66 |
|
|
67 |
|
MakeStamps *the_stamps; |
68 |
|
Globals* the_globals; |
69 |
< |
int i, j; |
69 |
> |
ExtendedSystem* the_extendedsystem; |
70 |
> |
int i, j, k, globalAtomIndex; |
71 |
|
|
72 |
|
// get the stamps and globals; |
73 |
|
the_stamps = stamps; |
81 |
|
// get the ones we know are there, yet still may need some work. |
82 |
|
n_components = the_globals->getNComponents(); |
83 |
|
strcpy( force_field, the_globals->getForceField() ); |
84 |
+ |
|
85 |
+ |
// get the ensemble and set up an extended system if we need it: |
86 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
87 |
+ |
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
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, |
145 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 |
+ |
"reverting to NVE for this simulation.\n", |
147 |
+ |
ensemble ); |
148 |
+ |
painCave.isFatal = 0; |
149 |
+ |
simError(); |
150 |
+ |
strcpy( ensemble, "NVE" ); |
151 |
+ |
} |
152 |
|
strcpy( simnfo->ensemble, ensemble ); |
153 |
|
|
154 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 |
|
simnfo->usePBC = the_globals->getPBC(); |
156 |
|
|
157 |
< |
|
158 |
< |
|
159 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
160 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
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, |
165 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
298 |
|
simnfo->n_torsions = tot_torsions; |
299 |
|
simnfo->n_SRI = tot_SRI; |
300 |
|
simnfo->n_mol = tot_nmol; |
231 |
– |
|
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 |
|
|
239 |
– |
|
240 |
– |
|
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 |
|
|
274 |
– |
|
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 |
|
} |
419 |
|
|
420 |
|
if( simnfo->n_SRI ){ |
421 |
|
|
339 |
– |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 |
– |
|
422 |
|
Exclude::createArray(simnfo->n_SRI); |
423 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
424 |
|
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
543 |
|
} |
544 |
|
simnfo->dielectric = the_globals->getDielectric(); |
545 |
|
} else { |
546 |
< |
if (simnfo->n_dipoles) { |
546 |
> |
if (usesDipoles) { |
547 |
|
|
548 |
|
if( !the_globals->haveECR() ){ |
549 |
|
sprintf( painCave.errMsg, |
550 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
550 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
551 |
|
"box length for the electrostaticCutoffRadius.\n" |
552 |
|
"I hope you have a very fast processor!\n"); |
553 |
|
painCave.isFatal = 0; |
563 |
|
|
564 |
|
if( !the_globals->haveEST() ){ |
565 |
|
sprintf( painCave.errMsg, |
566 |
< |
"SimSetup Warning: using default value of 5% of the" |
566 |
> |
"SimSetup Warning: using default value of 5%% of the " |
567 |
|
"electrostaticCutoffRadius for the " |
568 |
|
"electrostaticSkinThickness\n" |
569 |
|
); |
734 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
735 |
|
|
736 |
|
|
737 |
< |
// // make the longe range forces and the integrator |
737 |
> |
// make the integrator |
738 |
|
|
658 |
– |
// new AllLong( simnfo ); |
739 |
|
|
740 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
741 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
740 |
> |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
741 |
> |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
742 |
> |
} |
743 |
> |
else if( !strcmp( force_field, "LJ" ) ){ |
744 |
> |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
745 |
> |
} |
746 |
|
|
747 |
|
#ifdef IS_MPI |
748 |
|
mpiSim->mpiRefresh(); |