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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 905 by tim, Wed Jan 7 19:26:12 2004 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
11   #include "mpiSimulation.hpp"
10 – #define TAKE_THIS_TAG_CHAR 15
11 – #define TAKE_THIS_TAG_INT 20
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 29 | 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  
36 –    if( !outFile ){
37 –
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  
45 –    //outFile.setf( ios::scientific );
46 –
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 59 | 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 + /**
70 + * A hook function to load balancing
71 + */
72 +
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 + /**
86 + * Sorting the local index by global index
87 + */
88 +
89 + void DumpWriter::sortByGlobalIndex(){
90 +  Atom** atoms = entry_plug->atoms;
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 +  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 +  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 +  //}
102 +    
103 + }
104 +
105 + #endif
106 +
107 + void DumpWriter::writeDump(double currentTime){
108 +
109 +  ofstream finalOut;
110 +  vector<ofstream*> fileStreams;
111 +
112 + #ifdef IS_MPI
113 +  printf("Hello from node %d\n", worldRank);
114 +  sortByGlobalIndex();
115 +  if(worldRank == 0 ){
116 +    
117 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 +    if( !finalOut ){
119 +      sprintf( painCave.errMsg,
120 +               "Could not open \"%s\" for final dump output.\n",
121 +               entry_plug->finalName );
122 +      painCave.isFatal = 1;
123 +      simError();
124 +    }
125 +  }
126 + #endif // is_mpi
127 +
128 +  fileStreams.push_back(&finalOut);
129 +  fileStreams.push_back(&dumpFile);
130 +
131 +  writeFrame(fileStreams, currentTime);
132 +
133 + #ifdef IS_MPI
134 +  finalOut.close();
135 + #endif
136 +        
137 + }
138 +
139 + void DumpWriter::writeFinal(double currentTime){
140 +
141 +  ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143 +
144 + #ifdef IS_MPI
145 +  if(worldRank == 0 ){
146 + #endif // is_mpi
147 +
148 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149 +
150 +    if( !finalOut ){
151 +      sprintf( painCave.errMsg,
152 +               "Could not open \"%s\" for final dump output.\n",
153 +               entry_plug->finalName );
154 +      painCave.isFatal = 1;
155 +      simError();
156 +    }
157 +
158 + #ifdef IS_MPI
159 +  }
160 + #endif // is_mpi
161 +  
162 +  fileStreams.push_back(&finalOut);  
163 +  writeFrame(fileStreams, currentTime);
164 +
165 + #ifdef IS_MPI
166 +  finalOut.close();
167 + #endif
168 +  
169 + }
170 +
171 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172 +
173    const int BUFFERSIZE = 2000;
174 <  char tempBuffer[BUFFERSIZE];
174 >  const int MINIBUFFERSIZE = 100;
175 >
176 >  char tempBuffer[BUFFERSIZE];  
177    char writeLine[BUFFERSIZE];
178  
179 <  int i;
179 >  int i, k;
180 >
181   #ifdef IS_MPI
182 <  int j, which_node, done, which_atom, local_index;
182 >  
183 >  /*********************************************************************
184 >   * Documentation?  You want DOCUMENTATION?
185 >   *
186 >   * Why all the potatoes below?  
187 >   *
188 >   * To make a long story short, the original version of DumpWriter
189 >   * worked in the most inefficient way possible.  Node 0 would
190 >   * poke each of the node for an individual atom's formatted data
191 >   * as node 0 worked its way down the global index. This was particularly
192 >   * inefficient since the method blocked all processors at every atom
193 >   * (and did it twice!).
194 >   *
195 >   * An intermediate version of DumpWriter could be described from Node
196 >   * zero's perspective as follows:
197 >   *
198 >   *  1) Have 100 of your friends stand in a circle.
199 >   *  2) When you say go, have all of them start tossing potatoes at
200 >   *     you (one at a time).
201 >   *  3) Catch the potatoes.
