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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 905 by tim, Wed Jan 7 19:26:12 2004 UTC vs.
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC

# Line 3 | Line 3
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 15
11 – #define TAKE_THIS_TAG_INT 20
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 29 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
32 –    strcpy( outName, entry_plug->sampleName );
31  
32 <    outFile.open(outName, ios::out | ios::trunc );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    if( !outFile ){
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      }
# Line 47 | Line 45 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
45   #ifdef IS_MPI
46    }
47  
48 +  //sort the local atoms by global index
49 +  sortByGlobalIndex();
50 +  
51    sprintf( checkPointMsg,
52             "Sucessfully opened output file for dumping.\n");
53    MPIcheckPoint();
# Line 59 | Line 60 | DumpWriter::~DumpWriter( ){
60    if(worldRank == 0 ){
61   #endif // is_mpi
62  
63 <    outFile.close();
63 >    dumpFile.close();
64  
65   #ifdef IS_MPI
66    }
67   #endif // is_mpi
68   }
69  
70 < void DumpWriter::writeDump( double currentTime ){
70 > #ifdef IS_MPI
71  
72 + /**
73 + * A hook function to load balancing
74 + */
75 +
76 + void DumpWriter::update(){
77 +  sortByGlobalIndex();          
78 + }
79 +  
80 + /**
81 + * Auxiliary sorting function
82 + */
83 +
84 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
85 +  return p1.second < p2.second;
86 + }
87 +
88 + /**
89 + * Sorting the local index by global index
90 + */
91 +
92 + void DumpWriter::sortByGlobalIndex(){
93 +  Atom** atoms = entry_plug->atoms;
94 +  
95 +  indexArray.clear();
96 +  
97 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
98 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
99 +  
100 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
101 + }
102 + #endif
103 +
104 + void DumpWriter::writeDump(double currentTime){
105 +  
106 + // write to eor file
107 +  writeFinal(currentTime);
108 +
109 + //write to dump file
110 +  writeFrame(dumpFile, currentTime);
111 +        
112 + }
113 +
114 + void DumpWriter::writeFinal(double currentTime){
115 +
116 +  ofstream finalOut;    
117 +  
118 +  //Open eor file
119 + #ifdef IS_MPI
120 +  if(worldRank == 0 ){
121 + #endif // is_mpi
122 +
123 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
124 +    if( !finalOut ){
125 +      sprintf( painCave.errMsg,
126 +               "Could not open \"%s\" for final dump output.\n",
127 +               entry_plug->finalName );
128 +      painCave.isFatal = 1;
129 +      simError();
130 +    }
131 +    
132 + #ifdef IS_MPI
133 +  }
134 + #endif
135 +  
136 +  //write to eor file  
137 +  writeFrame(finalOut, currentTime);
138 +  
139 +  //close eor file      
140 + #ifdef IS_MPI
141 +  if(worldRank == 0 ){
142 +    finalOut.close();
143 +  }
144 + #endif // is_mpi
145 +
146 + }
147 +
148 + void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
149 +
150    const int BUFFERSIZE = 2000;
151 +  const int MINIBUFFERSIZE = 100;
152 +
153    char tempBuffer[BUFFERSIZE];
154    char writeLine[BUFFERSIZE];
155  
156    int i;
157 +
158   #ifdef IS_MPI
159 <  int j, which_node, done, which_atom, local_index;
159 >  
160 >  int *potatoes;
161 >  int myPotato;
162 >
163 >  int nProc;
164 >  int j, which_node, done, which_atom, local_index, currentIndex;
165 >  double atomData6[6];
166 >  double atomData13[13];
167 >  int isDirectional;
168 >  char* atomTypeString;
169 >  char MPIatomTypeString[MINIBUFFERSIZE];
170 >
171   #else //is_mpi
172    int nAtoms = entry_plug->n_atoms;
173   #endif //is_mpi
# Line 84 | Line 177 | void DumpWriter::writeDump( double currentTime ){
177    Atom** atoms = entry_plug->atoms;
178    double pos[3], vel[3];
179  
87 –
88 –  // write current frame to the eor file
89 –
90 –  this->writeFinal( currentTime );
91 –
180   #ifndef IS_MPI
181  
182    outFile << nAtoms << "\n";
# Line 146 | Line 234 | void DumpWriter::writeDump( double currentTime ){
234  
235      outFile << writeLine;
236    }
149 –  outFile.flush();
237  
238   #else // is_mpi
239  
240 <  // first thing first, suspend fatalities.
