# | 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 76 | Line 97 | void SimSetup::receiveParse(void){ | |
97 | ||
98 | #endif // is_mpi | |
99 | ||
100 | < | void SimSetup::createSim( void ){ |
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(); |
116 | < | |
118 | > | if( !isInfoArray ) initSystemCoords(); |
119 | ||
120 | // make the output filenames | |
121 | ||
122 | makeOutNames(); | |
123 | ||
122 | – | |
123 | – | |
124 | – | |
125 | – | |
126 | – | |
127 | – | |
128 | – | |
129 | – | |
124 | // make the integrator | |
125 | ||
126 | + | makeIntegrator(); |
127 | ||
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 | – | |
128 | #ifdef IS_MPI | |
129 | mpiSim->mpiRefresh(); | |
130 | #endif | |
131 | ||
132 | // initialize the Fortran | |
133 | ||
134 | + | initFortran(); |
135 | ||
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 | – | } |
136 | ||
137 | ||
333 | – | #ifdef IS_MPI |
334 | – | strcpy( checkPointMsg, |
335 | – | "Successfully intialized the mixingRule for Fortran." ); |
336 | – | MPIcheckPoint(); |
337 | – | #endif // is_mpi |
138 | } | |
139 | ||
140 | ||
141 | void SimSetup::makeMolecules( void ){ | |
142 | ||
143 | + | int k,l; |
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 364 | Line 165 | void SimSetup::makeMolecules( void ){ | |
165 | ||
166 | double ux, uy, uz, u, uSqr; | |
167 | ||
168 | < | atomOffset = 0; |
368 | < | excludeOffset = 0; |
369 | < | for(i=0; i<info->n_mol; i++){ |
168 | > | for(k=0; k<nInfo; k++){ |
169 | ||
170 | < | stampID = the_molecules[i].getStampID(); |
170 | > | the_ff->setSimInfo( &(info[k]) ); |
171 | ||
172 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
173 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
174 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
175 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
176 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
172 | > | atomOffset = 0; |
173 | > | excludeOffset = 0; |
174 | > | for(i=0; i<info[k].n_mol; i++){ |
175 | > | |
176 | > | stampID = info[k].molecules[i].getStampID(); |
177 | ||
178 | < | info.myAtoms = &the_atoms[atomOffset]; |
179 | < | info.myExcludes = &the_excludes[excludeOffset]; |
180 | < | info.myBonds = new Bond*[info.nBonds]; |
181 | < | info.myBends = new Bend*[info.nBends]; |
182 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
178 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
179 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
180 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
181 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
182 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
183 | > | |
184 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
185 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
186 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
187 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
188 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
189 | ||
190 | < | theBonds = new bond_pair[info.nBonds]; |
191 | < | theBends = new bend_set[info.nBends]; |
192 | < | theTorsions = new torsion_set[info.nTorsions]; |
190 | > | theBonds = new bond_pair[molInfo.nBonds]; |
191 | > | theBends = new bend_set[molInfo.nBends]; |
192 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
193 | ||
194 | < | // make the Atoms |
194 | > | // make the Atoms |
195 | ||
196 | < | for(j=0; j<info.nAtoms; j++){ |
392 | < | |
393 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
394 | < | if( currentAtom->haveOrientation() ){ |
196 | > | for(j=0; j<molInfo.nAtoms; j++){ |
197 | ||
198 | < | dAtom = new DirectionalAtom(j + atomOffset); |
199 | < | info->n_oriented++; |
200 | < | info.myAtoms[j] = dAtom; |
201 | < | |
202 | < | ux = currentAtom->getOrntX(); |
203 | < | uy = currentAtom->getOrntY(); |
204 | < | uz = currentAtom->getOrntZ(); |
205 | < | |
206 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
207 | < | |
208 | < | u = sqrt( uSqr ); |
209 | < | ux = ux / u; |