202 >   *
203 >   * It was an improvement, but MPI has buffers and caches that could
204 >   * best be described in this analogy as "potato nets", so there's no
205 >   * need to block the processors atom-by-atom.
206 >   *
207 >   * This new and improved DumpWriter works in an even more efficient
208 >   * way:
209 >   *
210 >   *  1) Have 100 of your friend stand in a circle.
211 >   *  2) When you say go, have them start tossing 5-pound bags of
212 >   *     potatoes at you.
213 >   *  3) Once you've caught a friend's bag of potatoes,
214 >   *     toss them a spud to let them know they can toss another bag.
215 >   *
216 >   * How's THAT for documentation?
217 >   *
218 >   *********************************************************************/
219 >
220 >  int *potatoes;
221 >  int myPotato;
222 >
223 >  int nProc;
224 >  int j, which_node, done, which_atom, local_index, currentIndex;
225 >  double atomData6[6];
226 >  double atomData13[13];
227 >  int isDirectional;
228 >  char* atomTypeString;
229 >  char MPIatomTypeString[MINIBUFFERSIZE];
230 >
231   #else //is_mpi
232    int nAtoms = entry_plug->n_atoms;
233   #endif //is_mpi
# Line 84 | Line 237 | void DumpWriter::writeDump( double currentTime ){
237    Atom** atoms = entry_plug->atoms;
238    double pos[3], vel[3];
239  
87 –
88 –  // write current frame to the eor file
89 –
90 –  this->writeFinal( currentTime );
91 –
240   #ifndef IS_MPI
241 +  
242 +  for(k = 0; k < outFile.size(); k++){
243 +    *outFile[k] << nAtoms << "\n";
244  
245 <  outFile << nAtoms << "\n";
245 >    *outFile[k] << currentTime << ";\t"
246 >               << entry_plug->Hmat[0][0] << "\t"
247 >                     << entry_plug->Hmat[1][0] << "\t"
248 >                     << entry_plug->Hmat[2][0] << ";\t"
249 >              
250 >               << entry_plug->Hmat[0][1] << "\t"
251 >                     << entry_plug->Hmat[1][1] << "\t"
252 >                     << entry_plug->Hmat[2][1] << ";\t"
253  
254 <  outFile << currentTime << ";\t"
255 <          << entry_plug->Hmat[0][0] << "\t"
256 <          << entry_plug->Hmat[1][0] << "\t"
99 <          << entry_plug->Hmat[2][0] << ";\t"
254 >                     << entry_plug->Hmat[0][2] << "\t"
255 >                     << entry_plug->Hmat[1][2] << "\t"
256 >                     << entry_plug->Hmat[2][2] << ";";
257  
258 <          << entry_plug->Hmat[0][1] << "\t"
259 <          << entry_plug->Hmat[1][1] << "\t"
260 <          << entry_plug->Hmat[2][1] << ";\t"
261 <
105 <          << entry_plug->Hmat[0][2] << "\t"
106 <          << entry_plug->Hmat[1][2] << "\t"
107 <          << entry_plug->Hmat[2][2] << ";";
108 <  //write out additional parameters, such as chi and eta
109 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
110 <  outFile << endl;
111 <
258 >    //write out additional parameters, such as chi and eta
259 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
260 >  }
261 >  
262    for( i=0; i<nAtoms; i++ ){
263  
264      atoms[i]->getPos(pos);
# Line 144 | Line 294 | void DumpWriter::writeDump( double currentTime ){
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296  
297 <    outFile << writeLine;
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
149 –  outFile.flush();
300  
301   #else // is_mpi
302  
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  /* code to find maximum tag value */
304 >  
305 >  int *tagub, flag, MAXTAG;
306 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
307 >  if (flag) {
308 >    MAXTAG = *tagub;
309 >  } else {
310 >    MAXTAG = 32767;
311 >  }  
312  
156 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313    int haveError;
314  
315    MPI_Status istatus;
# Line 162 | Line 318 | void DumpWriter::writeDump( double currentTime ){
318    // write out header and node 0's coordinates
319  
320    if( worldRank == 0 ){
165 –    outFile << mpiSim->getTotAtoms() << "\n";
321  
322 <    outFile << currentTime << ";\t"
168 <            << entry_plug->Hmat[0][0] << "\t"
169 <            << entry_plug->Hmat[1][0] << "\t"
170 <            << entry_plug->Hmat[2][0] << ";\t"
322 >    // Node 0 needs a list of the magic potatoes for each processor;
323  
324 <            << entry_plug->Hmat[0][1] << "\t"
325 <            << entry_plug->Hmat[1][1] << "\t"
174 <            << entry_plug->Hmat[2][1] << ";\t"
