# | 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 14 | Line 16 | |
16 | ||
17 | // some defines for ensemble and Forcefield cases | |
18 | ||
19 | < | #define NVE_ENS 0 |
20 | < | #define NVT_ENS 1 |
21 | < | #define NPTi_ENS 2 |
22 | < | #define NPTf_ENS 3 |
23 | < | #define NPTim_ENS 4 |
24 | < | #define NPTfm_ENS 5 |
19 | > | #define NVE_ENS 0 |
20 | > | #define NVT_ENS 1 |
21 | > | #define NPTi_ENS 2 |
22 | > | #define NPTf_ENS 3 |
23 | > | #define NPTim_ENS 4 |
24 | > | #define NPTfm_ENS 5 |
25 | > | #define NVEZCONS_ENS 6 |
26 | > | #define NVTZCONS_ENS 7 |
27 | > | #define NPTiZCONS_ENS 8 |
28 | > | #define NPTfZCONS_ENS 9 |
29 | > | #define NPTimZCONS_ENS 10 |
30 | > | #define NPTfmZCONS_ENS 11 |
31 | ||
24 | – | |
32 | #define FF_DUFF 0 | |
33 | #define FF_LJ 1 | |
34 | + | #define FF_EAM 2 |
35 | ||
36 | + | using namespace std; |
37 | ||
38 | SimSetup::SimSetup(){ | |
39 | + | |
40 | + | isInfoArray = 0; |
41 | + | nInfo = 1; |
42 | + | |
43 | stamps = new MakeStamps(); | |
44 | globals = new Globals(); | |
45 | ||
46 | + | |
47 | #ifdef IS_MPI | |
48 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
49 | MPIcheckPoint(); | |
# | Line 41 | Line 55 | SimSetup::~SimSetup(){ | |
55 | delete globals; | |
56 | } | |
57 | ||
58 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
59 | + | info = the_info; |
60 | + | nInfo = theNinfo; |
61 | + | isInfoArray = 1; |
62 | + | } |
63 | + | |
64 | + | |
65 | void SimSetup::parseFile( char* fileName ){ | |
66 | ||
67 | #ifdef IS_MPI | |
# | Line 78 | Line 99 | void SimSetup::createSim( void ){ | |
99 | ||
100 | void SimSetup::createSim( void ){ | |
101 | ||
81 | – | MakeStamps *the_stamps; |
82 | – | Globals* the_globals; |
102 | int i, j, k, globalAtomIndex; | |
103 | ||
104 | // gather all of the information from the Bass file | |
# | Line 90 | Line 109 | void SimSetup::createSim( void ){ | |
109 | ||
110 | sysObjectsCreation(); | |
111 | ||
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 | – | |
112 | // check on the post processing info | |
113 | ||
114 | finalInfoCheck(); | |
115 | ||
110 | – | |
111 | – | |
112 | – | |
116 | // initialize the system coordinates | |
117 | ||
118 | initSystemCoords(); | |
# | Line 119 | Line 122 | void SimSetup::createSim( void ){ | |
122 | ||
123 | makeOutNames(); | |
124 | ||
122 | – | |
123 | – | |
124 | – | |
125 | – | |
126 | – | |
127 | – | |
128 | – | |
129 | – | |
125 | // make the integrator | |
126 | ||
127 | + | makeIntegrator(); |
128 | ||
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 | – | |
129 | #ifdef IS_MPI | |
130 | mpiSim->mpiRefresh(); | |
131 | #endif | |
132 | ||
133 | // initialize the Fortran | |
134 | ||
135 | + | initFortran(); |
136 | ||
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 | – | } |
137 | ||
138 | ||
333 | – | #ifdef IS_MPI |
334 | – | strcpy( checkPointMsg, |
335 | – | "Successfully intialized the mixingRule for Fortran." ); |
336 | – | MPIcheckPoint(); |
337 | – | #endif // is_mpi |
139 | } | |
140 | ||
141 | ||
142 | void SimSetup::makeMolecules( void ){ | |
143 | ||
144 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
145 | < | molInit info; |
145 | > | molInit molInfo; |
146 | DirectionalAtom* dAtom; | |
147 | LinkedAssign* extras; | |
148 | LinkedAssign* current_extra; | |
# | Line 370 | Line 171 | void SimSetup::makeMolecules( void ){ | |
171 | ||
172 | stampID = the_molecules[i].getStampID(); | |
173 | ||
174 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
176 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
177 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
174 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
176 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
177 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
179 | ||
180 | < | info.myAtoms = &the_atoms[atomOffset]; |
181 | < | info.myExcludes = &the_excludes[excludeOffset]; |
182 | < | info.myBonds = new Bond*[info.nBonds]; |
183 | < | info.myBends = new Bend*[info.nBends]; |
184 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
180 | > | molInfo.myAtoms = &the_atoms[atomOffset]; |
181 | > | molInfo.myExcludes = &the_excludes[excludeOffset]; |
182 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
183 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
184 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
185 | ||
186 | < | theBonds = new bond_pair[info.nBonds]; |
187 | < | theBends = new bend_set[info.nBends]; |
188 | < | theTorsions = new torsion_set[info.nTorsions]; |
186 | > | theBonds = new bond_pair[molInfo.nBonds]; |
187 | > | theBends = new bend_set[molInfo.nBends]; |
188 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
189 | ||
190 | // make the Atoms | |
191 | ||
192 | < | for(j=0; j<info.nAtoms; j++){ |
192 | > | for(j=0; j<molInfo.nAtoms; j++){ |
193 | ||
194 | currentAtom = comp_stamps[stampID]->getAtom( j ); | |
195 | if( currentAtom->haveOrientation() ){ | |
196 | ||
197 | dAtom = new DirectionalAtom(j + atomOffset); | |
198 | info->n_oriented++; | |
199 | < | info.myAtoms[j] = dAtom; |
199 | > | molInfo.myAtoms[j] = dAtom; |
200 | ||
201 | ux = currentAtom->getOrntX(); | |
