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 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
92 |
+ |
the_extendedsystem->setTauRelax(the_globals->getTauRelax()); |
93 |
+ |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
94 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
95 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
96 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
97 |
+ |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
98 |
+ |
} else { |
99 |
+ |
sprintf( painCave.errMsg, |
100 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
101 |
+ |
"reverting to NVE for this simulation.\n", |
102 |
+ |
ensemble ); |
103 |
+ |
painCave.isFatal = 0; |
104 |
+ |
simError(); |
105 |
+ |
strcpy( ensemble, "NVE" ); |
106 |
+ |
} |
107 |
|
strcpy( simnfo->ensemble, ensemble ); |
108 |
|
|
109 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
110 |
|
simnfo->usePBC = the_globals->getPBC(); |
111 |
|
|
112 |
< |
|
113 |
< |
|
114 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
115 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
116 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
117 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
112 |
> |
int usesDipoles = 0; |
113 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
114 |
> |
the_ff = new TraPPE_ExFF(); |
115 |
> |
usesDipoles = 1; |
116 |
> |
} |
117 |
> |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
118 |
|
else{ |
119 |
|
sprintf( painCave.errMsg, |
120 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
265 |
|
|
266 |
|
globalIndex = mpiSim->divideLabor(); |
267 |
|
|
245 |
– |
|
246 |
– |
|
268 |
|
// set up the local variables |
269 |
|
|
270 |
|
int localMol, allMol; |
271 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
272 |
+ |
|
273 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
274 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
275 |
|
|
276 |
|
allMol = 0; |
277 |
|
localMol = 0; |
283 |
|
|
284 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
285 |
|
|
286 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
286 |
> |
if( mol2proc[j] == worldRank ){ |
287 |
|
|
288 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
289 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
302 |
|
if( local_atoms != simnfo->n_atoms ){ |
303 |
|
sprintf( painCave.errMsg, |
304 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
305 |
< |
" localAtom (%d) are note equal.\n", |
305 |
> |
" localAtom (%d) are not equal.\n", |
306 |
|
simnfo->n_atoms, |
307 |
|
local_atoms ); |
308 |
|
painCave.isFatal = 1; |
327 |
|
Atom::createArrays(simnfo->n_atoms); |
328 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
329 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
330 |
+ |
int molIndex; |
331 |
|
|
332 |
+ |
// initialize the molecule's stampID's |
333 |
|
|
334 |
+ |
#ifdef IS_MPI |
335 |
+ |
|
336 |
+ |
|
337 |
+ |
molIndex = 0; |
338 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
339 |
+ |
|
340 |
+ |
if(mol2proc[i] == worldRank ){ |
341 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
342 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
343 |
+ |
molIndex++; |
344 |
+ |
} |
345 |
+ |
} |
346 |
+ |
|
347 |
+ |
#else // is_mpi |
348 |
+ |
|
349 |
+ |
molIndex = 0; |
350 |
+ |
for(i=0; i<n_components; i++){ |
351 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
352 |
+ |
the_molecules[molIndex].setStampID( i ); |
353 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
354 |
+ |
molIndex++; |
355 |
+ |
} |
356 |
+ |
} |
357 |
+ |
|
358 |
+ |
|
359 |
+ |
#endif // is_mpi |
360 |
+ |
|
361 |
+ |
|
362 |
|
if( simnfo->n_SRI ){ |
363 |
+ |
|
364 |
|
Exclude::createArray(simnfo->n_SRI); |
365 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
366 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
367 |
|
simnfo->globalExcludes = new int; |
368 |
< |
simnfo->n_exclude = tot_SRI; |
368 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
369 |
|
} |
370 |
|
else{ |
371 |
|
|
381 |
|
// set the arrays into the SimInfo object |
382 |
|
|
383 |
|
simnfo->atoms = the_atoms; |
384 |
< |
simnfo->sr_interactions = the_sris; |
384 |
> |
simnfo->molecules = the_molecules; |
385 |
|
simnfo->nGlobalExcludes = 0; |
386 |
|
simnfo->excludes = the_excludes; |
387 |
|
|
438 |
|
|
439 |
|
the_ff->setSimInfo( simnfo ); |
440 |
|
|
441 |
< |
makeAtoms(); |
441 |
> |
makeMolecules(); |
442 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
443 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
444 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
445 |
|
} |
446 |
|
|
392 |
– |
if( tot_bonds ){ |
393 |
– |
makeBonds(); |
394 |
– |
} |
395 |
– |
|
396 |
– |
if( tot_bends ){ |
397 |
– |
makeBends(); |
398 |
– |
} |
399 |
– |
|
400 |
– |
if( tot_torsions ){ |
401 |
– |
makeTorsions(); |
402 |
– |
} |
403 |
– |
|
404 |
