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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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>
12   #include "mpiSimulation.hpp"
10 – #define TAKE_THIS_TAG_CHAR 1
11 – #define TAKE_THIS_TAG_INT 2
13  
14   namespace dWrite{
15 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
15 >  void DieDieDie( void );
16   }
17  
18   using namespace dWrite;
# Line 29 | 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  
36 –    if( !outFile ){
37 –
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  
45 –    //outFile.setf( ios::scientific );
46 –
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 59 | 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 +  Atom** atoms = entry_plug->atoms;
92 +  
93 +  indexArray.clear();
94 +  
95 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 +  
98 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 + }
100 +
101 + #endif
102 +
103 + void DumpWriter::writeDump(double currentTime){
104 +
105 +  ofstream finalOut;
106 +  vector<ofstream*> fileStreams;
107 +
108 + #ifdef IS_MPI
109 +  if(worldRank == 0 ){
110 + #endif    
111 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 +    if( !finalOut ){
113 +      sprintf( painCave.errMsg,
114 +               "Could not open \"%s\" for final dump output.\n",
115 +               entry_plug->finalName );
116 +      painCave.isFatal = 1;
117 +      simError();
118 +    }
119 + #ifdef IS_MPI
120 +  }
121 + #endif // is_mpi
122 +
123 +  fileStreams.push_back(&finalOut);
124 +  fileStreams.push_back(&dumpFile);
125 +
126 +  writeFrame(fileStreams, currentTime);
127 +
128 + #ifdef IS_MPI
129 +  finalOut.close();
130 + #endif
131 +        
132 + }
133 +
134 + void DumpWriter::writeFinal(double currentTime){
135 +
136 +  ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138 +
139 + #ifdef IS_MPI
140 +  if(worldRank == 0 ){
141 + #endif // is_mpi
142 +
143 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144 +
145 +    if( !finalOut ){
146 +      sprintf( painCave.errMsg,
147 +               "Could not open \"%s\" for final dump output.\n",
148 +               entry_plug->finalName );
149 +      painCave.isFatal = 1;
150 +      simError();
151 +    }
152 +
153 + #ifdef IS_MPI
154 +  }
155 + #endif // is_mpi
156 +  
157 +  fileStreams.push_back(&finalOut);  
158 +  writeFrame(fileStreams, currentTime);
159 +
160 + #ifdef IS_MPI
161 +  finalOut.close();
162 + #endif
163 +  
164 + }
165 +
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167 +
168    const int BUFFERSIZE = 2000;
169 <  char tempBuffer[BUFFERSIZE];
169 >  const int MINIBUFFERSIZE = 100;
170 >
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174 <  int i;
174 >  int i, k;
175 >
176   #ifdef IS_MPI
177 <  int j, which_node, done, which_atom, local_index;
177 >  
178 >  /*********************************************************************
179 >   * Documentation?  You want DOCUMENTATION?
180 >   *
181 >   * Why all the potatoes below?  
182 >   *
183 >   * To make a long story short, the original version of DumpWriter
184 >   * worked in the most inefficient way possible.  Node 0 would
185 >   * poke each of the node for an individual atom's formatted data
186 >   * as node 0 worked its way down the global index. This was particularly
187 >   * inefficient since the method blocked all processors at every atom
188 >   * (and did it twice!).
189 >   *
190 >   * An intermediate version of DumpWriter could be described from Node
191 >   * zero's perspective as follows:
192 >   *
193 >   *  1) Have 100 of your friends stand in a circle.
194 >   *  2) When you say go, have all of them start tossing potatoes at
195 >   *     you (one at a time).
196 >   *  3) Catch the potatoes.
197 >   *
198 >   * It was an improvement, but MPI has buffers and caches that could
199 >   * best be described in this analogy as "potato nets", so there's no
200 >   * need to block the processors atom-by-atom.
201 >   *
202 >   * This new and improved DumpWriter works in an even more efficient
203 >   * way:
204 >   *
205 >   *  1) Have 100 of your friend stand in a circle.
206 >   *  2) When you say go, have them start tossing 5-pound bags of
207 >   *     potatoes at you.
208 >   *  3) Once you've caught a friend's bag of potatoes,
209 >   *     toss them a spud to let them know they can toss another bag.
210 >   *
211 >   * How's THAT for documentation?
