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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _FILE_OFFSET_BITS 64
2 >
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"
8 – #define TAKE_THIS_TAG_CHAR 1
9 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
13 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 26 | 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 <    
34 <    if( !outFile ){
35 <      
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  
43 –    //outFile.setf( ios::scientific );
44 –
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 57 | 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 +  printf("Hello from node %d\n", worldRank);
114 +  sortByGlobalIndex();
115 +  if(worldRank == 0 ){
116 +    
117 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 +    if( !finalOut ){
119 +      sprintf( painCave.errMsg,
120 +               "Could not open \"%s\" for final dump output.\n",
121 +               entry_plug->finalName );
122 +      painCave.isFatal = 1;
123 +      simError();
124 +    }
125 +  }
126 + #endif // is_mpi
127 +
128 +  fileStreams.push_back(&finalOut);
129 +  fileStreams.push_back(&dumpFile);
130 +
131 +  writeFrame(fileStreams, currentTime);
132 +
133 + #ifdef IS_MPI
134 +  finalOut.close();
135 + #endif
136 +        
137 + }
138 +
139 + void DumpWriter::writeFinal(double currentTime){
140 +
141 +  ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143 +
144 + #ifdef IS_MPI
145 +  if(worldRank == 0 ){
146 + #endif // is_mpi
147 +
148 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149 +
150 +    if( !finalOut ){
151 +      sprintf( painCave.errMsg,
152 +               "Could not open \"%s\" for final dump output.\n",
153 +               entry_plug->finalName );
154 +      painCave.isFatal = 1;
155 +      simError();
156 +    }
157 +
158 + #ifdef IS_MPI
159 +  }
160 + #endif // is_mpi
161 +  
162 +  fileStreams.push_back(&finalOut);  
163 +  writeFrame(fileStreams, currentTime);
164 +
165 + #ifdef IS_MPI
166 +  finalOut.close();
167 + #endif
168 +  
169 + }
170 +
171 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172 +
173    const int BUFFERSIZE = 2000;
174 <  char tempBuffer[BUFFERSIZE];
174 >  const int MINIBUFFERSIZE = 100;
175 >
176 >  char tempBuffer[BUFFERSIZE];  
177    char writeLine[BUFFERSIZE];
178  
179 <  int i, j, which_node, done, which_atom, local_index;
179 >  int i, k;
180 >
181 > #ifdef IS_MPI
182 >  
183 >  /*********************************************************************
184 >   * Documentation?  You want DOCUMENTATION?
185 >   *
186 >   * Why all the potatoes below?  
187 >   *
188 >   * To make a long story short, the original version of DumpWriter
189 >   * worked in the most inefficient way possible.  Node 0 would
190 >   * poke each of the node for an individual atom's formatted data
191 >   * as node 0 worked its way down the global index. This was particularly
192 >   * inefficient since the method blocked all processors at every atom
193 >   * (and did it twice!).
194 >   *
195 >   * An intermediate version of DumpWriter could be described from Node
196 >   * zero's perspective as follows:
197 >   *
198 >   *  1) Have 100 of your friends stand in a circle.
199 >   *  2) When you say go, have all of them start tossing potatoes at
200 >   *     you (one at a time).
201 >   *  3) Catch the potatoes.
202 >   *
203 >   * It was an improvement, but MPI has buffers and caches that could
204 >   * best be described in this analogy as "potato nets", so there's no
205 >   * need to block the processors atom-by-atom.
206 >   *
207 >   * This new and improved DumpWriter works in an even more efficient
208 >   * way:
209 >   *
210 >   *  1) Have 100 of your friend stand in a circle.
211 >   *  2) When you say go, have them start tossing 5-pound bags of
212 >   *     potatoes at you.
213 >   *  3) Once you've caught a friend's bag of potatoes,
214 >   *     toss them a spud to let them know they can toss another bag.
215 >   *
216 >   * How's THAT for documentation?
