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 |
+ |
if (the_globals->haveTargetPressure()) |
91 |
+ |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 |
+ |
else { |
93 |
+ |
sprintf( painCave.errMsg, |
94 |
+ |
"SimSetup error: If you use the constant pressure\n" |
95 |
+ |
" ensemble, you must set targetPressure.\n" |
96 |
+ |
" This was found in the BASS file.\n"); |
97 |
+ |
painCave.isFatal = 1; |
98 |
+ |
simError(); |
99 |
+ |
} |
100 |
+ |
|
101 |
+ |
if (the_globals->haveTauThermostat()) |
102 |
+ |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 |
+ |
else if (the_globals->haveQmass()) |
104 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
105 |
+ |
else { |
106 |
+ |
sprintf( painCave.errMsg, |
107 |
+ |
"SimSetup error: If you use one of the constant temperature\n" |
108 |
+ |
" ensembles, you must set either tauThermostat or qMass.\n" |
109 |
+ |
" Neither of these was found in the BASS file.\n"); |
110 |
+ |
painCave.isFatal = 1; |
111 |
+ |
simError(); |
112 |
+ |
} |
113 |
+ |
|
114 |
+ |
if (the_globals->haveTauBarostat()) |
115 |
+ |
the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 |
+ |
else { |
117 |
+ |
sprintf( painCave.errMsg, |
118 |
+ |
"SimSetup error: If you use the constant pressure\n" |
119 |
+ |
" ensemble, you must set tauBarostat.\n" |
120 |
+ |
" This was found in the BASS file.\n"); |
121 |
+ |
painCave.isFatal = 1; |
122 |
+ |
simError(); |
123 |
+ |
} |
124 |
+ |
|
125 |
+ |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
126 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
127 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
128 |
+ |
|
129 |
+ |
if (the_globals->haveTauThermostat()) |
130 |
+ |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 |
+ |
else if (the_globals->haveQmass()) |
132 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
133 |
+ |
else { |
134 |
+ |
sprintf( painCave.errMsg, |
135 |
+ |
"SimSetup error: If you use one of the constant temperature\n" |
136 |
+ |
" ensembles, you must set either tauThermostat or qMass.\n" |
137 |
+ |
" Neither of these was found in the BASS file.\n"); |
138 |
+ |
painCave.isFatal = 1; |
139 |
+ |
simError(); |
140 |
+ |
} |
141 |
+ |
|
142 |
+ |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
143 |
+ |
} else { |
144 |
+ |
sprintf( painCave.errMsg, |
145 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 |
+ |
"reverting to NVE for this simulation.\n", |
147 |
+ |
ensemble ); |
148 |
+ |
painCave.isFatal = 0; |
149 |
+ |
simError(); |
150 |
+ |
strcpy( ensemble, "NVE" ); |
151 |
+ |
} |
152 |
|
strcpy( simnfo->ensemble, ensemble ); |
153 |
|
|
154 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 |
|
simnfo->usePBC = the_globals->getPBC(); |
156 |
|
|
157 |
< |
|
158 |
< |
|
159 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
160 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
161 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
162 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
157 |
> |
int usesDipoles = 0; |
158 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 |
> |
the_ff = new TraPPE_ExFF(); |
160 |
> |
usesDipoles = 1; |
161 |
> |
} |
162 |
> |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 |
|
else{ |
164 |
|
sprintf( painCave.errMsg, |
165 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
310 |
|
|
311 |
|
globalIndex = mpiSim->divideLabor(); |
312 |
|
|
245 |
– |
|
246 |
– |
|
313 |
|
// set up the local variables |
314 |
|
|
315 |
|
int localMol, allMol; |
316 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
317 |
+ |
|
318 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
319 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
320 |
|
|
321 |
|
allMol = 0; |
322 |
|
localMol = 0; |
328 |
|
|
329 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
330 |
|
|
331 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
