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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 952 by tim, Fri Jan 16 21:55:39 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 +  if(worldRank == 0 ){
114 + #endif    
115 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 +    if( !finalOut ){
117 +      sprintf( painCave.errMsg,
118 +               "Could not open \"%s\" for final dump output.\n",
119 +               entry_plug->finalName );
120 +      painCave.isFatal = 1;
121 +      simError();
122 +    }
123 + #ifdef IS_MPI
124 +  }
125 + #endif // is_mpi
126 +
127 +  fileStreams.push_back(&finalOut);
128 +  fileStreams.push_back(&dumpFile);
129 +
130 +  writeFrame(fileStreams, currentTime);
131 +
132 + #ifdef IS_MPI
133 +  finalOut.close();
134 + #endif
135 +        
136 + }
137 +
138 + void DumpWriter::writeFinal(double currentTime){
139 +
140 +  ofstream finalOut;
141 +  vector<ofstream*> fileStreams;
142 +
143 + #ifdef IS_MPI
144 +  if(worldRank == 0 ){
145 + #endif // is_mpi
146 +
147 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 +
149 +    if( !finalOut ){
150 +      sprintf( painCave.errMsg,
151 +               "Could not open \"%s\" for final dump output.\n",
152 +               entry_plug->finalName );
153 +      painCave.isFatal = 1;
154 +      simError();
155 +    }
156 +
157 + #ifdef IS_MPI
158 +  }
159 + #endif // is_mpi
160 +  
161 +  fileStreams.push_back(&finalOut);  
162 +  writeFrame(fileStreams, currentTime);
163 +
164 + #ifdef IS_MPI
165 +  finalOut.close();
166 + #endif
167 +  
168 + }
169 +
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171 +
172    const int BUFFERSIZE = 2000;
173 <  char tempBuffer[BUFFERSIZE];
173 >  const int MINIBUFFERSIZE = 100;
174 >
175 >  char tempBuffer[BUFFERSIZE];  
176    char writeLine[BUFFERSIZE];
177  
178 <  int i;
178 >  int i, k;
179 >
180   #ifdef IS_MPI
181 <  int j, which_node, done, which_atom, local_index;
181 >  
182 >  /*********************************************************************
183 >   * Documentation?  You want DOCUMENTATION?
184 >   *
185 >   * Why all the potatoes below?  
186 >   *
187 >   * To make a long story short, the original version of DumpWriter
188 >   * worked in the most inefficient way possible.  Node 0 would
189 >   * poke each of the node for an individual atom's formatted data
190 >   * as node 0 worked its way down the global index. This was particularly
191 >   * inefficient since the method blocked all processors at every atom
192 >   * (and did it twice!).
193 >   *
194 >   * An intermediate version of DumpWriter could be described from Node
195 >   * zero's perspective as follows:
196 >   *
197 >   *  1) Have 100 of your friends stand in a circle.
198 >   *  2) When you say go, have all of them start tossing potatoes at
199 >   *     you (one at a time).
200 >   *  3) Catch the potatoes.
201 >   *
202 >   * It was an improvement, but MPI has buffers and caches that could
203 >   * best be described in this analogy as "potato nets", so there's no
204 >   * need to block the processors atom-by-atom.
205 >   *
206 >   * This new and improved DumpWriter works in an even more efficient
207 >   * way:
208 >   *
209 >   *  1) Have 100 of your friend stand in a circle.
210 >   *  2) When you say go, have them start tossing 5-pound bags of
211 >   *     potatoes at you.
212 >   *  3) Once you've caught a friend's bag of potatoes,
213 >   *     toss them a spud to let them know they can toss another bag.
214 >   *
215 >   * How's THAT for documentation?