217 >   *
218 >   *********************************************************************/
219 >
220 >  int *potatoes;
221 >  int myPotato;
222 >
223 >  int nProc;
224 >  int j, which_node, done, which_atom, local_index, currentIndex;
225 >  double atomData6[6];
226 >  double atomData13[13];
227 >  int isDirectional;
228 >  char* atomTypeString;
229 >  char MPIatomTypeString[MINIBUFFERSIZE];
230 >
231 > #else //is_mpi
232 >  int nAtoms = entry_plug->n_atoms;
233 > #endif //is_mpi
234 >
235    double q[4];
236    DirectionalAtom* dAtom;
76 –  int nAtoms = entry_plug->n_atoms;
237    Atom** atoms = entry_plug->atoms;
78 –
238    double pos[3], vel[3];
80 –    
239  
240   #ifndef IS_MPI
241 <    
242 <  outFile << nAtoms << "\n";
243 <    
86 <  outFile << currentTime << ";\t"
87 <          << entry_plug->Hmat[0][0] << "\t"
88 <          << entry_plug->Hmat[1][0] << "\t"
89 <          << entry_plug->Hmat[2][0] << ";\t"
241 >  
242 >  for(k = 0; k < outFile.size(); k++){
243 >    *outFile[k] << nAtoms << "\n";
244  
245 <          << entry_plug->Hmat[0][1] << "\t"
246 <          << entry_plug->Hmat[1][1] << "\t"
247 <          << entry_plug->Hmat[2][1] << ";\t"
245 >    *outFile[k] << currentTime << ";\t"
246 >               << entry_plug->Hmat[0][0] << "\t"
247 >                     << entry_plug->Hmat[1][0] << "\t"
248 >                     << entry_plug->Hmat[2][0] << ";\t"
249 >              
250 >               << entry_plug->Hmat[0][1] << "\t"
251 >                     << entry_plug->Hmat[1][1] << "\t"
252 >                     << entry_plug->Hmat[2][1] << ";\t"
253  
254 <          << entry_plug->Hmat[0][2] << "\t"
255 <          << entry_plug->Hmat[1][2] << "\t"
256 <          << entry_plug->Hmat[2][2] << ";\n";
257 <    
254 >                     << entry_plug->Hmat[0][2] << "\t"
255 >                     << entry_plug->Hmat[1][2] << "\t"
256 >                     << entry_plug->Hmat[2][2] << ";";
257 >
258 >    //write out additional parameters, such as chi and eta
259 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
260 >  }
261 >  
262    for( i=0; i<nAtoms; i++ ){
263 <      
263 >
264      atoms[i]->getPos(pos);
265      atoms[i]->getVel(vel);
266  
# Line 113 | Line 276 | void DumpWriter::writeDump( double currentTime ){
276      strcpy( writeLine, tempBuffer );
277  
278      if( atoms[i]->isDirectional() ){
279 <        
279 >
280        dAtom = (DirectionalAtom *)atoms[i];
281        dAtom->getQ( q );
282 <        
282 >
283        sprintf( tempBuffer,
284                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
285                 q[0],
# Line 130 | Line 293 | void DumpWriter::writeDump( double currentTime ){
293      }
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296 <      
297 <    outFile << writeLine;
296 >
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
136 –  outFile.flush();
300  
301   #else // is_mpi
302  
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  /* code to find maximum tag value */
304 >  
305 >  int *tagub, flag, MAXTAG;
306 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
307 >  if (flag) {
308 >    MAXTAG = *tagub;
309 >  } else {
310 >    MAXTAG = 32767;
311 >  }  
312  
143 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313    int haveError;
314  
315    MPI_Status istatus;
316    int *AtomToProcMap = mpiSim->getAtomToProcMap();
317 <  
317 >
318    // write out header and node 0's coordinates
319 <  
319 >
320    if( worldRank == 0 ){
321 <    outFile << mpiSim->getTotAtoms() << "\n";
322 <  
323 <    outFile << currentTime << ";\t"
324 <            << entry_plug->Hmat[0][0] << "\t"
325 <            << entry_plug->Hmat[1][0] << "\t"
326 <            << entry_plug->Hmat[2][0] << ";\t"
327 <      
328 <            << entry_plug->Hmat[0][1] << "\t"
329 <            << entry_plug->Hmat[1][1] << "\t"
161 <            << entry_plug->Hmat[2][1] << ";\t"
162 <      
163 <            << entry_plug->Hmat[0][2] << "\t"
164 <            << entry_plug->Hmat[1][2] << "\t"
165 <            << entry_plug->Hmat[2][2] << ";\n";
321 >
322 >    // Node 0 needs a list of the magic potatoes for each processor;
323 >
324 >    nProc = mpiSim->getNumberProcessors();
325 >    potatoes = new int[nProc];
326 >
327 >    //write out the comment lines
328 >    for (i = 0; i < nProc; i++)
329 >      potatoes[i] = 0;
330      
331 <    outFile.flush();
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333 >
334 >        *outFile[k] << currentTime << ";\t"
335 >                         << entry_plug->Hmat[0][0] << "\t"
336 >                         << entry_plug->Hmat[1][0] << "\t"
337 >                         << entry_plug->Hmat[2][0] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][1] << "\t"
340 >                         << entry_plug->Hmat[1][1] << "\t"
