75 |
|
DirectionalAtom* dAtom; |
76 |
|
int nAtoms = entry_plug->n_atoms; |
77 |
|
Atom** atoms = entry_plug->atoms; |
78 |
+ |
|
79 |
+ |
double pos[3], vel[3]; |
80 |
|
|
81 |
|
|
82 |
|
#ifndef IS_MPI |
83 |
|
|
84 |
|
outFile << nAtoms << "\n"; |
85 |
|
|
86 |
< |
outFile << currentTime << "\t" |
87 |
< |
<< entry_plug->box_x << "\t" |
88 |
< |
<< entry_plug->box_y << "\t" |
89 |
< |
<< entry_plug->box_z << "\n"; |
86 |
> |
outFile << currentTime << ";\t" |
87 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
88 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
89 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
90 |
> |
|
91 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
92 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
93 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
94 |
> |
|
95 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
96 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
97 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
98 |
|
|
99 |
|
for( i=0; i<nAtoms; i++ ){ |
100 |
|
|
101 |
+ |
atoms[i]->getPos(pos); |
102 |
+ |
atoms[i]->getVel(vel); |
103 |
|
|
104 |
|
sprintf( tempBuffer, |
105 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
106 |
|
atoms[i]->getType(), |
107 |
< |
atoms[i]->getX(), |
108 |
< |
atoms[i]->getY(), |
109 |
< |
atoms[i]->getZ(), |
110 |
< |
atoms[i]->get_vx(), |
111 |
< |
atoms[i]->get_vy(), |
112 |
< |
atoms[i]->get_vz()); |
107 |
> |
pos[0], |
108 |
> |
pos[1], |
109 |
> |
pos[2], |
110 |
> |
vel[0], |
111 |
> |
vel[1], |
112 |
> |
vel[2]); |
113 |
|
strcpy( writeLine, tempBuffer ); |
114 |
|
|
115 |
|
if( atoms[i]->isDirectional() ){ |
150 |
|
|
151 |
|
if( worldRank == 0 ){ |
152 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
153 |
+ |
|
154 |
+ |
outFile << currentTime << ";\t" |
155 |
+ |
<< entry_plug->Hmat[0][0] << "\t" |
156 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
157 |
+ |
<< entry_plug->Hmat[2][0] << ";\t" |
158 |
+ |
|
159 |
+ |
<< entry_plug->Hmat[0][1] << "\t" |
160 |
+ |
<< entry_plug->Hmat[1][1] << "\t" |
161 |
+ |
<< entry_plug->Hmat[2][1] << ";\t" |
162 |
+ |
|
163 |
+ |
<< entry_plug->Hmat[0][2] << "\t" |
164 |
+ |
<< entry_plug->Hmat[1][2] << "\t" |
165 |
+ |
<< entry_plug->Hmat[2][2] << ";\n"; |
166 |
|
|
142 |
– |
outFile << currentTime << "\t" |
143 |
– |
<< entry_plug->box_x << "\t" |
144 |
– |
<< entry_plug->box_y << "\t" |
145 |
– |
<< entry_plug->box_z << "\n"; |
167 |
|
outFile.flush(); |
168 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
169 |
|
// Get the Node number which has this atom; |
180 |
|
} |
181 |
|
if (local_index != -1) { |
182 |
|
//format the line |
183 |
+ |
|
184 |
+ |
atoms[local_index]->getPos(pos); |
185 |
+ |
atoms[local_index]->getVel(vel); |
186 |
+ |
|
187 |
|
sprintf( tempBuffer, |
188 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
189 |
|
atoms[local_index]->getType(), |
190 |
< |
atoms[local_index]->getX(), |
191 |
< |
atoms[local_index]->getY(), |
192 |
< |
atoms[local_index]->getZ(), |
193 |
< |
atoms[local_index]->get_vx(), |
194 |
< |
atoms[local_index]->get_vy(), |
195 |
< |
atoms[local_index]->get_vz()); // check here. |
190 |
> |
pos[0], |
191 |
> |
pos[1], |
192 |
> |
pos[2], |
193 |
> |
vel[0], |
194 |
> |
vel[1], |
195 |
> |
vel[2]); // check here. |
196 |
|
strcpy( writeLine, tempBuffer ); |
197 |
|
|
198 |
|
if( atoms[local_index]->isDirectional() ){ |
274 |
|
} |
275 |
|
if (local_index != -1) { |
276 |
|
//format the line |
277 |
+ |
|
278 |
+ |
atoms[local_index]->getPos(pos); |
279 |
+ |
atoms[local_index]->getVel(vel); |
280 |
+ |
|
281 |
|
sprintf( tempBuffer, |
282 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
283 |
|
atoms[local_index]->getType(), |
284 |
< |
atoms[local_index]->getX(), |
285 |
< |
atoms[local_index]->getY(), |
286 |
< |
atoms[local_index]->getZ(), |
287 |
< |
atoms[local_index]->get_vx(), |
288 |
< |
atoms[local_index]->get_vy(), |
289 |
< |
atoms[local_index]->get_vz()); // check here. |
284 |
> |
pos[0], |
285 |
> |
pos[1], |
286 |
> |
pos[2], |
287 |
> |
vel[0], |
288 |
> |
vel[1], |
289 |
> |
vel[2]); // check here. |
290 |
|
strcpy( writeLine, tempBuffer ); |
291 |
|
|
292 |
|
if( atoms[local_index]->isDirectional() ){ |
336 |
|
#endif // is_mpi |
337 |
|
} |
338 |
|
|
339 |
< |
void DumpWriter::writeFinal(){ |
339 |
> |
void DumpWriter::writeFinal(double finalTime){ |
340 |
|
|
341 |
|