324 >    nProc = mpiSim->getNumberProcessors();
325 >    potatoes = new int[nProc];
326  
327 <            << entry_plug->Hmat[0][2] << "\t"
328 <            << entry_plug->Hmat[1][2] << "\t"
329 <            << entry_plug->Hmat[2][2] << ";";
327 >    //write out the comment lines
328 >    for (i = 0; i < nProc; i++)
329 >      potatoes[i] = 0;
330 >    
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333  
334 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
335 <    outFile << endl;
336 <    outFile.flush();
334 >        *outFile[k] << currentTime << ";\t"
335 >                         << entry_plug->Hmat[0][0] << "\t"
336 >                         << entry_plug->Hmat[1][0] << "\t"
337 >                         << entry_plug->Hmat[2][0] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][1] << "\t"
340 >                         << entry_plug->Hmat[1][1] << "\t"
341 >                         << entry_plug->Hmat[2][1] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][2] << "\t"
344 >                         << entry_plug->Hmat[1][2] << "\t"
345 >                         << entry_plug->Hmat[2][2] << ";";
346 >  
347 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
348 >    }
349 >
350 >    currentIndex = 0;
351 >
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
353 +      
354        // Get the Node number which has this atom;
355 <
355 >      
356        which_node = AtomToProcMap[i];
357 +      
358 +      if (which_node != 0) {
359  
360 <      if (which_node == 0 ) {
360 >        if (potatoes[which_node] + 3 >= MAXTAG) {
361 >          // The potato was going to exceed the maximum value,
362 >          // so wrap this processor potato back to 0:        
363  
364 <        haveError = 0;
365 <        which_atom = i;
366 <        local_index=-1;
193 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
194 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
364 >          potatoes[which_node] = 0;          
365 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
366 >          
367          }
196 –        if (local_index != -1) {
197 –          //format the line
368  
369 +        myPotato = potatoes[which_node];        
370 +        
371 +        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
372 +                 myPotato, MPI_COMM_WORLD, &istatus);
373 +        
374 +        atomTypeString = MPIatomTypeString;
375 +        
376 +        myPotato++;
377 +
378 +        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
379 +                 myPotato, MPI_COMM_WORLD, &istatus);
380 +              
381 +        myPotato++;
382 +
383 +        if (isDirectional) {          
384 +          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
385 +                   myPotato, MPI_COMM_WORLD, &istatus);
386 +        } else {
387 +          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
388 +                   myPotato, MPI_COMM_WORLD, &istatus);          
389 +        }
390 +        
391 +        myPotato++;
392 +        potatoes[which_node] = myPotato;
393 +
394 +      } else {
395 +        
396 +        haveError = 0;
397 +        which_atom = i;
398 +        
399 +        //local_index = -1;
400 +
401 +        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 +        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 +        //}
404 +        
405 +        //if (local_index != -1) {
406 +          
407 +          local_index = indexArray[currentIndex].first;        
408 +          
409 +          if (which_atom == indexArray[currentIndex].second) {
410 +            
411 +            atomTypeString = atoms[local_index]->getType();
412 +            
413            atoms[local_index]->getPos(pos);
414 <          atoms[local_index]->getVel(vel);
414 >          atoms[local_index]->getVel(vel);          
415 >          
416 >          atomData6[0] = pos[0];
417 >          atomData6[1] = pos[1];
418 >          atomData6[2] = pos[2];
419  
420 <          sprintf( tempBuffer,
421 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
422 <                   atoms[local_index]->getType(),
423 <                   pos[0],
424 <                   pos[1],
207 <                   pos[2],
208 <                   vel[0],
209 <                   vel[1],
210 <                   vel[2]); // check here.