210 | < | uy = uy / u; |
211 | < | uz = uz / u; |
212 | < | |
213 | < | dAtom->setSUx( ux ); |
214 | < | dAtom->setSUy( uy ); |
215 | < | dAtom->setSUz( uz ); |
216 | < | } |
217 | < | else{ |
218 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
219 | < | } |
220 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
198 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
199 | > | if( currentAtom->haveOrientation() ){ |
200 | > | |
201 | > | dAtom = new DirectionalAtom( (j + atomOffset), |
202 | > | info[k].getConfiguration() ); |
203 | > | info[k].n_oriented++; |
204 | > | molInfo.myAtoms[j] = dAtom; |
205 | > | |
206 | > | ux = currentAtom->getOrntX(); |
207 | > | uy = currentAtom->getOrntY(); |
208 | > | uz = currentAtom->getOrntZ(); |
209 | > | |
210 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
211 | > | |
212 | > | u = sqrt( uSqr ); |
213 | > | ux = ux / u; |
214 | > | uy = uy / u; |
215 | > | uz = uz / u; |
216 | > | |
217 | > | dAtom->setSUx( ux ); |
218 | > | dAtom->setSUy( uy ); |
219 | > | dAtom->setSUz( uz ); |
220 | > | } |
221 | > | else{ |
222 | > | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
223 | > | info[k].getConfiguration() ); |
224 | > | } |
225 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
226 | ||
227 | #ifdef IS_MPI | |
228 | ||
229 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
229 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
230 | ||
231 | #endif // is_mpi | |
232 | < | } |
232 | > | } |
233 | ||
234 | // make the bonds | |
235 | < | for(j=0; j<info.nBonds; j++){ |
235 | > | for(j=0; j<molInfo.nBonds; j++){ |
236 | ||
237 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
238 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
239 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
240 | < | |
241 | < | exI = theBonds[j].a; |
242 | < | exJ = theBonds[j].b; |
243 | < | |
244 | < | // exclude_I must always be the smaller of the pair |
245 | < | if( exI > exJ ){ |
246 | < | tempEx = exI; |
247 | < | exI = exJ; |
248 | < | exJ = tempEx; |
249 | < | } |
237 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
238 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
239 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
240 | > | |
241 | > | exI = theBonds[j].a; |
242 | > | exJ = theBonds[j].b; |
243 | > | |
244 | > | // exclude_I must always be the smaller of the pair |
245 | > | if( exI > exJ ){ |
246 | > | tempEx = exI; |
247 | > | exI = exJ; |
248 | > | exJ = tempEx; |
249 | > | } |
250 | #ifdef IS_MPI | |
251 | < | tempEx = exI; |
252 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
253 | < | tempEx = exJ; |
254 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
255 | < | |
256 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
251 | > | tempEx = exI; |
252 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
253 | > | tempEx = exJ; |
254 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
255 | > | |
256 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
257 | #else // isn't MPI | |
258 | < | |
259 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
258 | > | |
259 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
260 | #endif //is_mpi | |
261 | < | } |
262 | < | excludeOffset += info.nBonds; |
456 | < | |
457 | < | //make the bends |
458 | < | for(j=0; j<info.nBends; j++){ |
261 | > | } |
262 | > | excludeOffset += molInfo.nBonds; |
263 | ||
264 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
265 | < | theBends[j].a = currentBend->getA() + atomOffset; |
266 | < | theBends[j].b = currentBend->getB() + atomOffset; |
267 | < | theBends[j].c = currentBend->getC() + atomOffset; |
264 | > | //make the bends |
265 | > | for(j=0; j<molInfo.nBends; j++){ |
266 | > | |
267 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
268 | > | theBends[j].a = currentBend->getA() + atomOffset; |
269 | > | theBends[j].b = currentBend->getB() + atomOffset; |
270 | > | theBends[j].c = currentBend->getC() + atomOffset; |
