# | Line 1 | Line 1 | |
---|---|---|
1 | < | #include <cstring> |
1 | > | #define _FILE_OFFSET_BITS 64 |
2 | > | |
3 | > | #include <string.h> |
4 | #include <iostream> | |
5 | #include <fstream> | |
6 | ||
7 | #ifdef IS_MPI | |
8 | #include <mpi.h> | |
7 | – | #include <mpi++.h> |
9 | #include "mpiSimulation.hpp" | |
10 | < | #define TAKE_THIS_TAG 0 |
10 | > | #define TAKE_THIS_TAG_CHAR 1 |
11 | > | #define TAKE_THIS_TAG_INT 2 |
12 | > | |
13 | > | namespace dWrite{ |
14 | > | void nodeZeroError( void ); |
15 | > | void anonymousNodeDie( void ); |
16 | > | } |
17 | > | |
18 | > | using namespace dWrite; |
19 | #endif //is_mpi | |
20 | ||
21 | #include "ReadWrite.hpp" | |
# | Line 20 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
29 | if(worldRank == 0 ){ | |
30 | #endif // is_mpi | |
31 | ||
23 | – | |
24 | – | |
32 | strcpy( outName, entry_plug->sampleName ); | |
33 | ||
34 | outFile.open(outName, ios::out | ios::trunc ); | |
# | Line 34 | Line 41 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
41 | painCave.isFatal = 1; | |
42 | simError(); | |
43 | } | |
44 | < | |
44 | > | |
45 | //outFile.setf( ios::scientific ); | |
46 | ||
47 | #ifdef IS_MPI | |
# | Line 65 | Line 72 | void DumpWriter::writeDump( double currentTime ){ | |
72 | char tempBuffer[BUFFERSIZE]; | |
73 | char writeLine[BUFFERSIZE]; | |
74 | ||
75 | < | int i, j, which_node, done, game_over, which_atom; |
75 | > | int i; |
76 | > | #ifdef IS_MPI |
77 | > | int j, which_node, done, which_atom, local_index; |
78 | > | #else //is_mpi |
79 | > | int nAtoms = entry_plug->n_atoms; |
80 | > | #endif //is_mpi |
81 | > | |
82 | double q[4]; | |
83 | DirectionalAtom* dAtom; | |
71 | – | int nAtoms = entry_plug->n_atoms; |
84 | Atom** atoms = entry_plug->atoms; | |
85 | + | double pos[3], vel[3]; |
86 | ||
87 | + | |
88 | + | // write current frame to the eor file |
89 | ||
90 | + | this->writeFinal( currentTime ); |
91 | + | |
92 | #ifndef IS_MPI | |
93 | ||
94 | outFile << nAtoms << "\n"; | |
95 | ||
96 | < | outFile << currentTime << "\t" |
97 | < | << entry_plug->box_x << "\t" |
98 | < | << entry_plug->box_y << "\t" |
99 | < | << entry_plug->box_z << "\n"; |
96 | > | outFile << currentTime << ";\t" |
97 | > | << entry_plug->Hmat[0][0] << "\t" |
98 | > | << entry_plug->Hmat[1][0] << "\t" |
99 | > | << entry_plug->Hmat[2][0] << ";\t" |
100 | > | |
101 | > | << entry_plug->Hmat[0][1] << "\t" |
102 | > | << entry_plug->Hmat[1][1] << "\t" |
103 | > | << entry_plug->Hmat[2][1] << ";\t" |
104 | > | |
105 | > | << entry_plug->Hmat[0][2] << "\t" |
106 | > | << entry_plug->Hmat[1][2] << "\t" |
107 | > | << entry_plug->Hmat[2][2] << ";\n"; |
108 | ||
109 | for( i=0; i<nAtoms; i++ ){ | |
110 | ||
111 | + | atoms[i]->getPos(pos); |
112 | + | atoms[i]->getVel(vel); |
113 | ||
114 | sprintf( tempBuffer, | |
115 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
116 | atoms[i]->getType(), | |
117 | < | atoms[i]->getX(), |
118 | < | atoms[i]->getY(), |
119 | < | atoms[i]->getZ(), |
120 | < | atoms[i]->get_vx(), |
121 | < | atoms[i]->get_vy(), |
122 | < | atoms[i]->get_vz()); |
117 | > | pos[0], |
118 | > | pos[1], |
119 | > | pos[2], |
120 | > | vel[0], |
121 | > | vel[1], |
122 | > | vel[2]); |
123 | strcpy( writeLine, tempBuffer ); | |
124 | ||
125 | if( atoms[i]->isDirectional() ){ | |
# | Line 120 | Line 147 | void DumpWriter::writeDump( double currentTime ){ | |
147 | ||
148 | #else // is_mpi | |
149 | ||
150 | < | MPI::Status istatus; |
150 | > | // first thing first, suspend fatalities. |
151 | > | painCave.isEventLoop = 1; |
152 | > | |
153 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
154 | > | int haveError; |
155 | > | |
156 | > | MPI_Status istatus; |
157 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
158 | ||
159 | // write out header and node 0's coordinates | |
160 | ||
161 | if( worldRank == 0 ){ | |
