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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 829 by gezelter, Tue Oct 28 16:03:37 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 28 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28   #ifdef IS_MPI
29    if(worldRank == 0 ){
30   #endif // is_mpi
31 <    
32 <    strcpy( outName, entry_plug->sampleName );
33 <    
34 <    outFile.open(outName, ios::out | ios::trunc );
35 <    
36 <    if( !outFile ){
37 <      
31 >
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33 >
34 >    if( !dumpFile ){
35 >
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];
86 –    
87 –  
88 –  // write current frame to the eor file
234  
90 –  this->writeFinal( currentTime );
91 –
235   #ifndef IS_MPI
236 <    
237 <  outFile << nAtoms << "\n";
238 <    
96 <  outFile << currentTime << ";\t"
97 <          << entry_plug->Hmat[0][0] << "\t"
98 <          << entry_plug->Hmat[1][0] << "\t"
99 <          << entry_plug->Hmat[2][0] << ";\t"
236 >  
237 >  for(k = 0; k < outFile.size(); k++){
238 >    *outFile[k] << nAtoms << "\n";
239  
240 <          << entry_plug->Hmat[0][1] << "\t"
241 <          << entry_plug->Hmat[1][1] << "\t"
242 <          << entry_plug->Hmat[2][1] << ";\t"
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 <          << entry_plug->Hmat[0][2] << "\t"
250 <          << entry_plug->Hmat[1][2] << "\t"
251 <          << entry_plug->Hmat[2][2] << ";\n";
252 <    
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252 >
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 <      
258 >
259      atoms[i]->getPos(pos);
260      atoms[i]->getVel(vel);
261  
# Line 123 | Line 271 | void DumpWriter::writeDump( double currentTime ){
271      strcpy( writeLine, tempBuffer );
272  
273      if( atoms[i]->isDirectional() ){
274 <        
274 >
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 <        
277 >      dAtom->getJ( ji );
278 >
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
281                 q[0],
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;
292 >
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
146 –  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  
153 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
309    int haveError;
310  
311    MPI_Status istatus;
312    int *AtomToProcMap = mpiSim->getAtomToProcMap();
313 <  
313 >
314    // write out header and node 0's coordinates
315 <  
315 >
316    if( worldRank == 0 ){
317 <    outFile << mpiSim->getTotAtoms() << "\n";
318 <  
319 <    outFile << currentTime << ";\t"
320 <            << entry_plug->Hmat[0][0] << "\t"
321 <            << entry_plug->Hmat[1][0] << "\t"
322 <            << entry_plug->Hmat[2][0] << ";\t"
323 <      
324 <            << entry_plug->Hmat[0][1] << "\t"
325 <            << entry_plug->Hmat[1][1] << "\t"
171 <            << entry_plug->Hmat[2][1] << ";\t"
172 <      
173 <            << entry_plug->Hmat[0][2] << "\t"
174 <            << entry_plug->Hmat[1][2] << "\t"
175 <            << entry_plug->Hmat[2][2] << ";\n";
317 >
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319 >
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 <    outFile.flush();
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329 >
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 >                         << 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        
352 <      which_node = AtomToProcMap[i];    
352 >      which_node = AtomToProcMap[i];
353        
354 <      if (which_node == 0 ) {
354 >      if (which_node != 0) {
355 >
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 >          potatoes[which_node] = 0;          
361 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 >          
363 >        }
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 <        haveError = 0;
373 <        which_atom = i;
374 <        local_index=-1;        
375 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
376 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
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 <        if (local_index != -1) {
387 <          //format the line
388 <          
194 <          atoms[local_index]->getPos(pos);
195 <          atoms[local_index]->getVel(vel);
386 >        
387 >        myPotato++;
388 >        potatoes[which_node] = myPotato;
389  
390 <          sprintf( tempBuffer,
391 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392 <                   atoms[local_index]->getType(),
393 <                   pos[0],
394 <                   pos[1],
395 <                   pos[2],
396 <                   vel[0],
397 <                   vel[1],
398 <                   vel[2]); // check here.
