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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
# Line 28 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
31 –
32      dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34      if( !dumpFile ){
# Line 40 | Line 40 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
40        simError();
41      }
42  
43 –    //outFile.setf( ios::scientific );
44 –
43   #ifdef IS_MPI
44    }
45  
# Line 90 | Line 88 | void DumpWriter::sortByGlobalIndex(){
88   */
89  
90   void DumpWriter::sortByGlobalIndex(){
91 <  Atom** atoms = entry_plug->atoms;
94 <  
91 >  Molecule* mols = entry_plug->molecules;  
92    indexArray.clear();
93    
94 <  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 <    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
94 >  for(int i = 0; i < entry_plug->n_mol;i++)
95 >    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96    
97    sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98   }
99 +
100   #endif
101  
102   void DumpWriter::writeDump(double currentTime){
105 –  
106 – // write to eor file
107 –  writeFinal(currentTime);
103  
104 < //write to dump file
105 <  writeFrame(dumpFile, currentTime);
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106 >
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 > #ifdef IS_MPI
119 >  }
120 > #endif // is_mpi
121 >
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124 >
125 >  writeFrame(fileStreams, currentTime);
126 >
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130          
131   }
132  
133   void DumpWriter::writeFinal(double currentTime){
134  
135 <  ofstream finalOut;    
136 <  
137 <  //Open eor file
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137 >
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141  
142      finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 +
144      if( !finalOut ){
145        sprintf( painCave.errMsg,
146                 "Could not open \"%s\" for final dump output.\n",
# Line 128 | Line 148 | void DumpWriter::writeFinal(double currentTime){
148        painCave.isFatal = 1;
149        simError();
150      }
151 <    
151 >
152   #ifdef IS_MPI
153    }
134 – #endif
135 –  
136 –  //write to eor file  
137 –  writeFrame(finalOut, currentTime);
138 –  
139 –  //close eor file      
140 – #ifdef IS_MPI
141 –  if(worldRank == 0 ){
142 –    finalOut.close();
143 –  }
154   #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158  
159 + #ifdef IS_MPI
160 +  finalOut.close();
161 + #endif
162 +  
163   }
164  
165 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167    const int BUFFERSIZE = 2000;
168    const int MINIBUFFERSIZE = 100;
169  
170 <  char tempBuffer[BUFFERSIZE];
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  int i;
173 >  int i, k;
174  
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  
# Line 167 | Line 221 | void DumpWriter::writeFrame( ofstream& outFile, double
221    int isDirectional;
222    char* atomTypeString;
223    char MPIatomTypeString[MINIBUFFERSIZE];
224 <
171 < #else //is_mpi
172 <  int nAtoms = entry_plug->n_atoms;
224 >  int nObjects;
225   #endif //is_mpi
226  
227 <  double q[4];
227 >  double q[4], ji[3];
228    DirectionalAtom* dAtom;
177 –  Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230 <
230 >  int nTotObjects;
231 >  StuntDouble* sd;
232 >  char* molName;
233 >  vector<StuntDouble*> integrableObjects;
234 >  vector<StuntDouble*>::iterator iter;
235 >  nTotObjects = entry_plug->getTotIntegrableObjects();
236   #ifndef IS_MPI
237 +  
238 +  for(k = 0; k < outFile.size(); k++){
239 +    *outFile[k] << nTotObjects << "\n";
240  
241 <  outFile << nAtoms << "\n";
241 >    *outFile[k] << currentTime << ";\t"
242 >               << entry_plug->Hmat[0][0] << "\t"
243 >                     << entry_plug->Hmat[1][0] << "\t"
244 >                     << entry_plug->Hmat[2][0] << ";\t"
245 >              
246 >               << entry_plug->Hmat[0][1] << "\t"
247 >                     << entry_plug->Hmat[1][1] << "\t"
248 >                     << entry_plug->Hmat[2][1] << ";\t"
249  
250 <  outFile << currentTime << ";\t"
251 <          << entry_plug->Hmat[0][0] << "\t"
252 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << entry_plug->Hmat[2][0] << ";\t"
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253  
254 <          << entry_plug->Hmat[0][1] << "\t"
255 <          << entry_plug->Hmat[1][1] << "\t"
