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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 723 by mmeineke, Tue Aug 26 20:12:51 2003 UTC vs.
Revision 952 by tim, Fri Jan 16 21:55:39 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 <    
36 <    if( !outFile ){
37 <      
30 >
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32 >
33 >    if( !dumpFile ){
34 >
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
45 –    //outFile.setf( ios::scientific );
46 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 59 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68 >
69 > /**
70 > * A hook function to load balancing
71 > */
72 >
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 + /**
78 + * Auxiliary sorting function
79 + */
80 +
81 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 +  return p1.second < p2.second;
83 + }
84 +
85 + /**
86 + * Sorting the local index by global index
87 + */
88 +
89 + void DumpWriter::sortByGlobalIndex(){
90 +  Atom** atoms = entry_plug->atoms;
91 +  
92 +  indexArray.clear();
93 +  
94 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 +  
97 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 +
99 +  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 +  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 +  //}
102 +    
103 + }
104 +
105 + #endif
106 +
107 + void DumpWriter::writeDump(double currentTime){
108 +
109 +  ofstream finalOut;
110 +  vector<ofstream*> fileStreams;
111 +
112 + #ifdef IS_MPI
113 +  if(worldRank == 0 ){
114 + #endif    
115 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 +    if( !finalOut ){
117 +      sprintf( painCave.errMsg,
118 +               "Could not open \"%s\" for final dump output.\n",
119 +               entry_plug->finalName );
120 +      painCave.isFatal = 1;
121 +      simError();
122 +    }
123 + #ifdef IS_MPI
124 +  }
125 + #endif // is_mpi
126 +
127 +  fileStreams.push_back(&finalOut);
128 +  fileStreams.push_back(&dumpFile);
129 +
130 +  writeFrame(fileStreams, currentTime);
131 +
132 + #ifdef IS_MPI
133 +  finalOut.close();
134 + #endif
135 +        
136 + }
137 +
138 + void DumpWriter::writeFinal(double currentTime){
139 +
140 +  ofstream finalOut;
141 +  vector<ofstream*> fileStreams;
142 +
143 + #ifdef IS_MPI
144 +  if(worldRank == 0 ){
145 + #endif // is_mpi
146 +
147 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 +
149 +    if( !finalOut ){
150 +      sprintf( painCave.errMsg,
151 +               "Could not open \"%s\" for final dump output.\n",
152 +               entry_plug->finalName );
153 +      painCave.isFatal = 1;
154 +      simError();
155 +    }
156 +
157 + #ifdef IS_MPI
158 +  }
159 + #endif // is_mpi
160 +  
161 +  fileStreams.push_back(&finalOut);  
162 +  writeFrame(fileStreams, currentTime);
163 +
164 + #ifdef IS_MPI
165 +  finalOut.close();
166 + #endif
167 +  
168 + }
169 +
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171 +
172    const int BUFFERSIZE = 2000;
173 <  char tempBuffer[BUFFERSIZE];
173 >  const int MINIBUFFERSIZE = 100;
174 >
175 >  char tempBuffer[BUFFERSIZE];  
176    char writeLine[BUFFERSIZE];
177  
178 <  int i, j, which_node, done, which_atom, local_index;
178 >  int i, k;
179 >
180 > #ifdef IS_MPI
181 >  
182 >  /*********************************************************************
183 >   * Documentation?  You want DOCUMENTATION?
184 >   *
185 >   * Why all the potatoes below?  
186 >   *
187 >   * To make a long story short, the original version of DumpWriter
188 >   * worked in the most inefficient way possible.  Node 0 would
189 >   * poke each of the node for an individual atom's formatted data
190 >   * as node 0 worked its way down the global index. This was particularly
191 >   * inefficient since the method blocked all processors at every atom
192 >   * (and did it twice!).
193 >   *
194 >   * An intermediate version of DumpWriter could be described from Node
195 >   * zero's perspective as follows:
196 >   *
197 >   *  1) Have 100 of your friends stand in a circle.
198 >   *  2) When you say go, have all of them start tossing potatoes at
199 >   *     you (one at a time).
200 >   *  3) Catch the potatoes.