202 | uy = currentAtom->getOrntY(); | |
# | Line 413 | Line 214 | void SimSetup::makeMolecules( void ){ | |
214 | dAtom->setSUz( uz ); | |
215 | } | |
216 | else{ | |
217 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
217 | > | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
218 | } | |
219 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
219 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
220 | ||
221 | #ifdef IS_MPI | |
222 | ||
223 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
223 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 | ||
225 | #endif // is_mpi | |
226 | } | |
227 | ||
228 | // make the bonds | |
229 | < | for(j=0; j<info.nBonds; j++){ |
229 | > | for(j=0; j<molInfo.nBonds; j++){ |
230 | ||
231 | currentBond = comp_stamps[stampID]->getBond( j ); | |
232 | theBonds[j].a = currentBond->getA() + atomOffset; | |
# | Line 452 | Line 253 | void SimSetup::makeMolecules( void ){ | |
253 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
254 | #endif //is_mpi | |
255 | } | |
256 | < | excludeOffset += info.nBonds; |
256 | > | excludeOffset += molInfo.nBonds; |
257 | ||
258 | //make the bends | |
259 | < | for(j=0; j<info.nBends; j++){ |
259 | > | for(j=0; j<molInfo.nBends; j++){ |
260 | ||
261 | currentBend = comp_stamps[stampID]->getBend( j ); | |
262 | theBends[j].a = currentBend->getA() + atomOffset; | |
# | Line 538 | Line 339 | void SimSetup::makeMolecules( void ){ | |
339 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
340 | #endif //is_mpi | |
341 | } | |
342 | < | excludeOffset += info.nBends; |
342 | > | excludeOffset += molInfo.nBends; |
343 | ||
344 | < | for(j=0; j<info.nTorsions; j++){ |
344 | > | for(j=0; j<molInfo.nTorsions; j++){ |
345 | ||
346 | currentTorsion = comp_stamps[stampID]->getTorsion( j ); | |
347 | theTorsions[j].a = currentTorsion->getA() + atomOffset; | |
# | Line 568 | Line 369 | void SimSetup::makeMolecules( void ){ | |
369 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
370 | #endif //is_mpi | |
371 | } | |
372 | < | excludeOffset += info.nTorsions; |
372 | > | excludeOffset += molInfo.nTorsions; |
373 | ||
374 | ||
375 | // send the arrays off to the forceField for init. | |
376 | ||
377 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
378 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
379 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
380 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
377 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
378 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
379 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
380 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
381 | ||
382 | ||
383 | < | the_molecules[i].initialize( info ); |
383 | > | the_molecules[i].initialize( molInfo ); |
384 | ||
385 | ||
386 | < | atomOffset += info.nAtoms; |
386 | > | atomOffset += molInfo.nAtoms; |
387 | delete[] theBonds; | |
388 | delete[] theBends; | |
389 | delete[] theTorsions; | |
# | Line 618 | Line 419 | void SimSetup::initFromBass( void ){ | |
419 | have_extra =1; | |
420 | ||
421 | n_cells = (int)temp3 - 1; | |
422 | < | cellx = info->boxLx / temp3; |
423 | < | celly = info->boxLy / temp3; |
424 | < | cellz = info->boxLz / temp3; |
422 | > | cellx = info->boxL[0] / temp3; |
423 | > | celly = info->boxL[1] / temp3; |
424 | > | cellz = info->boxL[2] / temp3; |
425 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
426 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
427 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 635 | Line 436 | void SimSetup::initFromBass( void ){ | |
436 | } | |
437 | else{ | |
438 | n_cells = (int)temp3; | |
439 | < | cellx = info->boxLx / temp3; |
440 | < | celly = info->boxLy / temp3; |
441 | < | cellz = info->boxLz / temp3; |
439 | > | cellx = info->boxL[0] / temp3; |
440 | > | celly = info->boxL[1] / temp3; |
441 | > | cellz = info->boxL[2] / temp3; |
442 | } | |
443 | ||
444 | current_mol = 0; | |
# | Line 784 | Line 585 | void SimSetup::gatherInfo( void ){ | |
585 | ||
586 | ||
587 | void SimSetup::gatherInfo( void ){ | |
588 | + | int i,j,k; |
589 | ||
590 | ensembleCase = -1; | |
591 | ffCase = -1; | |
592 | ||
593 | // get the stamps and globals; | |
594 | < | the_stamps = stamps; |
595 | < | the_globals = globals; |
594 | > | stamps = stamps; |
595 | > | globals = globals; |
596 | ||
597 | // set the easy ones first | |
598 | < | info->target_temp = the_globals->getTargetTemp(); |
599 | < | info->dt = the_globals->getDt(); |
600 | < | info->run_time = the_globals->getRunTime(); |
601 | < | n_components = the_globals->getNComponents(); |
598 | > | info->target_temp = globals->getTargetTemp(); |
599 | > | info->dt = globals->getDt(); |
600 | > | info->run_time = globals->getRunTime(); |
601 | > | n_components = globals->getNComponents(); |
602 | ||
603 | ||
604 | // get the forceField | |
605 | ||
606 | < | strcpy( force_field, the_globals->getForceField() ); |
606 | > | strcpy( force_field, globals->getForceField() ); |
607 | ||
608 | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; | |
609 | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; | |
