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 |
|
} |
68 |
|
#endif // is_mpi |
69 |
|
|
70 |
|
dumpFile.close(); |
71 |
+ |
finalOut.close(); |
72 |
|
|
73 |
|
#ifdef IS_MPI |
74 |
|
} |
110 |
|
#endif |
111 |
|
|
112 |
|
void DumpWriter::writeDump(double currentTime){ |
105 |
– |
|
106 |
– |
// write to eor file |
107 |
– |
writeFinal(currentTime); |
113 |
|
|
114 |
< |
//write to dump file |
115 |
< |
writeFrame(dumpFile, currentTime); |
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 |
< |
ofstream finalOut; |
117 |
< |
|
118 |
< |
//Open eor file |
119 |
< |
#ifdef IS_MPI |
120 |
< |
if(worldRank == 0 ){ |
121 |
< |
#endif // is_mpi |
131 |
> |
vector<ofstream*> fileStreams; |
132 |
|
|
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 |
– |
|
133 |
|
#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 |
134 |
|
if(worldRank == 0 ){ |
135 |
< |
finalOut.close(); |
135 |
> |
finalOut.seekp(0); |
136 |
|
} |
137 |
|
#endif // is_mpi |
138 |
< |
|
138 |
> |
|
139 |
> |
fileStreams.push_back(&finalOut); |
140 |
> |
writeFrame(fileStreams, currentTime); |
141 |
> |
|
142 |
|
} |
143 |
|
|
144 |
< |
void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ |
144 |
> |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
145 |
|
|
146 |
|
const int BUFFERSIZE = 2000; |
147 |
|
const int MINIBUFFERSIZE = 100; |
149 |
|
char tempBuffer[BUFFERSIZE]; |
150 |
|
char writeLine[BUFFERSIZE]; |
151 |
|
|
152 |
< |
int i; |
152 |
> |
int i, k; |
153 |
|
|
154 |
|
#ifdef IS_MPI |
155 |
|
|
174 |
|
double pos[3], vel[3]; |
175 |
|
|
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" |
187 |
< |
<< 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 |
< |
|
193 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
194 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
195 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
196 |
< |
//write out additional parameters, such as chi and eta |
197 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
198 |
< |
outFile << endl; |
199 |
< |
|
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); |
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 |
|
} |
236 |
|
|
237 |
|
#else // is_mpi |
260 |
|
nProc = mpiSim->getNumberProcessors(); |
261 |
|
potatoes = new int[nProc]; |
262 |
|
|
263 |
+ |
//write out the comment lines |
264 |
|
for (i = 0; i < nProc; i++) |
265 |
|
potatoes[i] = 0; |
266 |
|
|
267 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
267 |
> |
for(k = 0; k < outFile.size(); k++){ |
268 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
269 |
|
|
270 |
< |
outFile << currentTime << ";\t" |
271 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
272 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
273 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
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" |
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] << ";"; |
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 |
|
|
282 |
– |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
283 |
– |
outFile << endl; |
284 |
– |
outFile.flush(); |
285 |
– |
|
286 |
|
currentIndex = 0; |
287 |
+ |
|
288 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
289 |
|
|
290 |
|
// Get the Node number which has this atom; |
329 |
|
|
330 |
|
} else { |
331 |
|
|
332 |
< |
haveError = 0; |
333 |
< |
which_atom = i; |
332 |
> |
haveError = 0; |
333 |
> |
which_atom = i; |
334 |
|
|
335 |
|
local_index = indexArray[currentIndex].first; |
336 |
|
|
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 |
|
atomData6[0] = pos[0]; |
345 |
|
atomData6[1] = pos[1]; |
372 |
|
} |
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 |
< |
} |
375 |
> |
sprintf(painCave.errMsg, |
376 |
> |
"Atom %d not found on processor %d\n", |
377 |
> |
i, worldRank ); |
378 |
> |
haveError= 1; |
379 |
> |
simError(); |
380 |
> |
} |
381 |
|
|
382 |
< |
if(haveError) DieDieDie(); |
382 |
> |
if(haveError) DieDieDie(); |
383 |
|
|
384 |
|
currentIndex ++; |
385 |
|
} |
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]); |
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 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
400 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
401 |
|
|
402 |
|
} else { |
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]); |
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 |
|
|
421 |
|
} |
422 |
|
|
423 |
< |
outFile << writeLine; |
423 |
> |
for(k = 0; k < outFile.size(); k++) |
424 |
> |
*outFile[k] << writeLine; |
425 |
|
} |
426 |
|
|
427 |
< |
|
428 |
< |
outFile.flush(); |
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 |
+ |
|
435 |
|
delete[] potatoes; |
436 |
+ |
|
437 |
|
} else { |
438 |
|
|
439 |
|
// worldRank != 0, so I'm a remote node. |
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 |
|
atomData6[0] = pos[0]; |
472 |
|
atomData6[1] = pos[1]; |
492 |
|
atomData13[7] = q[1]; |
493 |
|
atomData13[8] = q[2]; |
494 |
|
atomData13[9] = q[3]; |
495 |
< |
|
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 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
510 |
|
|
512 |
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
513 |
|
|
514 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
515 |
< |
myPotato, MPI_COMM_WORLD); |
515 |
> |
myPotato, MPI_COMM_WORLD); |
516 |
|
|
517 |
|
myPotato++; |
518 |
|
|
519 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
520 |
< |
myPotato, MPI_COMM_WORLD); |
520 |
> |
myPotato, MPI_COMM_WORLD); |
521 |
|
|
522 |
|
myPotato++; |
523 |
|
|