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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 927 by tim, Mon Jan 12 22:54:42 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>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 + /**
71 + * A hook function to load balancing
72 + */
73 +
74 + void DumpWriter::update(){
75 +  sortByGlobalIndex();          
76 + }
77 +  
78 + /**
79 + * Auxiliary sorting function
80 + */
81 +
82 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 +  return p1.second < p2.second;
84 + }
85 +
86 + /**
87 + * Sorting the local index by global index
88 + */
89 +
90 + void DumpWriter::sortByGlobalIndex(){
91 +  Molecule* mols = entry_plug->molecules;  
92 +  indexArray.clear();
93 +  
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){
103 +
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 +  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",
147 +               entry_plug->finalName );
148 +      painCave.isFatal = 1;
149 +      simError();
150 +    }
151 +
152 + #ifdef IS_MPI
153 +  }
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( 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  
217    int nProc;
218 <  int j, which_node, done, which_atom, local_index;
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 <
89 < #else //is_mpi
90 <  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;
95 –  Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230 <
231 <  // write current frame to the eor file
232 <
233 <  this->writeFinal( currentTime );
234 <
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"
109 <          << 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);
125 <    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",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    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(),
151 <               dAtom->getJz());
152 <      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      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298  
299 <    outFile << writeLine;
300 <  }
301 <  outFile.flush();
299 >    
300 >    for(k = 0; k < outFile.size(); k++)
301 >      *outFile[k] << writeLine;
302 > }
303  
304   #else // is_mpi
305  
# Line 173 | Line 316 | void DumpWriter::writeDump( double currentTime ){
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 184 | Line 328 | void DumpWriter::writeDump( double currentTime ){
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";
336 <
192 <    outFile << currentTime << ";\t"
193 <            << entry_plug->Hmat[0][0] << "\t"
194 <            << entry_plug->Hmat[1][0] << "\t"
195 <            << entry_plug->Hmat[2][0] << ";\t"
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <            << entry_plug->Hmat[0][1] << "\t"
339 <            << entry_plug->Hmat[1][1] << "\t"
340 <            << entry_plug->Hmat[2][1] << ";\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][2] << "\t"
344 <            << entry_plug->Hmat[1][2] << "\t"
345 <            << entry_plug->Hmat[2][2] << ";";
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
348 <    outFile << endl;
349 <    outFile.flush();
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  
354 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
354 >    currentIndex = 0;
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);
378 +        myPotato++;
379          
380 <        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 <        
233 <        // Null terminate the atomTypeString just in case:
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
383 <        atomTypeString = MPIatomTypeString;
384 <        
238 <        myPotato++;
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 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
387 <                 myPotato, MPI_COMM_WORLD, &istatus);
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          }
252 –        
253 –        myPotato++;
413          potatoes[which_node] = myPotato;
414  
415        } else {
416          
417 <        haveError = 0;
259 <        which_atom = i;
260 <        local_index=-1;
417 >        haveError = 0;
418          
419 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
263 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
264 <        }
265 <        
266 <        if (local_index != -1) {
267 <          
268 <          atomTypeString = atoms[local_index]->getType();
419 >            local_index = indexArray[currentIndex].first;        
420  
421 <          atoms[local_index]->getPos(pos);
271 <          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];
294 <            atomData13[7] = q[1];
295 <            atomData13[8] = q[2];
296 <            atomData13[9] = q[3];
297 <            
298 <            atomData13[10] = dAtom->getJx();
299 <            atomData13[11] = dAtom->getJy();
300 <            atomData13[12] = dAtom->getJz();
301 <          }
302 <          
303 <        } else {
304 <          sprintf(painCave.errMsg,
