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 |
+ |
|
22 |
+ |
|
23 |
+ |
#define FF_DUFF 0 |
24 |
+ |
#define FF_LJ 1 |
25 |
+ |
|
26 |
+ |
|
27 |
|
SimSetup::SimSetup(){ |
28 |
|
stamps = new MakeStamps(); |
29 |
|
globals = new Globals(); |
78 |
|
|
79 |
|
MakeStamps *the_stamps; |
80 |
|
Globals* the_globals; |
81 |
< |
int i, j; |
81 |
> |
int i, j, k, globalAtomIndex; |
82 |
> |
|
83 |
> |
int ensembleCase; |
84 |
> |
int ffCase; |
85 |
> |
|
86 |
> |
ensembleCase = -1; |
87 |
> |
ffCase = -1; |
88 |
|
|
89 |
|
// get the stamps and globals; |
90 |
|
the_stamps = stamps; |
98 |
|
// get the ones we know are there, yet still may need some work. |
99 |
|
n_components = the_globals->getNComponents(); |
100 |
|
strcpy( force_field, the_globals->getForceField() ); |
101 |
+ |
|
102 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
103 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
104 |
+ |
else{ |
105 |
+ |
sprintf( painCave.errMsg, |
106 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
107 |
+ |
force_field ); |
108 |
+ |
painCave.isFatal = 1; |
109 |
+ |
simError(); |
110 |
+ |
} |
111 |
+ |
|
112 |
+ |
// get the ensemble: |
113 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
114 |
+ |
|
115 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
116 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
117 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
118 |
+ |
ensembleCase = NPTi_ENS; |
119 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
120 |
+ |
else{ |
121 |
+ |
sprintf( painCave.errMsg, |
122 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
123 |
+ |
"reverting to NVE for this simulation.\n", |
124 |
+ |
ensemble ); |
125 |
+ |
painCave.isFatal = 0; |
126 |
+ |
simError(); |
127 |
+ |
strcpy( ensemble, "NVE" ); |
128 |
+ |
ensembleCase = NVE_ENS; |
129 |
+ |
} |
130 |
|
strcpy( simnfo->ensemble, ensemble ); |
131 |
+ |
|
132 |
+ |
|
133 |
+ |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
134 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
135 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
136 |
+ |
// if (the_globals->haveTargetPressure()) |
137 |
+ |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
138 |
+ |
// else { |
139 |
+ |
// sprintf( painCave.errMsg, |
140 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
141 |
+ |
// " ensemble, you must set targetPressure.\n" |
142 |
+ |
// " This was found in the BASS file.\n"); |
143 |
+ |
// painCave.isFatal = 1; |
144 |
+ |
// simError(); |
145 |
+ |
// } |
146 |
+ |
|
147 |
+ |
// if (the_globals->haveTauThermostat()) |
148 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
149 |
+ |
// else if (the_globals->haveQmass()) |
150 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
151 |
+ |
// else { |
152 |
+ |
// sprintf( painCave.errMsg, |
153 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
154 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
155 |
+ |
// " Neither of these was found in the BASS file.\n"); |
156 |
+ |
// painCave.isFatal = 1; |
157 |
+ |
// simError(); |
158 |
+ |
// } |
159 |
+ |
|
160 |
+ |
// if (the_globals->haveTauBarostat()) |
161 |
+ |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
162 |
+ |
// else { |
163 |
+ |
// sprintf( painCave.errMsg, |
164 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
165 |
+ |
// " ensemble, you must set tauBarostat.\n" |
166 |
+ |
// " This was found in the BASS file.\n"); |
167 |
+ |
// painCave.isFatal = 1; |
168 |
+ |
// simError(); |
169 |
+ |
// } |
170 |
|
|
171 |
+ |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
