# | Line 14 | Line 14 | |
---|---|---|
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 | ||
# | Line 112 | Line 116 | void SimSetup::createSim( void ){ | |
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, " | |
# | Line 479 | Line 487 | void SimSetup::createSim( void ){ | |
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() ){ | |
# | Line 500 | Line 512 | void SimSetup::createSim( void ){ | |
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, | |
# | Line 508 | Line 520 | void SimSetup::createSim( void ){ | |
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, | |
# | Line 516 | Line 528 | void SimSetup::createSim( void ){ | |
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 | |
# | Line 546 | Line 560 | void SimSetup::createSim( void ){ | |
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(); | |
# | Line 586 | Line 600 | void SimSetup::createSim( void ){ | |
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(); | |
# | Line 770 | Line 784 | void SimSetup::createSim( void ){ | |
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: | |
# | Line 783 | Line 801 | void SimSetup::createSim( void ){ | |
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"); | |
# | Line 1115 | Line 1238 | void SimSetup::initFromBass( void ){ | |
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 ); | |
# | Line 1132 | Line 1255 | void SimSetup::initFromBass( void ){ | |
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; |
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