241 <  painCave.isEventLoop = 1;
240 >  /* code to find maximum tag value */
241 >  
242 >  int *tagub, flag, MAXTAG;
243 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
244 >  if (flag) {
245 >    MAXTAG = *tagub;
246 >  } else {
247 >    MAXTAG = 32767;
248 >  }  
249  
156 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
250    int haveError;
251  
252    MPI_Status istatus;
# Line 162 | Line 255 | void DumpWriter::writeDump( double currentTime ){
255    // write out header and node 0's coordinates
256  
257    if( worldRank == 0 ){
258 +
259 +    // Node 0 needs a list of the magic potatoes for each processor;
260 +
261 +    nProc = mpiSim->getNumberProcessors();
262 +    potatoes = new int[nProc];
263 +
264 +    for (i = 0; i < nProc; i++)
265 +      potatoes[i] = 0;
266 +    
267      outFile << mpiSim->getTotAtoms() << "\n";
268  
269      outFile << currentTime << ";\t"
# Line 180 | Line 282 | void DumpWriter::writeDump( double currentTime ){
282      outFile << entry_plug->the_integrator->getAdditionalParameters();
283      outFile << endl;
284      outFile.flush();
285 +    
286 +    currentIndex = 0;
287      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
288 +      
289        // Get the Node number which has this atom;
290 <
290 >      
291        which_node = AtomToProcMap[i];
292 +      
293 +      if (which_node != 0) {
294  
295 <      if (which_node == 0 ) {
295 >        if (potatoes[which_node] + 3 >= MAXTAG) {
296 >          // The potato was going to exceed the maximum value,
297 >          // so wrap this processor potato back to 0:        
298  
299 +          potatoes[which_node] = 0;          
300 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
301 +          
302 +        }
303 +
304 +        myPotato = potatoes[which_node];        
305 +        
306 +        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307 +                 myPotato, MPI_COMM_WORLD, &istatus);
308 +        
309 +        atomTypeString = MPIatomTypeString;
310 +        
311 +        myPotato++;
312 +
313 +        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
314 +                 myPotato, MPI_COMM_WORLD, &istatus);
315 +              
316 +        myPotato++;
317 +
318 +        if (isDirectional) {          
319 +          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
320 +                   myPotato, MPI_COMM_WORLD, &istatus);
321 +        } else {
322 +          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
323 +                   myPotato, MPI_COMM_WORLD, &istatus);          
324 +        }
325 +        
326 +        myPotato++;
327 +        potatoes[which_node] = myPotato;
328 +
329 +      } else {
330 +        
331          haveError = 0;
332          which_atom = i;
333 <        local_index=-1;
334 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
335 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
336 <        }
337 <        if (local_index != -1) {
338 <          //format the line
333 >        
334 >        local_index = indexArray[currentIndex].first;        
335 >                
336 >        if (which_atom == indexArray[currentIndex].second) {
337 >          
338 >          atomTypeString = atoms[local_index]->getType();
339  
340            atoms[local_index]->getPos(pos);
341 <          atoms[local_index]->getVel(vel);
341 >          atoms[local_index]->getVel(vel);          
342  
343 <          sprintf( tempBuffer,
344 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
345 <                   atoms[local_index]->getType(),
205 <                   pos[0],
206 <                   pos[1],
207 <                   pos[2],
208 <                   vel[0],
209 <                   vel[1],
210 <                   vel[2]); // check here.
