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> |
9 |
#include "mpiSimulation.hpp" |
10 |
|
11 |
namespace dWrite{ |
12 |
void DieDieDie( void ); |
13 |
} |
14 |
|
15 |
using namespace dWrite; |
16 |
#endif //is_mpi |
17 |
|
18 |
#include "ReadWrite.hpp" |
19 |
#include "simError.h" |
20 |
|
21 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
22 |
|
23 |
entry_plug = the_entry_plug; |
24 |
|
25 |
#ifdef IS_MPI |
26 |
if(worldRank == 0 ){ |
27 |
#endif // is_mpi |
28 |
|
29 |
strcpy( outName, entry_plug->sampleName ); |
30 |
|
31 |
outFile.open(outName, ios::out | ios::trunc ); |
32 |
|
33 |
if( !outFile ){ |
34 |
|
35 |
sprintf( painCave.errMsg, |
36 |
"Could not open \"%s\" for dump output.\n", |
37 |
outName); |
38 |
painCave.isFatal = 1; |
39 |
simError(); |
40 |
} |
41 |
|
42 |
//outFile.setf( ios::scientific ); |
43 |
|
44 |
#ifdef IS_MPI |
45 |
} |
46 |
|
47 |
sprintf( checkPointMsg, |
48 |
"Sucessfully opened output file for dumping.\n"); |
49 |
MPIcheckPoint(); |
50 |
#endif // is_mpi |
51 |
} |
52 |
|
53 |
DumpWriter::~DumpWriter( ){ |
54 |
|
55 |
#ifdef IS_MPI |
56 |
if(worldRank == 0 ){ |
57 |
#endif // is_mpi |
58 |
|
59 |
outFile.close(); |
60 |
|
61 |
#ifdef IS_MPI |
62 |
} |
63 |
#endif // is_mpi |
64 |
} |
65 |
|
66 |
void DumpWriter::writeDump( double currentTime ){ |
67 |
|
68 |
const int BUFFERSIZE = 2000; |
69 |
const int MINIBUFFERSIZE = 100; |
70 |
|
71 |
char tempBuffer[BUFFERSIZE]; |
72 |
char writeLine[BUFFERSIZE]; |
73 |
|
74 |
int i; |
75 |
|
76 |
#ifdef IS_MPI |
77 |
|
78 |
int *potatoes; |
79 |
int myPotato; |
80 |
|
81 |
int nProc; |
82 |
int j, which_node, done, which_atom, local_index; |
83 |
double atomData6[6]; |
84 |
double atomData13[13]; |
85 |
int isDirectional; |
86 |
char* atomTypeString; |
87 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
88 |
|
89 |
#else //is_mpi |
90 |
int nAtoms = entry_plug->n_atoms; |
91 |
#endif //is_mpi |
92 |
|
93 |
double q[4]; |
94 |
DirectionalAtom* dAtom; |
95 |
Atom** atoms = entry_plug->atoms; |
96 |
double pos[3], vel[3]; |
97 |
|
98 |
// write current frame to the eor file |
99 |
|
100 |
this->writeFinal( currentTime ); |
101 |
|
102 |
#ifndef IS_MPI |
103 |
|
104 |
outFile << nAtoms << "\n"; |
105 |
|
106 |
outFile << currentTime << ";\t" |
107 |
<< entry_plug->Hmat[0][0] << "\t" |
108 |
<< entry_plug->Hmat[1][0] << "\t" |
109 |
<< entry_plug->Hmat[2][0] << ";\t" |
110 |
|
111 |
<< entry_plug->Hmat[0][1] << "\t" |
112 |
<< entry_plug->Hmat[1][1] << "\t" |
113 |
<< entry_plug->Hmat[2][1] << ";\t" |
114 |
|
115 |
<< entry_plug->Hmat[0][2] << "\t" |
116 |
<< entry_plug->Hmat[1][2] << "\t" |
117 |
<< entry_plug->Hmat[2][2] << ";"; |
118 |
//write out additional parameters, such as chi and eta |
119 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
120 |
outFile << endl; |
121 |
|
122 |
for( i=0; i<nAtoms; i++ ){ |
123 |
|
124 |
atoms[i]->getPos(pos); |
125 |
atoms[i]->getVel(vel); |
126 |
|
127 |
sprintf( tempBuffer, |
128 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
129 |
atoms[i]->getType(), |
130 |
pos[0], |
131 |
pos[1], |
132 |
pos[2], |
133 |
vel[0], |
134 |
vel[1], |
135 |
vel[2]); |
136 |
strcpy( writeLine, tempBuffer ); |
137 |
|
138 |
if( atoms[i]->isDirectional() ){ |
139 |
|
140 |
dAtom = (DirectionalAtom *)atoms[i]; |
141 |
dAtom->getQ( q ); |
142 |
|
143 |
sprintf( tempBuffer, |