341 >                         << entry_plug->Hmat[2][1] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][2] << "\t"
344 >                         << entry_plug->Hmat[1][2] << "\t"
345 >                         << entry_plug->Hmat[2][2] << ";";
346 >  
347 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
348 >    }
349 >
350 >    currentIndex = 0;
351 >
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
353 +      
354        // Get the Node number which has this atom;
355        
356 <      which_node = AtomToProcMap[i];    
356 >      which_node = AtomToProcMap[i];
357        
358 <      if (which_node == 0 ) {
358 >      if (which_node != 0) {
359 >
360 >        if (potatoes[which_node] + 3 >= MAXTAG) {
361 >          // The potato was going to exceed the maximum value,
362 >          // so wrap this processor potato back to 0:        
363 >
364 >          potatoes[which_node] = 0;          
365 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
366 >          
367 >        }
368 >
369 >        myPotato = potatoes[which_node];        
370 >        
371 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
372 >                 myPotato, MPI_COMM_WORLD, &istatus);
373 >        
374 >        atomTypeString = MPIatomTypeString;
375          
376 <        haveError = 0;
377 <        which_atom = i;
378 <        local_index=-1;        
379 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
380 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
376 >        myPotato++;
377 >
378 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
379 >                 myPotato, MPI_COMM_WORLD, &istatus);
380 >              
381 >        myPotato++;
382 >
383 >        if (isDirectional) {          
384 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
385 >                   myPotato, MPI_COMM_WORLD, &istatus);
386 >        } else {
387 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
388 >                   myPotato, MPI_COMM_WORLD, &istatus);          
389          }
390 <        if (local_index != -1) {
391 <          //format the line
390 >        
391 >        myPotato++;
392 >        potatoes[which_node] = myPotato;
393 >
394 >      } else {
395 >        
396 >        haveError = 0;
397 >        which_atom = i;
398 >        
399 >        //local_index = -1;
400 >
401 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 >        //}
404 >        
405 >        //if (local_index != -1) {
406            
407 +          local_index = indexArray[currentIndex].first;        
408 +          
409 +          if (which_atom == indexArray[currentIndex].second) {
410 +            
411 +            atomTypeString = atoms[local_index]->getType();
412 +            
413            atoms[local_index]->getPos(pos);
414 <          atoms[local_index]->getVel(vel);
186 <
187 <          sprintf( tempBuffer,
188 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
189 <                   atoms[local_index]->getType(),
190 <                   pos[0],
191 <                   pos[1],
192 <                   pos[2],
193 <                   vel[0],
194 <                   vel[1],
195 <                   vel[2]); // check here.
196 <          strcpy( writeLine, tempBuffer );
414 >          atoms[local_index]->getVel(vel);          
415            
416 +          atomData6[0] = pos[0];
417 +          atomData6[1] = pos[1];
418 +          atomData6[2] = pos[2];
419 +
420 +          atomData6[3] = vel[0];
421 +          atomData6[4] = vel[1];
422 +          atomData6[5] = vel[2];
423 +          
424 +          isDirectional = 0;
425 +
426            if( atoms[local_index]->isDirectional() ){
427 +
428 +            isDirectional = 1;
429              
430              dAtom = (DirectionalAtom *)atoms[local_index];
431              dAtom->getQ( q );
432 +
433 +            for (int j = 0; j < 6 ; j++)
434 +              atomData13[j] = atomData6[j];            
435              
436 <            sprintf( tempBuffer,
437 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
438 <                     q[0],
439 <                     q[1],
440 <                     q[2],
441 <                     q[3],
442 <                     dAtom->getJx(),
443 <                     dAtom->getJy(),
444 <                     dAtom->getJz());
445 <            strcat( writeLine, tempBuffer );
446 <            
214 <          }
215 <          else
216 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
217 <        }
218 <        else {
436 >            atomData13[6] = q[0];
437 >            atomData13[7] = q[1];
438 >            atomData13[8] = q[2];
439 >            atomData13[9] = q[3];
440 >            
441 >            atomData13[10] = dAtom->getJx();
442 >            atomData13[11] = dAtom->getJy();
443 >            atomData13[12] = dAtom->getJz();
444 >          }
445 >          
446 >        } else {