211 <          strcpy( writeLine, tempBuffer );
343 >          atomData6[0] = pos[0];
344 >          atomData6[1] = pos[1];
345 >          atomData6[2] = pos[2];
346  
347 +          atomData6[3] = vel[0];
348 +          atomData6[4] = vel[1];
349 +          atomData6[5] = vel[2];
350 +          
351 +          isDirectional = 0;
352 +
353            if( atoms[local_index]->isDirectional() ){
354  
355 +            isDirectional = 1;
356 +            
357              dAtom = (DirectionalAtom *)atoms[local_index];
358              dAtom->getQ( q );
359  
360 <            sprintf( tempBuffer,
361 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
362 <                     q[0],
363 <                     q[1],
364 <                     q[2],
365 <                     q[3],
366 <                     dAtom->getJx(),
367 <                     dAtom->getJy(),
368 <                     dAtom->getJz());
369 <            strcat( writeLine, tempBuffer );
370 <
371 <          }
372 <          else
373 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232 <        }
233 <        else {
360 >            for (int j = 0; j < 6 ; j++)
361 >              atomData13[j] = atomData6[j];            
362 >            
363 >            atomData13[6] = q[0];
364 >            atomData13[7] = q[1];
365 >            atomData13[8] = q[2];
366 >            atomData13[9] = q[3];
367 >            
368 >            atomData13[10] = dAtom->getJx();
369 >            atomData13[11] = dAtom->getJy();
370 >            atomData13[12] = dAtom->getJz();
371 >          }
372 >          
373 >        } else {
374            sprintf(painCave.errMsg,
375                    "Atom %d not found on processor %d\n",
376                    i, worldRank );
377            haveError= 1;
378            simError();
379          }
380 <
381 <        if(haveError) nodeZeroError();
382 <
380 >        
381 >        if(haveError) DieDieDie();
382 >        
383 >        currentIndex ++;
384        }
385 <      else {
386 <        myStatus = 1;
387 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
388 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
389 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
390 <                 MPI_COMM_WORLD);
391 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
392 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
393 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
394 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
385 >      // If we've survived to here, format the line:
386 >      
387 >      if (!isDirectional) {
388 >        
389 >        sprintf( writeLine,
390 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
391 >                 atomTypeString,
392 >                 atomData6[0],
393 >                 atomData6[1],
394 >                 atomData6[2],
395 >                 atomData6[3],
396 >                 atomData6[4],
397 >                 atomData6[5]);
398  
399 <        if(!myStatus) nodeZeroError();
400 <
399 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
400 >        
401 >      } else {
402 >        
403 >        sprintf( writeLine,
404 >                 "%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",
405 >                 atomTypeString,
406 >                 atomData13[0],
407 >                 atomData13[1],
408 >                 atomData13[2],
409 >                 atomData13[3],
410 >                 atomData13[4],
411 >                 atomData13[5],
412 >                 atomData13[6],
413 >                 atomData13[7],
414 >                 atomData13[8],
415 >                 atomData13[9],
416 >                 atomData13[10],
417 >                 atomData13[11],
418 >                 atomData13[12]);
419 >        
420        }
421 <
421 >      
422        outFile << writeLine;
260 –      outFile.flush();
423      }
424 +    
425  
426 <    // kill everyone off:
427 <    myStatus = -1;
428 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
429 <      MPI_Send(&myStatus, 1, MPI_INT, j,
430 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
268 <    }
269 <
426 >    outFile.flush();
427 >    sprintf( checkPointMsg,
428 >             "Sucessfully took a dump.\n");
429 >    MPIcheckPoint();        
430 >    delete[] potatoes;
431    } else {
432  
433 <    done = 0;
273 <    while (!done) {
433 >    // worldRank != 0, so I'm a remote node.  
434  
435 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
276 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
435 >    // Set my magic potato to 0:
436  
437 <      if(!myStatus) anonymousNodeDie();
437 >    myPotato = 0;
438 >    currentIndex = 0;
439 >    
440 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
441 >      
442 >      // Am I the node which has this atom?
443 >      
444 >      if (AtomToProcMap[i] == worldRank) {
445  
446 <      if(myStatus < 0) break;
446 >        if (myPotato + 3 >= MAXTAG) {
447  
448 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
449 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
448 >          // The potato was going to exceed the maximum value,
449 >          // so wrap this processor potato back to 0 (and block until
450 >          // node 0 says we can go:
451  
452 <      myStatus = 1;
453 <      local_index=-1;
454 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
455 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
456 <      }
457 <      if (local_index != -1) {
458 <        //format the line
452 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
453 >          
454 >        }
455 >        which_atom = i;
456 >        local_index = indexArray[currentIndex].first;        
457 >                
458 >        if (which_atom == indexArray[currentIndex].second) {
459 >        
460 >          atomTypeString = atoms[local_index]->getType();
461  
462 <        atoms[local_index]->getPos(pos);
463 <        atoms[local_index]->getVel(vel);
462 >          atoms[local_index]->getPos(pos);
463 >          atoms[local_index]->getVel(vel);
464  
465 <        sprintf( tempBuffer,
466 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
467 <                 atoms[local_index]->getType(),
299 <                 pos[0],
300 <                 pos[1],
301 <                 pos[2],
302 <                 vel[0],
303 <                 vel[1],
304 <                 vel[2]); // check here.