201 >   *
202 >   * It was an improvement, but MPI has buffers and caches that could
203 >   * best be described in this analogy as "potato nets", so there's no
204 >   * need to block the processors atom-by-atom.
205 >   *
206 >   * This new and improved DumpWriter works in an even more efficient
207 >   * way:
208 >   *
209 >   *  1) Have 100 of your friend stand in a circle.
210 >   *  2) When you say go, have them start tossing 5-pound bags of
211 >   *     potatoes at you.
212 >   *  3) Once you've caught a friend's bag of potatoes,
213 >   *     toss them a spud to let them know they can toss another bag.
214 >   *
215 >   * How's THAT for documentation?
216 >   *
217 >   *********************************************************************/
218 >
219 >  int *potatoes;
220 >  int myPotato;
221 >
222 >  int nProc;
223 >  int j, which_node, done, which_atom, local_index, currentIndex;
224 >  double atomData6[6];
225 >  double atomData13[13];
226 >  int isDirectional;
227 >  char* atomTypeString;
228 >  char MPIatomTypeString[MINIBUFFERSIZE];
229 >
230 > #else //is_mpi
231 >  int nAtoms = entry_plug->n_atoms;
232 > #endif //is_mpi
233 >
234    double q[4];
235    DirectionalAtom* dAtom;
78 –  int nAtoms = entry_plug->n_atoms;
236    Atom** atoms = entry_plug->atoms;
80 –
237    double pos[3], vel[3];
82 –    
238  
239   #ifndef IS_MPI
240 <    
241 <  outFile << nAtoms << "\n";
242 <    
88 <  outFile << currentTime << ";\t"
89 <          << entry_plug->Hmat[0][0] << "\t"
90 <          << entry_plug->Hmat[1][0] << "\t"
91 <          << entry_plug->Hmat[2][0] << ";\t"
240 >  
241 >  for(k = 0; k < outFile.size(); k++){
242 >    *outFile[k] << nAtoms << "\n";
243  
244 <          << entry_plug->Hmat[0][1] << "\t"
245 <          << entry_plug->Hmat[1][1] << "\t"
246 <          << entry_plug->Hmat[2][1] << ";\t"
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252  
253 <          << entry_plug->Hmat[0][2] << "\t"
254 <          << entry_plug->Hmat[1][2] << "\t"
255 <          << entry_plug->Hmat[2][2] << ";\n";
256 <    
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256 >
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 >  }
260 >  
261    for( i=0; i<nAtoms; i++ ){
262 <      
262 >
263      atoms[i]->getPos(pos);
264      atoms[i]->getVel(vel);
265  
# Line 115 | Line 275 | void DumpWriter::writeDump( double currentTime ){
275      strcpy( writeLine, tempBuffer );
276  
277      if( atoms[i]->isDirectional() ){
278 <        
278 >
279        dAtom = (DirectionalAtom *)atoms[i];
280        dAtom->getQ( q );
281 <        
281 >
282        sprintf( tempBuffer,
283                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
284                 q[0],
# Line 132 | Line 292 | void DumpWriter::writeDump( double currentTime ){
292      }
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295 <      
296 <    outFile << writeLine;
295 >
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
138 –  outFile.flush();
299  
300   #else // is_mpi
301  
302 <  // first thing first, suspend fatalities.
