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5 |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG 0 |
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#endif //is_mpi |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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#define GAME_OVER -1 |
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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|
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entry_plug = the_entry_plug; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
68 |
< |
int i; |
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int i, j, which_node, done, game_over, which_atom, local_index; |
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double q[4]; |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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outFile.flush(); |
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|
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#else // is_mpi |
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|
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MPI::Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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|
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// write out header and node 0's coordinates |
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|
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if( worldRank == 0 ){ |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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|
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for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
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// Get the Node number which has this molecule: |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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// Get the Node number which has this atom; |
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|
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which_node = AtomToProcMap[i]; |
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|
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if (which_node == mpiPlug->myNode) { |
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if (which_node == mpiSim->getMyNode()) { |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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} else { |
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|
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
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MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
176 |
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MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG, istatus); |
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} |
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|
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} |
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|
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// kill everyone off: |
184 |
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for (j = 0; j < mpiPlug->numberProcessors; j++) { |
185 |
< |
MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
184 |
> |
game_over = -1; |
185 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
186 |
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MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
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} |
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|
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} else { |
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|
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done = 0; |
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while (!done) { |
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MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
194 |
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TAKE_THIS_TAG, istatus); |
195 |
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|
196 |
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if (which_atom == GAME_OVER) { |
193 |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
194 |
> |
TAKE_THIS_TAG, istatus); |
195 |
> |
|
196 |
> |
if (which_atom == -1) { |
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done=1; |
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continue; |
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} else { |
200 |
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|
201 |
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//format the line |
202 |
< |
sprintf( tempBuffer, |
203 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
204 |
< |
atoms[which_atom]->getType(), |
205 |
< |
atoms[which_atom]->getX(), |
206 |
< |
atoms[which_atom]->getY(), |
207 |
< |
atoms[which_atom]->getZ(), |
208 |
< |
atoms[which_atom]->get_vx(), |
209 |
< |
atoms[which_atom]->get_vy(), |
210 |
< |
atoms[which_atom]->get_vz()); // check here. |
211 |
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strcpy( writeLine, tempBuffer ); |
200 |
> |
local_index=-1; |
201 |
> |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
202 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
203 |
> |
} |
204 |
> |
if (local_index != -1) { |
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//format the line |
206 |
> |
sprintf( tempBuffer, |
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> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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> |
atoms[local_index]->getType(), |
209 |
> |
atoms[local_index]->getX(), |
210 |
> |
atoms[local_index]->getY(), |
211 |
> |
atoms[local_index]->getZ(), |
212 |
> |
atoms[local_index]->get_vx(), |
213 |
> |
atoms[local_index]->get_vy(), |
214 |
> |
atoms[local_index]->get_vz()); // check here. |
215 |
> |
strcpy( writeLine, tempBuffer ); |
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|
217 |
< |
if( atoms[which_atom]->isDirectional() ){ |
218 |
< |
|
219 |
< |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
220 |
< |
dAtom->getQ( q ); |
221 |
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|
222 |
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
224 |
< |
q[0], |
225 |
< |
q[1], |
226 |
< |
q[2], |
227 |
< |
q[3], |
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< |
dAtom->getJx(), |
229 |
< |
dAtom->getJy(), |
230 |
< |
dAtom->getJz()); |
231 |
< |
strcat( writeLine, tempBuffer ); |
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} |
233 |
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else |
234 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
235 |
< |
|
236 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
237 |
< |
TAKE_THIS_TAG); |
217 |
> |