– |
|
447 |
|
if (the_globals->getUseRF() ) { |
448 |
|
simnfo->useReactionField = 1; |
449 |
|
|
485 |
|
} |
486 |
|
simnfo->dielectric = the_globals->getDielectric(); |
487 |
|
} else { |
488 |
< |
if (simnfo->n_dipoles) { |
488 |
> |
if (usesDipoles) { |
489 |
|
|
490 |
|
if( !the_globals->haveECR() ){ |
491 |
|
sprintf( painCave.errMsg, |
492 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
492 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
493 |
|
"box length for the electrostaticCutoffRadius.\n" |
494 |
|
"I hope you have a very fast processor!\n"); |
495 |
|
painCave.isFatal = 0; |
505 |
|
|
506 |
|
if( !the_globals->haveEST() ){ |
507 |
|
sprintf( painCave.errMsg, |
508 |
< |
"SimSetup Warning: using default value of 5% of the" |
508 |
> |
"SimSetup Warning: using default value of 5%% of the " |
509 |
|
"electrostaticCutoffRadius for the " |
510 |
|
"electrostaticSkinThickness\n" |
511 |
|
); |
680 |
|
|
681 |
|
// new AllLong( simnfo ); |
682 |
|
|
641 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
683 |
|
|
684 |
< |
|
684 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
685 |
> |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
686 |
> |
std::cerr << "called new Symplecic\n"; |
687 |
> |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
688 |
> |
} |
689 |
> |
else if( !strcmp( force_field, "LJ" ) ){ |
690 |
> |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
691 |
> |
std::cerr << "called new Verlet\n"; |
692 |
> |
fprintf( stderr, "called new Verlet. stderr\n" ); |
693 |
> |
} |
694 |
> |
else { |
695 |
> |
std::cerr << "I'm a bug.\n"; |
696 |
> |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
697 |
> |
} |
698 |
> |
#ifdef IS_MPI |
699 |
> |
mpiSim->mpiRefresh(); |
700 |
> |
#endif |
701 |
|
|
702 |
|
// initialize the Fortran |
703 |
< |
|
703 |
> |
|
704 |
> |
|
705 |
|
simnfo->refreshSim(); |
706 |
|
|
707 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
738 |
|
BondStamp* currentBond; |
739 |
|
BendStamp* currentBend; |
740 |
|
TorsionStamp* currentTorsion; |
741 |
+ |
|
742 |
+ |
bond_pair* theBonds; |
743 |
+ |
bend_set* theBends; |
744 |
+ |
torsion_set* theTorsions; |
745 |
+ |
|
746 |
|
|
747 |
|
//init the forceField paramters |
748 |
|
|
749 |
|
the_ff->readParams(); |
750 |
|
|
751 |
|
|
752 |
< |
// init the molecules |
752 |
> |
// init the atoms |
753 |
|
|
754 |
+ |
double ux, uy, uz, u, uSqr; |
755 |
+ |
|
756 |
|
atomOffset = 0; |
757 |
|
excludeOffset = 0; |
758 |
|
for(i=0; i<simnfo->n_mol; i++){ |
769 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
770 |
|
info.myBonds = new Bond*[info.nBonds]; |
771 |
|
info.myBends = new Bend*[info.nBends]; |
772 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
772 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
773 |
|
|
774 |
|
theBonds = new bond_pair[info.nBonds]; |
775 |
|
theBends = new bend_set[info.nBends]; |
779 |
|
|
780 |
|
for(j=0; j<info.nAtoms; j++){ |
781 |
|
|
782 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
782 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
783 |
|
if( currentAtom->haveOrientation() ){ |
784 |
|
|
785 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
820 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
821 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
822 |
|
|
823 |
< |
exI = theBonds[i].a; |
824 |
< |
exJ = theBonds[i].b; |
823 |
> |
exI = theBonds[j].a; |
824 |
> |
exJ = theBonds[j].b; |
825 |
|
|
826 |
|
// exclude_I must always be the smaller of the pair |
827 |
|
if( exI > exJ ){ |
837 |
|
|
838 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
839 |
|
#else // isn't MPI |
840 |
+ |
|
841 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
842 |
|
#endif //is_mpi |
843 |
|
} |
853 |
|
|
854 |
|
if( currentBend->haveExtras() ){ |
855 |
|
|
856 |
< |
extras = current_bend->getExtras(); |
856 |
> |
extras = currentBend->getExtras(); |
857 |
|
current_extra = extras; |
858 |
|
|
859 |
|
while( current_extra != NULL ){ |
875 |
|
|
876 |
|
default: |
877 |
|
sprintf( painCave.errMsg, |
878 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
878 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
879 |
|
"double nor an int.\n" |
880 |
|
"-->Bend[%d] in %s\n", |
881 |
|
j, comp_stamps[stampID]->getID() ); |
969 |
|
|
970 |
|
|
971 |
|
the_molecules[i].initialize( info ); |
972 |
+ |
|
973 |
+ |
|
974 |
|
atomOffset += info.nAtoms; |
975 |
+ |
delete[] theBonds; |
976 |
+ |
delete[] theBends; |
977 |
+ |
delete[] theTorsions; |
978 |
|
} |
979 |
|
|
980 |
+ |
#ifdef IS_MPI |
981 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
982 |
+ |
MPIcheckPoint(); |
983 |
+ |
#endif // is_mpi |
984 |
+ |
|
985 |
|
// clean up the forcefield |
986 |
|
the_ff->calcRcut(); |
987 |
|
the_ff->cleanMe(); |
988 |
+ |
|
989 |
|
} |
990 |
|
|
991 |
|
void SimSetup::initFromBass( void ){ |