479 |
|
|
480 |
|
// get some of the tricky things that may still be in the globals |
481 |
|
|
482 |
< |
|
482 |
> |
double boxVector[3]; |
483 |
|
if( the_globals->haveBox() ){ |
484 |
< |
simnfo->box_x = the_globals->getBox(); |
485 |
< |
simnfo->box_y = the_globals->getBox(); |
486 |
< |
simnfo->box_z = the_globals->getBox(); |
484 |
> |
boxVector[0] = the_globals->getBox(); |
485 |
> |
boxVector[1] = the_globals->getBox(); |
486 |
> |
boxVector[2] = the_globals->getBox(); |
487 |
> |
|
488 |
> |
simnfo->setBox( boxVector ); |
489 |
|
} |
490 |
|
else if( the_globals->haveDensity() ){ |
491 |
|
|
492 |
|
double vol; |
493 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
494 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
495 |
< |
simnfo->box_y = simnfo->box_x; |
496 |
< |
simnfo->box_z = simnfo->box_x; |
494 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
495 |
> |
boxVector[1] = boxVector[0]; |
496 |
> |
boxVector[2] = boxVector[0]; |
497 |
> |
|
498 |
> |
simnfo->setBox( boxVector ); |
499 |
|
} |
500 |
|
else{ |
501 |
|
if( !the_globals->haveBoxX() ){ |
504 |
|
painCave.isFatal = 1; |
505 |
|
simError(); |
506 |
|
} |
507 |
< |
simnfo->box_x = the_globals->getBoxX(); |
507 |
> |
boxVector[0] = the_globals->getBoxX(); |
508 |
|
|
509 |
|
if( !the_globals->haveBoxY() ){ |
510 |
|
sprintf( painCave.errMsg, |
512 |
|
painCave.isFatal = 1; |
513 |
|
simError(); |
514 |
|
} |
515 |
< |
simnfo->box_y = the_globals->getBoxY(); |
515 |
> |
boxVector[1] = the_globals->getBoxY(); |
516 |
|
|
517 |
|
if( !the_globals->haveBoxZ() ){ |
518 |
|
sprintf( painCave.errMsg, |
520 |
|
painCave.isFatal = 1; |
521 |
|
simError(); |
522 |
|
} |
523 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
523 |
> |
boxVector[2] = the_globals->getBoxZ(); |
524 |
> |
|
525 |
> |
simnfo->setBox( boxVector ); |
526 |
|
} |
527 |
|
|
528 |
|
#ifdef IS_MPI |
552 |
|
painCave.isFatal = 0; |
553 |
|
simError(); |
554 |
|
double smallest; |
555 |
< |
smallest = simnfo->box_x; |
556 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
557 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
555 |
> |
smallest = simnfo->boxLx; |
556 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
557 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
558 |
|
simnfo->ecr = 0.5 * smallest; |
559 |
|
} else { |
560 |
|
simnfo->ecr = the_globals->getECR(); |
592 |
|
painCave.isFatal = 0; |
593 |
|
simError(); |
594 |
|
double smallest; |
595 |
< |
smallest = simnfo->box_x; |
596 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
597 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
595 |
> |
smallest = simnfo->boxLx; |
596 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
597 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
598 |
|
simnfo->ecr = 0.5 * smallest; |
599 |
|
} else { |
600 |
|
simnfo->ecr = the_globals->getECR(); |
1121 |
|
have_extra =1; |
1122 |
|
|
1123 |
|
n_cells = (int)temp3 - 1; |
1124 |
< |
cellx = simnfo->box_x / temp3; |
1125 |
< |
celly = simnfo->box_y / temp3; |
1126 |
< |
cellz = simnfo->box_z / temp3; |
1124 |
> |
cellx = simnfo->boxLx / temp3; |
1125 |
> |
celly = simnfo->boxLy / temp3; |
1126 |
> |
cellz = simnfo->boxLz / temp3; |
1127 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1128 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1129 |
|
n_per_extra = (int)ceil( temp1 ); |
1138 |
|
} |
1139 |
|
else{ |
1140 |
|
n_cells = (int)temp3; |
1141 |
< |
cellx = simnfo->box_x / temp3; |
1142 |
< |
celly = simnfo->box_y / temp3; |
1143 |
< |
cellz = simnfo->box_z / temp3; |
1141 |
> |
cellx = simnfo->boxLx / temp3; |
1142 |
> |
celly = simnfo->boxLy / temp3; |
1143 |
> |
cellz = simnfo->boxLz / temp3; |
1144 |
|
} |
1145 |
|
|
1146 |
|
current_mol = 0; |