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 |
> |
#define NPTim_ENS 4 |
22 |
> |
#define NPTfm_ENS 5 |
23 |
|
|
24 |
+ |
|
25 |
|
#define FF_DUFF 0 |
26 |
|
#define FF_LJ 1 |
27 |
|
|
116 |
|
|
117 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
118 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
119 |
< |
else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
119 |
> |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
120 |
> |
ensembleCase = NPTi_ENS; |
121 |
> |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
122 |
> |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
123 |
> |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
124 |
|
else{ |
125 |
|
sprintf( painCave.errMsg, |
126 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
487 |
|
|
488 |
|
// get some of the tricky things that may still be in the globals |
489 |
|
|
490 |
< |
|
490 |
> |
double boxVector[3]; |
491 |
|
if( the_globals->haveBox() ){ |
492 |
< |
simnfo->box_x = the_globals->getBox(); |
493 |
< |
simnfo->box_y = the_globals->getBox(); |
494 |
< |
simnfo->box_z = the_globals->getBox(); |
492 |
> |
boxVector[0] = the_globals->getBox(); |
493 |
> |
boxVector[1] = the_globals->getBox(); |
494 |
> |
boxVector[2] = the_globals->getBox(); |
495 |
> |
|
496 |
> |
simnfo->setBox( boxVector ); |
497 |
|
} |
498 |
|
else if( the_globals->haveDensity() ){ |
499 |
|
|
500 |
|
double vol; |
501 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
502 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
503 |
< |
simnfo->box_y = simnfo->box_x; |
504 |
< |
simnfo->box_z = simnfo->box_x; |
502 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
503 |
> |
boxVector[1] = boxVector[0]; |
504 |
> |
boxVector[2] = boxVector[0]; |
505 |
> |
|
506 |
> |
simnfo->setBox( boxVector ); |
507 |
|
} |
508 |
|
else{ |
509 |
|
if( !the_globals->haveBoxX() ){ |
512 |
|
painCave.isFatal = 1; |
513 |
|
simError(); |
514 |
|
} |
515 |
< |
simnfo->box_x = the_globals->getBoxX(); |
515 |
> |
boxVector[0] = the_globals->getBoxX(); |
516 |
|
|
517 |
|
if( !the_globals->haveBoxY() ){ |
518 |
|
sprintf( painCave.errMsg, |
520 |
|
painCave.isFatal = 1; |
521 |
|
simError(); |
522 |
|
} |
523 |
< |
simnfo->box_y = the_globals->getBoxY(); |
523 |
> |
boxVector[1] = the_globals->getBoxY(); |
524 |
|
|
525 |
|
if( !the_globals->haveBoxZ() ){ |
526 |
|
sprintf( painCave.errMsg, |
528 |
|
painCave.isFatal = 1; |
529 |
|
simError(); |
530 |
|
} |
531 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
531 |
> |
boxVector[2] = the_globals->getBoxZ(); |
532 |
> |
|
533 |
> |
simnfo->setBox( boxVector ); |
534 |
|
} |
535 |
|
|
536 |
|
#ifdef IS_MPI |
560 |
|
painCave.isFatal = 0; |
561 |
|
simError(); |
562 |
|
double smallest; |
563 |
< |
smallest = simnfo->box_x; |
564 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
565 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
563 |
> |
smallest = simnfo->boxLx; |
564 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
565 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
566 |
|
simnfo->ecr = 0.5 * smallest; |
567 |
|
} else { |
568 |
|
simnfo->ecr = the_globals->getECR(); |
600 |
|
painCave.isFatal = 0; |
601 |
|
simError(); |
602 |
|
double smallest; |
603 |
< |
smallest = simnfo->box_x; |
604 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
605 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
603 |
> |
smallest = simnfo->boxLx; |
604 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
605 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
606 |
|
simnfo->ecr = 0.5 * smallest; |
607 |
|
} else { |
608 |
|
simnfo->ecr = the_globals->getECR(); |
784 |
|
// make the integrator |
785 |
|
|
786 |
|
|
787 |
< |
NVT* myNVT = NULL; |
787 |
> |
NVT* myNVT = NULL; |
788 |
> |
NPTi* myNPTi = NULL; |
789 |
> |
NPTf* myNPTf = NULL; |
790 |
> |
NPTim* myNPTim = NULL; |
791 |
> |
|
792 |
|
switch( ensembleCase ){ |
793 |
|
|
794 |
|
case NVE_ENS: |
801 |
|
|
802 |
|
if (the_globals->haveTauThermostat()) |
803 |
|
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
804 |
< |
// else if (the_globals->haveQmass()) |
787 |
< |
// myNVT->setQmass(the_globals->getQmass()); |
804 |
> |
|
805 |
|
else { |
806 |
|
sprintf( painCave.errMsg, |
807 |
|
"SimSetup error: If you use the NVT\n" |
808 |
< |
" ensemble, you must set either tauThermostat or qMass.\n" |
792 |
< |
" Neither of these was found in the BASS file.\n"); |
808 |
> |
" ensemble, you must set tauThermostat.\n"); |
809 |
|
painCave.isFatal = 1; |
810 |
|
simError(); |
811 |
|
} |
812 |
|
break; |
813 |
|
|
814 |
+ |
case NPTi_ENS: |
815 |
+ |
myNPTi = new NPTi( simnfo, the_ff ); |
816 |
+ |
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
