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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 2004 UTC vs.
Revision 934 by tim, Tue Jan 13 20:04:28 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>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
29 –    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      }
42  
43 <    //outFile.setf( ios::scientific );
43 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
44 >    if( !finalOut ){
45 >      sprintf( painCave.errMsg,
46 >               "Could not open \"%s\" for final dump output.\n",
47 >               entry_plug->finalName );
48 >      painCave.isFatal = 1;
49 >      simError();
50 >    }
51  
52   #ifdef IS_MPI
53    }
54  
55 +  //sort the local atoms by global index
56 +  sortByGlobalIndex();
57 +  
58    sprintf( checkPointMsg,
59             "Sucessfully opened output file for dumping.\n");
60    MPIcheckPoint();
# Line 56 | Line 67 | DumpWriter::~DumpWriter( ){
67    if(worldRank == 0 ){
68   #endif // is_mpi
69  
70 <    outFile.close();
70 >    dumpFile.close();
71 >    finalOut.close();
72  
73   #ifdef IS_MPI
74    }
75   #endif // is_mpi
76   }
77  
78 < void DumpWriter::writeDump( double currentTime ){
78 > #ifdef IS_MPI
79  
80 + /**
81 + * A hook function to load balancing
82 + */
83 +
84 + void DumpWriter::update(){
85 +  sortByGlobalIndex();          
86 + }
87 +  
88 + /**
89 + * Auxiliary sorting function
90 + */
91 +
92 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
93 +  return p1.second < p2.second;
94 + }
95 +
96 + /**
97 + * Sorting the local index by global index
98 + */
99 +
100 + void DumpWriter::sortByGlobalIndex(){
101 +  Atom** atoms = entry_plug->atoms;
102 +  
103 +  indexArray.clear();
104 +  
105 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
106 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
107 +  
108 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
109 + }
110 + #endif
111 +
112 + void DumpWriter::writeDump(double currentTime){
113 +
114 +  vector<ofstream*> fileStreams;
115 +
116 + #ifdef IS_MPI
117 +  if(worldRank == 0 ){
118 +    finalOut.seekp(0);
119 +  }
120 + #endif // is_mpi
121 +
122 +  fileStreams.push_back(&finalOut);
123 +  fileStreams.push_back(&dumpFile);
124 +
125 +  writeFrame(fileStreams, currentTime);
126 +        
127 + }
128 +
129 + void DumpWriter::writeFinal(double currentTime){
130 +
131 +  vector<ofstream*> fileStreams;
132 +
133 + #ifdef IS_MPI
134 +  if(worldRank == 0 ){
135 +    finalOut.seekp(0);
136 +  }
137 + #endif // is_mpi
138 +  
139 +  fileStreams.push_back(&finalOut);  
140 +  writeFrame(fileStreams, currentTime);
141 +  
142 + }
143 +
144 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
145 +
146    const int BUFFERSIZE = 2000;
147 <  const int MINIBUFFERSIZE = 10;
147 >  const int MINIBUFFERSIZE = 100;
148  
149    char tempBuffer[BUFFERSIZE];
150    char writeLine[BUFFERSIZE];
151  
152 <  int i;
152 >  int i, k;
153 >
154   #ifdef IS_MPI
155 <  int j, which_node, done, which_atom, local_index;
156 <  double atomTransData[6];
157 <  double atomOrientData[7];
155 >  
156 >  int *potatoes;
157 >  int myPotato;
158 >
159 >  int nProc;
160 >  int j, which_node, done, which_atom, local_index, currentIndex;
161 >  double atomData6[6];
162 >  double atomData13[13];
163    int isDirectional;
164    char* atomTypeString;
165 <  int me;
166 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
165 >  char MPIatomTypeString[MINIBUFFERSIZE];
166 >
167   #else //is_mpi
168    int nAtoms = entry_plug->n_atoms;
169   #endif //is_mpi
# Line 92 | Line 173 | void DumpWriter::writeDump( double currentTime ){
173    Atom** atoms = entry_plug->atoms;
174    double pos[3], vel[3];
175  
95 –  // write current frame to the eor file
96 –
97 –  this->writeFinal( currentTime );
98 –
176   #ifndef IS_MPI
177 +  
178 +  for(k = 0; k < outFile.size(); k++){
179 +    *outFile[k] << nAtoms << "\n";
180  
181 <  outFile << nAtoms << "\n";
181 >    *outFile[k] << currentTime << ";\t"
