| 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()); |
| 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, |
| 154 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
| 155 |
|
simnfo->usePBC = the_globals->getPBC(); |
| 156 |
|
|
| 157 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
| 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, |
| 485 |
|
|
| 486 |
|
makeMolecules(); |
| 487 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 488 |
+ |
simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
| 489 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 490 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 491 |
+ |
} |
| 492 |
+ |
for(i=0; i< simnfo->n_mol; i++) { |
| 493 |
+ |
the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
| 494 |
|
} |
| 495 |
|
|
| 496 |
|
if (the_globals->getUseRF() ) { |
| 534 |
|
} |
| 535 |
|
simnfo->dielectric = the_globals->getDielectric(); |
| 536 |
|
} else { |
| 537 |
< |
if (simnfo->n_dipoles) { |
| 537 |
> |
if (usesDipoles) { |
| 538 |
|
|
| 539 |
|
if( !the_globals->haveECR() ){ |
| 540 |
|
sprintf( painCave.errMsg, |
| 541 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
| 541 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 542 |
|
"box length for the electrostaticCutoffRadius.\n" |
| 543 |
|
"I hope you have a very fast processor!\n"); |
| 544 |
|
painCave.isFatal = 0; |
| 554 |
|
|
| 555 |
|
if( !the_globals->haveEST() ){ |
| 556 |
|
sprintf( painCave.errMsg, |
| 557 |
< |
"SimSetup Warning: using default value of 5% of the" |
| 557 |
> |
"SimSetup Warning: using default value of 5%% of the " |
| 558 |
|
"electrostaticCutoffRadius for the " |
| 559 |
|
"electrostaticSkinThickness\n" |
| 560 |
|
); |
| 729 |
|
|
| 730 |
|
// new AllLong( simnfo ); |
| 731 |
|
|
| 676 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, |
| 677 |
– |
the_ff, |
| 678 |
– |
the_extendedsystem); |
| 679 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, |
| 680 |
– |
the_ff, |
| 681 |
– |
the_extendedsystem ); |
| 732 |
|
|
| 733 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 734 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
| 735 |
+ |
} |
| 736 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
| 737 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
| 738 |
+ |
} |
| 739 |
+ |
else { |
| 740 |
+ |
std::cerr << "I'm a bug.\n"; |
| 741 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
| 742 |
+ |
} |
| 743 |
|
#ifdef IS_MPI |
| 744 |
|
mpiSim->mpiRefresh(); |
| 745 |
|
#endif |
