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 = 10; |
70 |
|
71 |
char tempBuffer[BUFFERSIZE]; |
72 |
char writeLine[BUFFERSIZE]; |
73 |
|
74 |
int i; |
75 |
#ifdef IS_MPI |
76 |
int j, which_node, done, which_atom, local_index; |
77 |
double atomTransData[6]; |
78 |
double atomOrientData[7]; |
79 |
int isDirectional; |
80 |
char* atomTypeString; |
81 |
int me; |
82 |
int atomTypeTag; |
83 |
int atomIsDirectionalTag; |
84 |
int atomTransDataTag; |
85 |
int atomOrientDataTag; |
86 |
#else //is_mpi |
87 |
int nAtoms = entry_plug->n_atoms; |
88 |
#endif //is_mpi |
89 |
|
90 |
double q[4]; |
91 |
DirectionalAtom* dAtom; |
92 |
Atom** atoms = entry_plug->atoms; |
93 |
double pos[3], vel[3]; |
94 |
|
95 |
// write current frame to the eor file |
96 |
|
97 |
this->writeFinal( currentTime ); |
98 |
|
99 |
#ifndef IS_MPI |
100 |
|
101 |
outFile << nAtoms << "\n"; |
102 |
|
103 |
outFile << currentTime << ";\t" |
104 |
<< entry_plug->Hmat[0][0] << "\t" |
105 |
<< entry_plug->Hmat[1][0] << "\t" |
106 |
<< entry_plug->Hmat[2][0] << ";\t" |
107 |
|
108 |
<< entry_plug->Hmat[0][1] << "\t" |
109 |
<< entry_plug->Hmat[1][1] << "\t" |
110 |
<< entry_plug->Hmat[2][1] << ";\t" |
111 |
|
112 |
<< entry_plug->Hmat[0][2] << "\t" |
113 |
<< entry_plug->Hmat[1][2] << "\t" |
114 |
<< entry_plug->Hmat[2][2] << ";"; |
115 |
//write out additional parameters, such as chi and eta |
116 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
117 |
outFile << endl; |
118 |
|
119 |
for( i=0; i<nAtoms; i++ ){ |
120 |
|
121 |
atoms[i]->getPos(pos); |
122 |
atoms[i]->getVel(vel); |
123 |
|
124 |
sprintf( tempBuffer, |
125 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
126 |
atoms[i]->getType(), |
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pos[0], |
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pos[1], |
129 |
pos[2], |
130 |
vel[0], |
131 |
vel[1], |
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vel[2]); |
133 |
strcpy( writeLine, tempBuffer ); |
134 |
|
135 |
if( atoms[i]->isDirectional() ){ |
136 |
|
137 |
dAtom = (DirectionalAtom *)atoms[i]; |
138 |
dAtom->getQ( q ); |
139 |
|
140 |
sprintf( tempBuffer, |
141 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
143 |
q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
148 |
dAtom->getJz()); |
149 |
strcat( writeLine, tempBuffer ); |
150 |
} |
151 |
else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
153 |
|
154 |
outFile << writeLine; |
155 |
} |
156 |
outFile.flush(); |
157 |
|
158 |
#else // is_mpi |
159 |
|
160 |
// first thing first, suspend fatalities. |
161 |
painCave.isEventLoop = 1; |
162 |
|
163 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
164 |
int haveError; |
165 |
|
166 |
MPI_Status istatus; |
167 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
168 |
|
169 |
// write out header and node 0's coordinates |
170 |
|
171 |
if( worldRank == 0 ){ |
172 |
outFile << mpiSim->getTotAtoms() << "\n"; |
173 |
|
174 |
outFile << currentTime << ";\t" |
175 |
<< entry_plug->Hmat[0][0] << "\t" |
176 |
<< entry_plug->Hmat[1][0] << "\t" |
177 |
<< entry_plug->Hmat[2][0] << ";\t" |
178 |
|
179 |
<< entry_plug->Hmat[0][1] << "\t" |
180 |
<< entry_plug->Hmat[1][1] << "\t" |
181 |
<< entry_plug->Hmat[2][1] << ";\t" |
182 |
|
183 |