172 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
173 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
174 |
+ |
|
175 |
+ |
// if (the_globals->haveTauThermostat()) |
176 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
177 |
+ |
// else if (the_globals->haveQmass()) |
178 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
179 |
+ |
// else { |
180 |
+ |
// sprintf( painCave.errMsg, |
181 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
182 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
183 |
+ |
// " Neither of these was found in the BASS file.\n"); |
184 |
+ |
// painCave.isFatal = 1; |
185 |
+ |
// simError(); |
186 |
+ |
// } |
187 |
+ |
|
188 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
189 |
|
simnfo->usePBC = the_globals->getPBC(); |
190 |
|
|
191 |
+ |
int usesDipoles = 0; |
192 |
+ |
switch( ffCase ){ |
193 |
|
|
194 |
+ |
case FF_DUFF: |
195 |
+ |
the_ff = new DUFF(); |
196 |
+ |
usesDipoles = 1; |
197 |
+ |
break; |
198 |
|
|
199 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
200 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
201 |
< |
else{ |
199 |
> |
case FF_LJ: |
200 |
> |
the_ff = new LJFF(); |
201 |
> |
break; |
202 |
> |
|
203 |
> |
default: |
204 |
|
sprintf( painCave.errMsg, |
205 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
96 |
< |
force_field ); |
205 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
206 |
|
painCave.isFatal = 1; |
207 |
|
simError(); |
208 |
|
} |
212 |
|
MPIcheckPoint(); |
213 |
|
#endif // is_mpi |
214 |
|
|
106 |
– |
|
107 |
– |
|
215 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
216 |
|
the_components = the_globals->getComponents(); |
217 |
|
components_nmol = new int[n_components]; |
335 |
|
simnfo->n_torsions = tot_torsions; |
336 |
|
simnfo->n_SRI = tot_SRI; |
337 |
|
simnfo->n_mol = tot_nmol; |
231 |
– |
|
338 |
|
|
339 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
340 |
+ |
|
341 |
|
#ifdef IS_MPI |
342 |
|
|
343 |
|
// divide the molecules among processors here. |
344 |
|
|
345 |
|
mpiSim = new mpiSimulation( simnfo ); |
346 |
|
|
239 |
– |
|
240 |
– |
|
347 |
|
globalIndex = mpiSim->divideLabor(); |
348 |
|
|
349 |
|
// set up the local variables |
360 |
|
local_bonds = 0; |
361 |
|
local_bends = 0; |
362 |
|
local_torsions = 0; |
363 |
+ |
globalAtomIndex = 0; |
364 |
+ |
|
365 |
+ |
|
366 |
|
for( i=0; i<n_components; i++ ){ |
367 |
|
|
368 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
369 |
|
|
370 |
< |
if( mol2proc[j] == worldRank ){ |
370 |
> |
if( mol2proc[allMol] == worldRank ){ |
371 |
|
|
372 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
373 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
375 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
376 |
|
localMol++; |
377 |
|
} |
378 |
< |
allMol++; |
378 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
379 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
380 |
> |
globalAtomIndex++; |
381 |
> |
} |
382 |
> |
|
383 |
> |
allMol++; |
384 |
|
} |
385 |
|
} |
386 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
387 |
|
|
274 |
– |
|
388 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
389 |
|
|
390 |
|
if( local_atoms != simnfo->n_atoms ){ |
427 |
|
|
428 |
|
if(mol2proc[i] == worldRank ){ |
429 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
430 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
431 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
432 |
|
molIndex++; |
433 |
|
} |
434 |
|
} |
436 |
|
#else // is_mpi |
437 |
|
|
438 |
|
molIndex = 0; |
439 |
+ |
globalAtomIndex = 0; |
440 |
|
for(i=0; i<n_components; i++){ |