216 >   *
217 >   *********************************************************************/
218 >
219 >  int *potatoes;
220 >  int myPotato;
221 >
222 >  int nProc;
223 >  int j, which_node, done, which_atom, local_index, currentIndex;
224 >  double atomData6[6];
225 >  double atomData13[13];
226 >  int isDirectional;
227 >  char* atomTypeString;
228 >  char MPIatomTypeString[MINIBUFFERSIZE];
229 >
230   #else //is_mpi
231    int nAtoms = entry_plug->n_atoms;
232   #endif //is_mpi
# Line 84 | Line 236 | void DumpWriter::writeDump( double currentTime ){
236    Atom** atoms = entry_plug->atoms;
237    double pos[3], vel[3];
238  
87 –
88 –  // write current frame to the eor file
89 –
90 –  this->writeFinal( currentTime );
91 –
239   #ifndef IS_MPI
240 +  
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243  
244 <  outFile << nAtoms << "\n";
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252  
253 <  outFile << currentTime << ";\t"
254 <          << entry_plug->Hmat[0][0] << "\t"
255 <          << entry_plug->Hmat[1][0] << "\t"
99 <          << entry_plug->Hmat[2][0] << ";\t"
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256  
257 <          << entry_plug->Hmat[0][1] << "\t"
258 <          << entry_plug->Hmat[1][1] << "\t"
259 <          << entry_plug->Hmat[2][1] << ";\t"
260 <
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 <
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 >  }
260 >  
261    for( i=0; i<nAtoms; i++ ){
262  
263      atoms[i]->getPos(pos);
# Line 144 | Line 293 | void DumpWriter::writeDump( double currentTime ){
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295  
296 <    outFile << writeLine;
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
149 –  outFile.flush();
299  
300   #else // is_mpi
301  
302 <  // first thing first, suspend fatalities.
303 <  painCave.isEventLoop = 1;
302 >  /* code to find maximum tag value */
303 >  
304 >  int *tagub, flag, MAXTAG;
305 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306 >  if (flag) {
307 >    MAXTAG = *tagub;
308 >  } else {
309 >    MAXTAG = 32767;
310 >  }  
311  
156 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
312    int haveError;
313  
314    MPI_Status istatus;
# Line 162 | Line 317 | void DumpWriter::writeDump( double currentTime ){
317    // write out header and node 0's coordinates
318  
319    if( worldRank == 0 ){
165 –    outFile << mpiSim->getTotAtoms() << "\n";
320  
321 <    outFile << currentTime << ";\t"
168 <            << entry_plug->Hmat[0][0] << "\t"
169 <            << entry_plug->Hmat[1][0] << "\t"
170 <            << entry_plug->Hmat[2][0] << ";\t"
321 >    // Node 0 needs a list of the magic potatoes for each processor;
322  
323 <            << entry_plug->Hmat[0][1] << "\t"
324 <            << entry_plug->Hmat[1][1] << "\t"
174 <            << entry_plug->Hmat[2][1] << ";\t"
323 >    nProc = mpiSim->getNumberProcessors();
324 >    potatoes = new int[nProc];
325  
326 <            << entry_plug->Hmat[0][2] << "\t"
327 <            << entry_plug->Hmat[1][2] << "\t"
328 <            << entry_plug->Hmat[2][2] << ";";
326 >    //write out the comment lines
327 >    for (i = 0; i < nProc; i++)
328 >      potatoes[i] = 0;
329 >    
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332  
333 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
334 <    outFile << endl;
335 <    outFile.flush();
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341 >
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348 >
349 >    currentIndex = 0;
350 >
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352 +      
353        // Get the Node number which has this atom;
354 <
354 >      
355        which_node = AtomToProcMap[i];
356 +      
357 +      if (which_node != 0) {
358  
359 <      if (which_node == 0 ) {
359 >        if (potatoes[which_node] + 3 >= MAXTAG) {
360 >          // The potato was going to exceed the maximum value,
361 >          // so wrap this processor potato back to 0:        
362  
363 <        haveError = 0;
364 <        which_atom = i;
365 <        local_index=-1;
193 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
194 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
363 >          potatoes[which_node] = 0;          
364 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
365 >          
366          }
196 –        if (local_index != -1) {
197 –          //format the line
367  
368 +        myPotato = potatoes[which_node];        
369 +        
370 +        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371 +                 myPotato, MPI_COMM_WORLD, &istatus);
372 +        
373 +        atomTypeString = MPIatomTypeString;
374 +        
375 +        myPotato++;
376 +
377 +        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
378 +                 myPotato, MPI_COMM_WORLD, &istatus);
379 +              
380 +        myPotato++;
381 +
382 +        if (isDirectional) {          
383 +          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384 +                   myPotato, MPI_COMM_WORLD, &istatus);
385 +        } else {
386 +          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387 +                   myPotato, MPI_COMM_WORLD, &istatus);          
388 +        }
389 +        
390 +        myPotato++;
391 +        potatoes[which_node] = myPotato;
392 +
393 +      } else {
394 +        
395 +        haveError = 0;
396 +        which_atom = i;
397 +        
398 +        //local_index = -1;
399 +
400 +        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 +        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 +        //}
403 +        
404 +        //if (local_index != -1) {
405 +          
406 +          local_index = indexArray[currentIndex].first;        
407 +          
408 +          if (which_atom == indexArray[currentIndex].second) {
409 +            
410 +            atomTypeString = atoms[local_index]->getType();
411 +            
412            atoms[local_index]->getPos(pos);
413 <          atoms[local_index]->getVel(vel);
413 >          atoms[local_index]->getVel(vel);          
414 >          
415 >          atomData6[0] = pos[0];
416 >          atomData6[1] = pos[1];
417 >          atomData6[2] = pos[2];
418  
419 <          sprintf( tempBuffer,
420 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
421 <                   atoms[local_index]->getType(),
422 <                   pos[0],
423 <                   pos[1],
207 <                   pos[2],
208 <                   vel[0],
209 <                   vel[1],
210 <                   vel[2]); // check here.
