97 |
|
n_components = the_globals->getNComponents(); |
98 |
|
strcpy( force_field, the_globals->getForceField() ); |
99 |
|
|
100 |
< |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
100 |
> |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 |
|
else{ |
103 |
|
sprintf( painCave.errMsg, |
110 |
|
// get the ensemble: |
111 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
112 |
|
|
113 |
< |
if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
114 |
< |
else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
115 |
< |
else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
113 |
> |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
114 |
> |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
115 |
> |
else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
116 |
|
else{ |
117 |
|
sprintf( painCave.errMsg, |
118 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
193 |
|
break; |
194 |
|
|
195 |
|
case FF_LJ: |
196 |
< |
the_ff = LJFF(); |
196 |
> |
the_ff = new LJFF(); |
197 |
|
break; |
198 |
|
|
199 |
|
default: |
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(); |
774 |
|
|
775 |
|
|
776 |
|
// make the integrator |
777 |
+ |
|
778 |
+ |
|
779 |
+ |
NVT* myNVT = NULL; |
780 |
+ |
switch( ensembleCase ){ |
781 |
|
|
782 |
+ |
case NVE_ENS: |
783 |
+ |
new NVE( simnfo, the_ff ); |
784 |
+ |
break; |
785 |
|
|
786 |
< |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
787 |
< |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
788 |
< |
} |
789 |
< |
else if( !strcmp( force_field, "LJ" ) ){ |
790 |
< |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
786 |
> |
case NVT_ENS: |
787 |
> |
myNVT = new NVT( simnfo, the_ff ); |
788 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
789 |
> |
|
790 |
> |
if (the_globals->haveTauThermostat()) |
791 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
792 |
> |
// else if (the_globals->haveQmass()) |
793 |
> |
// myNVT->setQmass(the_globals->getQmass()); |
794 |
> |
else { |
795 |
> |
sprintf( painCave.errMsg, |
796 |
> |
"SimSetup error: If you use the NVT\n" |
797 |
> |
" ensemble, you must set either tauThermostat or qMass.\n" |
798 |
> |
" Neither of these was found in the BASS file.\n"); |
799 |
> |
painCave.isFatal = 1; |
800 |
> |
simError(); |
801 |
> |
} |
802 |
> |
break; |
803 |
> |
|
804 |
> |
default: |
805 |
> |
sprintf( painCave.errMsg, |
806 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
807 |
> |
painCave.isFatal = 1; |
808 |
> |
simError(); |
809 |
|
} |
810 |
|
|
811 |
+ |
|
812 |
|
#ifdef IS_MPI |
813 |
|
mpiSim->mpiRefresh(); |
814 |
|
#endif |
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; |