| 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, |
| 328 |
|
|
| 329 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 330 |
|
|
| 331 |
< |
if( mol2proc[j] == worldRank ){ |
| 331 |
> |
if( mol2proc[allMol] == worldRank ){ |
| 332 |
|
|
| 333 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 334 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 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 |
|
} |
| 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 |
|
} |
| 487 |
|
|
| 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 |
+ |
for(i=0; i< simnfo->n_mol; i++) { |
| 495 |
+ |
the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
| 496 |
+ |
} |
| 497 |
|
|
| 498 |
|
if (the_globals->getUseRF() ) { |
| 499 |
|
simnfo->useReactionField = 1; |
| 734 |
|
|
| 735 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 736 |
|
new Symplectic(simnfo, the_ff, the_extendedsystem); |
| 686 |
– |
std::cerr << "called new Symplecic\n"; |
| 687 |
– |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
| 737 |
|
} |
| 738 |
|
else if( !strcmp( force_field, "LJ" ) ){ |
| 739 |
|
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
| 691 |
– |
std::cerr << "called new Verlet\n"; |
| 692 |
– |
fprintf( stderr, "called new Verlet. stderr\n" ); |
| 740 |
|
} |
| 741 |
|
else { |
| 742 |
|
std::cerr << "I'm a bug.\n"; |