182 >               << entry_plug->Hmat[0][0] << "\t"
183 >                     << entry_plug->Hmat[1][0] << "\t"
184 >                     << entry_plug->Hmat[2][0] << ";\t"
185 >              
186 >               << entry_plug->Hmat[0][1] << "\t"
187 >                     << entry_plug->Hmat[1][1] << "\t"
188 >                     << entry_plug->Hmat[2][1] << ";\t"
189  
190 <  outFile << currentTime << ";\t"
191 <          << entry_plug->Hmat[0][0] << "\t"
192 <          << entry_plug->Hmat[1][0] << "\t"
106 <          << entry_plug->Hmat[2][0] << ";\t"
190 >                     << entry_plug->Hmat[0][2] << "\t"
191 >                     << entry_plug->Hmat[1][2] << "\t"
192 >                     << entry_plug->Hmat[2][2] << ";";
193  
194 <          << entry_plug->Hmat[0][1] << "\t"
195 <          << entry_plug->Hmat[1][1] << "\t"
196 <          << entry_plug->Hmat[2][1] << ";\t"
197 <
112 <          << entry_plug->Hmat[0][2] << "\t"
113 <          << entry_plug->Hmat[1][2] << "\t"
114 <          << entry_plug->Hmat[2][2] << ";";
115 <  //write out additional parameters, such as chi and eta
116 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
117 <  outFile << endl;
118 <
194 >    //write out additional parameters, such as chi and eta
195 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
196 >  }
197 >  
198    for( i=0; i<nAtoms; i++ ){
199  
200      atoms[i]->getPos(pos);
# Line 151 | Line 230 | void DumpWriter::writeDump( double currentTime ){
230      else
231        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232  
233 <    outFile << writeLine;
233 >    for(k = 0; k < outFile.size(); k++)
234 >      *outFile[k] << writeLine;
235    }
156 –  outFile.flush();
236  
237   #else // is_mpi
238  
239 <  // first thing first, suspend fatalities.
240 <  painCave.isEventLoop = 1;
239 >  /* code to find maximum tag value */
240 >  
241 >  int *tagub, flag, MAXTAG;
242 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
243 >  if (flag) {
244 >    MAXTAG = *tagub;
245 >  } else {
246 >    MAXTAG = 32767;
247 >  }  
248  
163 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
249    int haveError;
250  
251    MPI_Status istatus;
# Line 169 | Line 254 | void DumpWriter::writeDump( double currentTime ){
254    // write out header and node 0's coordinates
255  
256    if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
257  
258 <    outFile << currentTime << ";\t"
175 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << entry_plug->Hmat[2][0] << ";\t"
258 >    // Node 0 needs a list of the magic potatoes for each processor;
259  
260 <            << entry_plug->Hmat[0][1] << "\t"
261 <            << entry_plug->Hmat[1][1] << "\t"
181 <            << entry_plug->Hmat[2][1] << ";\t"
260 >    nProc = mpiSim->getNumberProcessors();
261 >    potatoes = new int[nProc];
262  
263 <            << entry_plug->Hmat[0][2] << "\t"
264 <            << entry_plug->Hmat[1][2] << "\t"
265 <            << entry_plug->Hmat[2][2] << ";";
263 >    //write out the comment lines
264 >    for (i = 0; i < nProc; i++)
265 >      potatoes[i] = 0;
266 >    
267 >      for(k = 0; k < outFile.size(); k++){
268 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
269  
270 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
271 <    outFile << endl;
272 <    outFile.flush();
270 >        *outFile[k] << currentTime << ";\t"
271 >                         << entry_plug->Hmat[0][0] << "\t"
272 >                         << entry_plug->Hmat[1][0] << "\t"
273 >                         << entry_plug->Hmat[2][0] << ";\t"
274 >
275 >                         << entry_plug->Hmat[0][1] << "\t"
276 >                         << entry_plug->Hmat[1][1] << "\t"
277 >                         << entry_plug->Hmat[2][1] << ";\t"
278 >
279 >                         << entry_plug->Hmat[0][2] << "\t"
280 >                         << entry_plug->Hmat[1][2] << "\t"
281 >                         << entry_plug->Hmat[2][2] << ";";
282 >  