162 | outFile << mpiSim->getTotAtoms() << "\n"; | |
163 | + | |
164 | + | outFile << currentTime << ";\t" |
165 | + | << entry_plug->Hmat[0][0] << "\t" |
166 | + | << entry_plug->Hmat[1][0] << "\t" |
167 | + | << entry_plug->Hmat[2][0] << ";\t" |
168 | + | |
169 | + | << entry_plug->Hmat[0][1] << "\t" |
170 | + | << entry_plug->Hmat[1][1] << "\t" |
171 | + | << entry_plug->Hmat[2][1] << ";\t" |
172 | + | |
173 | + | << entry_plug->Hmat[0][2] << "\t" |
174 | + | << entry_plug->Hmat[1][2] << "\t" |
175 | + | << entry_plug->Hmat[2][2] << ";\n"; |
176 | ||
177 | < | outFile << currentTime << "\t" |
132 | < | << entry_plug->box_x << "\t" |
133 | < | << entry_plug->box_y << "\t" |
134 | < | << entry_plug->box_z << "\n"; |
135 | < | |
177 | > | outFile.flush(); |
178 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
179 | < | // Get the Node number which has this molecule: |
179 | > | // Get the Node number which has this atom; |
180 | ||
181 | which_node = AtomToProcMap[i]; | |
182 | ||
183 | < | if (which_node == mpiSim->getMyNode()) { |
142 | < | |
143 | < | sprintf( tempBuffer, |
144 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
145 | < | atoms[i]->getType(), |
146 | < | atoms[i]->getX(), |
147 | < | atoms[i]->getY(), |
148 | < | atoms[i]->getZ(), |
149 | < | atoms[i]->get_vx(), |
150 | < | atoms[i]->get_vy(), |
151 | < | atoms[i]->get_vz()); |
152 | < | strcpy( writeLine, tempBuffer ); |
183 | > | if (which_node == 0 ) { |
184 | ||
185 | < | if( atoms[i]->isDirectional() ){ |
185 | > | haveError = 0; |
186 | > | which_atom = i; |
187 | > | local_index=-1; |
188 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
189 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
190 | > | } |
191 | > | if (local_index != -1) { |
192 | > | //format the line |
193 | ||
194 | < | dAtom = (DirectionalAtom *)atoms[i]; |
195 | < | dAtom->getQ( q ); |
196 | < | |
194 | > | atoms[local_index]->getPos(pos); |
195 | > | atoms[local_index]->getVel(vel); |
196 | > | |
197 | sprintf( tempBuffer, | |
198 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
199 | < | q[0], |
200 | < | q[1], |
201 | < | q[2], |
202 | < | q[3], |
203 | < | dAtom->getJx(), |
204 | < | dAtom->getJy(), |
205 | < | dAtom->getJz()); |
206 | < | strcat( writeLine, tempBuffer ); |
207 | < | } |
208 | < | else |
209 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
210 | < | |
211 | < | } else { |
212 | < | |
213 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
214 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
215 | < | TAKE_THIS_TAG, istatus); |
198 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
199 | > | atoms[local_index]->getType(), |
200 | > | pos[0], |
201 | > | pos[1], |
202 | > | pos[2], |
203 | > | vel[0], |
204 | > | vel[1], |
205 | > | vel[2]); // check here. |
206 | > | strcpy( writeLine, tempBuffer ); |
207 | > | |
208 | > | if( atoms[local_index]->isDirectional() ){ |
209 | > | |
210 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
211 | > | dAtom->getQ( q ); |
212 | > | |
213 | > | sprintf( tempBuffer, |
214 | > | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
215 | > | q[0], |
216 | > | q[1], |
217 | > | q[2], |
218 | > | q[3], |
219 | > | dAtom->getJx(), |
220 | > | dAtom->getJy(), |
221 | > | dAtom->getJz()); |
222 | > | strcat( writeLine, tempBuffer ); |
223 | > | |
224 | > | } |
225 | > | else |
226 | > | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
227 | > | } |
228 | > | else { |
229 | > | sprintf(painCave.errMsg, |
230 | > | "Atom %d not found on processor %d\n", |
231 | > | i, worldRank ); |
232 | > | haveError= 1; |
233 | > | simError(); |
234 | > | } |
235 | > | |
236 | > | if(haveError) nodeZeroError(); |
237 | > | |
238 | } | |
239 | + | else { |
240 | + | myStatus = 1; |
241 | + | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
242 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
