78 |
|
|
79 |
|
void SimSetup::createSim( void ){ |
80 |
|
|
81 |
– |
MakeStamps *the_stamps; |
82 |
– |
Globals* the_globals; |
81 |
|
int i, j, k, globalAtomIndex; |
82 |
|
|
83 |
|
// gather all of the information from the Bass file |
88 |
|
|
89 |
|
sysObjectsCreation(); |
90 |
|
|
93 |
– |
|
94 |
– |
|
95 |
– |
// initialize the arrays |
96 |
– |
|
97 |
– |
|
98 |
– |
|
99 |
– |
makeMolecules(); |
100 |
– |
info->identArray = new int[info->n_atoms]; |
101 |
– |
for(i=0; i<info->n_atoms; i++){ |
102 |
– |
info->identArray[i] = the_atoms[i]->getIdent(); |
103 |
– |
} |
104 |
– |
|
105 |
– |
|
91 |
|
// check on the post processing info |
92 |
|
|
93 |
|
finalInfoCheck(); |
94 |
|
|
110 |
– |
|
111 |
– |
|
112 |
– |
|
95 |
|
// initialize the system coordinates |
96 |
|
|
97 |
|
initSystemCoords(); |
101 |
|
|
102 |
|
makeOutNames(); |
103 |
|
|
122 |
– |
|
123 |
– |
|
124 |
– |
|
125 |
– |
|
126 |
– |
|
127 |
– |
|
128 |
– |
|
129 |
– |
|
104 |
|
// make the integrator |
105 |
|
|
106 |
+ |
makeIntegrator(); |
107 |
|
|
133 |
– |
NVT* myNVT = NULL; |
134 |
– |
NPTi* myNPTi = NULL; |
135 |
– |
NPTf* myNPTf = NULL; |
136 |
– |
NPTim* myNPTim = NULL; |
137 |
– |
NPTfm* myNPTfm = NULL; |
138 |
– |
|
139 |
– |
switch( ensembleCase ){ |
140 |
– |
|
141 |
– |
case NVE_ENS: |
142 |
– |
new NVE( info, the_ff ); |
143 |
– |
break; |
144 |
– |
|
145 |
– |
case NVT_ENS: |
146 |
– |
myNVT = new NVT( info, the_ff ); |
147 |
– |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
148 |
– |
|
149 |
– |
if (the_globals->haveTauThermostat()) |
150 |
– |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
151 |
– |
|
152 |
– |
else { |
153 |
– |
sprintf( painCave.errMsg, |
154 |
– |
"SimSetup error: If you use the NVT\n" |
155 |
– |
" ensemble, you must set tauThermostat.\n"); |
156 |
– |
painCave.isFatal = 1; |
157 |
– |
simError(); |
158 |
– |
} |
159 |
– |
break; |
160 |
– |
|
161 |
– |
case NPTi_ENS: |
162 |
– |
myNPTi = new NPTi( info, the_ff ); |
163 |
– |
myNPTi->setTargetTemp( the_globals->getTargetTemp() ); |
164 |
– |
|
165 |
– |
if (the_globals->haveTargetPressure()) |
166 |
– |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
167 |
– |
else { |
168 |
– |
sprintf( painCave.errMsg, |
169 |
– |
"SimSetup error: If you use a constant pressure\n" |
170 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
171 |
– |
painCave.isFatal = 1; |
172 |
– |
simError(); |
173 |
– |
} |
174 |
– |
|
175 |
– |
if( the_globals->haveTauThermostat() ) |
176 |
– |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
177 |
– |
else{ |
178 |
– |
sprintf( painCave.errMsg, |
179 |
– |
"SimSetup error: If you use an NPT\n" |
180 |
– |
" ensemble, you must set tauThermostat.\n"); |
181 |
– |
painCave.isFatal = 1; |
182 |
– |
simError(); |
183 |
– |
} |
184 |
– |
|
185 |
– |
if( the_globals->haveTauBarostat() ) |
186 |
– |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
187 |
– |
else{ |
188 |
– |
sprintf( painCave.errMsg, |
189 |
– |
"SimSetup error: If you use an NPT\n" |
190 |
– |
" ensemble, you must set tauBarostat.\n"); |
191 |
– |
painCave.isFatal = 1; |
192 |
– |
simError(); |
193 |
– |
} |
194 |
– |
break; |
195 |
– |
|
196 |
– |
case NPTf_ENS: |
197 |
– |
myNPTf = new NPTf( info, the_ff ); |
198 |
– |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
199 |
– |
|
200 |
– |
if (the_globals->haveTargetPressure()) |
201 |
– |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
202 |
– |
else { |
203 |
– |
sprintf( painCave.errMsg, |
204 |
– |
"SimSetup error: If you use a constant pressure\n" |
205 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
206 |
– |
painCave.isFatal = 1; |
207 |
– |
simError(); |
208 |
– |
} |
209 |
– |
|
210 |
– |
if( the_globals->haveTauThermostat() ) |
211 |
– |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
212 |
– |
else{ |
213 |
– |
sprintf( painCave.errMsg, |
214 |
– |