144 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
145 |
q[0], |
146 |
q[1], |
147 |
q[2], |
148 |
q[3], |
149 |
dAtom->getJx(), |
150 |
dAtom->getJy(), |
151 |
dAtom->getJz()); |
152 |
strcat( writeLine, tempBuffer ); |
153 |
} |
154 |
else |
155 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
156 |
|
157 |
outFile << writeLine; |
158 |
} |
159 |
outFile.flush(); |
160 |
|
161 |
#else // is_mpi |
162 |
|
163 |
/* code to find maximum tag value */ |
164 |
int *tagub, flag, MAXTAG; |
165 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
166 |
if (flag) { |
167 |
MAXTAG = *tagub; |
168 |
} else { |
169 |
MAXTAG = 32767; |
170 |
} |
171 |
|
172 |
int haveError; |
173 |
|
174 |
MPI_Status istatus; |
175 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
176 |
|
177 |
// write out header and node 0's coordinates |
178 |
|
179 |
if( worldRank == 0 ){ |
180 |
|
181 |
// Node 0 needs a list of the magic potatoes for each processor; |
182 |
|
183 |
nProc = mpiSim->getNumberProcessors(); |
184 |
potatoes = new int[nProc]; |
185 |
|
186 |
for (i = 0; i < nProc; i++) |
187 |
potatoes[i] = 0; |
188 |
|
189 |
outFile << mpiSim->getTotAtoms() << "\n"; |
190 |
|
191 |
outFile << currentTime << ";\t" |
192 |
<< entry_plug->Hmat[0][0] << "\t" |
193 |
<< entry_plug->Hmat[1][0] << "\t" |
194 |
<< entry_plug->Hmat[2][0] << ";\t" |
195 |
|
196 |
<< entry_plug->Hmat[0][1] << "\t" |
197 |
<< entry_plug->Hmat[1][1] << "\t" |
198 |
<< entry_plug->Hmat[2][1] << ";\t" |
199 |
|
200 |
<< entry_plug->Hmat[0][2] << "\t" |
201 |
<< entry_plug->Hmat[1][2] << "\t" |
202 |
<< entry_plug->Hmat[2][2] << ";"; |
203 |
|
204 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
205 |
outFile << endl; |
206 |
outFile.flush(); |
207 |
|
208 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
209 |
|
210 |
// Get the Node number which has this atom; |
211 |
|
212 |
which_node = AtomToProcMap[i]; |
213 |
|
214 |
if (which_node != 0) { |
215 |
|
216 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
217 |
// The potato was going to exceed the maximum value, |
218 |
// so wrap this processor potato back to 0: |
219 |
|
220 |
potatoes[which_node] = 0; |
221 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
222 |
|
223 |
} |
224 |
|
225 |
myPotato = potatoes[which_node]; |
226 |
|
227 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
228 |
myPotato, MPI_COMM_WORLD, &istatus); |
229 |
|
230 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
231 |
|
232 |
// Null terminate the atomTypeString just in case: |
233 |
|
234 |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
235 |
|
236 |
myPotato++; |
237 |
|
238 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
239 |
myPotato, MPI_COMM_WORLD, &istatus); |
240 |
|
241 |
myPotato++; |
242 |
|
243 |
if (isDirectional) { |
244 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
245 |
myPotato, MPI_COMM_WORLD, &istatus); |
246 |
} else { |
247 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
248 |
myPotato, MPI_COMM_WORLD, &istatus); |
249 |
} |
250 |
|
251 |
myPotato++; |
252 |
potatoes[which_node] = myPotato; |
253 |
|
254 |
} else { |
255 |
|
256 |
haveError = 0; |
257 |
which_atom = i; |
258 |
local_index=-1; |
259 |
|
260 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
261 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
262 |
} |
263 |
|
264 |
if (local_index != -1) { |
265 |
|