283 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
284 >    }
285 >
286 >    currentIndex = 0;
287 >
288      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
289 +      
290        // Get the Node number which has this atom;
291 <
291 >      
292        which_node = AtomToProcMap[i];
293 <
293 >      
294        if (which_node != 0) {
196 –        
197 –        atomTypeTag          = 4*i;
198 –        atomIsDirectionalTag = 4*i + 1;
199 –        atomTransDataTag     = 4*i + 2;
200 –        atomOrientDataTag    = 4*i + 3;
295  
296 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
297 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
298 <        
205 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
206 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
207 <        
208 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
209 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
296 >        if (potatoes[which_node] + 3 >= MAXTAG) {
297 >          // The potato was going to exceed the maximum value,
298 >          // so wrap this processor potato back to 0:        
299  
300 <        if (isDirectional) {
301 <
302 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
214 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
215 <
300 >          potatoes[which_node] = 0;          
301 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
302 >          
303          }
304  
305 <      } else {
305 >        myPotato = potatoes[which_node];        
306          
307 <        haveError = 0;
308 <        which_atom = i;
222 <        local_index=-1;
223 <
224 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
225 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
226 <        }
227 <
228 <        if (local_index != -1) {
229 <
230 <          atomTypeString = atoms[local_index]->getType();
231 <
232 <          atoms[local_index]->getPos(pos);
233 <          atoms[local_index]->getVel(vel);
234 <
235 <          atomTransData[0] = pos[0];
236 <          atomTransData[1] = pos[1];
237 <          atomTransData[2] = pos[2];
238 <
239 <          atomTransData[3] = vel[0];
240 <          atomTransData[4] = vel[1];
241 <          atomTransData[5] = vel[2];
242 <          
243 <          isDirectional = 0;
244 <
245 <          if( atoms[local_index]->isDirectional() ){
246 <
247 <            isDirectional = 1;
248 <            
249 <            dAtom = (DirectionalAtom *)atoms[local_index];
250 <            dAtom->getQ( q );
251 <            
252 <            atomOrientData[0] = q[0];
253 <            atomOrientData[1] = q[1];
254 <            atomOrientData[2] = q[2];
255 <            atomOrientData[3] = q[3];
256 <
257 <            atomOrientData[4] = dAtom->getJx();
258 <            atomOrientData[5] = dAtom->getJy();
259 <            atomOrientData[6] = dAtom->getJz();
260 <          }
261 <
262 <        } else {
263 <          sprintf(painCave.errMsg,
264 <                  "Atom %d not found on processor %d\n",
265 <                  i, worldRank );
266 <          haveError= 1;
267 <          simError();
268 <        }
269 <
270 <        if(haveError) DieDieDie();
271 <                              
272 <        // If we've survived to here, format the line:
307 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
308 >                 myPotato, MPI_COMM_WORLD, &istatus);
309          
310 <        sprintf( tempBuffer,
311 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
312 <                 atomTypeString,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 atomTransData[5]);
310 >        atomTypeString = MPIatomTypeString;
311 >        
312 >        myPotato++;
313  
314 <        strcpy( writeLine, tempBuffer );
314 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
315 >                 myPotato, MPI_COMM_WORLD, &istatus);
316 >              
317 >        myPotato++;
318  
319 <        if (isDirectional) {
320 <
321 <          sprintf( tempBuffer,
289 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
