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; |
301 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
302 |
|
|
232 |
– |
|
303 |
|
#ifdef IS_MPI |
304 |
|
|
305 |
|
// divide the molecules among processors here. |
306 |
|
|
307 |
|
mpiSim = new mpiSimulation( simnfo ); |
308 |
|
|
239 |
– |
|
240 |
– |
|
309 |
|
globalIndex = mpiSim->divideLabor(); |
310 |
|
|
243 |
– |
|
244 |
– |
|
311 |
|
// set up the local variables |
312 |
|
|
313 |
|
int localMol, allMol; |
322 |
|
local_bonds = 0; |
323 |
|
local_bends = 0; |
324 |
|
local_torsions = 0; |
325 |
+ |
globalAtomIndex = 0; |
326 |
+ |
|
327 |
+ |
|
328 |
|
for( i=0; i<n_components; i++ ){ |
329 |
|
|
330 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
331 |
|
|
332 |
< |
if( mol2proc[j] == worldRank ){ |
332 |
> |
if( mol2proc[allMol] == worldRank ){ |
333 |
|
|
334 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
335 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
337 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
338 |
|
localMol++; |
339 |
|
} |
340 |
< |
allMol++; |
340 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
341 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
342 |
> |
globalAtomIndex++; |
343 |
> |
} |
344 |
> |
|
345 |
> |
allMol++; |
346 |
|
} |
347 |
|
} |
348 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
349 |
|
|
350 |
+ |
if (worldRank != 0) { |
351 |
+ |
for (i =0; i < tot_atoms; i++){ |
352 |
+ |
std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n"; |
353 |
+ |
} |
354 |
+ |
} |
355 |
|
|
356 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
357 |
|
|
395 |
|
|
396 |
|
if(mol2proc[i] == worldRank ){ |
397 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
398 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
399 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
400 |
|
molIndex++; |
401 |
|
} |
402 |
|
} |
404 |
|
#else // is_mpi |
405 |
|
|
406 |
|
molIndex = 0; |
407 |
+ |
globalAtomIndex = 0; |
408 |
|
for(i=0; i<n_components; i++){ |
409 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
410 |
|
the_molecules[molIndex].setStampID( i ); |
411 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
412 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
413 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
414 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
415 |
+ |
globalAtomIndex++; |
416 |
+ |
} |
417 |
|
molIndex++; |
418 |
|
} |
419 |
|
} |
423 |
|
|
424 |
|
|
425 |
|
if( simnfo->n_SRI ){ |
426 |
+ |
|
427 |
|
Exclude::createArray(simnfo->n_SRI); |
428 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
429 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
430 |
|
simnfo->globalExcludes = new int; |
431 |
< |
simnfo->n_exclude = tot_SRI; |
431 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
432 |
|
} |
433 |
|
else{ |
434 |
|
|
444 |
|
// set the arrays into the SimInfo object |
445 |
|
|
446 |
|
simnfo->atoms = the_atoms; |
447 |
+ |
simnfo->molecules = the_molecules; |
448 |
|
simnfo->nGlobalExcludes = 0; |
449 |
|
simnfo->excludes = the_excludes; |
450 |
|
|
548 |
|
} |
549 |
|
simnfo->dielectric = the_globals->getDielectric(); |
550 |
|
} else { |
551 |
< |
if (simnfo->n_dipoles) { |
551 |
> |
if (usesDipoles) { |
552 |
|
|
553 |
|
if( !the_globals->haveECR() ){ |
554 |
|
sprintf( painCave.errMsg, |
555 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
555 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
556 |
|
"box length for the electrostaticCutoffRadius.\n" |
557 |
|
"I hope you have a very fast processor!\n"); |
558 |
|
painCave.isFatal = 0; |
568 |
|
|
569 |
|
if( !the_globals->haveEST() ){ |
570 |
|
sprintf( painCave.errMsg, |
571 |
< |
"SimSetup Warning: using default value of 5% of the" |
571 |
> |
"SimSetup Warning: using default value of 5%% of the " |
572 |
|
"electrostaticCutoffRadius for the " |
573 |
|
"electrostaticSkinThickness\n" |
574 |
|
); |
743 |
|
|
744 |
|
// new AllLong( simnfo ); |
745 |
|
|
655 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
656 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
746 |
|
|
747 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
748 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
749 |
+ |
} |
750 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
751 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
752 |
+ |
} |
753 |
+ |
else { |
754 |
+ |
std::cerr << "I'm a bug.\n"; |
755 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
756 |
+ |
} |
757 |
+ |
#ifdef IS_MPI |
758 |
+ |
mpiSim->mpiRefresh(); |
759 |
+ |
#endif |
760 |
|
|
659 |
– |
|
761 |
|
// initialize the Fortran |
762 |
< |
|
762 |
> |
|
763 |
> |
|
764 |
|
simnfo->refreshSim(); |
765 |
|
|
766 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
879 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
880 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
881 |
|
|
882 |
< |
exI = theBonds[i].a; |
883 |
< |
exJ = theBonds[i].b; |
882 |
> |
exI = theBonds[j].a; |
883 |
> |
exJ = theBonds[j].b; |
884 |
|
|
885 |
|
// exclude_I must always be the smaller of the pair |
886 |
|
if( exI > exJ ){ |
896 |
|
|
897 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
898 |
|
#else // isn't MPI |
899 |
+ |
|
900 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
901 |
|
#endif //is_mpi |
902 |
|
} |
934 |
|
|
935 |
|
default: |
936 |
|
sprintf( painCave.errMsg, |
937 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
937 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
938 |
|
"double nor an int.\n" |
939 |
|
"-->Bend[%d] in %s\n", |
940 |
|
j, comp_stamps[stampID]->getID() ); |
1028 |
|
|
1029 |
|
|
1030 |
|
the_molecules[i].initialize( info ); |
1031 |
+ |
|
1032 |
+ |
|
1033 |
|
atomOffset += info.nAtoms; |
1034 |
|
delete[] theBonds; |
1035 |
|
delete[] theBends; |
1036 |
|
delete[] theTorsions; |
1037 |
|
} |
1038 |
+ |
|
1039 |
+ |
#ifdef IS_MPI |
1040 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1041 |
+ |
MPIcheckPoint(); |
1042 |
+ |
#endif // is_mpi |
1043 |
|
|
1044 |
|
// clean up the forcefield |
1045 |
|
the_ff->calcRcut(); |
1046 |
|
the_ff->cleanMe(); |
1047 |
+ |
|
1048 |
|
} |
1049 |
|
|
1050 |
|
void SimSetup::initFromBass( void ){ |