447            sprintf(painCave.errMsg,
448 <                  "Atom %d not found on processor %d\n",
449 <                  i, worldRank );
448 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
449 >                  which_atom, worldRank, currentIndex, local_index );
450            haveError= 1;
451            simError();
452 <        }
453 <        
454 <        if(haveError) nodeZeroError();
455 <
452 >        }
453 >        
454 >        if(haveError) DieDieDie();
455 >        
456 >        currentIndex++;
457        }
458 <      else {
459 <        myStatus = 1;
460 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
232 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
233 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
234 <                 MPI_COMM_WORLD);
235 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
236 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
237 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
238 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
458 >      // If we've survived to here, format the line:
459 >      
460 >      if (!isDirectional) {
461          
462 <        if(!myStatus) nodeZeroError();
463 <
462 >        sprintf( writeLine,
463 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 >                 atomTypeString,
465 >                 atomData6[0],
466 >                 atomData6[1],
467 >                 atomData6[2],
468 >                 atomData6[3],
469 >                 atomData6[4],
470 >                 atomData6[5]);
471 >        
472 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 >        
474 >      } else {
475 >        
476 >        sprintf( writeLine,
477 >                 "%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",
478 >                 atomTypeString,
479 >                 atomData13[0],
480 >                 atomData13[1],
481 >                 atomData13[2],
482 >                 atomData13[3],
483 >                 atomData13[4],
484 >                 atomData13[5],
485 >                 atomData13[6],
486 >                 atomData13[7],
487 >                 atomData13[8],
488 >                 atomData13[9],
489 >                 atomData13[10],
490 >                 atomData13[11],
491 >                 atomData13[12]);
492 >        
493        }
494        
495 <      outFile << writeLine;
496 <      outFile.flush();
495 >      for(k = 0; k < outFile.size(); k++)
496 >        *outFile[k] << writeLine;
497      }
498      
499 <    // kill everyone off:
500 <    myStatus = -1;
501 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
502 <      MPI_Send(&myStatus, 1, MPI_INT, j,
503 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
504 <    }
505 <
499 >    for(k = 0; k < outFile.size(); k++)
500 >      outFile[k]->flush();
501 >    
502 >    sprintf( checkPointMsg,
503 >             "Sucessfully took a dump.\n");
504 >    
505 >    MPIcheckPoint();        
506 >    
507 >    delete[] potatoes;
508 >    
509    } else {
510 +
511 +    // worldRank != 0, so I'm a remote node.  
512 +
513 +    // Set my magic potato to 0:
514 +
515 +    myPotato = 0;
516 +    currentIndex = 0;
517      
518 <    done = 0;
258 <    while (!done) {
518 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
519        
520 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
261 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
262 <
263 <      if(!myStatus) anonymousNodeDie();
520 >      // Am I the node which has this atom?
521        
522 <      if(myStatus < 0) break;
522 >      if (AtomToProcMap[i] == worldRank) {
523  
524 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
525 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
526 <      
527 <      myStatus = 1;
528 <      local_index=-1;        
529 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
530 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
531 <      }
532 <      if (local_index != -1) {
533 <        //format the line
524 >        if (myPotato + 3 >= MAXTAG) {
525 >          
526 >          // The potato was going to exceed the maximum value,
527 >          // so wrap this processor potato back to 0 (and block until
528 >          // node 0 says we can go:
529 >          
530 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531 >          
532 >        }
533 >        which_atom = i;
534  
535 <        atoms[local_index]->getPos(pos);
279 <        atoms[local_index]->getVel(vel);
535 >        //local_index = -1;
536  
537 <        sprintf( tempBuffer,
538 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
539 <                 atoms[local_index]->getType(),
540 <                 pos[0],
541 <                 pos[1],
542 <                 pos[2],
543 <                 vel[0],
544 <                 vel[1],
545 <                 vel[2]); // check here.