817 |
+ |
|
818 |
+ |
if (the_globals->haveTargetPressure()) |
819 |
+ |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
820 |
+ |
else { |
821 |
+ |
sprintf( painCave.errMsg, |
822 |
+ |
"SimSetup error: If you use a constant pressure\n" |
823 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
824 |
+ |
painCave.isFatal = 1; |
825 |
+ |
simError(); |
826 |
+ |
} |
827 |
+ |
|
828 |
+ |
if( the_globals->haveTauThermostat() ) |
829 |
+ |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
830 |
+ |
else{ |
831 |
+ |
sprintf( painCave.errMsg, |
832 |
+ |
"SimSetup error: If you use an NPT\n" |
833 |
+ |
" ensemble, you must set tauThermostat.\n"); |
834 |
+ |
painCave.isFatal = 1; |
835 |
+ |
simError(); |
836 |
+ |
} |
837 |
+ |
|
838 |
+ |
if( the_globals->haveTauBarostat() ) |
839 |
+ |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
840 |
+ |
else{ |
841 |
+ |
sprintf( painCave.errMsg, |
842 |
+ |
"SimSetup error: If you use an NPT\n" |
843 |
+ |
" ensemble, you must set tauBarostat.\n"); |
844 |
+ |
painCave.isFatal = 1; |
845 |
+ |
simError(); |
846 |
+ |
} |
847 |
+ |
break; |
848 |
+ |
|
849 |
+ |
case NPTf_ENS: |
850 |
+ |
myNPTf = new NPTf( simnfo, the_ff ); |
851 |
+ |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
852 |
+ |
|
853 |
+ |
if (the_globals->haveTargetPressure()) |
854 |
+ |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
855 |
+ |
else { |
856 |
+ |
sprintf( painCave.errMsg, |
857 |
+ |
"SimSetup error: If you use a constant pressure\n" |
858 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
859 |
+ |
painCave.isFatal = 1; |
860 |
+ |
simError(); |
861 |
+ |
} |
862 |
+ |
|
863 |
+ |
if( the_globals->haveTauThermostat() ) |
864 |
+ |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
865 |
+ |
else{ |
866 |
+ |
sprintf( painCave.errMsg, |
867 |
+ |
"SimSetup error: If you use an NPT\n" |
868 |
+ |
" ensemble, you must set tauThermostat.\n"); |
869 |
+ |
painCave.isFatal = 1; |
870 |
+ |
simError(); |
871 |
+ |
} |
872 |
+ |
|
873 |
+ |
if( the_globals->haveTauBarostat() ) |
874 |
+ |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
875 |
+ |
else{ |
876 |
+ |
sprintf( painCave.errMsg, |
877 |
+ |
"SimSetup error: If you use an NPT\n" |
878 |
+ |
" ensemble, you must set tauBarostat.\n"); |
879 |
+ |
painCave.isFatal = 1; |
880 |
+ |
simError(); |
881 |
+ |
} |
882 |
+ |
break; |
883 |
+ |
|
884 |
+ |
case NPTim_ENS: |
885 |
+ |
myNPTim = new NPTim( simnfo, the_ff ); |
886 |
+ |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
887 |
+ |
|
888 |
+ |
if (the_globals->haveTargetPressure()) |
889 |
+ |
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
890 |
+ |
else { |
891 |
+ |
sprintf( painCave.errMsg, |
892 |
+ |
"SimSetup error: If you use a constant pressure\n" |
893 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
894 |
+ |
painCave.isFatal = 1; |
895 |
+ |
simError(); |
896 |
+ |
} |
897 |
+ |
|
898 |
+ |
if( the_globals->haveTauThermostat() ) |
899 |
+ |
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
900 |
+ |
else{ |
901 |
+ |
sprintf( painCave.errMsg, |
902 |
+ |
"SimSetup error: If you use an NPT\n" |
903 |
+ |
" ensemble, you must set tauThermostat.\n"); |
904 |
+ |
painCave.isFatal = 1; |
905 |
+ |
simError(); |
906 |
+ |
} |
907 |
+ |
|
908 |
+ |
if( the_globals->haveTauBarostat() ) |
909 |
+ |
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
910 |
+ |
else{ |
911 |
+ |
sprintf( painCave.errMsg, |
912 |
+ |
"SimSetup error: If you use an NPT\n" |
913 |
+ |
" ensemble, you must set tauBarostat.\n"); |
914 |
+ |
painCave.isFatal = 1; |
915 |
+ |
simError(); |
916 |
+ |
} |
917 |
+ |
break; |
918 |
+ |
|
919 |
+ |
|
920 |
+ |
|
921 |
|
default: |
922 |
|
sprintf( painCave.errMsg, |
923 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1238 |
|
have_extra =1; |
1239 |
|
|
1240 |
|
n_cells = (int)temp3 - 1; |
1241 |
< |
cellx = simnfo->box_x / temp3; |
1242 |
< |
celly = simnfo->box_y / temp3; |
1243 |
< |
cellz = simnfo->box_z / temp3; |
1241 |
> |
cellx = simnfo->boxLx / temp3; |
1242 |
> |
celly = simnfo->boxLy / temp3; |
1243 |
> |
cellz = simnfo->boxLz / temp3; |
1244 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1245 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1246 |
|
n_per_extra = (int)ceil( temp1 ); |
1255 |
|
} |
1256 |
|
else{ |
1257 |
|
n_cells = (int)temp3; |
1258 |
< |
cellx = simnfo->box_x / temp3; |
1259 |
< |
celly = simnfo->box_y / temp3; |
1260 |
< |
cellz = simnfo->box_z / temp3; |
1258 |
> |
cellx = simnfo->boxLx / temp3; |
1259 |
> |
celly = simnfo->boxLy / temp3; |
1260 |
> |
cellz = simnfo->boxLz / temp3; |
1261 |
|
} |
1262 |
|
|
1263 |
|
current_mol = 0; |