212 >   *
213 >   *********************************************************************/
214 >
215 >  int *potatoes;
216 >  int myPotato;
217 >
218 >  int nProc;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220 >  double atomData6[6];
221 >  double atomData13[13];
222 >  int isDirectional;
223 >  char* atomTypeString;
224 >  char MPIatomTypeString[MINIBUFFERSIZE];
225 >
226   #else //is_mpi
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 <  double q[4];
230 >  double q[4], ji[3];
231    DirectionalAtom* dAtom;
232    Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
87 –
88 –  // write current frame to the eor file
89 –
90 –  this->writeFinal( currentTime );
91 –
235   #ifndef IS_MPI
236 +  
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239  
240 <  outFile << nAtoms << "\n";
240 >    *outFile[k] << currentTime << ";\t"
241 >               << entry_plug->Hmat[0][0] << "\t"
242 >                     << entry_plug->Hmat[1][0] << "\t"
243 >                     << entry_plug->Hmat[2][0] << ";\t"
244 >              
245 >               << entry_plug->Hmat[0][1] << "\t"
246 >                     << entry_plug->Hmat[1][1] << "\t"
247 >                     << entry_plug->Hmat[2][1] << ";\t"
248  
249 <  outFile << currentTime << ";\t"
250 <          << entry_plug->Hmat[0][0] << "\t"
251 <          << entry_plug->Hmat[1][0] << "\t"
99 <          << entry_plug->Hmat[2][0] << ";\t"
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252  
253 <          << entry_plug->Hmat[0][1] << "\t"
254 <          << entry_plug->Hmat[1][1] << "\t"
255 <          << entry_plug->Hmat[2][1] << ";\t"
256 <
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 <
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 >  }
256 >  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 129 | Line 274 | void DumpWriter::writeDump( double currentTime ){
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 136 | Line 282 | void DumpWriter::writeDump( double currentTime ){
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292  
293 <    outFile << writeLine;
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
149 –  outFile.flush();
296  
297   #else // is_mpi
298  
299 <  // first thing first, suspend fatalities.
300 <  painCave.isEventLoop = 1;
299 >  /* code to find maximum tag value */
300 >  
301 >  int *tagub, flag, MAXTAG;
302 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303 >  if (flag) {
304 >    MAXTAG = *tagub;
305 >  } else {
306 >    MAXTAG = 32767;
307 >  }  
308  
156 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
309    int haveError;
310  
311    MPI_Status istatus;
# Line 162 | Line 314 | void DumpWriter::writeDump( double currentTime ){
314    // write out header and node 0's coordinates
315  
316    if( worldRank == 0 ){
165 –    outFile << mpiSim->getTotAtoms() << "\n";
317  
318 <    outFile << currentTime << ";\t"
168 <            << entry_plug->Hmat[0][0] << "\t"
169 <            << entry_plug->Hmat[1][0] << "\t"
170 <            << entry_plug->Hmat[2][0] << ";\t"
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319  
320 <            << entry_plug->Hmat[0][1] << "\t"
321 <            << entry_plug->Hmat[1][1] << "\t"
322 <            << entry_plug->Hmat[2][1] << ";\t"
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322 >
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326 >    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <            << entry_plug->Hmat[0][2] << "\t"
331 <            << entry_plug->Hmat[1][2] << "\t"
332 <            << entry_plug->Hmat[2][2] << ";";
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334  
335 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
336 <    outFile << endl;
337 <    outFile.flush();
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345 >
346 >    currentIndex = 0;
347 >
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349 +      
350        // Get the Node number which has this atom;
351 <
351 >      
352        which_node = AtomToProcMap[i];
353 +      
354 +      if (which_node != 0) {
355  
356 <      if (which_node == 0 ) {
356 >        if (potatoes[which_node] + 3 >= MAXTAG) {
357 >          // The potato was going to exceed the maximum value,
358 >          // so wrap this processor potato back to 0:        
359  
360 <        haveError = 0;
361 <        which_atom = i;
362 <        local_index=-1;
193 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
194 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
360 >          potatoes[which_node] = 0;          
361 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 >          
363          }
196 –        if (local_index != -1) {
197 –          //format the line
364  
365 +        myPotato = potatoes[which_node];        
366 +        
367 +        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 +                 myPotato, MPI_COMM_WORLD, &istatus);
369 +        
370 +        atomTypeString = MPIatomTypeString;
371 +        
372 +        myPotato++;
373 +
374 +        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 +                 myPotato, MPI_COMM_WORLD, &istatus);
376 +              
377 +        myPotato++;
378 +
379 +        if (isDirectional) {          
380 +          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 +                   myPotato, MPI_COMM_WORLD, &istatus);
382 +        } else {
383 +          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 +                   myPotato, MPI_COMM_WORLD, &istatus);          
385 +        }
386 +        
387 +        myPotato++;
388 +        potatoes[which_node] = myPotato;
389 +
390 +      } else {
391 +        
392 +        haveError = 0;
393 +        which_atom = i;
394 +        
395 +          local_index = indexArray[currentIndex].first;        
396 +          
397 +          if (which_atom == indexArray[currentIndex].second) {
398 +            
399 +            atomTypeString = atoms[local_index]->getType();
400 +            
401            atoms[local_index]->getPos(pos);
402 <          atoms[local_index]->getVel(vel);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407  
408 <          sprintf( tempBuffer,
409 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
410 <                   atoms[local_index]->getType(),
411 <                   pos[0],
412 <                   pos[1],
207 <                   pos[2],
208 <                   vel[0],
209 <                   vel[1],
210 <                   vel[2]); // check here.
