1 |
+ |
#define _FILE_OFFSET_BITS 64 |
2 |
+ |
|
3 |
|
#include <cstring> |
4 |
|
#include <iostream> |
5 |
|
#include <fstream> |
77 |
|
DirectionalAtom* dAtom; |
78 |
|
int nAtoms = entry_plug->n_atoms; |
79 |
|
Atom** atoms = entry_plug->atoms; |
80 |
+ |
|
81 |
+ |
double pos[3], vel[3]; |
82 |
|
|
83 |
|
|
84 |
|
#ifndef IS_MPI |
100 |
|
|
101 |
|
for( i=0; i<nAtoms; i++ ){ |
102 |
|
|
103 |
+ |
atoms[i]->getPos(pos); |
104 |
+ |
atoms[i]->getVel(vel); |
105 |
|
|
106 |
|
sprintf( tempBuffer, |
107 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
108 |
|
atoms[i]->getType(), |
109 |
< |
atoms[i]->getX(), |
110 |
< |
atoms[i]->getY(), |
111 |
< |
atoms[i]->getZ(), |
112 |
< |
atoms[i]->get_vx(), |
113 |
< |
atoms[i]->get_vy(), |
114 |
< |
atoms[i]->get_vz()); |
109 |
> |
pos[0], |
110 |
> |
pos[1], |
111 |
> |
pos[2], |
112 |
> |
vel[0], |
113 |
> |
vel[1], |
114 |
> |
vel[2]); |
115 |
|
strcpy( writeLine, tempBuffer ); |
116 |
|
|
117 |
|
if( atoms[i]->isDirectional() ){ |
153 |
|
if( worldRank == 0 ){ |
154 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
155 |
|
|
156 |
< |
outFile << currentTime << "\t" |
157 |
< |
<< entry_plug->Hmat[0] << "\t" |
158 |
< |
<< entry_plug->Hmat[1] << "\t" |
159 |
< |
<< entry_plug->Hmat[2] << "\t" |
156 |
> |
outFile << currentTime << ";\t" |
157 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
158 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
159 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
160 |
|
|
161 |
< |
<< entry_plug->Hmat[3] << "\t" |
162 |
< |
<< entry_plug->Hmat[4] << "\t" |
163 |
< |
<< entry_plug->Hmat[5] << "\t" |
161 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
162 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
163 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
164 |
|
|
165 |
< |
<< entry_plug->Hmat[6] << "\t" |
166 |
< |
<< entry_plug->Hmat[7] << "\t" |
167 |
< |
<< entry_plug->Hmat[8] << "\n"; |
168 |
< |
; |
165 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
166 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
167 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
168 |
> |
|
169 |
|
outFile.flush(); |
170 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
171 |
|
// Get the Node number which has this atom; |
182 |
|
} |
183 |
|
if (local_index != -1) { |
184 |
|
//format the line |
185 |
+ |
|
186 |
+ |
atoms[local_index]->getPos(pos); |
187 |
+ |
atoms[local_index]->getVel(vel); |
188 |
+ |
|
189 |
|
sprintf( tempBuffer, |
190 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
191 |
|
atoms[local_index]->getType(), |
192 |
< |
atoms[local_index]->getX(), |
193 |
< |
atoms[local_index]->getY(), |
194 |
< |
atoms[local_index]->getZ(), |
195 |
< |
atoms[local_index]->get_vx(), |
196 |
< |
atoms[local_index]->get_vy(), |
197 |
< |
atoms[local_index]->get_vz()); // check here. |
192 |
> |
pos[0], |
193 |
> |
pos[1], |
194 |
> |
pos[2], |
195 |
> |
vel[0], |
196 |
> |
vel[1], |
197 |
> |
vel[2]); // check here. |
198 |
|
strcpy( writeLine, tempBuffer ); |
199 |
|
|
200 |
|
if( atoms[local_index]->isDirectional() ){ |
276 |
|
} |
277 |
|
if (local_index != -1) { |
278 |
|
//format the line |
279 |
+ |
|
280 |
+ |
atoms[local_index]->getPos(pos); |
281 |
+ |
atoms[local_index]->getVel(vel); |
282 |
+ |
|
283 |
|
sprintf( tempBuffer, |
284 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
285 |
|
atoms[local_index]->getType(), |
286 |
< |
atoms[local_index]->getX(), |
287 |
< |
atoms[local_index]->getY(), |
288 |
< |
atoms[local_index]->getZ(), |
289 |
< |
atoms[local_index]->get_vx(), |
290 |
< |
atoms[local_index]->get_vy(), |
291 |
< |
atoms[local_index]->get_vz()); // check here. |
286 |
> |
pos[0], |
287 |
> |
pos[1], |
288 |
> |
pos[2], |
289 |
> |
vel[0], |
290 |
> |
vel[1], |
291 |
> |
vel[2]); // check here. |
292 |
|
strcpy( writeLine, tempBuffer ); |
293 |
|
|
294 |
|
if( atoms[local_index]->isDirectional() ){ |
353 |
|
Atom** atoms = entry_plug->atoms; |
354 |
|
int i, j, which_node, done, game_over, which_atom, local_index; |
355 |
|
|
356 |
+ |
double pos[3], vel[3]; |
357 |
|
|
358 |
|
#ifdef IS_MPI |
359 |
|
if(worldRank == 0 ){ |
385 |
|
|
386 |
|
finalOut << nAtoms << "\n"; |