610 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
611 | else{ | |
612 | sprintf( painCave.errMsg, | |
613 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 815 | Line 618 | void SimSetup::gatherInfo( void ){ | |
618 | ||
619 | // get the ensemble | |
620 | ||
621 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
621 | > | strcpy( ensemble, globals->getEnsemble() ); |
622 | ||
623 | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; | |
624 | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; | |
# | Line 824 | Line 627 | void SimSetup::gatherInfo( void ){ | |
627 | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; | |
628 | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; | |
629 | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; | |
630 | + | |
631 | + | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
632 | + | else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
633 | + | else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS")) |
634 | + | ensembleCase = NPTiZCONS_ENS; |
635 | + | else if( !strcasecmp( ensemble, "NPTfZCONS")) ensembleCase = NPTfZCONS_ENS; |
636 | + | else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
637 | + | else if( !strcasecmp( ensemble, "NPTfmZCONS")) ensembleCase = NPTfmZCONS_ENS; |
638 | + | |
639 | else{ | |
640 | sprintf( painCave.errMsg, | |
641 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 838 | Line 650 | void SimSetup::gatherInfo( void ){ | |
650 | ||
651 | // get the mixing rule | |
652 | ||
653 | < | strcpy( info->mixingRule, the_globals->getMixingRule() ); |
654 | < | info->usePBC = the_globals->getPBC(); |
653 | > | strcpy( info->mixingRule, globals->getMixingRule() ); |
654 | > | info->usePBC = globals->getPBC(); |
655 | ||
656 | ||
657 | // get the components and calculate the tot_nMol and indvidual n_mol | |
658 | ||
659 | < | the_components = the_globals->getComponents(); |
659 | > | the_components = globals->getComponents(); |
660 | components_nmol = new int[n_components]; | |
661 | ||
662 | ||
663 | < | if( !the_globals->haveNMol() ){ |
663 | > | if( !globals->haveNMol() ){ |
664 | // we don't have the total number of molecules, so we assume it is | |
665 | // given in each component | |
666 | ||
# | Line 881 | Line 693 | void SimSetup::gatherInfo( void ){ | |
693 | ||
694 | // set the status, sample, and thermal kick times | |
695 | ||
696 | < | if( the_globals->haveSampleTime() ){ |
697 | < | info->sampleTime = the_globals->getSampleTime(); |
696 | > | if( globals->haveSampleTime() ){ |
697 | > | info->sampleTime = globals->getSampleTime(); |
698 | info->statusTime = info->sampleTime; | |
699 | info->thermalTime = info->sampleTime; | |
700 | } | |
701 | else{ | |
702 | < | info->sampleTime = the_globals->getRunTime(); |
702 | > | info->sampleTime = globals->getRunTime(); |
703 | info->statusTime = info->sampleTime; | |
704 | info->thermalTime = info->sampleTime; | |
705 | } | |
706 | ||
707 | < | if( the_globals->haveStatusTime() ){ |
708 | < | info->statusTime = the_globals->getStatusTime(); |
707 | > | if( globals->haveStatusTime() ){ |
708 | > | info->statusTime = globals->getStatusTime(); |
709 | } | |
710 | ||
711 | < | if( the_globals->haveThermalTime() ){ |
712 | < | info->thermalTime = the_globals->getThermalTime(); |
711 | > | if( globals->haveThermalTime() ){ |
712 | > | info->thermalTime = globals->getThermalTime(); |
713 | } | |
714 | ||
715 | // check for the temperature set flag | |
716 | ||
717 | < | if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
717 | > | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
718 | ||
719 | // get some of the tricky things that may still be in the globals | |
720 | ||
721 | double boxVector[3]; | |
722 | < | if( the_globals->haveBox() ){ |
723 | < | boxVector[0] = the_globals->getBox(); |
724 | < | boxVector[1] = the_globals->getBox(); |
725 | < | boxVector[2] = the_globals->getBox(); |
722 | > | if( globals->haveBox() ){ |
723 | > | boxVector[0] = globals->getBox(); |
724 | > | boxVector[1] = globals->getBox(); |
725 | > | boxVector[2] = globals->getBox(); |
726 | ||
727 | info->setBox( boxVector ); | |
728 | } | |
729 | < | else if( the_globals->haveDensity() ){ |
729 | > | else if( globals->haveDensity() ){ |
730 | ||
731 | double vol; | |
732 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
732 | > | vol = (double)tot_nmol / globals->getDensity(); |
733 | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); | |
734 | boxVector[1] = boxVector[0]; | |
735 | boxVector[2] = boxVector[0]; | |
# | Line 925 | Line 737 | void SimSetup::gatherInfo( void ){ | |
737 | info->setBox( boxVector ); | |
738 | } | |
739 | else{ | |
740 | < | if( !the_globals->haveBoxX() ){ |
740 | > | if( !globals->haveBoxX() ){ |
741 | sprintf( painCave.errMsg, | |
742 | "SimSetup error, no periodic BoxX size given.\n" ); | |
743 | painCave.isFatal = 1; | |
744 | simError(); | |
745 | } | |
746 | < | boxVector[0] = the_globals->getBoxX(); |
746 | > | boxVector[0] = globals->getBoxX(); |
747 | ||
748 | < | if( !the_globals->haveBoxY() ){ |
748 | > | if( !globals->haveBoxY() ){ |
749 | sprintf( painCave.errMsg, | |
