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(); |
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; |
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 |
|
} |
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]; |
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 |
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(); |
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 ){ |
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 |
|
} |
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 |
|
} |
460 |
|
|
461 |
|
if( simnfo->n_SRI ){ |
462 |
|
|
339 |
– |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 |
– |
|
463 |
|
Exclude::createArray(simnfo->n_SRI); |
464 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
465 |
|
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
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(); |
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(); |
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 |
|
); |
781 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
782 |
|
|
783 |
|
|
784 |
< |
// // make the longe range forces and the integrator |
785 |
< |
|
786 |
< |
// new AllLong( simnfo ); |
784 |
> |
// make the integrator |
785 |
> |
|
786 |
> |
|
787 |
> |
NVT* myNVT = NULL; |
788 |
> |
NPTi* myNPTi = NULL; |
789 |
> |
NPTf* myNPTf = NULL; |
790 |
> |
NPTim* myNPTim = NULL; |
791 |
|
|
792 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
793 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
792 |
> |
switch( ensembleCase ){ |
793 |
> |
|
794 |
> |
case NVE_ENS: |
795 |
> |
new NVE( simnfo, the_ff ); |
796 |
> |
break; |
797 |
> |
|
798 |
> |
case NVT_ENS: |
799 |
> |
myNVT = new NVT( simnfo, the_ff ); |
800 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
801 |
> |
|
802 |
> |
if (the_globals->haveTauThermostat()) |
803 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
804 |
> |
|
805 |
> |
else { |
806 |
> |
sprintf( painCave.errMsg, |
807 |
> |
"SimSetup error: If you use the NVT\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"); |
924 |
+ |
painCave.isFatal = 1; |
925 |
+ |
simError(); |
926 |
+ |
} |
927 |
+ |
|
928 |
+ |
|
929 |
|
#ifdef IS_MPI |
930 |
|
mpiSim->mpiRefresh(); |
931 |
|
#endif |
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; |