66 |
|
|
67 |
|
MakeStamps *the_stamps; |
68 |
|
Globals* the_globals; |
69 |
+ |
ExtendedSystem* the_extendedsystem; |
70 |
|
int i, j; |
71 |
|
|
72 |
|
// get the stamps and globals; |
81 |
|
// get the ones we know are there, yet still may need some work. |
82 |
|
n_components = the_globals->getNComponents(); |
83 |
|
strcpy( force_field, the_globals->getForceField() ); |
84 |
+ |
|
85 |
+ |
// get the ensemble and set up an extended system if we need it: |
86 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
87 |
+ |
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 |
+ |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 |
+ |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
92 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
93 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
94 |
+ |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
95 |
+ |
} else { |
96 |
+ |
sprintf( painCave.errMsg, |
97 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
98 |
+ |
"reverting to NVE for this simulation.\n", |
99 |
+ |
ensemble ); |
100 |
+ |
painCave.isFatal = 0; |
101 |
+ |
simError(); |
102 |
+ |
strcpy( ensemble, "NVE" ); |
103 |
+ |
} |
104 |
|
strcpy( simnfo->ensemble, ensemble ); |
105 |
|
|
106 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
107 |
|
simnfo->usePBC = the_globals->getPBC(); |
108 |
|
|
109 |
< |
|
110 |
< |
|
111 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
112 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
109 |
> |
int usesDipoles = 0; |
110 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
111 |
> |
the_ff = new TraPPE_ExFF(); |
112 |
> |
usesDipoles = 1; |
113 |
> |
} |
114 |
> |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
115 |
|
else{ |
116 |
|
sprintf( painCave.errMsg, |
117 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
336 |
|
|
337 |
|
if(mol2proc[i] == worldRank ){ |
338 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
339 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
340 |
|
molIndex++; |
341 |
|
} |
342 |
|
} |
347 |
|
for(i=0; i<n_components; i++){ |
348 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
349 |
|
the_molecules[molIndex].setStampID( i ); |
350 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
351 |
|
molIndex++; |
352 |
|
} |
353 |
|
} |
358 |
|
|
359 |
|
if( simnfo->n_SRI ){ |
360 |
|
|
337 |
– |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 |
– |
|
361 |
|
Exclude::createArray(simnfo->n_SRI); |
362 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
363 |
|
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
364 |
|
simnfo->globalExcludes = new int; |
365 |
< |
simnfo->n_exclude = tot_SRI; |
365 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
366 |
|
} |
367 |
|
else{ |
368 |
|
|
482 |
|
} |
483 |
|
simnfo->dielectric = the_globals->getDielectric(); |
484 |
|
} else { |
485 |
< |
if (simnfo->n_dipoles) { |
485 |
> |
if (usesDipoles) { |
486 |
|
|
487 |
|
if( !the_globals->haveECR() ){ |
488 |
|
sprintf( painCave.errMsg, |
489 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
489 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
490 |
|
"box length for the electrostaticCutoffRadius.\n" |
491 |
|
"I hope you have a very fast processor!\n"); |
492 |
|
painCave.isFatal = 0; |
502 |
|
|
503 |
|
if( !the_globals->haveEST() ){ |
504 |
|
sprintf( painCave.errMsg, |
505 |
< |
"SimSetup Warning: using default value of 5% of the" |
505 |
> |
"SimSetup Warning: using default value of 5%% of the " |
506 |
|
"electrostaticCutoffRadius for the " |
507 |
|
"electrostaticSkinThickness\n" |
508 |
|
); |
677 |
|
|
678 |
|
// new AllLong( simnfo ); |
679 |
|
|
658 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
659 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
680 |
|
|
681 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
682 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
683 |
+ |
std::cerr << "called new Symplecic\n"; |
684 |
+ |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
685 |
+ |
} |
686 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
687 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
688 |
+ |
std::cerr << "called new Verlet\n"; |
689 |
+ |
fprintf( stderr, "called new Verlet. stderr\n" ); |
690 |
+ |
} |
691 |
+ |
else { |
692 |
+ |
std::cerr << "I'm a bug.\n"; |
693 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
694 |
+ |
} |
695 |
|
#ifdef IS_MPI |
696 |
|
mpiSim->mpiRefresh(); |
697 |
|
#endif |
817 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
818 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
819 |
|
|
820 |
< |
exI = theBonds[i].a; |
821 |
< |
exJ = theBonds[i].b; |
820 |
> |
exI = theBonds[j].a; |
821 |
> |
exJ = theBonds[j].b; |
822 |
|
|
823 |
|
// exclude_I must always be the smaller of the pair |
824 |
|
if( exI > exJ ){ |
834 |
|
|
835 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
836 |
|
#else // isn't MPI |
837 |
+ |
|
838 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
839 |
|
#endif //is_mpi |
840 |
|
} |
966 |
|
|
967 |
|
|
968 |
|
the_molecules[i].initialize( info ); |
969 |
+ |
|
970 |
+ |
|
971 |
|
atomOffset += info.nAtoms; |
972 |
|
delete[] theBonds; |
973 |
|
delete[] theBends; |