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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 947 by gezelter, Thu Jan 15 14:22:16 2004 UTC

# Line 1 | Line 1
1   #define _FILE_OFFSET_BITS 64
2  
3 < #include <cstring>
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 1
11 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 28 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <    strcpy( outName, entry_plug->sampleName );
32 <    
33 <    outFile.open(outName, ios::out | ios::trunc );
34 <    
35 <    if( !outFile ){
37 <      
30 >
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 + #endif
101 +
102 + void DumpWriter::writeDump(double currentTime){
103 +
104 +  ofstream finalOut;
105 +  vector<ofstream*> fileStreams;
106 +
107 + #ifdef IS_MPI
108 +  if(worldRank == 0 ){
109 +    
110 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 +    if( !finalOut ){
112 +      sprintf( painCave.errMsg,
113 +               "Could not open \"%s\" for final dump output.\n",
114 +               entry_plug->finalName );
115 +      painCave.isFatal = 1;
116 +      simError();
117 +    }
118 +  }
119 + #endif // is_mpi
120 +
121 +  fileStreams.push_back(&finalOut);
122 +  fileStreams.push_back(&dumpFile);
123 +
124 +  writeFrame(fileStreams, currentTime);
125 +
126 + #ifdef IS_MPI
127 +  finalOut.close();
128 + #endif
129 +        
130 + }
131 +
132 + void DumpWriter::writeFinal(double currentTime){
133 +
134 +  ofstream finalOut;
135 +  vector<ofstream*> fileStreams;
136 +
137 + #ifdef IS_MPI
138 +  if(worldRank == 0 ){
139 +
140 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141 +
142 +    if( !finalOut ){
143 +      sprintf( painCave.errMsg,
144 +               "Could not open \"%s\" for final dump output.\n",
145 +               entry_plug->finalName );
146 +      painCave.isFatal = 1;
147 +      simError();
148 +    }
149 +
150 +  }
151 + #endif // is_mpi
152 +  
153 +  fileStreams.push_back(&finalOut);  
154 +  writeFrame(fileStreams, currentTime);
155 +
156 + #ifdef IS_MPI
157 +  finalOut.close();
158 + #endif
159 +  
160 + }
161 +
162 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163 +
164    const int BUFFERSIZE = 2000;
165 <  char tempBuffer[BUFFERSIZE];
165 >  const int MINIBUFFERSIZE = 100;
166 >
167 >  char tempBuffer[BUFFERSIZE];  
168    char writeLine[BUFFERSIZE];
169  
170 <  int i;
170 >  int i, k;
171 >
172   #ifdef IS_MPI
173 <  int j, which_node, done, which_atom, local_index;
173 >  
174 >  /*********************************************************************
175 >   * Documentation?  You want DOCUMENTATION?
176 >   *
177 >   * Why all the potatoes below?  
178 >   *
179 >   * To make a long story short, the original version of DumpWriter
180 >   * worked in the most inefficient way possible.  Node 0 would
181 >   * poke each of the node for an individual atom's formatted data
182 >   * as node 0 worked its way down the global index. This was particularly
183 >   * inefficient since the method blocked all processors at every atom
184 >   * (and did it twice!).
185 >   *
186 >   * An intermediate version of DumpWriter could be described from Node
187 >   * zero's perspective as follows:
188 >   *
189 >   *  1) Have 100 of your friends stand in a circle.
190 >   *  2) When you say go, have all of them start tossing potatoes at
191 >   *     you (one at a time).
192 >   *  3) Catch the potatoes.
193 >   *
194 >   * It was an improvement, but MPI has buffers and caches that could
195 >   * best be described in this analogy as "potato nets", so there's no
196 >   * need to block the processors atom-by-atom.
197 >   *
198 >   * This new and improved DumpWriter works in an even more efficient
199 >   * way:
200 >   *
201 >   *  1) Have 100 of your friend stand in a circle.
202 >   *  2) When you say go, have them start tossing 5-pound bags of
203 >   *     potatoes at you.
204 >   *  3) Once you've caught a friend's bag of potatoes,
205 >   *     toss them a spud to let them know they can toss another bag.
206 >   *
207 >   * How's THAT for documentation?