271 | > | |
272 | > | if( currentBend->haveExtras() ){ |
273 | ||
274 | < | if( currentBend->haveExtras() ){ |
275 | < | |
276 | < | extras = currentBend->getExtras(); |
277 | < | current_extra = extras; |
278 | < | |
279 | < | while( current_extra != NULL ){ |
280 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 | > | extras = currentBend->getExtras(); |
275 | > | current_extra = extras; |
276 | > | |
277 | > | while( current_extra != NULL ){ |
278 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
279 | > | |
280 | > | switch( current_extra->getType() ){ |
281 | ||
282 | < | switch( current_extra->getType() ){ |
282 | > | case 0: |
283 | > | theBends[j].ghost = |
284 | > | current_extra->getInt() + atomOffset; |
285 | > | theBends[j].isGhost = 1; |
286 | > | break; |
287 | > | |
288 | > | case 1: |
289 | > | theBends[j].ghost = |
290 | > | (int)current_extra->getDouble() + atomOffset; |
291 | > | theBends[j].isGhost = 1; |
292 | > | break; |
293 | > | |
294 | > | default: |
295 | > | sprintf( painCave.errMsg, |
296 | > | "SimSetup Error: ghostVectorSource was neither a " |
297 | > | "double nor an int.\n" |
298 | > | "-->Bend[%d] in %s\n", |
299 | > | j, comp_stamps[stampID]->getID() ); |
300 | > | painCave.isFatal = 1; |
301 | > | simError(); |
302 | > | } |
303 | > | } |
304 | > | |
305 | > | else{ |
306 | ||
475 | – | case 0: |
476 | – | theBends[j].ghost = |
477 | – | current_extra->getInt() + atomOffset; |
478 | – | theBends[j].isGhost = 1; |
479 | – | break; |
480 | – | |
481 | – | case 1: |
482 | – | theBends[j].ghost = |
483 | – | (int)current_extra->getDouble() + atomOffset; |
484 | – | theBends[j].isGhost = 1; |
485 | – | break; |
486 | – | |
487 | – | default: |
307 | sprintf( painCave.errMsg, | |
308 | < | "SimSetup Error: ghostVectorSource was neither a " |
309 | < | "double nor an int.\n" |
310 | < | "-->Bend[%d] in %s\n", |
308 | > | "SimSetup Error: unhandled bend assignment:\n" |
309 | > | " -->%s in Bend[%d] in %s\n", |
310 | > | current_extra->getlhs(), |
311 | j, comp_stamps[stampID]->getID() ); | |
312 | painCave.isFatal = 1; | |
313 | simError(); | |
314 | } | |
496 | – | } |
497 | – | |
498 | – | else{ |
315 | ||
316 | < | sprintf( painCave.errMsg, |
501 | < | "SimSetup Error: unhandled bend assignment:\n" |
502 | < | " -->%s in Bend[%d] in %s\n", |
503 | < | current_extra->getlhs(), |
504 | < | j, comp_stamps[stampID]->getID() ); |
505 | < | painCave.isFatal = 1; |
506 | < | simError(); |
316 | > | current_extra = current_extra->getNext(); |
317 | } | |
318 | + | } |
319 | + | |
320 | + | if( !theBends[j].isGhost ){ |
321 | ||
322 | < | current_extra = current_extra->getNext(); |
322 | > | exI = theBends[j].a; |
323 | > | exJ = theBends[j].c; |
324 | } | |
325 | < | } |
325 | > | else{ |
326 | ||
327 | < | if( !theBends[j].isGhost ){ |
328 | < | |
329 | < | exI = theBends[j].a; |
516 | < | exJ = theBends[j].c; |
517 | < | } |
518 | < | else{ |
327 | > | exI = theBends[j].a; |
328 | > | exJ = theBends[j].b; |
329 | > | } |
330 | ||
331 | < | exI = theBends[j].a; |
332 | < | exJ = theBends[j].b; |
333 | < | } |
334 | < | |
335 | < | // exclude_I must always be the smaller of the pair |
336 | < | if( exI > exJ ){ |
526 | < | tempEx = exI; |
527 | < | exI = exJ; |
528 | < | exJ = tempEx; |
529 | < | } |
331 | > | // exclude_I must always be the smaller of the pair |
332 | > | if( exI > exJ ){ |
333 | > | tempEx = exI; |
334 | > | exI = exJ; |
335 | > | exJ = tempEx; |
336 | > | } |
337 | #ifdef IS_MPI | |
338 | < | tempEx = exI; |
339 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
340 | < | tempEx = exJ; |
341 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
338 | > | tempEx = exI; |
339 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
340 | > | tempEx = exJ; |
341 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
342 | ||
343 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
343 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