331 |
> |
if( mol2proc[allMol] == worldRank ){ |
332 |
|
|
333 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
334 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
347 |
|
if( local_atoms != simnfo->n_atoms ){ |
348 |
|
sprintf( painCave.errMsg, |
349 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
350 |
< |
" localAtom (%d) are note equal.\n", |
350 |
> |
" localAtom (%d) are not equal.\n", |
351 |
|
simnfo->n_atoms, |
352 |
|
local_atoms ); |
353 |
|
painCave.isFatal = 1; |
372 |
|
Atom::createArrays(simnfo->n_atoms); |
373 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
374 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
375 |
+ |
int molIndex; |
376 |
|
|
377 |
+ |
// initialize the molecule's stampID's |
378 |
|
|
379 |
+ |
#ifdef IS_MPI |
380 |
+ |
|
381 |
+ |
|
382 |
+ |
molIndex = 0; |
383 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
384 |
+ |
|
385 |
+ |
if(mol2proc[i] == worldRank ){ |
386 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
387 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
388 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
389 |
+ |
molIndex++; |
390 |
+ |
} |
391 |
+ |
} |
392 |
+ |
|
393 |
+ |
#else // is_mpi |
394 |
+ |
|
395 |
+ |
molIndex = 0; |
396 |
+ |
for(i=0; i<n_components; i++){ |
397 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
398 |
+ |
the_molecules[molIndex].setStampID( i ); |
399 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
400 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
401 |
+ |
molIndex++; |
402 |
+ |
} |
403 |
+ |
} |
404 |
+ |
|
405 |
+ |
|
406 |
+ |
#endif // is_mpi |
407 |
+ |
|
408 |
+ |
|
409 |
|
if( simnfo->n_SRI ){ |
410 |
+ |
|
411 |
|
Exclude::createArray(simnfo->n_SRI); |
412 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
413 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
414 |
|
simnfo->globalExcludes = new int; |
415 |
< |
simnfo->n_exclude = tot_SRI; |
415 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
416 |
|
} |
417 |
|
else{ |
418 |
|
|
428 |
|
// set the arrays into the SimInfo object |
429 |
|
|
430 |
|
simnfo->atoms = the_atoms; |
431 |
< |
simnfo->sr_interactions = the_sris; |
431 |
> |
simnfo->molecules = the_molecules; |
432 |
|
simnfo->nGlobalExcludes = 0; |
433 |
|
simnfo->excludes = the_excludes; |
434 |
|
|
485 |
|
|
486 |
|
the_ff->setSimInfo( simnfo ); |
487 |
|
|
488 |
< |
makeAtoms(); |
488 |
> |
makeMolecules(); |
489 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
490 |
+ |
simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
491 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
492 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
493 |
|
} |
494 |
< |
|
495 |
< |
if( tot_bonds ){ |
393 |
< |
makeBonds(); |
494 |
> |
for(i=0; i< simnfo->n_mol; i++) { |
495 |
> |
the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
496 |
|
} |
497 |
< |
|
396 |
< |
if( tot_bends ){ |
397 |
< |
makeBends(); |
398 |
< |
} |
399 |
< |
|
400 |
< |
if( tot_torsions ){ |
401 |
< |
makeTorsions(); |
402 |
< |
} |
403 |
< |
|
404 |
< |
|
497 |
> |
|
498 |
|
if (the_globals->getUseRF() ) { |
499 |
|
simnfo->useReactionField = 1; |
500 |
|
|
536 |
|
} |
537 |
|
simnfo->dielectric = the_globals->getDielectric(); |
538 |
|
} else { |
539 |
< |
if (simnfo->n_dipoles) { |
539 |
> |
if (usesDipoles) { |
540 |
|
|
541 |
|
if( !the_globals->haveECR() ){ |
542 |
|
sprintf( painCave.errMsg, |
543 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
543 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
544 |
|
"box length for the electrostaticCutoffRadius.\n" |
545 |
|
"I hope you have a very fast processor!\n"); |
546 |
|
painCave.isFatal = 0; |
556 |
|
|
557 |
|
if( !the_globals->haveEST() ){ |
558 |
|
sprintf( painCave.errMsg, |
559 |
< |
"SimSetup Warning: using default value of 5% of the" |
559 |
> |
"SimSetup Warning: using default value of 5%% of the " |