290 <                   atomOrientData[0],
291 <                   atomOrientData[1],
292 <                   atomOrientData[2],
293 <                   atomOrientData[3],
294 <                   atomOrientData[4],
295 <                   atomOrientData[5],
296 <                   atomOrientData[6]);
297 <          strcat( writeLine, tempBuffer );
298 <
319 >        if (isDirectional) {          
320 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
321 >                   myPotato, MPI_COMM_WORLD, &istatus);
322          } else {
323 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
323 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
324 >                   myPotato, MPI_COMM_WORLD, &istatus);          
325          }
326 +        
327 +        myPotato++;
328 +        potatoes[which_node] = myPotato;
329  
330 <        outFile << writeLine;
331 <        outFile.flush();
332 <      }
333 <    }
334 <
335 <    outFile.flush();
336 <    sprintf( checkPointMsg,
337 <             "Sucessfully took a dump.\n");
338 <    MPIcheckPoint();        
312 <    
313 <  } else {
314 <
315 <    // worldRank != 0, so I'm a remote node.  
316 <    
317 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
318 <      
319 <      // Am I the node which has this atom?
320 <      
321 <      if (AtomToProcMap[i] == worldRank) {
322 <
323 <        local_index=-1;
324 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
325 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
326 <        }
327 <        if (local_index != -1) {
328 <        
330 >      } else {
331 >        
332 >        haveError = 0;
333 >              which_atom = i;
334 >        
335 >        local_index = indexArray[currentIndex].first;        
336 >                
337 >        if (which_atom == indexArray[currentIndex].second) {
338 >          
339            atomTypeString = atoms[local_index]->getType();
340  
341 <          atoms[local_index]->getPos(pos);
342 <          atoms[local_index]->getVel(vel);
341 >                atoms[local_index]->getPos(pos);
342 >                atoms[local_index]->getVel(vel);          
343  
344 <          atomTransData[0] = pos[0];
345 <          atomTransData[1] = pos[1];
346 <          atomTransData[2] = pos[2];
344 >          atomData6[0] = pos[0];
345 >          atomData6[1] = pos[1];
346 >          atomData6[2] = pos[2];
347  
348 <          atomTransData[3] = vel[0];
349 <          atomTransData[4] = vel[1];
350 <          atomTransData[5] = vel[2];
348 >          atomData6[3] = vel[0];
349 >          atomData6[4] = vel[1];
350 >          atomData6[5] = vel[2];
351            
352            isDirectional = 0;
353  
# Line 347 | Line 357 | void DumpWriter::writeDump( double currentTime ){
357              
358              dAtom = (DirectionalAtom *)atoms[local_index];
359              dAtom->getQ( q );
350 –            
351 –            atomOrientData[0] = q[0];
352 –            atomOrientData[1] = q[1];
353 –            atomOrientData[2] = q[2];
354 –            atomOrientData[3] = q[3];
360  
361 <            atomOrientData[4] = dAtom->getJx();
362 <            atomOrientData[5] = dAtom->getJy();
363 <            atomOrientData[6] = dAtom->getJz();
361 >            for (int j = 0; j < 6 ; j++)
362 >              atomData13[j] = atomData6[j];            
363 >            
364 >            atomData13[6] = q[0];
365 >            atomData13[7] = q[1];
366 >            atomData13[8] = q[2];
367 >            atomData13[9] = q[3];
368 >            
369 >            atomData13[10] = dAtom->getJx();
370 >            atomData13[11] = dAtom->getJy();
371 >            atomData13[12] = dAtom->getJz();
372            }
373 <
373 >          
374          } else {
375 <          sprintf(painCave.errMsg,
376 <                  "Atom %d not found on processor %d\n",
377 <                  i, worldRank );
378 <          haveError= 1;
379 <          simError();
380 <        }
368 <
369 <        // I've survived this far, so send off the data!
