ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 913 by chuckv, Thu Jan 8 22:25:52 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 = 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    char MPIatomTypeString[MINIBUFFERSIZE];
166 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
166 >
167   #else //is_mpi
168    int nAtoms = entry_plug->n_atoms;
169   #endif //is_mpi
# Line 93 | Line 173 | void DumpWriter::writeDump( double currentTime ){
173    Atom** atoms = entry_plug->atoms;
174    double pos[3], vel[3];
175  
96 –  // write current frame to the eor file
97 –
98 –  this->writeFinal( currentTime );
99 –
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"
107 <          << 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 <
113 <          << entry_plug->Hmat[0][2] << "\t"
114 <          << entry_plug->Hmat[1][2] << "\t"
115 <          << entry_plug->Hmat[2][2] << ";";
116 <  //write out additional parameters, such as chi and eta
117 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
118 <  outFile << endl;
119 <
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 152 | 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    }
157 –  outFile.flush();
236  
237   #else // is_mpi
238  
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 <  }
247 >  }  
248  
249    int haveError;
250  
# Line 175 | Line 254 | void DumpWriter::writeDump( double currentTime ){
254    // write out header and node 0's coordinates
255  
256    if( worldRank == 0 ){
178 –    outFile << mpiSim->getTotAtoms() << "\n";
257  
258 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << 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"
187 <            << 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 <    tag = 0;
275 >                         << entry_plug->Hmat[0][1] << "\t"
276 >                         << entry_plug->Hmat[1][1] << "\t"
277 >                         << entry_plug->Hmat[2][1] << ";\t"
278  
279 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
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 <      if (tag + 2 >= MAXTAG) {
287 <        // The tag was going to exceed the maximum value, so wrap around to 0:
288 <        tag = 0;
204 <        // Send the newly zeroed tag on to the other nodes:
205 <        MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 <      }
286 >    currentIndex = 0;
287 >
288 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
289        
290        // Get the Node number which has this atom;
291        
292        which_node = AtomToProcMap[i];
293        
294        if (which_node != 0) {
295 +
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 +          potatoes[which_node] = 0;          
301 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
302 +          
303 +        }
304 +
305 +        myPotato = potatoes[which_node];        
306          
307          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
308 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
308 >                 myPotato, MPI_COMM_WORLD, &istatus);
309          
310 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
311 <        
312 <        // Null terminate the atomTypeString just in case:
310 >        atomTypeString = MPIatomTypeString;
311 >        
312 >        myPotato++;
313  
221 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
222 –
314          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
315 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
316 <        
317 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
228 <
229 <        if (isDirectional) {
315 >                 myPotato, MPI_COMM_WORLD, &istatus);
316 >              
317 >        myPotato++;
318  
319 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
320 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
321 <
319 >        if (isDirectional) {          
320 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
321 >                   myPotato, MPI_COMM_WORLD, &istatus);
322 >        } else {
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        } else {
331          
332 <        haveError = 0;
333 <        which_atom = i;
334 <        local_index=-1;
335 <
336 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
337 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