<< entry_plug->Hmat[0][2] << "\t" |
184 |
<< entry_plug->Hmat[1][2] << "\t" |
185 |
<< entry_plug->Hmat[2][2] << ";"; |
186 |
|
187 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
188 |
outFile << endl; |
189 |
outFile.flush(); |
190 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
191 |
// Get the Node number which has this atom; |
192 |
|
193 |
which_node = AtomToProcMap[i]; |
194 |
|
195 |
if (which_node != 0) { |
196 |
|
197 |
atomTypeTag = 4*i; |
198 |
atomIsDirectionalTag = 4*i + 1; |
199 |
atomTransDataTag = 4*i + 2; |
200 |
atomOrientDataTag = 4*i + 3; |
201 |
|
202 |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
203 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
204 |
|
205 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
206 |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
207 |
|
208 |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
209 |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
210 |
|
211 |
if (isDirectional) { |
212 |
|
213 |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
214 |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
215 |
|
216 |
} |
217 |
|
218 |
} else { |
219 |
|
220 |
haveError = 0; |
221 |
which_atom = i; |
222 |
local_index=-1; |
223 |
|
224 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
225 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
226 |
} |
227 |
|
228 |
if (local_index != -1) { |
229 |
|
230 |
atomTypeString = atoms[local_index]->getType(); |
231 |
|
232 |
atoms[local_index]->getPos(pos); |
233 |
atoms[local_index]->getVel(vel); |
234 |
|
235 |
atomTransData[0] = pos[0]; |
236 |
atomTransData[1] = pos[1]; |
237 |
atomTransData[2] = pos[2]; |
238 |
|
239 |
atomTransData[3] = vel[0]; |
240 |
atomTransData[4] = vel[1]; |
241 |
atomTransData[5] = vel[2]; |
242 |
|
243 |
isDirectional = 0; |
244 |
|
245 |
if( atoms[local_index]->isDirectional() ){ |
246 |
|
247 |
isDirectional = 1; |
248 |
|
249 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
250 |
dAtom->getQ( q ); |
251 |
|
252 |
atomOrientData[0] = q[0]; |
253 |
atomOrientData[1] = q[1]; |
254 |
atomOrientData[2] = q[2]; |
255 |
atomOrientData[3] = q[3]; |
256 |
|
257 |
atomOrientData[4] = dAtom->getJx(); |
258 |
atomOrientData[5] = dAtom->getJy(); |
259 |
atomOrientData[6] = dAtom->getJz(); |
260 |
} |
261 |
|
262 |
} else { |
263 |
sprintf(painCave.errMsg, |
264 |
"Atom %d not found on processor %d\n", |
265 |
i, worldRank ); |
266 |
haveError= 1; |
267 |
simError(); |
268 |
} |
269 |
|
270 |
if(haveError) DieDieDie(); |
271 |
|
272 |
// If we've survived to here, format the line: |
273 |
|
274 |
sprintf( tempBuffer, |
275 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
276 |
atomTypeString, |
277 |
atomTransData[0], |
278 |
atomTransData[1], |
279 |
atomTransData[2], |
280 |
atomTransData[3], |
281 |
atomTransData[4], |
282 |
atomTransData[5]); |
283 |
|
284 |
strcpy( writeLine, tempBuffer ); |
285 |
|
286 |
if (isDirectional) { |
287 |
|
288 |
sprintf( tempBuffer, |
289 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
290 |
atomOrientData[0], |
291 |
atomOrientData[1], |
292 |
atomOrientData[2], |
293 |
atomOrientData[3], |
294 |
atomOrientData[4], |
295 |
atomOrientData[5], |
296 |
atomOrientData[6]); |
297 |
