| 67 |
|
MakeStamps *the_stamps; |
| 68 |
|
Globals* the_globals; |
| 69 |
|
ExtendedSystem* the_extendedsystem; |
| 70 |
< |
int i, j; |
| 70 |
> |
int i, j, k, globalAtomIndex; |
| 71 |
|
|
| 72 |
|
// get the stamps and globals; |
| 73 |
|
the_stamps = stamps; |
| 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()); |
| 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 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
| 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, |
| 298 |
|
simnfo->n_torsions = tot_torsions; |
| 299 |
|
simnfo->n_SRI = tot_SRI; |
| 300 |
|
simnfo->n_mol = tot_nmol; |
| 256 |
– |
|
| 301 |
|
|
| 302 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
| 303 |
+ |
|
| 304 |
|
#ifdef IS_MPI |
| 305 |
|
|
| 306 |
|
// divide the molecules among processors here. |
| 307 |
|
|
| 308 |
|
mpiSim = new mpiSimulation( simnfo ); |
| 309 |
|
|
| 264 |
– |
|
| 265 |
– |
|
| 310 |
|
globalIndex = mpiSim->divideLabor(); |
| 311 |
|
|
| 312 |
|
// set up the local variables |
| 323 |
|
local_bonds = 0; |
| 324 |
|
local_bends = 0; |
| 325 |
|
local_torsions = 0; |
| 326 |
+ |
globalAtomIndex = 0; |
| 327 |
+ |
|
| 328 |
+ |
|
| 329 |
|
for( i=0; i<n_components; i++ ){ |
| 330 |
|
|
| 331 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 332 |
|
|
| 333 |
< |
if( mol2proc[j] == worldRank ){ |
| 333 |
> |
if( mol2proc[allMol] == worldRank ){ |
| 334 |
|
|
| 335 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 336 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 338 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
| 339 |
|
localMol++; |
| 340 |
|
} |
| 341 |
< |
allMol++; |
| 341 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 342 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
| 343 |
> |
globalAtomIndex++; |
| 344 |
> |
} |
| 345 |
> |
|
| 346 |
> |
allMol++; |
| 347 |
|
} |
| 348 |
|
} |
| 349 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
| 350 |
|
|
| 299 |
– |
|
| 351 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
| 352 |
|
|
| 353 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 391 |
|
if(mol2proc[i] == worldRank ){ |
| 392 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 393 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
| 394 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
| 395 |
|
molIndex++; |
| 396 |
|
} |
| 397 |
|
} |
| 399 |
|
#else // is_mpi |
| 400 |
|
|
| 401 |
|
molIndex = 0; |
| 402 |
+ |
globalAtomIndex = 0; |
| 403 |
|
for(i=0; i<n_components; i++){ |
| 404 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
| 405 |
|
the_molecules[molIndex].setStampID( i ); |
| 406 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
| 407 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
| 408 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 409 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
| 410 |
+ |
globalAtomIndex++; |
| 411 |
+ |
} |
| 412 |
|
molIndex++; |
| 413 |
|
} |
| 414 |
|
} |
| 732 |
|
// check for the temperature set flag |
| 733 |
|
|
| 734 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
| 677 |
– |
|
| 735 |
|
|
| 679 |
– |
// // make the longe range forces and the integrator |
| 736 |
|
|
| 737 |
< |
// new AllLong( simnfo ); |
| 737 |
> |
// make the integrator |
| 738 |
|
|
| 739 |
|
|
| 740 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 740 |
> |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
| 741 |
|
new Symplectic(simnfo, the_ff, the_extendedsystem); |
| 686 |
– |
std::cerr << "called new Symplecic\n"; |
| 687 |
– |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
| 742 |
|
} |
| 743 |
|
else if( !strcmp( force_field, "LJ" ) ){ |
| 744 |
|
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
| 691 |
– |
std::cerr << "called new Verlet\n"; |
| 692 |
– |
fprintf( stderr, "called new Verlet. stderr\n" ); |
| 745 |
|
} |
| 746 |
< |
else { |
| 695 |
< |
std::cerr << "I'm a bug.\n"; |
| 696 |
< |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
| 697 |
< |
} |
| 746 |
> |
|
| 747 |
|
#ifdef IS_MPI |
| 748 |
|
mpiSim->mpiRefresh(); |
| 749 |
|
#endif |