256 <          << entry_plug->Hmat[2][1] << ";\t"
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 >  }
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259  
260 <          << entry_plug->Hmat[0][2] << "\t"
261 <          << entry_plug->Hmat[1][2] << "\t"
262 <          << entry_plug->Hmat[2][2] << ";";
263 <  //write out additional parameters, such as chi and eta
264 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
265 <  outFile << endl;
260 >    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 >    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262 >    
263 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 >      sd = *iter;
265 >      sd->getPos(pos);
266 >      sd->getVel(vel);
267  
268 <  for( i=0; i<nAtoms; i++ ){
268 >      sprintf( tempBuffer,
269 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 >             sd->getType(),
271 >             pos[0],
272 >             pos[1],
273 >             pos[2],
274 >             vel[0],
275 >             vel[1],
276 >             vel[2]);
277 >      strcpy( writeLine, tempBuffer );
278  
279 <    atoms[i]->getPos(pos);
203 <    atoms[i]->getVel(vel);
279 >      if( sd->isDirectional() ){
280  
281 <    sprintf( tempBuffer,
282 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
207 <             atoms[i]->getType(),
208 <             pos[0],
209 <             pos[1],
210 <             pos[2],
211 <             vel[0],
212 <             vel[1],
213 <             vel[2]);
214 <    strcpy( writeLine, tempBuffer );
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283  
284 <    if( atoms[i]->isDirectional() ){
285 <
286 <      dAtom = (DirectionalAtom *)atoms[i];
287 <      dAtom->getQ( q );
288 <
289 <      sprintf( tempBuffer,
290 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
291 <               q[0],
292 <               q[1],
293 <               q[2],
294 <               q[3],
295 <               dAtom->getJx(),
296 <               dAtom->getJy(),
229 <               dAtom->getJz());
230 <      strcat( writeLine, tempBuffer );
284 >        sprintf( tempBuffer,
285 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 >               q[0],
287 >               q[1],
288 >               q[2],
289 >               q[3],
290 >                 ji[0],
291 >                 ji[1],
292 >                 ji[2]);
293 >        strcat( writeLine, tempBuffer );
294 >      }
295 >      else
296 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297      }
232 –    else
233 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298  
299 <    outFile << writeLine;
300 <  }
299 >    
300 >    for(k = 0; k < outFile.size(); k++)
301 >      *outFile[k] << writeLine;
302 > }
303  
304   #else // is_mpi
305  
# Line 250 | Line 316 | void DumpWriter::writeFrame( ofstream& outFile, double
316    int haveError;
317  
318    MPI_Status istatus;
319 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321  
322    // write out header and node 0's coordinates
323  
# Line 261 | Line 328 | void DumpWriter::writeFrame( ofstream& outFile, double
328      nProc = mpiSim->getNumberProcessors();
329      potatoes = new int[nProc];
330  
331 +    //write out the comment lines
332      for (i = 0; i < nProc; i++)
333        potatoes[i] = 0;
334      
335 <    outFile << mpiSim->getTotAtoms() << "\n";
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <    outFile << currentTime << ";\t"
339 <            << entry_plug->Hmat[0][0] << "\t"
340 <            << entry_plug->Hmat[1][0] << "\t"
341 <            << entry_plug->Hmat[2][0] << ";\t"
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342  
343 <            << entry_plug->Hmat[0][1] << "\t"
344 <            << entry_plug->Hmat[1][1] << "\t"
345 <            << entry_plug->Hmat[2][1] << ";\t"
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <            << entry_plug->Hmat[0][2] << "\t"
348 <            << entry_plug->Hmat[1][2] << "\t"
349 <            << entry_plug->Hmat[2][2] << ";";
347 >                         << entry_plug->Hmat[0][2] << "\t"
348 >                         << entry_plug->Hmat[1][2] << "\t"
349 >                         << entry_plug->Hmat[2][2] << ";";
350 >  
351 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352 >    }
353  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
354      currentIndex = 0;
355 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
355 >
