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"; |