# | Line 1 | Line 1 | |
---|---|---|
1 | + | #include <algorithm> |
2 | #include <cstdlib> | |
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | + | #include <string> |
6 | ||
7 | #include "SimSetup.hpp" | |
8 | #include "parse_me.h" | |
# | Line 20 | Line 22 | |
22 | #define NPTf_ENS 3 | |
23 | #define NPTim_ENS 4 | |
24 | #define NPTfm_ENS 5 | |
25 | + | #define NVEZCONS_ENS 6 |
26 | ||
27 | ||
28 | #define FF_DUFF 0 | |
29 | #define FF_LJ 1 | |
30 | + | #define FF_EAM 2 |
31 | ||
32 | + | using namespace std; |
33 | ||
34 | SimSetup::SimSetup(){ | |
35 | + | |
36 | + | isInfoArray = 0; |
37 | + | nInfo = 1; |
38 | + | |
39 | stamps = new MakeStamps(); | |
40 | globals = new Globals(); | |
41 | ||
42 | + | |
43 | #ifdef IS_MPI | |
44 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
45 | MPIcheckPoint(); | |
# | Line 41 | Line 51 | SimSetup::~SimSetup(){ | |
51 | delete globals; | |
52 | } | |
53 | ||
54 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
55 | + | info = the_info; |
56 | + | nInfo = theNinfo; |
57 | + | isInfoArray = 1; |
58 | + | } |
59 | + | |
60 | + | |
61 | void SimSetup::parseFile( char* fileName ){ | |
62 | ||
63 | #ifdef IS_MPI | |
# | Line 78 | Line 95 | void SimSetup::createSim( void ){ | |
95 | ||
96 | void SimSetup::createSim( void ){ | |
97 | ||
81 | – | MakeStamps *the_stamps; |
82 | – | Globals* the_globals; |
98 | int i, j, k, globalAtomIndex; | |
99 | ||
100 | // gather all of the information from the Bass file | |
# | Line 90 | Line 105 | void SimSetup::createSim( void ){ | |
105 | ||
106 | sysObjectsCreation(); | |
107 | ||
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 | – | |
108 | // check on the post processing info | |
109 | ||
110 | finalInfoCheck(); | |
111 | ||
110 | – | |
111 | – | |
112 | – | |
112 | // initialize the system coordinates | |
113 | ||
114 | initSystemCoords(); | |
# | Line 119 | Line 118 | void SimSetup::createSim( void ){ | |
118 | ||
119 | makeOutNames(); | |
120 | ||
122 | – | |
123 | – | |
124 | – | |
125 | – | |
126 | – | |
127 | – | |
128 | – | |
129 | – | |
121 | // make the integrator | |
122 | ||
123 | + | makeIntegrator(); |
124 | ||
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 | – | |
125 | #ifdef IS_MPI | |
126 | mpiSim->mpiRefresh(); | |
127 | #endif | |
128 | ||
129 | // initialize the Fortran | |
130 | ||
131 | + | initFortran(); |
132 | ||
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 | – | } |
133 | ||
134 | ||
333 | – | #ifdef IS_MPI |
334 | – | strcpy( checkPointMsg, |
335 | – | "Successfully intialized the mixingRule for Fortran." ); |
336 | – | MPIcheckPoint(); |
337 | – | #endif // is_mpi |
135 | } | |
136 | ||
137 | ||
138 | void SimSetup::makeMolecules( void ){ | |
139 | ||
140 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
141 | < | molInit info; |
141 | > | molInit molInfo; |
142 | DirectionalAtom* dAtom; | |
143 | LinkedAssign* extras; | |
144 | LinkedAssign* current_extra; | |
# | Line 370 | Line 167 | void SimSetup::makeMolecules( void ){ | |
167 | ||
168 | stampID = the_molecules[i].getStampID(); | |
169 | ||
170 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
172 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
173 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
170 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
172 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
173 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
175 | ||
176 | < | info.myAtoms = &the_atoms[atomOffset]; |
177 | < | info.myExcludes = &the_excludes[excludeOffset]; |
178 | < | info.myBonds = new Bond*[info.nBonds]; |
179 | < | info.myBends = new Bend*[info.nBends]; |
180 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
176 | > | molInfo.myAtoms = &the_atoms[atomOffset]; |
177 | > | molInfo.myExcludes = &the_excludes[excludeOffset]; |
178 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
179 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
180 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
181 | ||
182 | < | theBonds = new bond_pair[info.nBonds]; |
183 | < | theBends = new bend_set[info.nBends]; |
184 | < | theTorsions = new torsion_set[info.nTorsions]; |