266 |
atomTypeString = atoms[local_index]->getType(); |
267 |
|
268 |
atoms[local_index]->getPos(pos); |
269 |
atoms[local_index]->getVel(vel); |
270 |
|
271 |
atomData6[0] = pos[0]; |
272 |
atomData6[1] = pos[1]; |
273 |
atomData6[2] = pos[2]; |
274 |
|
275 |
atomData6[3] = vel[0]; |
276 |
atomData6[4] = vel[1]; |
277 |
atomData6[5] = vel[2]; |
278 |
|
279 |
isDirectional = 0; |
280 |
|
281 |
if( atoms[local_index]->isDirectional() ){ |
282 |
|
283 |
isDirectional = 1; |
284 |
|
285 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
286 |
dAtom->getQ( q ); |
287 |
|
288 |
for (int j = 0; j < 6 ; j++) |
289 |
atomData13[j] = atomData6[j]; |
290 |
|
291 |
atomData13[6] = q[0]; |
292 |
atomData13[7] = q[1]; |
293 |
atomData13[8] = q[2]; |
294 |
atomData13[9] = q[3]; |
295 |
|
296 |
atomData13[10] = dAtom->getJx(); |
297 |
atomData13[11] = dAtom->getJy(); |
298 |
atomData13[12] = dAtom->getJz(); |
299 |
} |
300 |
|
301 |
} else { |
302 |
sprintf(painCave.errMsg, |
303 |
"Atom %d not found on processor %d\n", |
304 |
i, worldRank ); |
305 |
haveError= 1; |
306 |
simError(); |
307 |
} |
308 |
|
309 |
if(haveError) DieDieDie(); |
310 |
|
311 |
// If we've survived to here, format the line: |
312 |
|
313 |
if (!isDirectional) { |
314 |
|
315 |
sprintf( tempBuffer, |
316 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
317 |
atomTypeString, |
318 |
atomData6[0], |
319 |
atomData6[1], |
320 |
atomData6[2], |
321 |
atomData6[3], |
322 |
atomData6[4], |
323 |
atomData6[5]); |
324 |
|
325 |
strcpy( writeLine, tempBuffer ); |
326 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
327 |
|
328 |
} else { |
329 |
|
330 |
sprintf( tempBuffer, |
331 |
"%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", |
332 |
atomTypeString, |
333 |
atomData13[0], |
334 |
atomData13[1], |
335 |
atomData13[2], |
336 |
atomData13[3], |
337 |
atomData13[4], |
338 |
atomData13[5], |
339 |
atomData13[6], |
340 |
atomData13[7], |
341 |
atomData13[8], |
342 |
atomData13[9], |
343 |
atomData13[10], |
344 |
atomData13[11], |
345 |
atomData13[12]); |
346 |
|
347 |
strcat( writeLine, tempBuffer ); |
348 |
|
349 |
} |
350 |
|
351 |
outFile << writeLine; |
352 |
outFile.flush(); |
353 |
} |
354 |
} |
355 |
|
356 |
outFile.flush(); |
357 |
sprintf( checkPointMsg, |
358 |
"Sucessfully took a dump.\n"); |
359 |
MPIcheckPoint(); |
360 |
|
361 |
} else { |
362 |
|
363 |
// worldRank != 0, so I'm a remote node. |
364 |
|
365 |
// Set my magic potato to 0: |
366 |
|
367 |
myPotato = 0; |
368 |
|
369 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
370 |
|
371 |
// Am I the node which has this atom? |
372 |
|
373 |
if (AtomToProcMap[i] == worldRank) { |
374 |
|
375 |
if (myPotato + 3 >= MAXTAG) { |
376 |
|
377 |
// The potato was going to exceed the maximum value, |
378 |
// so wrap this processor potato back to 0 (and block until |
379 |
// node 0 says we can go: |
380 |
|
381 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
382 |
|
383 |
} |
384 |
|
385 |
local_index=-1; |
386 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
387 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
388 |
} |
389 |
if (local_index != -1) { |
390 |
|
391 |
atomTypeString = atoms[local_index]->getType(); |
392 |
|
393 |
atoms[local_index]->getPos(pos); |
394 |
atoms[local_index]->getVel(vel); |
395 |
|
396 |
atomData6[0] = pos[0]; |
397 |
atomData6[1] = pos[1]; |