344 | #else // isn't MPI | |
345 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
345 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
346 | #endif //is_mpi | |
540 | – | } |
541 | – | excludeOffset += info.nBends; |
542 | – | |
543 | – | for(j=0; j<info.nTorsions; j++){ |
544 | – | |
545 | – | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
546 | – | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
547 | – | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
548 | – | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
549 | – | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
550 | – | |
551 | – | exI = theTorsions[j].a; |
552 | – | exJ = theTorsions[j].d; |
553 | – | |
554 | – | // exclude_I must always be the smaller of the pair |
555 | – | if( exI > exJ ){ |
556 | – | tempEx = exI; |
557 | – | exI = exJ; |
558 | – | exJ = tempEx; |
347 | } | |
348 | < | #ifdef IS_MPI |
561 | < | tempEx = exI; |
562 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
563 | < | tempEx = exJ; |
564 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
348 | > | excludeOffset += molInfo.nBends; |
349 | ||
350 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
350 | > | for(j=0; j<molInfo.nTorsions; j++){ |
351 | > | |
352 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
353 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
354 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
355 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
356 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
357 | > | |
358 | > | exI = theTorsions[j].a; |
359 | > | exJ = theTorsions[j].d; |
360 | > | |
361 | > | // exclude_I must always be the smaller of the pair |
362 | > | if( exI > exJ ){ |
363 | > | tempEx = exI; |
364 | > | exI = exJ; |
365 | > | exJ = tempEx; |
366 | > | } |
367 | > | #ifdef IS_MPI |
368 | > | tempEx = exI; |
369 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
370 | > | tempEx = exJ; |
371 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
372 | > | |
373 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
374 | #else // isn't MPI | |
375 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
375 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
376 | #endif //is_mpi | |
377 | < | } |
378 | < | excludeOffset += info.nTorsions; |
377 | > | } |
378 | > | excludeOffset += molInfo.nTorsions; |
379 | > | |
380 | > | |
381 | > | // send the arrays off to the forceField for init. |
382 | > | |
383 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
384 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
385 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
386 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
387 | > | |
388 | > | |
389 | > | info[k].molecules[i].initialize( molInfo ); |
390 | ||
391 | < | |
392 | < | // send the arrays off to the forceField for init. |
393 | < | |
394 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
395 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
396 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
579 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
580 | < | |
581 | < | |
582 | < | the_molecules[i].initialize( info ); |
583 | < | |
584 | < | |
585 | < | atomOffset += info.nAtoms; |
586 | < | delete[] theBonds; |
587 | < | delete[] theBends; |
588 | < | delete[] theTorsions; |
391 | > | |
392 | > | atomOffset += molInfo.nAtoms; |
393 | > | delete[] theBonds; |
394 | > | delete[] theBends; |
395 | > | delete[] theTorsions; |
396 | > | } |
397 | } | |
398 | < | |
398 | > | |
399 | #ifdef IS_MPI | |
400 | sprintf( checkPointMsg, "all molecules initialized succesfully" ); | |
401 | MPIcheckPoint(); | |
402 | #endif // is_mpi | |
403 | < | |
403 | > | |
404 | // clean up the forcefield | |
405 | + | |
406 | the_ff->calcRcut(); | |
407 | the_ff->cleanMe(); | |
408 | < | |
408 | > | |
409 | } | |
410 | ||
411 | void SimSetup::initFromBass( void ){ | |