560 |
|
"electrostaticCutoffRadius for the " |
561 |
|
"electrostaticSkinThickness\n" |
562 |
|
); |
730 |
|
// // make the longe range forces and the integrator |
731 |
|
|
732 |
|
// new AllLong( simnfo ); |
640 |
– |
|
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 ); |
733 |
|
|
734 |
|
|
735 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
736 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
737 |
+ |
} |
738 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
739 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
740 |
+ |
} |
741 |
+ |
else { |
742 |
+ |
std::cerr << "I'm a bug.\n"; |
743 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
744 |
+ |
} |
745 |
+ |
#ifdef IS_MPI |
746 |
+ |
mpiSim->mpiRefresh(); |
747 |
+ |
#endif |
748 |
|
|
749 |
|
// initialize the Fortran |
750 |
< |
|
750 |
> |
|
751 |
> |
|
752 |
|
simnfo->refreshSim(); |
753 |
|
|
754 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
785 |
|
BondStamp* currentBond; |
786 |
|
BendStamp* currentBend; |
787 |
|
TorsionStamp* currentTorsion; |
788 |
+ |
|
789 |
+ |
bond_pair* theBonds; |
790 |
+ |
bend_set* theBends; |
791 |
+ |
torsion_set* theTorsions; |
792 |
+ |
|
793 |
|
|
794 |
|
//init the forceField paramters |
795 |
|
|
796 |
|
the_ff->readParams(); |
797 |
|
|
798 |
|
|
799 |
< |
// init the molecules |
799 |
> |
// init the atoms |
800 |
|
|
801 |
+ |
double ux, uy, uz, u, uSqr; |
802 |
+ |
|
803 |
|
atomOffset = 0; |
804 |
|
excludeOffset = 0; |
805 |
|
for(i=0; i<simnfo->n_mol; i++){ |
816 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
817 |
|
info.myBonds = new Bond*[info.nBonds]; |
818 |
|
info.myBends = new Bend*[info.nBends]; |
819 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
819 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
820 |
|
|
821 |
|
theBonds = new bond_pair[info.nBonds]; |
822 |
|
theBends = new bend_set[info.nBends]; |
826 |
|
|
827 |
|
for(j=0; j<info.nAtoms; j++){ |
828 |
|
|
829 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
829 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
830 |
|
if( currentAtom->haveOrientation() ){ |
831 |
|
|
832 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
867 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
868 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
869 |
|
|
870 |
< |
exI = theBonds[i].a; |
871 |
< |
exJ = theBonds[i].b; |
870 |
> |
exI = theBonds[j].a; |
871 |
> |
exJ = theBonds[j].b; |
872 |
|
|
873 |
|
// exclude_I must always be the smaller of the pair |
874 |
|
if( exI > exJ ){ |
884 |
|
|
885 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
886 |
|
#else // isn't MPI |
887 |
+ |
|
888 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
889 |
|
#endif //is_mpi |
890 |
|
} |
900 |
|
|
901 |
|
if( currentBend->haveExtras() ){ |
902 |
|
|
903 |
< |
extras = current_bend->getExtras(); |
903 |
> |
extras = currentBend->getExtras(); |
904 |
|
current_extra = extras; |
905 |
|
|
906 |
|
while( current_extra != NULL ){ |
922 |
|
|
923 |
|
default: |
924 |
|
sprintf( painCave.errMsg, |
925 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
925 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
926 |
|
"double nor an int.\n" |
927 |
|
"-->Bend[%d] in %s\n", |
928 |
|
j, comp_stamps[stampID]->getID() ); |
1016 |
|
|
1017 |
|
|
1018 |
|
the_molecules[i].initialize( info ); |
1019 |
+ |
|
1020 |
+ |
|
1021 |
|
atomOffset += info.nAtoms; |
1022 |
+ |
delete[] theBonds; |
1023 |
+ |
delete[] theBends; |
1024 |
+ |
delete[] theTorsions; |
1025 |
|
} |
1026 |
|
|
1027 |
+ |
#ifdef IS_MPI |
1028 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1029 |
+ |
MPIcheckPoint(); |
1030 |
+ |
#endif // is_mpi |
1031 |
+ |
|
1032 |
|
// clean up the forcefield |
1033 |
|
the_ff->calcRcut(); |
1034 |
|
the_ff->cleanMe(); |
1035 |
+ |
|
1036 |
|
} |
1037 |
|
|
1038 |
|
void SimSetup::initFromBass( void ){ |