370 <
371 <        atomTypeTag          = 4*i;
372 <        atomIsDirectionalTag = 4*i + 1;
373 <        atomTransDataTag     = 4*i + 2;
374 <        atomOrientDataTag    = 4*i + 3;
375 <
376 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
377 <                 atomTypeTag, MPI_COMM_WORLD);
375 >          sprintf(painCave.errMsg,
376 >                              "Atom %d not found on processor %d\n",
377 >                              i, worldRank );
378 >                haveError= 1;
379 >                simError();
380 >              }
381          
382 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
380 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
382 >        if(haveError) DieDieDie();
383          
384 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
383 <                 atomTransDataTag, MPI_COMM_WORLD);
384 <
385 <        if (isDirectional) {
386 <
387 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
388 <                   atomOrientDataTag, MPI_COMM_WORLD);
389 <          
390 <        }
391 <      
384 >        currentIndex ++;
385        }
386 <    }
387 <
388 <    sprintf( checkPointMsg,
389 <             "Sucessfully took a dump.\n");
390 <    MPIcheckPoint();        
391 <    
392 <  }
393 <  
394 <  painCave.isEventLoop = 0;
386 >      // If we've survived to here, format the line:
387 >      
388 >      if (!isDirectional) {
389 >        
390 >        sprintf( writeLine,
391 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392 >                             atomTypeString,
393 >                             atomData6[0],
394 >                             atomData6[1],
395 >                             atomData6[2],
396 >                             atomData6[3],
397 >                             atomData6[4],
398 >                             atomData6[5]);
399  
400 < #endif // is_mpi
401 < }
405 <
406 < void DumpWriter::writeFinal(double finalTime){
407 <
408 <  char finalName[500];
409 <  ofstream finalOut;
410 <
411 <  const int BUFFERSIZE = 2000;
412 <  const int MINIBUFFERSIZE = 10;
413 <  char tempBuffer[BUFFERSIZE];
414 <  char writeLine[BUFFERSIZE];
415 <
416 <  double q[4];
417 <  DirectionalAtom* dAtom;
418 <  Atom** atoms = entry_plug->atoms;
419 <  int i;
420 < #ifdef IS_MPI
421 <  int j, which_node, done, which_atom, local_index;
422 <  double atomTransData[6];
423 <  double atomOrientData[7];
424 <  int isDirectional;
425 <  char* atomTypeString;
426 <  int atomTypeTag;
427 <  int atomIsDirectionalTag;
428 <  int atomTransDataTag;
429 <  int atomOrientDataTag;
430 < #else //is_mpi
431 <  int nAtoms = entry_plug->n_atoms;
432 < #endif //is_mpi
433 <
434 <  double pos[3], vel[3];
435 <
436 < #ifdef IS_MPI
437 <  if(worldRank == 0 ){
438 < #endif // is_mpi
439 <
440 <    strcpy( finalName, entry_plug->finalName );
441 <
442 <    finalOut.open( finalName, ios::out | ios::trunc );
443 <    if( !finalOut ){
444 <      sprintf( painCave.errMsg,
445 <               "Could not open \"%s\" for final dump output.\n",
446 <               finalName );
447 <      painCave.isFatal = 1;
448 <      simError();
449 <    }
450 <
451 <    // finalOut.setf( ios::scientific );
452 <
453 < #ifdef IS_MPI
454 <  }
455 <
456 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 <  MPIcheckPoint();
458 <
459 < #endif //is_mpi
460 <
461 <
462 < #ifndef IS_MPI
463 <
464 <  finalOut << nAtoms << "\n";
465 <
466 <  finalOut << finalTime << ";\t"
467 <           << entry_plug->Hmat[0][0] << "\t"
468 <           << entry_plug->Hmat[1][0] << "\t"
469 <           << entry_plug->Hmat[2][0] << ";\t"