211 <          strcpy( writeLine, tempBuffer );
420 >          atomData6[3] = vel[0];
421 >          atomData6[4] = vel[1];
422 >          atomData6[5] = vel[2];
423 >          
424 >          isDirectional = 0;
425  
426            if( atoms[local_index]->isDirectional() ){
427  
428 +            isDirectional = 1;
429 +            
430              dAtom = (DirectionalAtom *)atoms[local_index];
431              dAtom->getQ( q );
432  
433 <            sprintf( tempBuffer,
434 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
435 <                     q[0],
436 <                     q[1],
437 <                     q[2],
438 <                     q[3],
439 <                     dAtom->getJx(),
440 <                     dAtom->getJy(),
441 <                     dAtom->getJz());
442 <            strcat( writeLine, tempBuffer );
443 <
444 <          }
445 <          else
446 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232 <        }
233 <        else {
433 >            for (int j = 0; j < 6 ; j++)
434 >              atomData13[j] = atomData6[j];            
435 >            
436 >            atomData13[6] = q[0];
437 >            atomData13[7] = q[1];
438 >            atomData13[8] = q[2];
439 >            atomData13[9] = q[3];
440 >            
441 >            atomData13[10] = dAtom->getJx();
442 >            atomData13[11] = dAtom->getJy();
443 >            atomData13[12] = dAtom->getJz();
444 >          }
445 >          
446 >        } else {
447            sprintf(painCave.errMsg,
448 <                  "Atom %d not found on processor %d\n",
449 <                  i, worldRank );
448 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
449 >                  which_atom, worldRank, currentIndex, local_index );
450            haveError= 1;
451            simError();
452          }
453 <
454 <        if(haveError) nodeZeroError();
455 <
453 >        
454 >        if(haveError) DieDieDie();
455 >        
456 >        currentIndex++;
457        }
458 <      else {
459 <        myStatus = 1;
460 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
461 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
462 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
463 <                 MPI_COMM_WORLD);
464 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
465 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
466 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
467 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
468 <
469 <        if(!myStatus) nodeZeroError();
470 <
458 >      // If we've survived to here, format the line:
459 >      
460 >      if (!isDirectional) {
461 >        
462 >        sprintf( writeLine,
463 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 >                 atomTypeString,
465 >                 atomData6[0],
466 >                 atomData6[1],
467 >                 atomData6[2],
468 >                 atomData6[3],
469 >                 atomData6[4],
470 >                 atomData6[5]);
471 >        
472 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 >        
474 >      } else {
475 >        
476 >        sprintf( writeLine,
477 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
478 >                 atomTypeString,
479 >                 atomData13[0],
480 >                 atomData13[1],
481 >                 atomData13[2],
482 >                 atomData13[3],
483 >                 atomData13[4],
484 >                 atomData13[5],
485 >                 atomData13[6],
486 >                 atomData13[7],
487 >                 atomData13[8],
488 >                 atomData13[9],
489 >                 atomData13[10],
490 >                 atomData13[11],
491 >                 atomData13[12]);
492 >        
493        }
494 <
495 <      outFile << writeLine;
496 <      outFile.flush();
494 >      
495 >      for(k = 0; k < outFile.size(); k++)
496 >        *outFile[k] << writeLine;
497      }
498 <
499 <    // kill everyone off:
500 <    myStatus = -1;
501 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
502 <      MPI_Send(&myStatus, 1, MPI_INT, j,
503 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
504 <    }
505 <
498 >    
499 >    for(k = 0; k < outFile.size(); k++)
500 >      outFile[k]->flush();
501 >    
502 >    sprintf( checkPointMsg,
503 >             "Sucessfully took a dump.\n");
504 >    
505 >    MPIcheckPoint();        
506 >    
507 >    delete[] potatoes;
508 >    
509    } else {
510  
511 <    done = 0;
273 <    while (!done) {
511 >    // worldRank != 0, so I'm a remote node.  