303 <  painCave.isEventLoop = 1;
302 >  /* code to find maximum tag value */
303 >  
304 >  int *tagub, flag, MAXTAG;
305 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306 >  if (flag) {
307 >    MAXTAG = *tagub;
308 >  } else {
309 >    MAXTAG = 32767;
310 >  }  
311  
145 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
312    int haveError;
313  
314    MPI_Status istatus;
315    int *AtomToProcMap = mpiSim->getAtomToProcMap();
316 <  
316 >
317    // write out header and node 0's coordinates
318 <  
318 >
319    if( worldRank == 0 ){
320 <    outFile << mpiSim->getTotAtoms() << "\n";
321 <  
322 <    outFile << currentTime << ";\t"
323 <            << entry_plug->Hmat[0][0] << "\t"
324 <            << entry_plug->Hmat[1][0] << "\t"
325 <            << entry_plug->Hmat[2][0] << ";\t"
326 <      
327 <            << entry_plug->Hmat[0][1] << "\t"
328 <            << entry_plug->Hmat[1][1] << "\t"
163 <            << entry_plug->Hmat[2][1] << ";\t"
164 <      
165 <            << entry_plug->Hmat[0][2] << "\t"
166 <            << entry_plug->Hmat[1][2] << "\t"
167 <            << entry_plug->Hmat[2][2] << ";\n";
320 >
321 >    // Node 0 needs a list of the magic potatoes for each processor;
322 >
323 >    nProc = mpiSim->getNumberProcessors();
324 >    potatoes = new int[nProc];
325 >
326 >    //write out the comment lines
327 >    for (i = 0; i < nProc; i++)
328 >      potatoes[i] = 0;
329      
330 <    outFile.flush();
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332 >
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341 >
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348 >
349 >    currentIndex = 0;
350 >
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352 +      
353        // Get the Node number which has this atom;
354        
355 <      which_node = AtomToProcMap[i];    
355 >      which_node = AtomToProcMap[i];
356        
357 <      if (which_node == 0 ) {
357 >      if (which_node != 0) {
358 >
359 >        if (potatoes[which_node] + 3 >= MAXTAG) {
360 >          // The potato was going to exceed the maximum value,
361 >          // so wrap this processor potato back to 0:        
362 >
363 >          potatoes[which_node] = 0;          
364 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
365 >          
366 >        }
367 >
368 >        myPotato = potatoes[which_node];        
369 >        
370 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371 >                 myPotato, MPI_COMM_WORLD, &istatus);
372 >        
373 >        atomTypeString = MPIatomTypeString;
374          
375 <        haveError = 0;
376 <        which_atom = i;
377 <        local_index=-1;        
378 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
379 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
375 >        myPotato++;
376 >
377 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >              
380 >        myPotato++;
381 >
382 >        if (isDirectional) {          
383 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);
385 >        } else {
386 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387 >                   myPotato, MPI_COMM_WORLD, &istatus);          
388          }
389 <        if (local_index != -1) {
390 <          //format the line
389 >        
390 >        myPotato++;
391 >        potatoes[which_node] = myPotato;
392 >
393 >      } else {
394 >        
395 >        haveError = 0;
396 >        which_atom = i;
397 >        
398 >        //local_index = -1;
399 >
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403 >        
404 >        //if (local_index != -1) {
405            
406 +          local_index = indexArray[currentIndex].first;        
407 +          
408 +          if (which_atom == indexArray[currentIndex].second) {
409 +            
410 +            atomTypeString = atoms[local_index]->getType();
411 +            
412            atoms[local_index]->getPos(pos);
413 <          atoms[local_index]->getVel(vel);
188 <
189 <          sprintf( tempBuffer,
190 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
191 <                   atoms[local_index]->getType(),
192 <                   pos[0],
193 <                   pos[1],
194 <                   pos[2],
195 <                   vel[0],
196 <                   vel[1],
197 <                   vel[2]); // check here.