182 | > | theBonds = new bond_pair[molInfo.nBonds]; |
183 | > | theBends = new bend_set[molInfo.nBends]; |
184 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
185 | ||
186 | // make the Atoms | |
187 | ||
188 | < | for(j=0; j<info.nAtoms; j++){ |
188 | > | for(j=0; j<molInfo.nAtoms; j++){ |
189 | ||
190 | currentAtom = comp_stamps[stampID]->getAtom( j ); | |
191 | if( currentAtom->haveOrientation() ){ | |
192 | ||
193 | dAtom = new DirectionalAtom(j + atomOffset); | |
194 | info->n_oriented++; | |
195 | < | info.myAtoms[j] = dAtom; |
195 | > | molInfo.myAtoms[j] = dAtom; |
196 | ||
197 | ux = currentAtom->getOrntX(); | |
198 | uy = currentAtom->getOrntY(); | |
# | Line 413 | Line 210 | void SimSetup::makeMolecules( void ){ | |
210 | dAtom->setSUz( uz ); | |
211 | } | |
212 | else{ | |
213 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
213 | > | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
214 | } | |
215 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
215 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
216 | ||
217 | #ifdef IS_MPI | |
218 | ||
219 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
219 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
220 | ||
221 | #endif // is_mpi | |
222 | } | |
223 | ||
224 | // make the bonds | |
225 | < | for(j=0; j<info.nBonds; j++){ |
225 | > | for(j=0; j<molInfo.nBonds; j++){ |
226 | ||
227 | currentBond = comp_stamps[stampID]->getBond( j ); | |
228 | theBonds[j].a = currentBond->getA() + atomOffset; | |
# | Line 452 | Line 249 | void SimSetup::makeMolecules( void ){ | |
249 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
250 | #endif //is_mpi | |
251 | } | |
252 | < | excludeOffset += info.nBonds; |
252 | > | excludeOffset += molInfo.nBonds; |
253 | ||
254 | //make the bends | |
255 | < | for(j=0; j<info.nBends; j++){ |
255 | > | for(j=0; j<molInfo.nBends; j++){ |
256 | ||
257 | currentBend = comp_stamps[stampID]->getBend( j ); | |
258 | theBends[j].a = currentBend->getA() + atomOffset; | |
# | Line 538 | Line 335 | void SimSetup::makeMolecules( void ){ | |
335 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
336 | #endif //is_mpi | |
337 | } | |
338 | < | excludeOffset += info.nBends; |
338 | > | excludeOffset += molInfo.nBends; |
339 | ||
340 | < | for(j=0; j<info.nTorsions; j++){ |
340 | > | for(j=0; j<molInfo.nTorsions; j++){ |
341 | ||
342 | currentTorsion = comp_stamps[stampID]->getTorsion( j ); | |
343 | theTorsions[j].a = currentTorsion->getA() + atomOffset; | |
# | Line 568 | Line 365 | void SimSetup::makeMolecules( void ){ | |
365 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
366 | #endif //is_mpi | |
367 | } | |
368 | < | excludeOffset += info.nTorsions; |
368 | > | excludeOffset += molInfo.nTorsions; |
369 | ||
370 | ||
371 | // send the arrays off to the forceField for init. | |
372 | ||
373 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
374 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
375 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
376 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
373 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
374 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
375 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
376 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
377 | ||
378 | ||
379 | < | the_molecules[i].initialize( info ); |
379 | > | the_molecules[i].initialize( molInfo ); |
380 | ||
381 | ||
382 | < | atomOffset += info.nAtoms; |
382 | > | atomOffset += molInfo.nAtoms; |
383 | delete[] theBonds; | |
384 | delete[] theBends; | |
385 | delete[] theTorsions; | |
# | Line 618 | Line 415 | void SimSetup::initFromBass( void ){ | |
415 | have_extra =1; | |
416 | ||
417 | n_cells = (int)temp3 - 1; | |
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 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
422 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
423 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 635 | Line 432 | void SimSetup::initFromBass( void ){ | |
432 | } | |
433 | else{ | |
434 | n_cells = (int)temp3; | |
435 | < | cellx = info->boxLx / temp3; |