305 <        strcpy( writeLine, tempBuffer );
465 >          atomData6[0] = pos[0];
466 >          atomData6[1] = pos[1];
467 >          atomData6[2] = pos[2];
468  
469 <        if( atoms[local_index]->isDirectional() ){
469 >          atomData6[3] = vel[0];
470 >          atomData6[4] = vel[1];
471 >          atomData6[5] = vel[2];
472 >          
473 >          isDirectional = 0;
474  
475 <          dAtom = (DirectionalAtom *)atoms[local_index];
310 <          dAtom->getQ( q );
475 >          if( atoms[local_index]->isDirectional() ){
476  
477 <          sprintf( tempBuffer,
478 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
479 <                   q[0],
480 <                   q[1],
481 <                   q[2],
482 <                   q[3],
483 <                   dAtom->getJx(),
484 <                   dAtom->getJy(),
485 <                   dAtom->getJz());
486 <          strcat( writeLine, tempBuffer );
487 <        }
488 <        else{
324 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
325 <        }
326 <      }
327 <      else {
328 <        sprintf(painCave.errMsg,
329 <                "Atom %d not found on processor %d\n",
330 <                which_atom, worldRank );
331 <        myStatus = 0;
332 <        simError();
477 >            isDirectional = 1;
478 >            
479 >            dAtom = (DirectionalAtom *)atoms[local_index];
480 >            dAtom->getQ( q );
481 >            
482 >            for (int j = 0; j < 6 ; j++)
483 >              atomData13[j] = atomData6[j];
484 >            
485 >            atomData13[6] = q[0];
486 >            atomData13[7] = q[1];
487 >            atomData13[8] = q[2];
488 >            atomData13[9] = q[3];
489  
490 <        strcpy( writeLine, "Hello, I'm an error.\n");
491 <      }
490 >            atomData13[10] = dAtom->getJx();
491 >            atomData13[11] = dAtom->getJy();
492 >            atomData13[12] = dAtom->getJz();
493 >          }
494  
495 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
338 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
339 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
340 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
341 <    }
342 <  }
343 <  outFile.flush();
344 <  sprintf( checkPointMsg,
345 <           "Sucessfully took a dump.\n");
346 <  MPIcheckPoint();
347 <
348 < // last  thing last, enable  fatalities.
349 <  painCave.isEventLoop = 0;
350 <
351 < #endif // is_mpi
352 < }
353 <
354 < void DumpWriter::writeFinal(double finalTime){
355 <
356 <  char finalName[500];
357 <  ofstream finalOut;
358 <
359 <  const int BUFFERSIZE = 2000;
360 <  char tempBuffer[BUFFERSIZE];
361 <  char writeLine[BUFFERSIZE];
362 <
363 <  double q[4];
364 <  DirectionalAtom* dAtom;
365 <  Atom** atoms = entry_plug->atoms;
366 <  int i;
367 < #ifdef IS_MPI
368 <  int j, which_node, done, which_atom, local_index;
369 < #else //is_mpi
370 <  int nAtoms = entry_plug->n_atoms;
371 < #endif //is_mpi
372 <
373 <  double pos[3], vel[3];
374 <
375 < #ifdef IS_MPI
376 <  if(worldRank == 0 ){
377 < #endif // is_mpi
378 <
379 <    strcpy( finalName, entry_plug->finalName );
380 <
381 <    finalOut.open( finalName, ios::out | ios::trunc );
382 <    if( !finalOut ){
383 <      sprintf( painCave.errMsg,
384 <               "Could not open \"%s\" for final dump output.\n",
385 <               finalName );
386 <      painCave.isFatal = 1;
387 <      simError();
388 <    }
389 <
390 <    // finalOut.setf( ios::scientific );
391 <
392 < #ifdef IS_MPI
393 <  }
394 <
395 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
396 <  MPIcheckPoint();
397 <
398 < #endif //is_mpi
399 <
400 <
401 < #ifndef IS_MPI
402 <
403 <  finalOut << nAtoms << "\n";
404 <
405 <  finalOut << finalTime << ";\t"
406 <           << entry_plug->Hmat[0][0] << "\t"
407 <           << entry_plug->Hmat[1][0] << "\t"
408 <           << entry_plug->Hmat[2][0] << ";\t"
409 <
410 <           << entry_plug->Hmat[0][1] << "\t"
411 <           << entry_plug->Hmat[1][1] << "\t"
412 <           << entry_plug->Hmat[2][1] << ";\t"
413 <
414 <           << entry_plug->Hmat[0][2] << "\t"
415 <           << entry_plug->Hmat[1][2] << "\t"
416 <           << entry_plug->Hmat[2][2] << ";";
417 <
418 <  //write out additional parameters, such as chi and eta
419 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
420 <  finalOut << endl;
421 <
422 <  for( i=0; i<nAtoms; i++ ){
423 <
424 <    atoms[i]->getPos(pos);
425 <    atoms[i]->getVel(vel);
426 <
427 <    sprintf( tempBuffer,
428 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