208 >   *
209 >   *********************************************************************/
210 >
211 >  int *potatoes;
212 >  int myPotato;
213 >
214 >  int nProc;
215 >  int j, which_node, done, which_atom, local_index, currentIndex;
216 >  double atomData6[6];
217 >  double atomData13[13];
218 >  int isDirectional;
219 >  char* atomTypeString;
220 >  char MPIatomTypeString[MINIBUFFERSIZE];
221 >
222   #else //is_mpi
223    int nAtoms = entry_plug->n_atoms;
224   #endif //is_mpi
# Line 83 | Line 227 | void DumpWriter::writeDump( double currentTime ){
227    DirectionalAtom* dAtom;
228    Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
86 –    
230  
231   #ifndef IS_MPI
232 <    
233 <  outFile << nAtoms << "\n";
234 <    
92 <  outFile << currentTime << ";\t"
93 <          << entry_plug->Hmat[0][0] << "\t"
94 <          << entry_plug->Hmat[1][0] << "\t"
95 <          << entry_plug->Hmat[2][0] << ";\t"
232 >  
233 >  for(k = 0; k < outFile.size(); k++){
234 >    *outFile[k] << nAtoms << "\n";
235  
236 <          << entry_plug->Hmat[0][1] << "\t"
237 <          << entry_plug->Hmat[1][1] << "\t"
238 <          << entry_plug->Hmat[2][1] << ";\t"
236 >    *outFile[k] << currentTime << ";\t"
237 >               << entry_plug->Hmat[0][0] << "\t"
238 >                     << entry_plug->Hmat[1][0] << "\t"
239 >                     << entry_plug->Hmat[2][0] << ";\t"
240 >              
241 >               << entry_plug->Hmat[0][1] << "\t"
242 >                     << entry_plug->Hmat[1][1] << "\t"
243 >                     << entry_plug->Hmat[2][1] << ";\t"
244  
245 <          << entry_plug->Hmat[0][2] << "\t"
246 <          << entry_plug->Hmat[1][2] << "\t"
247 <          << entry_plug->Hmat[2][2] << ";\n";
248 <    
245 >                     << entry_plug->Hmat[0][2] << "\t"
246 >                     << entry_plug->Hmat[1][2] << "\t"
247 >                     << entry_plug->Hmat[2][2] << ";";
248 >
249 >    //write out additional parameters, such as chi and eta
250 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251 >  }
252 >  
253    for( i=0; i<nAtoms; i++ ){
254 <      
254 >
255      atoms[i]->getPos(pos);
256      atoms[i]->getVel(vel);
257  
# Line 119 | Line 267 | void DumpWriter::writeDump( double currentTime ){
267      strcpy( writeLine, tempBuffer );
268  
269      if( atoms[i]->isDirectional() ){
270 <        
270 >
271        dAtom = (DirectionalAtom *)atoms[i];
272        dAtom->getQ( q );
273 <        
273 >
274        sprintf( tempBuffer,
275                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
276                 q[0],
# Line 136 | Line 284 | void DumpWriter::writeDump( double currentTime ){
284      }
285      else
286        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287 <      
288 <    outFile << writeLine;
287 >
288 >    for(k = 0; k < outFile.size(); k++)
289 >      *outFile[k] << writeLine;
290    }
142 –  outFile.flush();
291  
292   #else // is_mpi
293  
294 <  // first thing first, suspend fatalities.
