120 |
|
double dt2; // half the dt |
121 |
|
|
122 |
|
double vx, vy, vz; // the velocities |
123 |
< |
double vx2, vy2, vz2; // the square of the velocities |
123 |
> |
// double vx2, vy2, vz2; // the square of the velocities |
124 |
|
double rx, ry, rz; // the postitions |
125 |
|
|
126 |
|
double ji[3]; // the body frame angular momentum |
129 |
|
double angle; // the angle through which to rotate the rotation matrix |
130 |
|
double A[3][3]; // the rotation matrix |
131 |
|
|
132 |
+ |
int time; |
133 |
|
|
134 |
|
double dt = entry_plug->dt; |
135 |
|
double runTime = entry_plug->run_time; |
171 |
|
tStats->velocitize(); |
172 |
|
} |
173 |
|
|
174 |
+ |
dump_out->writeDump( 0.0 ); |
175 |
+ |
e_out->writeStat( 0.0 ); |
176 |
+ |
|
177 |
|
if( n_constrained ){ |
178 |
|
|
179 |
|
double *Rx = new double[nAtoms]; |
362 |
|
dAtom->setJz( ji[2] ); |
363 |
|
} |
364 |
|
} |
365 |
< |
|
366 |
< |
if( entry_plug->setTemp ){ |
367 |
< |
if( !(tl % vel_n) ) tStats->velocitize(); |
365 |
> |
|
366 |
> |
time = tl + 1; |
367 |
> |
|
368 |
> |
if( entry_plug->setTemp ){ |
369 |
> |
if( !(time % vel_n) ) tStats->velocitize(); |
370 |
|
} |
371 |
< |
if( !(tl % sample_n) ) dump_out->writeDump( tl * dt ); |
372 |
< |
if( !(tl % status_n) ) e_out->writeStat( tl * dt ); |
371 |
> |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
372 |
> |
if( !(time % status_n) ) e_out->writeStat( time * dt ); |
373 |
|
} |
374 |
|
} |
375 |
|
else{ |
492 |
|
atoms[i]->set_vy( vy ); |
493 |
|
atoms[i]->set_vz( vz ); |
494 |
|
|
495 |
< |
vx2 = vx * vx; |
496 |
< |
vy2 = vy * vy; |
497 |
< |
vz2 = vz * vz; |
495 |
> |
// vx2 = vx * vx; |
496 |
> |
// vy2 = vy * vy; |
497 |
> |
// vz2 = vz * vz; |
498 |
|
|
499 |
|
if( atoms[i]->isDirectional() ){ |
500 |
|
|
527 |
|
dAtom->setJz( ji[2] ); |
528 |
|
} |
529 |
|
} |
530 |
< |
|
530 |
> |
|
531 |
> |
time = tl + 1; |
532 |
> |
|
533 |
|
if( entry_plug->setTemp ){ |
534 |
< |
if( !(tl % vel_n) ) tStats->velocitize(); |
534 |
> |
if( !(time % vel_n) ) tStats->velocitize(); |
535 |
|
} |
536 |
< |
if( !(tl % sample_n) ) dump_out->writeDump( tl * dt ); |
537 |
< |
if( !(tl % status_n) ) e_out->writeStat( tl * dt ); |
536 |
> |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
537 |
> |
if( !(time % status_n) ) e_out->writeStat( time * dt ); |
538 |
|
} |
539 |
|
} |
540 |
|
|