char finalName[500]; |
342 |
|
ofstream finalOut; |
351 |
|
Atom** atoms = entry_plug->atoms; |
352 |
|
int i, j, which_node, done, game_over, which_atom, local_index; |
353 |
|
|
354 |
+ |
double pos[3], vel[3]; |
355 |
|
|
356 |
|
#ifdef IS_MPI |
357 |
|
if(worldRank == 0 ){ |
383 |
|
|
384 |
|
finalOut << nAtoms << "\n"; |
385 |
|
|
386 |
< |
finalOut << entry_plug->box_x << "\t" |
387 |
< |
<< entry_plug->box_y << "\t" |
388 |
< |
<< entry_plug->box_z << "\n"; |
386 |
> |
finalOut << finalTime << ";\t" |
387 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
388 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
389 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
390 |
> |
|
391 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
392 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
393 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
394 |
> |
|
395 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
396 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
397 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
398 |
|
|
399 |
|
for( i=0; i<nAtoms; i++ ){ |
400 |
|
|
401 |
+ |
atoms[i]->getPos(pos); |
402 |
+ |
atoms[i]->getVel(vel); |
403 |
+ |
|
404 |
|
sprintf( tempBuffer, |
405 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
406 |
|
atoms[i]->getType(), |
407 |
< |
atoms[i]->getX(), |
408 |
< |
atoms[i]->getY(), |
409 |
< |
atoms[i]->getZ(), |
410 |
< |
atoms[i]->get_vx(), |
411 |
< |
atoms[i]->get_vy(), |
412 |
< |
atoms[i]->get_vz()); |
407 |
> |
pos[0], |
408 |
> |
pos[1], |
409 |
> |
pos[2], |
410 |
> |
vel[0], |
411 |
> |
vel[1], |
412 |
> |
vel[2]); |
413 |
|
strcpy( writeLine, tempBuffer ); |
414 |
|
|
415 |
|
if( atoms[i]->isDirectional() ){ |
453 |
|
if( worldRank == 0 ){ |
454 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
455 |
|
|
456 |
< |
finalOut << entry_plug->box_x << "\t" |
457 |
< |
<< entry_plug->box_y << "\t" |
458 |
< |
<< entry_plug->box_z << "\n"; |
456 |
> |
finalOut << finalTime << ";\t" |
457 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
458 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
459 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
460 |
> |
|
461 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
462 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
463 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
464 |
> |
|
465 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
466 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
467 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
468 |
|
|
469 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
470 |
|
// Get the Node number which has this molecule: |
478 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
479 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
480 |
|
} |
481 |
< |
if (local_index != -1) { |
481 |
> |
if (local_index != -1) { |
482 |
> |
|
483 |
> |
atoms[local_index]->getPos(pos); |
484 |
> |
atoms[local_index]->getVel(vel); |
485 |
> |
|
486 |
|
sprintf( tempBuffer, |
487 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
488 |
|
atoms[local_index]->getType(), |
489 |
< |
atoms[local_index]->getX(), |
490 |
< |
atoms[local_index]->getY(), |
491 |
< |
atoms[local_index]->getZ(), |
492 |
< |
atoms[local_index]->get_vx(), |
493 |
< |
atoms[local_index]->get_vy(), |
494 |
< |
atoms[local_index]->get_vz()); |
489 |
> |
pos[0], |
490 |
> |
pos[1], |
491 |
> |
pos[2], |
492 |
> |
vel[0], |
493 |
> |
vel[1], |
494 |
> |
vel[2]); |
495 |
|
strcpy( writeLine, tempBuffer ); |
496 |
|
|
497 |
|
if( atoms[local_index]->isDirectional() ){ |
571 |
|
} |
572 |
|
if (local_index != -1) { |
573 |
|
|
574 |
+ |
atoms[local_index]->getPos(pos); |
575 |
+ |
atoms[local_index]->getVel(vel); |
576 |
+ |
|
577 |
|
//format the line |
578 |
|
sprintf( tempBuffer, |
579 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
580 |
|
atoms[local_index]->getType(), |
581 |
< |
atoms[local_index]->getX(), |
582 |
< |
atoms[local_index]->getY(), |
583 |
< |
atoms[local_index]->getZ(), |
584 |
< |
atoms[local_index]->get_vx(), |
585 |
< |
atoms[local_index]->get_vy(), |
586 |
< |
atoms[local_index]->get_vz()); // check here. |
581 |
> |
pos[0], |
582 |
> |
pos[1], |
583 |
> |
pos[2], |
584 |
> |
vel[0], |
585 |
> |
vel[1], |
586 |
> |
vel[2]); // check here. |
587 |
|
strcpy( writeLine, tempBuffer ); |
588 |
|
|
589 |
|
if( atoms[local_index]->isDirectional() ){ |