198 <          strcpy( writeLine, tempBuffer );
413 >          atoms[local_index]->getVel(vel);          
414            
415 +          atomData6[0] = pos[0];
416 +          atomData6[1] = pos[1];
417 +          atomData6[2] = pos[2];
418 +
419 +          atomData6[3] = vel[0];
420 +          atomData6[4] = vel[1];
421 +          atomData6[5] = vel[2];
422 +          
423 +          isDirectional = 0;
424 +
425            if( atoms[local_index]->isDirectional() ){
426 +
427 +            isDirectional = 1;
428              
429              dAtom = (DirectionalAtom *)atoms[local_index];
430              dAtom->getQ( q );
431 +
432 +            for (int j = 0; j < 6 ; j++)
433 +              atomData13[j] = atomData6[j];            
434              
435 <            sprintf( tempBuffer,
436 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
437 <                     q[0],
438 <                     q[1],
439 <                     q[2],
440 <                     q[3],
441 <                     dAtom->getJx(),
442 <                     dAtom->getJy(),
443 <                     dAtom->getJz());
444 <            strcat( writeLine, tempBuffer );
445 <            
216 <          }
217 <          else
218 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
219 <        }
220 <        else {
435 >            atomData13[6] = q[0];
436 >            atomData13[7] = q[1];
437 >            atomData13[8] = q[2];
438 >            atomData13[9] = q[3];
439 >            
440 >            atomData13[10] = dAtom->getJx();
441 >            atomData13[11] = dAtom->getJy();
442 >            atomData13[12] = dAtom->getJz();
443 >          }
444 >          
445 >        } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451 <        }
452 <        
453 <        if(haveError) nodeZeroError();
454 <
451 >        }
452 >        
453 >        if(haveError) DieDieDie();
454 >        
455 >        currentIndex++;
456        }
457 <      else {
458 <        myStatus = 1;
459 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
234 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
235 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
236 <                 MPI_COMM_WORLD);
237 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
238 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
239 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
240 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
457 >      // If we've survived to here, format the line:
458 >      
459 >      if (!isDirectional) {
460          
461 <        if(!myStatus) nodeZeroError();
462 <
461 >        sprintf( writeLine,
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470 >        
471 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 >        
473 >      } else {
474 >        
475 >        sprintf( writeLine,
476 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
477 >                 atomTypeString,
478 >                 atomData13[0],
479 >                 atomData13[1],
480 >                 atomData13[2],
481 >                 atomData13[3],
482 >                 atomData13[4],
483 >                 atomData13[5],
484 >                 atomData13[6],
485 >                 atomData13[7],
486 >                 atomData13[8],
487 >                 atomData13[9],
488 >                 atomData13[10],
489 >                 atomData13[11],
490 >                 atomData13[12]);
491 >        
492        }
493        
494 <      outFile << writeLine;
495 <      outFile.flush();
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
497      
498 <    // kill everyone off:
499 <    myStatus = -1;
500 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
501 <      MPI_Send(&myStatus, 1, MPI_INT, j,
502 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
503 <    }
504 <
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501 >    sprintf( checkPointMsg,
502 >             "Sucessfully took a dump.\n");
503 >    
504 >    MPIcheckPoint();        
505 >    
506 >    delete[] potatoes;
507 >    
508    } else {
509 +
510 +    // worldRank != 0, so I'm a remote node.  
511 +
512 +    // Set my magic potato to 0:
513 +
514 +    myPotato = 0;
515 +    currentIndex = 0;
516      
517 <    done = 0;
260 <    while (!done) {
517 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518        
519 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
263 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
264 <
265 <      if(!myStatus) anonymousNodeDie();
519 >      // Am I the node which has this atom?
520        
521 <      if(myStatus < 0) break;
521 >      if (AtomToProcMap[i] == worldRank) {
522  
523 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
524 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
525 <      
526 <      myStatus = 1;
527 <      local_index=-1;        
528 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
529 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
530 <      }
531 <      if (local_index != -1) {
532 <        //format the line
523 >        if (myPotato + 3 >= MAXTAG) {
524 >          
525 >          // The potato was going to exceed the maximum value,
526 >          // so wrap this processor potato back to 0 (and block until
527 >          // node 0 says we can go:
528 >          
529 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530 >          
531 >        }
532 >        which_atom = i;
533  
534 <        atoms[local_index]->getPos(pos);
281 <        atoms[local_index]->getVel(vel);
534 >        //local_index = -1;
535  
536 <        sprintf( tempBuffer,
537 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
538 <                 atoms[local_index]->getType(),
539 <                 pos[0],
540 <                 pos[1],
541 <                 pos[2],
542 <                 vel[0],
543 <                 vel[1],
544 <                 vel[2]); // check here.