399 <          strcpy( writeLine, tempBuffer );
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);          
403            
404 +          atomData6[0] = pos[0];
405 +          atomData6[1] = pos[1];
406 +          atomData6[2] = pos[2];
407 +
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 +            for (int j = 0; j < 6 ; j++)
423 +              atomData13[j] = atomData6[j];            
424              
425 <            sprintf( tempBuffer,
426 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
427 <                     q[0],
428 <                     q[1],
429 <                     q[2],
430 <                     q[3],
431 <                     dAtom->getJx(),
432 <                     dAtom->getJy(),
433 <                     dAtom->getJz());
434 <            strcat( writeLine, tempBuffer );
435 <            
224 <          }
225 <          else
226 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
227 <        }
228 <        else {
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 <
441 >        }
442 >        
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 <      else {
448 <        myStatus = 1;
449 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
242 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
243 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
244 <                 MPI_COMM_WORLD);
245 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
246 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
247 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
248 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
447 >      // If we've survived to here, format the line:
448 >      
449 >      if (!isDirectional) {
450          
451 <        if(!myStatus) nodeZeroError();
452 <
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();
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 <
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 +    // worldRank != 0, so I'm a remote node.  
501 +
502 +    // Set my magic potato to 0:
503 +
504 +    myPotato = 0;
505 +    currentIndex = 0;
506      
507 <    done = 0;
268 <    while (!done) {
507 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
509 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
271 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272 <
273 <      if(!myStatus) anonymousNodeDie();
509 >      // Am I the node which has this atom?
510        
511 <      if(myStatus < 0) break;
511 >      if (AtomToProcMap[i] == worldRank) {
512  
513 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
514 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
515 <      
516 <      myStatus = 1;
517 <      local_index=-1;        
518 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
519 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
520 <      }
521 <      if (local_index != -1) {
522 <        //format the line
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 <        atoms[local_index]->getPos(pos);
525 <        atoms[local_index]->getVel(vel);
526 <
527 <        sprintf( tempBuffer,
528 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
293 <                 atoms[local_index]->getType(),
294 <                 pos[0],
295 <                 pos[1],
296 <                 pos[2],
297 <                 vel[0],
298 <                 vel[1],
299 <                 vel[2]); // check here.
300 <        strcpy( writeLine, tempBuffer );
301 <        
302 <        if( atoms[local_index]->isDirectional() ){
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527 >        
528 >          atomTypeString = atoms[local_index]->getType();
529            
530 <          dAtom = (DirectionalAtom *)atoms[local_index];
531 <          dAtom->getQ( q );
530 >          atoms[local_index]->getPos(pos);
531 >          atoms[local_index]->getVel(vel);
532            
533 <          sprintf( tempBuffer,
534 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
535 <                   q[0],
310 <                   q[1],
311 <                   q[2],
312 <                   q[3],
313 <                   dAtom->getJx(),
314 <                   dAtom->getJy(),
315 <                   dAtom->getJz());
316 <          strcat( writeLine, tempBuffer );
317 <        }
318 <        else{
319 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
320 <        }
321 <      }
322 <      else {
323 <        sprintf(painCave.errMsg,
324 <                "Atom %d not found on processor %d\n",
325 <                which_atom, worldRank );
326 <        myStatus = 0;
327 <        simError();
533 >          atomData6[0] = pos[0];
534 >          atomData6[1] = pos[1];
535 >          atomData6[2] = pos[2];
536  
537 <        strcpy( writeLine, "Hello, I'm an error.\n");
538 <      }
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540 >          
541 >          isDirectional = 0;
542  
543 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
333 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
334 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
335 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
336 <    }
337 <  }  
338 <  outFile.flush();
339 <  sprintf( checkPointMsg,
340 <           "Sucessfully took a dump.\n");
341 <  MPIcheckPoint();
543 >          if( atoms[local_index]->isDirectional() ){
544  
545 < // last  thing last, enable  fatalities.