436 | < | celly = info->boxLy / temp3; |
437 | < | cellz = info->boxLz / temp3; |
435 | > | cellx = info->boxL[0] / temp3; |
436 | > | celly = info->boxL[1] / temp3; |
437 | > | cellz = info->boxL[2] / temp3; |
438 | } | |
439 | ||
440 | current_mol = 0; | |
# | Line 784 | Line 581 | void SimSetup::gatherInfo( void ){ | |
581 | ||
582 | ||
583 | void SimSetup::gatherInfo( void ){ | |
584 | + | int i,j,k; |
585 | ||
586 | ensembleCase = -1; | |
587 | ffCase = -1; | |
588 | ||
589 | // get the stamps and globals; | |
590 | < | the_stamps = stamps; |
591 | < | the_globals = globals; |
590 | > | stamps = stamps; |
591 | > | globals = globals; |
592 | ||
593 | // set the easy ones first | |
594 | < | info->target_temp = the_globals->getTargetTemp(); |
595 | < | info->dt = the_globals->getDt(); |
596 | < | info->run_time = the_globals->getRunTime(); |
597 | < | n_components = the_globals->getNComponents(); |
594 | > | info->target_temp = globals->getTargetTemp(); |
595 | > | info->dt = globals->getDt(); |
596 | > | info->run_time = globals->getRunTime(); |
597 | > | n_components = globals->getNComponents(); |
598 | ||
599 | ||
600 | // get the forceField | |
601 | ||
602 | < | strcpy( force_field, the_globals->getForceField() ); |
602 | > | strcpy( force_field, globals->getForceField() ); |
603 | ||
604 | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; | |
605 | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; | |
606 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
607 | else{ | |
608 | sprintf( painCave.errMsg, | |
609 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 815 | Line 614 | void SimSetup::gatherInfo( void ){ | |
614 | ||
615 | // get the ensemble | |
616 | ||
617 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
617 | > | strcpy( ensemble, globals->getEnsemble() ); |
618 | ||
619 | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; | |
620 | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; | |
# | Line 824 | Line 623 | void SimSetup::gatherInfo( void ){ | |
623 | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; | |
624 | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; | |
625 | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; | |
626 | + | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
627 | else{ | |
628 | sprintf( painCave.errMsg, | |
629 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 838 | Line 638 | void SimSetup::gatherInfo( void ){ | |
638 | ||
639 | // get the mixing rule | |
640 | ||
641 | < | strcpy( info->mixingRule, the_globals->getMixingRule() ); |
642 | < | info->usePBC = the_globals->getPBC(); |
641 | > | strcpy( info->mixingRule, globals->getMixingRule() ); |
642 | > | info->usePBC = globals->getPBC(); |
643 | ||
644 | ||
645 | // get the components and calculate the tot_nMol and indvidual n_mol | |
646 | ||
647 | < | the_components = the_globals->getComponents(); |
647 | > | the_components = globals->getComponents(); |
648 | components_nmol = new int[n_components]; | |
649 | ||
650 | ||
651 | < | if( !the_globals->haveNMol() ){ |
651 | > | if( !globals->haveNMol() ){ |
652 | // we don't have the total number of molecules, so we assume it is | |
653 | // given in each component | |
654 | ||
# | Line 881 | Line 681 | void SimSetup::gatherInfo( void ){ | |
681 | ||
682 | // set the status, sample, and thermal kick times | |
683 | ||
684 | < | if( the_globals->haveSampleTime() ){ |
685 | < | info->sampleTime = the_globals->getSampleTime(); |
684 | > | if( globals->haveSampleTime() ){ |
685 | > | info->sampleTime = globals->getSampleTime(); |
686 | info->statusTime = info->sampleTime; | |
687 | info->thermalTime = info->sampleTime; | |
688 | } | |
689 | else{ | |
690 | < | info->sampleTime = the_globals->getRunTime(); |
690 | > | info->sampleTime = globals->getRunTime(); |
691 | info->statusTime = info->sampleTime; | |
692 | info->thermalTime = info->sampleTime; | |
693 | } | |
694 | ||
695 | < | if( the_globals->haveStatusTime() ){ |
696 | < | info->statusTime = the_globals->getStatusTime(); |
695 | > | if( globals->haveStatusTime() ){ |
696 | > | info->statusTime = globals->getStatusTime(); |
697 | } | |
698 | ||