512  
513 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
276 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
513 >    // Set my magic potato to 0:
514  
515 <      if(!myStatus) anonymousNodeDie();
516 <
517 <      if(myStatus < 0) break;
515 >    myPotato = 0;
516 >    currentIndex = 0;
517 >    
518 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
519 >      
520 >      // Am I the node which has this atom?
521 >      
522 >      if (AtomToProcMap[i] == worldRank) {
523  
524 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
525 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
524 >        if (myPotato + 3 >= MAXTAG) {
525 >          
526 >          // The potato was going to exceed the maximum value,
527 >          // so wrap this processor potato back to 0 (and block until
528 >          // node 0 says we can go:
529 >          
530 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531 >          
532 >        }
533 >        which_atom = i;
534  
535 <      myStatus = 1;
286 <      local_index=-1;
287 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
288 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
289 <      }
290 <      if (local_index != -1) {
291 <        //format the line
535 >        //local_index = -1;
536  
537 <        atoms[local_index]->getPos(pos);
538 <        atoms[local_index]->getVel(vel);
537 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
538 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
539 >        //}
540 >        
541 >        //if (local_index != -1) {
542  
543 <        sprintf( tempBuffer,
544 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
545 <                 atoms[local_index]->getType(),
546 <                 pos[0],
547 <                 pos[1],
548 <                 pos[2],
549 <                 vel[0],
550 <                 vel[1],
551 <                 vel[2]); // check here.
552 <        strcpy( writeLine, tempBuffer );
543 >        local_index = indexArray[currentIndex].first;        
544 >                
545 >        if (which_atom == indexArray[currentIndex].second) {
546 >        
547 >          atomTypeString = atoms[local_index]->getType();
548 >          
549 >          atoms[local_index]->getPos(pos);
550 >          atoms[local_index]->getVel(vel);
551 >          
552 >          atomData6[0] = pos[0];
553 >          atomData6[1] = pos[1];
554 >          atomData6[2] = pos[2];
555  
556 <        if( atoms[local_index]->isDirectional() ){
556 >          atomData6[3] = vel[0];
557 >          atomData6[4] = vel[1];
558 >          atomData6[5] = vel[2];
559 >          
560 >          isDirectional = 0;
561  
562 <          dAtom = (DirectionalAtom *)atoms[local_index];
310 <          dAtom->getQ( q );
562 >          if( atoms[local_index]->isDirectional() ){
563  
564 <          sprintf( tempBuffer,
565 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
566 <                   q[0],
567 <                   q[1],
568 <                   q[2],
569 <                   q[3],
570 <                   dAtom->getJx(),
571 <                   dAtom->getJy(),
572 <                   dAtom->getJz());
573 <          strcat( writeLine, tempBuffer );
564 >            isDirectional = 1;
565 >            
566 >            dAtom = (DirectionalAtom *)atoms[local_index];
567 >            dAtom->getQ( q );
568 >            
569 >            for (int j = 0; j < 6 ; j++)
570 >              atomData13[j] = atomData6[j];
571 >            
572 >            atomData13[6] = q[0];
573 >            atomData13[7] = q[1];
574 >            atomData13[8] = q[2];
575 >            atomData13[9] = q[3];
576 >  
577 >            atomData13[10] = dAtom->getJx();
578 >            atomData13[11] = dAtom->getJy();
579 >            atomData13[12] = dAtom->getJz();
580 >          }
581 >
582 >        } else {
583 >          sprintf(painCave.errMsg,
584 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
585 >                  which_atom, worldRank, currentIndex, local_index );
586 >          haveError= 1;
587 >          simError();
588          }
589 <        else{
590 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
325 <        }
326 <      }
327 <      else {
328 <        sprintf(painCave.errMsg,
329 <                "Atom %d not found on processor %d\n",
330 <                which_atom, worldRank );
331 <        myStatus = 0;
332 <        simError();
589 >        
590 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591  
592 <        strcpy( writeLine, "Hello, I'm an error.\n");
593 <      }
592 >        // null terminate the string before sending (just in case):
593 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
594  
595 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
596 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
597 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
598 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
341 <    }
342 <  }
343 <  outFile.flush();
344 <  sprintf( checkPointMsg,
345 <           "Sucessfully took a dump.\n");
346 <  MPIcheckPoint();
595 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
596 >                             myPotato, MPI_COMM_WORLD);
597 >        
598 >        myPotato++;
599  
600 < // last  thing last, enable  fatalities.
