# | Line 12 | Line 12 | |
---|---|---|
12 | #include "mpiSimulation.hpp" | |
13 | #endif | |
14 | ||
15 | + | // some defines for ensemble and Forcefield cases |
16 | + | |
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 | + | |
28 | + | |
29 | SimSetup::SimSetup(){ | |
30 | stamps = new MakeStamps(); | |
31 | globals = new Globals(); | |
# | Line 66 | Line 80 | void SimSetup::createSim( void ){ | |
80 | ||
81 | MakeStamps *the_stamps; | |
82 | Globals* the_globals; | |
83 | < | int i, j; |
83 | > | int i, j, k, globalAtomIndex; |
84 | > | |
85 | > | int ensembleCase; |
86 | > | int ffCase; |
87 | > | |
88 | > | ensembleCase = -1; |
89 | > | ffCase = -1; |
90 | ||
91 | // get the stamps and globals; | |
92 | the_stamps = stamps; | |
# | Line 80 | Line 100 | void SimSetup::createSim( void ){ | |
100 | // get the ones we know are there, yet still may need some work. | |
101 | n_components = the_globals->getNComponents(); | |
102 | strcpy( force_field, the_globals->getForceField() ); | |
103 | + | |
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, |
108 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
109 | + | force_field ); |
110 | + | painCave.isFatal = 1; |
111 | + | simError(); |
112 | + | } |
113 | + | |
114 | + | // get the ensemble: |
115 | strcpy( ensemble, the_globals->getEnsemble() ); | |
116 | + | |
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, " |
127 | + | "reverting to NVE for this simulation.\n", |
128 | + | ensemble ); |
129 | + | painCave.isFatal = 0; |
130 | + | simError(); |
131 | + | strcpy( ensemble, "NVE" ); |
132 | + | ensembleCase = NVE_ENS; |
133 | + | } |
134 | strcpy( simnfo->ensemble, ensemble ); | |
135 | ||
136 | + | |
137 | + | // if( !strcasecmp( ensemble, "NPT" ) ) { |
138 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
139 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
140 | + | // if (the_globals->haveTargetPressure()) |
141 | + | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
142 | + | // else { |
143 | + | // sprintf( painCave.errMsg, |
144 | + | // "SimSetup error: If you use the constant pressure\n" |
145 | + | // " ensemble, you must set targetPressure.\n" |
146 | + | // " This was found in the BASS file.\n"); |
147 | + | // painCave.isFatal = 1; |
148 | + | // simError(); |
149 | + | // } |
150 | + | |
151 | + | // if (the_globals->haveTauThermostat()) |
152 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
153 | + | // else if (the_globals->haveQmass()) |
154 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
155 | + | // else { |
156 | + | // sprintf( painCave.errMsg, |
157 | + | // "SimSetup error: If you use one of the constant temperature\n" |
158 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
159 | + | // " Neither of these was found in the BASS file.\n"); |
160 | + | // painCave.isFatal = 1; |
161 | + | // simError(); |
162 | + | // } |
163 | + | |
164 | + | // if (the_globals->haveTauBarostat()) |
165 | + | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 | + | // else { |
167 | + | // sprintf( painCave.errMsg, |
168 | + | // "SimSetup error: If you use the constant pressure\n" |
169 | + | // " ensemble, you must set tauBarostat.\n" |
170 | + | // " This was found in the BASS file.\n"); |
171 | + | // painCave.isFatal = 1; |
172 | + | // simError(); |
173 | + | // } |
174 | + | |
175 | + | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
176 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
177 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
178 | + | |
179 | + | // if (the_globals->haveTauThermostat()) |
180 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
181 | + | // else if (the_globals->haveQmass()) |
182 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
183 | + | // else { |
184 | + | // sprintf( painCave.errMsg, |
185 | + | // "SimSetup error: If you use one of the constant temperature\n" |
186 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
187 | + | // " Neither of these was found in the BASS file.\n"); |
188 | + | // painCave.isFatal = 1; |
189 | + | // simError(); |
190 | + | // } |
191 | + | |
192 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
193 | simnfo->usePBC = the_globals->getPBC(); | |
194 | ||
195 | + | int usesDipoles = 0; |
196 | + | switch( ffCase ){ |
197 | ||
198 | + | case FF_DUFF: |
199 | + | the_ff = new DUFF(); |
200 | + | usesDipoles = 1; |
201 | + | break; |
202 | ||
203 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
204 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
205 | < | else{ |
203 | > | case FF_LJ: |
204 | > | the_ff = new LJFF(); |
205 | > | break; |
206 | > | |
207 | > | default: |
208 | sprintf( painCave.errMsg, | |
209 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
96 | < | force_field ); |
209 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
210 | painCave.isFatal = 1; | |
211 | simError(); | |
212 | } | |