699 | < | if( the_globals->haveThermalTime() ){ |
700 | < | info->thermalTime = the_globals->getThermalTime(); |
699 | > | if( globals->haveThermalTime() ){ |
700 | > | info->thermalTime = globals->getThermalTime(); |
701 | } | |
702 | ||
703 | // check for the temperature set flag | |
704 | ||
705 | < | if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
705 | > | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
706 | ||
707 | // get some of the tricky things that may still be in the globals | |
708 | ||
709 | double boxVector[3]; | |
710 | < | if( the_globals->haveBox() ){ |
711 | < | boxVector[0] = the_globals->getBox(); |
712 | < | boxVector[1] = the_globals->getBox(); |
713 | < | boxVector[2] = the_globals->getBox(); |
710 | > | if( globals->haveBox() ){ |
711 | > | boxVector[0] = globals->getBox(); |
712 | > | boxVector[1] = globals->getBox(); |
713 | > | boxVector[2] = globals->getBox(); |
714 | ||
715 | info->setBox( boxVector ); | |
716 | } | |
717 | < | else if( the_globals->haveDensity() ){ |
717 | > | else if( globals->haveDensity() ){ |
718 | ||
719 | double vol; | |
720 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
720 | > | vol = (double)tot_nmol / globals->getDensity(); |
721 | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); | |
722 | boxVector[1] = boxVector[0]; | |
723 | boxVector[2] = boxVector[0]; | |
# | Line 925 | Line 725 | void SimSetup::gatherInfo( void ){ | |
725 | info->setBox( boxVector ); | |
726 | } | |
727 | else{ | |
728 | < | if( !the_globals->haveBoxX() ){ |
728 | > | if( !globals->haveBoxX() ){ |
729 | sprintf( painCave.errMsg, | |
730 | "SimSetup error, no periodic BoxX size given.\n" ); | |
731 | painCave.isFatal = 1; | |
732 | simError(); | |
733 | } | |
734 | < | boxVector[0] = the_globals->getBoxX(); |
734 | > | boxVector[0] = globals->getBoxX(); |
735 | ||
736 | < | if( !the_globals->haveBoxY() ){ |
736 | > | if( !globals->haveBoxY() ){ |
737 | sprintf( painCave.errMsg, | |
738 | "SimSetup error, no periodic BoxY size given.\n" ); | |
739 | painCave.isFatal = 1; | |
740 | simError(); | |
741 | } | |
742 | < | boxVector[1] = the_globals->getBoxY(); |
742 | > | boxVector[1] = globals->getBoxY(); |
743 | ||
744 | < | if( !the_globals->haveBoxZ() ){ |
744 | > | if( !globals->haveBoxZ() ){ |
745 | sprintf( painCave.errMsg, | |
746 | "SimSetup error, no periodic BoxZ size given.\n" ); | |
747 | painCave.isFatal = 1; | |
748 | simError(); | |
749 | } | |
750 | < | boxVector[2] = the_globals->getBoxZ(); |
750 | > | boxVector[2] = globals->getBoxZ(); |
751 | ||
752 | info->setBox( boxVector ); | |
753 | } | |
# | Line 977 | Line 777 | void SimSetup::finalInfoCheck( void ){ | |
777 | } | |
778 | ||
779 | #ifdef IS_MPI | |
780 | < | int myUse = usesDipoles |
781 | < | MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
780 | > | int myUse = usesDipoles; |
781 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
782 | #endif //is_mpi | |
783 | ||
784 | + | double theEcr, theEst; |
785 | ||
786 | < | if (the_globals->getUseRF() ) { |
786 | > | if (globals->getUseRF() ) { |
787 | info->useReactionField = 1; | |
788 | ||
789 | < | if( !the_globals->haveECR() ){ |
789 | > | if( !globals->haveECR() ){ |
790 | sprintf( painCave.errMsg, | |
791 | "SimSetup Warning: using default value of 1/2 the smallest " | |
792 | "box length for the electrostaticCutoffRadius.\n" | |
# | Line 993 | Line 794 | void SimSetup::finalInfoCheck( void ){ | |
794 | painCave.isFatal = 0; | |
795 | simError(); | |
796 | double smallest; | |
797 | < | smallest = info->boxLx; |
798 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
799 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
800 | < | info->ecr = 0.5 * smallest; |
797 | > | smallest = info->boxL[0]; |
798 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
799 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
800 | > | theEcr = 0.5 * smallest; |
801 | } else { | |
802 | < | info->ecr = the_globals->getECR(); |
802 | > | theEcr = globals->getECR(); |
803 | } | |
804 | ||
805 | < | if( !the_globals->haveEST() ){ |
805 | > | if( !globals->haveEST() ){ |
806 | sprintf( painCave.errMsg, | |