601 <  painCave.isEventLoop = 0;
600 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 >                             myPotato, MPI_COMM_WORLD);
602 >        
603 >        myPotato++;
604 >        
605 >        if (isDirectional) {
606  
607 < #endif // is_mpi
608 < }
607 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
608 >                   myPotato, MPI_COMM_WORLD);
609 >          
610 >        } else {
611  
612 < void DumpWriter::writeFinal(double finalTime){
613 <
356 <  char finalName[500];
357 <  ofstream finalOut;
358 <
359 <  const int BUFFERSIZE = 2000;
360 <  char tempBuffer[BUFFERSIZE];
361 <  char writeLine[BUFFERSIZE];
362 <
363 <  double q[4];
364 <  DirectionalAtom* dAtom;
365 <  Atom** atoms = entry_plug->atoms;
366 <  int i;
367 < #ifdef IS_MPI
368 <  int j, which_node, done, which_atom, local_index;
369 < #else //is_mpi
370 <  int nAtoms = entry_plug->n_atoms;
371 < #endif //is_mpi
372 <
373 <  double pos[3], vel[3];
374 <
375 < #ifdef IS_MPI
376 <  if(worldRank == 0 ){
377 < #endif // is_mpi
378 <
379 <    strcpy( finalName, entry_plug->finalName );
380 <
381 <    finalOut.open( finalName, ios::out | ios::trunc );
382 <    if( !finalOut ){
383 <      sprintf( painCave.errMsg,
384 <               "Could not open \"%s\" for final dump output.\n",
385 <               finalName );
386 <      painCave.isFatal = 1;
387 <      simError();
388 <    }
389 <
390 <    // finalOut.setf( ios::scientific );
391 <
392 < #ifdef IS_MPI
393 <  }
394 <
395 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
396 <  MPIcheckPoint();
397 <
398 < #endif //is_mpi
399 <
400 <
401 < #ifndef IS_MPI
402 <
403 <  finalOut << nAtoms << "\n";
404 <
405 <  finalOut << finalTime << ";\t"
406 <           << entry_plug->Hmat[0][0] << "\t"
407 <           << entry_plug->Hmat[1][0] << "\t"
408 <           << entry_plug->Hmat[2][0] << ";\t"
409 <
410 <           << entry_plug->Hmat[0][1] << "\t"
411 <           << entry_plug->Hmat[1][1] << "\t"
412 <           << entry_plug->Hmat[2][1] << ";\t"
413 <
414 <           << entry_plug->Hmat[0][2] << "\t"
415 <           << entry_plug->Hmat[1][2] << "\t"
416 <           << entry_plug->Hmat[2][2] << ";";
417 <
418 <  //write out additional parameters, such as chi and eta
419 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
420 <  finalOut << endl;
421 <
422 <  for( i=0; i<nAtoms; i++ ){
423 <
424 <    atoms[i]->getPos(pos);
425 <    atoms[i]->getVel(vel);
426 <
427 <    sprintf( tempBuffer,
428 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
429 <             atoms[i]->getType(),
430 <             pos[0],
431 <             pos[1],
432 <             pos[2],
433 <             vel[0],
434 <             vel[1],
435 <             vel[2]);
436 <    strcpy( writeLine, tempBuffer );
437 <
438 <    if( atoms[i]->isDirectional() ){
439 <
440 <      dAtom = (DirectionalAtom *)atoms[i];
441 <      dAtom->getQ( q );
442 <
443 <      sprintf( tempBuffer,
444 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
445 <               q[0],
446 <               q[1],
447 <               q[2],
448 <               q[3],
449 <               dAtom->getJx(),
450 <               dAtom->getJy(),
451 <               dAtom->getJz());
452 <      strcat( writeLine, tempBuffer );
453 <    }
454 <    else
455 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 <
457 <    finalOut << writeLine;
458 <  }
459 <  finalOut.flush();
460 <  finalOut.close();
461 <
462 < #else // is_mpi
463 <
464 <  // first thing first, suspend fatalities.
465 <  painCave.isEventLoop = 1;
466 <
467 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
468 <  int haveError;
469 <
470 <  MPI_Status istatus;