441 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
442 |
|
the_molecules[molIndex].setStampID( i ); |
443 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
444 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
445 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
446 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
447 |
+ |
globalAtomIndex++; |
448 |
+ |
} |
449 |
|
molIndex++; |
450 |
|
} |
451 |
|
} |
456 |
|
|
457 |
|
if( simnfo->n_SRI ){ |
458 |
|
|
337 |
– |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 |
– |
|
459 |
|
Exclude::createArray(simnfo->n_SRI); |
460 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
461 |
|
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
462 |
|
simnfo->globalExcludes = new int; |
463 |
< |
simnfo->n_exclude = tot_SRI; |
463 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
464 |
|
} |
465 |
|
else{ |
466 |
|
|
483 |
|
|
484 |
|
// get some of the tricky things that may still be in the globals |
485 |
|
|
486 |
< |
|
486 |
> |
double boxVector[3]; |
487 |
|
if( the_globals->haveBox() ){ |
488 |
< |
simnfo->box_x = the_globals->getBox(); |
489 |
< |
simnfo->box_y = the_globals->getBox(); |
490 |
< |
simnfo->box_z = the_globals->getBox(); |
488 |
> |
boxVector[0] = the_globals->getBox(); |
489 |
> |
boxVector[1] = the_globals->getBox(); |
490 |
> |
boxVector[2] = the_globals->getBox(); |
491 |
> |
|
492 |
> |
simnfo->setBox( boxVector ); |
493 |
|
} |
494 |
|
else if( the_globals->haveDensity() ){ |
495 |
|
|
496 |
|
double vol; |
497 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
498 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
499 |
< |
simnfo->box_y = simnfo->box_x; |
500 |
< |
simnfo->box_z = simnfo->box_x; |
498 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
499 |
> |
boxVector[1] = boxVector[0]; |
500 |
> |
boxVector[2] = boxVector[0]; |
501 |
> |
|
502 |
> |
simnfo->setBox( boxVector ); |
503 |
|
} |
504 |
|
else{ |
505 |
|
if( !the_globals->haveBoxX() ){ |
508 |
|
painCave.isFatal = 1; |
509 |
|
simError(); |
510 |
|
} |
511 |
< |
simnfo->box_x = the_globals->getBoxX(); |
511 |
> |
boxVector[0] = the_globals->getBoxX(); |
512 |
|
|
513 |
|
if( !the_globals->haveBoxY() ){ |
514 |
|
sprintf( painCave.errMsg, |
516 |
|
painCave.isFatal = 1; |
517 |
|
simError(); |
518 |
|
} |
519 |
< |
simnfo->box_y = the_globals->getBoxY(); |
519 |
> |
boxVector[1] = the_globals->getBoxY(); |
520 |
|
|
521 |
|
if( !the_globals->haveBoxZ() ){ |
522 |
|
sprintf( painCave.errMsg, |
524 |
|
painCave.isFatal = 1; |
525 |
|
simError(); |
526 |
|
} |
527 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
527 |
> |
boxVector[2] = the_globals->getBoxZ(); |
528 |
> |
|
529 |
> |
simnfo->setBox( boxVector ); |
530 |
|
} |
531 |
|
|
532 |
|
#ifdef IS_MPI |
556 |
|
painCave.isFatal = 0; |
557 |
|
simError(); |
558 |
|
double smallest; |
559 |
< |
smallest = simnfo->box_x; |
560 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
561 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 |
> |
smallest = simnfo->boxLx; |
560 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
561 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
562 |
|
simnfo->ecr = 0.5 * smallest; |
563 |
|
} else { |
564 |
|
simnfo->ecr = the_globals->getECR(); |
586 |
|
} |
587 |
|
simnfo->dielectric = the_globals->getDielectric(); |
588 |
|
} else { |
589 |
< |
if (simnfo->n_dipoles) { |
589 |
> |
if (usesDipoles) { |
590 |
|
|
591 |
|
if( !the_globals->haveECR() ){ |
592 |
|
sprintf( painCave.errMsg, |
593 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
593 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