305 <                  "Atom %d not found on processor %d\n",
306 <                  i, worldRank );
307 <          haveError= 1;
308 <          simError();
309 <        }
460 >        }
461          
462 <        if(haveError) DieDieDie();
312 <        
462 >      currentIndex++;
463        }
464        // If we've survived to here, format the line:
465        
466        if (!isDirectional) {
467          
468 <        sprintf( tempBuffer,
468 >        sprintf( writeLine,
469                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
470                   atomTypeString,
471                   atomData6[0],
# Line 325 | Line 475 | void DumpWriter::writeDump( double currentTime ){
475                   atomData6[4],
476                   atomData6[5]);
477          
328 –        strcpy( writeLine, tempBuffer );
478          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
479          
480        } else {
481          
482 <        sprintf( tempBuffer,
482 >        sprintf( writeLine,
483                   "%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",
484                   atomTypeString,
485                   atomData13[0],
# Line 346 | Line 495 | void DumpWriter::writeDump( double currentTime ){
495                   atomData13[10],
496                   atomData13[11],
497                   atomData13[12]);
349 –        
350 –        strcpy( writeLine, tempBuffer );
498          
499        }
500        
501 <      outFile << writeLine;
502 <      outFile.flush();
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 368 | Line 519 | void DumpWriter::writeDump( double currentTime ){
519      // Set my magic potato to 0:
520  
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  
378 –        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          }
387 –        which_atom = i;
388 –        local_index=-1;
389 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
390 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
391 –        }
392 –        if (local_index != -1) {
393 –        
394 –          atomTypeString = atoms[local_index]->getType();
540  
541 <          atoms[local_index]->getPos(pos);
542 <          atoms[local_index]->getVel(vel);
398 <
399 <          atomData6[0] = pos[0];
400 <          atomData6[1] = pos[1];
401 <          atomData6[2] = pos[2];
402 <
403 <          atomData6[3] = vel[0];
404 <          atomData6[4] = vel[1];
405 <          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];
414 <            dAtom->getQ( q );
562 >            sd = *iter;
563              
564 <            for (int j = 0; j < 6 ; j++)
565 <              atomData13[j] = atomData6[j];
566 <            
567 <            atomData13[6] = q[0];
568 <            atomData13[7] = q[1];
569 <            atomData13[8] = q[2];
570 <            atomData13[9] = q[3];
564 >            atomTypeString = sd->getType();
565 >
566 >            sd->getPos(pos);
567 >            sd->getVel(vel);
568 >
569 >            atomData6[0] = pos[0];
570 >            atomData6[1] = pos[1];
571 >            atomData6[2] = pos[2];
572 >
573 >            atomData6[3] = vel[0];
574 >            atomData6[4] = vel[1];
575 >            atomData6[5] = vel[2];
576 >              
577 >            isDirectional = 0;
578  
579 <            atomData13[10] = dAtom->getJx();
425 <            atomData13[11] = dAtom->getJy();
426 <            atomData13[12] = dAtom->getJz();
427 <          }
579 >            if( sd->isDirectional() ){
580  
581 <        } else {
582 <          sprintf(painCave.errMsg,
583 <                  "Atom %d not found on processor %d\n",
584 <                  i, worldRank );
585 <          haveError= 1;
586 <          simError();
587 <        }
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 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
599 >            
600 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
601  
602 <        // null terminate the string before sending (just in case):
603 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
602 >            // null terminate the string before sending (just in case):
603 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
604  
605 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
606 <                 myPotato, MPI_COMM_WORLD);
607 <        
608 <        myPotato++;
605 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
606 >                             myPotato, MPI_COMM_WORLD);
607 >            
608 >            myPotato++;
609  
610 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
611 <                 myPotato, MPI_COMM_WORLD);
612 <        
613 <        myPotato++;
614 <        
615 <        if (isDirectional) {
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 {
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 <        }
622 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
623 >                       myPotato, MPI_COMM_WORLD);
624 >            }
625  
626 <        myPotato++;      
464 <      }
465 <    }
466 <