471 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
472 <
473 <  // write out header and node 0's coordinates
474 <
475 <  haveError = 0;
476 <  if( worldRank == 0 ){
477 <    finalOut << mpiSim->getTotAtoms() << "\n";
478 <
479 <    finalOut << finalTime << ";\t"
480 <             << entry_plug->Hmat[0][0] << "\t"
481 <             << entry_plug->Hmat[1][0] << "\t"
482 <             << entry_plug->Hmat[2][0] << ";\t"
483 <
484 <             << entry_plug->Hmat[0][1] << "\t"
485 <             << entry_plug->Hmat[1][1] << "\t"
486 <             << entry_plug->Hmat[2][1] << ";\t"
487 <
488 <             << entry_plug->Hmat[0][2] << "\t"
489 <             << entry_plug->Hmat[1][2] << "\t"
490 <             << entry_plug->Hmat[2][2] << ";";
491 <
492 <    //write out additional parameters, such as chi and eta
493 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
494 <    finalOut << endl;
495 <
496 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
497 <      // Get the Node number which has this molecule:
498 <
499 <      which_node = AtomToProcMap[i];
500 <
501 <      if (which_node == mpiSim->getMyNode()) {
502 <
503 <        which_atom = i;
504 <        local_index=-1;
505 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
506 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
612 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
613 >                   myPotato, MPI_COMM_WORLD);
614          }
508 –        if (local_index != -1) {
615  
616 <          atoms[local_index]->getPos(pos);
617 <          atoms[local_index]->getVel(vel);
512 <
513 <          sprintf( tempBuffer,
514 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <                   atoms[local_index]->getType(),
516 <                   pos[0],
517 <                   pos[1],
518 <                   pos[2],
519 <                   vel[0],
520 <                   vel[1],
521 <                   vel[2]);
522 <          strcpy( writeLine, tempBuffer );
523 <
524 <          if( atoms[local_index]->isDirectional() ){
525 <
526 <            dAtom = (DirectionalAtom *)atoms[local_index];
527 <            dAtom->getQ( q );
528 <
529 <            sprintf( tempBuffer,
530 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <                     q[0],
532 <                     q[1],
533 <                     q[2],
534 <                     q[3],
535 <                     dAtom->getJx(),
536 <                     dAtom->getJy(),
537 <                     dAtom->getJz());
538 <            strcat( writeLine, tempBuffer );
539 <          }
540 <          else
541 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
542 <        }
543 <        else {
544 <          sprintf(painCave.errMsg,
545 <                  "Atom %d not found on processor %d\n",
546 <                  i, worldRank );
547 <          haveError= 1;
548 <          simError();
549 <        }
550 <
551 <        if(haveError) nodeZeroError();
552 <
616 >        myPotato++;  
617 >        currentIndex++;    
618        }
554 –      else {
555 –
556 –        myStatus = 1;
557 –        MPI_Send(&myStatus, 1, MPI_INT, which_node,
558 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
559 –        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
560 –                 MPI_COMM_WORLD);
561 –        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
562 –                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
563 –        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
564 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
565 –
566 –        if(!myStatus) nodeZeroError();
567 –      }
568 –
569 –      finalOut << writeLine;