398 |
atomData6[2] = pos[2]; |
399 |
|
400 |
atomData6[3] = vel[0]; |
401 |
atomData6[4] = vel[1]; |
402 |
atomData6[5] = vel[2]; |
403 |
|
404 |
isDirectional = 0; |
405 |
|
406 |
if( atoms[local_index]->isDirectional() ){ |
407 |
|
408 |
isDirectional = 1; |
409 |
|
410 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
411 |
dAtom->getQ( q ); |
412 |
|
413 |
for (int j = 0; j < 6 ; j++) |
414 |
atomData13[j] = atomData6[j]; |
415 |
|
416 |
atomData13[6] = q[0]; |
417 |
atomData13[7] = q[1]; |
418 |
atomData13[8] = q[2]; |
419 |
atomData13[9] = q[3]; |
420 |
|
421 |
atomData13[10] = dAtom->getJx(); |
422 |
atomData13[11] = dAtom->getJy(); |
423 |
atomData13[12] = dAtom->getJz(); |
424 |
} |
425 |
|
426 |
} else { |
427 |
sprintf(painCave.errMsg, |
428 |
"Atom %d not found on processor %d\n", |
429 |
i, worldRank ); |
430 |
haveError= 1; |
431 |
simError(); |
432 |
} |
433 |
|
434 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
435 |
|
436 |
// null terminate the string before sending (just in case): |
437 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
438 |
|
439 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
440 |
myPotato, MPI_COMM_WORLD); |
441 |
|
442 |
myPotato++; |
443 |
|
444 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
445 |
myPotato, MPI_COMM_WORLD); |
446 |
|
447 |
myPotato++; |
448 |
|
449 |
if (isDirectional) { |
450 |
|
451 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
452 |
myPotato, MPI_COMM_WORLD); |
453 |
|
454 |
} else { |
455 |
|
456 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
457 |
myPotato, MPI_COMM_WORLD); |
458 |
} |
459 |
|
460 |
myPotato++; |
461 |
} |
462 |
} |
463 |
|
464 |
sprintf( checkPointMsg, |
465 |
"Sucessfully took a dump.\n"); |
466 |
MPIcheckPoint(); |
467 |
|
468 |
} |
469 |
|
470 |
#endif // is_mpi |
471 |
} |
472 |
|
473 |
void DumpWriter::writeFinal(double finalTime){ |
474 |
|
475 |
char finalName[500]; |
476 |
ofstream finalOut; |
477 |
|
478 |
const int BUFFERSIZE = 2000; |
479 |
const int MINIBUFFERSIZE = 100; |
480 |
char tempBuffer[BUFFERSIZE]; |
481 |
char writeLine[BUFFERSIZE]; |
482 |
|
483 |
double q[4]; |
484 |
DirectionalAtom* dAtom; |
485 |
Atom** atoms = entry_plug->atoms; |
486 |
int i; |
487 |
#ifdef IS_MPI |
488 |
|
489 |
int *potatoes; |
490 |
int myPotato; |
491 |
|
492 |
int nProc; |
493 |
int j, which_node, done, which_atom, local_index; |
494 |
double atomData6[6]; |
495 |
double atomData13[13]; |
496 |
int isDirectional; |
497 |
char* atomTypeString; |
498 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
499 |
|
500 |
#else //is_mpi |
501 |
int nAtoms = entry_plug->n_atoms; |
502 |
#endif //is_mpi |
503 |
|
504 |
double pos[3], vel[3]; |
505 |
|
506 |
#ifdef IS_MPI |
507 |
if(worldRank == 0 ){ |
508 |
#endif // is_mpi |
509 |
|
510 |
strcpy( finalName, entry_plug->finalName ); |
511 |
|
512 |
finalOut.open( finalName, ios::out | ios::trunc ); |
513 |
if( !finalOut ){ |
514 |
sprintf( painCave.errMsg, |
515 |
"Could not open \"%s\" for final dump output.\n", |
516 |
finalName ); |
517 |
painCave.isFatal = 1; |
518 |
simError(); |
519 |
} |
520 |
|
521 |
// finalOut.setf( ios::scientific ); |
522 |
|
523 |
#ifdef IS_MPI |
524 |
} |
525 |
|
526 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
527 |
MPIcheckPoint(); |
528 |
|
529 |
#endif //is_mpi |
530 |
|
531 |
|
532 |
#ifndef IS_MPI |
533 |