243 | + | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
244 | + | MPI_COMM_WORLD); |
245 | + | MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
246 | + | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
247 | + | MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
248 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
249 | + | |
250 | + | if(!myStatus) nodeZeroError(); |
251 | + | |
252 | + | } |
253 | ||
254 | outFile << writeLine; | |
255 | + | outFile.flush(); |
256 | } | |
257 | ||
258 | // kill everyone off: | |
259 | < | game_over = -1; |
259 | > | myStatus = -1; |
260 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
261 | < | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
261 | > | MPI_Send(&myStatus, 1, MPI_INT, j, |
262 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
263 | } | |
264 | ||
265 | } else { | |
266 | ||
267 | done = 0; | |
268 | while (!done) { | |
269 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
270 | < | TAKE_THIS_TAG, istatus); |
269 | > | |
270 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
271 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
272 | ||
273 | < | if (which_atom == -1) { |
274 | < | done=1; |
275 | < | continue; |
199 | < | } else { |
273 | > | if(!myStatus) anonymousNodeDie(); |
274 | > | |
275 | > | if(myStatus < 0) break; |
276 | ||
277 | < | //format the line |
277 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
278 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
279 | > | |
280 | > | myStatus = 1; |
281 | > | local_index=-1; |
282 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
283 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
284 | > | } |
285 | > | if (local_index != -1) { |
286 | > | //format the line |
287 | > | |
288 | > | atoms[local_index]->getPos(pos); |
289 | > | atoms[local_index]->getVel(vel); |
290 | > | |
291 | sprintf( tempBuffer, | |
292 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
293 | < | atoms[which_atom]->getType(), |
294 | < | atoms[which_atom]->getX(), |
295 | < | atoms[which_atom]->getY(), |
296 | < | atoms[which_atom]->getZ(), |
297 | < | atoms[which_atom]->get_vx(), |
298 | < | atoms[which_atom]->get_vy(), |
299 | < | atoms[which_atom]->get_vz()); // check here. |
293 | > | atoms[local_index]->getType(), |
294 | > | pos[0], |
295 | > | pos[1], |
296 | > | pos[2], |
297 | > | vel[0], |
298 | > | vel[1], |
299 | > | vel[2]); // check here. |
300 | strcpy( writeLine, tempBuffer ); | |
301 | + | |
302 | + | if( atoms[local_index]->isDirectional() ){ |
303 | ||
304 | < | if( atoms[which_atom]->isDirectional() ){ |
214 | < | |
215 | < | dAtom = (DirectionalAtom *)atoms[which_atom]; |
304 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
305 | dAtom->getQ( q ); | |
306 | < | |
306 | > | |
307 | sprintf( tempBuffer, | |
308 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
309 | q[0], | |
# | Line 226 | Line 315 | void DumpWriter::writeDump( double currentTime ){ | |
315 | dAtom->getJz()); | |
316 | strcat( writeLine, tempBuffer ); | |
317 | } | |
318 | < | else |
318 | > | else{ |
319 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
320 | < | |
321 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
322 | < | TAKE_THIS_TAG); |
320 | > | } |
321 | > | } |
322 | > | else { |
323 | > | sprintf(painCave.errMsg, |
324 | > | "Atom %d not found on processor %d\n", |
325 | > | which_atom, worldRank ); |
326 | > | myStatus = 0; |
327 | > | simError(); |
328 | > | |
329 | > | strcpy( writeLine, "Hello, I'm an error.\n"); |
330 | } | |
331 | + | |
332 | + | MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
333 | + | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
334 | + | MPI_Send( &myStatus, 1, MPI_INT, 0, |
335 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
336 | } | |
337 | } | |