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357        
358        // Get the Node number which has this atom;
359        
360 <      which_node = AtomToProcMap[i];
360 >      which_node = MolToProcMap[i];
361        
362        if (which_node != 0) {
363 <
364 <        if (potatoes[which_node] + 3 >= MAXTAG) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365            // The potato was going to exceed the maximum value,
366            // so wrap this processor potato back to 0:        
367  
368            potatoes[which_node] = 0;          
369 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370            
371          }
372  
373          myPotato = potatoes[which_node];        
374 <        
375 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
374 >
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377                   myPotato, MPI_COMM_WORLD, &istatus);
308 –        
309 –        atomTypeString = MPIatomTypeString;
310 –        
378          myPotato++;
379 +        
380 +        for(int l = 0; l < nCurObj; l++){
381  
382 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
383 <                 myPotato, MPI_COMM_WORLD, &istatus);
382 >          if (potatoes[which_node] + 3 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385 >
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390 >
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393 >
394 >          atomTypeString = MPIatomTypeString;
395 >
396 >          myPotato++;
397 >
398 >          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
399 >          myPotato, MPI_COMM_WORLD, &istatus);
400                
401 <        myPotato++;
401 >          myPotato++;
402  
403 <        if (isDirectional) {          
403 >          if (isDirectional) {          
404            MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
405                     myPotato, MPI_COMM_WORLD, &istatus);
406 <        } else {
406 >          } else {
407            MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
408                     myPotato, MPI_COMM_WORLD, &istatus);          
409 +          }
410 +
411 +          myPotato++;
412          }
325 –        
326 –        myPotato++;
413          potatoes[which_node] = myPotato;
414  
415        } else {
416          
417 <        haveError = 0;
332 <        which_atom = i;
417 >        haveError = 0;
418          
419 <        local_index = indexArray[currentIndex].first;        
335 <                
336 <        if (which_atom == indexArray[currentIndex].second) {
337 <          
338 <          atomTypeString = atoms[local_index]->getType();
419 >            local_index = indexArray[currentIndex].first;        
420  
421 <          atoms[local_index]->getPos(pos);
341 <          atoms[local_index]->getVel(vel);          
421 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
422  
423 <          atomData6[0] = pos[0];
424 <          atomData6[1] = pos[1];
425 <          atomData6[2] = pos[2];
423 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
424 >                sd = *iter;
425 >            atomTypeString = sd->getType();
426 >            
427 >            sd->getPos(pos);
428 >            sd->getVel(vel);          
429 >          
430 >            atomData6[0] = pos[0];
431 >            atomData6[1] = pos[1];
432 >            atomData6[2] = pos[2];
433  
434 <          atomData6[3] = vel[0];
435 <          atomData6[4] = vel[1];
436 <          atomData6[5] = vel[2];
437 <          
438 <          isDirectional = 0;
434 >            atomData6[3] = vel[0];
435 >            atomData6[4] = vel[1];
436 >            atomData6[5] = vel[2];
437 >              
438 >            isDirectional = 0;
439  
440 <          if( atoms[local_index]->isDirectional() ){
440 >            if( sd->isDirectional() ){
441  
442 <            isDirectional = 1;
443 <            
444 <            dAtom = (DirectionalAtom *)atoms[local_index];
445 <            dAtom->getQ( q );
442 >              isDirectional = 1;
443 >                
444 >              sd->getQ( q );
445 >              sd->getJ( ji );
446  
447 <            for (int j = 0; j < 6 ; j++)
448 <              atomData13[j] = atomData6[j];            
447 >              for (int j = 0; j < 6 ; j++)
448 >                atomData13[j] = atomData6[j];            
449 >              
450 >              atomData13[6] = q[0];
451 >              atomData13[7] = q[1];
452 >              atomData13[8] = q[2];