295 <  painCave.isEventLoop = 1;
294 >  /* code to find maximum tag value */
295 >  
296 >  int *tagub, flag, MAXTAG;
297 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
298 >  if (flag) {
299 >    MAXTAG = *tagub;
300 >  } else {
301 >    MAXTAG = 32767;
302 >  }  
303  
149 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
304    int haveError;
305  
306    MPI_Status istatus;
307    int *AtomToProcMap = mpiSim->getAtomToProcMap();
308 <  
308 >
309    // write out header and node 0's coordinates
310 <  
310 >
311    if( worldRank == 0 ){
312 <    outFile << mpiSim->getTotAtoms() << "\n";
313 <  
314 <    outFile << currentTime << ";\t"
315 <            << entry_plug->Hmat[0][0] << "\t"
316 <            << entry_plug->Hmat[1][0] << "\t"
317 <            << entry_plug->Hmat[2][0] << ";\t"
318 <      
319 <            << entry_plug->Hmat[0][1] << "\t"
320 <            << entry_plug->Hmat[1][1] << "\t"
167 <            << entry_plug->Hmat[2][1] << ";\t"
168 <      
169 <            << entry_plug->Hmat[0][2] << "\t"
170 <            << entry_plug->Hmat[1][2] << "\t"
171 <            << entry_plug->Hmat[2][2] << ";\n";
312 >
313 >    // Node 0 needs a list of the magic potatoes for each processor;
314 >
315 >    nProc = mpiSim->getNumberProcessors();
316 >    potatoes = new int[nProc];
317 >
318 >    //write out the comment lines
319 >    for (i = 0; i < nProc; i++)
320 >      potatoes[i] = 0;
321      
322 <    outFile.flush();
322 >      for(k = 0; k < outFile.size(); k++){
323 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
324 >
325 >        *outFile[k] << currentTime << ";\t"
326 >                         << entry_plug->Hmat[0][0] << "\t"
327 >                         << entry_plug->Hmat[1][0] << "\t"
328 >                         << entry_plug->Hmat[2][0] << ";\t"
329 >
330 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333 >
334 >                         << entry_plug->Hmat[0][2] << "\t"
335 >                         << entry_plug->Hmat[1][2] << "\t"
336 >                         << entry_plug->Hmat[2][2] << ";";
337 >  
338 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339 >    }
340 >
341 >    currentIndex = 0;
342 >
343      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344 +      
345        // Get the Node number which has this atom;
346        
347 <      which_node = AtomToProcMap[i];    
347 >      which_node = AtomToProcMap[i];
348        
349 <      if (which_node == 0 ) {
349 >      if (which_node != 0) {
350 >
351 >        if (potatoes[which_node] + 3 >= MAXTAG) {
352 >          // The potato was going to exceed the maximum value,
353 >          // so wrap this processor potato back to 0:        
354 >
355 >          potatoes[which_node] = 0;          
356 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
357 >          
358 >        }
359 >
360 >        myPotato = potatoes[which_node];        
361 >        
362 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363 >                 myPotato, MPI_COMM_WORLD, &istatus);
364 >        
365 >        atomTypeString = MPIatomTypeString;
366          
367 <        haveError = 0;
368 <        which_atom = i;
369 <        local_index=-1;        
370 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
371 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
367 >        myPotato++;
368 >
369 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >              
372 >        myPotato++;
373 >
374 >        if (isDirectional) {          
375 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
376 >                   myPotato, MPI_COMM_WORLD, &istatus);
377 >        } else {
378 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);          
380          }
381 <        if (local_index != -1) {
382 <          //format the line
383 <          
190 <          atoms[local_index]->getPos(pos);
191 <          atoms[local_index]->getVel(vel);
381 >        
382 >        myPotato++;
383 >        potatoes[which_node] = myPotato;
384  
385 <          sprintf( tempBuffer,
386 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
387 <                   atoms[local_index]->getType(),
388 <                   pos[0],
389 <                   pos[1],
390 <                   pos[2],
391 <                   vel[0],
392 <                   vel[1],
393 <                   vel[2]); // check here.
394 <          strcpy( writeLine, tempBuffer );
395 <          
385 >      } else {
386 >        
387 >        haveError = 0;
388 >              which_atom = i;
389 >        
390 >        local_index = indexArray[currentIndex].first;        
391 >                
392 >        if (which_atom == indexArray[currentIndex].second) {
393 >          
394 >          atomTypeString = atoms[local_index]->getType();
395 >
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398 >
399 >          atomData6[0] = pos[0];
400 >          atomData6[1] = pos[1];
401 >          atomData6[2] = pos[2];
402 >
403 >          atomData6[3] = vel[0];
404 >          atomData6[4] = vel[1];
405 >          atomData6[5] = vel[2];
406 >          
407 >          isDirectional = 0;
408 >
409            if( atoms[local_index]->isDirectional() ){
410 +
411 +            isDirectional = 1;
412              
413              dAtom = (DirectionalAtom *)atoms[local_index];
414              dAtom->getQ( q );
208 –            
209 –            sprintf( tempBuffer,
210 –                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
211 –                     q[0],
212 –                     q[1],
213 –                     q[2],
214 –                     q[3],
215 –                     dAtom->getJx(),
216 –                     dAtom->getJy(),
217 –                     dAtom->getJz());
218 –            strcat( writeLine, tempBuffer );
219 –            
220 –          }
221 –          else
222 –            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
223 –        }
224 –        else {
225 –          sprintf(painCave.errMsg,