211 <          strcpy( writeLine, tempBuffer );
419 >          atomData6[3] = vel[0];
420 >          atomData6[4] = vel[1];
421 >          atomData6[5] = vel[2];
422 >          
423 >          isDirectional = 0;
424  
425            if( atoms[local_index]->isDirectional() ){
426  
427 +            isDirectional = 1;
428 +            
429              dAtom = (DirectionalAtom *)atoms[local_index];
430              dAtom->getQ( q );
431  
432 <            sprintf( tempBuffer,
433 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
434 <                     q[0],
435 <                     q[1],
436 <                     q[2],
437 <                     q[3],
438 <                     dAtom->getJx(),
439 <                     dAtom->getJy(),
440 <                     dAtom->getJz());
441 <            strcat( writeLine, tempBuffer );
442 <
443 <          }
444 <          else
445 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232 <        }
233 <        else {
432 >            for (int j = 0; j < 6 ; j++)
433 >              atomData13[j] = atomData6[j];            
434 >            
435 >            atomData13[6] = q[0];
436 >            atomData13[7] = q[1];
437 >            atomData13[8] = q[2];
438 >            atomData13[9] = q[3];
439 >            
440 >            atomData13[10] = dAtom->getJx();
441 >            atomData13[11] = dAtom->getJy();
442 >            atomData13[12] = dAtom->getJz();
443 >          }
444 >          
445 >        } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451          }
452 <
453 <        if(haveError) nodeZeroError();
454 <
452 >        
453 >        if(haveError) DieDieDie();
454 >        
455 >        currentIndex++;
456        }
457 <      else {
458 <        myStatus = 1;
459 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
460 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
461 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
462 <                 MPI_COMM_WORLD);
463 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
464 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
465 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
466 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
467 <
468 <        if(!myStatus) nodeZeroError();
469 <
457 >      // If we've survived to here, format the line:
458 >      
459 >      if (!isDirectional) {
460 >        
461 >        sprintf( writeLine,
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470 >        
471 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 >        
473 >      } else {
474 >        
475 >        sprintf( writeLine,
476 >                 "%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",
477 >                 atomTypeString,
478 >                 atomData13[0],
479 >                 atomData13[1],
480 >                 atomData13[2],
481 >                 atomData13[3],
482 >                 atomData13[4],
483 >                 atomData13[5],
484 >                 atomData13[6],
485 >                 atomData13[7],
486 >                 atomData13[8],
487 >                 atomData13[9],
488 >                 atomData13[10],
489 >                 atomData13[11],
490 >                 atomData13[12]);
491 >        
492        }
493 <
494 <      outFile << writeLine;
495 <      outFile.flush();
493 >      
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
497 <
498 <    // kill everyone off:
499 <    myStatus = -1;
500 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
501 <      MPI_Send(&myStatus, 1, MPI_INT, j,
502 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
503 <    }
504 <
497 >    
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501 >    sprintf( checkPointMsg,
502 >             "Sucessfully took a dump.\n");
503 >    
504 >    MPIcheckPoint();        
505 >    
506 >    delete[] potatoes;
507 >    
508    } else {
509  
510 <    done = 0;
273 <    while (!done) {
510 >    // worldRank != 0, so I'm a remote node.  
511  
512 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
276 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
512 >    // Set my magic potato to 0:
513  
514 <      if(!myStatus) anonymousNodeDie();
515 <
516 <      if(myStatus < 0) break;
514 >    myPotato = 0;
515 >    currentIndex = 0;
516 >    
517 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518 >      
519 >      // Am I the node which has this atom?
520 >      
521 >      if (AtomToProcMap[i] == worldRank) {
522  
523 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
524 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
523 >        if (myPotato + 3 >= MAXTAG) {
524 >          
525 >          // The potato was going to exceed the maximum value,
526 >          // so wrap this processor potato back to 0 (and block until
527 >          // node 0 says we can go:
528 >          
529 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530 >          
531 >        }
532 >        which_atom = i;
533  
534 <      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
534 >        //local_index = -1;
535  
536 <        atoms[local_index]->getPos(pos);
537 <        atoms[local_index]->getVel(vel);
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541  
542 <        sprintf( tempBuffer,
543 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
544 <                 atoms[local_index]->getType(),
545 <                 pos[0],
546 <                 pos[1],
547 <                 pos[2],
548 <                 vel[0],
549 <                 vel[1],
550 <                 vel[2]); // check here.