467 <    sprintf( checkPointMsg,
468 <             "Sucessfully took a dump.\n");
469 <    MPIcheckPoint();        
470 <    
471 <  }
472 <  
473 < #endif // is_mpi
474 < }
475 <
476 < void DumpWriter::writeFinal(double finalTime){
477 <
478 <  char finalName[500];
479 <  ofstream finalOut;
480 <
481 <  const int BUFFERSIZE = 2000;
482 <  const int MINIBUFFERSIZE = 100;
483 <  char tempBuffer[BUFFERSIZE];
484 <  char writeLine[BUFFERSIZE];
485 <
486 <  double q[4];
487 <  DirectionalAtom* dAtom;
488 <  Atom** atoms = entry_plug->atoms;
489 <  int i;
490 < #ifdef IS_MPI
491 <  
492 <  int *potatoes;
493 <  int myPotato;
494 <
495 <  int nProc;
496 <  int j, which_node, done, which_atom, local_index;
497 <  double atomData6[6];
498 <  double atomData13[13];
499 <  int isDirectional;
500 <  char* atomTypeString;
501 <  char MPIatomTypeString[MINIBUFFERSIZE];
502 <
503 < #else //is_mpi
504 <  int nAtoms = entry_plug->n_atoms;
505 < #endif //is_mpi
506 <
507 <  double pos[3], vel[3];
508 <
509 < #ifdef IS_MPI
510 <  if(worldRank == 0 ){
511 < #endif // is_mpi
512 <
513 <    strcpy( finalName, entry_plug->finalName );
514 <
515 <    finalOut.open( finalName, ios::out | ios::trunc );
516 <    if( !finalOut ){
517 <      sprintf( painCave.errMsg,
518 <               "Could not open \"%s\" for final dump output.\n",
519 <               finalName );
520 <      painCave.isFatal = 1;
521 <      simError();
522 <    }
523 <
524 <    // finalOut.setf( ios::scientific );
525 <
526 < #ifdef IS_MPI
527 <  }
528 <
529 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
530 <  MPIcheckPoint();
531 <
532 < #endif //is_mpi
533 <
534 <
535 < #ifndef IS_MPI
536 <
537 <  finalOut << nAtoms << "\n";
538 <
539 <  finalOut << finalTime << ";\t"
540 <           << entry_plug->Hmat[0][0] << "\t"
541 <           << entry_plug->Hmat[1][0] << "\t"
542 <           << entry_plug->Hmat[2][0] << ";\t"
543 <
544 <           << entry_plug->Hmat[0][1] << "\t"
545 <           << entry_plug->Hmat[1][1] << "\t"
546 <           << entry_plug->Hmat[2][1] << ";\t"
547 <
548 <           << entry_plug->Hmat[0][2] << "\t"
549 <           << entry_plug->Hmat[1][2] << "\t"
550 <           << entry_plug->Hmat[2][2] << ";";
551 <
552 <  //write out additional parameters, such as chi and eta
553 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
554 <  finalOut << endl;
555 <
556 <  for( i=0; i<nAtoms; i++ ){
557 <
558 <    atoms[i]->getPos(pos);
559 <    atoms[i]->getVel(vel);
560 <
561 <    sprintf( tempBuffer,
562 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563 <             atoms[i]->getType(),
564 <             pos[0],
565 <             pos[1],
566 <             pos[2],
567 <             vel[0],
568 <             vel[1],
569 <             vel[2]);
570 <    strcpy( writeLine, tempBuffer );
571 <
572 <    if( atoms[i]->isDirectional() ){
573 <
574 <      dAtom = (DirectionalAtom *)atoms[i];
575 <      dAtom->getQ( q );
576 <
577 <      sprintf( tempBuffer,
578 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
579 <               q[0],
580 <               q[1],
581 <               q[2],
582 <               q[3],
583 <               dAtom->getJx(),
584 <               dAtom->getJy(),
585 <               dAtom->getJz());
586 <      strcat( writeLine, tempBuffer );
587 <    }
588 <    else
589 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
590 <
591 <    finalOut << writeLine;
592 <  }
593 <  finalOut.flush();
594 <  finalOut.close();
595 <
596 < #else // is_mpi
597 <
598 <  /* code to find maximum tag value */
599 <  int *tagub, flag, MAXTAG;
600 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
601 <  if (flag) {
602 <    MAXTAG = *tagub;
603 <  } else {
604 <    MAXTAG = 32767;
605 <  }  
606 <
607 <  int haveError;
608 <
609 <  MPI_Status istatus;
610 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
611 <
612 <  // write out header and node 0's coordinates
613 <
614 <  if( worldRank == 0 ){
615 <
616 <    // Node 0 needs a list of the magic potatoes for each processor;
617 <
618 <    nProc = mpiSim->getNumberProcessors();
619 <    potatoes = new int[nProc];
620 <
621 <    for (i = 0; i < nProc; i++)
622 <      potatoes[i] = 0;
623 <    
624 <    finalOut << mpiSim->getTotAtoms() << "\n";
625 <
626 <    finalOut << finalTime << ";\t"
627 <            << entry_plug->Hmat[0][0] << "\t"
628 <            << entry_plug->Hmat[1][0] << "\t"
629 <            << entry_plug->Hmat[2][0] << ";\t"
630 <
631 <            << entry_plug->Hmat[0][1] << "\t"
632 <            << entry_plug->Hmat[1][1] << "\t"
633 <            << entry_plug->Hmat[2][1] << ";\t"
634 <
635 <            << entry_plug->Hmat[0][2] << "\t"
636 <            << entry_plug->Hmat[1][2] << "\t"
637 <            << entry_plug->Hmat[2][2] << ";";
638 <
639 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
640 <    finalOut << endl;
641 <    finalOut.flush();
642 <
643 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
644 <      
645 <      // Get the Node number which has this atom;
646 <      