453 >              atomData13[9] = q[3];
454 >              
455 >              atomData13[10] = ji[0];
456 >              atomData13[11] = ji[1];
457 >              atomData13[12] = ji[2];
458 >            }
459              
460 <            atomData13[6] = q[0];
364 <            atomData13[7] = q[1];
365 <            atomData13[8] = q[2];
366 <            atomData13[9] = q[3];
367 <            
368 <            atomData13[10] = dAtom->getJx();
369 <            atomData13[11] = dAtom->getJy();
370 <            atomData13[12] = dAtom->getJz();
371 <          }
372 <          
373 <        } else {
374 <          sprintf(painCave.errMsg,
375 <                  "Atom %d not found on processor %d\n",
376 <                  i, worldRank );
377 <          haveError= 1;
378 <          simError();
379 <        }
460 >        }
461          
462 <        if(haveError) DieDieDie();
382 <        
383 <        currentIndex ++;
462 >      currentIndex++;
463        }
464        // If we've survived to here, format the line:
465        
466        if (!isDirectional) {
467          
468 <        sprintf( writeLine,
468 >        sprintf( writeLine,
469                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
470                   atomTypeString,
471                   atomData6[0],
# Line 395 | Line 474 | void DumpWriter::writeFrame( ofstream& outFile, double
474                   atomData6[3],
475                   atomData6[4],
476                   atomData6[5]);
477 <
477 >        
478          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
479          
480        } else {
# Line 419 | Line 498 | void DumpWriter::writeFrame( ofstream& outFile, double
498          
499        }
500        
501 <      outFile << writeLine;
501 >      for(k = 0; k < outFile.size(); k++)
502 >        *outFile[k] << writeLine;
503      }
504      
505 <
506 <    outFile.flush();
505 >    for(k = 0; k < outFile.size(); k++)
506 >      outFile[k]->flush();
507 >    
508      sprintf( checkPointMsg,
509               "Sucessfully took a dump.\n");
510 +    
511      MPIcheckPoint();        
512 +    
513      delete[] potatoes;
514 +    
515    } else {
516  
517      // worldRank != 0, so I'm a remote node.  
# Line 437 | Line 521 | void DumpWriter::writeFrame( ofstream& outFile, double
521      myPotato = 0;
522      currentIndex = 0;
523      
524 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
524 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
525        
526 <      // Am I the node which has this atom?
526 >      // Am I the node which has this integrableObject?
527        
528 <      if (AtomToProcMap[i] == worldRank) {
528 >      if (MolToProcMap[i] == worldRank) {
529  
446 –        if (myPotato + 3 >= MAXTAG) {
530  
531 +        if (myPotato + 1 >= MAXTAG) {
532 +          
533            // The potato was going to exceed the maximum value,
534            // so wrap this processor potato back to 0 (and block until
535            // node 0 says we can go:
536 <
536 >          
537            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
538            
539          }
455 –        which_atom = i;
456 –        local_index = indexArray[currentIndex].first;        
457 –                
458 –        if (which_atom == indexArray[currentIndex].second) {
459 –        
460 –          atomTypeString = atoms[local_index]->getType();
540  
541 <          atoms[local_index]->getPos(pos);
542 <          atoms[local_index]->getVel(vel);
464 <
465 <          atomData6[0] = pos[0];
466 <          atomData6[1] = pos[1];
467 <          atomData6[2] = pos[2];
468 <
469 <          atomData6[3] = vel[0];
470 <          atomData6[4] = vel[1];
471 <          atomData6[5] = vel[2];
541 >          local_index = indexArray[currentIndex].first;        
542 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
543            
544 <          isDirectional = 0;
544 >          nCurObj = integrableObjects.size();
545 >                      
546 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
547 >                             myPotato, MPI_COMM_WORLD);
548 >          myPotato++;
549  
550 <          if( atoms[local_index]->isDirectional() ){
550 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
551  
552 <            isDirectional = 1;
552 >            if (myPotato + 3 >= MAXTAG) {
553 >          
554 >              // The potato was going to exceed the maximum value,
