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 |
|
|
101 |
|
n_components = the_globals->getNComponents(); |
102 |
|
strcpy( force_field, the_globals->getForceField() ); |
103 |
|
|
104 |
< |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
104 |
> |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
105 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
106 |
|
else{ |
107 |
|
sprintf( painCave.errMsg, |
114 |
|
// get the ensemble: |
115 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
116 |
|
|
117 |
< |
if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
118 |
< |
else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
119 |
< |
else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
117 |
> |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
118 |
> |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_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, " |
201 |
|
break; |
202 |
|
|
203 |
|
case FF_LJ: |
204 |
< |
the_ff = LJFF(); |
204 |
> |
the_ff = new LJFF(); |
205 |
|
break; |
206 |
|
|
207 |
|
default: |
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(); |
782 |
|
|
783 |
|
|
784 |
|
// make the integrator |
785 |
+ |
|
786 |
+ |
|
787 |
+ |
NVT* myNVT = NULL; |
788 |
+ |
NPTi* myNPTi = NULL; |
789 |
+ |
NPTf* myNPTf = NULL; |
790 |
+ |
NPTim* myNPTim = NULL; |
791 |
+ |
NPTfm* myNPTfm = NULL; |
792 |
|
|
793 |
+ |
switch( ensembleCase ){ |
794 |
|
|
795 |
< |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
796 |
< |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
797 |
< |
} |
798 |
< |
else if( !strcmp( force_field, "LJ" ) ){ |
799 |
< |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
795 |
> |
case NVE_ENS: |
796 |
> |
new NVE( simnfo, the_ff ); |
797 |
> |
break; |
798 |
> |
|
799 |
> |
case NVT_ENS: |
800 |
> |
myNVT = new NVT( simnfo, the_ff ); |
801 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
802 |
> |
|
803 |
> |
if (the_globals->haveTauThermostat()) |
804 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
805 |
> |
|
806 |
> |
else { |
807 |
> |
sprintf( painCave.errMsg, |
808 |
> |
"SimSetup error: If you use the NVT\n" |
809 |
> |
" ensemble, you must set tauThermostat.\n"); |
810 |
> |
painCave.isFatal = 1; |
811 |
> |
simError(); |
812 |
> |
} |
813 |
> |
break; |
814 |
> |
|
815 |
> |
case NPTi_ENS: |
816 |
> |
myNPTi = new NPTi( simnfo, the_ff ); |
817 |
> |
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
818 |
> |
|
819 |
> |
if (the_globals->haveTargetPressure()) |
820 |
> |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
821 |
> |
else { |
822 |
> |
sprintf( painCave.errMsg, |
823 |
> |
"SimSetup error: If you use a constant pressure\n" |
824 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
825 |
> |
painCave.isFatal = 1; |
826 |
> |
simError(); |
827 |
> |
} |
828 |
> |
|
829 |
> |
if( the_globals->haveTauThermostat() ) |
830 |
> |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
831 |
> |
else{ |
832 |
> |
sprintf( painCave.errMsg, |
833 |
> |
"SimSetup error: If you use an NPT\n" |
834 |
> |
" ensemble, you must set tauThermostat.\n"); |
835 |
> |
painCave.isFatal = 1; |
836 |
> |
simError(); |
837 |
> |
} |
838 |
> |
|
839 |
> |
if( the_globals->haveTauBarostat() ) |
840 |
> |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
841 |
> |
else{ |
842 |
> |
sprintf( painCave.errMsg, |
843 |
> |
"SimSetup error: If you use an NPT\n" |
844 |
> |
" ensemble, you must set tauBarostat.\n"); |
845 |
> |
painCave.isFatal = 1; |
846 |
> |
simError(); |
847 |
> |
} |
848 |
> |
break; |
849 |
> |
|
850 |
> |
case NPTf_ENS: |
851 |
> |
myNPTf = new NPTf( simnfo, the_ff ); |
852 |
> |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
853 |
> |
|
854 |
> |
if (the_globals->haveTargetPressure()) |
855 |
> |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
856 |
> |
else { |
857 |
> |
sprintf( painCave.errMsg, |
858 |
> |
"SimSetup error: If you use a constant pressure\n" |
859 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
860 |
> |
painCave.isFatal = 1; |
861 |
> |
simError(); |
862 |
> |
} |
863 |
> |
|
864 |
> |
if( the_globals->haveTauThermostat() ) |
865 |
> |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
866 |
> |
else{ |
867 |
> |
sprintf( painCave.errMsg, |