# | Line 103 | Line 216 | void SimSetup::createSim( void ){ | |
216 | MPIcheckPoint(); | |
217 | #endif // is_mpi | |
218 | ||
106 | – | |
107 | – | |
219 | // get the components and calculate the tot_nMol and indvidual n_mol | |
220 | the_components = the_globals->getComponents(); | |
221 | components_nmol = new int[n_components]; | |
# | Line 228 | Line 339 | void SimSetup::createSim( void ){ | |
339 | simnfo->n_torsions = tot_torsions; | |
340 | simnfo->n_SRI = tot_SRI; | |
341 | simnfo->n_mol = tot_nmol; | |
231 | – | |
342 | ||
343 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
344 | + | |
345 | #ifdef IS_MPI | |
346 | ||
347 | // divide the molecules among processors here. | |
348 | ||
349 | mpiSim = new mpiSimulation( simnfo ); | |
350 | ||
239 | – | |
240 | – | |
351 | globalIndex = mpiSim->divideLabor(); | |
352 | ||
353 | // set up the local variables | |
# | Line 254 | Line 364 | void SimSetup::createSim( void ){ | |
364 | local_bonds = 0; | |
365 | local_bends = 0; | |
366 | local_torsions = 0; | |
367 | + | globalAtomIndex = 0; |
368 | + | |
369 | + | |
370 | for( i=0; i<n_components; i++ ){ | |
371 | ||
372 | for( j=0; j<components_nmol[i]; j++ ){ | |
373 | ||
374 | < | if( mol2proc[j] == worldRank ){ |
374 | > | if( mol2proc[allMol] == worldRank ){ |
375 | ||
376 | local_atoms += comp_stamps[i]->getNAtoms(); | |
377 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 266 | Line 379 | void SimSetup::createSim( void ){ | |
379 | local_torsions += comp_stamps[i]->getNTorsions(); | |
380 | localMol++; | |
381 | } | |
382 | < | allMol++; |
382 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 | > | globalAtomIndex++; |
385 | > | } |
386 | > | |
387 | > | allMol++; |
388 | } | |
389 | } | |
390 | local_SRI = local_bonds + local_bends + local_torsions; | |
391 | ||
274 | – | |
392 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
393 | ||
394 | if( local_atoms != simnfo->n_atoms ){ | |
# | Line 315 | Line 432 | void SimSetup::createSim( void ){ | |
432 | if(mol2proc[i] == worldRank ){ | |
433 | the_molecules[molIndex].setStampID( molCompType[i] ); | |
434 | the_molecules[molIndex].setMyIndex( molIndex ); | |
435 | + | the_molecules[molIndex].setGlobalIndex( i ); |
436 | molIndex++; | |
437 | } | |
438 | } | |
# | Line 322 | Line 440 | void SimSetup::createSim( void ){ | |
440 | #else // is_mpi | |
441 | ||
442 | molIndex = 0; | |
443 | + | globalAtomIndex = 0; |
444 | for(i=0; i<n_components; i++){ | |
445 | for(j=0; j<components_nmol[i]; j++ ){ | |
446 | the_molecules[molIndex].setStampID( i ); | |
447 | the_molecules[molIndex].setMyIndex( molIndex ); | |
448 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 | + | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 | + | globalAtomIndex++; |
452 | + | } |
453 | molIndex++; | |
454 | } | |
455 | } | |
# | Line 363 | 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 384 | 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 392 | 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 400 | 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 430 | 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 460 | Line 590 | void SimSetup::createSim( void ){ | |
590 | } | |
591 | simnfo->dielectric = the_globals->getDielectric(); | |
592 | } else { | |
593 | < | if (simnfo->n_dipoles) { |
593 | > | if (usesDipoles) { |
594 | ||
595 | if( !the_globals->haveECR() ){ | |
596 | sprintf( painCave.errMsg, | |
597 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
597 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
598 | "box length for the electrostaticCutoffRadius.\n" | |
599 | "I hope you have a very fast processor!\n"); | |
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 480 | Line 610 | void SimSetup::createSim( void ){ | |
610 | ||
611 | if( !the_globals->haveEST() ){ | |
612 | sprintf( painCave.errMsg, | |
613 | < | "SimSetup Warning: using default value of 5% of the" |
613 | > | "SimSetup Warning: using default value of 5%% of the " |
614 | "electrostaticCutoffRadius for the " | |
615 | "electrostaticSkinThickness\n" | |
616 | ); | |
# | Line 651 | Line 781 | void SimSetup::createSim( void ){ | |
781 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
782 | ||
783 | ||
784 | < | // // make the longe range forces and the integrator |
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 | < | // new AllLong( simnfo ); |
793 | > | switch( ensembleCase ){ |
794 | ||
795 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
796 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
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 | |
# | Line 970 | Line 1272 | void SimSetup::initFromBass( void ){ | |
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 ); | |
# | Line 987 | Line 1289 | void SimSetup::initFromBass( void ){ | |
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; |
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