"SimSetup error: If you use an NPT\n" |
215 |
– |
" ensemble, you must set tauThermostat.\n"); |
216 |
– |
painCave.isFatal = 1; |
217 |
– |
simError(); |
218 |
– |
} |
219 |
– |
|
220 |
– |
if( the_globals->haveTauBarostat() ) |
221 |
– |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
222 |
– |
else{ |
223 |
– |
sprintf( painCave.errMsg, |
224 |
– |
"SimSetup error: If you use an NPT\n" |
225 |
– |
" ensemble, you must set tauBarostat.\n"); |
226 |
– |
painCave.isFatal = 1; |
227 |
– |
simError(); |
228 |
– |
} |
229 |
– |
break; |
230 |
– |
|
231 |
– |
case NPTim_ENS: |
232 |
– |
myNPTim = new NPTim( info, the_ff ); |
233 |
– |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
234 |
– |
|
235 |
– |
if (the_globals->haveTargetPressure()) |
236 |
– |
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
237 |
– |
else { |
238 |
– |
sprintf( painCave.errMsg, |
239 |
– |
"SimSetup error: If you use a constant pressure\n" |
240 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
241 |
– |
painCave.isFatal = 1; |
242 |
– |
simError(); |
243 |
– |
} |
244 |
– |
|
245 |
– |
if( the_globals->haveTauThermostat() ) |
246 |
– |
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
247 |
– |
else{ |
248 |
– |
sprintf( painCave.errMsg, |
249 |
– |
"SimSetup error: If you use an NPT\n" |
250 |
– |
" ensemble, you must set tauThermostat.\n"); |
251 |
– |
painCave.isFatal = 1; |
252 |
– |
simError(); |
253 |
– |
} |
254 |
– |
|
255 |
– |
if( the_globals->haveTauBarostat() ) |
256 |
– |
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
257 |
– |
else{ |
258 |
– |
sprintf( painCave.errMsg, |
259 |
– |
"SimSetup error: If you use an NPT\n" |
260 |
– |
" ensemble, you must set tauBarostat.\n"); |
261 |
– |
painCave.isFatal = 1; |
262 |
– |
simError(); |
263 |
– |
} |
264 |
– |
break; |
265 |
– |
|
266 |
– |
case NPTfm_ENS: |
267 |
– |
myNPTfm = new NPTfm( info, the_ff ); |
268 |
– |
myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
269 |
– |
|
270 |
– |
if (the_globals->haveTargetPressure()) |
271 |
– |
myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
272 |
– |
else { |
273 |
– |
sprintf( painCave.errMsg, |
274 |
– |
"SimSetup error: If you use a constant pressure\n" |
275 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
276 |
– |
painCave.isFatal = 1; |
277 |
– |
simError(); |
278 |
– |
} |
279 |
– |
|
280 |
– |
if( the_globals->haveTauThermostat() ) |
281 |
– |
myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
282 |
– |
else{ |
283 |
– |
sprintf( painCave.errMsg, |
284 |
– |
"SimSetup error: If you use an NPT\n" |
285 |
– |
" ensemble, you must set tauThermostat.\n"); |
286 |
– |
painCave.isFatal = 1; |
287 |
– |
simError(); |
288 |
– |
} |
289 |
– |
|
290 |
– |
if( the_globals->haveTauBarostat() ) |
291 |
– |
myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
292 |
– |
else{ |
293 |
– |
sprintf( painCave.errMsg, |
294 |
– |
"SimSetup error: If you use an NPT\n" |
295 |
– |
" ensemble, you must set tauBarostat.\n"); |
296 |
– |
painCave.isFatal = 1; |
297 |
– |
simError(); |
298 |
– |
} |
299 |
– |
break; |
300 |
– |
|
301 |
– |
default: |
302 |
– |
sprintf( painCave.errMsg, |
303 |
– |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
304 |
– |
painCave.isFatal = 1; |
305 |
– |
simError(); |
306 |
– |
} |
307 |
– |
|
308 |
– |
|
108 |
|
#ifdef IS_MPI |
109 |
|
mpiSim->mpiRefresh(); |
110 |
|
#endif |
111 |
|
|
112 |
|
// initialize the Fortran |
113 |
|
|
114 |
+ |
initFortran(); |
115 |
|
|
316 |
– |
info->refreshSim(); |
317 |
– |
|
318 |
– |
if( !strcmp( info->mixingRule, "standard") ){ |
319 |
– |
the_ff->initForceField( LB_MIXING_RULE ); |
320 |
– |
} |
321 |
– |
else if( !strcmp( info->mixingRule, "explicit") ){ |
322 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
323 |
– |
} |
324 |
– |
else{ |
325 |
– |
sprintf( painCave.errMsg, |
326 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
327 |
– |
info->mixingRule ); |
328 |
– |
painCave.isFatal = 1; |
329 |
– |
simError(); |
330 |
– |
} |
116 |
|
|
117 |
|
|
333 |
– |
#ifdef IS_MPI |
334 |
– |
strcpy( checkPointMsg, |
335 |
– |
"Successfully intialized the mixingRule for Fortran." ); |
336 |
– |
MPIcheckPoint(); |
337 |
– |
#endif // is_mpi |
118 |
|
} |
119 |
|
|
120 |
|
|
121 |
|
void SimSetup::makeMolecules( void ){ |
122 |
|
|
123 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
124 |
< |
molInit info; |
124 |
> |
molInit molInfo; |
125 |
|
DirectionalAtom* dAtom; |
126 |
|
LinkedAssign* extras; |
127 |
|
LinkedAssign* current_extra; |
150 |
|
|
151 |
|
stampID = the_molecules[i].getStampID(); |
152 |
|
|
153 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
156 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
153 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
156 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
158 |
|
|
159 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
160 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
161 |
< |
info.myBonds = new Bond*[info.nBonds]; |
162 |
< |
info.myBends = new Bend*[info.nBends]; |
163 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
159 |
> |
molInfo.myAtoms = &the_atoms[atomOffset]; |
160 |
> |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
161 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
162 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
163 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
164 |
|
|
165 |
< |
theBonds = new bond_pair[info.nBonds]; |
166 |
< |
theBends = new bend_set[info.nBends]; |
167 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
165 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
166 |
> |
theBends = new bend_set[molInfo.nBends]; |
167 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
168 |
|
|
169 |
|
// make the Atoms |
170 |
|
|
171 |
< |
for(j=0; j<info.nAtoms; j++){ |
171 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
172 |
|
|
173 |
|
currentAtom = comp_stamps[stampID]->getAtom( j ); |
174 |
|
if( currentAtom->haveOrientation() ){ |
175 |
|
|
176 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
177 |
|
info->n_oriented++; |
178 |
< |
info.myAtoms[j] = dAtom; |
178 |
> |
molInfo.myAtoms[j] = dAtom; |
179 |
|
|
180 |
|
ux = currentAtom->getOrntX(); |
181 |
|
uy = currentAtom->getOrntY(); |
193 |
|
dAtom->setSUz( uz ); |
194 |
|
} |
195 |
|
else{ |
196 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
196 |
> |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
197 |
|
} |
198 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
198 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
199 |
|
|
200 |
|
#ifdef IS_MPI |
201 |
|
|
202 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
202 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
203 |
|
|
204 |
|
#endif // is_mpi |
205 |
|
} |
206 |
|
|
207 |
|
// make the bonds |
208 |
< |
for(j=0; j<info.nBonds; j++){ |
208 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
209 |
|
|
210 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
211 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
232 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
233 |
|
#endif //is_mpi |
234 |
|
} |
235 |
< |
excludeOffset += info.nBonds; |
235 |
> |
excludeOffset += molInfo.nBonds; |
236 |
|
|
237 |
|
//make the bends |
238 |
< |
for(j=0; j<info.nBends; j++){ |
238 |
> |
for(j=0; j<molInfo.nBends; j++){ |
239 |
|
|
240 |
|
currentBend = comp_stamps[stampID]->getBend( j ); |
241 |
|
theBends[j].a = currentBend->getA() + atomOffset; |
318 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
319 |
|
#endif //is_mpi |
320 |
|
} |
321 |
< |
excludeOffset += info.nBends; |
321 |
> |
excludeOffset += molInfo.nBends; |
322 |
|
|
323 |
< |
for(j=0; j<info.nTorsions; j++){ |
323 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
324 |
|
|
325 |
|
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
326 |
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
348 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 |
|
#endif //is_mpi |
350 |
|
} |
351 |
< |
excludeOffset += info.nTorsions; |
351 |
> |
excludeOffset += molInfo.nTorsions; |
352 |
|
|
353 |
|
|
354 |
|
// send the arrays off to the forceField for init. |
355 |
|
|
356 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
357 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
358 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
359 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
356 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
360 |
|
|
361 |
|
|
362 |
< |
the_molecules[i].initialize( info ); |
362 |
> |
the_molecules[i].initialize( molInfo ); |
363 |
|
|
364 |
|
|
365 |
< |
atomOffset += info.nAtoms; |
365 |
> |
atomOffset += molInfo.nAtoms; |
366 |
|
delete[] theBonds; |
367 |
|
delete[] theBends; |
368 |
|
delete[] theTorsions; |
564 |
|
|
565 |
|
|
566 |
|
void SimSetup::gatherInfo( void ){ |
567 |
+ |
int i,j,k; |
568 |
|
|
569 |
|
ensembleCase = -1; |
570 |
|
ffCase = -1; |
571 |
|
|
572 |
|
// get the stamps and globals; |
573 |
< |
the_stamps = stamps; |
574 |
< |
the_globals = globals; |
573 |
> |
stamps = stamps; |
574 |
> |
globals = globals; |
575 |
|
|
576 |
|
// set the easy ones first |
577 |
< |
info->target_temp = the_globals->getTargetTemp(); |
578 |
< |
info->dt = the_globals->getDt(); |
579 |
< |
info->run_time = the_globals->getRunTime(); |
580 |
< |
n_components = the_globals->getNComponents(); |
577 |
> |
info->target_temp = globals->getTargetTemp(); |
578 |
> |
info->dt = globals->getDt(); |
579 |
> |
info->run_time = globals->getRunTime(); |
580 |
> |
n_components = globals->getNComponents(); |
581 |
|
|
582 |
|
|
583 |
|
// get the forceField |
584 |
|
|
585 |
< |
strcpy( force_field, the_globals->getForceField() ); |
585 |
> |
strcpy( force_field, globals->getForceField() ); |
586 |
|
|
587 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
588 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
596 |
|
|
597 |
|
// get the ensemble |
598 |
|
|
599 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
599 |
> |
strcpy( ensemble, globals->getEnsemble() ); |
600 |
|
|
601 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
602 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
619 |
|
|
620 |
|
// get the mixing rule |
621 |
|
|
622 |
< |
strcpy( info->mixingRule, the_globals->getMixingRule() ); |
623 |
< |
info->usePBC = the_globals->getPBC(); |
622 |
> |
strcpy( info->mixingRule, globals->getMixingRule() ); |
623 |
> |
info->usePBC = globals->getPBC(); |
624 |
|
|
625 |
|
|
626 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
627 |
|
|
628 |
< |
the_components = the_globals->getComponents(); |
628 |
> |
the_components = globals->getComponents(); |
629 |
|
components_nmol = new int[n_components]; |
630 |
|
|
631 |
|
|
632 |
< |
if( !the_globals->haveNMol() ){ |
632 |
> |
if( !globals->haveNMol() ){ |
633 |
|
// we don't have the total number of molecules, so we assume it is |
634 |
|
// given in each component |
635 |
|
|
662 |
|
|
663 |
|
// set the status, sample, and thermal kick times |
664 |
|
|
665 |
< |
if( the_globals->haveSampleTime() ){ |
666 |
< |
info->sampleTime = the_globals->getSampleTime(); |
665 |
> |
if( globals->haveSampleTime() ){ |
666 |
> |
info->sampleTime = globals->getSampleTime(); |
667 |
|
info->statusTime = info->sampleTime; |
668 |
|
info->thermalTime = info->sampleTime; |
669 |
|
} |
670 |
|
else{ |
671 |
< |
info->sampleTime = the_globals->getRunTime(); |
671 |
> |
info->sampleTime = globals->getRunTime(); |
672 |
|
info->statusTime = info->sampleTime; |
673 |
|
info->thermalTime = info->sampleTime; |
674 |
|
} |
675 |
|
|
676 |
< |
if( the_globals->haveStatusTime() ){ |
677 |
< |
info->statusTime = the_globals->getStatusTime(); |
676 |
> |
if( globals->haveStatusTime() ){ |
677 |
> |
info->statusTime = globals->getStatusTime(); |
678 |
|
} |
679 |
|
|
680 |
< |
if( the_globals->haveThermalTime() ){ |
681 |
< |
info->thermalTime = the_globals->getThermalTime(); |
680 |
> |
if( globals->haveThermalTime() ){ |
681 |
> |
info->thermalTime = globals->getThermalTime(); |
682 |
|
} |
683 |
|
|
684 |
|
// check for the temperature set flag |
685 |
|
|
686 |
< |
if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
686 |
> |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
687 |
|
|
688 |
|
// get some of the tricky things that may still be in the globals |
689 |
|
|
690 |
|
double boxVector[3]; |
691 |
< |
if( the_globals->haveBox() ){ |
692 |
< |
boxVector[0] = the_globals->getBox(); |
693 |
< |
boxVector[1] = the_globals->getBox(); |
694 |
< |
boxVector[2] = the_globals->getBox(); |
691 |
> |
if( globals->haveBox() ){ |
692 |
> |
boxVector[0] = globals->getBox(); |
693 |
> |
boxVector[1] = globals->getBox(); |
694 |
> |
boxVector[2] = globals->getBox(); |
695 |
|
|
696 |
|
info->setBox( boxVector ); |
697 |
|
} |
698 |
< |
else if( the_globals->haveDensity() ){ |
698 |
> |
else if( globals->haveDensity() ){ |
699 |
|
|
700 |
|
double vol; |
701 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
701 |
> |
vol = (double)tot_nmol / globals->getDensity(); |
702 |
|
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
703 |
|
boxVector[1] = boxVector[0]; |
704 |
|
boxVector[2] = boxVector[0]; |
706 |
|
info->setBox( boxVector ); |
707 |
|
} |
708 |
|
else{ |
709 |
< |
if( !the_globals->haveBoxX() ){ |
709 |
> |
if( !globals->haveBoxX() ){ |
710 |
|
sprintf( painCave.errMsg, |
711 |
|
"SimSetup error, no periodic BoxX size given.\n" ); |
712 |
|
painCave.isFatal = 1; |
713 |
|
simError(); |
714 |
|
} |
715 |
< |
boxVector[0] = the_globals->getBoxX(); |
715 |
> |
boxVector[0] = globals->getBoxX(); |
716 |
|
|
717 |
< |
if( !the_globals->haveBoxY() ){ |
717 |
> |
if( !globals->haveBoxY() ){ |
718 |
|
sprintf( painCave.errMsg, |
719 |
|
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
|
painCave.isFatal = 1; |
721 |
|
simError(); |
722 |
|
} |
723 |
< |
boxVector[1] = the_globals->getBoxY(); |
723 |
> |
boxVector[1] = globals->getBoxY(); |
724 |
|
|
725 |
< |
if( !the_globals->haveBoxZ() ){ |
725 |
> |
if( !globals->haveBoxZ() ){ |
726 |
|
sprintf( painCave.errMsg, |
727 |
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
728 |
|
painCave.isFatal = 1; |
729 |
|
simError(); |
730 |
|
} |
731 |
< |
boxVector[2] = the_globals->getBoxZ(); |
731 |
> |
boxVector[2] = globals->getBoxZ(); |
732 |
|
|
733 |
|
info->setBox( boxVector ); |
734 |
|
} |
758 |
|
} |
759 |
|
|
760 |
|
#ifdef IS_MPI |
761 |
< |
int myUse = usesDipoles |
762 |
< |
MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
761 |
> |
int myUse = usesDipoles; |
762 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
763 |
|
#endif //is_mpi |
764 |
|
|
765 |
|
|
766 |
< |
if (the_globals->getUseRF() ) { |
766 |
> |
if (globals->getUseRF() ) { |
767 |
|
info->useReactionField = 1; |
768 |
|
|
769 |
< |
if( !the_globals->haveECR() ){ |
769 |
> |
if( !globals->haveECR() ){ |
770 |
|
sprintf( painCave.errMsg, |
771 |
|
"SimSetup Warning: using default value of 1/2 the smallest " |
772 |
|
"box length for the electrostaticCutoffRadius.\n" |
779 |
|
if (info->boxLz <= smallest) smallest = info->boxLz; |
780 |
|
info->ecr = 0.5 * smallest; |
781 |
|
} else { |
782 |
< |
info->ecr = the_globals->getECR(); |
782 |
> |
info->ecr = globals->getECR(); |
783 |
|
} |
784 |
|
|
785 |
< |
if( !the_globals->haveEST() ){ |
785 |
> |
if( !globals->haveEST() ){ |
786 |
|
sprintf( painCave.errMsg, |
787 |
|
"SimSetup Warning: using default value of 0.05 * the " |
788 |
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
791 |
|
simError(); |
792 |
|
info->est = 0.05 * info->ecr; |
793 |
|
} else { |
794 |
< |
info->est = the_globals->getEST(); |
794 |
> |
info->est = globals->getEST(); |
795 |
|
} |
796 |
|
|
797 |
< |
if(!the_globals->haveDielectric() ){ |
797 |
> |
if(!globals->haveDielectric() ){ |
798 |
|
sprintf( painCave.errMsg, |
799 |
|
"SimSetup Error: You are trying to use Reaction Field without" |
800 |
|
"setting a dielectric constant!\n" |
802 |
|
painCave.isFatal = 1; |
803 |
|
simError(); |
804 |
|
} |
805 |
< |
info->dielectric = the_globals->getDielectric(); |
805 |
> |
info->dielectric = globals->getDielectric(); |
806 |
|
} |
807 |
|
else { |
808 |
|
if (usesDipoles) { |
809 |
|
|
810 |
< |
if( !the_globals->haveECR() ){ |
810 |
> |
if( !globals->haveECR() ){ |
811 |
|
sprintf( painCave.errMsg, |
812 |
|
"SimSetup Warning: using default value of 1/2 the smallest " |
813 |
|
"box length for the electrostaticCutoffRadius.\n" |
820 |
|
if (info->boxLz <= smallest) smallest = info->boxLz; |
821 |
|
info->ecr = 0.5 * smallest; |
822 |
|
} else { |
823 |
< |
info->ecr = the_globals->getECR(); |
823 |
> |
info->ecr = globals->getECR(); |
824 |
|
} |
825 |
|
|
826 |
< |
if( !the_globals->haveEST() ){ |
826 |
> |
if( !globals->haveEST() ){ |
827 |
|
sprintf( painCave.errMsg, |
828 |
|
"SimSetup Warning: using default value of 5%% of the " |
829 |
|
"electrostaticCutoffRadius for the " |
833 |
|
simError(); |
834 |
|
info->est = 0.05 * info->ecr; |
835 |
|
} else { |
836 |
< |
info->est = the_globals->getEST(); |
836 |
> |
info->est = globals->getEST(); |
837 |
|
} |
838 |
|
} |
839 |
|
} |
847 |
|
|
848 |
|
void SimSetup::initSystemCoords( void ){ |
849 |
|
|
850 |
< |
if( the_globals->haveInitialConfig() ){ |
850 |
> |
if( globals->haveInitialConfig() ){ |
851 |
|
|
852 |
|
InitializeFromFile* fileInit; |
853 |
|
#ifdef IS_MPI // is_mpi |
854 |
|
if( worldRank == 0 ){ |
855 |
|
#endif //is_mpi |
856 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
856 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
857 |
|
#ifdef IS_MPI |
858 |
|
}else fileInit = new InitializeFromFile( NULL ); |
859 |
|
#endif |
894 |
|
if( worldRank == 0 ){ |
895 |
|
#endif // is_mpi |
896 |
|
|
897 |
< |
if( the_globals->haveFinalConfig() ){ |
898 |
< |
strcpy( info->finalName, the_globals->getFinalConfig() ); |
897 |
> |
if( globals->haveFinalConfig() ){ |
898 |
> |
strcpy( info->finalName, globals->getFinalConfig() ); |
899 |
|
} |
900 |
|
else{ |
901 |
|
strcpy( info->finalName, inFileName ); |
978 |
|
|
979 |
|
void SimSetup::sysObjectsCreation( void ){ |
980 |
|
|
981 |
+ |
int i; |
982 |
+ |
|
983 |
|
// create the forceField |
984 |
|
|
985 |
|
createFF(); |
1002 |
|
|
1003 |
|
makeSysArrays(); |
1004 |
|
|
1005 |
+ |
// make and initialize the molecules (all but atomic coordinates) |
1006 |
|
|
1007 |
+ |
makeMolecules(); |
1008 |
+ |
info->identArray = new int[info->n_atoms]; |
1009 |
+ |
for(i=0; i<info->n_atoms; i++){ |
1010 |
+ |
info->identArray[i] = the_atoms[i]->getIdent(); |
1011 |
+ |
} |
1012 |
+ |
|
1013 |
|
|
1014 |
|
|
1015 |
|
} |
1044 |
|
|
1045 |
|
void SimSetup::compList( void ){ |
1046 |
|
|
1047 |
+ |
int i; |
1048 |
+ |
|
1049 |
|
comp_stamps = new MoleculeStamp*[n_components]; |
1050 |
|
|
1051 |
|
// make an array of molecule stamps that match the components used. |
1071 |
|
|
1072 |
|
// extract the component from the list; |
1073 |
|
|
1074 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
1074 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1075 |
|
if( currentStamp == NULL ){ |
1076 |
|
sprintf( painCave.errMsg, |
1077 |
|
"SimSetup error: Component \"%s\" was not found in the " |
1095 |
|
} |
1096 |
|
|
1097 |
|
void SimSetup::calcSysValues( void ){ |
1098 |
+ |
int i, j, k; |
1099 |
|
|
1100 |
+ |
|
1101 |
|
tot_atoms = 0; |
1102 |
|
tot_bonds = 0; |
1103 |
|
tot_bends = 0; |
1127 |
|
|
1128 |
|
void SimSetup::mpiMolDivide( void ){ |
1129 |
|
|
1130 |
+ |
int i, j, k; |
1131 |
|
int localMol, allMol; |
1132 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1133 |
|
|
1197 |
|
|
1198 |
|
|
1199 |
|
void SimSetup::makeSysArrays( void ){ |
1200 |
+ |
int i, j, k; |
1201 |
|
|
1202 |
+ |
|
1203 |
|
// create the atom and short range interaction arrays |
1204 |
|
|
1205 |
|
Atom::createArrays(info->n_atoms); |
1271 |
|
info->excludes = the_excludes; |
1272 |
|
|
1273 |
|
the_ff->setSimInfo( info ); |
1274 |
+ |
|
1275 |
+ |
} |
1276 |
+ |
|
1277 |
+ |
void SimSetup::makeIntegrator( void ){ |
1278 |
+ |
|
1279 |
+ |
NVT* myNVT = NULL; |
1280 |
+ |
NPTi* myNPTi = NULL; |
1281 |
+ |
NPTf* myNPTf = NULL; |
1282 |
+ |
NPTim* myNPTim = NULL; |
1283 |
+ |
NPTfm* myNPTfm = NULL; |
1284 |
+ |
|
1285 |
+ |
switch( ensembleCase ){ |
1286 |
+ |
|
1287 |
+ |
case NVE_ENS: |
1288 |
+ |
new NVE( info, the_ff ); |
1289 |
+ |
break; |
1290 |
+ |
|
1291 |
+ |
case NVT_ENS: |
1292 |
+ |
myNVT = new NVT( info, the_ff ); |
1293 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1294 |
+ |
|
1295 |
+ |
if (globals->haveTauThermostat()) |
1296 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1297 |
+ |
|
1298 |
+ |
else { |
1299 |
+ |
sprintf( painCave.errMsg, |
1300 |
+ |
"SimSetup error: If you use the NVT\n" |
1301 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1302 |
+ |
painCave.isFatal = 1; |
1303 |
+ |
simError(); |
1304 |
+ |
} |
1305 |
+ |
break; |
1306 |
+ |
|
1307 |
+ |
case NPTi_ENS: |
1308 |
+ |
myNPTi = new NPTi( info, the_ff ); |
1309 |
+ |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1310 |
+ |
|
1311 |
+ |
if (globals->haveTargetPressure()) |
1312 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1313 |
+ |
else { |
1314 |
+ |
sprintf( painCave.errMsg, |
1315 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1316 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1317 |
+ |
painCave.isFatal = 1; |
1318 |
+ |
simError(); |
1319 |
+ |
} |
1320 |
+ |
|
1321 |
+ |
if( globals->haveTauThermostat() ) |
1322 |
+ |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1323 |
+ |
else{ |
1324 |
+ |
sprintf( painCave.errMsg, |
1325 |
+ |
"SimSetup error: If you use an NPT\n" |
1326 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1327 |
+ |
painCave.isFatal = 1; |
1328 |
+ |
simError(); |
1329 |
+ |
} |
1330 |
|
|
1331 |
+ |
if( globals->haveTauBarostat() ) |
1332 |
+ |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1333 |
+ |
else{ |
1334 |
+ |
sprintf( painCave.errMsg, |
1335 |
+ |
"SimSetup error: If you use an NPT\n" |
1336 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1337 |
+ |
painCave.isFatal = 1; |
1338 |
+ |
simError(); |
1339 |
+ |
} |
1340 |
+ |
break; |
1341 |
+ |
|
1342 |
+ |
case NPTf_ENS: |
1343 |
+ |
myNPTf = new NPTf( info, the_ff ); |
1344 |
+ |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1345 |
+ |
|
1346 |
+ |
if (globals->haveTargetPressure()) |
1347 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1348 |
+ |
else { |
1349 |
+ |
sprintf( painCave.errMsg, |
1350 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1351 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1352 |
+ |
painCave.isFatal = 1; |
1353 |
+ |
simError(); |
1354 |
+ |
} |
1355 |
+ |
|
1356 |
+ |
if( globals->haveTauThermostat() ) |
1357 |
+ |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1358 |
+ |
else{ |
1359 |
+ |
sprintf( painCave.errMsg, |
1360 |
+ |
"SimSetup error: If you use an NPT\n" |
1361 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1362 |
+ |
painCave.isFatal = 1; |
1363 |
+ |
simError(); |
1364 |
+ |
} |
1365 |
+ |
|
1366 |
+ |
if( globals->haveTauBarostat() ) |
1367 |
+ |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1368 |
+ |
else{ |
1369 |
+ |
sprintf( painCave.errMsg, |
1370 |
+ |
"SimSetup error: If you use an NPT\n" |
1371 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1372 |
+ |
painCave.isFatal = 1; |
1373 |
+ |
simError(); |
1374 |
+ |
} |
1375 |
+ |
break; |
1376 |
+ |
|
1377 |
+ |
case NPTim_ENS: |
1378 |
+ |
myNPTim = new NPTim( info, the_ff ); |
1379 |
+ |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1380 |
+ |
|
1381 |
+ |
if (globals->haveTargetPressure()) |
1382 |
+ |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1383 |
+ |
else { |
1384 |
+ |
sprintf( painCave.errMsg, |
1385 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1386 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1387 |
+ |
painCave.isFatal = 1; |
1388 |
+ |
simError(); |
1389 |
+ |
} |
1390 |
+ |
|
1391 |
+ |
if( globals->haveTauThermostat() ) |
1392 |
+ |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1393 |
+ |
else{ |
1394 |
+ |
sprintf( painCave.errMsg, |
1395 |
+ |
"SimSetup error: If you use an NPT\n" |
1396 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1397 |
+ |
painCave.isFatal = 1; |
1398 |
+ |
simError(); |
1399 |
+ |
} |
1400 |
+ |
|
1401 |
+ |
if( globals->haveTauBarostat() ) |
1402 |
+ |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1403 |
+ |
else{ |
1404 |
+ |
sprintf( painCave.errMsg, |
1405 |
+ |
"SimSetup error: If you use an NPT\n" |
1406 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1407 |
+ |
painCave.isFatal = 1; |
1408 |
+ |
simError(); |
1409 |
+ |
} |
1410 |
+ |
break; |
1411 |
+ |
|
1412 |
+ |
case NPTfm_ENS: |
1413 |
+ |
myNPTfm = new NPTfm( info, the_ff ); |
1414 |
+ |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1415 |
+ |
|
1416 |
+ |
if (globals->haveTargetPressure()) |
1417 |
+ |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1418 |
+ |
else { |
1419 |
+ |
sprintf( painCave.errMsg, |
1420 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1421 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1422 |
+ |
painCave.isFatal = 1; |
1423 |
+ |
simError(); |
1424 |
+ |
} |
1425 |
+ |
|
1426 |
+ |
if( globals->haveTauThermostat() ) |
1427 |
+ |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1428 |
+ |
else{ |
1429 |
+ |
sprintf( painCave.errMsg, |
1430 |
+ |
"SimSetup error: If you use an NPT\n" |
1431 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1432 |
+ |
painCave.isFatal = 1; |
1433 |
+ |
simError(); |
1434 |
+ |
} |
1435 |
+ |
|
1436 |
+ |
if( globals->haveTauBarostat() ) |
1437 |
+ |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1438 |
+ |
else{ |
1439 |
+ |
sprintf( painCave.errMsg, |
1440 |
+ |
"SimSetup error: If you use an NPT\n" |
1441 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1442 |
+ |
painCave.isFatal = 1; |
1443 |
+ |
simError(); |
1444 |
+ |
} |
1445 |
+ |
break; |
1446 |
+ |
|
1447 |
+ |
default: |
1448 |
+ |
sprintf( painCave.errMsg, |
1449 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1450 |
+ |
painCave.isFatal = 1; |
1451 |
+ |
simError(); |
1452 |
+ |
} |
1453 |
+ |
|
1454 |
|
} |
1455 |
+ |
|
1456 |
+ |
void SimSetup::initFortran( void ){ |
1457 |
+ |
|
1458 |
+ |
info->refreshSim(); |
1459 |
+ |
|
1460 |
+ |
if( !strcmp( info->mixingRule, "standard") ){ |
1461 |
+ |
the_ff->initForceField( LB_MIXING_RULE ); |
1462 |
+ |
} |
1463 |
+ |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1464 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1465 |
+ |
} |
1466 |
+ |
else{ |
1467 |
+ |
sprintf( painCave.errMsg, |
1468 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1469 |
+ |
info->mixingRule ); |
1470 |
+ |
painCave.isFatal = 1; |
1471 |
+ |
simError(); |
1472 |
+ |
} |
1473 |
+ |
|
1474 |
+ |
|
1475 |
+ |
#ifdef IS_MPI |
1476 |
+ |
strcpy( checkPointMsg, |
1477 |
+ |
"Successfully intialized the mixingRule for Fortran." ); |
1478 |
+ |
MPIcheckPoint(); |
1479 |
+ |
#endif // is_mpi |
1480 |
+ |
|
1481 |
+ |
} |