# | Line 609 | Line 418 | void SimSetup::initFromBass( void ){ | |
418 | int n_extra; | |
419 | int have_extra, done; | |
420 | ||
421 | + | double vel[3]; |
422 | + | vel[0] = 0.0; |
423 | + | vel[1] = 0.0; |
424 | + | vel[2] = 0.0; |
425 | + | |
426 | temp1 = (double)tot_nmol / 4.0; | |
427 | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); | |
428 | temp3 = ceil( temp2 ); | |
# | Line 618 | Line 432 | void SimSetup::initFromBass( void ){ | |
432 | have_extra =1; | |
433 | ||
434 | n_cells = (int)temp3 - 1; | |
435 | < | cellx = info->boxLx / temp3; |
436 | < | celly = info->boxLy / temp3; |
437 | < | cellz = info->boxLz / temp3; |
435 | > | cellx = info[0].boxL[0] / temp3; |
436 | > | celly = info[0].boxL[1] / temp3; |
437 | > | cellz = info[0].boxL[2] / temp3; |
438 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
439 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
440 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 635 | Line 449 | void SimSetup::initFromBass( void ){ | |
449 | } | |
450 | else{ | |
451 | n_cells = (int)temp3; | |
452 | < | cellx = info->boxLx / temp3; |
453 | < | celly = info->boxLy / temp3; |
454 | < | cellz = info->boxLz / temp3; |
452 | > | cellx = info[0].boxL[0] / temp3; |
453 | > | celly = info[0].boxL[1] / temp3; |
454 | > | cellz = info[0].boxL[2] / temp3; |
455 | } | |
456 | ||
457 | current_mol = 0; | |
# | Line 716 | Line 530 | void SimSetup::initFromBass( void ){ | |
530 | } | |
531 | } | |
532 | ||
533 | < | |
534 | < | for( i=0; i<info->n_atoms; i++ ){ |
721 | < | info->atoms[i]->set_vx( 0.0 ); |
722 | < | info->atoms[i]->set_vy( 0.0 ); |
723 | < | info->atoms[i]->set_vz( 0.0 ); |
533 | > | for( i=0; i<info[0].n_atoms; i++ ){ |
534 | > | info[0].atoms[i]->setVel( vel ); |
535 | } | |
536 | } | |
537 | ||
# | Line 730 | Line 541 | void SimSetup::makeElement( double x, double y, double | |
541 | AtomStamp* current_atom; | |
542 | DirectionalAtom* dAtom; | |
543 | double rotMat[3][3]; | |
544 | + | double pos[3]; |
545 | ||
546 | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ | |
547 | ||
# | Line 745 | Line 557 | void SimSetup::makeElement( double x, double y, double | |
557 | painCave.isFatal = 1; | |
558 | simError(); | |
559 | } | |
560 | + | |
561 | + | pos[0] = x + current_atom->getPosX(); |
562 | + | pos[1] = y + current_atom->getPosY(); |
563 | + | pos[2] = z + current_atom->getPosZ(); |
564 | + | |
565 | + | info[0].atoms[current_atom_ndx]->setPos( pos ); |
566 | ||
567 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
750 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
751 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
567 | > | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
568 | ||
569 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
569 | > | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
570 | ||
755 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
756 | – | |
571 | rotMat[0][0] = 1.0; | |
572 | rotMat[0][1] = 0.0; | |
573 | rotMat[0][2] = 0.0; | |
# | Line 784 | Line 598 | void SimSetup::gatherInfo( void ){ | |
598 | ||
599 | ||
600 | void SimSetup::gatherInfo( void ){ | |
601 | + | int i,j,k; |
602 | ||
603 | ensembleCase = -1; | |
604 | ffCase = -1; | |
605 | ||
791 | – | // get the stamps and globals; |
792 | – | the_stamps = stamps; |
793 | – | the_globals = globals; |
794 | – | |
606 | // set the easy ones first | |
607 | < | info->target_temp = the_globals->getTargetTemp(); |
608 | < | info->dt = the_globals->getDt(); |
609 | < | info->run_time = the_globals->getRunTime(); |
610 | < | n_components = the_globals->getNComponents(); |
607 | > | |
608 | > | for( i=0; i<nInfo; i++){ |
609 | > | info[i].target_temp = globals->getTargetTemp(); |
610 | > | info[i].dt = globals->getDt(); |
611 | > | info[i].run_time = globals->getRunTime(); |
612 | > | } |
613 | > | n_components = globals->getNComponents(); |
614 | ||
615 | ||
616 | // get the forceField | |
617 | ||
618 | < | strcpy( force_field, the_globals->getForceField() ); |