|
534 |
finalOut << nAtoms << "\n"; |
535 |
|
536 |
finalOut << finalTime << ";\t" |
537 |
<< entry_plug->Hmat[0][0] << "\t" |
538 |
<< entry_plug->Hmat[1][0] << "\t" |
539 |
<< entry_plug->Hmat[2][0] << ";\t" |
540 |
|
541 |
<< entry_plug->Hmat[0][1] << "\t" |
542 |
<< entry_plug->Hmat[1][1] << "\t" |
543 |
<< entry_plug->Hmat[2][1] << ";\t" |
544 |
|
545 |
<< entry_plug->Hmat[0][2] << "\t" |
546 |
<< entry_plug->Hmat[1][2] << "\t" |
547 |
<< entry_plug->Hmat[2][2] << ";"; |
548 |
|
549 |
//write out additional parameters, such as chi and eta |
550 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
551 |
finalOut << endl; |
552 |
|
553 |
for( i=0; i<nAtoms; i++ ){ |
554 |
|
555 |
atoms[i]->getPos(pos); |
556 |
atoms[i]->getVel(vel); |
557 |
|
558 |
sprintf( tempBuffer, |
559 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
560 |
atoms[i]->getType(), |
561 |
pos[0], |
562 |
pos[1], |
563 |
pos[2], |
564 |
vel[0], |
565 |
vel[1], |
566 |
vel[2]); |
567 |
strcpy( writeLine, tempBuffer ); |
568 |
|
569 |
if( atoms[i]->isDirectional() ){ |
570 |
|
571 |
dAtom = (DirectionalAtom *)atoms[i]; |
572 |
dAtom->getQ( q ); |
573 |
|
574 |
sprintf( tempBuffer, |
575 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
576 |
q[0], |
577 |
q[1], |
578 |
q[2], |
579 |
q[3], |
580 |
dAtom->getJx(), |
581 |
dAtom->getJy(), |
582 |
dAtom->getJz()); |
583 |
strcat( writeLine, tempBuffer ); |
584 |
} |
585 |
else |
586 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
587 |
|
588 |
finalOut << writeLine; |
589 |
} |
590 |
finalOut.flush(); |
591 |
finalOut.close(); |
592 |
|
593 |
#else // is_mpi |
594 |
|
595 |
/* code to find maximum tag value */ |
596 |
int *tagub, flag, MAXTAG; |
597 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
598 |
if (flag) { |
599 |
MAXTAG = *tagub; |
600 |
} else { |
601 |
MAXTAG = 32767; |
602 |
} |
603 |
|
604 |
int haveError; |
605 |
|
606 |
MPI_Status istatus; |
607 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
608 |
|
609 |
// write out header and node 0's coordinates |
610 |
|
611 |
if( worldRank == 0 ){ |
612 |
|
613 |
// Node 0 needs a list of the magic potatoes for each processor; |
614 |
|
615 |
nProc = mpiSim->getNumberProcessors(); |
616 |
potatoes = new int[nProc]; |
617 |
|
618 |
for (i = 0; i < nProc; i++) |
619 |
potatoes[i] = 0; |
620 |
|
621 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
622 |
|
623 |
finalOut << finalTime << ";\t" |
624 |
<< entry_plug->Hmat[0][0] << "\t" |
625 |
<< entry_plug->Hmat[1][0] << "\t" |
626 |
<< entry_plug->Hmat[2][0] << ";\t" |
627 |
|
628 |
<< entry_plug->Hmat[0][1] << "\t" |
629 |
<< entry_plug->Hmat[1][1] << "\t" |
630 |
<< entry_plug->Hmat[2][1] << ";\t" |
631 |
|
632 |
<< entry_plug->Hmat[0][2] << "\t" |
633 |
<< entry_plug->Hmat[1][2] << "\t" |
634 |
<< entry_plug->Hmat[2][2] << ";"; |
635 |
|
636 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
637 |
finalOut << endl; |
638 |
finalOut.flush(); |
639 |
|
640 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
641 |
|
642 |
// Get the Node number which has this atom; |
643 |
|
644 |
which_node = AtomToProcMap[i]; |
645 |
|
646 |
if (which_node != 0) { |
647 |
|
648 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
649 |
// The potato was going to exceed the maximum value, |
650 |
// so wrap this processor potato back to 0: |
651 |
|
652 |
potatoes[which_node] = 0; |