338 | outFile.flush(); | |
339 | sprintf( checkPointMsg, | |
340 | "Sucessfully took a dump.\n"); | |
341 | MPIcheckPoint(); | |
342 | + | |
343 | + | // last thing last, enable fatalities. |
344 | + | painCave.isEventLoop = 0; |
345 | + | |
346 | #endif // is_mpi | |
347 | } | |
348 | ||
349 | < | void DumpWriter::writeFinal(){ |
349 | > | void DumpWriter::writeFinal(double finalTime){ |
350 | ||
351 | char finalName[500]; | |
352 | ofstream finalOut; | |
# | Line 252 | Line 357 | void DumpWriter::writeFinal(){ | |
357 | ||
358 | double q[4]; | |
359 | DirectionalAtom* dAtom; | |
255 | – | int nAtoms = entry_plug->n_atoms; |
360 | Atom** atoms = entry_plug->atoms; | |
361 | < | int i, j, which_node, done, game_over, which_atom; |
361 | > | int i; |
362 | > | #ifdef IS_MPI |
363 | > | int j, which_node, done, which_atom, local_index; |
364 | > | #else //is_mpi |
365 | > | int nAtoms = entry_plug->n_atoms; |
366 | > | #endif //is_mpi |
367 | ||
368 | + | double pos[3], vel[3]; |
369 | ||
370 | #ifdef IS_MPI | |
371 | if(worldRank == 0 ){ | |
# | Line 287 | Line 397 | void DumpWriter::writeFinal(){ | |
397 | ||
398 | finalOut << nAtoms << "\n"; | |
399 | ||
400 | < | finalOut << entry_plug->box_x << "\t" |
401 | < | << entry_plug->box_y << "\t" |
402 | < | << entry_plug->box_z << "\n"; |
400 | > | finalOut << finalTime << ";\t" |
401 | > | << entry_plug->Hmat[0][0] << "\t" |
402 | > | << entry_plug->Hmat[1][0] << "\t" |
403 | > | << entry_plug->Hmat[2][0] << ";\t" |
404 | > | |
405 | > | << entry_plug->Hmat[0][1] << "\t" |
406 | > | << entry_plug->Hmat[1][1] << "\t" |
407 | > | << entry_plug->Hmat[2][1] << ";\t" |
408 | > | |
409 | > | << entry_plug->Hmat[0][2] << "\t" |
410 | > | << entry_plug->Hmat[1][2] << "\t" |
411 | > | << entry_plug->Hmat[2][2] << ";\n"; |
412 | ||
413 | for( i=0; i<nAtoms; i++ ){ | |
414 | ||
415 | + | atoms[i]->getPos(pos); |
416 | + | atoms[i]->getVel(vel); |
417 | + | |
418 | sprintf( tempBuffer, | |
419 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
420 | atoms[i]->getType(), | |
421 | < | atoms[i]->getX(), |
422 | < | atoms[i]->getY(), |
423 | < | atoms[i]->getZ(), |
424 | < | atoms[i]->get_vx(), |
425 | < | atoms[i]->get_vy(), |
426 | < | atoms[i]->get_vz()); |
421 | > | pos[0], |
422 | > | pos[1], |
423 | > | pos[2], |
424 | > | vel[0], |
425 | > | vel[1], |
426 | > | vel[2]); |
427 | strcpy( writeLine, tempBuffer ); | |
428 | ||
429 | if( atoms[i]->isDirectional() ){ | |
# | Line 330 | Line 452 | void DumpWriter::writeFinal(){ | |
452 | ||
453 | #else // is_mpi | |
454 | ||
455 | < | MPI::Status istatus; |
455 | > | // first thing first, suspend fatalities. |
456 | > | painCave.isEventLoop = 1; |
457 | > | |
458 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
459 | > | int haveError; |
460 | > | |
461 | > | MPI_Status istatus; |
462 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
463 | ||
464 | // write out header and node 0's coordinates | |
465 | ||
466 | + | haveError = 0; |
467 | if( worldRank == 0 ){ | |
468 | finalOut << mpiSim->getTotAtoms() << "\n"; | |
469 | ||
470 | < | finalOut << entry_plug->box_x << "\t" |
471 | < | << entry_plug->box_y << "\t" |
472 | < | << entry_plug->box_z << "\n"; |
470 | > | finalOut << finalTime << ";\t" |
471 | > | << entry_plug->Hmat[0][0] << "\t" |
472 | > | << entry_plug->Hmat[1][0] << "\t" |
473 | > | << entry_plug->Hmat[2][0] << ";\t" |
474 | > | |
475 | > | << entry_plug->Hmat[0][1] << "\t" |
476 | > | << entry_plug->Hmat[1][1] << "\t" |
477 | > | << entry_plug->Hmat[2][1] << ";\t" |
478 | > | |
479 | > | << entry_plug->Hmat[0][2] << "\t" |
480 | > | << entry_plug->Hmat[1][2] << "\t" |
481 | > | << entry_plug->Hmat[2][2] << ";\n"; |
482 | ||
483 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
484 | // Get the Node number which has this molecule: | |
# | Line 348 | Line 486 | void DumpWriter::writeFinal(){ | |
486 | which_node = AtomToProcMap[i]; | |