618 | > | strcpy( force_field, globals->getForceField() ); |
619 | ||
620 | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; | |
621 | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; | |
622 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
623 | else{ | |
624 | sprintf( painCave.errMsg, | |
625 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 815 | Line 630 | void SimSetup::gatherInfo( void ){ | |
630 | ||
631 | // get the ensemble | |
632 | ||
633 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
633 | > | strcpy( ensemble, globals->getEnsemble() ); |
634 | ||
635 | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; | |
636 | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; | |
# | Line 824 | Line 639 | void SimSetup::gatherInfo( void ){ | |
639 | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; | |
640 | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; | |
641 | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; | |
642 | + | |
643 | + | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
644 | + | else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
645 | + | else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS")) |
646 | + | ensembleCase = NPTiZCONS_ENS; |
647 | + | else if( !strcasecmp( ensemble, "NPTfZCONS")) ensembleCase = NPTfZCONS_ENS; |
648 | + | else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
649 | + | else if( !strcasecmp( ensemble, "NPTfmZCONS")) ensembleCase = NPTfmZCONS_ENS; |
650 | + | |
651 | else{ | |
652 | sprintf( painCave.errMsg, | |
653 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 834 | Line 658 | void SimSetup::gatherInfo( void ){ | |
658 | strcpy( ensemble, "NVE" ); | |
659 | ensembleCase = NVE_ENS; | |
660 | } | |
661 | < | strcpy( info->ensemble, ensemble ); |
661 | > | |
662 | > | for(i=0; i<nInfo; i++){ |
663 | > | |
664 | > | strcpy( info[i].ensemble, ensemble ); |
665 | ||
666 | < | // get the mixing rule |
666 | > | // get the mixing rule |
667 | ||
668 | < | strcpy( info->mixingRule, the_globals->getMixingRule() ); |
669 | < | info->usePBC = the_globals->getPBC(); |
670 | < | |
668 | > | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
669 | > | info[i].usePBC = globals->getPBC(); |
670 | > | } |
671 | ||
672 | // get the components and calculate the tot_nMol and indvidual n_mol | |
673 | ||
674 | < | the_components = the_globals->getComponents(); |
674 | > | the_components = globals->getComponents(); |
675 | components_nmol = new int[n_components]; | |
676 | ||
677 | ||
678 | < | if( !the_globals->haveNMol() ){ |
678 | > | if( !globals->haveNMol() ){ |
679 | // we don't have the total number of molecules, so we assume it is | |
680 | // given in each component | |
681 | ||
# | Line 881 | Line 708 | void SimSetup::gatherInfo( void ){ | |
708 | ||
709 | // set the status, sample, and thermal kick times | |
710 | ||
711 | < | if( the_globals->haveSampleTime() ){ |
885 | < | info->sampleTime = the_globals->getSampleTime(); |
886 | < | info->statusTime = info->sampleTime; |
887 | < | info->thermalTime = info->sampleTime; |
888 | < | } |
889 | < | else{ |
890 | < | info->sampleTime = the_globals->getRunTime(); |
891 | < | info->statusTime = info->sampleTime; |
892 | < | info->thermalTime = info->sampleTime; |
893 | < | } |
711 | > | for(i=0; i<nInfo; i++){ |
712 | ||
713 | < | if( the_globals->haveStatusTime() ){ |
714 | < | info->statusTime = the_globals->getStatusTime(); |
715 | < | } |
716 | < | |
717 | < | if( the_globals->haveThermalTime() ){ |
718 | < | info->thermalTime = the_globals->getThermalTime(); |
719 | < | } |
720 | < | |
721 | < | // check for the temperature set flag |
722 | < | |
905 | < | if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
906 | < | |
907 | < | // get some of the tricky things that may still be in the globals |
908 | < | |
909 | < | double boxVector[3]; |
910 | < | if( the_globals->haveBox() ){ |
911 | < | boxVector[0] = the_globals->getBox(); |