619      }
620  
621 <    // kill everyone off:
622 <    myStatus = -1;
623 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
624 <      MPI_Send(&myStatus, 1, MPI_INT, j,
625 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
626 <    }
578 <
579 <  } else {
580 <
581 <    done = 0;
582 <    while (!done) {
583 <
584 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
585 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
586 <
587 <      if(!myStatus) anonymousNodeDie();
588 <
589 <      if(myStatus < 0) break;
590 <
591 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
592 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
593 <
594 <      myStatus = 1;
595 <      local_index=-1;
596 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
597 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
598 <      }
599 <      if (local_index != -1) {
600 <
601 <        atoms[local_index]->getPos(pos);
602 <        atoms[local_index]->getVel(vel);
603 <
604 <        //format the line
605 <        sprintf( tempBuffer,
606 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
607 <                 atoms[local_index]->getType(),
608 <                 pos[0],
609 <                 pos[1],
610 <                 pos[2],
611 <                 vel[0],
612 <                 vel[1],
613 <                 vel[2]); // check here.
614 <        strcpy( writeLine, tempBuffer );
615 <
616 <        if( atoms[local_index]->isDirectional() ){
617 <
618 <          dAtom = (DirectionalAtom *)atoms[local_index];
619 <          dAtom->getQ( q );
620 <
621 <          sprintf( tempBuffer,
622 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
623 <                   q[0],
624 <                   q[1],
625 <                   q[2],
626 <                   q[3],
627 <                   dAtom->getJx(),
628 <                   dAtom->getJy(),
629 <                   dAtom->getJz());
630 <          strcat( writeLine, tempBuffer );
631 <        }
632 <        else{
633 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
634 <        }
635 <      }
636 <      else {
637 <        sprintf(painCave.errMsg,
638 <                "Atom %d not found on processor %d\n",
639 <                which_atom, worldRank );
640 <        myStatus = 0;
641 <        simError();
642 <
643 <        strcpy( writeLine, "Hello, I'm an error.\n");
644 <      }
645 <
646 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
647 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
648 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
649 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
650 <    }
651 <  }
652 <  finalOut.flush();
653 <  sprintf( checkPointMsg,
654 <           "Sucessfully took a dump.\n");
655 <  MPIcheckPoint();
656 <
657 <  if( worldRank == 0 ) finalOut.close();
621 >    sprintf( checkPointMsg,
622 >             "Sucessfully took a dump.\n");
623 >    MPIcheckPoint();        
624 >    
625 >  }
626 >  
627   #endif // is_mpi
628   }
629  
661 –
662 –
630   #ifdef IS_MPI
631  
632   // a couple of functions to let us escape the write loop
633  
634 < void dWrite::nodeZeroError( void ){
668 <  int j, myStatus;
634 > void dWrite::DieDieDie( void ){
635  
670 –  myStatus = 0;
671 –  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
672 –    MPI_Send( &myStatus, 1, MPI_INT, j,
673 –              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
674 –  }
675 –
676 –
636    MPI_Finalize();
637    exit (0);
679 –
638   }
639  
682 – void dWrite::anonymousNodeDie( void ){
683 –
684 –  MPI_Finalize();
685 –  exit (0);
686 – }
687 –
640   #endif //is_mpi

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