750 | "SimSetup error, no periodic BoxY size given.\n" ); | |
751 | painCave.isFatal = 1; | |
752 | simError(); | |
753 | } | |
754 | < | boxVector[1] = the_globals->getBoxY(); |
754 | > | boxVector[1] = globals->getBoxY(); |
755 | ||
756 | < | if( !the_globals->haveBoxZ() ){ |
756 | > | if( !globals->haveBoxZ() ){ |
757 | sprintf( painCave.errMsg, | |
758 | "SimSetup error, no periodic BoxZ size given.\n" ); | |
759 | painCave.isFatal = 1; | |
760 | simError(); | |
761 | } | |
762 | < | boxVector[2] = the_globals->getBoxZ(); |
762 | > | boxVector[2] = globals->getBoxZ(); |
763 | ||
764 | info->setBox( boxVector ); | |
765 | } | |
# | Line 977 | Line 789 | void SimSetup::finalInfoCheck( void ){ | |
789 | } | |
790 | ||
791 | #ifdef IS_MPI | |
792 | < | int myUse = usesDipoles |
793 | < | MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
792 | > | int myUse = usesDipoles; |
793 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
794 | #endif //is_mpi | |
795 | ||
796 | + | double theEcr, theEst; |
797 | ||
798 | < | if (the_globals->getUseRF() ) { |
798 | > | if (globals->getUseRF() ) { |
799 | info->useReactionField = 1; | |
800 | ||
801 | < | if( !the_globals->haveECR() ){ |
801 | > | if( !globals->haveECR() ){ |
802 | sprintf( painCave.errMsg, | |
803 | "SimSetup Warning: using default value of 1/2 the smallest " | |
804 | "box length for the electrostaticCutoffRadius.\n" | |
# | Line 993 | Line 806 | void SimSetup::finalInfoCheck( void ){ | |
806 | painCave.isFatal = 0; | |
807 | simError(); | |
808 | double smallest; | |
809 | < | smallest = info->boxLx; |
810 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
811 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
812 | < | info->ecr = 0.5 * smallest; |
809 | > | smallest = info->boxL[0]; |
810 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
811 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
812 | > | theEcr = 0.5 * smallest; |
813 | } else { | |
814 | < | info->ecr = the_globals->getECR(); |
814 | > | theEcr = globals->getECR(); |
815 | } | |
816 | ||
817 | < | if( !the_globals->haveEST() ){ |
817 | > | if( !globals->haveEST() ){ |
818 | sprintf( painCave.errMsg, | |
819 | "SimSetup Warning: using default value of 0.05 * the " | |
820 | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" | |
821 | ); | |
822 | painCave.isFatal = 0; | |
823 | simError(); | |
824 | < | info->est = 0.05 * info->ecr; |
824 | > | theEst = 0.05 * theEcr; |
825 | } else { | |
826 | < | info->est = the_globals->getEST(); |
826 | > | theEst= globals->getEST(); |
827 | } | |
828 | + | |
829 | + | info->setEcr( theEcr, theEst ); |
830 | ||
831 | < | if(!the_globals->haveDielectric() ){ |
831 | > | if(!globals->haveDielectric() ){ |
832 | sprintf( painCave.errMsg, | |
833 | "SimSetup Error: You are trying to use Reaction Field without" | |
834 | "setting a dielectric constant!\n" | |
# | Line 1021 | Line 836 | void SimSetup::finalInfoCheck( void ){ | |
836 | painCave.isFatal = 1; | |
837 | simError(); | |
838 | } | |
839 | < | info->dielectric = the_globals->getDielectric(); |
839 | > | info->dielectric = globals->getDielectric(); |
840 | } | |
841 | else { | |
842 | if (usesDipoles) { | |
843 | ||
844 | < | if( !the_globals->haveECR() ){ |
845 | < | sprintf( painCave.errMsg, |
846 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
847 | < | "box length for the electrostaticCutoffRadius.\n" |
848 | < | "I hope you have a very fast processor!\n"); |
849 | < | painCave.isFatal = 0; |
850 | < | simError(); |
851 | < | double smallest; |
852 | < | smallest = info->boxLx; |
853 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
854 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
855 | < | info->ecr = 0.5 * smallest; |
844 | > | if( !globals->haveECR() ){ |
845 | > | sprintf( painCave.errMsg, |
846 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
847 | > | "box length for the electrostaticCutoffRadius.\n" |
848 | > | "I hope you have a very fast processor!\n"); |
849 | > | painCave.isFatal = 0; |
850 | > | simError(); |
851 | > | double smallest; |
852 | > | smallest = info->boxL[0]; |
853 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
854 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
855 | > | theEcr = 0.5 * smallest; |
856 | } else { | |
857 | < | info->ecr = the_globals->getECR(); |
857 | > | theEcr = globals->getECR(); |
858 | } | |
859 | ||
860 | < | if( !the_globals->haveEST() ){ |
861 | < | sprintf( painCave.errMsg, |
862 | < | "SimSetup Warning: using default value of 5%% of the " |
863 | < | "electrostaticCutoffRadius for the " |
864 | < | "electrostaticSkinThickness\n" |
865 | < | ); |
866 | < | painCave.isFatal = 0; |
867 | < | simError(); |
868 | < | info->est = 0.05 * info->ecr; |
860 | > | if( !globals->haveEST() ){ |
861 | > | sprintf( painCave.errMsg, |
862 | > | "SimSetup Warning: using default value of 0.05 * the " |
863 | > | "electrostaticCutoffRadius for the " |
864 | > | "electrostaticSkinThickness\n" |
865 | > | ); |
866 | > | painCave.isFatal = 0; |
867 | > | simError(); |
868 | > | theEst = 0.05 * theEcr; |
869 | } else { | |