868 |
> |
"SimSetup error: If you use an NPT\n" |
869 |
> |
" ensemble, you must set tauThermostat.\n"); |
870 |
> |
painCave.isFatal = 1; |
871 |
> |
simError(); |
872 |
> |
} |
873 |
> |
|
874 |
> |
if( the_globals->haveTauBarostat() ) |
875 |
> |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
876 |
> |
else{ |
877 |
> |
sprintf( painCave.errMsg, |
878 |
> |
"SimSetup error: If you use an NPT\n" |
879 |
> |
" ensemble, you must set tauBarostat.\n"); |
880 |
> |
painCave.isFatal = 1; |
881 |
> |
simError(); |
882 |
> |
} |
883 |
> |
break; |
884 |
> |
|
885 |
> |
case NPTim_ENS: |
886 |
> |
myNPTim = new NPTim( simnfo, the_ff ); |
887 |
> |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
888 |
> |
|
889 |
> |
if (the_globals->haveTargetPressure()) |
890 |
> |
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
891 |
> |
else { |
892 |
> |
sprintf( painCave.errMsg, |
893 |
> |
"SimSetup error: If you use a constant pressure\n" |
894 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
895 |
> |
painCave.isFatal = 1; |
896 |
> |
simError(); |
897 |
> |
} |
898 |
> |
|
899 |
> |
if( the_globals->haveTauThermostat() ) |
900 |
> |
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
901 |
> |
else{ |
902 |
> |
sprintf( painCave.errMsg, |
903 |
> |
"SimSetup error: If you use an NPT\n" |
904 |
> |
" ensemble, you must set tauThermostat.\n"); |
905 |
> |
painCave.isFatal = 1; |
906 |
> |
simError(); |
907 |
> |
} |
908 |
> |
|
909 |
> |
if( the_globals->haveTauBarostat() ) |
910 |
> |
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
911 |
> |
else{ |
912 |
> |
sprintf( painCave.errMsg, |
913 |
> |
"SimSetup error: If you use an NPT\n" |
914 |
> |
" ensemble, you must set tauBarostat.\n"); |
915 |
> |
painCave.isFatal = 1; |
916 |
> |
simError(); |
917 |
> |
} |
918 |
> |
break; |
919 |
> |
|
920 |
> |
case NPTfm_ENS: |
921 |
> |
myNPTfm = new NPTfm( simnfo, the_ff ); |
922 |
> |
myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
923 |
> |
|
924 |
> |
if (the_globals->haveTargetPressure()) |
925 |
> |
myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
926 |
> |
else { |
927 |
> |
sprintf( painCave.errMsg, |
928 |
> |
"SimSetup error: If you use a constant pressure\n" |
929 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
930 |
> |
painCave.isFatal = 1; |
931 |
> |
simError(); |
932 |
> |
} |
933 |
> |
|
934 |
> |
if( the_globals->haveTauThermostat() ) |
935 |
> |
myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
936 |
> |
else{ |
937 |
> |
sprintf( painCave.errMsg, |
938 |
> |
"SimSetup error: If you use an NPT\n" |
939 |
> |
" ensemble, you must set tauThermostat.\n"); |
940 |
> |
painCave.isFatal = 1; |
941 |
> |
simError(); |
942 |
> |
} |
943 |
> |
|
944 |
> |
if( the_globals->haveTauBarostat() ) |
945 |
> |
myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
946 |
> |
else{ |
947 |
> |
sprintf( painCave.errMsg, |
948 |
> |
"SimSetup error: If you use an NPT\n" |
949 |
> |
" ensemble, you must set tauBarostat.\n"); |
950 |
> |
painCave.isFatal = 1; |
951 |
> |
simError(); |
952 |
> |
} |
953 |
> |
break; |
954 |
> |
|
955 |
> |
default: |
956 |
> |
sprintf( painCave.errMsg, |
957 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
958 |
> |
painCave.isFatal = 1; |
959 |
> |
simError(); |
960 |
|
} |
961 |
|
|
962 |
+ |
|
963 |
|
#ifdef IS_MPI |
964 |
|
mpiSim->mpiRefresh(); |
965 |
|
#endif |
1272 |
|
have_extra =1; |
1273 |
|
|
1274 |
|
n_cells = (int)temp3 - 1; |
1275 |
< |
cellx = simnfo->box_x / temp3; |
1276 |
< |
celly = simnfo->box_y / temp3; |
1277 |
< |
cellz = simnfo->box_z / temp3; |
1275 |
> |
cellx = simnfo->boxLx / temp3; |
1276 |
> |
celly = simnfo->boxLy / temp3; |
1277 |
> |
cellz = simnfo->boxLz / temp3; |
1278 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1279 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1280 |
|
n_per_extra = (int)ceil( temp1 ); |
1289 |
|
} |
1290 |
|
else{ |
1291 |
|
n_cells = (int)temp3; |
1292 |
< |
cellx = simnfo->box_x / temp3; |
1293 |
< |
celly = simnfo->box_y / temp3; |
1294 |
< |
cellz = simnfo->box_z / temp3; |
1292 |
> |
cellx = simnfo->boxLx / temp3; |
1293 |
> |
celly = simnfo->boxLy / temp3; |
1294 |
> |
cellz = simnfo->boxLz / temp3; |
1295 |
|
} |
1296 |
|
|
1297 |
|
current_mol = 0; |