807 | "SimSetup Warning: using default value of 0.05 * the " | |
808 | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" | |
809 | ); | |
810 | painCave.isFatal = 0; | |
811 | simError(); | |
812 | < | info->est = 0.05 * info->ecr; |
812 | > | theEst = 0.05 * theEcr; |
813 | } else { | |
814 | < | info->est = the_globals->getEST(); |
814 | > | theEst= globals->getEST(); |
815 | } | |
816 | + | |
817 | + | info->setEcr( theEcr, theEst ); |
818 | ||
819 | < | if(!the_globals->haveDielectric() ){ |
819 | > | if(!globals->haveDielectric() ){ |
820 | sprintf( painCave.errMsg, | |
821 | "SimSetup Error: You are trying to use Reaction Field without" | |
822 | "setting a dielectric constant!\n" | |
# | Line 1021 | Line 824 | void SimSetup::finalInfoCheck( void ){ | |
824 | painCave.isFatal = 1; | |
825 | simError(); | |
826 | } | |
827 | < | info->dielectric = the_globals->getDielectric(); |
827 | > | info->dielectric = globals->getDielectric(); |
828 | } | |
829 | else { | |
830 | if (usesDipoles) { | |
831 | ||
832 | < | if( !the_globals->haveECR() ){ |
833 | < | sprintf( painCave.errMsg, |
834 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
835 | < | "box length for the electrostaticCutoffRadius.\n" |
836 | < | "I hope you have a very fast processor!\n"); |
837 | < | painCave.isFatal = 0; |
838 | < | simError(); |
839 | < | double smallest; |
840 | < | smallest = info->boxLx; |
841 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
842 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
843 | < | info->ecr = 0.5 * smallest; |
832 | > | if( !globals->haveECR() ){ |
833 | > | sprintf( painCave.errMsg, |
834 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
835 | > | "box length for the electrostaticCutoffRadius.\n" |
836 | > | "I hope you have a very fast processor!\n"); |
837 | > | painCave.isFatal = 0; |
838 | > | simError(); |
839 | > | double smallest; |
840 | > | smallest = info->boxL[0]; |
841 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
842 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
843 | > | theEcr = 0.5 * smallest; |
844 | } else { | |
845 | < | info->ecr = the_globals->getECR(); |
845 | > | theEcr = globals->getECR(); |
846 | } | |
847 | ||
848 | < | if( !the_globals->haveEST() ){ |
849 | < | sprintf( painCave.errMsg, |
850 | < | "SimSetup Warning: using default value of 5%% of the " |
851 | < | "electrostaticCutoffRadius for the " |
852 | < | "electrostaticSkinThickness\n" |
853 | < | ); |
854 | < | painCave.isFatal = 0; |
855 | < | simError(); |
856 | < | info->est = 0.05 * info->ecr; |
848 | > | if( !globals->haveEST() ){ |
849 | > | sprintf( painCave.errMsg, |
850 | > | "SimSetup Warning: using default value of 0.05 * the " |
851 | > | "electrostaticCutoffRadius for the " |
852 | > | "electrostaticSkinThickness\n" |
853 | > | ); |
854 | > | painCave.isFatal = 0; |
855 | > | simError(); |
856 | > | theEst = 0.05 * theEcr; |
857 | } else { | |
858 | < | info->est = the_globals->getEST(); |
858 | > | theEst= globals->getEST(); |
859 | } | |
860 | + | |
861 | + | info->setEcr( theEcr, theEst ); |
862 | } | |
863 | } | |
864 | ||
# | Line 1066 | Line 871 | void SimSetup::initSystemCoords( void ){ | |
871 | ||
872 | void SimSetup::initSystemCoords( void ){ | |
873 | ||
874 | < | if( the_globals->haveInitialConfig() ){ |
874 | > | if( globals->haveInitialConfig() ){ |
875 | ||
876 | InitializeFromFile* fileInit; | |
877 | #ifdef IS_MPI // is_mpi | |
878 | if( worldRank == 0 ){ | |
879 | #endif //is_mpi | |
880 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
880 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
881 | #ifdef IS_MPI | |
882 | }else fileInit = new InitializeFromFile( NULL ); | |
883 | #endif | |
884 | < | fileInit->read_xyz( info ); // default velocities on |
884 | > | fileInit->readInit( info ); // default velocities on |
885 | ||
886 | delete fileInit; | |
887 | } | |
# | Line 1113 | Line 918 | void SimSetup::makeOutNames( void ){ | |
918 | if( worldRank == 0 ){ | |
919 | #endif // is_mpi | |
920 | ||
921 | < | if( the_globals->haveFinalConfig() ){ |
922 | < | strcpy( info->finalName, the_globals->getFinalConfig() ); |
921 | > | if( globals->haveFinalConfig() ){ |