870 | < | info->est = the_globals->getEST(); |
870 | > | theEst= globals->getEST(); |
871 | } | |
872 | + | |
873 | + | info->setEcr( theEcr, theEst ); |
874 | } | |
875 | } | |
876 | ||
# | Line 1066 | Line 883 | void SimSetup::initSystemCoords( void ){ | |
883 | ||
884 | void SimSetup::initSystemCoords( void ){ | |
885 | ||
886 | < | if( the_globals->haveInitialConfig() ){ |
886 | > | if( globals->haveInitialConfig() ){ |
887 | ||
888 | InitializeFromFile* fileInit; | |
889 | #ifdef IS_MPI // is_mpi | |
890 | if( worldRank == 0 ){ | |
891 | #endif //is_mpi | |
892 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
892 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
893 | #ifdef IS_MPI | |
894 | }else fileInit = new InitializeFromFile( NULL ); | |
895 | #endif | |
896 | < | fileInit->read_xyz( info ); // default velocities on |
896 | > | fileInit->readInit( info ); // default velocities on |
897 | ||
898 | delete fileInit; | |
899 | } | |
# | Line 1113 | Line 930 | void SimSetup::makeOutNames( void ){ | |
930 | if( worldRank == 0 ){ | |
931 | #endif // is_mpi | |
932 | ||
933 | < | if( the_globals->haveFinalConfig() ){ |
934 | < | strcpy( info->finalName, the_globals->getFinalConfig() ); |
933 | > | if( globals->haveFinalConfig() ){ |
934 | > | strcpy( info->finalName, globals->getFinalConfig() ); |
935 | } | |
936 | else{ | |
937 | strcpy( info->finalName, inFileName ); | |
# | Line 1197 | Line 1014 | void SimSetup::sysObjectsCreation( void ){ | |
1014 | ||
1015 | void SimSetup::sysObjectsCreation( void ){ | |
1016 | ||
1017 | + | int i; |
1018 | + | |
1019 | // create the forceField | |
1020 | ||
1021 | createFF(); | |
# | Line 1219 | Line 1038 | void SimSetup::sysObjectsCreation( void ){ | |
1038 | ||
1039 | makeSysArrays(); | |
1040 | ||
1041 | + | // make and initialize the molecules (all but atomic coordinates) |
1042 | + | |
1043 | + | makeMolecules(); |
1044 | + | info->identArray = new int[info->n_atoms]; |
1045 | + | for(i=0; i<info->n_atoms; i++){ |
1046 | + | info->identArray[i] = the_atoms[i]->getIdent(); |
1047 | + | } |
1048 | ||
1049 | ||
1050 | ||
# | Line 1237 | Line 1063 | void SimSetup::createFF( void ){ | |
1063 | the_ff = new LJFF(); | |
1064 | break; | |
1065 | ||
1066 | + | case FF_EAM: |
1067 | + | the_ff = new EAM_FF(); |
1068 | + | break; |
1069 | + | |
1070 | default: | |
1071 | sprintf( painCave.errMsg, | |
1072 | "SimSetup Error. Unrecognized force field in case statement.\n"); | |
# | Line 1254 | Line 1084 | void SimSetup::compList( void ){ | |
1084 | ||
1085 | void SimSetup::compList( void ){ | |
1086 | ||
1087 | + | int i; |
1088 | + | |
1089 | comp_stamps = new MoleculeStamp*[n_components]; | |
1090 | ||
1091 | // make an array of molecule stamps that match the components used. | |
# | Line 1279 | Line 1111 | void SimSetup::compList( void ){ | |
1111 | ||
1112 | // extract the component from the list; | |
1113 | ||
1114 | < | currentStamp = the_stamps->extractMolStamp( id ); |
1114 | > | currentStamp = stamps->extractMolStamp( id ); |
1115 | if( currentStamp == NULL ){ | |
1116 | sprintf( painCave.errMsg, | |
1117 | "SimSetup error: Component \"%s\" was not found in the " | |
# | Line 1303 | Line 1135 | void SimSetup::calcSysValues( void ){ | |
1135 | } | |
1136 | ||
1137 | void SimSetup::calcSysValues( void ){ | |
1138 | + | int i, j, k; |
1139 | ||
1140 | + | |
1141 | tot_atoms = 0; | |
1142 | tot_bonds = 0; | |
1143 | tot_bends = 0; | |
# | Line 1333 | Line 1167 | void SimSetup::mpiMolDivide( void ){ | |
1167 | ||
1168 | void SimSetup::mpiMolDivide( void ){ | |
1169 | ||
1170 | + | int i, j, k; |
1171 | int localMol, allMol; | |
1172 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1173 | ||
# | Line 1402 | Line 1237 | void SimSetup::makeSysArrays( void ){ | |
1237 | ||
1238 | ||
1239 | void SimSetup::makeSysArrays( void ){ | |
1240 | + | int i, j, k; |
1241 | + | |
1242 | ||
1243 | // create the atom and short range interaction arrays | |
1244 | ||
# | Line 1476 | Line 1313 | void SimSetup::makeSysArrays( void ){ | |
1313 | the_ff->setSimInfo( info ); | |
1314 | ||
1315 | } | |
1316 | + | |
1317 | + | void SimSetup::makeIntegrator( void ){ |
1318 | + | |
1319 | + | NVT<RealIntegrator>* myNVT = NULL; |
1320 | + | NPTi<RealIntegrator>* myNPTi = NULL; |
1321 | + | NPTf<RealIntegrator>* myNPTf = NULL; |
1322 | + | NPTim<RealIntegrator>* myNPTim = NULL; |
1323 | + | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1324 | + | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1325 | + | ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1326 | + | ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1327 | + | ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1328 | + | ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1329 | + | ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1330 | + | |
1331 | + | switch( ensembleCase ){ |
1332 | + | |
1333 | + | case NVE_ENS: |
1334 | + | new NVE<RealIntegrator>( info, the_ff ); |
1335 | + | break; |
1336 | + | |
1337 | + | case NVT_ENS: |
1338 | + | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1339 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1340 | + | |