546 <        strcpy( writeLine, tempBuffer );
547 <        
292 <        if( atoms[local_index]->isDirectional() ){
537 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
538 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
539 >        //}
540 >        
541 >        //if (local_index != -1) {
542 >
543 >        local_index = indexArray[currentIndex].first;        
544 >                
545 >        if (which_atom == indexArray[currentIndex].second) {
546 >        
547 >          atomTypeString = atoms[local_index]->getType();
548            
549 <          dAtom = (DirectionalAtom *)atoms[local_index];
550 <          dAtom->getQ( q );
549 >          atoms[local_index]->getPos(pos);
550 >          atoms[local_index]->getVel(vel);
551            
552 <          sprintf( tempBuffer,
553 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
554 <                   q[0],
300 <                   q[1],
301 <                   q[2],
302 <                   q[3],
303 <                   dAtom->getJx(),
304 <                   dAtom->getJy(),
305 <                   dAtom->getJz());
306 <          strcat( writeLine, tempBuffer );
307 <        }
308 <        else{
309 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
310 <        }
311 <      }
312 <      else {
313 <        sprintf(painCave.errMsg,
314 <                "Atom %d not found on processor %d\n",
315 <                which_atom, worldRank );
316 <        myStatus = 0;
317 <        simError();
552 >          atomData6[0] = pos[0];
553 >          atomData6[1] = pos[1];
554 >          atomData6[2] = pos[2];
555  
556 <        strcpy( writeLine, "Hello, I'm an error.\n");
557 <      }
556 >          atomData6[3] = vel[0];
557 >          atomData6[4] = vel[1];
558 >          atomData6[5] = vel[2];
559 >          
560 >          isDirectional = 0;
561  
562 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
323 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
324 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
325 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
326 <    }
327 <  }  
328 <  outFile.flush();
329 <  sprintf( checkPointMsg,
330 <           "Sucessfully took a dump.\n");
331 <  MPIcheckPoint();
562 >          if( atoms[local_index]->isDirectional() ){
563  
564 < // last  thing last, enable  fatalities.
565 <  painCave.isEventLoop = 0;
564 >            isDirectional = 1;
565 >            
566 >            dAtom = (DirectionalAtom *)atoms[local_index];
567 >            dAtom->getQ( q );
568 >            
569 >            for (int j = 0; j < 6 ; j++)
570 >              atomData13[j] = atomData6[j];
571 >            
572 >            atomData13[6] = q[0];
573 >            atomData13[7] = q[1];
574 >            atomData13[8] = q[2];
575 >            atomData13[9] = q[3];
576 >  
577 >            atomData13[10] = dAtom->getJx();
578 >            atomData13[11] = dAtom->getJy();
579 >            atomData13[12] = dAtom->getJz();
580 >          }
581  
582 < #endif // is_mpi
583 < }
582 >        } else {
583 >          sprintf(painCave.errMsg,
584 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
585 >                  which_atom, worldRank, currentIndex, local_index );
586 >          haveError= 1;
587 >          simError();
588 >        }
589 >        
590 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591  
592 < void DumpWriter::writeFinal(double finalTime){
592 >        // null terminate the string before sending (just in case):
593 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
594  
595 <  char finalName[500];
596 <  ofstream finalOut;
595 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
596 >                             myPotato, MPI_COMM_WORLD);
597 >        
598 >        myPotato++;
599  
600 <  const int BUFFERSIZE = 2000;
601 <  char tempBuffer[BUFFERSIZE];
602 <  char writeLine[BUFFERSIZE];  
600 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 >                             myPotato, MPI_COMM_WORLD);
602 >        
603 >        myPotato++;
604 >        
605 >        if (isDirectional) {
606  
607 <  double q[4];
608 <  DirectionalAtom* dAtom;
609 <  int nAtoms = entry_plug->n_atoms;
610 <  Atom** atoms = entry_plug->atoms;
352 <  int i, j, which_node, done, game_over, which_atom, local_index;
353 <  
354 <  double pos[3], vel[3];
355 <  
356 < #ifdef IS_MPI
357 <  if(worldRank == 0 ){
358 < #endif // is_mpi
359 <    
360 <    strcpy( finalName, entry_plug->finalName );
361 <    
362 <    finalOut.open( finalName, ios::out | ios::trunc );
363 <    if( !finalOut ){
364 <      sprintf( painCave.errMsg,
365 <               "Could not open \"%s\" for final dump output.\n",
366 <               finalName );
367 <      painCave.isFatal = 1;
368 <      simError();
369 <    }
370 <    