211 <          strcpy( writeLine, tempBuffer );
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411 >          
412 >          isDirectional = 0;
413  
414            if( atoms[local_index]->isDirectional() ){
415  
416 +            isDirectional = 1;
417 +            
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 +            dAtom->getJ( ji );
421  
422 <            sprintf( tempBuffer,
423 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
424 <                     q[0],
425 <                     q[1],
426 <                     q[2],
427 <                     q[3],
428 <                     dAtom->getJx(),
429 <                     dAtom->getJy(),
430 <                     dAtom->getJz());
431 <            strcat( writeLine, tempBuffer );
432 <
433 <          }
434 <          else
435 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232 <        }
233 <        else {
422 >            for (int j = 0; j < 6 ; j++)
423 >              atomData13[j] = atomData6[j];            
424 >            
425 >            atomData13[6] = q[0];
426 >            atomData13[7] = q[1];
427 >            atomData13[8] = q[2];
428 >            atomData13[9] = q[3];
429 >            
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433 >          }
434 >          
435 >        } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441          }
442 <
443 <        if(haveError) nodeZeroError();
444 <
442 >        
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 <      else {
448 <        myStatus = 1;
449 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
450 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
451 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
452 <                 MPI_COMM_WORLD);
453 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
454 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
455 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
456 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
457 <
458 <        if(!myStatus) nodeZeroError();
459 <
447 >      // If we've survived to here, format the line:
448 >      
449 >      if (!isDirectional) {
450 >        
451 >        sprintf( writeLine,
452 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                 atomTypeString,
454 >                 atomData6[0],
455 >                 atomData6[1],
456 >                 atomData6[2],
457 >                 atomData6[3],
458 >                 atomData6[4],
459 >                 atomData6[5]);
460 >        
461 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 >        
463 >      } else {
464 >        
465 >        sprintf( writeLine,
466 >                 "%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",
467 >                 atomTypeString,
468 >                 atomData13[0],
469 >                 atomData13[1],
470 >                 atomData13[2],
471 >                 atomData13[3],
472 >                 atomData13[4],
473 >                 atomData13[5],
474 >                 atomData13[6],
475 >                 atomData13[7],
476 >                 atomData13[8],
477 >                 atomData13[9],
478 >                 atomData13[10],
479 >                 atomData13[11],
480 >                 atomData13[12]);
481 >        
482        }
483 <
484 <      outFile << writeLine;
485 <      outFile.flush();
483 >      
484 >      for(k = 0; k < outFile.size(); k++)
485 >        *outFile[k] << writeLine;
486      }
487 <
488 <    // kill everyone off:
489 <    myStatus = -1;
490 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
491 <      MPI_Send(&myStatus, 1, MPI_INT, j,
492 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
493 <    }
494 <
487 >    
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491 >    sprintf( checkPointMsg,
492 >             "Sucessfully took a dump.\n");
493 >    
494 >    MPIcheckPoint();        
495 >    
496 >    delete[] potatoes;
497 >    
498    } else {
499  
500 <    done = 0;
273 <    while (!done) {
500 >    // worldRank != 0, so I'm a remote node.  
501  
502 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
276 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
502 >    // Set my magic potato to 0:
503  
504 <      if(!myStatus) anonymousNodeDie();
504 >    myPotato = 0;
505 >    currentIndex = 0;
506 >    
507 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508 >      
509 >      // Am I the node which has this atom?