1341 | + | if (globals->haveTauThermostat()) |
1342 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1343 | + | |
1344 | + | else { |
1345 | + | sprintf( painCave.errMsg, |
1346 | + | "SimSetup error: If you use the NVT\n" |
1347 | + | " ensemble, you must set tauThermostat.\n"); |
1348 | + | painCave.isFatal = 1; |
1349 | + | simError(); |
1350 | + | } |
1351 | + | break; |
1352 | + | |
1353 | + | case NPTi_ENS: |
1354 | + | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1355 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1356 | + | |
1357 | + | if (globals->haveTargetPressure()) |
1358 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1359 | + | else { |
1360 | + | sprintf( painCave.errMsg, |
1361 | + | "SimSetup error: If you use a constant pressure\n" |
1362 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1363 | + | painCave.isFatal = 1; |
1364 | + | simError(); |
1365 | + | } |
1366 | + | |
1367 | + | if( globals->haveTauThermostat() ) |
1368 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1369 | + | else{ |
1370 | + | sprintf( painCave.errMsg, |
1371 | + | "SimSetup error: If you use an NPT\n" |
1372 | + | " ensemble, you must set tauThermostat.\n"); |
1373 | + | painCave.isFatal = 1; |
1374 | + | simError(); |
1375 | + | } |
1376 | + | |
1377 | + | if( globals->haveTauBarostat() ) |
1378 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1379 | + | else{ |
1380 | + | sprintf( painCave.errMsg, |
1381 | + | "SimSetup error: If you use an NPT\n" |
1382 | + | " ensemble, you must set tauBarostat.\n"); |
1383 | + | painCave.isFatal = 1; |
1384 | + | simError(); |
1385 | + | } |
1386 | + | break; |
1387 | + | |
1388 | + | case NPTf_ENS: |
1389 | + | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1390 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1391 | + | |
1392 | + | if (globals->haveTargetPressure()) |
1393 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1394 | + | else { |
1395 | + | sprintf( painCave.errMsg, |
1396 | + | "SimSetup error: If you use a constant pressure\n" |
1397 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1398 | + | painCave.isFatal = 1; |
1399 | + | simError(); |
1400 | + | } |
1401 | + | |
1402 | + | if( globals->haveTauThermostat() ) |
1403 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1404 | + | else{ |
1405 | + | sprintf( painCave.errMsg, |
1406 | + | "SimSetup error: If you use an NPT\n" |
1407 | + | " ensemble, you must set tauThermostat.\n"); |
1408 | + | painCave.isFatal = 1; |
1409 | + | simError(); |
1410 | + | } |
1411 | + | |
1412 | + | if( globals->haveTauBarostat() ) |
1413 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1414 | + | else{ |
1415 | + | sprintf( painCave.errMsg, |
1416 | + | "SimSetup error: If you use an NPT\n" |
1417 | + | " ensemble, you must set tauBarostat.\n"); |
1418 | + | painCave.isFatal = 1; |
1419 | + | simError(); |
1420 | + | } |
1421 | + | break; |
1422 | + | |
1423 | + | case NPTim_ENS: |
1424 | + | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1425 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1426 | + | |
1427 | + | if (globals->haveTargetPressure()) |
1428 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1429 | + | else { |
1430 | + | sprintf( painCave.errMsg, |
1431 | + | "SimSetup error: If you use a constant pressure\n" |
1432 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1433 | + | painCave.isFatal = 1; |
1434 | + | simError(); |
1435 | + | } |
1436 | + | |
1437 | + | if( globals->haveTauThermostat() ) |
1438 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1439 | + | else{ |
1440 | + | sprintf( painCave.errMsg, |
1441 | + | "SimSetup error: If you use an NPT\n" |
1442 | + | " ensemble, you must set tauThermostat.\n"); |
1443 | + | painCave.isFatal = 1; |
1444 | + | simError(); |
1445 | + | } |
1446 | + | |
1447 | + | if( globals->haveTauBarostat() ) |
1448 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1449 | + | else{ |
1450 | + | sprintf( painCave.errMsg, |
1451 | + | "SimSetup error: If you use an NPT\n" |
1452 | + | " ensemble, you must set tauBarostat.\n"); |
1453 | + | painCave.isFatal = 1; |
1454 | + | simError(); |
1455 | + | } |
1456 | + | break; |
1457 | + | |
1458 | + | case NPTfm_ENS: |
1459 | + | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1460 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1461 | + | |
1462 | + | if (globals->haveTargetPressure()) |
1463 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1464 | + | else { |
1465 | + | sprintf( painCave.errMsg, |
1466 | + | "SimSetup error: If you use a constant pressure\n" |
1467 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1468 | + | painCave.isFatal = 1; |
1469 | + | simError(); |
1470 | + | } |
1471 | + | |
1472 | + | if( globals->haveTauThermostat() ) |
1473 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1474 | + | else{ |
1475 | + | sprintf( painCave.errMsg, |
1476 | + | "SimSetup error: If you use an NPT\n" |
1477 | + | " ensemble, you must set tauThermostat.\n"); |
1478 | + | painCave.isFatal = 1; |
1479 | + | simError(); |
1480 | + | } |
1481 | + | |
1482 | + | if( globals->haveTauBarostat() ) |