912 | < | boxVector[1] = the_globals->getBox(); |
913 | < | boxVector[2] = the_globals->getBox(); |
713 | > | if( globals->haveSampleTime() ){ |
714 | > | info[i].sampleTime = globals->getSampleTime(); |
715 | > | info[i].statusTime = info[i].sampleTime; |
716 | > | info[i].thermalTime = info[i].sampleTime; |
717 | > | } |
718 | > | else{ |
719 | > | info[i].sampleTime = globals->getRunTime(); |
720 | > | info[i].statusTime = info[i].sampleTime; |
721 | > | info[i].thermalTime = info[i].sampleTime; |
722 | > | } |
723 | ||
724 | < | info->setBox( boxVector ); |
725 | < | } |
917 | < | else if( the_globals->haveDensity() ){ |
918 | < | |
919 | < | double vol; |
920 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
921 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
922 | < | boxVector[1] = boxVector[0]; |
923 | < | boxVector[2] = boxVector[0]; |
924 | < | |
925 | < | info->setBox( boxVector ); |
926 | < | } |
927 | < | else{ |
928 | < | if( !the_globals->haveBoxX() ){ |
929 | < | sprintf( painCave.errMsg, |
930 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
931 | < | painCave.isFatal = 1; |
932 | < | simError(); |
724 | > | if( globals->haveStatusTime() ){ |
725 | > | info[i].statusTime = globals->getStatusTime(); |
726 | } | |
727 | < | boxVector[0] = the_globals->getBoxX(); |
728 | < | |
729 | < | if( !the_globals->haveBoxY() ){ |
937 | < | sprintf( painCave.errMsg, |
938 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
939 | < | painCave.isFatal = 1; |
940 | < | simError(); |
727 | > | |
728 | > | if( globals->haveThermalTime() ){ |
729 | > | info[i].thermalTime = globals->getThermalTime(); |
730 | } | |
942 | – | boxVector[1] = the_globals->getBoxY(); |
731 | ||
732 | < | if( !the_globals->haveBoxZ() ){ |
945 | < | sprintf( painCave.errMsg, |
946 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
947 | < | painCave.isFatal = 1; |
948 | < | simError(); |
949 | < | } |
950 | < | boxVector[2] = the_globals->getBoxZ(); |
732 | > | // check for the temperature set flag |
733 | ||
734 | < | info->setBox( boxVector ); |
734 | > | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
735 | > | |
736 | > | // get some of the tricky things that may still be in the globals |
737 | > | |
738 | > | double boxVector[3]; |
739 | > | if( globals->haveBox() ){ |
740 | > | boxVector[0] = globals->getBox(); |
741 | > | boxVector[1] = globals->getBox(); |
742 | > | boxVector[2] = globals->getBox(); |
743 | > | |
744 | > | info[i].setBox( boxVector ); |
745 | > | } |
746 | > | else if( globals->haveDensity() ){ |
747 | > | |
748 | > | double vol; |
749 | > | vol = (double)tot_nmol / globals->getDensity(); |
750 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
751 | > | boxVector[1] = boxVector[0]; |
752 | > | boxVector[2] = boxVector[0]; |
753 | > | |
754 | > | info[i].setBox( boxVector ); |
755 | } | |
756 | + | else{ |
757 | + | if( !globals->haveBoxX() ){ |
758 | + | sprintf( painCave.errMsg, |
759 | + | "SimSetup error, no periodic BoxX size given.\n" ); |
760 | + | painCave.isFatal = 1; |
761 | + | simError(); |
762 | + | } |
763 | + | boxVector[0] = globals->getBoxX(); |
764 | + | |
765 | + | if( !globals->haveBoxY() ){ |
766 | + | sprintf( painCave.errMsg, |
767 | + | "SimSetup error, no periodic BoxY size given.\n" ); |
768 | + | painCave.isFatal = 1; |
769 | + | simError(); |
770 | + | } |
771 | + | boxVector[1] = globals->getBoxY(); |
772 | + | |
773 | + | if( !globals->haveBoxZ() ){ |
774 | + | sprintf( painCave.errMsg, |
775 | + | "SimSetup error, no periodic BoxZ size given.\n" ); |
776 | + | painCave.isFatal = 1; |
777 | + | simError(); |
778 | + | } |
779 | + | boxVector[2] = globals->getBoxZ(); |
780 | + | |
781 | + | info[i].setBox( boxVector ); |
782 | + | } |
783 | ||
784 | < | |
784 | > | } |
785 | ||
786 | #ifdef IS_MPI | |
787 | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); | |
# | Line 965 | Line 794 | void SimSetup::finalInfoCheck( void ){ | |
794 | void SimSetup::finalInfoCheck( void ){ | |