594 |
|
"box length for the electrostaticCutoffRadius.\n" |
595 |
|
"I hope you have a very fast processor!\n"); |
596 |
|
painCave.isFatal = 0; |
597 |
|
simError(); |
598 |
|
double smallest; |
599 |
< |
smallest = simnfo->box_x; |
600 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
601 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
599 |
> |
smallest = simnfo->boxLx; |
600 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
601 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
602 |
|
simnfo->ecr = 0.5 * smallest; |
603 |
|
} else { |
604 |
|
simnfo->ecr = the_globals->getECR(); |
606 |
|
|
607 |
|
if( !the_globals->haveEST() ){ |
608 |
|
sprintf( painCave.errMsg, |
609 |
< |
"SimSetup Warning: using default value of 5% of the" |
609 |
> |
"SimSetup Warning: using default value of 5%% of the " |
610 |
|
"electrostaticCutoffRadius for the " |
611 |
|
"electrostaticSkinThickness\n" |
612 |
|
); |
777 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
778 |
|
|
779 |
|
|
780 |
< |
// // make the longe range forces and the integrator |
780 |
> |
// make the integrator |
781 |
> |
|
782 |
> |
|
783 |
> |
NVT* myNVT = NULL; |
784 |
> |
NPTi* myNPTi = NULL; |
785 |
> |
NPTf* myNPTf = NULL; |
786 |
> |
switch( ensembleCase ){ |
787 |
|
|
788 |
< |
// new AllLong( simnfo ); |
788 |
> |
case NVE_ENS: |
789 |
> |
new NVE( simnfo, the_ff ); |
790 |
> |
break; |
791 |
> |
|
792 |
> |
case NVT_ENS: |
793 |
> |
myNVT = new NVT( simnfo, the_ff ); |
794 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
795 |
|
|
796 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
797 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
796 |
> |
if (the_globals->haveTauThermostat()) |
797 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
798 |
|
|
799 |
+ |
else { |
800 |
+ |
sprintf( painCave.errMsg, |
801 |
+ |
"SimSetup error: If you use the NVT\n" |
802 |
+ |
" ensemble, you must set tauThermostat.\n"); |
803 |
+ |
painCave.isFatal = 1; |
804 |
+ |
simError(); |
805 |
+ |
} |
806 |
+ |
break; |
807 |
+ |
|
808 |
+ |
case NPTi_ENS: |
809 |
+ |
myNPTi = new NPTi( simnfo, the_ff ); |
810 |
+ |
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
811 |
+ |
|
812 |
+ |
if (the_globals->haveTargetPressure()) |
813 |
+ |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
814 |
+ |
else { |
815 |
+ |
sprintf( painCave.errMsg, |
816 |
+ |
"SimSetup error: If you use a constant pressure\n" |
817 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
818 |
+ |
painCave.isFatal = 1; |
819 |
+ |
simError(); |
820 |
+ |
} |
821 |
+ |
|
822 |
+ |
if( the_globals->haveTauThermostat() ) |
823 |
+ |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
824 |
+ |
else{ |
825 |
+ |
sprintf( painCave.errMsg, |
826 |
+ |
"SimSetup error: If you use an NPT\n" |
827 |
+ |
" ensemble, you must set tauThermostat.\n"); |
828 |
+ |
painCave.isFatal = 1; |
829 |
+ |
simError(); |
830 |
+ |
} |
831 |
+ |
|
832 |
+ |
if( the_globals->haveTauBarostat() ) |
833 |
+ |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
834 |
+ |
else{ |
835 |
+ |
sprintf( painCave.errMsg, |
836 |
+ |
"SimSetup error: If you use an NPT\n" |
837 |
+ |
" ensemble, you must set tauBarostat.\n"); |
838 |
+ |
painCave.isFatal = 1; |
839 |
+ |
simError(); |
840 |
+ |
} |
841 |
+ |
break; |
842 |
+ |
|
843 |
+ |
case NPTf_ENS: |
844 |
+ |
myNPTf = new NPTf( simnfo, the_ff ); |
845 |
+ |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
846 |
+ |
|
847 |
+ |
if (the_globals->haveTargetPressure()) |
848 |
+ |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
849 |
+ |
else { |
850 |
+ |