510 >      
511 >      if (AtomToProcMap[i] == worldRank) {
512  
513 <      if(myStatus < 0) break;
513 >        if (myPotato + 3 >= MAXTAG) {
514 >          
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518 >          
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521 >        }
522 >        which_atom = i;
523  
524 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
525 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527 >        
528 >          atomTypeString = atoms[local_index]->getType();
529 >          
530 >          atoms[local_index]->getPos(pos);
531 >          atoms[local_index]->getVel(vel);
532 >          
533 >          atomData6[0] = pos[0];
534 >          atomData6[1] = pos[1];
535 >          atomData6[2] = pos[2];
536  
537 <      myStatus = 1;
538 <      local_index=-1;
539 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
540 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
541 <      }
290 <      if (local_index != -1) {
291 <        //format the line
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540 >          
541 >          isDirectional = 0;
542  
543 <        atoms[local_index]->getPos(pos);
294 <        atoms[local_index]->getVel(vel);
543 >          if( atoms[local_index]->isDirectional() ){
544  
545 <        sprintf( tempBuffer,
546 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
547 <                 atoms[local_index]->getType(),
548 <                 pos[0],
549 <                 pos[1],
550 <                 pos[2],
551 <                 vel[0],
552 <                 vel[1],
553 <                 vel[2]); // check here.
554 <        strcpy( writeLine, tempBuffer );
545 >            isDirectional = 1;
546 >            
547 >            dAtom = (DirectionalAtom *)atoms[local_index];
548 >            dAtom->getQ( q );
549 >            dAtom->getJ( ji );
550 >            
551 >            for (int j = 0; j < 6 ; j++)
552 >              atomData13[j] = atomData6[j];
553 >            
554 >            atomData13[6] = q[0];
555 >            atomData13[7] = q[1];
556 >            atomData13[8] = q[2];
557 >            atomData13[9] = q[3];
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562 >          }
563  
564 <        if( atoms[local_index]->isDirectional() ){
565 <
566 <          dAtom = (DirectionalAtom *)atoms[local_index];
567 <          dAtom->getQ( q );
568 <
569 <          sprintf( tempBuffer,
313 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
314 <                   q[0],
315 <                   q[1],
316 <                   q[2],
317 <                   q[3],
318 <                   dAtom->getJx(),
319 <                   dAtom->getJy(),
320 <                   dAtom->getJz());
321 <          strcat( writeLine, tempBuffer );
564 >        } else {
565 >          sprintf(painCave.errMsg,
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568 >          haveError= 1;
569 >          simError();
570          }
571 <        else{
572 <          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();
571 >        
572 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574 <        strcpy( writeLine, "Hello, I'm an error.\n");
575 <      }
574 >        // null terminate the string before sending (just in case):
575 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576  
577 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
578 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
579 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
580 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
341 <    }
342 <  }
343 <  outFile.flush();
344 <  sprintf( checkPointMsg,
345 <           "Sucessfully took a dump.\n");
346 <  MPIcheckPoint();
577 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 >                             myPotato, MPI_COMM_WORLD);
579 >        
580 >        myPotato++;
581  
582 < // last  thing last, enable  fatalities.
583 <  painCave.isEventLoop = 0;
582 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 >                             myPotato, MPI_COMM_WORLD);
584 >        
585 >        myPotato++;
586 >        
587 >        if (isDirectional) {
588  
589 < #endif // is_mpi
590 < }
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591 >          
592 >        } else {
593  
594 < void DumpWriter::writeFinal(double finalTime){
595 <
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;
594 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 >                   myPotato, MPI_COMM_WORLD);
596          }
508 –        if (local_index != -1) {
597  
598 <          atoms[local_index]->getPos(pos);
599 <          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 <
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
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;
601      }
602  
603 <    // kill everyone off:
604 <    myStatus = -1;
605 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
606 <      MPI_Send(&myStatus, 1, MPI_INT, j,
607 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
608 <    }
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();
603 >    sprintf( checkPointMsg,
604 >             "Sucessfully took a dump.\n");
605 >    MPIcheckPoint();        
606 >    
607 >  }
608 >  
609   #endif // is_mpi
610   }
611  
661 –
662 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop
615  
616 < void dWrite::nodeZeroError( void ){
668 <  int j, myStatus;
616 > void dWrite::DieDieDie( void ){
617  
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 –
618    MPI_Finalize();
619    exit (0);
679 –
620   }
621  
682 – void dWrite::anonymousNodeDie( void ){
683 –
684 –  MPI_Finalize();
685 –  exit (0);
686 – }
687 –
622   #endif //is_mpi

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