strcat( writeLine, tempBuffer ); |
298 |
|
299 |
} else { |
300 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
301 |
} |
302 |
|
303 |
outFile << writeLine; |
304 |
outFile.flush(); |
305 |
} |
306 |
} |
307 |
|
308 |
outFile.flush(); |
309 |
sprintf( checkPointMsg, |
310 |
"Sucessfully took a dump.\n"); |
311 |
MPIcheckPoint(); |
312 |
|
313 |
} else { |
314 |
|
315 |
// worldRank != 0, so I'm a remote node. |
316 |
|
317 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
318 |
|
319 |
// Am I the node which has this atom? |
320 |
|
321 |
if (AtomToProcMap[i] == worldRank) { |
322 |
|
323 |
local_index=-1; |
324 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
325 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
326 |
} |
327 |
if (local_index != -1) { |
328 |
|
329 |
atomTypeString = atoms[local_index]->getType(); |
330 |
|
331 |
atoms[local_index]->getPos(pos); |
332 |
atoms[local_index]->getVel(vel); |
333 |
|
334 |
atomTransData[0] = pos[0]; |
335 |
atomTransData[1] = pos[1]; |
336 |
atomTransData[2] = pos[2]; |
337 |
|
338 |
atomTransData[3] = vel[0]; |
339 |
atomTransData[4] = vel[1]; |
340 |
atomTransData[5] = vel[2]; |
341 |
|
342 |
isDirectional = 0; |
343 |
|
344 |
if( atoms[local_index]->isDirectional() ){ |
345 |
|
346 |
isDirectional = 1; |
347 |
|
348 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
349 |
dAtom->getQ( q ); |
350 |
|
351 |
atomOrientData[0] = q[0]; |
352 |
atomOrientData[1] = q[1]; |
353 |
atomOrientData[2] = q[2]; |
354 |
atomOrientData[3] = q[3]; |
355 |
|
356 |
atomOrientData[4] = dAtom->getJx(); |
357 |
atomOrientData[5] = dAtom->getJy(); |
358 |
atomOrientData[6] = dAtom->getJz(); |
359 |
} |
360 |
|
361 |
} else { |
362 |
sprintf(painCave.errMsg, |
363 |
"Atom %d not found on processor %d\n", |
364 |
i, worldRank ); |
365 |
haveError= 1; |
366 |
simError(); |
367 |
} |
368 |
|
369 |
// I've survived this far, so send off the data! |
370 |
|
371 |
atomTypeTag = 4*i; |
372 |
atomIsDirectionalTag = 4*i + 1; |
373 |
atomTransDataTag = 4*i + 2; |
374 |
atomOrientDataTag = 4*i + 3; |
375 |
|
376 |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
377 |
atomTypeTag, MPI_COMM_WORLD); |
378 |
|
379 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
380 |
atomIsDirectionalTag, MPI_COMM_WORLD); |
381 |
|
382 |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
383 |
atomTransDataTag, MPI_COMM_WORLD); |
384 |
|
385 |
if (isDirectional) { |
386 |
|
387 |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
388 |
atomOrientDataTag, MPI_COMM_WORLD); |
389 |
|
390 |
} |
391 |
|
392 |
} |
393 |
} |
394 |
|
395 |
sprintf( checkPointMsg, |
396 |
"Sucessfully took a dump.\n"); |
397 |
MPIcheckPoint(); |
398 |
|
399 |
} |
400 |
|
401 |
painCave.isEventLoop = 0; |
402 |
|
403 |
#endif // is_mpi |
404 |
} |
405 |
|
406 |
void DumpWriter::writeFinal(double finalTime){ |
407 |
|
408 |
char finalName[500]; |
409 |
ofstream finalOut; |
410 |
|
411 |
const int BUFFERSIZE = 2000; |
412 |
const int MINIBUFFERSIZE = 10; |
413 |
char tempBuffer[BUFFERSIZE]; |
414 |
char writeLine[BUFFERSIZE]; |
415 |
|
416 |
double q[4]; |
417 |
DirectionalAtom* dAtom; |
418 |
Atom** atoms = entry_plug->atoms; |
419 |
int i; |
420 |
#ifdef IS_MPI |
421 |
int j, which_node, done, which_atom, local_index; |