653 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
654 |
|
655 |
} |
656 |
|
657 |
myPotato = potatoes[which_node]; |
658 |
|
659 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
660 |
myPotato, MPI_COMM_WORLD, &istatus); |
661 |
|
662 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
663 |
|
664 |
// Null terminate the atomTypeString just in case: |
665 |
|
666 |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
667 |
|
668 |
myPotato++; |
669 |
|
670 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
671 |
myPotato, MPI_COMM_WORLD, &istatus); |
672 |
|
673 |
myPotato++; |
674 |
|
675 |
if (isDirectional) { |
676 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
677 |
myPotato, MPI_COMM_WORLD, &istatus); |
678 |
} else { |
679 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
680 |
myPotato, MPI_COMM_WORLD, &istatus); |
681 |
} |
682 |
|
683 |
myPotato++; |
684 |
potatoes[which_node] = myPotato; |
685 |
|
686 |
} else { |
687 |
|
688 |
haveError = 0; |
689 |
which_atom = i; |
690 |
local_index=-1; |
691 |
|
692 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
693 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
694 |
} |
695 |
|
696 |
if (local_index != -1) { |
697 |
|
698 |
atomTypeString = atoms[local_index]->getType(); |
699 |
|
700 |
atoms[local_index]->getPos(pos); |
701 |
atoms[local_index]->getVel(vel); |
702 |
|
703 |
atomData6[0] = pos[0]; |
704 |
atomData6[1] = pos[1]; |
705 |
atomData6[2] = pos[2]; |
706 |
|
707 |
atomData6[3] = vel[0]; |
708 |
atomData6[4] = vel[1]; |
709 |
atomData6[5] = vel[2]; |
710 |
|
711 |
isDirectional = 0; |
712 |
|
713 |
if( atoms[local_index]->isDirectional() ){ |
714 |
|
715 |
isDirectional = 1; |
716 |
|
717 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
718 |
dAtom->getQ( q ); |
719 |
|
720 |
for (int j = 0; j < 6 ; j++) |
721 |
atomData13[j] = atomData6[j]; |
722 |
|
723 |
atomData13[6] = q[0]; |
724 |
atomData13[7] = q[1]; |
725 |
atomData13[8] = q[2]; |
726 |
atomData13[9] = q[3]; |
727 |
|
728 |
atomData13[10] = dAtom->getJx(); |
729 |
atomData13[11] = dAtom->getJy(); |
730 |
atomData13[12] = dAtom->getJz(); |
731 |
} |
732 |
|
733 |
} else { |
734 |
sprintf(painCave.errMsg, |
735 |
"Atom %d not found on processor %d\n", |
736 |
i, worldRank ); |
737 |
haveError= 1; |
738 |
simError(); |
739 |
} |
740 |
|
741 |
if(haveError) DieDieDie(); |
742 |
|
743 |
// If we've survived to here, format the line: |
744 |
|
745 |
if (!isDirectional) { |
746 |
|
747 |
sprintf( tempBuffer, |
748 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
749 |
atomTypeString, |
750 |
atomData6[0], |
751 |
atomData6[1], |
752 |
atomData6[2], |
753 |
atomData6[3], |
754 |
atomData6[4], |
755 |
atomData6[5]); |
756 |
|
757 |
strcpy( writeLine, tempBuffer ); |
758 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
759 |
|
760 |
} else { |
761 |
|
762 |
sprintf( tempBuffer, |
763 |
"%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", |
764 |
atomTypeString, |
765 |
atomData13[0], |
766 |
atomData13[1], |
767 |
atomData13[2], |
768 |
atomData13[3], |
769 |
atomData13[4], |
770 |
atomData13[5], |
771 |
atomData13[6], |
772 |
atomData13[7], |
773 |
atomData13[8], |
774 |
atomData13[9], |
775 |
atomData13[10], |
776 |
atomData13[11], |
777 |
atomData13[12]); |
778 |
|
779 |
strcat( writeLine, tempBuffer ); |
780 |
|
781 |
} |
782 |
|
783 |
