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 |
|
|
114 |
|
|
115 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
116 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
117 |
< |
else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_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, " |
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(); |
780 |
|
// make the integrator |
781 |
|
|
782 |
|
|
783 |
< |
NVT* myNVT = NULL; |
783 |
> |
NVT* myNVT = NULL; |
784 |
> |
NPTi* myNPTi = NULL; |
785 |
> |
NPTf* myNPTf = NULL; |
786 |
|
switch( ensembleCase ){ |
787 |
|
|
788 |
|
case NVE_ENS: |
795 |
|
|
796 |
|
if (the_globals->haveTauThermostat()) |
797 |
|
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
798 |
< |
else if (the_globals->haveQmass()) |
787 |
< |
myNVT->setQmass(the_globals->getQmass()); |
798 |
> |
|
799 |
|
else { |
800 |
|
sprintf( painCave.errMsg, |
801 |
|
"SimSetup error: If you use the NVT\n" |
802 |
< |
" ensemble, you must set either tauThermostat or qMass.\n" |
803 |
< |
" Neither of these was found in the BASS file.\n"); |
802 |
> |
" ensemble, you must set tauThermostat.\n"); |
803 |
> |
painCave.isFatal = 1; |
804 |
> |
simError(); |
805 |
> |
} |
806 |
> |
break; |
807 |
> |
|
808 |
> |
case NPTi_ENS: |
809 |
> |
myNPTi = new NPTi( simnfo, the_ff ); |
810 |
> |
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
811 |
> |
|
812 |
> |
if (the_globals->haveTargetPressure()) |
813 |
> |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
814 |
> |
else { |
815 |
> |
sprintf( painCave.errMsg, |
816 |
> |
"SimSetup error: If you use a constant pressure\n" |
817 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
818 |
|
painCave.isFatal = 1; |
819 |
|
simError(); |
820 |
|
} |
821 |
+ |
|
822 |
+ |
if( the_globals->haveTauThermostat() ) |
823 |
+ |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
824 |
+ |
else{ |
825 |
+ |
sprintf( painCave.errMsg, |
826 |
+ |
"SimSetup error: If you use an NPT\n" |
827 |
+ |
" ensemble, you must set tauThermostat.\n"); |
828 |
+ |
painCave.isFatal = 1; |
829 |
+ |
simError(); |
830 |
+ |
} |
831 |
+ |
|
832 |
+ |
if( the_globals->haveTauBarostat() ) |
833 |
+ |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
834 |
+ |
else{ |
835 |
+ |
sprintf( painCave.errMsg, |
836 |
+ |
"SimSetup error: If you use an NPT\n" |
837 |
+ |
" ensemble, you must set tauBarostat.\n"); |
838 |
+ |
painCave.isFatal = 1; |
839 |
+ |
simError(); |
840 |
+ |
} |
841 |
|
break; |
842 |
|
|
843 |
+ |
case NPTf_ENS: |
844 |
+ |
myNPTf = new NPTf( simnfo, the_ff ); |
845 |
+ |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
846 |
+ |
|
847 |
+ |
if (the_globals->haveTargetPressure()) |
848 |
+ |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
849 |
+ |
else { |
850 |
+ |
sprintf( painCave.errMsg, |
851 |
+ |
"SimSetup error: If you use a constant pressure\n" |
852 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
853 |
+ |
painCave.isFatal = 1; |
854 |
+ |
simError(); |
855 |
+ |
} |
856 |
+ |
|
857 |
+ |
if( the_globals->haveTauThermostat() ) |
858 |
+ |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
859 |
+ |
else{ |
860 |
+ |
sprintf( painCave.errMsg, |
861 |
+ |
"SimSetup error: If you use an NPT\n" |
862 |
+ |
" ensemble, you must set tauThermostat.\n"); |
863 |
+ |
painCave.isFatal = 1; |
864 |
+ |
simError(); |
865 |
+ |
} |
866 |
+ |
|
867 |
+ |
if( the_globals->haveTauBarostat() ) |
868 |
+ |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
869 |
+ |
else{ |
870 |
+ |
sprintf( painCave.errMsg, |
871 |
+ |
"SimSetup error: If you use an NPT\n" |
872 |
+ |
" ensemble, you must set tauBarostat.\n"); |
873 |
+ |
painCave.isFatal = 1; |
874 |
+ |
simError(); |
875 |
+ |
} |
876 |
+ |
break; |
877 |
+ |
|
878 |
+ |
|
879 |
+ |
|
880 |
|
default: |
881 |
|
sprintf( painCave.errMsg, |
882 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1197 |
|
have_extra =1; |
1198 |
|
|
1199 |
|
n_cells = (int)temp3 - 1; |
1200 |
< |
cellx = simnfo->box_x / temp3; |
1201 |
< |
celly = simnfo->box_y / temp3; |
1202 |
< |
cellz = simnfo->box_z / temp3; |
1200 |
> |
cellx = simnfo->boxLx / temp3; |
1201 |
> |
celly = simnfo->boxLy / temp3; |
1202 |
> |
cellz = simnfo->boxLz / temp3; |
1203 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1204 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1205 |
|
n_per_extra = (int)ceil( temp1 ); |
1214 |
|
} |
1215 |
|
else{ |
1216 |
|
n_cells = (int)temp3; |
1217 |
< |
cellx = simnfo->box_x / temp3; |
1218 |
< |
celly = simnfo->box_y / temp3; |
1219 |
< |
cellz = simnfo->box_z / temp3; |
1217 |
> |
cellx = simnfo->boxLx / temp3; |
1218 |
> |
celly = simnfo->boxLy / temp3; |
1219 |
> |
cellz = simnfo->boxLz / temp3; |
1220 |
|
} |
1221 |
|
|
1222 |
|
current_mol = 0; |