647 <      which_node = AtomToProcMap[i];
648 <      
649 <      if (which_node != 0) {
626 >            myPotato++;  
627  
628 <        if (potatoes[which_node] + 3 >= MAXTAG) {
652 <          // The potato was going to exceed the maximum value,
653 <          // so wrap this processor potato back to 0:        
628 >          }
629  
630 <          potatoes[which_node] = 0;          
656 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
630 >          currentIndex++;    
631            
632          }
659 –
660 –        myPotato = potatoes[which_node];        
661 –        
662 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
663 –                 myPotato, MPI_COMM_WORLD, &istatus);
664 –        
665 –        atomTypeString = MPIatomTypeString;
666 –                
667 –        myPotato++;
668 –
669 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
670 –                 myPotato, MPI_COMM_WORLD, &istatus);
671 –              
672 –        myPotato++;
673 –
674 –        if (isDirectional) {          
675 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
676 –                   myPotato, MPI_COMM_WORLD, &istatus);
677 –        } else {
678 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
679 –                   myPotato, MPI_COMM_WORLD, &istatus);          
680 –        }
681 –        
682 –        myPotato++;
683 –        potatoes[which_node] = myPotato;
684 –
685 –      } else {
686 –        
687 –        haveError = 0;
688 –        which_atom = i;
689 –        local_index=-1;
690 –        
691 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
692 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
693 –        }
694 –        
695 –        if (local_index != -1) {
696 –          
697 –          atomTypeString = atoms[local_index]->getType();
698 –
699 –          atoms[local_index]->getPos(pos);
700 –          atoms[local_index]->getVel(vel);          
701 –
702 –          atomData6[0] = pos[0];
703 –          atomData6[1] = pos[1];
704 –          atomData6[2] = pos[2];
705 –
706 –          atomData6[3] = vel[0];
707 –          atomData6[4] = vel[1];
708 –          atomData6[5] = vel[2];
709 –          
710 –          isDirectional = 0;
711 –
712 –          if( atoms[local_index]->isDirectional() ){
713 –
714 –            isDirectional = 1;
715 –            
716 –            dAtom = (DirectionalAtom *)atoms[local_index];
717 –            dAtom->getQ( q );
718 –
719 –            for (int j = 0; j < 6 ; j++)
720 –              atomData13[j] = atomData6[j];            
721 –            
722 –            atomData13[6] = q[0];
723 –            atomData13[7] = q[1];
724 –            atomData13[8] = q[2];
725 –            atomData13[9] = q[3];
726 –            
727 –            atomData13[10] = dAtom->getJx();
728 –            atomData13[11] = dAtom->getJy();
729 –            atomData13[12] = dAtom->getJz();
730 –          }
731 –          
732 –        } else {
733 –          sprintf(painCave.errMsg,
734 –                  "Atom %d not found on processor %d\n",
735 –                  i, worldRank );
736 –          haveError= 1;
737 –          simError();
738 –        }
739 –        
740 –        if(haveError) DieDieDie();
741 –        
742 –      }
743 –
744 –
745 –      // If we've survived to here, format the line:
633        
747 –      if (!isDirectional) {
748 –        
749 –        sprintf( tempBuffer,
750 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
751 –                 atomTypeString,
752 –                 atomData6[0],
753 –                 atomData6[1],
754 –                 atomData6[2],
755 –                 atomData6[3],
756 –                 atomData6[4],
757 –                 atomData6[5]);
758 –        
759 –        strcpy( writeLine, tempBuffer );
760 –        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
761 –        
762 –      } else {
763 –        
764 –        sprintf( tempBuffer,
765 –                 "%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",
766 –                 atomTypeString,
767 –                 atomData13[0],
768 –                 atomData13[1],
769 –                 atomData13[2],
770 –                 atomData13[3],
771 –                 atomData13[4],
772 –                 atomData13[5],
773 –                 atomData13[6],
774 –                 atomData13[7],
775 –                 atomData13[8],
776 –                 atomData13[9],
777 –                 atomData13[10],
778 –                 atomData13[11],
779 –                 atomData13[12]);
780 –        
781 –        strcpy( writeLine, tempBuffer );
782 –        
634        }
635 <        
785 <      finalOut << writeLine;
786 <      finalOut.flush();
787 <    }
788 <  
789 <    finalOut.flush();
635 >
636      sprintf( checkPointMsg,
637               "Sucessfully took a dump.\n");
638 <    delete[] potatoes;
638 >    MPIcheckPoint();                
639      
794 –    MPIcheckPoint();        
795 –    
796 –  } else {
797 –
798 –    // worldRank != 0, so I'm a remote node.  