545 <        strcpy( writeLine, tempBuffer );
546 <        
294 <        if( atoms[local_index]->isDirectional() ){
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541 >
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545 >        
546 >          atomTypeString = atoms[local_index]->getType();
547            
548 <          dAtom = (DirectionalAtom *)atoms[local_index];
549 <          dAtom->getQ( q );
548 >          atoms[local_index]->getPos(pos);
549 >          atoms[local_index]->getVel(vel);
550            
551 <          sprintf( tempBuffer,
552 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
553 <                   q[0],
302 <                   q[1],
303 <                   q[2],
304 <                   q[3],
305 <                   dAtom->getJx(),
306 <                   dAtom->getJy(),
307 <                   dAtom->getJz());
308 <          strcat( writeLine, tempBuffer );
309 <        }
310 <        else{
311 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
312 <        }
313 <      }
314 <      else {
315 <        sprintf(painCave.errMsg,
316 <                "Atom %d not found on processor %d\n",
317 <                which_atom, worldRank );
318 <        myStatus = 0;
319 <        simError();
551 >          atomData6[0] = pos[0];
552 >          atomData6[1] = pos[1];
553 >          atomData6[2] = pos[2];
554  
555 <        strcpy( writeLine, "Hello, I'm an error.\n");
556 <      }
555 >          atomData6[3] = vel[0];
556 >          atomData6[4] = vel[1];
557 >          atomData6[5] = vel[2];
558 >          
559 >          isDirectional = 0;
560  
561 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
325 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
326 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
327 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
328 <    }
329 <  }  
330 <  outFile.flush();
331 <  sprintf( checkPointMsg,
332 <           "Sucessfully took a dump.\n");
333 <  MPIcheckPoint();
561 >          if( atoms[local_index]->isDirectional() ){
562  
563 < // last  thing last, enable  fatalities.
564 <  painCave.isEventLoop = 0;
563 >            isDirectional = 1;
564 >            
565 >            dAtom = (DirectionalAtom *)atoms[local_index];
566 >            dAtom->getQ( q );
567 >            
568 >            for (int j = 0; j < 6 ; j++)
569 >              atomData13[j] = atomData6[j];
570 >            
571 >            atomData13[6] = q[0];
572 >            atomData13[7] = q[1];
573 >            atomData13[8] = q[2];
574 >            atomData13[9] = q[3];
575 >  
576 >            atomData13[10] = dAtom->getJx();
577 >            atomData13[11] = dAtom->getJy();
578 >            atomData13[12] = dAtom->getJz();
579 >          }
580  
581 < #endif // is_mpi
582 < }
581 >        } else {
582 >          sprintf(painCave.errMsg,
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585 >          haveError= 1;
586 >          simError();
587 >        }
588 >        
589 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591 < void DumpWriter::writeFinal(double finalTime){
591 >        // null terminate the string before sending (just in case):
592 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593  
594 <  char finalName[500];
595 <  ofstream finalOut;
594 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 >                             myPotato, MPI_COMM_WORLD);
596 >        
597 >        myPotato++;
598  
599 <  const int BUFFERSIZE = 2000;
600 <  char tempBuffer[BUFFERSIZE];
601 <  char writeLine[BUFFERSIZE];  
599 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >        
602 >        myPotato++;
603 >        
604 >        if (isDirectional) {
605  
606 <  double q[4];
607 <  DirectionalAtom* dAtom;
608 <  int nAtoms = entry_plug->n_atoms;
609 <  Atom** atoms = entry_plug->atoms;
354 <  int i, j, which_node, done, game_over, which_atom, local_index;
355 <  
356 <  double pos[3], vel[3];
357 <  
358 < #ifdef IS_MPI
359 <  if(worldRank == 0 ){
360 < #endif // is_mpi
361 <    
362 <    strcpy( finalName, entry_plug->finalName );
363 <    
364 <    finalOut.open( finalName, ios::out | ios::trunc );
365 <    if( !finalOut ){
366 <      sprintf( painCave.errMsg,
367 <               "Could not open \"%s\" for final dump output.\n",
368 <               finalName );
369 <      painCave.isFatal = 1;
370 <      simError();
371 <    }
372 <    
373 <    // finalOut.setf( ios::scientific );
374 <    
375 < #ifdef IS_MPI
376 <  }
377 <  
378 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
379 <  MPIcheckPoint();  