1483 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1484 | + | else{ |
1485 | + | sprintf( painCave.errMsg, |
1486 | + | "SimSetup error: If you use an NPT\n" |
1487 | + | " ensemble, you must set tauBarostat.\n"); |
1488 | + | painCave.isFatal = 1; |
1489 | + | simError(); |
1490 | + | } |
1491 | + | break; |
1492 | + | |
1493 | + | case NVEZCONS_ENS: |
1494 | + | |
1495 | + | |
1496 | + | //setup index of z-constraint molecules, z-constraint sampel time |
1497 | + | //and z-constraint force output name. These parameter should be known |
1498 | + | //before constructing the z-constraint integrator |
1499 | + | setupZConstraint(); |
1500 | + | |
1501 | + | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1502 | + | |
1503 | + | break; |
1504 | + | |
1505 | + | |
1506 | + | case NVTZCONS_ENS: |
1507 | + | |
1508 | + | setupZConstraint(); |
1509 | + | |
1510 | + | myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff ); |
1511 | + | myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1512 | + | |
1513 | + | if (globals->haveTauThermostat()) |
1514 | + | myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1515 | + | |
1516 | + | else { |
1517 | + | sprintf( painCave.errMsg, |
1518 | + | "SimSetup error: If you use the NVT\n" |
1519 | + | " ensemble, you must set tauThermostat.\n"); |
1520 | + | painCave.isFatal = 1; |
1521 | + | simError(); |
1522 | + | } |
1523 | + | break; |
1524 | + | |
1525 | + | case NPTiZCONS_ENS: |
1526 | + | |
1527 | + | setupZConstraint(); |
1528 | + | |
1529 | + | myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff ); |
1530 | + | myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1531 | + | |
1532 | + | if (globals->haveTargetPressure()) |
1533 | + | myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1534 | + | else { |
1535 | + | sprintf( painCave.errMsg, |
1536 | + | "SimSetup error: If you use a constant pressure\n" |
1537 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1538 | + | painCave.isFatal = 1; |
1539 | + | simError(); |
1540 | + | } |
1541 | + | |
1542 | + | if( globals->haveTauThermostat() ) |
1543 | + | myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1544 | + | else{ |
1545 | + | sprintf( painCave.errMsg, |
1546 | + | "SimSetup error: If you use an NPT\n" |
1547 | + | " ensemble, you must set tauThermostat.\n"); |
1548 | + | painCave.isFatal = 1; |
1549 | + | simError(); |
1550 | + | } |
1551 | + | |
1552 | + | if( globals->haveTauBarostat() ) |
1553 | + | myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1554 | + | else{ |
1555 | + | sprintf( painCave.errMsg, |
1556 | + | "SimSetup error: If you use an NPT\n" |
1557 | + | " ensemble, you must set tauBarostat.\n"); |
1558 | + | painCave.isFatal = 1; |
1559 | + | simError(); |
1560 | + | } |
1561 | + | |
1562 | + | break; |
1563 | + | |
1564 | + | case NPTfZCONS_ENS: |
1565 | + | |
1566 | + | setupZConstraint(); |
1567 | + | |
1568 | + | myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff ); |
1569 | + | myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1570 | + | |
1571 | + | if (globals->haveTargetPressure()) |
1572 | + | myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1573 | + | else { |
1574 | + | sprintf( painCave.errMsg, |
1575 | + | "SimSetup error: If you use a constant pressure\n" |
1576 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1577 | + | painCave.isFatal = 1; |
1578 | + | simError(); |
1579 | + | } |
1580 | + | |
1581 | + | if( globals->haveTauThermostat() ) |
1582 | + | myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1583 | + | else{ |
1584 | + | sprintf( painCave.errMsg, |
1585 | + | "SimSetup error: If you use an NPT\n" |
1586 | + | " ensemble, you must set tauThermostat.\n"); |
1587 | + | painCave.isFatal = 1; |
1588 | + | simError(); |
1589 | + | } |
1590 | + | |
1591 | + | if( globals->haveTauBarostat() ) |
1592 | + | myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1593 | + | else{ |
1594 | + | sprintf( painCave.errMsg, |
1595 | + | "SimSetup error: If you use an NPT\n" |
1596 | + | " ensemble, you must set tauBarostat.\n"); |
1597 | + | painCave.isFatal = 1; |
1598 | + | simError(); |
1599 | + | } |
1600 | + | |
1601 | + | break; |
1602 | + | |
1603 | + | case NPTimZCONS_ENS: |
1604 | + | |
1605 | + | setupZConstraint(); |
1606 | + | |
1607 | + | myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff ); |
1608 | + | myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1609 | + | |
1610 | + | if (globals->haveTargetPressure()) |
1611 | + | myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1612 | + | else { |
1613 | + | sprintf( painCave.errMsg, |
1614 | + | "SimSetup error: If you use a constant pressure\n" |
1615 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1616 | + | painCave.isFatal = 1; |
1617 | + | simError(); |
1618 | + | } |
1619 | + | |
1620 | + | if( globals->haveTauThermostat() ) |
1621 | + | myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1622 | + | else{ |
1623 | + | sprintf( painCave.errMsg, |
1624 | + | "SimSetup error: If you use an NPT\n" |
1625 | + | " ensemble, you must set tauThermostat.\n"); |