338 <        }
245 <
246 <        if (local_index != -1) {
247 <
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 266 | Line 357 | void DumpWriter::writeDump( double currentTime ){
357              
358              dAtom = (DirectionalAtom *)atoms[local_index];
359              dAtom->getQ( q );
269 –            
270 –            atomOrientData[0] = q[0];
271 –            atomOrientData[1] = q[1];
272 –            atomOrientData[2] = q[2];
273 –            atomOrientData[3] = q[3];
360  
361 <            atomOrientData[4] = dAtom->getJx();
362 <            atomOrientData[5] = dAtom->getJy();
277 <            atomOrientData[6] = dAtom->getJz();
278 <          }
279 <
280 <        } else {
281 <          sprintf(painCave.errMsg,
282 <                  "Atom %d not found on processor %d\n",
283 <                  i, worldRank );
284 <          haveError= 1;
285 <          simError();
286 <        }
287 <
288 <        if(haveError) DieDieDie();
289 <                              
290 <        // If we've survived to here, format the line:
291 <        
292 <        sprintf( tempBuffer,
293 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
294 <                 atomTypeString,
295 <                 atomTransData[0],
296 <                 atomTransData[1],
297 <                 atomTransData[2],
298 <                 atomTransData[3],
299 <                 atomTransData[4],
300 <                 atomTransData[5]);
301 <
302 <        strcpy( writeLine, tempBuffer );
303 <
304 <        if (isDirectional) {
305 <
306 <          sprintf( tempBuffer,
307 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
308 <                   atomOrientData[0],
309 <                   atomOrientData[1],
310 <                   atomOrientData[2],
311 <                   atomOrientData[3],
312 <                   atomOrientData[4],
313 <                   atomOrientData[5],
314 <                   atomOrientData[6]);
315 <          strcat( writeLine, tempBuffer );
316 <
317 <        } else {
318 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
319 <        }
320 <
321 <        outFile << writeLine;
322 <        outFile.flush();
323 <      }
324 <    }
325 <
326 <    outFile.flush();
327 <    sprintf( checkPointMsg,
328 <             "Sucessfully took a dump.\n");
329 <    MPIcheckPoint();        
330 <    
331 <  } else {
332 <
333 <    // worldRank != 0, so I'm a remote node.  
334 <    
335 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
336 <      
337 <      // Am I the node which has this atom?
338 <      
339 <      if (AtomToProcMap[i] == worldRank) {
340 <
341 <        local_index=-1;
342 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
343 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
344 <        }
345 <        if (local_index != -1) {
346 <        
347 <          atomTypeString = atoms[local_index]->getType();
348 <
349 <          atoms[local_index]->getPos(pos);
350 <          atoms[local_index]->getVel(vel);
351 <
352 <          atomTransData[0] = pos[0];
353 <          atomTransData[1] = pos[1];
354 <          atomTransData[2] = pos[2];
355 <
356 <          atomTransData[3] = vel[0];
357 <          atomTransData[4] = vel[1];
358 <          atomTransData[5] = vel[2];
359 <          
360 <          isDirectional = 0;
361 <
362 <          if( atoms[local_index]->isDirectional() ){
363 <
364 <            isDirectional = 1;
361 >            for (int j = 0; j < 6 ; j++)
362 >              atomData13[j] = atomData6[j];            
363              
364 <            dAtom = (DirectionalAtom *)atoms[local_index];
365 <            dAtom->getQ( q );
364 >            atomData13[6] = q[0];
365 >            atomData13[7] = q[1];
366 >            atomData13[8] = q[2];
367 >            atomData13[9] = q[3];
368              
369 <            atomOrientData[0] = q[0];
370 <            atomOrientData[1] = q[1];
371 <            atomOrientData[2] = q[2];
372 <            atomOrientData[3] = q[3];
373 <
374 <            atomOrientData[4] = dAtom->getJx();
375 <            atomOrientData[5] = dAtom->getJy();
376 <            atomOrientData[6] = dAtom->getJz();
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 <        }
386 <
387 <        // I've survived this far, so send off the data!