546 <  painCave.isEventLoop = 0;
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 < #endif // is_mpi
565 < }
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 >        
572 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574 < void DumpWriter::writeFinal(double finalTime){
574 >        // null terminate the string before sending (just in case):
575 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576  
577 <  char finalName[500];
578 <  ofstream finalOut;
577 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 >                             myPotato, MPI_COMM_WORLD);
579 >        
580 >        myPotato++;
581  
582 <  const int BUFFERSIZE = 2000;
583 <  char tempBuffer[BUFFERSIZE];
584 <  char writeLine[BUFFERSIZE];  
582 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 >                             myPotato, MPI_COMM_WORLD);
584 >        
585 >        myPotato++;
586 >        
587 >        if (isDirectional) {
588  
589 <  double q[4];
590 <  DirectionalAtom* dAtom;
591 <  Atom** atoms = entry_plug->atoms;
592 <  int i;
362 < #ifdef IS_MPI
363 <  int j, which_node, done, which_atom, local_index;
364 < #else //is_mpi
365 <  int nAtoms = entry_plug->n_atoms;
366 < #endif //is_mpi
367 <  
368 <  double pos[3], vel[3];
369 <  
370 < #ifdef IS_MPI
371 <  if(worldRank == 0 ){
372 < #endif // is_mpi
373 <    
374 <    strcpy( finalName, entry_plug->finalName );
375 <    
376 <    finalOut.open( finalName, ios::out | ios::trunc );
377 <    if( !finalOut ){
378 <      sprintf( painCave.errMsg,
379 <               "Could not open \"%s\" for final dump output.\n",
380 <               finalName );
381 <      painCave.isFatal = 1;
382 <      simError();
383 <    }
384 <    
385 <    // finalOut.setf( ios::scientific );
386 <    
387 < #ifdef IS_MPI
388 <  }
389 <  
390 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
391 <  MPIcheckPoint();  
392 <  
393 < #endif //is_mpi
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591 >          
592 >        } else {
593  
594 <  
595 < #ifndef IS_MPI
397 <    
398 <  finalOut << nAtoms << "\n";
399 <    
400 <  finalOut << finalTime << ";\t"
401 <           << entry_plug->Hmat[0][0] << "\t"
402 <           << entry_plug->Hmat[1][0] << "\t"
403 <           << entry_plug->Hmat[2][0] << ";\t"
404 <    
405 <           << entry_plug->Hmat[0][1] << "\t"
406 <           << entry_plug->Hmat[1][1] << "\t"
407 <           << entry_plug->Hmat[2][1] << ";\t"
408 <    
409 <           << entry_plug->Hmat[0][2] << "\t"
410 <           << entry_plug->Hmat[1][2] << "\t"
411 <           << entry_plug->Hmat[2][2] << ";\n";
412 <  
413 <  for( i=0; i<nAtoms; i++ ){
414 <      
415 <    atoms[i]->getPos(pos);
416 <    atoms[i]->getVel(vel);
417 <    
418 <    sprintf( tempBuffer,
419 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
420 <             atoms[i]->getType(),
421 <             pos[0],
422 <             pos[1],
423 <             pos[2],
424 <             vel[0],
425 <             vel[1],
426 <             vel[2]);
427 <    strcpy( writeLine, tempBuffer );
428 <
429 <    if( atoms[i]->isDirectional() ){
430 <        
431 <      dAtom = (DirectionalAtom *)atoms[i];
432 <      dAtom->getQ( q );
433 <        
434 <      sprintf( tempBuffer,
435 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
436 <               q[0],
437 <               q[1],
438 <               q[2],
439 <               q[3],
440 <               dAtom->getJx(),
441 <               dAtom->getJy(),
442 <               dAtom->getJz());
443 <      strcat( writeLine, tempBuffer );
444 <    }
445 <    else
446 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
447 <      
448 <    finalOut << writeLine;
449 <  }
450 <  finalOut.flush();
451 <  finalOut.close();
452 <
453 < #else // is_mpi
454 <  
455 <  // first thing first, suspend fatalities.
456 <  painCave.isEventLoop = 1;
457 <
458 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
459 <  int haveError;
460 <
461 <  MPI_Status istatus;
462 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
463 <
464 <  // write out header and node 0's coordinates
465 <  
466 <  haveError = 0;
467 <  if( worldRank == 0 ){
468 <    finalOut << mpiSim->getTotAtoms() << "\n";
469 <    
470 <    finalOut << finalTime << ";\t"
471 <             << entry_plug->Hmat[0][0] << "\t"
472 <             << entry_plug->Hmat[1][0] << "\t"
473 <             << entry_plug->Hmat[2][0] << ";\t"
474 <      
475 <             << entry_plug->Hmat[0][1] << "\t"
476 <             << entry_plug->Hmat[1][1] << "\t"
477 <             << entry_plug->Hmat[2][1] << ";\t"
478 <      
479 <             << entry_plug->Hmat[0][2] << "\t"
480 <             << entry_plug->Hmat[1][2] << "\t"
481 <             << entry_plug->Hmat[2][2] << ";\n";
482 <    
483 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
484 <      // Get the Node number which has this molecule:
485 <      
486 <      which_node = AtomToProcMap[i];    
487 <      
488 <      if (which_node == mpiSim->getMyNode()) {
489 <
490 <        which_atom = i;
491 <        local_index=-1;        
492 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
493 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
594 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 >                   myPotato, MPI_COMM_WORLD);
596          }
495 –        if (local_index != -1) {    
597  
598 <          atoms[local_index]->getPos(pos);
599 <          atoms[local_index]->getVel(vel);
499 <          
500 <          sprintf( tempBuffer,
501 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
502 <                   atoms[local_index]->getType(),