429 <             atoms[i]->getType(),
430 <             pos[0],
431 <             pos[1],
432 <             pos[2],
433 <             vel[0],
434 <             vel[1],
435 <             vel[2]);
436 <    strcpy( writeLine, tempBuffer );
437 <
438 <    if( atoms[i]->isDirectional() ){
439 <
440 <      dAtom = (DirectionalAtom *)atoms[i];
441 <      dAtom->getQ( q );
442 <
443 <      sprintf( tempBuffer,
444 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
445 <               q[0],
446 <               q[1],
447 <               q[2],
448 <               q[3],
449 <               dAtom->getJx(),
450 <               dAtom->getJy(),
451 <               dAtom->getJz());
452 <      strcat( writeLine, tempBuffer );
453 <    }
454 <    else
455 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 <
457 <    finalOut << writeLine;
458 <  }
459 <  finalOut.flush();
460 <  finalOut.close();
461 <
462 < #else // is_mpi
463 <
464 <  // first thing first, suspend fatalities.
465 <  painCave.isEventLoop = 1;
466 <
467 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
468 <  int haveError;
469 <
470 <  MPI_Status istatus;
471 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
472 <
473 <  // write out header and node 0's coordinates
474 <
475 <  haveError = 0;
476 <  if( worldRank == 0 ){
477 <    finalOut << mpiSim->getTotAtoms() << "\n";
478 <
479 <    finalOut << finalTime << ";\t"
480 <             << entry_plug->Hmat[0][0] << "\t"
481 <             << entry_plug->Hmat[1][0] << "\t"
482 <             << entry_plug->Hmat[2][0] << ";\t"
483 <
484 <             << entry_plug->Hmat[0][1] << "\t"
485 <             << entry_plug->Hmat[1][1] << "\t"
486 <             << entry_plug->Hmat[2][1] << ";\t"
487 <
488 <             << entry_plug->Hmat[0][2] << "\t"
489 <             << entry_plug->Hmat[1][2] << "\t"
490 <             << entry_plug->Hmat[2][2] << ";";
491 <
492 <    //write out additional parameters, such as chi and eta
493 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
494 <    finalOut << endl;
495 <
496 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
497 <      // Get the Node number which has this molecule:
498 <
499 <      which_node = AtomToProcMap[i];
500 <
501 <      if (which_node == mpiSim->getMyNode()) {
502 <
503 <        which_atom = i;
504 <        local_index=-1;
505 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
506 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
507 <        }
508 <        if (local_index != -1) {
509 <
510 <          atoms[local_index]->getPos(pos);
511 <          atoms[local_index]->getVel(vel);
512 <
513 <          sprintf( tempBuffer,
514 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <                   atoms[local_index]->getType(),
516 <                   pos[0],
517 <                   pos[1],
518 <                   pos[2],
519 <                   vel[0],
520 <                   vel[1],
521 <                   vel[2]);
522 <          strcpy( writeLine, tempBuffer );
523 <
524 <          if( atoms[local_index]->isDirectional() ){
525 <
526 <            dAtom = (DirectionalAtom *)atoms[local_index];
527 <            dAtom->getQ( q );
528 <
529 <            sprintf( tempBuffer,
530 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <                     q[0],
532 <                     q[1],
533 <                     q[2],
534 <                     q[3],
535 <                     dAtom->getJx(),
536 <                     dAtom->getJy(),
537 <                     dAtom->getJz());
538 <            strcat( writeLine, tempBuffer );
539 <          }
540 <          else
541 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
542 <        }
543 <        else {
495 >        } else {
496            sprintf(painCave.errMsg,
497                    "Atom %d not found on processor %d\n",
498                    i, worldRank );
# Line 548 | Line 500 | void DumpWriter::writeFinal(double finalTime){
500            simError();
501          }
502  
503 <        if(haveError) nodeZeroError();
503 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
504  
505 <      }
506 <      else {
505 >        // null terminate the string before sending (just in case):
506 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
507  
508 <        myStatus = 1;
509 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
510 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
511 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
560 <                 MPI_COMM_WORLD);
561 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