922 | > | strcpy( info->finalName, globals->getFinalConfig() ); |
923 | } | |
924 | else{ | |
925 | strcpy( info->finalName, inFileName ); | |
# | Line 1197 | Line 1002 | void SimSetup::sysObjectsCreation( void ){ | |
1002 | ||
1003 | void SimSetup::sysObjectsCreation( void ){ | |
1004 | ||
1005 | + | int i; |
1006 | + | |
1007 | // create the forceField | |
1008 | ||
1009 | createFF(); | |
# | Line 1219 | Line 1026 | void SimSetup::sysObjectsCreation( void ){ | |
1026 | ||
1027 | makeSysArrays(); | |
1028 | ||
1029 | + | // make and initialize the molecules (all but atomic coordinates) |
1030 | + | |
1031 | + | makeMolecules(); |
1032 | + | info->identArray = new int[info->n_atoms]; |
1033 | + | for(i=0; i<info->n_atoms; i++){ |
1034 | + | info->identArray[i] = the_atoms[i]->getIdent(); |
1035 | + | } |
1036 | ||
1037 | ||
1038 | ||
# | Line 1237 | Line 1051 | void SimSetup::createFF( void ){ | |
1051 | the_ff = new LJFF(); | |
1052 | break; | |
1053 | ||
1054 | + | case FF_EAM: |
1055 | + | the_ff = new EAM_FF(); |
1056 | + | break; |
1057 | + | |
1058 | default: | |
1059 | sprintf( painCave.errMsg, | |
1060 | "SimSetup Error. Unrecognized force field in case statement.\n"); | |
# | Line 1254 | Line 1072 | void SimSetup::compList( void ){ | |
1072 | ||
1073 | void SimSetup::compList( void ){ | |
1074 | ||
1075 | + | int i; |
1076 | + | |
1077 | comp_stamps = new MoleculeStamp*[n_components]; | |
1078 | ||
1079 | // make an array of molecule stamps that match the components used. | |
# | Line 1279 | Line 1099 | void SimSetup::compList( void ){ | |
1099 | ||
1100 | // extract the component from the list; | |
1101 | ||
1102 | < | currentStamp = the_stamps->extractMolStamp( id ); |
1102 | > | currentStamp = stamps->extractMolStamp( id ); |
1103 | if( currentStamp == NULL ){ | |
1104 | sprintf( painCave.errMsg, | |
1105 | "SimSetup error: Component \"%s\" was not found in the " | |
# | Line 1303 | Line 1123 | void SimSetup::calcSysValues( void ){ | |
1123 | } | |
1124 | ||
1125 | void SimSetup::calcSysValues( void ){ | |
1126 | + | int i, j, k; |
1127 | ||
1128 | + | |
1129 | tot_atoms = 0; | |
1130 | tot_bonds = 0; | |
1131 | tot_bends = 0; | |
# | Line 1333 | Line 1155 | void SimSetup::mpiMolDivide( void ){ | |
1155 | ||
1156 | void SimSetup::mpiMolDivide( void ){ | |
1157 | ||
1158 | + | int i, j, k; |
1159 | int localMol, allMol; | |
1160 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1161 | ||
# | Line 1402 | Line 1225 | void SimSetup::makeSysArrays( void ){ | |
1225 | ||
1226 | ||
1227 | void SimSetup::makeSysArrays( void ){ | |
1228 | + | int i, j, k; |
1229 | ||
1230 | + | |
1231 | // create the atom and short range interaction arrays | |
1232 | ||
1233 | Atom::createArrays(info->n_atoms); | |
# | Line 1476 | Line 1301 | void SimSetup::makeSysArrays( void ){ | |
1301 | the_ff->setSimInfo( info ); | |
1302 | ||
1303 | } | |
1304 | + | |
1305 | + | void SimSetup::makeIntegrator( void ){ |
1306 | + | |
1307 | + | NVT<RealIntegrator>* myNVT = NULL; |
1308 | + | NPTi<RealIntegrator>* myNPTi = NULL; |
1309 | + | NPTf<RealIntegrator>* myNPTf = NULL; |
1310 | + | NPTim<RealIntegrator>* myNPTim = NULL; |
1311 | + | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1312 | + | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1313 | + | |
1314 | + | cerr << "setting integrator" <<endl; |
1315 | + | |
1316 | + | switch( ensembleCase ){ |
1317 | + | |
1318 | + | case NVE_ENS: |
1319 | + | new NVE<RealIntegrator>( info, the_ff ); |
1320 | + | break; |
1321 | + | |
1322 | + | case NVT_ENS: |
1323 | + | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1324 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1325 | + | |
1326 | + | if (globals->haveTauThermostat()) |
1327 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1328 | + | |
1329 | + | else { |
1330 | + | sprintf( painCave.errMsg, |
1331 | + | "SimSetup error: If you use the NVT\n" |
1332 | + | " ensemble, you must set tauThermostat.\n"); |
1333 | + | painCave.isFatal = 1; |
1334 | + | simError(); |
1335 | + | } |
1336 | + | break; |
1337 | + | |
1338 | + | case NPTi_ENS: |
