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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 1000 by tim, Fri Jan 30 21:47:22 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  
100 <  // write current frame to the eor file
100 > #endif
101  
102 <  this->writeFinal( currentTime );
102 > void DumpWriter::writeDump(double currentTime){
103  
104 < #ifndef IS_MPI
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <  outFile << nAtoms << "\n";
108 <
109 <  outFile << currentTime << ";\t"
110 <          << entry_plug->Hmat[0][0] << "\t"
111 <          << entry_plug->Hmat[1][0] << "\t"
112 <          << entry_plug->Hmat[2][0] << ";\t"
113 <
114 <          << entry_plug->Hmat[0][1] << "\t"
115 <          << entry_plug->Hmat[1][1] << "\t"
116 <          << entry_plug->Hmat[2][1] << ";\t"
111 <
112 <          << 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;
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 );
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 > #endif    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117      }
118 <    else
152 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
153 <
154 <    outFile << writeLine;
118 > #ifdef IS_MPI
119    }
120 <  outFile.flush();
120 > #endif // is_mpi
121  
122 < #else // is_mpi
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  // first thing first, suspend fatalities.
161 <  painCave.isEventLoop = 1;
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
128 <  int haveError;
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  MPI_Status istatus;
167 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
133 > void DumpWriter::writeFinal(double currentTime){
134  
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];
135    ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137  
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;
138   #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
139    if(worldRank == 0 ){
140   #endif // is_mpi
141  
142 <    strcpy( finalName, entry_plug->finalName );
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
442 –    finalOut.open( finalName, ios::out | ios::trunc );
144      if( !finalOut ){
145        sprintf( painCave.errMsg,
146                 "Could not open \"%s\" for final dump output.\n",
147 <               finalName );
147 >               entry_plug->finalName );
148        painCave.isFatal = 1;
149        simError();
150      }
151  
451 –    // finalOut.setf( ios::scientific );
452 –
152   #ifdef IS_MPI
153    }
154 + #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158  
159 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
160 <  MPIcheckPoint();
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 < #endif //is_mpi
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167 +  const int BUFFERSIZE = 2000;
168 +  const int MINIBUFFERSIZE = 100;
169  
170 < #ifndef IS_MPI
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172  
173 <  finalOut << nAtoms << "\n";
173 >  int i, k;
174  
175 <  finalOut << finalTime << ";\t"
176 <           << entry_plug->Hmat[0][0] << "\t"
177 <           << entry_plug->Hmat[1][0] << "\t"
178 <           << entry_plug->Hmat[2][0] << ";\t"
179 <
180 <           << entry_plug->Hmat[0][1] << "\t"
181 <           << entry_plug->Hmat[1][1] << "\t"
182 <           << entry_plug->Hmat[2][1] << ";\t"
183 <
184 <           << entry_plug->Hmat[0][2] << "\t"
185 <           << entry_plug->Hmat[1][2] << "\t"
186 <           << entry_plug->Hmat[2][2] << ";";
187 <
188 <  //write out additional parameters, such as chi and eta
189 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
190 <  finalOut << endl;
175 > #ifdef IS_MPI
176 >  
177 >  /*********************************************************************
178 >   * Documentation?  You want DOCUMENTATION?
179 >   *
180 >   * Why all the potatoes below?  
181 >   *
182 >   * To make a long story short, the original version of DumpWriter
183 >   * worked in the most inefficient way possible.  Node 0 would
184 >   * poke each of the node for an individual atom's formatted data
185 >   * as node 0 worked its way down the global index. This was particularly
186 >   * inefficient since the method blocked all processors at every atom
187 >   * (and did it twice!).
188 >   *
189 >   * An intermediate version of DumpWriter could be described from Node
190 >   * zero's perspective as follows:
191 >   *
192 >   *  1) Have 100 of your friends stand in a circle.
193 >   *  2) When you say go, have all of them start tossing potatoes at
194 >   *     you (one at a time).
195 >   *  3) Catch the potatoes.
196 >   *
197 >   * It was an improvement, but MPI has buffers and caches that could
198 >   * best be described in this analogy as "potato nets", so there's no
199 >   * need to block the processors atom-by-atom.
200 >   *
201 >   * This new and improved DumpWriter works in an even more efficient
202 >   * way:
203 >   *
204 >   *  1) Have 100 of your friend stand in a circle.
205 >   *  2) When you say go, have them start tossing 5-pound bags of
206 >   *     potatoes at you.