1626 | + | painCave.isFatal = 1; |
1627 | + | simError(); |
1628 | + | } |
1629 | + | |
1630 | + | if( globals->haveTauBarostat() ) |
1631 | + | myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1632 | + | else{ |
1633 | + | sprintf( painCave.errMsg, |
1634 | + | "SimSetup error: If you use an NPT\n" |
1635 | + | " ensemble, you must set tauBarostat.\n"); |
1636 | + | painCave.isFatal = 1; |
1637 | + | simError(); |
1638 | + | } |
1639 | + | |
1640 | + | break; |
1641 | + | |
1642 | + | case NPTfmZCONS_ENS: |
1643 | + | |
1644 | + | setupZConstraint(); |
1645 | + | |
1646 | + | myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff ); |
1647 | + | myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1648 | + | |
1649 | + | if (globals->haveTargetPressure()) |
1650 | + | myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1651 | + | else { |
1652 | + | sprintf( painCave.errMsg, |
1653 | + | "SimSetup error: If you use a constant pressure\n" |
1654 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1655 | + | painCave.isFatal = 1; |
1656 | + | simError(); |
1657 | + | } |
1658 | + | |
1659 | + | if( globals->haveTauThermostat() ) |
1660 | + | myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1661 | + | else{ |
1662 | + | sprintf( painCave.errMsg, |
1663 | + | "SimSetup error: If you use an NPT\n" |
1664 | + | " ensemble, you must set tauThermostat.\n"); |
1665 | + | painCave.isFatal = 1; |
1666 | + | simError(); |
1667 | + | } |
1668 | + | |
1669 | + | if( globals->haveTauBarostat() ) |
1670 | + | myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1671 | + | else{ |
1672 | + | sprintf( painCave.errMsg, |
1673 | + | "SimSetup error: If you use an NPT\n" |
1674 | + | " ensemble, you must set tauBarostat.\n"); |
1675 | + | painCave.isFatal = 1; |
1676 | + | simError(); |
1677 | + | } |
1678 | + | break; |
1679 | + | |
1680 | + | |
1681 | + | |
1682 | + | default: |
1683 | + | sprintf( painCave.errMsg, |
1684 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1685 | + | painCave.isFatal = 1; |
1686 | + | simError(); |
1687 | + | } |
1688 | + | |
1689 | + | } |
1690 | + | |
1691 | + | void SimSetup::initFortran( void ){ |
1692 | + | |
1693 | + | info->refreshSim(); |
1694 | + | |
1695 | + | if( !strcmp( info->mixingRule, "standard") ){ |
1696 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1697 | + | } |
1698 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1699 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1700 | + | } |
1701 | + | else{ |
1702 | + | sprintf( painCave.errMsg, |
1703 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1704 | + | info->mixingRule ); |
1705 | + | painCave.isFatal = 1; |
1706 | + | simError(); |
1707 | + | } |
1708 | + | |
1709 | + | |
1710 | + | #ifdef IS_MPI |
1711 | + | strcpy( checkPointMsg, |
1712 | + | "Successfully intialized the mixingRule for Fortran." ); |
1713 | + | MPIcheckPoint(); |
1714 | + | #endif // is_mpi |
1715 | + | |
1716 | + | } |
1717 | + | |
1718 | + | void SimSetup::setupZConstraint() |
1719 | + | { |
1720 | + | if(globals->haveZConsTime()){ |
1721 | + | |
1722 | + | //add sample time of z-constraint into SimInfo's property list |
1723 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1724 | + | zconsTimeProp->setID("zconstime"); |
1725 | + | zconsTimeProp->setData(globals->getZConsTime()); |
1726 | + | info->addProperty(zconsTimeProp); |
1727 | + | } |
1728 | + | else{ |
1729 | + | sprintf( painCave.errMsg, |
1730 | + | "ZConstraint error: If you use an ZConstraint\n" |
1731 | + | " , you must set sample time.\n"); |
1732 | + | painCave.isFatal = 1; |
1733 | + | simError(); |
1734 | + | } |
1735 | + | |
1736 | + | if(globals->haveIndexOfAllZConsMols()){ |
1737 | + | |
1738 | + | //add index of z-constraint molecules into SimInfo's property list |
1739 | + | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1740 | + | |
1741 | + | //sort the index |
1742 | + | sort(tempIndex.begin(), tempIndex.end()); |
1743 | + | |
1744 | + | IndexData* zconsIndex = new IndexData(); |
1745 | + | zconsIndex->setID("zconsindex"); |
1746 | + | zconsIndex->setIndexData(tempIndex); |
1747 | + | info->addProperty(zconsIndex); |
1748 | + | } |
1749 | + | else{ |
1750 | + | sprintf( painCave.errMsg, |
1751 | + | "SimSetup error: If you use an ZConstraint\n" |
1752 | + | " , you must set index of z-constraint molecules.\n"); |
1753 | + | painCave.isFatal = 1; |
1754 | + | simError(); |
1755 | + | |
1756 | + | } |
1757 | + | |
1758 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1759 | + | //Be careful, do not use inFileName, since it is a pointer which |
1760 | + | //point to a string at master node, and slave nodes do not contain that string |
1761 | + | |
1762 | + | string zconsOutput(info->finalName); |
1763 | + | |
1764 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1765 | + | |
1766 | + | StringData* zconsFilename = new StringData(); |
1767 | + | zconsFilename->setID("zconsfilename"); |
1768 | + | zconsFilename->setData(zconsOutput); |
1769 | + | |
1770 | + | info->addProperty(zconsFilename); |
1771 | + | |
1772 | + | } |
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