226 –                  "Atom %d not found on processor %d\n",
227 –                  i, worldRank );
228 –          haveError= 1;
229 –          simError();
230 –        }
231 –        
232 –        if(haveError) nodeZeroError();
415  
416 +            for (int j = 0; j < 6 ; j++)
417 +              atomData13[j] = atomData6[j];            
418 +            
419 +            atomData13[6] = q[0];
420 +            atomData13[7] = q[1];
421 +            atomData13[8] = q[2];
422 +            atomData13[9] = q[3];
423 +            
424 +            atomData13[10] = dAtom->getJx();
425 +            atomData13[11] = dAtom->getJy();
426 +            atomData13[12] = dAtom->getJz();
427 +          }
428 +          
429 +        } else {
430 +          sprintf(painCave.errMsg,
431 +                              "Atom %d not found on processor %d\n",
432 +                              i, worldRank );
433 +                haveError= 1;
434 +                simError();
435 +              }
436 +        
437 +        if(haveError) DieDieDie();
438 +        
439 +        currentIndex ++;
440        }
441 <      else {
442 <        myStatus = 1;
443 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
238 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
239 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
240 <                 MPI_COMM_WORLD);
241 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
242 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
243 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
244 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
441 >      // If we've survived to here, format the line:
442 >      
443 >      if (!isDirectional) {
444          
445 <        if(!myStatus) nodeZeroError();
445 >        sprintf( writeLine,
446 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 >                             atomTypeString,
448 >                             atomData6[0],
449 >                             atomData6[1],
450 >                             atomData6[2],
451 >                             atomData6[3],
452 >                             atomData6[4],
453 >                             atomData6[5]);
454  
455 +              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 +        
457 +      } else {
458 +        
459 +              sprintf( writeLine,
460 +                             "%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",
461 +                             atomTypeString,
462 +                             atomData13[0],
463 +                             atomData13[1],
464 +                             atomData13[2],
465 +                             atomData13[3],
466 +                             atomData13[4],
467 +                             atomData13[5],
468 +                             atomData13[6],
469 +                             atomData13[7],
470 +                             atomData13[8],
471 +                             atomData13[9],
472 +                             atomData13[10],
473 +                             atomData13[11],
474 +                             atomData13[12]);
475 +        
476        }
477        
478 <      outFile << writeLine;
479 <      outFile.flush();
478 >      for(k = 0; k < outFile.size(); k++)
479 >        *outFile[k] << writeLine;
480      }
481      
482 <    // kill everyone off:
483 <    myStatus = -1;
256 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
257 <      MPI_Send(&myStatus, 1, MPI_INT, j,
258 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
259 <    }
260 <
261 <  } else {
482 >    for(k = 0; k < outFile.size(); k++)
483 >      outFile[k]->flush();
484      
485 <    done = 0;
486 <    while (!done) {
265 <      
266 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
267 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
485 >    sprintf( checkPointMsg,
486 >             "Sucessfully took a dump.\n");
487  
488 <      if(!myStatus) anonymousNodeDie();
270 <      
271 <      if(myStatus < 0) break;
488 >    MPIcheckPoint();        
489  
490 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
274 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
275 <      
276 <      myStatus = 1;
277 <      local_index=-1;        
278 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
279 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
280 <      }
281 <      if (local_index != -1) {
282 <        //format the line
490 >    delete[] potatoes;
491  
492 <        atoms[local_index]->getPos(pos);
285 <        atoms[local_index]->getVel(vel);
492 >  } else {
493  
494 <        sprintf( tempBuffer,
288 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
289 <                 atoms[local_index]->getType(),
290 <                 pos[0],
291 <                 pos[1],
292 <                 pos[2],
293 <                 vel[0],
294 <                 vel[1],
295 <                 vel[2]); // check here.
296 <        strcpy( writeLine, tempBuffer );
297 <        
298 <        if( atoms[local_index]->isDirectional() ){
299 <          
300 <          dAtom = (DirectionalAtom *)atoms[local_index];
301 <          dAtom->getQ( q );
302 <          
303 <          sprintf( tempBuffer,
304 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
305 <                   q[0],
306 <                   q[1],
307 <                   q[2],
308 <                   q[3],
309 <                   dAtom->getJx(),
310 <                   dAtom->getJy(),
311 <                   dAtom->getJz());
312 <          strcat( writeLine, tempBuffer );
313 <        }
314 <        else{
315 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
316 <        }
317 <      }
318 <      else {
319 <        sprintf(painCave.errMsg,
320 <                "Atom %d not found on processor %d\n",
321 <                which_atom, worldRank );
322 <        myStatus = 0;
323 <        simError();
494 >    // worldRank != 0, so I'm a remote node.  