555 >              // so wrap this processor potato back to 0 (and block until
556 >              // node 0 says we can go:
557 >          
558 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
559 >              
560 >            }
561              
562 <            dAtom = (DirectionalAtom *)atoms[local_index];
480 <            dAtom->getQ( q );
562 >            sd = *iter;
563              
564 <            for (int j = 0; j < 6 ; j++)
483 <              atomData13[j] = atomData6[j];
484 <            
485 <            atomData13[6] = q[0];
486 <            atomData13[7] = q[1];
487 <            atomData13[8] = q[2];
488 <            atomData13[9] = q[3];
564 >            atomTypeString = sd->getType();
565  
566 <            atomData13[10] = dAtom->getJx();
567 <            atomData13[11] = dAtom->getJy();
492 <            atomData13[12] = dAtom->getJz();
493 <          }
566 >            sd->getPos(pos);
567 >            sd->getVel(vel);
568  
569 <        } else {
570 <          sprintf(painCave.errMsg,
571 <                  "Atom %d not found on processor %d\n",
498 <                  i, worldRank );
499 <          haveError= 1;
500 <          simError();
501 <        }
569 >            atomData6[0] = pos[0];
570 >            atomData6[1] = pos[1];
571 >            atomData6[2] = pos[2];
572  
573 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573 >            atomData6[3] = vel[0];
574 >            atomData6[4] = vel[1];
575 >            atomData6[5] = vel[2];
576 >              
577 >            isDirectional = 0;
578  
579 <        // null terminate the string before sending (just in case):
506 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
579 >            if( sd->isDirectional() ){
580  
581 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
582 <                 myPotato, MPI_COMM_WORLD);
583 <        
584 <        myPotato++;
581 >                isDirectional = 1;
582 >                
583 >                sd->getQ( q );
584 >                sd->getJ( ji );
585 >                
586 >                for (int j = 0; j < 6 ; j++)
587 >                  atomData13[j] = atomData6[j];
588 >                
589 >                atomData13[6] = q[0];
590 >                atomData13[7] = q[1];
591 >                atomData13[8] = q[2];
592 >                atomData13[9] = q[3];
593 >      
594 >                atomData13[10] = ji[0];
595 >                atomData13[11] = ji[1];
596 >                atomData13[12] = ji[2];
597 >              }
598  
599 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 <                 myPotato, MPI_COMM_WORLD);
515 <        
516 <        myPotato++;
517 <        
518 <        if (isDirectional) {
599 >            
600 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
601  
602 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
603 <                   myPotato, MPI_COMM_WORLD);
522 <          
523 <        } else {
602 >            // null terminate the string before sending (just in case):
603 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
604  
605 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
606 <                   myPotato, MPI_COMM_WORLD);
607 <        }
605 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
606 >                             myPotato, MPI_COMM_WORLD);
607 >            
608 >            myPotato++;
609  
610 <        myPotato++;  
611 <        currentIndex++;    
610 >            MPI_Send(&isDirectional, 1, MPI_INT, 0,
611 >                             myPotato, MPI_COMM_WORLD);
612 >            
613 >            myPotato++;
614 >            
615 >            if (isDirectional) {
616 >
617 >              MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
618 >                       myPotato, MPI_COMM_WORLD);
619 >              
620 >            } else {
621 >
622 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
623 >                       myPotato, MPI_COMM_WORLD);
624 >            }
625 >
626 >            myPotato++;  
627 >
628 >          }
629 >
630 >          currentIndex++;    
631 >          
632 >        }
633 >      
634        }
532 –    }
635  
636      sprintf( checkPointMsg,
637               "Sucessfully took a dump.\n");
638 <    MPIcheckPoint();        
638 >    MPIcheckPoint();                
639      
640 <  }
640 >    }
641 >
642 >
643    
644   #endif // is_mpi
645   }

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