388 <
389 <        atomTypeTag          = 4*i;
390 <        atomIsDirectionalTag = 4*i + 1;
391 <        atomTransDataTag     = 4*i + 2;
392 <        atomOrientDataTag    = 4*i + 3;
393 <
394 <
395 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
396 <
397 <        // null terminate the string before sending (just in case):
398 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
399 <
400 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
401 <                 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,
404 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
382 >        if(haveError) DieDieDie();
383          
384 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
407 <                 atomTransDataTag, MPI_COMM_WORLD);
408 <
409 <        if (isDirectional) {
410 <
411 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
412 <                   atomOrientDataTag, MPI_COMM_WORLD);
413 <          
414 <        }
415 <      
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 < }
429 <
430 < void DumpWriter::writeFinal(double finalTime){
431 <
432 <  char finalName[500];
433 <  ofstream finalOut;
434 <
435 <  const int BUFFERSIZE = 2000;
436 <  const int MINIBUFFERSIZE = 100;
437 <  char tempBuffer[BUFFERSIZE];
438 <  char writeLine[BUFFERSIZE];
439 <
440 <  double q[4];
441 <  DirectionalAtom* dAtom;
442 <  Atom** atoms = entry_plug->atoms;
443 <  int i;
444 < #ifdef IS_MPI
445 <  int j, which_node, done, which_atom, local_index;
446 <  double atomTransData[6];
447 <  double atomOrientData[7];
448 <  int isDirectional;
449 <  char* atomTypeString;
450 <  char MPIatomTypeString[MINIBUFFERSIZE];
451 <  int atomTypeTag;
452 <  int atomIsDirectionalTag;
453 <  int atomTransDataTag;
454 <  int atomOrientDataTag;
455 < #else //is_mpi
456 <  int nAtoms = entry_plug->n_atoms;
457 < #endif //is_mpi
458 <
459 <  double pos[3], vel[3];
460 <
461 < #ifdef IS_MPI
462 <  if(worldRank == 0 ){
463 < #endif // is_mpi
464 <
465 <    strcpy( finalName, entry_plug->finalName );
466 <
467 <    finalOut.open( finalName, ios::out | ios::trunc );
468 <    if( !finalOut ){
469 <      sprintf( painCave.errMsg,
470 <               "Could not open \"%s\" for final dump output.\n",
471 <               finalName );
472 <      painCave.isFatal = 1;
473 <      simError();
474 <    }
475 <
476 <    // finalOut.setf( ios::scientific );
477 <
478 < #ifdef IS_MPI
479 <  }
480 <
481 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
482 <  MPIcheckPoint();
483 <
484 < #endif //is_mpi
485 <
486 <
487 < #ifndef IS_MPI
488 <
489 <  finalOut << nAtoms << "\n";
490 <
491 <  finalOut << finalTime << ";\t"
492 <           << entry_plug->Hmat[0][0] << "\t"
493 <           << entry_plug->Hmat[1][0] << "\t"
494 <           << entry_plug->Hmat[2][0] << ";\t"
495 <
496 <           << entry_plug->Hmat[0][1] << "\t"
497 <           << entry_plug->Hmat[1][1] << "\t"
498 <           << entry_plug->Hmat[2][1] << ";\t"
499 <
500 <           << entry_plug->Hmat[0][2] << "\t"
501 <           << entry_plug->Hmat[1][2] << "\t"
502 <           << entry_plug->Hmat[2][2] << ";";
503 <
504 <  //write out additional parameters, such as chi and eta
505 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
506 <  finalOut << endl;
507 <
508 <  for( i=0; i<nAtoms; i++ ){
509 <
510 <    atoms[i]->getPos(pos);
511 <    atoms[i]->getVel(vel);
512 <
513 <    sprintf( tempBuffer,
514 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <             atoms[i]->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[i]->isDirectional() ){
525 <
526 <      dAtom = (DirectionalAtom *)atoms[i];
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 <    finalOut << writeLine;
544 <  }
545 <  finalOut.flush();
546 <  finalOut.close();
547 <
548 < #else // is_mpi
549 <
550 <  // first thing first, suspend fatalities.