371 <    // finalOut.setf( ios::scientific );
372 <    
373 < #ifdef IS_MPI
374 <  }
375 <  
376 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
377 <  MPIcheckPoint();  
378 <  
379 < #endif //is_mpi
607 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
608 >                   myPotato, MPI_COMM_WORLD);
609 >          
610 >        } else {
611  
612 <  
613 < #ifndef IS_MPI
383 <    
384 <  finalOut << nAtoms << "\n";
385 <    
386 <  finalOut << finalTime << ";\t"
387 <           << entry_plug->Hmat[0][0] << "\t"
388 <           << entry_plug->Hmat[1][0] << "\t"
389 <           << entry_plug->Hmat[2][0] << ";\t"
390 <    
391 <           << entry_plug->Hmat[0][1] << "\t"
392 <           << entry_plug->Hmat[1][1] << "\t"
393 <           << entry_plug->Hmat[2][1] << ";\t"
394 <    
395 <           << entry_plug->Hmat[0][2] << "\t"
396 <           << entry_plug->Hmat[1][2] << "\t"
397 <           << entry_plug->Hmat[2][2] << ";\n";
398 <  
399 <  for( i=0; i<nAtoms; i++ ){
400 <      
401 <    atoms[i]->getPos(pos);
402 <    atoms[i]->getVel(vel);
403 <    
404 <    sprintf( tempBuffer,
405 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
406 <             atoms[i]->getType(),
407 <             pos[0],
408 <             pos[1],
409 <             pos[2],
410 <             vel[0],
411 <             vel[1],
412 <             vel[2]);
413 <    strcpy( writeLine, tempBuffer );
414 <
415 <    if( atoms[i]->isDirectional() ){
416 <        
417 <      dAtom = (DirectionalAtom *)atoms[i];
418 <      dAtom->getQ( q );
419 <        
420 <      sprintf( tempBuffer,
421 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
422 <               q[0],
423 <               q[1],
424 <               q[2],
425 <               q[3],
426 <               dAtom->getJx(),
427 <               dAtom->getJy(),
428 <               dAtom->getJz());
429 <      strcat( writeLine, tempBuffer );
430 <    }
431 <    else
432 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
433 <      
434 <    finalOut << writeLine;
435 <  }
436 <  finalOut.flush();
437 <  finalOut.close();
438 <
439 < #else // is_mpi
440 <  
441 <  // first thing first, suspend fatalities.
442 <  painCave.isEventLoop = 1;
443 <
444 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
445 <  int haveError;
446 <
447 <  MPI_Status istatus;
448 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
449 <
450 <  // write out header and node 0's coordinates
451 <  
452 <  haveError = 0;
453 <  if( worldRank == 0 ){
454 <    finalOut << mpiSim->getTotAtoms() << "\n";
455 <    
456 <    finalOut << finalTime << ";\t"
457 <             << entry_plug->Hmat[0][0] << "\t"
458 <             << entry_plug->Hmat[1][0] << "\t"
459 <             << entry_plug->Hmat[2][0] << ";\t"
460 <      
461 <             << entry_plug->Hmat[0][1] << "\t"
462 <             << entry_plug->Hmat[1][1] << "\t"
463 <             << entry_plug->Hmat[2][1] << ";\t"
464 <      
465 <             << entry_plug->Hmat[0][2] << "\t"
466 <             << entry_plug->Hmat[1][2] << "\t"
467 <             << entry_plug->Hmat[2][2] << ";\n";
468 <    
469 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
470 <      // Get the Node number which has this molecule:
471 <      
472 <      which_node = AtomToProcMap[i];    
473 <      
474 <      if (which_node == mpiSim->getMyNode()) {
475 <
476 <        which_atom = i;
477 <        local_index=-1;        
478 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
479 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
612 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
613 >                   myPotato, MPI_COMM_WORLD);
614          }
481 –        if (local_index != -1) {    
615  
616 <          atoms[local_index]->getPos(pos);
617 <          atoms[local_index]->getVel(vel);
485 <          
486 <          sprintf( tempBuffer,
487 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
488 <                   atoms[local_index]->getType(),
489 <                   pos[0],
490 <                   pos[1],
491 <                   pos[2],
492 <                   vel[0],
493 <                   vel[1],
494 <                   vel[2]);
495 <          strcpy( writeLine, tempBuffer );
496 <          
497 <          if( atoms[local_index]->isDirectional() ){
498 <            
499 <            dAtom = (DirectionalAtom *)atoms[local_index];
500 <            dAtom->getQ( q );
501 <            
502 <            sprintf( tempBuffer,
503 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
504 <                     q[0],
505 <                     q[1],
506 <                     q[2],
507 <                     q[3],
508 <                     dAtom->getJx(),
509 <                     dAtom->getJy(),
510 <                     dAtom->getJz());
511 <            strcat( writeLine, tempBuffer );