1339 | + | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1340 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1341 | + | |
1342 | + | if (globals->haveTargetPressure()) |
1343 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1344 | + | else { |
1345 | + | sprintf( painCave.errMsg, |
1346 | + | "SimSetup error: If you use a constant pressure\n" |
1347 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1348 | + | painCave.isFatal = 1; |
1349 | + | simError(); |
1350 | + | } |
1351 | + | |
1352 | + | if( globals->haveTauThermostat() ) |
1353 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1354 | + | else{ |
1355 | + | sprintf( painCave.errMsg, |
1356 | + | "SimSetup error: If you use an NPT\n" |
1357 | + | " ensemble, you must set tauThermostat.\n"); |
1358 | + | painCave.isFatal = 1; |
1359 | + | simError(); |
1360 | + | } |
1361 | + | |
1362 | + | if( globals->haveTauBarostat() ) |
1363 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1364 | + | else{ |
1365 | + | sprintf( painCave.errMsg, |
1366 | + | "SimSetup error: If you use an NPT\n" |
1367 | + | " ensemble, you must set tauBarostat.\n"); |
1368 | + | painCave.isFatal = 1; |
1369 | + | simError(); |
1370 | + | } |
1371 | + | break; |
1372 | + | |
1373 | + | case NPTf_ENS: |
1374 | + | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1375 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1376 | + | |
1377 | + | if (globals->haveTargetPressure()) |
1378 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1379 | + | else { |
1380 | + | sprintf( painCave.errMsg, |
1381 | + | "SimSetup error: If you use a constant pressure\n" |
1382 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1383 | + | painCave.isFatal = 1; |
1384 | + | simError(); |
1385 | + | } |
1386 | + | |
1387 | + | if( globals->haveTauThermostat() ) |
1388 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1389 | + | else{ |
1390 | + | sprintf( painCave.errMsg, |
1391 | + | "SimSetup error: If you use an NPT\n" |
1392 | + | " ensemble, you must set tauThermostat.\n"); |
1393 | + | painCave.isFatal = 1; |
1394 | + | simError(); |
1395 | + | } |
1396 | + | |
1397 | + | if( globals->haveTauBarostat() ) |
1398 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1399 | + | else{ |
1400 | + | sprintf( painCave.errMsg, |
1401 | + | "SimSetup error: If you use an NPT\n" |
1402 | + | " ensemble, you must set tauBarostat.\n"); |
1403 | + | painCave.isFatal = 1; |
1404 | + | simError(); |
1405 | + | } |
1406 | + | break; |
1407 | + | |
1408 | + | case NPTim_ENS: |
1409 | + | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1410 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1411 | + | |
1412 | + | if (globals->haveTargetPressure()) |
1413 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1414 | + | else { |
1415 | + | sprintf( painCave.errMsg, |
1416 | + | "SimSetup error: If you use a constant pressure\n" |
1417 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1418 | + | painCave.isFatal = 1; |
1419 | + | simError(); |
1420 | + | } |
1421 | + | |
1422 | + | if( globals->haveTauThermostat() ) |
1423 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1424 | + | else{ |
1425 | + | sprintf( painCave.errMsg, |
1426 | + | "SimSetup error: If you use an NPT\n" |
1427 | + | " ensemble, you must set tauThermostat.\n"); |
1428 | + | painCave.isFatal = 1; |
1429 | + | simError(); |
1430 | + | } |
1431 | + | |
1432 | + | if( globals->haveTauBarostat() ) |
1433 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1434 | + | else{ |
1435 | + | sprintf( painCave.errMsg, |
1436 | + | "SimSetup error: If you use an NPT\n" |
1437 | + | " ensemble, you must set tauBarostat.\n"); |
1438 | + | painCave.isFatal = 1; |
1439 | + | simError(); |
1440 | + | } |
1441 | + | break; |
1442 | + | |
1443 | + | case NPTfm_ENS: |
1444 | + | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1445 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 | + | |
1447 | + | if (globals->haveTargetPressure()) |
1448 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1449 | + | else { |
1450 | + | sprintf( painCave.errMsg, |
1451 | + | "SimSetup error: If you use a constant pressure\n" |