487 | ||
488 | if (which_node == mpiSim->getMyNode()) { | |
489 | < | |
490 | < | sprintf( tempBuffer, |
491 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
492 | < | atoms[i]->getType(), |
493 | < | atoms[i]->getX(), |
494 | < | atoms[i]->getY(), |
495 | < | atoms[i]->getZ(), |
496 | < | atoms[i]->get_vx(), |
497 | < | atoms[i]->get_vy(), |
498 | < | atoms[i]->get_vz()); |
361 | < | strcpy( writeLine, tempBuffer ); |
362 | < | |
363 | < | if( atoms[i]->isDirectional() ){ |
489 | > | |
490 | > | which_atom = i; |
491 | > | local_index=-1; |
492 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
493 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
494 | > | } |
495 | > | if (local_index != -1) { |
496 | > | |
497 | > | atoms[local_index]->getPos(pos); |
498 | > | atoms[local_index]->getVel(vel); |
499 | ||
500 | < | dAtom = (DirectionalAtom *)atoms[i]; |
501 | < | dAtom->getQ( q ); |
500 | > | sprintf( tempBuffer, |
501 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
502 | > | atoms[local_index]->getType(), |
503 | > | pos[0], |
504 | > | pos[1], |
505 | > | pos[2], |
506 | > | vel[0], |
507 | > | vel[1], |
508 | > | vel[2]); |
509 | > | strcpy( writeLine, tempBuffer ); |
510 | ||
511 | < | sprintf( tempBuffer, |
512 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
513 | < | q[0], |
514 | < | q[1], |
515 | < | q[2], |
516 | < | q[3], |
517 | < | dAtom->getJx(), |
518 | < | dAtom->getJy(), |
519 | < | dAtom->getJz()); |
520 | < | strcat( writeLine, tempBuffer ); |
521 | < | } |
522 | < | else |
523 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
511 | > | if( atoms[local_index]->isDirectional() ){ |
512 | > | |
513 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
514 | > | dAtom->getQ( q ); |
515 | > | |
516 | > | sprintf( tempBuffer, |
517 | > | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
518 | > | q[0], |
519 | > | q[1], |
520 | > | q[2], |
521 | > | q[3], |
522 | > | dAtom->getJx(), |
523 | > | dAtom->getJy(), |
524 | > | dAtom->getJz()); |
525 | > | strcat( writeLine, tempBuffer ); |
526 | > | } |
527 | > | else |
528 | > | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
529 | > | } |
530 | > | else { |
531 | > | sprintf(painCave.errMsg, |
532 | > | "Atom %d not found on processor %d\n", |
533 | > | i, worldRank ); |
534 | > | haveError= 1; |
535 | > | simError(); |
536 | > | } |
537 | > | |
538 | > | if(haveError) nodeZeroError(); |
539 | > | |
540 | > | } |
541 | > | else { |
542 | ||
543 | < | } else { |
544 | < | |
545 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
546 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
547 | < | TAKE_THIS_TAG, istatus); |
543 | > | myStatus = 1; |
544 | > | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
545 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
546 | > | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
547 | > | MPI_COMM_WORLD); |
548 | > | MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
549 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
550 | > | MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
551 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
552 | > | |
553 | > | if(!myStatus) nodeZeroError(); |
554 | } | |
555 | ||
556 | finalOut << writeLine; | |
557 | } | |
558 | ||
559 | // kill everyone off: | |
560 | < | game_over = -1; |
561 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
562 | < | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
560 | > | myStatus = -1; |
561 | > | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
562 | > | MPI_Send(&myStatus, 1, MPI_INT, j, |
563 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
564 | } | |
565 | ||
566 | } else { | |
567 | ||
568 | done = 0; | |
569 | while (!done) { | |
402 | – | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