207 >   *  3) Once you've caught a friend's bag of potatoes,
208 >   *     toss them a spud to let them know they can toss another bag.
209 >   *
210 >   * How's THAT for documentation?
211 >   *
212 >   *********************************************************************/
213  
214 +  int *potatoes;
215 +  int myPotato;
216 +
217 +  int nProc;
218 +  int j, which_node, done, which_atom, local_index, currentIndex;
219 +  double atomData6[6];
220 +  double atomData13[13];
221 +  int isDirectional;
222 +  char* atomTypeString;
223 +  char MPIatomTypeString[MINIBUFFERSIZE];
224 +
225 + #else //is_mpi
226 +  int nAtoms = entry_plug->n_atoms;
227 + #endif //is_mpi
228 +
229 +  double q[4];
230 +  DirectionalAtom* dAtom;
231 +  Atom** atoms = entry_plug->atoms;
232 +  double pos[3], vel[3];
233 +
234 + #ifndef IS_MPI
235 +  
236 +  for(k = 0; k < outFile.size(); k++){
237 +    *outFile[k] << nAtoms << "\n";
238 +
239 +    *outFile[k] << currentTime << ";\t"
240 +               << entry_plug->Hmat[0][0] << "\t"
241 +                     << entry_plug->Hmat[1][0] << "\t"
242 +                     << entry_plug->Hmat[2][0] << ";\t"
243 +              
244 +               << entry_plug->Hmat[0][1] << "\t"
245 +                     << entry_plug->Hmat[1][1] << "\t"
246 +                     << entry_plug->Hmat[2][1] << ";\t"
247 +
248 +                     << entry_plug->Hmat[0][2] << "\t"
249 +                     << entry_plug->Hmat[1][2] << "\t"
250 +                     << entry_plug->Hmat[2][2] << ";";
251 +
252 +    //write out additional parameters, such as chi and eta
253 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 +  }
255 +  
256    for( i=0; i<nAtoms; i++ ){
257  
258      atoms[i]->getPos(pos);
# Line 515 | Line 288 | void DumpWriter::writeFinal(double finalTime){
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290  
291 <    finalOut << writeLine;
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
520 –  finalOut.flush();
521 –  finalOut.close();
294  
295   #else // is_mpi
296  
297 <  // first thing first, suspend fatalities.
298 <  painCave.isEventLoop = 1;
297 >  /* code to find maximum tag value */
298 >  
299 >  int *tagub, flag, MAXTAG;
300 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301 >  if (flag) {
302 >    MAXTAG = *tagub;
303 >  } else {
304 >    MAXTAG = 32767;
305 >  }  
306  
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
307    int haveError;
308  
309    MPI_Status istatus;
# Line 534 | Line 312 | void DumpWriter::writeFinal(double finalTime){
312    // write out header and node 0's coordinates
313  
314    if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\n";
315  
316 <    finalOut << finalTime << ";\t"
540 <            << entry_plug->Hmat[0][0] << "\t"
541 <            << entry_plug->Hmat[1][0] << "\t"
542 <            << entry_plug->Hmat[2][0] << ";\t"
316 >    // Node 0 needs a list of the magic potatoes for each processor;
317  
318 <            << entry_plug->Hmat[0][1] << "\t"
319 <            << entry_plug->Hmat[1][1] << "\t"
546 <            << entry_plug->Hmat[2][1] << ";\t"
318 >    nProc = mpiSim->getNumberProcessors();
319 >    potatoes = new int[nProc];
320  
321 <            << entry_plug->Hmat[0][2] << "\t"
322 <            << entry_plug->Hmat[1][2] << "\t"
323 <            << entry_plug->Hmat[2][2] << ";";
321 >    //write out the comment lines
322 >    for (i = 0; i < nProc; i++)
323 >      potatoes[i] = 0;
324 >    
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327  
328 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
329 <    finalOut << endl;
330 <    finalOut.flush();
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332 >
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343 >
344 >    currentIndex = 0;
345 >
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
347 +      
348        // Get the Node number which has this atom;
349 <
349 >      
350        which_node = AtomToProcMap[i];
351 <
351 >      
352        if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
353  
354 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
355 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
354 >        if (potatoes[which_node] + 3 >= MAXTAG) {
355 >          // The potato was going to exceed the maximum value,
356 >          // so wrap this processor potato back to 0:        
357 >
358 >          potatoes[which_node] = 0;          
359 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
360 >          
361 >        }
362 >
363 >        myPotato = potatoes[which_node];        
364          
365 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
366 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
365 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366 >                 myPotato, MPI_COMM_WORLD, &istatus);
367          
368 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
369 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
368 >        atomTypeString = MPIatomTypeString;
369 >        
370 >        myPotato++;
371  
372 <        if (isDirectional) {
372 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