495  
496 <        strcpy( writeLine, "Hello, I'm an error.\n");
326 <      }
496 >    // Set my magic potato to 0:
497  
498 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
499 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
500 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
501 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
502 <    }
503 <  }  
504 <  outFile.flush();
505 <  sprintf( checkPointMsg,
336 <           "Sucessfully took a dump.\n");
337 <  MPIcheckPoint();
498 >    myPotato = 0;
499 >    currentIndex = 0;
500 >    
501 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
502 >      
503 >      // Am I the node which has this atom?
504 >      
505 >      if (AtomToProcMap[i] == worldRank) {
506  
507 < // last  thing last, enable  fatalities.
340 <  painCave.isEventLoop = 0;
507 >        if (myPotato + 3 >= MAXTAG) {
508  
509 < #endif // is_mpi
510 < }
509 >          // The potato was going to exceed the maximum value,
510 >          // so wrap this processor potato back to 0 (and block until
511 >          // node 0 says we can go:
512  
513 < void DumpWriter::writeFinal(double finalTime){
513 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514 >          
515 >        }
516 >        which_atom = i;
517 >        local_index = indexArray[currentIndex].first;        
518 >                
519 >        if (which_atom == indexArray[currentIndex].second) {
520 >        
521 >          atomTypeString = atoms[local_index]->getType();
522  
523 <  char finalName[500];
524 <  ofstream finalOut;
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525  
526 <  const int BUFFERSIZE = 2000;
527 <  char tempBuffer[BUFFERSIZE];
528 <  char writeLine[BUFFERSIZE];  
526 >          atomData6[0] = pos[0];
527 >          atomData6[1] = pos[1];
528 >          atomData6[2] = pos[2];
529  
530 <  double q[4];
531 <  DirectionalAtom* dAtom;
532 <  Atom** atoms = entry_plug->atoms;
533 <  int i;
534 < #ifdef IS_MPI
359 <  int j, which_node, done, which_atom, local_index;
360 < #else //is_mpi
361 <  int nAtoms = entry_plug->n_atoms;
362 < #endif //is_mpi
363 <  
364 <  double pos[3], vel[3];
365 <  
366 < #ifdef IS_MPI
367 <  if(worldRank == 0 ){
368 < #endif // is_mpi
369 <    
370 <    strcpy( finalName, entry_plug->finalName );
371 <    
372 <    finalOut.open( finalName, ios::out | ios::trunc );
373 <    if( !finalOut ){
374 <      sprintf( painCave.errMsg,
375 <               "Could not open \"%s\" for final dump output.\n",
376 <               finalName );
377 <      painCave.isFatal = 1;
378 <      simError();
379 <    }
380 <    
381 <    // finalOut.setf( ios::scientific );
382 <    
383 < #ifdef IS_MPI
384 <  }
385 <  
386 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
387 <  MPIcheckPoint();  
388 <  
389 < #endif //is_mpi
530 >          atomData6[3] = vel[0];
531 >          atomData6[4] = vel[1];
532 >          atomData6[5] = vel[2];
533 >          
534 >          isDirectional = 0;
535  
536 <  
392 < #ifndef IS_MPI
393 <    
394 <  finalOut << nAtoms << "\n";
395 <    
396 <  finalOut << finalTime << ";\t"
397 <           << entry_plug->Hmat[0][0] << "\t"
398 <           << entry_plug->Hmat[1][0] << "\t"
399 <           << entry_plug->Hmat[2][0] << ";\t"
400 <    
401 <           << entry_plug->Hmat[0][1] << "\t"
402 <           << entry_plug->Hmat[1][1] << "\t"
403 <           << entry_plug->Hmat[2][1] << ";\t"
404 <    
405 <           << entry_plug->Hmat[0][2] << "\t"
406 <           << entry_plug->Hmat[1][2] << "\t"
407 <           << entry_plug->Hmat[2][2] << ";\n";
408 <  
409 <  for( i=0; i<nAtoms; i++ ){
410 <      
411 <    atoms[i]->getPos(pos);
412 <    atoms[i]->getVel(vel);
413 <    
414 <    sprintf( tempBuffer,
415 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
416 <             atoms[i]->getType(),
417 <             pos[0],
418 <             pos[1],
419 <             pos[2],
420 <             vel[0],
421 <             vel[1],
422 <             vel[2]);
423 <    strcpy( writeLine, tempBuffer );
536 >          if( atoms[local_index]->isDirectional() ){
537  
538 <    if( atoms[i]->isDirectional() ){
539 <        
540 <      dAtom = (DirectionalAtom *)atoms[i];
541 <      dAtom->getQ( q );
542 <        
543 <      sprintf( tempBuffer,
544 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
545 <               q[0],
546 <               q[1],
547 <               q[2],
548 <               q[3],
549 <               dAtom->getJx(),
437 <               dAtom->getJy(),
438 <               dAtom->getJz());