sprintf( painCave.errMsg, |
851 |
+ |
"SimSetup error: If you use a constant pressure\n" |
852 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
853 |
+ |
painCave.isFatal = 1; |
854 |
+ |
simError(); |
855 |
+ |
} |
856 |
+ |
|
857 |
+ |
if( the_globals->haveTauThermostat() ) |
858 |
+ |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
859 |
+ |
else{ |
860 |
+ |
sprintf( painCave.errMsg, |
861 |
+ |
"SimSetup error: If you use an NPT\n" |
862 |
+ |
" ensemble, you must set tauThermostat.\n"); |
863 |
+ |
painCave.isFatal = 1; |
864 |
+ |
simError(); |
865 |
+ |
} |
866 |
+ |
|
867 |
+ |
if( the_globals->haveTauBarostat() ) |
868 |
+ |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
869 |
+ |
else{ |
870 |
+ |
sprintf( painCave.errMsg, |
871 |
+ |
"SimSetup error: If you use an NPT\n" |
872 |
+ |
" ensemble, you must set tauBarostat.\n"); |
873 |
+ |
painCave.isFatal = 1; |
874 |
+ |
simError(); |
875 |
+ |
} |
876 |
+ |
break; |
877 |
+ |
|
878 |
+ |
|
879 |
+ |
|
880 |
+ |
default: |
881 |
+ |
sprintf( painCave.errMsg, |
882 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
883 |
+ |
painCave.isFatal = 1; |
884 |
+ |
simError(); |
885 |
+ |
} |
886 |
+ |
|
887 |
+ |
|
888 |
|
#ifdef IS_MPI |
889 |
|
mpiSim->mpiRefresh(); |
890 |
|
#endif |
1010 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
1011 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
1012 |
|
|
1013 |
< |
exI = theBonds[i].a; |
1014 |
< |
exJ = theBonds[i].b; |
1013 |
> |
exI = theBonds[j].a; |
1014 |
> |
exJ = theBonds[j].b; |
1015 |
|
|
1016 |
|
// exclude_I must always be the smaller of the pair |
1017 |
|
if( exI > exJ ){ |
1027 |
|
|
1028 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1029 |
|
#else // isn't MPI |
1030 |
+ |
|
1031 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1032 |
|
#endif //is_mpi |
1033 |
|
} |
1065 |
|
|
1066 |
|
default: |
1067 |
|
sprintf( painCave.errMsg, |
1068 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
1068 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
1069 |
|
"double nor an int.\n" |
1070 |
|
"-->Bend[%d] in %s\n", |
1071 |
|
j, comp_stamps[stampID]->getID() ); |
1159 |
|
|
1160 |
|
|
1161 |
|
the_molecules[i].initialize( info ); |
1162 |
+ |
|
1163 |
+ |
|
1164 |
|
atomOffset += info.nAtoms; |
1165 |
|
delete[] theBonds; |
1166 |
|
delete[] theBends; |
1167 |
|
delete[] theTorsions; |
1168 |
|
} |
1169 |
|
|
1170 |
+ |
#ifdef IS_MPI |
1171 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1172 |
+ |
MPIcheckPoint(); |
1173 |
+ |
#endif // is_mpi |
1174 |
+ |
|
1175 |
|
// clean up the forcefield |
1176 |
|
the_ff->calcRcut(); |
1177 |
|
the_ff->cleanMe(); |
1178 |
+ |
|
1179 |
|
} |
1180 |
|
|
1181 |
|
void SimSetup::initFromBass( void ){ |
1197 |
|
have_extra =1; |
1198 |
|
|
1199 |
|
n_cells = (int)temp3 - 1; |
1200 |
< |
cellx = simnfo->box_x / temp3; |
1201 |
< |
celly = simnfo->box_y / temp3; |
1202 |
< |
cellz = simnfo->box_z / temp3; |
1200 |
> |
cellx = simnfo->boxLx / temp3; |
1201 |
> |
celly = simnfo->boxLy / temp3; |
1202 |
> |
cellz = simnfo->boxLz / temp3; |
1203 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1204 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1205 |
|
n_per_extra = (int)ceil( temp1 ); |
1214 |
|
} |
1215 |
|
else{ |
1216 |
|
n_cells = (int)temp3; |
1217 |
< |
cellx = simnfo->box_x / temp3; |
1218 |
< |
celly = simnfo->box_y / temp3; |
1219 |
< |
cellz = simnfo->box_z / temp3; |
1217 |
> |
cellx = simnfo->boxLx / temp3; |
1218 |
> |
celly = simnfo->boxLy / temp3; |
1219 |
> |
cellz = simnfo->boxLz / temp3; |
1220 |
|
} |
1221 |
|
|
1222 |
|
current_mol = 0; |