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()); |
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, |
298 |
|
simnfo->n_torsions = tot_torsions; |
299 |
|
simnfo->n_SRI = tot_SRI; |
300 |
|
simnfo->n_mol = tot_nmol; |
253 |
– |
|
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 |
|
|
261 |
– |
|
262 |
– |
|
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 |
|
|
296 |
– |
|
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 |
|
} |
741 |
|
|
742 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
743 |
|
new Symplectic(simnfo, the_ff, the_extendedsystem); |
683 |
– |
std::cerr << "called new Symplecic\n"; |
684 |
– |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
744 |
|
} |
745 |
|
else if( !strcmp( force_field, "LJ" ) ){ |
746 |
|
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
688 |
– |
std::cerr << "called new Verlet\n"; |
689 |
– |
fprintf( stderr, "called new Verlet. stderr\n" ); |
747 |
|
} |
748 |
|
else { |
749 |
|
std::cerr << "I'm a bug.\n"; |