439 <      strcat( writeLine, tempBuffer );
440 <    }
441 <    else
442 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
443 <      
444 <    finalOut << writeLine;
445 <  }
446 <  finalOut.flush();
447 <  finalOut.close();
448 <
449 < #else // is_mpi
538 >            isDirectional = 1;
539 >            
540 >            dAtom = (DirectionalAtom *)atoms[local_index];
541 >            dAtom->getQ( q );
542 >            
543 >            for (int j = 0; j < 6 ; j++)
544 >              atomData13[j] = atomData6[j];
545 >            
546 >            atomData13[6] = q[0];
547 >            atomData13[7] = q[1];
548 >            atomData13[8] = q[2];
549 >            atomData13[9] = q[3];
550    
551 <  // first thing first, suspend fatalities.
552 <  painCave.isEventLoop = 1;
551 >            atomData13[10] = dAtom->getJx();
552 >            atomData13[11] = dAtom->getJy();
553 >            atomData13[12] = dAtom->getJz();
554 >          }
555  
556 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
557 <  int haveError;
556 >        } else {
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563  
564 <  MPI_Status istatus;
458 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
564 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565  
566 <  // write out header and node 0's coordinates
567 <  
462 <  haveError = 0;
463 <  if( worldRank == 0 ){
464 <    finalOut << mpiSim->getTotAtoms() << "\n";
465 <    
466 <    finalOut << finalTime << ";\t"
467 <             << entry_plug->Hmat[0][0] << "\t"
468 <             << entry_plug->Hmat[1][0] << "\t"
469 <             << entry_plug->Hmat[2][0] << ";\t"
470 <      
471 <             << entry_plug->Hmat[0][1] << "\t"
472 <             << entry_plug->Hmat[1][1] << "\t"
473 <             << entry_plug->Hmat[2][1] << ";\t"
474 <      
475 <             << entry_plug->Hmat[0][2] << "\t"
476 <             << entry_plug->Hmat[1][2] << "\t"
477 <             << entry_plug->Hmat[2][2] << ";\n";
478 <    
479 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
480 <      // Get the Node number which has this molecule:
481 <      
482 <      which_node = AtomToProcMap[i];    
483 <      
484 <      if (which_node == mpiSim->getMyNode()) {
566 >        // null terminate the string before sending (just in case):
567 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568  
569 <        which_atom = i;
570 <        local_index=-1;        
571 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
572 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
490 <        }
491 <        if (local_index != -1) {    
569 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 >                             myPotato, MPI_COMM_WORLD);
571 >        
572 >        myPotato++;
573  
574 <          atoms[local_index]->getPos(pos);
575 <          atoms[local_index]->getVel(vel);
495 <          
496 <          sprintf( tempBuffer,
497 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
498 <                   atoms[local_index]->getType(),
499 <                   pos[0],
500 <                   pos[1],
501 <                   pos[2],
502 <                   vel[0],
503 <                   vel[1],
504 <                   vel[2]);
505 <          strcpy( writeLine, tempBuffer );
506 <          
507 <          if( atoms[local_index]->isDirectional() ){
508 <            
509 <            dAtom = (DirectionalAtom *)atoms[local_index];
510 <            dAtom->getQ( q );
511 <            
512 <            sprintf( tempBuffer,
513 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
514 <                     q[0],
515 <                     q[1],
516 <                     q[2],
517 <                     q[3],
518 <                     dAtom->getJx(),
519 <                     dAtom->getJy(),
520 <                     dAtom->getJz());
521 <            strcat( writeLine, tempBuffer );
522 <          }
523 <          else
524 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
525 <        }
526 <        else {
527 <          sprintf(painCave.errMsg,
528 <                  "Atom %d not found on processor %d\n",
529 <                  i, worldRank );
530 <          haveError= 1;
531 <          simError();
532 <        }
533 <
534 <        if(haveError) nodeZeroError();
535 <    
536 <      }
537 <      else {
574 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576          
577 <        myStatus = 1;
578 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
579 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