373 >                 myPotato, MPI_COMM_WORLD, &istatus);
374 >              
375 >        myPotato++;
376  
377 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
378 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
379 <
377 >        if (isDirectional) {          
378 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);
380 >        } else {
381 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
382 >                   myPotato, MPI_COMM_WORLD, &istatus);          
383          }
384 +        
385 +        myPotato++;
386 +        potatoes[which_node] = myPotato;
387  
388        } else {
389          
390 <        haveError = 0;
390 >        haveError = 0;
391          which_atom = i;
392 <        local_index=-1;
393 <
394 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
395 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
396 <        }
397 <
398 <        if (local_index != -1) {
594 <
595 <          atomTypeString = atoms[local_index]->getType();
596 <
392 >        
393 >          local_index = indexArray[currentIndex].first;        
394 >          
395 >          if (which_atom == indexArray[currentIndex].second) {
396 >            
397 >            atomTypeString = atoms[local_index]->getType();
398 >            
399            atoms[local_index]->getPos(pos);
400 <          atoms[local_index]->getVel(vel);
400 >          atoms[local_index]->getVel(vel);          
401 >          
402 >          atomData6[0] = pos[0];
403 >          atomData6[1] = pos[1];
404 >          atomData6[2] = pos[2];
405  
406 <          atomTransData[0] = pos[0];
407 <          atomTransData[1] = pos[1];
408 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
406 >          atomData6[3] = vel[0];
407 >          atomData6[4] = vel[1];
408 >          atomData6[5] = vel[2];
409            
410            isDirectional = 0;
411  
# Line 613 | Line 415 | void DumpWriter::writeFinal(double finalTime){
415              
416              dAtom = (DirectionalAtom *)atoms[local_index];
417              dAtom->getQ( q );
418 +
419 +            for (int j = 0; j < 6 ; j++)
420 +              atomData13[j] = atomData6[j];            
421              
422 <            atomOrientData[0] = q[0];
423 <            atomOrientData[1] = q[1];
424 <            atomOrientData[2] = q[2];
425 <            atomOrientData[3] = q[3];
426 <
427 <            atomOrientData[4] = dAtom->getJx();
428 <            atomOrientData[5] = dAtom->getJy();
429 <            atomOrientData[6] = dAtom->getJz();
422 >            atomData13[6] = q[0];
423 >            atomData13[7] = q[1];
424 >            atomData13[8] = q[2];
425 >            atomData13[9] = q[3];
426 >            
427 >            atomData13[10] = dAtom->getJx();
428 >            atomData13[11] = dAtom->getJy();
429 >            atomData13[12] = dAtom->getJz();
430            }
431 <
431 >          
432          } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438          }
634 –
635 –        if(haveError) DieDieDie();
636 –                              
637 –        // If we've survived to here, format the line:
439          
440 <        sprintf( tempBuffer,
441 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
442 <                 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();
440 >        if(haveError) DieDieDie();
441 >        
442 >        currentIndex++;
443        }
444 +      // If we've survived to here, format the line:
445 +      
446 +      if (!isDirectional) {
447 +        
448 +        sprintf( writeLine,
449 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 +                 atomTypeString,
451 +                 atomData6[0],
452 +                 atomData6[1],
453 +                 atomData6[2],
454 +                 atomData6[3],
455 +                 atomData6[4],
456 +                 atomData6[5]);
457 +        
458 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 +        
460 +      } else {
461 +        
462 +        sprintf( writeLine,
463 +                 "%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",
464 +                 atomTypeString,
465 +                 atomData13[0],
466 +                 atomData13[1],
467 +                 atomData13[2],
468 +                 atomData13[3],
469 +                 atomData13[4],
470 +                 atomData13[5],
471 +                 atomData13[6],
472 +                 atomData13[7],
473 +                 atomData13[8],
474 +                 atomData13[9],
475 +                 atomData13[10],
476 +                 atomData13[11],
477 +                 atomData13[12]);
478 +        
479 +      }
480 +      
481 +      for(k = 0; k < outFile.size(); k++)
482 +        *outFile[k] << writeLine;
483      }
484 <
485 <    finalOut.flush();
484 >    
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487 >    
488      sprintf( checkPointMsg,
489               "Sucessfully took a dump.\n");
490 +    
491      MPIcheckPoint();        
492      
493 +    delete[] potatoes;
494 +    
495    } else {
496  
497      // worldRank != 0, so I'm a remote node.  