503 <                   pos[0],
504 <                   pos[1],
505 <                   pos[2],
506 <                   vel[0],
507 <                   vel[1],
508 <                   vel[2]);
509 <          strcpy( writeLine, tempBuffer );
510 <          
511 <          if( atoms[local_index]->isDirectional() ){
512 <            
513 <            dAtom = (DirectionalAtom *)atoms[local_index];
514 <            dAtom->getQ( q );
515 <            
516 <            sprintf( tempBuffer,
517 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
518 <                     q[0],
519 <                     q[1],
520 <                     q[2],
521 <                     q[3],
522 <                     dAtom->getJx(),
523 <                     dAtom->getJy(),
524 <                     dAtom->getJz());
525 <            strcat( writeLine, tempBuffer );
526 <          }
527 <          else
528 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
529 <        }
530 <        else {
531 <          sprintf(painCave.errMsg,
532 <                  "Atom %d not found on processor %d\n",
533 <                  i, worldRank );
534 <          haveError= 1;
535 <          simError();
536 <        }
537 <
538 <        if(haveError) nodeZeroError();
539 <    
540 <      }
541 <      else {
542 <        
543 <        myStatus = 1;
544 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
545 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
546 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
547 <                 MPI_COMM_WORLD);
548 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
549 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
550 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
551 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
552 <        
553 <        if(!myStatus) nodeZeroError();
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
555 –      
556 –      finalOut << writeLine;
601      }
558 –    
559 –    // kill everyone off:
560 –    myStatus = -1;
561 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
562 –      MPI_Send(&myStatus, 1, MPI_INT, j,
563 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
564 –    }
602  
603 <  } else {
603 >    sprintf( checkPointMsg,
604 >             "Sucessfully took a dump.\n");
605 >    MPIcheckPoint();        
606      
607 <    done = 0;
569 <    while (!done) {
570 <
571 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
572 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
573 <      
574 <      if(!myStatus) anonymousNodeDie();
575 <      
576 <      if(myStatus < 0) break;
577 <      
578 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
579 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
580 <      
581 <      myStatus = 1;
582 <      local_index=-1;        
583 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
584 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
585 <      }
586 <      if (local_index != -1) {
587 <
588 <        atoms[local_index]->getPos(pos);
589 <        atoms[local_index]->getVel(vel);
590 <
591 <        //format the line
592 <        sprintf( tempBuffer,
593 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
594 <                 atoms[local_index]->getType(),
595 <                 pos[0],
596 <                 pos[1],
597 <                 pos[2],
598 <                 vel[0],
599 <                 vel[1],
600 <                 vel[2]); // check here.
601 <        strcpy( writeLine, tempBuffer );
602 <        
603 <        if( atoms[local_index]->isDirectional() ){
604 <          
605 <          dAtom = (DirectionalAtom *)atoms[local_index];
606 <          dAtom->getQ( q );
607 <          
608 <          sprintf( tempBuffer,
609 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
610 <                   q[0],
611 <                   q[1],
612 <                   q[2],
613 <                   q[3],
614 <                   dAtom->getJx(),
615 <                   dAtom->getJy(),
616 <                   dAtom->getJz());
617 <          strcat( writeLine, tempBuffer );
618 <        }
619 <        else{
620 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
621 <        }
622 <      }
623 <      else {
624 <        sprintf(painCave.errMsg,
625 <                "Atom %d not found on processor %d\n",
626 <                which_atom, worldRank );
627 <        myStatus = 0;
628 <        simError();
629 <        
630 <        strcpy( writeLine, "Hello, I'm an error.\n");
631 <      }
632 <
633 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
634 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
635 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
636 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
637 <    }
638 <  }
639 <  finalOut.flush();
640 <  sprintf( checkPointMsg,
641 <           "Sucessfully took a dump.\n");
642 <  MPIcheckPoint();
607 >  }
608    
644 –  if( worldRank == 0 ) finalOut.close();    
609   #endif // is_mpi
610   }
611  
648 –
649 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop
615  
616 < void dWrite::nodeZeroError( void ){
655 <  int j, myStatus;
656 <  
657 <  myStatus = 0;
658 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
659 <    MPI_Send( &myStatus, 1, MPI_INT, j,
660 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661 <  }  
662 <  
616 > void dWrite::DieDieDie( void ){
617  
618    MPI_Finalize();
619    exit (0);
666 –  
620   }
621  
669 – void dWrite::anonymousNodeDie( void ){
670 –
671 –  MPI_Finalize();
672 –  exit (0);
673 – }
674 –
622   #endif //is_mpi

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