380 <  
381 < #endif //is_mpi
606 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
607 >                   myPotato, MPI_COMM_WORLD);
608 >          
609 >        } else {
610  
611 <  
612 < #ifndef IS_MPI
385 <    
386 <  finalOut << nAtoms << "\n";
387 <    
388 <  finalOut << finalTime << ";\t"
389 <           << entry_plug->Hmat[0][0] << "\t"
390 <           << entry_plug->Hmat[1][0] << "\t"
391 <           << entry_plug->Hmat[2][0] << ";\t"
392 <    
393 <           << entry_plug->Hmat[0][1] << "\t"
394 <           << entry_plug->Hmat[1][1] << "\t"
395 <           << entry_plug->Hmat[2][1] << ";\t"
396 <    
397 <           << entry_plug->Hmat[0][2] << "\t"
398 <           << entry_plug->Hmat[1][2] << "\t"
399 <           << entry_plug->Hmat[2][2] << ";\n";
400 <  
401 <  for( i=0; i<nAtoms; i++ ){
402 <      
403 <    atoms[i]->getPos(pos);
404 <    atoms[i]->getVel(vel);
405 <    
406 <    sprintf( tempBuffer,
407 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
408 <             atoms[i]->getType(),
409 <             pos[0],
410 <             pos[1],
411 <             pos[2],
412 <             vel[0],
413 <             vel[1],
414 <             vel[2]);
415 <    strcpy( writeLine, tempBuffer );
416 <
417 <    if( atoms[i]->isDirectional() ){
418 <        
419 <      dAtom = (DirectionalAtom *)atoms[i];
420 <      dAtom->getQ( q );
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 <    else
434 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
435 <      
436 <    finalOut << writeLine;
437 <  }
438 <  finalOut.flush();
439 <  finalOut.close();
440 <
441 < #else // is_mpi
442 <  
443 <  // first thing first, suspend fatalities.
444 <  painCave.isEventLoop = 1;
445 <
446 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
447 <  int haveError;
448 <
449 <  MPI_Status istatus;
450 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
451 <
452 <  // write out header and node 0's coordinates
453 <  
454 <  haveError = 0;
455 <  if( worldRank == 0 ){
456 <    finalOut << mpiSim->getTotAtoms() << "\n";
457 <    
458 <    finalOut << finalTime << ";\t"
459 <             << entry_plug->Hmat[0][0] << "\t"
460 <             << entry_plug->Hmat[1][0] << "\t"
461 <             << entry_plug->Hmat[2][0] << ";\t"
462 <      
463 <             << entry_plug->Hmat[0][1] << "\t"
464 <             << entry_plug->Hmat[1][1] << "\t"
465 <             << entry_plug->Hmat[2][1] << ";\t"
466 <      
467 <             << entry_plug->Hmat[0][2] << "\t"
468 <             << entry_plug->Hmat[1][2] << "\t"
469 <             << entry_plug->Hmat[2][2] << ";\n";
470 <    
471 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
472 <      // Get the Node number which has this molecule:
473 <      
474 <      which_node = AtomToProcMap[i];    
475 <      
476 <      if (which_node == mpiSim->getMyNode()) {
477 <
478 <        which_atom = i;
479 <        local_index=-1;        
480 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
481 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
611 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
612 >                   myPotato, MPI_COMM_WORLD);
613          }
483 –        if (local_index != -1) {    
614  
615 <          atoms[local_index]->getPos(pos);
616 <          atoms[local_index]->getVel(vel);
487 <          
488 <          sprintf( tempBuffer,
489 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 <                   atoms[local_index]->getType(),
491 <                   pos[0],
492 <                   pos[1],
493 <                   pos[2],
494 <                   vel[0],
495 <                   vel[1],
496 <                   vel[2]);
497 <          strcpy( writeLine, tempBuffer );
498 <          
499 <          if( atoms[local_index]->isDirectional() ){
500 <            
501 <            dAtom = (DirectionalAtom *)atoms[local_index];
502 <            dAtom->getQ( q );
503 <            
504 <            sprintf( tempBuffer,
505 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 <                     q[0],
507 <                     q[1],
508 <                     q[2],
509 <                     q[3],
510 <                     dAtom->getJx(),
511 <                     dAtom->getJy(),
512 <                     dAtom->getJz());
513 <            strcat( writeLine, tempBuffer );
514 <          }
515 <          else
516 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
517 <        }
518 <        else {
519 <          sprintf(painCave.errMsg,
520 <                  "Atom %d not found on processor %d\n",