if( atoms[local_index]->isDirectional() ){ |
218 |
> |
|
219 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
220 |
> |
dAtom->getQ( q ); |
221 |
> |
|
222 |
> |
sprintf( tempBuffer, |
223 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
224 |
> |
q[0], |
225 |
> |
q[1], |
226 |
> |
q[2], |
227 |
> |
q[3], |
228 |
> |
dAtom->getJx(), |
229 |
> |
dAtom->getJy(), |
230 |
> |
dAtom->getJz()); |
231 |
> |
strcat( writeLine, tempBuffer ); |
232 |
> |
} |
233 |
> |
else |
234 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
235 |
> |
|
236 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
237 |
> |
TAKE_THIS_TAG); |
238 |
> |
} else { |
239 |
> |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
240 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
241 |
> |
TAKE_THIS_TAG); |
242 |
> |
} |
243 |
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} |
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} |
245 |
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} |
251 |
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} |
252 |
|
|
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void DumpWriter::writeFinal(){ |
254 |
< |
|
254 |
> |
|
255 |
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char finalName[500]; |
256 |
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ofstream finalOut; |
257 |
+ |
|
258 |
+ |
const int BUFFERSIZE = 2000; |
259 |
+ |
char tempBuffer[BUFFERSIZE]; |
260 |
+ |
char writeLine[BUFFERSIZE]; |
261 |
+ |
|
262 |
+ |
double q[4]; |
263 |
+ |
DirectionalAtom* dAtom; |
264 |
+ |
int nAtoms = entry_plug->n_atoms; |
265 |
+ |
Atom** atoms = entry_plug->atoms; |
266 |
+ |
int i, j, which_node, done, game_over, which_atom, local_index; |
267 |
|
|
268 |
+ |
|
269 |
|
#ifdef IS_MPI |
270 |
|
if(worldRank == 0 ){ |
271 |
|
#endif // is_mpi |
299 |
|
finalOut << entry_plug->box_x << "\t" |
300 |
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<< entry_plug->box_y << "\t" |
301 |
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<< entry_plug->box_z << "\n"; |
302 |
< |
|
302 |
> |
|
303 |
|
for( i=0; i<nAtoms; i++ ){ |
304 |
|
|
305 |
|
sprintf( tempBuffer, |
339 |
|
|
340 |
|
#else // is_mpi |
341 |
|
|
342 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
343 |
< |
|
342 |
> |
MPI::Status istatus; |
343 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
344 |
> |
|
345 |
|
// write out header and node 0's coordinates |
346 |
|
|
347 |
|
if( worldRank == 0 ){ |
351 |
|
<< entry_plug->box_y << "\t" |
352 |
|
<< entry_plug->box_z << "\n"; |
353 |
|
|
354 |
< |
for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
354 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
355 |
|
// Get the Node number which has this molecule: |
356 |
|
|
357 |
|
which_node = AtomToProcMap[i]; |
358 |
|
|
359 |
< |
if (which_node == mpiPlug->myNode) { |
359 |
> |
if (which_node == mpiSim->getMyNode()) { |
360 |
|
|
361 |
|
sprintf( tempBuffer, |
362 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
391 |
|
} else { |
392 |
|
|
393 |
|
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
394 |
< |
MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
394 |
> |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
395 |
|
TAKE_THIS_TAG, istatus); |
396 |
|
} |
397 |
|
|
399 |
|
} |
400 |
|
|
401 |
|
// kill everyone off: |
402 |
< |
for (j = 0; j < mpiPlug->numberProcessors; j++) { |
403 |
< |
MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
402 |
> |
game_over = -1; |
403 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
404 |
> |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
405 |
|
} |
406 |
|
|
407 |
|
} else { |
408 |
|
|
409 |
|
done = 0; |
410 |
|
while (!done) { |
411 |
< |
MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
412 |
< |
TAKE_THIS_TAG, istatus); |
411 |
> |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
412 |
> |
TAKE_THIS_TAG, istatus); |
413 |
|
|
414 |
< |
if (which_atom == GAME_OVER) { |
414 |
> |
if (which_atom == -1) { |
415 |
|
done=1; |
416 |
|
continue; |
417 |
|
} else { |
418 |
|
|
419 |
< |
//format the line |
420 |
< |
sprintf( tempBuffer, |
421 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
422 |
< |
atoms[which_atom]->getType(), |
423 |
< |
atoms[which_atom]->getX(), |
424 |
< |
atoms[which_atom]->getY(), |
425 |
< |
atoms[which_atom]->getZ(), |
426 |
< |
atoms[which_atom]->get_vx(), |
427 |
< |
atoms[which_atom]->get_vy(), |
428 |
< |
atoms[which_atom]->get_vz()); // check here. |
429 |
< |
strcpy( writeLine, tempBuffer ); |
419 |
> |
local_index=-1; |
420 |
> |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
421 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
422 |
> |
} |
423 |
> |
if (local_index != -1) { |
424 |
> |
|
425 |
> |
//format the line |
426 |
> |
sprintf( tempBuffer, |
427 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
428 |
> |
atoms[local_index]->getType(), |
429 |
> |
atoms[local_index]->getX(), |
430 |
> |
atoms[local_index]->getY(), |
431 |
> |
atoms[local_index]->getZ(), |
432 |
> |
atoms[local_index]->get_vx(), |
433 |
> |
atoms[local_index]->get_vy(), |
434 |
> |
atoms[local_index]->get_vz()); // check here. |
435 |
> |
strcpy( writeLine, tempBuffer ); |
436 |
|
|
437 |
< |
if( atoms[which_atom]->isDirectional() ){ |
437 |
> |
if( atoms[local_index]->isDirectional() ){ |
438 |
> |
|
439 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
440 |
> |
dAtom->getQ( q ); |
441 |
|
|
442 |
< |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
443 |
< |
dAtom->getQ( q ); |
444 |
< |
|
445 |
< |
sprintf( tempBuffer, |
446 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
447 |
< |
q[0], |
448 |
< |
q[1], |
449 |
< |
q[2], |
450 |
< |
q[3], |
451 |
< |
dAtom->getJx(), |
452 |
< |
dAtom->getJy(), |
453 |
< |
dAtom->getJz()); |
454 |
< |
strcat( writeLine, tempBuffer ); |
455 |
< |
} |
456 |
< |
else |
457 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
458 |
< |
|
459 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
460 |
< |
TAKE_THIS_TAG); |
442 |
> |
sprintf( tempBuffer, |
443 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
444 |
> |
q[0], |
445 |
> |
q[1], |
446 |
> |
q[2], |
447 |
> |
q[3], |
448 |
> |
dAtom->getJx(), |
449 |
> |
dAtom->getJy(), |
450 |
> |
dAtom->getJz()); |
451 |
> |
strcat( writeLine, tempBuffer ); |
452 |
> |
} |
453 |
> |
else |
454 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
455 |
> |
|
456 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
457 |
> |
TAKE_THIS_TAG); |
458 |
> |
} else { |
459 |
> |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
460 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
461 |
> |
TAKE_THIS_TAG); |
462 |
> |
} |
463 |
|
} |
464 |
|
} |
465 |
< |
} |
465 |
> |
} |
466 |
|
finalOut.flush(); |
467 |
|
sprintf( checkPointMsg, |
468 |
|
"Sucessfully took a dump.\n"); |