551 <  painCave.isEventLoop = 1;
552 <
553 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
554 <  int haveError;
555 <
556 <  MPI_Status istatus;
557 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
558 <
559 <  // write out header and node 0's coordinates
560 <
561 <  if( worldRank == 0 ){
562 <    finalOut << mpiSim->getTotAtoms() << "\n";
563 <
564 <    finalOut << finalTime << ";\t"
565 <            << entry_plug->Hmat[0][0] << "\t"
566 <            << entry_plug->Hmat[1][0] << "\t"
567 <            << entry_plug->Hmat[2][0] << ";\t"
568 <
569 <            << entry_plug->Hmat[0][1] << "\t"
570 <            << entry_plug->Hmat[1][1] << "\t"
571 <            << entry_plug->Hmat[2][1] << ";\t"
572 <
573 <            << entry_plug->Hmat[0][2] << "\t"
574 <            << entry_plug->Hmat[1][2] << "\t"
575 <            << entry_plug->Hmat[2][2] << ";";
576 <
577 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
578 <    finalOut << endl;
579 <    finalOut.flush();
580 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
581 <      // Get the Node number which has this atom;
582 <
583 <      which_node = AtomToProcMap[i];
584 <
585 <      if (which_node != 0) {
586 <        
587 <        atomTypeTag          = 4*i;
588 <        atomIsDirectionalTag = 4*i + 1;
589 <        atomTransDataTag     = 4*i + 2;
590 <        atomOrientDataTag    = 4*i + 3;
591 <
592 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
593 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
594 <        
595 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
596 <
597 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
598 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
599 <        
600 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
601 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
602 <
603 <        if (isDirectional) {
604 <
605 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
606 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
607 <
608 <        }
609 <
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];
628 <          atomTransData[1] = pos[1];
629 <          atomTransData[2] = pos[2];
630 <
631 <          atomTransData[3] = vel[0];
632 <          atomTransData[4] = vel[1];
633 <          atomTransData[5] = vel[2];
634 <          
635 <          isDirectional = 0;
636 <
637 <          if( atoms[local_index]->isDirectional() ){
638 <
639 <            isDirectional = 1;
640 <            
641 <            dAtom = (DirectionalAtom *)atoms[local_index];
642 <            dAtom->getQ( q );
643 <            
644 <            atomOrientData[0] = q[0];
645 <            atomOrientData[1] = q[1];
646 <            atomOrientData[2] = q[2];
647 <            atomOrientData[3] = q[3];
648 <
649 <            atomOrientData[4] = dAtom->getJx();
650 <            atomOrientData[5] = dAtom->getJy();
651 <            atomOrientData[6] = dAtom->getJz();
652 <          }
653 <
654 <        } else {
655 <          sprintf(painCave.errMsg,
656 <                  "Atom %d not found on processor %d\n",
657 <                  i, worldRank );
658 <          haveError= 1;
659 <          simError();
660 <        }
661 <
662 <        if(haveError) DieDieDie();
663 <                              
664 <        // 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          
666 –        sprintf( tempBuffer,
667 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
668 –                 atomTypeString,
669 –                 atomTransData[0],
670 –                 atomTransData[1],
671 –                 atomTransData[2],
672 –                 atomTransData[3],
673 –                 atomTransData[4],
674 –                 atomTransData[5]);
675 –
676 –        strcpy( writeLine, tempBuffer );
677 –
678 –        if (isDirectional) {
679 –
680 –          sprintf( tempBuffer,
681 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
682 –                   atomOrientData[0],
683 –                   atomOrientData[1],
684 –                   atomOrientData[2],
685 –                   atomOrientData[3],
686 –                   atomOrientData[4],
687 –                   atomOrientData[5],
688 –                   atomOrientData[6]);
689 –          strcat( writeLine, tempBuffer );
690 –
691 –        } else {
692 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
693 –        }
694 –
695 –        finalOut << writeLine;
696 –        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 712 | 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 740 | 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  
761 –        // I've survived this far, so send off the data!
762 –
763 –        atomTypeTag          = 4*i;
764 –        atomIsDirectionalTag = 4*i + 1;
765 –        atomTransDataTag     = 4*i + 2;
766 –        atomOrientDataTag    = 4*i + 3;
767 –
509          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
510  
511 +        // null terminate the string before sending (just in case):
512 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
513 +
514          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
515 <                 atomTypeTag, MPI_COMM_WORLD);
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);
778 <
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    
795 –  painCave.isEventLoop = 0;
796 –
797 –  if( worldRank == 0 ) finalOut.close();
546   #endif // is_mpi
547   }
548  
801 –
802 –
549   #ifdef IS_MPI
550  
551   // a couple of functions to let us escape the write loop

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines