# | Line 78 | Line 78 | void SimSetup::createSim( void ){ | |
---|---|---|
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 | |
# | Line 90 | Line 88 | void SimSetup::createSim( void ){ | |
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(); | |
# | Line 119 | Line 101 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 370 | Line 150 | void SimSetup::makeMolecules( void ){ | |
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(); | |
# | Line 413 | Line 193 | void SimSetup::makeMolecules( void ){ | |
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; | |
# | Line 452 | Line 232 | void SimSetup::makeMolecules( void ){ | |
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; | |
# | Line 538 | Line 318 | void SimSetup::makeMolecules( void ){ | |
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; | |
# | Line 568 | Line 348 | void SimSetup::makeMolecules( void ){ | |
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; | |
# | Line 618 | Line 398 | void SimSetup::initFromBass( void ){ | |
398 | have_extra =1; | |
399 | ||
400 | n_cells = (int)temp3 - 1; | |
401 | < | cellx = info->boxLx / temp3; |
402 | < | celly = info->boxLy / temp3; |
403 | < | cellz = info->boxLz / temp3; |
401 | > | cellx = info->boxL[0] / temp3; |
402 | > | celly = info->boxL[1] / temp3; |
403 | > | cellz = info->boxL[2] / temp3; |
404 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
405 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
406 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 635 | Line 415 | void SimSetup::initFromBass( void ){ | |
415 | } | |
416 | else{ | |
417 | n_cells = (int)temp3; | |
418 | < | cellx = info->boxLx / temp3; |
419 | < | celly = info->boxLy / temp3; |
420 | < | cellz = info->boxLz / temp3; |
418 | > | cellx = info->boxL[0] / temp3; |
419 | > | celly = info->boxL[1] / temp3; |
420 | > | cellz = info->boxL[2] / temp3; |
421 | } | |
422 | ||
423 | current_mol = 0; | |
# | Line 784 | Line 564 | void SimSetup::gatherInfo( void ){ | |
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; | |
# | Line 815 | Line 596 | void SimSetup::gatherInfo( void ){ | |
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; | |
# | Line 838 | Line 619 | void SimSetup::gatherInfo( void ){ | |
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 | ||
# | Line 881 | Line 662 | void SimSetup::gatherInfo( void ){ | |
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]; | |
# | Line 925 | Line 706 | void SimSetup::gatherInfo( void ){ | |
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 | } | |
# | Line 977 | Line 758 | void SimSetup::finalInfoCheck( void ){ | |
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 | + | double theEcr, theEst; |
766 | ||
767 | < | if (the_globals->getUseRF() ) { |
767 | > | if (globals->getUseRF() ) { |
768 | info->useReactionField = 1; | |
769 | ||
770 | < | if( !the_globals->haveECR() ){ |
770 | > | if( !globals->haveECR() ){ |
771 | sprintf( painCave.errMsg, | |
772 | "SimSetup Warning: using default value of 1/2 the smallest " | |
773 | "box length for the electrostaticCutoffRadius.\n" | |
# | Line 993 | Line 775 | void SimSetup::finalInfoCheck( void ){ | |
775 | painCave.isFatal = 0; | |
776 | simError(); | |
777 | double smallest; | |
778 | < | smallest = info->boxLx; |
779 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
780 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
781 | < | info->ecr = 0.5 * smallest; |
778 | > | smallest = info->boxL[0]; |
779 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
780 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
781 | > | theEcr = 0.5 * smallest; |
782 | } else { | |
783 | < | info->ecr = the_globals->getECR(); |
783 | > | theEcr = globals->getECR(); |
784 | } | |
785 | ||
786 | < | if( !the_globals->haveEST() ){ |
786 | > | if( !globals->haveEST() ){ |
787 | sprintf( painCave.errMsg, | |
788 | "SimSetup Warning: using default value of 0.05 * the " | |
789 | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" | |
790 | ); | |
791 | painCave.isFatal = 0; | |
792 | simError(); | |
793 | < | info->est = 0.05 * info->ecr; |
793 | > | theEst = 0.05 * theEcr; |
794 | } else { | |
795 | < | info->est = the_globals->getEST(); |
795 | > | theEst= globals->getEST(); |
796 | } | |
797 | + | |
798 | + | info->setEcr( theEcr, theEst ); |
799 | ||
800 | < | if(!the_globals->haveDielectric() ){ |
800 | > | if(!globals->haveDielectric() ){ |
801 | sprintf( painCave.errMsg, | |
802 | "SimSetup Error: You are trying to use Reaction Field without" | |
803 | "setting a dielectric constant!\n" | |
# | Line 1021 | Line 805 | void SimSetup::finalInfoCheck( void ){ | |
805 | painCave.isFatal = 1; | |
806 | simError(); | |
807 | } | |
808 | < | info->dielectric = the_globals->getDielectric(); |
808 | > | info->dielectric = globals->getDielectric(); |
809 | } | |
810 | else { | |
811 | if (usesDipoles) { | |
812 | ||
813 | < | if( !the_globals->haveECR() ){ |
814 | < | sprintf( painCave.errMsg, |
815 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
816 | < | "box length for the electrostaticCutoffRadius.\n" |
817 | < | "I hope you have a very fast processor!\n"); |
818 | < | painCave.isFatal = 0; |
819 | < | simError(); |
820 | < | double smallest; |
821 | < | smallest = info->boxLx; |
822 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
823 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
824 | < | info->ecr = 0.5 * smallest; |
813 | > | if( !globals->haveECR() ){ |
814 | > | sprintf( painCave.errMsg, |
815 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
816 | > | "box length for the electrostaticCutoffRadius.\n" |
817 | > | "I hope you have a very fast processor!\n"); |
818 | > | painCave.isFatal = 0; |
819 | > | simError(); |
820 | > | double smallest; |
821 | > | smallest = info->boxL[0]; |
822 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
823 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
824 | > | theEcr = 0.5 * smallest; |
825 | } else { | |
826 | < | info->ecr = the_globals->getECR(); |
826 | > | theEcr = globals->getECR(); |
827 | } | |
828 | ||
829 | < | if( !the_globals->haveEST() ){ |
830 | < | sprintf( painCave.errMsg, |
831 | < | "SimSetup Warning: using default value of 5%% of the " |
832 | < | "electrostaticCutoffRadius for the " |
833 | < | "electrostaticSkinThickness\n" |
834 | < | ); |
835 | < | painCave.isFatal = 0; |
836 | < | simError(); |
837 | < | info->est = 0.05 * info->ecr; |
829 | > | if( !globals->haveEST() ){ |
830 | > | sprintf( painCave.errMsg, |
831 | > | "SimSetup Warning: using default value of 0.05 * the " |
832 | > | "electrostaticCutoffRadius for the " |
833 | > | "electrostaticSkinThickness\n" |
834 | > | ); |
835 | > | painCave.isFatal = 0; |
836 | > | simError(); |
837 | > | theEst = 0.05 * theEcr; |
838 | } else { | |
839 | < | info->est = the_globals->getEST(); |
839 | > | theEst= globals->getEST(); |
840 | } | |
841 | + | |
842 | + | info->setEcr( theEcr, theEst ); |
843 | } | |
844 | } | |
845 | ||
# | Line 1066 | Line 852 | void SimSetup::initSystemCoords( void ){ | |
852 | ||
853 | void SimSetup::initSystemCoords( void ){ | |
854 | ||
855 | < | if( the_globals->haveInitialConfig() ){ |
855 | > | if( globals->haveInitialConfig() ){ |
856 | ||
857 | InitializeFromFile* fileInit; | |
858 | #ifdef IS_MPI // is_mpi | |
859 | if( worldRank == 0 ){ | |
860 | #endif //is_mpi | |
861 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
861 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
862 | #ifdef IS_MPI | |
863 | }else fileInit = new InitializeFromFile( NULL ); | |
864 | #endif | |
865 | < | fileInit->read_xyz( info ); // default velocities on |
865 | > | fileInit->readInit( info ); // default velocities on |
866 | ||
867 | delete fileInit; | |
868 | } | |
# | Line 1113 | Line 899 | void SimSetup::makeOutNames( void ){ | |
899 | if( worldRank == 0 ){ | |
900 | #endif // is_mpi | |
901 | ||
902 | < | if( the_globals->haveFinalConfig() ){ |
903 | < | strcpy( info->finalName, the_globals->getFinalConfig() ); |
902 | > | if( globals->haveFinalConfig() ){ |
903 | > | strcpy( info->finalName, globals->getFinalConfig() ); |
904 | } | |
905 | else{ | |
906 | strcpy( info->finalName, inFileName ); | |
# | Line 1197 | Line 983 | void SimSetup::sysObjectsCreation( void ){ | |
983 | ||
984 | void SimSetup::sysObjectsCreation( void ){ | |
985 | ||
986 | + | int i; |
987 | + | |
988 | // create the forceField | |
989 | ||
990 | createFF(); | |
# | Line 1219 | Line 1007 | void SimSetup::sysObjectsCreation( void ){ | |
1007 | ||
1008 | makeSysArrays(); | |
1009 | ||
1010 | + | // make and initialize the molecules (all but atomic coordinates) |
1011 | ||
1012 | + | makeMolecules(); |
1013 | + | info->identArray = new int[info->n_atoms]; |
1014 | + | for(i=0; i<info->n_atoms; i++){ |
1015 | + | info->identArray[i] = the_atoms[i]->getIdent(); |
1016 | + | } |
1017 | + | |
1018 | ||
1019 | ||
1020 | } | |
# | Line 1254 | Line 1049 | void SimSetup::compList( void ){ | |
1049 | ||
1050 | void SimSetup::compList( void ){ | |
1051 | ||
1052 | + | int i; |
1053 | + | |
1054 | comp_stamps = new MoleculeStamp*[n_components]; | |
1055 | ||
1056 | // make an array of molecule stamps that match the components used. | |
# | Line 1279 | Line 1076 | void SimSetup::compList( void ){ | |
1076 | ||
1077 | // extract the component from the list; | |
1078 | ||
1079 | < | currentStamp = the_stamps->extractMolStamp( id ); |
1079 | > | currentStamp = stamps->extractMolStamp( id ); |
1080 | if( currentStamp == NULL ){ | |
1081 | sprintf( painCave.errMsg, | |
1082 | "SimSetup error: Component \"%s\" was not found in the " | |
# | Line 1303 | Line 1100 | void SimSetup::calcSysValues( void ){ | |
1100 | } | |
1101 | ||
1102 | void SimSetup::calcSysValues( void ){ | |
1103 | + | int i, j, k; |
1104 | ||
1105 | + | |
1106 | tot_atoms = 0; | |
1107 | tot_bonds = 0; | |
1108 | tot_bends = 0; | |
# | Line 1333 | Line 1132 | void SimSetup::mpiMolDivide( void ){ | |
1132 | ||
1133 | void SimSetup::mpiMolDivide( void ){ | |
1134 | ||
1135 | + | int i, j, k; |
1136 | int localMol, allMol; | |
1137 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1138 | ||
# | Line 1402 | Line 1202 | void SimSetup::makeSysArrays( void ){ | |
1202 | ||
1203 | ||
1204 | void SimSetup::makeSysArrays( void ){ | |
1205 | + | int i, j, k; |
1206 | ||
1207 | + | |
1208 | // create the atom and short range interaction arrays | |
1209 | ||
1210 | Atom::createArrays(info->n_atoms); | |
# | Line 1476 | Line 1278 | void SimSetup::makeSysArrays( void ){ | |
1278 | the_ff->setSimInfo( info ); | |
1279 | ||
1280 | } | |
1281 | + | |
1282 | + | void SimSetup::makeIntegrator( void ){ |
1283 | + | |
1284 | + | NVT* myNVT = NULL; |
1285 | + | NPTi* myNPTi = NULL; |
1286 | + | NPTf* myNPTf = NULL; |
1287 | + | NPTim* myNPTim = NULL; |
1288 | + | NPTfm* myNPTfm = NULL; |
1289 | + | |
1290 | + | switch( ensembleCase ){ |
1291 | + | |
1292 | + | case NVE_ENS: |
1293 | + | new NVE( info, the_ff ); |
1294 | + | break; |
1295 | + | |
1296 | + | case NVT_ENS: |
1297 | + | myNVT = new NVT( info, the_ff ); |
1298 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1299 | + | |
1300 | + | if (globals->haveTauThermostat()) |
1301 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1302 | + | |
1303 | + | else { |
1304 | + | sprintf( painCave.errMsg, |
1305 | + | "SimSetup error: If you use the NVT\n" |
1306 | + | " ensemble, you must set tauThermostat.\n"); |
1307 | + | painCave.isFatal = 1; |
1308 | + | simError(); |
1309 | + | } |
1310 | + | break; |
1311 | + | |
1312 | + | case NPTi_ENS: |
1313 | + | myNPTi = new NPTi( info, the_ff ); |
1314 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1315 | + | |
1316 | + | if (globals->haveTargetPressure()) |
1317 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1318 | + | else { |
1319 | + | sprintf( painCave.errMsg, |
1320 | + | "SimSetup error: If you use a constant pressure\n" |
1321 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1322 | + | painCave.isFatal = 1; |
1323 | + | simError(); |
1324 | + | } |
1325 | + | |
1326 | + | if( globals->haveTauThermostat() ) |
1327 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1328 | + | else{ |
1329 | + | sprintf( painCave.errMsg, |
1330 | + | "SimSetup error: If you use an NPT\n" |
1331 | + | " ensemble, you must set tauThermostat.\n"); |
1332 | + | painCave.isFatal = 1; |
1333 | + | simError(); |
1334 | + | } |
1335 | + | |
1336 | + | if( globals->haveTauBarostat() ) |
1337 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1338 | + | else{ |
1339 | + | sprintf( painCave.errMsg, |
1340 | + | "SimSetup error: If you use an NPT\n" |
1341 | + | " ensemble, you must set tauBarostat.\n"); |
1342 | + | painCave.isFatal = 1; |
1343 | + | simError(); |
1344 | + | } |
1345 | + | break; |
1346 | + | |
1347 | + | case NPTf_ENS: |
1348 | + | myNPTf = new NPTf( info, the_ff ); |
1349 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1350 | + | |
1351 | + | if (globals->haveTargetPressure()) |
1352 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1353 | + | else { |
1354 | + | sprintf( painCave.errMsg, |
1355 | + | "SimSetup error: If you use a constant pressure\n" |
1356 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1357 | + | painCave.isFatal = 1; |
1358 | + | simError(); |
1359 | + | } |
1360 | + | |
1361 | + | if( globals->haveTauThermostat() ) |
1362 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1363 | + | else{ |
1364 | + | sprintf( painCave.errMsg, |
1365 | + | "SimSetup error: If you use an NPT\n" |
1366 | + | " ensemble, you must set tauThermostat.\n"); |
1367 | + | painCave.isFatal = 1; |
1368 | + | simError(); |
1369 | + | } |
1370 | + | |
1371 | + | if( globals->haveTauBarostat() ) |
1372 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1373 | + | else{ |
1374 | + | sprintf( painCave.errMsg, |
1375 | + | "SimSetup error: If you use an NPT\n" |
1376 | + | " ensemble, you must set tauBarostat.\n"); |
1377 | + | painCave.isFatal = 1; |
1378 | + | simError(); |
1379 | + | } |
1380 | + | break; |
1381 | + | |
1382 | + | case NPTim_ENS: |
1383 | + | myNPTim = new NPTim( info, the_ff ); |
1384 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1385 | + | |
1386 | + | if (globals->haveTargetPressure()) |
1387 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1388 | + | else { |
1389 | + | sprintf( painCave.errMsg, |
1390 | + | "SimSetup error: If you use a constant pressure\n" |
1391 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1392 | + | painCave.isFatal = 1; |
1393 | + | simError(); |
1394 | + | } |
1395 | + | |
1396 | + | if( globals->haveTauThermostat() ) |
1397 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1398 | + | else{ |
1399 | + | sprintf( painCave.errMsg, |
1400 | + | "SimSetup error: If you use an NPT\n" |
1401 | + | " ensemble, you must set tauThermostat.\n"); |
1402 | + | painCave.isFatal = 1; |
1403 | + | simError(); |
1404 | + | } |
1405 | + | |
1406 | + | if( globals->haveTauBarostat() ) |
1407 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1408 | + | else{ |
1409 | + | sprintf( painCave.errMsg, |
1410 | + | "SimSetup error: If you use an NPT\n" |
1411 | + | " ensemble, you must set tauBarostat.\n"); |
1412 | + | painCave.isFatal = 1; |
1413 | + | simError(); |
1414 | + | } |
1415 | + | break; |
1416 | + | |
1417 | + | case NPTfm_ENS: |
1418 | + | myNPTfm = new NPTfm( info, the_ff ); |
1419 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1420 | + | |
1421 | + | if (globals->haveTargetPressure()) |
1422 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1423 | + | else { |
1424 | + | sprintf( painCave.errMsg, |
1425 | + | "SimSetup error: If you use a constant pressure\n" |
1426 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1427 | + | painCave.isFatal = 1; |
1428 | + | simError(); |
1429 | + | } |
1430 | + | |
1431 | + | if( globals->haveTauThermostat() ) |
1432 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1433 | + | else{ |
1434 | + | sprintf( painCave.errMsg, |
1435 | + | "SimSetup error: If you use an NPT\n" |
1436 | + | " ensemble, you must set tauThermostat.\n"); |
1437 | + | painCave.isFatal = 1; |
1438 | + | simError(); |
1439 | + | } |
1440 | + | |
1441 | + | if( globals->haveTauBarostat() ) |
1442 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1443 | + | else{ |
1444 | + | sprintf( painCave.errMsg, |
1445 | + | "SimSetup error: If you use an NPT\n" |
1446 | + | " ensemble, you must set tauBarostat.\n"); |
1447 | + | painCave.isFatal = 1; |
1448 | + | simError(); |
1449 | + | } |
1450 | + | break; |
1451 | + | |
1452 | + | default: |
1453 | + | sprintf( painCave.errMsg, |
1454 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1455 | + | painCave.isFatal = 1; |
1456 | + | simError(); |
1457 | + | } |
1458 | + | |
1459 | + | } |
1460 | + | |
1461 | + | void SimSetup::initFortran( void ){ |
1462 | + | |
1463 | + | info->refreshSim(); |
1464 | + | |
1465 | + | if( !strcmp( info->mixingRule, "standard") ){ |
1466 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1467 | + | } |
1468 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1469 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1470 | + | } |
1471 | + | else{ |
1472 | + | sprintf( painCave.errMsg, |
1473 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1474 | + | info->mixingRule ); |
1475 | + | painCave.isFatal = 1; |
1476 | + | simError(); |
1477 | + | } |
1478 | + | |
1479 | + | |
1480 | + | #ifdef IS_MPI |
1481 | + | strcpy( checkPointMsg, |
1482 | + | "Successfully intialized the mixingRule for Fortran." ); |
1483 | + | MPIcheckPoint(); |
1484 | + | #endif // is_mpi |
1485 | + | |
1486 | + | } |
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