422 |
double atomTransData[6]; |
423 |
double atomOrientData[7]; |
424 |
int isDirectional; |
425 |
char* atomTypeString; |
426 |
int atomTypeTag; |
427 |
int atomIsDirectionalTag; |
428 |
int atomTransDataTag; |
429 |
int atomOrientDataTag; |
430 |
#else //is_mpi |
431 |
int nAtoms = entry_plug->n_atoms; |
432 |
#endif //is_mpi |
433 |
|
434 |
double pos[3], vel[3]; |
435 |
|
436 |
#ifdef IS_MPI |
437 |
if(worldRank == 0 ){ |
438 |
#endif // is_mpi |
439 |
|
440 |
strcpy( finalName, entry_plug->finalName ); |
441 |
|
442 |
finalOut.open( finalName, ios::out | ios::trunc ); |
443 |
if( !finalOut ){ |
444 |
sprintf( painCave.errMsg, |
445 |
"Could not open \"%s\" for final dump output.\n", |
446 |
finalName ); |
447 |
painCave.isFatal = 1; |
448 |
simError(); |
449 |
} |
450 |
|
451 |
// finalOut.setf( ios::scientific ); |
452 |
|
453 |
#ifdef IS_MPI |
454 |
} |
455 |
|
456 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
457 |
MPIcheckPoint(); |
458 |
|
459 |
#endif //is_mpi |
460 |
|
461 |
|
462 |
#ifndef IS_MPI |
463 |
|
464 |
finalOut << nAtoms << "\n"; |
465 |
|
466 |
finalOut << finalTime << ";\t" |
467 |
<< entry_plug->Hmat[0][0] << "\t" |
468 |
<< entry_plug->Hmat[1][0] << "\t" |
469 |
<< entry_plug->Hmat[2][0] << ";\t" |
470 |
|
471 |
<< entry_plug->Hmat[0][1] << "\t" |
472 |
<< entry_plug->Hmat[1][1] << "\t" |
473 |
<< entry_plug->Hmat[2][1] << ";\t" |
474 |
|
475 |
<< entry_plug->Hmat[0][2] << "\t" |
476 |
<< entry_plug->Hmat[1][2] << "\t" |
477 |
<< entry_plug->Hmat[2][2] << ";"; |
478 |
|
479 |
//write out additional parameters, such as chi and eta |
480 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
481 |
finalOut << endl; |
482 |
|
483 |
for( i=0; i<nAtoms; i++ ){ |
484 |
|
485 |
atoms[i]->getPos(pos); |
486 |
atoms[i]->getVel(vel); |
487 |
|
488 |
sprintf( tempBuffer, |
489 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
490 |
atoms[i]->getType(), |
491 |
pos[0], |
492 |
pos[1], |
493 |
pos[2], |
494 |
vel[0], |
495 |
vel[1], |
496 |
vel[2]); |
497 |
strcpy( writeLine, tempBuffer ); |
498 |
|
499 |
if( atoms[i]->isDirectional() ){ |
500 |
|
501 |
dAtom = (DirectionalAtom *)atoms[i]; |
502 |
dAtom->getQ( q ); |
503 |
|
504 |
sprintf( tempBuffer, |
505 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
506 |
q[0], |
507 |
q[1], |
508 |
q[2], |
509 |
q[3], |
510 |
dAtom->getJx(), |
511 |
dAtom->getJy(), |
512 |
dAtom->getJz()); |
513 |
strcat( writeLine, tempBuffer ); |
514 |
} |
515 |
else |
516 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
517 |
|
518 |
finalOut << writeLine; |
519 |
} |
520 |
finalOut.flush(); |
521 |
finalOut.close(); |
522 |
|
523 |
#else // is_mpi |
524 |
|
525 |
// first thing first, suspend fatalities. |
526 |
painCave.isEventLoop = 1; |
527 |
|
528 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
529 |
int haveError; |
530 |
|
531 |
MPI_Status istatus; |
532 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
533 |
|
534 |
// write out header and node 0's coordinates |
535 |
|
536 |
if( worldRank == 0 ){ |
537 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
538 |
|
539 |
finalOut << finalTime << ";\t" |
540 |
<< entry_plug->Hmat[0][0] << "\t" |
541 |
<< entry_plug->Hmat[1][0] << "\t" |
542 |
<< entry_plug->Hmat[2][0] << ";\t" |