387 |
|
|
388 |
< |
finalOut << finalTime << "\t" |
388 |
> |
finalOut << finalTime << ";\t" |
389 |
|
<< entry_plug->Hmat[0][0] << "\t" |
390 |
|
<< entry_plug->Hmat[1][0] << "\t" |
391 |
< |
<< entry_plug->Hmat[2][0] << "\t" |
391 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
392 |
|
|
393 |
|
<< entry_plug->Hmat[0][1] << "\t" |
394 |
|
<< entry_plug->Hmat[1][1] << "\t" |
395 |
< |
<< entry_plug->Hmat[2][1] << "\t" |
395 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
396 |
|
|
397 |
|
<< entry_plug->Hmat[0][2] << "\t" |
398 |
|
<< entry_plug->Hmat[1][2] << "\t" |
399 |
< |
<< entry_plug->Hmat[2][2] << "\n"; |
399 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
400 |
|
|
401 |
|
for( i=0; i<nAtoms; i++ ){ |
402 |
|
|
403 |
+ |
atoms[i]->getPos(pos); |
404 |
+ |
atoms[i]->getVel(vel); |
405 |
+ |
|
406 |
|
sprintf( tempBuffer, |
407 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
408 |
|
atoms[i]->getType(), |
409 |
< |
atoms[i]->getX(), |
410 |
< |
atoms[i]->getY(), |
411 |
< |
atoms[i]->getZ(), |
412 |
< |
atoms[i]->get_vx(), |
413 |
< |
atoms[i]->get_vy(), |
414 |
< |
atoms[i]->get_vz()); |
409 |
> |
pos[0], |
410 |
> |
pos[1], |
411 |
> |
pos[2], |
412 |
> |
vel[0], |
413 |
> |
vel[1], |
414 |
> |
vel[2]); |
415 |
|
strcpy( writeLine, tempBuffer ); |
416 |
|
|
417 |
|
if( atoms[i]->isDirectional() ){ |
455 |
|
if( worldRank == 0 ){ |
456 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
457 |
|
|
458 |
< |
finalOut << finalTime << "\t" |
459 |
< |
<< entry_plug->Hmat[0] << "\t" |
460 |
< |
<< entry_plug->Hmat[1] << "\t" |
461 |
< |
<< entry_plug->Hmat[2] << "\t" |
458 |
> |
finalOut << finalTime << ";\t" |
459 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
460 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
461 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
462 |
|
|
463 |
< |
<< entry_plug->Hmat[3] << "\t" |
464 |
< |
<< entry_plug->Hmat[4] << "\t" |
465 |
< |
<< entry_plug->Hmat[5] << "\t" |
463 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
464 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
465 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
466 |
|
|
467 |
< |
<< entry_plug->Hmat[6] << "\t" |
468 |
< |
<< entry_plug->Hmat[7] << "\t" |
469 |
< |
<< entry_plug->Hmat[8] << "\n"; |
467 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
468 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
469 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
470 |
|
|
471 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
472 |
|
// Get the Node number which has this molecule: |
480 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
481 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
482 |
|
} |
483 |
< |
if (local_index != -1) { |
483 |
> |
if (local_index != -1) { |
484 |
> |
|
485 |
> |
atoms[local_index]->getPos(pos); |
486 |
> |
atoms[local_index]->getVel(vel); |
487 |
> |
|
488 |
|
sprintf( tempBuffer, |
489 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
490 |
|
atoms[local_index]->getType(), |
491 |
< |
atoms[local_index]->getX(), |
492 |
< |
atoms[local_index]->getY(), |
493 |
< |
atoms[local_index]->getZ(), |
494 |
< |
atoms[local_index]->get_vx(), |
495 |
< |
atoms[local_index]->get_vy(), |
496 |
< |
atoms[local_index]->get_vz()); |
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[local_index]->isDirectional() ){ |
573 |
|
} |
574 |
|
if (local_index != -1) { |
575 |
|
|
576 |
+ |
atoms[local_index]->getPos(pos); |
577 |
+ |
atoms[local_index]->getVel(vel); |
578 |
+ |
|
579 |
|
//format the line |
580 |
|
sprintf( tempBuffer, |
581 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
582 |
|
atoms[local_index]->getType(), |
583 |
< |
atoms[local_index]->getX(), |
584 |
< |
atoms[local_index]->getY(), |
585 |
< |
atoms[local_index]->getZ(), |
586 |
< |
atoms[local_index]->get_vx(), |
587 |
< |
atoms[local_index]->get_vy(), |
588 |
< |
atoms[local_index]->get_vz()); // check here. |
583 |
> |
pos[0], |
584 |
> |
pos[1], |
585 |
> |
pos[2], |
586 |
> |
vel[0], |
587 |
> |
vel[1], |
588 |
> |
vel[2]); // check here. |
589 |
|
strcpy( writeLine, tempBuffer ); |
590 |
|
|
591 |
|
if( atoms[local_index]->isDirectional() ){ |