542 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
543 <                 MPI_COMM_WORLD);
544 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
545 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
546 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
547 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
548 <        
549 <        if(!myStatus) nodeZeroError();
550 <      }
551 <      
552 <      finalOut << writeLine;
553 <    }
554 <    
555 <    // kill everyone off:
556 <    myStatus = -1;
557 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
558 <      MPI_Send(&myStatus, 1, MPI_INT, j,
559 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
560 <    }
577 >        myPotato++;
578 >        
579 >        if (isDirectional) {
580  
581 <  } else {
582 <    
583 <    done = 0;
584 <    while (!done) {
581 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
582 >                   myPotato, MPI_COMM_WORLD);
583 >          
584 >        } else {
585  
586 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
587 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
588 <      
570 <      if(!myStatus) anonymousNodeDie();
571 <      
572 <      if(myStatus < 0) break;
573 <      
574 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
575 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
576 <      
577 <      myStatus = 1;
578 <      local_index=-1;        
579 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
580 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
581 <      }
582 <      if (local_index != -1) {
586 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588 >        }
589  
590 <        atoms[local_index]->getPos(pos);
591 <        atoms[local_index]->getVel(vel);
586 <
587 <        //format the line
588 <        sprintf( tempBuffer,
589 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
590 <                 atoms[local_index]->getType(),
591 <                 pos[0],
592 <                 pos[1],
593 <                 pos[2],
594 <                 vel[0],
595 <                 vel[1],
596 <                 vel[2]); // check here.
597 <        strcpy( writeLine, tempBuffer );
598 <        
599 <        if( atoms[local_index]->isDirectional() ){
600 <          
601 <          dAtom = (DirectionalAtom *)atoms[local_index];
602 <          dAtom->getQ( q );
603 <          
604 <          sprintf( tempBuffer,
605 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
606 <                   q[0],
607 <                   q[1],
608 <                   q[2],
609 <                   q[3],
610 <                   dAtom->getJx(),
611 <                   dAtom->getJy(),
612 <                   dAtom->getJz());
613 <          strcat( writeLine, tempBuffer );
614 <        }
615 <        else{
616 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
617 <        }
618 <      }
619 <      else {
620 <        sprintf(painCave.errMsg,
621 <                "Atom %d not found on processor %d\n",
622 <                which_atom, worldRank );
623 <        myStatus = 0;
624 <        simError();
625 <        
626 <        strcpy( writeLine, "Hello, I'm an error.\n");
590 >        myPotato++;  
591 >        currentIndex++;    
592        }
628 –
629 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
630 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
631 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
632 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
593      }
594 <  }
595 <  finalOut.flush();
596 <  sprintf( checkPointMsg,
597 <           "Sucessfully took a dump.\n");
598 <  MPIcheckPoint();
594 >
595 >    sprintf( checkPointMsg,
596 >             "Sucessfully took a dump.\n");
597 >    MPIcheckPoint();        
598 >    
599 >  }
600    
640 –  if( worldRank == 0 ) finalOut.close();    
601   #endif // is_mpi
602   }
603  
644 –
645 –
604   #ifdef IS_MPI
605  
606   // a couple of functions to let us escape the write loop
607  
608 < void dWrite::nodeZeroError( void ){
651 <  int j, myStatus;
652 <  
653 <  myStatus = 0;
654 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
655 <    MPI_Send( &myStatus, 1, MPI_INT, j,
656 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
657 <  }  
658 <  
608 > void dWrite::DieDieDie( void ){
609  
610    MPI_Finalize();
611    exit (0);
662 –  
612   }
613  
665 – void dWrite::anonymousNodeDie( void ){
666 –
667 –  MPI_Finalize();
668 –  exit (0);
669 – }
670 –
614   #endif //is_mpi

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