543 |
|
544 |
<< entry_plug->Hmat[0][1] << "\t" |
545 |
<< entry_plug->Hmat[1][1] << "\t" |
546 |
<< entry_plug->Hmat[2][1] << ";\t" |
547 |
|
548 |
<< entry_plug->Hmat[0][2] << "\t" |
549 |
<< entry_plug->Hmat[1][2] << "\t" |
550 |
<< entry_plug->Hmat[2][2] << ";"; |
551 |
|
552 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
553 |
finalOut << endl; |
554 |
finalOut.flush(); |
555 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
556 |
// Get the Node number which has this atom; |
557 |
|
558 |
which_node = AtomToProcMap[i]; |
559 |
|
560 |
if (which_node != 0) { |
561 |
|
562 |
atomTypeTag = 4*i; |
563 |
atomIsDirectionalTag = 4*i + 1; |
564 |
atomTransDataTag = 4*i + 2; |
565 |
atomOrientDataTag = 4*i + 3; |
566 |
|
567 |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
568 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
569 |
|
570 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
571 |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
572 |
|
573 |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
574 |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
575 |
|
576 |
if (isDirectional) { |
577 |
|
578 |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
579 |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
580 |
|
581 |
} |
582 |
|
583 |
} else { |
584 |
|
585 |
haveError = 0; |
586 |
which_atom = i; |
587 |
local_index=-1; |
588 |
|
589 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
590 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
591 |
} |
592 |
|
593 |
if (local_index != -1) { |
594 |
|
595 |
atomTypeString = atoms[local_index]->getType(); |
596 |
|
597 |
atoms[local_index]->getPos(pos); |
598 |
atoms[local_index]->getVel(vel); |
599 |
|
600 |
atomTransData[0] = pos[0]; |
601 |
atomTransData[1] = pos[1]; |
602 |
atomTransData[2] = pos[2]; |
603 |
|
604 |
atomTransData[3] = vel[0]; |
605 |
atomTransData[4] = vel[1]; |
606 |
atomTransData[5] = vel[2]; |
607 |
|
608 |
isDirectional = 0; |
609 |
|
610 |
if( atoms[local_index]->isDirectional() ){ |
611 |
|
612 |
isDirectional = 1; |
613 |
|
614 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
615 |
dAtom->getQ( q ); |
616 |
|
617 |
atomOrientData[0] = q[0]; |
618 |
atomOrientData[1] = q[1]; |
619 |
atomOrientData[2] = q[2]; |
620 |
atomOrientData[3] = q[3]; |
621 |
|
622 |
atomOrientData[4] = dAtom->getJx(); |
623 |
atomOrientData[5] = dAtom->getJy(); |
624 |
atomOrientData[6] = dAtom->getJz(); |
625 |
} |
626 |
|
627 |
} else { |
628 |
sprintf(painCave.errMsg, |
629 |
"Atom %d not found on processor %d\n", |
630 |
i, worldRank ); |
631 |
haveError= 1; |
632 |
simError(); |
633 |
} |
634 |
|
635 |
if(haveError) DieDieDie(); |
636 |
|
637 |
// If we've survived to here, format the line: |
638 |
|
639 |
sprintf( tempBuffer, |
640 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
641 |
atomTypeString, |
642 |
atomTransData[0], |
643 |
atomTransData[1], |
644 |
atomTransData[2], |
645 |
atomTransData[3], |
646 |
atomTransData[4], |
647 |
atomTransData[5]); |
648 |
|
649 |
strcpy( writeLine, tempBuffer ); |
650 |
|
651 |
if (isDirectional) { |
652 |
|
653 |
sprintf( tempBuffer, |
654 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
655 |
atomOrientData[0], |
656 |
atomOrientData[1], |