521 <                  i, worldRank );
522 <          haveError= 1;
523 <          simError();
524 <        }
525 <
526 <        if(haveError) nodeZeroError();
527 <    
528 <      }
529 <      else {
530 <        
531 <        myStatus = 1;
532 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
533 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
534 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
535 <                 MPI_COMM_WORLD);
536 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
537 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
538 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
539 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
540 <        
541 <        if(!myStatus) nodeZeroError();
615 >        myPotato++;  
616 >        currentIndex++;    
617        }
543 –      
544 –      finalOut << writeLine;
618      }
546 –    
547 –    // kill everyone off:
548 –    myStatus = -1;
549 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
550 –      MPI_Send(&myStatus, 1, MPI_INT, j,
551 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
552 –    }
619  
620 <  } else {
620 >    sprintf( checkPointMsg,
621 >             "Sucessfully took a dump.\n");
622 >    MPIcheckPoint();        
623      
624 <    done = 0;
557 <    while (!done) {
558 <
559 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
560 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
561 <      
562 <      if(!myStatus) anonymousNodeDie();
563 <      
564 <      if(myStatus < 0) break;
565 <      
566 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
567 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
568 <      
569 <      myStatus = 1;
570 <      local_index=-1;        
571 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
572 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
573 <      }
574 <      if (local_index != -1) {
575 <
576 <        atoms[local_index]->getPos(pos);
577 <        atoms[local_index]->getVel(vel);
578 <
579 <        //format the line
580 <        sprintf( tempBuffer,
581 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
582 <                 atoms[local_index]->getType(),
583 <                 pos[0],
584 <                 pos[1],
585 <                 pos[2],
586 <                 vel[0],
587 <                 vel[1],
588 <                 vel[2]); // check here.
589 <        strcpy( writeLine, tempBuffer );
590 <        
591 <        if( atoms[local_index]->isDirectional() ){
592 <          
593 <          dAtom = (DirectionalAtom *)atoms[local_index];
594 <          dAtom->getQ( q );
595 <          
596 <          sprintf( tempBuffer,
597 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
598 <                   q[0],
599 <                   q[1],
600 <                   q[2],
601 <                   q[3],
602 <                   dAtom->getJx(),
603 <                   dAtom->getJy(),
604 <                   dAtom->getJz());
605 <          strcat( writeLine, tempBuffer );
606 <        }
607 <        else{
608 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
609 <        }
610 <      }
611 <      else {
612 <        sprintf(painCave.errMsg,
613 <                "Atom %d not found on processor %d\n",
614 <                which_atom, worldRank );
615 <        myStatus = 0;
616 <        simError();
617 <        
618 <        strcpy( writeLine, "Hello, I'm an error.\n");
619 <      }
620 <
621 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
622 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
623 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
624 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
625 <    }
626 <  }
627 <  finalOut.flush();
628 <  sprintf( checkPointMsg,
629 <           "Sucessfully took a dump.\n");
630 <  MPIcheckPoint();
624 >  }
625    
632 –  if( worldRank == 0 ) finalOut.close();    
626   #endif // is_mpi
627   }
628  
636 –
637 –
629   #ifdef IS_MPI
630  
631   // a couple of functions to let us escape the write loop
632  
633 < void dWrite::nodeZeroError( void ){
643 <  int j, myStatus;
644 <  
645 <  myStatus = 0;
646 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
647 <    MPI_Send( &myStatus, 1, MPI_INT, j,
648 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
649 <  }  
650 <  
633 > void dWrite::DieDieDie( void ){
634  
635    MPI_Finalize();
636    exit (0);
654 –  
637   }
638  
657 – void dWrite::anonymousNodeDie( void ){
658 –
659 –  MPI_Finalize();
660 –  exit (0);
661 – }
662 –
639   #endif //is_mpi

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