470 <
471 <           << entry_plug->Hmat[0][1] << "\t"
472 <           << entry_plug->Hmat[1][1] << "\t"
473 <           << entry_plug->Hmat[2][1] << ";\t"
474 <
475 <           << entry_plug->Hmat[0][2] << "\t"
476 <           << entry_plug->Hmat[1][2] << "\t"
477 <           << entry_plug->Hmat[2][2] << ";";
478 <
479 <  //write out additional parameters, such as chi and eta
480 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 <  finalOut << endl;
482 <
483 <  for( i=0; i<nAtoms; i++ ){
484 <
485 <    atoms[i]->getPos(pos);
486 <    atoms[i]->getVel(vel);
487 <
488 <    sprintf( tempBuffer,
489 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 <             atoms[i]->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[i]->isDirectional() ){
500 <
501 <      dAtom = (DirectionalAtom *)atoms[i];
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 <    finalOut << writeLine;
519 <  }
520 <  finalOut.flush();
521 <  finalOut.close();
522 <
523 < #else // is_mpi
524 <
525 <  // first thing first, suspend fatalities.
526 <  painCave.isEventLoop = 1;
527 <
528 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
529 <  int haveError;
530 <
531 <  MPI_Status istatus;
532 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
533 <
534 <  // write out header and node 0's coordinates
535 <
536 <  if( worldRank == 0 ){
537 <    finalOut << mpiSim->getTotAtoms() << "\n";
538 <
539 <    finalOut << finalTime << ";\t"
540 <            << entry_plug->Hmat[0][0] << "\t"
541 <            << entry_plug->Hmat[1][0] << "\t"
542 <            << entry_plug->Hmat[2][0] << ";\t"
543 <
544 <            << entry_plug->Hmat[0][1] << "\t"
545 <            << entry_plug->Hmat[1][1] << "\t"
546 <            << entry_plug->Hmat[2][1] << ";\t"
547 <
548 <            << entry_plug->Hmat[0][2] << "\t"
549 <            << entry_plug->Hmat[1][2] << "\t"
550 <            << entry_plug->Hmat[2][2] << ";";
551 <
552 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 <    finalOut << endl;
554 <    finalOut.flush();
555 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
556 <      // Get the Node number which has this atom;
557 <
558 <      which_node = AtomToProcMap[i];
559 <
560 <      if (which_node != 0) {
561 <        
562 <        atomTypeTag          = 4*i;
563 <        atomIsDirectionalTag = 4*i + 1;
564 <        atomTransDataTag     = 4*i + 2;
565 <        atomOrientDataTag    = 4*i + 3;
566 <
567 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
568 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
569 <        
570 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
571 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
572 <        
573 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
574 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
575 <
576 <        if (isDirectional) {
577 <
578 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
579 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
580 <
581 <        }
582 <
400 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
401 >        
402        } else {
403 <        
404 <        haveError = 0;
405 <        which_atom = i;
406 <        local_index=-1;
407 <
408 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
409 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
410 <        }
411 <
412 <        if (local_index != -1) {
413 <
414 <          atomTypeString = atoms[local_index]->getType();
415 <
416 <          atoms[local_index]->getPos(pos);
417 <          atoms[local_index]->getVel(vel);
418 <