512 <          }
513 <          else
514 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
515 <        }
516 <        else {
517 <          sprintf(painCave.errMsg,
518 <                  "Atom %d not found on processor %d\n",
519 <                  i, worldRank );
520 <          haveError= 1;
521 <          simError();
522 <        }
523 <
524 <        if(haveError) nodeZeroError();
525 <    
526 <      }
527 <      else {
528 <        
529 <        myStatus = 1;
530 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
531 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
532 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
533 <                 MPI_COMM_WORLD);
534 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
535 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
536 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
537 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
538 <        
539 <        if(!myStatus) nodeZeroError();
616 >        myPotato++;  
617 >        currentIndex++;    
618        }
541 –      
542 –      finalOut << writeLine;
619      }
544 –    
545 –    // kill everyone off:
546 –    myStatus = -1;
547 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
548 –      MPI_Send(&myStatus, 1, MPI_INT, j,
549 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
550 –    }
620  
621 <  } else {
621 >    sprintf( checkPointMsg,
622 >             "Sucessfully took a dump.\n");
623 >    MPIcheckPoint();        
624      
625 <    done = 0;
555 <    while (!done) {
556 <
557 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
558 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
559 <      
560 <      if(!myStatus) anonymousNodeDie();
561 <      
562 <      if(myStatus < 0) break;
563 <      
564 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
565 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
566 <      
567 <      myStatus = 1;
568 <      local_index=-1;        
569 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
570 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
571 <      }
572 <      if (local_index != -1) {
573 <
574 <        atoms[local_index]->getPos(pos);
575 <        atoms[local_index]->getVel(vel);
576 <
577 <        //format the line
578 <        sprintf( tempBuffer,
579 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
580 <                 atoms[local_index]->getType(),
581 <                 pos[0],
582 <                 pos[1],
583 <                 pos[2],
584 <                 vel[0],
585 <                 vel[1],
586 <                 vel[2]); // check here.
587 <        strcpy( writeLine, tempBuffer );
588 <        
589 <        if( atoms[local_index]->isDirectional() ){
590 <          
591 <          dAtom = (DirectionalAtom *)atoms[local_index];
592 <          dAtom->getQ( q );
593 <          
594 <          sprintf( tempBuffer,
595 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
596 <                   q[0],
597 <                   q[1],
598 <                   q[2],
599 <                   q[3],
600 <                   dAtom->getJx(),
601 <                   dAtom->getJy(),
602 <                   dAtom->getJz());
603 <          strcat( writeLine, tempBuffer );
604 <        }
605 <        else{
606 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
607 <        }
608 <      }
609 <      else {
610 <        sprintf(painCave.errMsg,
611 <                "Atom %d not found on processor %d\n",
612 <                which_atom, worldRank );
613 <        myStatus = 0;
614 <        simError();
615 <        
616 <        strcpy( writeLine, "Hello, I'm an error.\n");
617 <      }
618 <
619 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
620 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
621 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
622 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
623 <    }
624 <  }
625 <  finalOut.flush();
626 <  sprintf( checkPointMsg,
627 <           "Sucessfully took a dump.\n");
628 <  MPIcheckPoint();
625 >  }
626    
630 –  if( worldRank == 0 ) finalOut.close();    
627   #endif // is_mpi
628   }
629  
634 –
635 –
630   #ifdef IS_MPI
631  
632   // a couple of functions to let us escape the write loop
633  
634 < void dWrite::nodeZeroError( void ){
641 <  int j, myStatus;
642 <  
643 <  myStatus = 0;
644 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
645 <    MPI_Send( &myStatus, 1, MPI_INT, j,
646 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
647 <  }  
648 <  
634 > void dWrite::DieDieDie( void ){
635  
636    MPI_Finalize();
637    exit (0);
652 –  
638   }
639  
655 – void dWrite::anonymousNodeDie( void ){
656 –
657 –  MPI_Finalize();
658 –  exit (0);
659 – }
660 –
640   #endif //is_mpi

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