14 |
|
|
15 |
|
// some defines for ensemble and Forcefield cases |
16 |
|
|
17 |
< |
#define NVE_ENS 0 |
18 |
< |
#define NVT_ENS 1 |
19 |
< |
#define NPT_ENS 2 |
17 |
> |
#define NVE_ENS 0 |
18 |
> |
#define NVT_ENS 1 |
19 |
> |
#define NPTi_ENS 2 |
20 |
> |
#define NPTf_ENS 3 |
21 |
|
|
22 |
+ |
|
23 |
|
#define FF_DUFF 0 |
24 |
|
#define FF_LJ 1 |
25 |
|
|
99 |
|
n_components = the_globals->getNComponents(); |
100 |
|
strcpy( force_field, the_globals->getForceField() ); |
101 |
|
|
102 |
< |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
102 |
> |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
103 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
104 |
|
else{ |
105 |
|
sprintf( painCave.errMsg, |
112 |
|
// get the ensemble: |
113 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
114 |
|
|
115 |
< |
if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
116 |
< |
else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
117 |
< |
else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
115 |
> |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
116 |
> |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
117 |
> |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
118 |
> |
ensembleCase = NPTi_ENS; |
119 |
> |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
120 |
|
else{ |
121 |
|
sprintf( painCave.errMsg, |
122 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
197 |
|
break; |
198 |
|
|
199 |
|
case FF_LJ: |
200 |
< |
the_ff = LJFF(); |
200 |
> |
the_ff = new LJFF(); |
201 |
|
break; |
202 |
|
|
203 |
|
default: |
483 |
|
|
484 |
|
// get some of the tricky things that may still be in the globals |
485 |
|
|
486 |
< |
|
486 |
> |
double boxVector[3]; |
487 |
|
if( the_globals->haveBox() ){ |
488 |
< |
simnfo->box_x = the_globals->getBox(); |
489 |
< |
simnfo->box_y = the_globals->getBox(); |
490 |
< |
simnfo->box_z = the_globals->getBox(); |
488 |
> |
boxVector[0] = the_globals->getBox(); |
489 |
> |
boxVector[1] = the_globals->getBox(); |
490 |
> |
boxVector[2] = the_globals->getBox(); |
491 |
> |
|
492 |
> |
simnfo->setBox( boxVector ); |
493 |
|
} |
494 |
|
else if( the_globals->haveDensity() ){ |
495 |
|
|
496 |
|
double vol; |
497 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
498 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
499 |
< |
simnfo->box_y = simnfo->box_x; |
500 |
< |
simnfo->box_z = simnfo->box_x; |
498 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
499 |
> |
boxVector[1] = boxVector[0]; |
500 |
> |
boxVector[2] = boxVector[0]; |
501 |
> |
|
502 |
> |
simnfo->setBox( boxVector ); |
503 |
|
} |
504 |
|
else{ |
505 |
|
if( !the_globals->haveBoxX() ){ |
508 |
|
painCave.isFatal = 1; |
509 |
|
simError(); |
510 |
|
} |
511 |
< |
simnfo->box_x = the_globals->getBoxX(); |
511 |
> |
boxVector[0] = the_globals->getBoxX(); |
512 |
|
|
513 |
|
if( !the_globals->haveBoxY() ){ |
514 |
|
sprintf( painCave.errMsg, |
516 |
|
painCave.isFatal = 1; |
517 |
|
simError(); |
518 |
|
} |
519 |
< |
simnfo->box_y = the_globals->getBoxY(); |
519 |
> |
boxVector[1] = the_globals->getBoxY(); |
520 |
|
|
521 |
|
if( !the_globals->haveBoxZ() ){ |
522 |
|
sprintf( painCave.errMsg, |
524 |
|
painCave.isFatal = 1; |
525 |
|
simError(); |
526 |
|
} |
527 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
527 |
> |
boxVector[2] = the_globals->getBoxZ(); |
528 |
> |
|
529 |
> |
simnfo->setBox( boxVector ); |
530 |
|
} |
531 |
|
|
532 |
|
#ifdef IS_MPI |
556 |
|
painCave.isFatal = 0; |
557 |
|
simError(); |
558 |
|
double smallest; |
559 |
< |
smallest = simnfo->box_x; |
560 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
561 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 |
> |
smallest = simnfo->boxLx; |
560 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
561 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
562 |
|
simnfo->ecr = 0.5 * smallest; |
563 |
|
} else { |
564 |
|
simnfo->ecr = the_globals->getECR(); |
596 |
|
painCave.isFatal = 0; |
597 |
|
simError(); |
598 |
|
double smallest; |
599 |
< |
smallest = simnfo->box_x; |
600 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
601 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
599 |
> |
smallest = simnfo->boxLx; |
600 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
601 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
602 |
|
simnfo->ecr = 0.5 * smallest; |
603 |
|
} else { |
604 |
|
simnfo->ecr = the_globals->getECR(); |
778 |
|
|
779 |
|
|
780 |
|
// make the integrator |
781 |
< |
|
781 |
> |
|
782 |
> |
|
783 |
> |
NVT* myNVT = NULL; |
784 |
|
switch( ensembleCase ){ |
785 |
|
|
786 |
|
case NVE_ENS: |
787 |
|
new NVE( simnfo, the_ff ); |
788 |
+ |
break; |
789 |
+ |
|
790 |
+ |
case NVT_ENS: |
791 |
+ |
myNVT = new NVT( simnfo, the_ff ); |
792 |
+ |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
793 |
+ |
|
794 |
+ |
if (the_globals->haveTauThermostat()) |
795 |
+ |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
796 |
+ |
// else if (the_globals->haveQmass()) |
797 |
+ |
// myNVT->setQmass(the_globals->getQmass()); |
798 |
+ |
else { |
799 |
+ |
sprintf( painCave.errMsg, |
800 |
+ |
"SimSetup error: If you use the NVT\n" |
801 |
+ |
" ensemble, you must set either tauThermostat or qMass.\n" |
802 |
+ |
" Neither of these was found in the BASS file.\n"); |
803 |
+ |
painCave.isFatal = 1; |
804 |
+ |
simError(); |
805 |
+ |
} |
806 |
|
break; |
807 |
|
|
808 |
|
default: |
1125 |
|
have_extra =1; |
1126 |
|
|
1127 |
|
n_cells = (int)temp3 - 1; |
1128 |
< |
cellx = simnfo->box_x / temp3; |
1129 |
< |
celly = simnfo->box_y / temp3; |
1130 |
< |
cellz = simnfo->box_z / temp3; |
1128 |
> |
cellx = simnfo->boxLx / temp3; |
1129 |
> |
celly = simnfo->boxLy / temp3; |
1130 |
> |
cellz = simnfo->boxLz / temp3; |
1131 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1132 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1133 |
|
n_per_extra = (int)ceil( temp1 ); |
1142 |
|
} |
1143 |
|
else{ |
1144 |
|
n_cells = (int)temp3; |
1145 |
< |
cellx = simnfo->box_x / temp3; |
1146 |
< |
celly = simnfo->box_y / temp3; |
1147 |
< |
cellz = simnfo->box_z / temp3; |
1145 |
> |
cellx = simnfo->boxLx / temp3; |
1146 |
> |
celly = simnfo->boxLy / temp3; |
1147 |
> |
cellz = simnfo->boxLz / temp3; |
1148 |
|
} |
1149 |
|
|
1150 |
|
current_mol = 0; |