551 <        strcpy( writeLine, tempBuffer );
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545 >        
546 >          atomTypeString = atoms[local_index]->getType();
547 >          
548 >          atoms[local_index]->getPos(pos);
549 >          atoms[local_index]->getVel(vel);
550 >          
551 >          atomData6[0] = pos[0];
552 >          atomData6[1] = pos[1];
553 >          atomData6[2] = pos[2];
554  
555 <        if( atoms[local_index]->isDirectional() ){
555 >          atomData6[3] = vel[0];
556 >          atomData6[4] = vel[1];
557 >          atomData6[5] = vel[2];
558 >          
559 >          isDirectional = 0;
560  
561 <          dAtom = (DirectionalAtom *)atoms[local_index];
310 <          dAtom->getQ( q );
561 >          if( atoms[local_index]->isDirectional() ){
562  
563 <          sprintf( tempBuffer,
564 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
565 <                   q[0],
566 <                   q[1],
567 <                   q[2],
568 <                   q[3],
569 <                   dAtom->getJx(),
570 <                   dAtom->getJy(),
571 <                   dAtom->getJz());
572 <          strcat( writeLine, tempBuffer );
563 >            isDirectional = 1;
564 >            
565 >            dAtom = (DirectionalAtom *)atoms[local_index];
566 >            dAtom->getQ( q );
567 >            
568 >            for (int j = 0; j < 6 ; j++)
569 >              atomData13[j] = atomData6[j];
570 >            
571 >            atomData13[6] = q[0];
572 >            atomData13[7] = q[1];
573 >            atomData13[8] = q[2];
574 >            atomData13[9] = q[3];
575 >  
576 >            atomData13[10] = dAtom->getJx();
577 >            atomData13[11] = dAtom->getJy();
578 >            atomData13[12] = dAtom->getJz();
579 >          }
580 >
581 >        } else {
582 >          sprintf(painCave.errMsg,
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585 >          haveError= 1;
586 >          simError();
587          }
588 <        else{
589 <          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();
588 >        
589 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591 <        strcpy( writeLine, "Hello, I'm an error.\n");
592 <      }
591 >        // null terminate the string before sending (just in case):
592 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593  
594 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
595 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
596 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
597 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
341 <    }
342 <  }
343 <  outFile.flush();
344 <  sprintf( checkPointMsg,
345 <           "Sucessfully took a dump.\n");
346 <  MPIcheckPoint();
594 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 >                             myPotato, MPI_COMM_WORLD);
596 >        
597 >        myPotato++;
598  
599 < // last  thing last, enable  fatalities.
600 <  painCave.isEventLoop = 0;
599 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >        
602 >        myPotato++;
603 >        
604 >        if (isDirectional) {
605  
606 < #endif // is_mpi
607 < }
606 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
607 >                   myPotato, MPI_COMM_WORLD);
608 >          
609 >        } else {
610  
611 < void DumpWriter::writeFinal(double finalTime){
612 <
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;
611 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
612 >                   myPotato, MPI_COMM_WORLD);
613          }
508 –        if (local_index != -1) {
614  
615 <          atoms[local_index]->getPos(pos);
616 <          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 <
615 >        myPotato++;  
616 >        currentIndex++;    
617        }
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;
618      }
619  
620 <    // kill everyone off:
621 <    myStatus = -1;
622 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
623 <      MPI_Send(&myStatus, 1, MPI_INT, j,
624 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
625 <    }
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();
620 >    sprintf( checkPointMsg,
621 >             "Sucessfully took a dump.\n");
622 >    MPIcheckPoint();        
623 >    
624 >  }
625 >  
626   #endif // is_mpi
627   }
628  
661 –
662 –
629   #ifdef IS_MPI
630  
631   // a couple of functions to let us escape the write loop
632  
633 < void dWrite::nodeZeroError( void ){
668 <  int j, myStatus;
633 > void dWrite::DieDieDie( void ){
634  
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 –
635    MPI_Finalize();
636    exit (0);
679 –
637   }
638  
682 – void dWrite::anonymousNodeDie( void ){
683 –
684 –  MPI_Finalize();
685 –  exit (0);
686 – }
687 –
639   #endif //is_mpi

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