1452 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1453 | + | painCave.isFatal = 1; |
1454 | + | simError(); |
1455 | + | } |
1456 | + | |
1457 | + | if( globals->haveTauThermostat() ) |
1458 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1459 | + | else{ |
1460 | + | sprintf( painCave.errMsg, |
1461 | + | "SimSetup error: If you use an NPT\n" |
1462 | + | " ensemble, you must set tauThermostat.\n"); |
1463 | + | painCave.isFatal = 1; |
1464 | + | simError(); |
1465 | + | } |
1466 | + | |
1467 | + | if( globals->haveTauBarostat() ) |
1468 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1469 | + | else{ |
1470 | + | sprintf( painCave.errMsg, |
1471 | + | "SimSetup error: If you use an NPT\n" |
1472 | + | " ensemble, you must set tauBarostat.\n"); |
1473 | + | painCave.isFatal = 1; |
1474 | + | simError(); |
1475 | + | } |
1476 | + | break; |
1477 | + | |
1478 | + | case NVEZCONS_ENS: |
1479 | + | { |
1480 | + | |
1481 | + | if(globals->haveZConsTime()){ |
1482 | + | |
1483 | + | //add sample time of z-constraint into SimInfo's property list |
1484 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1485 | + | zconsTimeProp->setID("zconstime"); |
1486 | + | zconsTimeProp->setData(globals->getZConsTime()); |
1487 | + | info->addProperty(zconsTimeProp); |
1488 | + | } |
1489 | + | else{ |
1490 | + | sprintf( painCave.errMsg, |
1491 | + | "ZConstraint error: If you use an ZConstraint\n" |
1492 | + | " , you must set sample time.\n"); |
1493 | + | painCave.isFatal = 1; |
1494 | + | simError(); |
1495 | + | } |
1496 | + | |
1497 | + | if(globals->haveIndexOfAllZConsMols()){ |
1498 | + | |
1499 | + | //add index of z-constraint molecules into SimInfo's property list |
1500 | + | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1501 | + | sort(tempIndex.begin(), tempIndex.end()); |
1502 | + | |
1503 | + | IndexData* zconsIndex = new IndexData(); |
1504 | + | zconsIndex->setID("zconsindex"); |
1505 | + | zconsIndex->setIndexData(tempIndex); |
1506 | + | info->addProperty(zconsIndex); |
1507 | + | } |
1508 | + | else{ |
1509 | + | sprintf( painCave.errMsg, |
1510 | + | "SimSetup error: If you use an ZConstraint\n" |
1511 | + | " , you must set index of z-constraint molecules.\n"); |
1512 | + | painCave.isFatal = 1; |
1513 | + | simError(); |
1514 | + | |
1515 | + | } |
1516 | + | |
1517 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1518 | + | //Be careful, do not use inFileName, since it is a pointer which |
1519 | + | //point to a string at master node, and slave nodes do not contain that string |
1520 | + | |
1521 | + | string zconsOutput(info->finalName); |
1522 | + | |
1523 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1524 | + | |
1525 | + | StringData* zconsFilename = new StringData(); |
1526 | + | zconsFilename->setID("zconsfilename"); |
1527 | + | zconsFilename->setData(zconsOutput); |
1528 | + | |
1529 | + | info->addProperty(zconsFilename); |
1530 | + | |
1531 | + | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1532 | + | |
1533 | + | break; |
1534 | + | } |
1535 | + | |
1536 | + | default: |
1537 | + | sprintf( painCave.errMsg, |
1538 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1539 | + | painCave.isFatal = 1; |
1540 | + | simError(); |
1541 | + | } |
1542 | + | |
1543 | + | } |
1544 | + | |
1545 | + | void SimSetup::initFortran( void ){ |
1546 | + | |
1547 | + | info->refreshSim(); |
1548 | + | |
1549 | + | if( !strcmp( info->mixingRule, "standard") ){ |
1550 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1551 | + | } |
1552 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1553 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1554 | + | } |
1555 | + | else{ |
1556 | + | sprintf( painCave.errMsg, |
1557 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1558 | + | info->mixingRule ); |
1559 | + | painCave.isFatal = 1; |
1560 | + | simError(); |
1561 | + | } |
1562 | + | |
1563 | + | |
1564 | + | #ifdef IS_MPI |
1565 | + | strcpy( checkPointMsg, |
1566 | + | "Successfully intialized the mixingRule for Fortran." ); |
1567 | + | MPIcheckPoint(); |
1568 | + | #endif // is_mpi |
1569 | + | |
1570 | + | } |
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