498 +
499 +    // Set my magic potato to 0:
500 +
501 +    myPotato = 0;
502 +    currentIndex = 0;
503      
504      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
505        
# Line 685 | Line 507 | void DumpWriter::writeFinal(double finalTime){
507        
508        if (AtomToProcMap[i] == worldRank) {
509  
510 <        local_index=-1;
511 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
512 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
510 >        if (myPotato + 3 >= MAXTAG) {
511 >          
512 >          // The potato was going to exceed the maximum value,
513 >          // so wrap this processor potato back to 0 (and block until
514 >          // node 0 says we can go:
515 >          
516 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517 >          
518          }
519 <        if (local_index != -1) {
519 >        which_atom = i;
520 >
521 >        local_index = indexArray[currentIndex].first;        
522 >                
523 >        if (which_atom == indexArray[currentIndex].second) {
524          
525            atomTypeString = atoms[local_index]->getType();
526 <
526 >          
527            atoms[local_index]->getPos(pos);
528            atoms[local_index]->getVel(vel);
529 +          
530 +          atomData6[0] = pos[0];
531 +          atomData6[1] = pos[1];
532 +          atomData6[2] = pos[2];
533  
534 <          atomTransData[0] = pos[0];
535 <          atomTransData[1] = pos[1];
536 <          atomTransData[2] = pos[2];
702 <
703 <          atomTransData[3] = vel[0];
704 <          atomTransData[4] = vel[1];
705 <          atomTransData[5] = vel[2];
534 >          atomData6[3] = vel[0];
535 >          atomData6[4] = vel[1];
536 >          atomData6[5] = vel[2];
537            
538            isDirectional = 0;
539  
# Line 713 | Line 544 | void DumpWriter::writeFinal(double finalTime){
544              dAtom = (DirectionalAtom *)atoms[local_index];
545              dAtom->getQ( q );
546              
547 <            atomOrientData[0] = q[0];
548 <            atomOrientData[1] = q[1];
549 <            atomOrientData[2] = q[2];
550 <            atomOrientData[3] = q[3];
551 <
552 <            atomOrientData[4] = dAtom->getJx();
553 <            atomOrientData[5] = dAtom->getJy();
554 <            atomOrientData[6] = dAtom->getJz();
547 >            for (int j = 0; j < 6 ; j++)
548 >              atomData13[j] = atomData6[j];
549 >            
550 >            atomData13[6] = q[0];
551 >            atomData13[7] = q[1];
552 >            atomData13[8] = q[2];
553 >            atomData13[9] = q[3];
554 >  
555 >            atomData13[10] = dAtom->getJx();
556 >            atomData13[11] = dAtom->getJy();
557 >            atomData13[12] = dAtom->getJz();
558            }
559  
560          } else {
561            sprintf(painCave.errMsg,
562 <                  "Atom %d not found on processor %d\n",
563 <                  i, worldRank );
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564            haveError= 1;
565            simError();
566          }
567 +        
568 +        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570 <        // I've survived this far, so send off the data!
570 >        // null terminate the string before sending (just in case):
571 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572  
573 <        atomTypeTag          = 4*i;
574 <        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);
573 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 >                             myPotato, MPI_COMM_WORLD);
575          
576 +        myPotato++;
577 +
578          MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
579 >                             myPotato, MPI_COMM_WORLD);
580          
581 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
582 <                 atomTransDataTag, MPI_COMM_WORLD);
749 <
581 >        myPotato++;
582 >        
583          if (isDirectional) {
584  
585 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
586 <                   atomOrientDataTag, MPI_COMM_WORLD);
585 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
586 >                   myPotato, MPI_COMM_WORLD);
587            
588 +        } else {
589 +
590 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
591 +                   myPotato, MPI_COMM_WORLD);
592          }
593 <      
593 >
594 >        myPotato++;  
595 >        currentIndex++;    
596        }
597      }
598  
599      sprintf( checkPointMsg,
600 <             "Sucessfully wrote final file.\n");
600 >             "Sucessfully took a dump.\n");
601      MPIcheckPoint();        
602      
603 <  }
603 >  }
604    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
605   #endif // is_mpi
606   }
607  
772 –
773 –
608   #ifdef IS_MPI
609  
610   // a couple of functions to let us escape the write loop

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