657 |
atomOrientData[2], |
658 |
atomOrientData[3], |
659 |
atomOrientData[4], |
660 |
atomOrientData[5], |
661 |
atomOrientData[6]); |
662 |
strcat( writeLine, tempBuffer ); |
663 |
|
664 |
} else { |
665 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
666 |
} |
667 |
|
668 |
finalOut << writeLine; |
669 |
finalOut.flush(); |
670 |
} |
671 |
} |
672 |
|
673 |
finalOut.flush(); |
674 |
sprintf( checkPointMsg, |
675 |
"Sucessfully took a dump.\n"); |
676 |
MPIcheckPoint(); |
677 |
|
678 |
} else { |
679 |
|
680 |
// worldRank != 0, so I'm a remote node. |
681 |
|
682 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
683 |
|
684 |
// Am I the node which has this atom? |
685 |
|
686 |
if (AtomToProcMap[i] == worldRank) { |
687 |
|
688 |
local_index=-1; |
689 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
690 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
691 |
} |
692 |
if (local_index != -1) { |
693 |
|
694 |
atomTypeString = atoms[local_index]->getType(); |
695 |
|
696 |
atoms[local_index]->getPos(pos); |
697 |
atoms[local_index]->getVel(vel); |
698 |
|
699 |
atomTransData[0] = pos[0]; |
700 |
atomTransData[1] = pos[1]; |
701 |
atomTransData[2] = pos[2]; |
702 |
|
703 |
atomTransData[3] = vel[0]; |
704 |
atomTransData[4] = vel[1]; |
705 |
atomTransData[5] = vel[2]; |
706 |
|
707 |
isDirectional = 0; |
708 |
|
709 |
if( atoms[local_index]->isDirectional() ){ |
710 |
|
711 |
isDirectional = 1; |
712 |
|
713 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
714 |
dAtom->getQ( q ); |
715 |
|
716 |
atomOrientData[0] = q[0]; |
717 |
atomOrientData[1] = q[1]; |
718 |
atomOrientData[2] = q[2]; |
719 |
atomOrientData[3] = q[3]; |
720 |
|
721 |
atomOrientData[4] = dAtom->getJx(); |
722 |
atomOrientData[5] = dAtom->getJy(); |
723 |
atomOrientData[6] = dAtom->getJz(); |
724 |
} |
725 |
|
726 |
} else { |
727 |
sprintf(painCave.errMsg, |
728 |
"Atom %d not found on processor %d\n", |
729 |
i, worldRank ); |
730 |
haveError= 1; |
731 |
simError(); |
732 |
} |
733 |
|
734 |
// I've survived this far, so send off the data! |
735 |
|
736 |
atomTypeTag = 4*i; |
737 |
atomIsDirectionalTag = 4*i + 1; |
738 |
atomTransDataTag = 4*i + 2; |
739 |
atomOrientDataTag = 4*i + 3; |
740 |
|
741 |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
742 |
atomTypeTag, MPI_COMM_WORLD); |
743 |
|
744 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
745 |
atomIsDirectionalTag, MPI_COMM_WORLD); |
746 |
|
747 |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
748 |
atomTransDataTag, MPI_COMM_WORLD); |
749 |
|
750 |
if (isDirectional) { |
751 |
|
752 |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
753 |
atomOrientDataTag, MPI_COMM_WORLD); |
754 |
|
755 |
} |
756 |
|
757 |
} |
758 |
} |
759 |
|
760 |
sprintf( checkPointMsg, |
761 |
"Sucessfully wrote final file.\n"); |
762 |
MPIcheckPoint(); |
763 |
|
764 |
} |
765 |
|
766 |
painCave.isEventLoop = 0; |
767 |
|
768 |
if( worldRank == 0 ) finalOut.close(); |
769 |
#endif // is_mpi |
770 |
} |
771 |
|
772 |
|
773 |
|
774 |
#ifdef IS_MPI |
775 |
|
776 |
// a couple of functions to let us escape the write loop |
777 |
|
778 |
void dWrite::DieDieDie( void ){ |
779 |
|
780 |
MPI_Finalize(); |
781 |
exit (0); |
782 |
} |
783 |
|
784 |
#endif //is_mpi |