419 <          atomTransData[0] = pos[0];
601 <          atomTransData[1] = pos[1];
602 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
607 <          
608 <          isDirectional = 0;
609 <
610 <          if( atoms[local_index]->isDirectional() ){
611 <
612 <            isDirectional = 1;
613 <            
614 <            dAtom = (DirectionalAtom *)atoms[local_index];
615 <            dAtom->getQ( q );
616 <            
617 <            atomOrientData[0] = q[0];
618 <            atomOrientData[1] = q[1];
619 <            atomOrientData[2] = q[2];
620 <            atomOrientData[3] = q[3];
621 <
622 <            atomOrientData[4] = dAtom->getJx();
623 <            atomOrientData[5] = dAtom->getJy();
624 <            atomOrientData[6] = dAtom->getJz();
625 <          }
626 <
627 <        } else {
628 <          sprintf(painCave.errMsg,
629 <                  "Atom %d not found on processor %d\n",
630 <                  i, worldRank );
631 <          haveError= 1;
632 <          simError();
633 <        }
634 <
635 <        if(haveError) DieDieDie();
636 <                              
637 <        // If we've survived to here, format the line:
403 >        
404 >              sprintf( writeLine,
405 >                             "%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",
406 >                             atomTypeString,
407 >                             atomData13[0],
408 >                             atomData13[1],
409 >                             atomData13[2],
410 >                             atomData13[3],
411 >                             atomData13[4],
412 >                             atomData13[5],
413 >                             atomData13[6],
414 >                             atomData13[7],
415 >                             atomData13[8],
416 >                             atomData13[9],
417 >                             atomData13[10],
418 >                             atomData13[11],
419 >                             atomData13[12]);
420          
639 –        sprintf( tempBuffer,
640 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
641 –                 atomTypeString,
642 –                 atomTransData[0],
643 –                 atomTransData[1],
644 –                 atomTransData[2],
645 –                 atomTransData[3],
646 –                 atomTransData[4],
647 –                 atomTransData[5]);
648 –
649 –        strcpy( writeLine, tempBuffer );
650 –
651 –        if (isDirectional) {
652 –
653 –          sprintf( tempBuffer,
654 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 –                   atomOrientData[0],
656 –                   atomOrientData[1],
657 –                   atomOrientData[2],
658 –                   atomOrientData[3],
659 –                   atomOrientData[4],
660 –                   atomOrientData[5],
661 –                   atomOrientData[6]);
662 –          strcat( writeLine, tempBuffer );
663 –
664 –        } else {
665 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
666 –        }
667 –
668 –        finalOut << writeLine;
669 –        finalOut.flush();
421        }
422 +      
423 +      for(k = 0; k < outFile.size(); k++)
424 +        *outFile[k] << writeLine;
425      }
426 <
427 <    finalOut.flush();
426 >    
427 >    for(k = 0; k < outFile.size(); k++)
428 >      outFile[k]->flush();
429 >    
430      sprintf( checkPointMsg,
431               "Sucessfully took a dump.\n");
432 +
433      MPIcheckPoint();        
434 <    
434 >
435 >    delete[] potatoes;
436 >
437    } else {
438  
439      // worldRank != 0, so I'm a remote node.  