finalOut << writeLine; |
784 |
finalOut.flush(); |
785 |
} |
786 |
} |
787 |
|
788 |
finalOut.flush(); |
789 |
sprintf( checkPointMsg, |
790 |
"Sucessfully took a dump.\n"); |
791 |
MPIcheckPoint(); |
792 |
|
793 |
} else { |
794 |
|
795 |
// worldRank != 0, so I'm a remote node. |
796 |
|
797 |
// Set my magic potato to 0: |
798 |
|
799 |
myPotato = 0; |
800 |
|
801 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
802 |
|
803 |
// Am I the node which has this atom? |
804 |
|
805 |
if (AtomToProcMap[i] == worldRank) { |
806 |
|
807 |
if (myPotato + 3 >= MAXTAG) { |
808 |
|
809 |
// The potato was going to exceed the maximum value, |
810 |
// so wrap this processor potato back to 0 (and block until |
811 |
// node 0 says we can go: |
812 |
|
813 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
814 |
|
815 |
} |
816 |
|
817 |
local_index=-1; |
818 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
819 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
820 |
} |
821 |
if (local_index != -1) { |
822 |
|
823 |
atomTypeString = atoms[local_index]->getType(); |
824 |
|
825 |
atoms[local_index]->getPos(pos); |
826 |
atoms[local_index]->getVel(vel); |
827 |
|
828 |
atomData6[0] = pos[0]; |
829 |
atomData6[1] = pos[1]; |
830 |
atomData6[2] = pos[2]; |
831 |
|
832 |
atomData6[3] = vel[0]; |
833 |
atomData6[4] = vel[1]; |
834 |
atomData6[5] = vel[2]; |
835 |
|
836 |
isDirectional = 0; |
837 |
|
838 |
if( atoms[local_index]->isDirectional() ){ |
839 |
|
840 |
isDirectional = 1; |
841 |
|
842 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
843 |
dAtom->getQ( q ); |
844 |
|
845 |
for (int j = 0; j < 6 ; j++) |
846 |
atomData13[j] = atomData6[j]; |
847 |
|
848 |
atomData13[6] = q[0]; |
849 |
atomData13[7] = q[1]; |
850 |
atomData13[8] = q[2]; |
851 |
atomData13[9] = q[3]; |
852 |
|
853 |
atomData13[10] = dAtom->getJx(); |
854 |
atomData13[11] = dAtom->getJy(); |
855 |
atomData13[12] = dAtom->getJz(); |
856 |
} |
857 |
|
858 |
} else { |
859 |
sprintf(painCave.errMsg, |
860 |
"Atom %d not found on processor %d\n", |
861 |
i, worldRank ); |
862 |
haveError= 1; |
863 |
simError(); |
864 |
} |
865 |
|
866 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
867 |
|
868 |
// null terminate the string before sending (just in case): |
869 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
870 |
|
871 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
872 |
myPotato, MPI_COMM_WORLD); |
873 |
|
874 |
myPotato++; |
875 |
|
876 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
877 |
myPotato, MPI_COMM_WORLD); |
878 |
|
879 |
myPotato++; |
880 |
|
881 |
if (isDirectional) { |
882 |
|
883 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
884 |
myPotato, MPI_COMM_WORLD); |
885 |
|
886 |
} else { |
887 |
|
888 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
889 |
myPotato, MPI_COMM_WORLD); |
890 |
} |
891 |
|
892 |
myPotato++; |
893 |
} |
894 |
} |
895 |
|
896 |
sprintf( checkPointMsg, |
897 |
"Sucessfully took a dump.\n"); |
898 |
MPIcheckPoint(); |
899 |
|
900 |
} |
901 |
|
902 |
if( worldRank == 0 ) finalOut.close(); |
903 |
#endif // is_mpi |
904 |
} |
905 |
|
906 |
|
907 |
|
908 |
#ifdef IS_MPI |
909 |
|
910 |
// a couple of functions to let us escape the write loop |
911 |
|
912 |
void dWrite::DieDieDie( void ){ |
913 |
|
914 |
MPI_Finalize(); |
915 |
exit (0); |
916 |
} |
917 |
|
918 |
#endif //is_mpi |