562 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
563 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
564 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
508 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
509 >                 myPotato, MPI_COMM_WORLD);
510 >        
511 >        myPotato++;
512  
513 <        if(!myStatus) nodeZeroError();
514 <      }
513 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
514 >                 myPotato, MPI_COMM_WORLD);
515 >        
516 >        myPotato++;
517 >        
518 >        if (isDirectional) {
519  
520 <      finalOut << writeLine;
521 <    }
520 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
521 >                   myPotato, MPI_COMM_WORLD);
522 >          
523 >        } else {
524  
525 <    // kill everyone off:
526 <    myStatus = -1;
527 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
575 <      MPI_Send(&myStatus, 1, MPI_INT, j,
576 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
577 <    }
525 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
526 >                   myPotato, MPI_COMM_WORLD);
527 >        }
528  
529 <  } else {
530 <
581 <    done = 0;
582 <    while (!done) {
583 <
584 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
585 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
586 <
587 <      if(!myStatus) anonymousNodeDie();
588 <
589 <      if(myStatus < 0) break;
590 <
591 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
592 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
593 <
594 <      myStatus = 1;
595 <      local_index=-1;
596 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
597 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
529 >        myPotato++;  
530 >        currentIndex++;    
531        }
599 –      if (local_index != -1) {
600 –
601 –        atoms[local_index]->getPos(pos);
602 –        atoms[local_index]->getVel(vel);
603 –
604 –        //format the line
605 –        sprintf( tempBuffer,
606 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
607 –                 atoms[local_index]->getType(),
608 –                 pos[0],
609 –                 pos[1],
610 –                 pos[2],
611 –                 vel[0],
612 –                 vel[1],
613 –                 vel[2]); // check here.
614 –        strcpy( writeLine, tempBuffer );
615 –
616 –        if( atoms[local_index]->isDirectional() ){
617 –
618 –          dAtom = (DirectionalAtom *)atoms[local_index];
619 –          dAtom->getQ( q );
620 –
621 –          sprintf( tempBuffer,
622 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
623 –                   q[0],
624 –                   q[1],
625 –                   q[2],
626 –                   q[3],
627 –                   dAtom->getJx(),
628 –                   dAtom->getJy(),
629 –                   dAtom->getJz());
630 –          strcat( writeLine, tempBuffer );
631 –        }
632 –        else{
633 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
634 –        }
635 –      }
636 –      else {
637 –        sprintf(painCave.errMsg,
638 –                "Atom %d not found on processor %d\n",
639 –                which_atom, worldRank );
640 –        myStatus = 0;
641 –        simError();
642 –
643 –        strcpy( writeLine, "Hello, I'm an error.\n");
644 –      }
645 –
646 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
647 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
648 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
649 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
532      }
651 –  }
652 –  finalOut.flush();
653 –  sprintf( checkPointMsg,
654 –           "Sucessfully took a dump.\n");
655 –  MPIcheckPoint();
533  
534 <  if( worldRank == 0 ) finalOut.close();
534 >    sprintf( checkPointMsg,
535 >             "Sucessfully took a dump.\n");
536 >    MPIcheckPoint();        
537 >    
538 >  }
539 >  
540   #endif // is_mpi
541   }
542  
661 –
662 –
543   #ifdef IS_MPI
544  
545   // a couple of functions to let us escape the write loop
546  
547 < void dWrite::nodeZeroError( void ){
668 <  int j, myStatus;
547 > void dWrite::DieDieDie( void ){
548  
670 –  myStatus = 0;
671 –  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
672 –    MPI_Send( &myStatus, 1, MPI_INT, j,
673 –              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
674 –  }
675 –
676 –
549    MPI_Finalize();
550    exit (0);
679 –
551   }
552  
682 – void dWrite::anonymousNodeDie( void ){
683 –
684 –  MPI_Finalize();
685 –  exit (0);
686 – }
687 –
553   #endif //is_mpi

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