799 –
800 –    // Set my magic potato to 0:
801 –
802 –    myPotato = 0;
803 –    
804 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
805 –      
806 –      // Am I the node which has this atom?
807 –      
808 –      if (AtomToProcMap[i] == worldRank) {
809 –
810 –        if (myPotato + 3 >= MAXTAG) {
811 –
812 –          // The potato was going to exceed the maximum value,
813 –          // so wrap this processor potato back to 0 (and block until
814 –          // node 0 says we can go:
815 –
816 –          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
817 –          
818 –        }
819 –        which_atom = i;  
820 –        local_index=-1;
821 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
822 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
823 –        }
824 –        if (local_index != -1) {
825 –        
826 –          atomTypeString = atoms[local_index]->getType();
827 –
828 –          atoms[local_index]->getPos(pos);
829 –          atoms[local_index]->getVel(vel);
830 –
831 –          atomData6[0] = pos[0];
832 –          atomData6[1] = pos[1];
833 –          atomData6[2] = pos[2];
834 –
835 –          atomData6[3] = vel[0];
836 –          atomData6[4] = vel[1];
837 –          atomData6[5] = vel[2];
838 –          
839 –          isDirectional = 0;
840 –
841 –          if( atoms[local_index]->isDirectional() ){
842 –
843 –            isDirectional = 1;
844 –            
845 –            dAtom = (DirectionalAtom *)atoms[local_index];
846 –            dAtom->getQ( q );
847 –            
848 –            for (int j = 0; j < 6 ; j++)
849 –              atomData13[j] = atomData6[j];
850 –            
851 –            atomData13[6] = q[0];
852 –            atomData13[7] = q[1];
853 –            atomData13[8] = q[2];
854 –            atomData13[9] = q[3];
855 –
856 –            atomData13[10] = dAtom->getJx();
857 –            atomData13[11] = dAtom->getJy();
858 –            atomData13[12] = dAtom->getJz();
859 –          }
860 –
861 –        } else {
862 –          sprintf(painCave.errMsg,
863 –                  "Atom %d not found on processor %d\n",
864 –                  i, worldRank );
865 –          haveError= 1;
866 –          simError();
867 –        }
868 –
869 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
870 –
871 –        // null terminate the string before sending (just in case):
872 –        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
873 –
874 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
875 –                 myPotato, MPI_COMM_WORLD);
876 –        
877 –        myPotato++;
878 –
879 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
880 –                 myPotato, MPI_COMM_WORLD);
881 –        
882 –        myPotato++;
883 –        
884 –        if (isDirectional) {
885 –
886 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
887 –                   myPotato, MPI_COMM_WORLD);
888 –          
889 –        } else {
890 –
891 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
892 –                   myPotato, MPI_COMM_WORLD);
893 –        }
894 –
895 –        myPotato++;      
896 –      }
640      }
641  
642 <    sprintf( checkPointMsg,
900 <             "Sucessfully took a dump.\n");
901 <    MPIcheckPoint();        
902 <    
903 <  }
642 >
643    
905 –  if( worldRank == 0 ) finalOut.close();
644   #endif // is_mpi
645   }
646  
909 –
910 –
647   #ifdef IS_MPI
648  
649   // a couple of functions to let us escape the write loop

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