403 | – | TAKE_THIS_TAG, istatus); |
570 | ||
571 | < | if (which_atom == -1) { |
572 | < | done=1; |
573 | < | continue; |
574 | < | } else { |
571 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
572 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
573 | > | |
574 | > | if(!myStatus) anonymousNodeDie(); |
575 | > | |
576 | > | if(myStatus < 0) break; |
577 | > | |
578 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
579 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
580 | > | |
581 | > | myStatus = 1; |
582 | > | local_index=-1; |
583 | > | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
584 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
585 | > | } |
586 | > | if (local_index != -1) { |
587 | ||
588 | < | //format the line |
588 | > | atoms[local_index]->getPos(pos); |
589 | > | atoms[local_index]->getVel(vel); |
590 | > | |
591 | > | //format the line |
592 | sprintf( tempBuffer, | |
593 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
594 | < | atoms[which_atom]->getType(), |
595 | < | atoms[which_atom]->getX(), |
596 | < | atoms[which_atom]->getY(), |
597 | < | atoms[which_atom]->getZ(), |
598 | < | atoms[which_atom]->get_vx(), |
599 | < | atoms[which_atom]->get_vy(), |
600 | < | atoms[which_atom]->get_vz()); // check here. |
594 | > | atoms[local_index]->getType(), |
595 | > | pos[0], |
596 | > | pos[1], |
597 | > | pos[2], |
598 | > | vel[0], |
599 | > | vel[1], |
600 | > | vel[2]); // check here. |
601 | strcpy( writeLine, tempBuffer ); | |
602 | + | |
603 | + | if( atoms[local_index]->isDirectional() ){ |
604 | ||
605 | < | if( atoms[which_atom]->isDirectional() ){ |
423 | < | |
424 | < | dAtom = (DirectionalAtom *)atoms[which_atom]; |
605 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
606 | dAtom->getQ( q ); | |
607 | < | |
607 | > | |
608 | sprintf( tempBuffer, | |
609 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
610 | q[0], | |
# | Line 435 | Line 616 | void DumpWriter::writeFinal(){ | |
616 | dAtom->getJz()); | |
617 | strcat( writeLine, tempBuffer ); | |
618 | } | |
619 | < | else |
619 | > | else{ |
620 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
621 | < | |
622 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
623 | < | TAKE_THIS_TAG); |
621 | > | } |
622 | > | } |
623 | > | else { |
624 | > | sprintf(painCave.errMsg, |
625 | > | "Atom %d not found on processor %d\n", |
626 | > | which_atom, worldRank ); |
627 | > | myStatus = 0; |
628 | > | simError(); |
629 | > | |
630 | > | strcpy( writeLine, "Hello, I'm an error.\n"); |
631 | } | |
632 | + | |
633 | + | MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
634 | + | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
635 | + | MPI_Send( &myStatus, 1, MPI_INT, 0, |
636 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
637 | } | |
638 | < | } |
638 | > | } |
639 | finalOut.flush(); | |
640 | sprintf( checkPointMsg, | |
641 | "Sucessfully took a dump.\n"); | |
642 | MPIcheckPoint(); | |
643 | < | |
643 | > | |
644 | if( worldRank == 0 ) finalOut.close(); | |
645 | #endif // is_mpi | |
646 | } | |
647 | + | |
648 | + | |
649 | + | |
650 | + | #ifdef IS_MPI |
651 | + | |
652 | + | // a couple of functions to let us escape the write loop |
653 | + | |
654 | + | void dWrite::nodeZeroError( void ){ |
655 | + | int j, myStatus; |
656 | + | |
657 | + | myStatus = 0; |
658 | + | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
659 | + | MPI_Send( &myStatus, 1, MPI_INT, j, |
660 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 | + | } |
662 | + | |
663 | + | |
664 | + | MPI_Finalize(); |
665 | + | exit (0); |
666 | + | |
667 | + | } |
668 | + | |
669 | + | void dWrite::anonymousNodeDie( void ){ |
670 | + | |
671 | + | MPI_Finalize(); |
672 | + | exit (0); |
673 | + | } |
674 | + | |
675 | + | #endif //is_mpi |
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