440 +
441 +    // Set my magic potato to 0:
442 +
443 +    myPotato = 0;
444 +    currentIndex = 0;
445      
446      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
447        
# Line 685 | Line 449 | void DumpWriter::writeFinal(double finalTime){
449        
450        if (AtomToProcMap[i] == worldRank) {
451  
452 <        local_index=-1;
453 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
454 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
452 >        if (myPotato + 3 >= MAXTAG) {
453 >
454 >          // The potato was going to exceed the maximum value,
455 >          // so wrap this processor potato back to 0 (and block until
456 >          // node 0 says we can go:
457 >
458 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
459 >          
460          }
461 <        if (local_index != -1) {
461 >        which_atom = i;
462 >        local_index = indexArray[currentIndex].first;        
463 >                
464 >        if (which_atom == indexArray[currentIndex].second) {
465          
466            atomTypeString = atoms[local_index]->getType();
467  
468 <          atoms[local_index]->getPos(pos);
469 <          atoms[local_index]->getVel(vel);
468 >                atoms[local_index]->getPos(pos);
469 >                atoms[local_index]->getVel(vel);
470  
471 <          atomTransData[0] = pos[0];
472 <          atomTransData[1] = pos[1];
473 <          atomTransData[2] = pos[2];
471 >          atomData6[0] = pos[0];
472 >          atomData6[1] = pos[1];
473 >          atomData6[2] = pos[2];
474  
475 <          atomTransData[3] = vel[0];
476 <          atomTransData[4] = vel[1];
477 <          atomTransData[5] = vel[2];
475 >          atomData6[3] = vel[0];
476 >          atomData6[4] = vel[1];
477 >          atomData6[5] = vel[2];
478            
479            isDirectional = 0;
480  
# Line 713 | Line 485 | void DumpWriter::writeFinal(double finalTime){
485              dAtom = (DirectionalAtom *)atoms[local_index];
486              dAtom->getQ( q );
487              
488 <            atomOrientData[0] = q[0];
489 <            atomOrientData[1] = q[1];
490 <            atomOrientData[2] = q[2];
491 <            atomOrientData[3] = q[3];
492 <
493 <            atomOrientData[4] = dAtom->getJx();
494 <            atomOrientData[5] = dAtom->getJy();
495 <            atomOrientData[6] = dAtom->getJz();
488 >            for (int j = 0; j < 6 ; j++)
489 >              atomData13[j] = atomData6[j];
490 >            
491 >            atomData13[6] = q[0];
492 >            atomData13[7] = q[1];
493 >            atomData13[8] = q[2];
494 >            atomData13[9] = q[3];
495 >  
496 >            atomData13[10] = dAtom->getJx();
497 >            atomData13[11] = dAtom->getJy();
498 >            atomData13[12] = dAtom->getJz();
499            }
500  
501          } else {
502 <          sprintf(painCave.errMsg,
503 <                  "Atom %d not found on processor %d\n",
504 <                  i, worldRank );
505 <          haveError= 1;
506 <          simError();
507 <        }
502 >                sprintf(painCave.errMsg,
503 >                              "Atom %d not found on processor %d\n",
504 >                              i, worldRank );
505 >                haveError= 1;
506 >                simError();
507 >              }
508  
509 <        // I've survived this far, so send off the data!
509 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
510  
511 <        atomTypeTag          = 4*i;
512 <        atomIsDirectionalTag = 4*i + 1;
738 <        atomTransDataTag     = 4*i + 2;
739 <        atomOrientDataTag    = 4*i + 3;
511 >        // null terminate the string before sending (just in case):
512 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
513  
514 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
515 <                 atomTypeTag, MPI_COMM_WORLD);
514 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
515 >                             myPotato, MPI_COMM_WORLD);
516          
517 +        myPotato++;
518 +
519          MPI_Send(&isDirectional, 1, MPI_INT, 0,
520 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
520 >                             myPotato, MPI_COMM_WORLD);
521          
522 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
523 <                 atomTransDataTag, MPI_COMM_WORLD);
749 <
522 >        myPotato++;
523 >        
524          if (isDirectional) {
525  
526 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
527 <                   atomOrientDataTag, MPI_COMM_WORLD);
526 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
527 >                   myPotato, MPI_COMM_WORLD);
528            
529 +        } else {
530 +
531 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
532 +                   myPotato, MPI_COMM_WORLD);
533          }
534 <      
534 >
535 >        myPotato++;  
536 >        currentIndex++;    
537        }
538      }
539  
540      sprintf( checkPointMsg,
541 <             "Sucessfully wrote final file.\n");
541 >             "Sucessfully took a dump.\n");
542      MPIcheckPoint();        
543      
544 <  }
544 >  }
545    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
546   #endif // is_mpi
547   }
548  
772 –
773 –
549   #ifdef IS_MPI
550  
551   // a couple of functions to let us escape the write loop

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