],
488 +                 atomData13[9],
489 +                 atomData13[10],
490 +                 atomData13[11],
491 +                 atomData13[12]);
492 +        
493 +      }
494 +      
495 +      for(k = 0; k < outFile.size(); k++)
496 +        *outFile[k] << writeLine;
497      }
498 <
499 <    finalOut.flush();
498 >    
499 >    for(k = 0; k < outFile.size(); k++)
500 >      outFile[k]->flush();
501 >    
502      sprintf( checkPointMsg,
503               "Sucessfully took a dump.\n");
504 +    
505      MPIcheckPoint();        
506      
507 +    delete[] potatoes;
508 +    
509    } else {
510  
511      // worldRank != 0, so I'm a remote node.  
512 +
513 +    // Set my magic potato to 0:
514 +
515 +    myPotato = 0;
516 +    currentIndex = 0;
517      
518      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
519        
# Line 685 | Line 521 | void DumpWriter::writeFinal(double finalTime){
521        
522        if (AtomToProcMap[i] == worldRank) {
523  
524 <        local_index=-1;
525 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
526 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
524 >        if (myPotato + 3 >= MAXTAG) {
525 >          
526 >          // The potato was going to exceed the maximum value,
527 >          // so wrap this processor potato back to 0 (and block until
528 >          // node 0 says we can go:
529 >          
530 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531 >          
532          }
533 <        if (local_index != -1) {
533 >        which_atom = i;
534 >
535 >        //local_index = -1;
536 >
537 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
538 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
539 >        //}
540 >        
541 >        //if (local_index != -1) {
542 >
543 >        local_index = indexArray[currentIndex].first;        
544 >                
545 >        if (which_atom == indexArray[currentIndex].second) {
546          
547            atomTypeString = atoms[local_index]->getType();
548 <
548 >          
549            atoms[local_index]->getPos(pos);
550            atoms[local_index]->getVel(vel);
551 +          
552 +          atomData6[0] = pos[0];
553 +          atomData6[1] = pos[1];
554 +          atomData6[2] = pos[2];
555  
556 <          atomTransData[0] = pos[0];
557 <          atomTransData[1] = pos[1];
558 <          atomTransData[2] = pos[2];
702 <
703 <          atomTransData[3] = vel[0];
704 <          atomTransData[4] = vel[1];
705 <          atomTransData[5] = vel[2];
556 >          atomData6[3] = vel[0];
557 >          atomData6[4] = vel[1];
558 >          atomData6[5] = vel[2];
559            
560            isDirectional = 0;
561  
# Line 713 | Line 566 | void DumpWriter::writeFinal(double finalTime){
566              dAtom = (DirectionalAtom *)atoms[local_index];
567              dAtom->getQ( q );
568              
569 <            atomOrientData[0] = q[0];
570 <            atomOrientData[1] = q[1];
571 <            atomOrientData[2] = q[2];
572 <            atomOrientData[3] = q[3];
573 <
574 <            atomOrientData[4] = dAtom->getJx();
575 <            atomOrientData[5] = dAtom->getJy();
576 <            atomOrientData[6] = dAtom->getJz();
569 >            for (int j = 0; j < 6 ; j++)
570 >              atomData13[j] = atomData6[j];
571 >            
572 >            atomData13[6] = q[0];
573 >            atomData13[7] = q[1];
574 >            atomData13[8] = q[2];
575 >            atomData13[9] = q[3];
576 >  
577 >            atomData13[10] = dAtom->getJx();
578 >            atomData13[11] = dAtom->getJy();
579 >            atomData13[12] = dAtom->getJz();
580            }
581  
582          } else {
583            sprintf(painCave.errMsg,
584 <                  "Atom %d not found on processor %d\n",
585 <                  i, worldRank );
584 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
585 >                  which_atom, worldRank, currentIndex, local_index );
586            haveError= 1;
587            simError();
588          }
589 +        
590 +        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591  
592 <        // I've survived this far, so send off the data!
592 >        // null terminate the string before sending (just in case):
593 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
594  
595 <        atomTypeTag          = 4*i;
596 <        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);
595 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
596 >                             myPotato, MPI_COMM_WORLD);
597          
598 +        myPotato++;
599 +
600          MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
601 >                             myPotato, MPI_COMM_WORLD);
602          
603 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
604 <                 atomTransDataTag, MPI_COMM_WORLD);
749 <
603 >        myPotato++;
604 >        
605          if (isDirectional) {
606  
607 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
608 <                   atomOrientDataTag, MPI_COMM_WORLD);
607 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
608 >                   myPotato, MPI_COMM_WORLD);
609            
610 +        } else {
611 +
612 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
613 +                   myPotato, MPI_COMM_WORLD);
614          }
615 <      
615 >
616 >        myPotato++;  
617 >        currentIndex++;    
618        }
619      }
620  
621      sprintf( checkPointMsg,
622 <             "Sucessfully wrote final file.\n");
622 >             "Sucessfully took a dump.\n");
623      MPIcheckPoint();        
624      
625 <  }
625 >  }
626    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
627   #endif // is_mpi
628   }
629  
772 –
773 –
630   #ifdef IS_MPI
631  
632   // a couple of functions to let us escape the write loop

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