795 | int index; | |
796 | int usesDipoles; | |
797 | < | |
797 | > | int i; |
798 | ||
799 | < | // check electrostatic parameters |
800 | < | |
972 | < | index = 0; |
973 | < | usesDipoles = 0; |
974 | < | while( (index < info->n_atoms) && !usesDipoles ){ |
975 | < | usesDipoles = ((info->atoms)[index])->hasDipole(); |
976 | < | index++; |
977 | < | } |
978 | < | |
979 | < | #ifdef IS_MPI |
980 | < | int myUse = usesDipoles |
981 | < | MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
982 | < | #endif //is_mpi |
983 | < | |
984 | < | |
985 | < | if (the_globals->getUseRF() ) { |
986 | < | info->useReactionField = 1; |
799 | > | for(i=0; i<nInfo; i++){ |
800 | > | // check electrostatic parameters |
801 | ||
802 | < | if( !the_globals->haveECR() ){ |
803 | < | sprintf( painCave.errMsg, |
804 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
805 | < | "box length for the electrostaticCutoffRadius.\n" |
806 | < | "I hope you have a very fast processor!\n"); |
993 | < | painCave.isFatal = 0; |
994 | < | simError(); |
995 | < | double smallest; |
996 | < | smallest = info->boxLx; |
997 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
998 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
999 | < | info->ecr = 0.5 * smallest; |
1000 | < | } else { |
1001 | < | info->ecr = the_globals->getECR(); |
802 | > | index = 0; |
803 | > | usesDipoles = 0; |
804 | > | while( (index < info[i].n_atoms) && !usesDipoles ){ |
805 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
806 | > | index++; |
807 | } | |
1003 | – | |
1004 | – | if( !the_globals->haveEST() ){ |
1005 | – | sprintf( painCave.errMsg, |
1006 | – | "SimSetup Warning: using default value of 0.05 * the " |
1007 | – | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
1008 | – | ); |
1009 | – | painCave.isFatal = 0; |
1010 | – | simError(); |
1011 | – | info->est = 0.05 * info->ecr; |
1012 | – | } else { |
1013 | – | info->est = the_globals->getEST(); |
1014 | – | } |
808 | ||
809 | < | if(!the_globals->haveDielectric() ){ |
810 | < | sprintf( painCave.errMsg, |
811 | < | "SimSetup Error: You are trying to use Reaction Field without" |
812 | < | "setting a dielectric constant!\n" |
813 | < | ); |
814 | < | painCave.isFatal = 1; |
815 | < | simError(); |
816 | < | } |
817 | < | info->dielectric = the_globals->getDielectric(); |
1025 | < | } |
1026 | < | else { |
1027 | < | if (usesDipoles) { |
809 | > | #ifdef IS_MPI |
810 | > | int myUse = usesDipoles; |
811 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
812 | > | #endif //is_mpi |
813 | > | |
814 | > | double theEcr, theEst; |
815 | > | |
816 | > | if (globals->getUseRF() ) { |
817 | > | info[i].useReactionField = 1; |
818 | ||
819 | < | if( !the_globals->haveECR() ){ |
820 | < | sprintf( painCave.errMsg, |
821 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
822 | < | "box length for the electrostaticCutoffRadius.\n" |
823 | < | "I hope you have a very fast processor!\n"); |
824 | < | painCave.isFatal = 0; |
825 | < | simError(); |
826 | < | double smallest; |
827 | < | smallest = info->boxLx; |
828 | < | if (info->boxLy <= smallest) smallest = info->boxLy; |
829 | < | if (info->boxLz <= smallest) smallest = info->boxLz; |
830 | < | info->ecr = 0.5 * smallest; |
819 | > | if( !globals->haveECR() ){ |
820 | > | sprintf( painCave.errMsg, |
821 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
822 | > | "box length for the electrostaticCutoffRadius.\n" |
823 | > | "I hope you have a very fast processor!\n"); |
824 | > | painCave.isFatal = 0; |
825 | > | simError(); |
826 | > | double smallest; |
827 | > | smallest = info[i].boxL[0]; |
828 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
829 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
830 | > | theEcr = 0.5 * smallest; |
831 | } else { | |
832 | < | info->ecr = the_globals->getECR(); |
832 | > | theEcr = globals->getECR(); |
833 | } | |
834 | ||
835 | < | if( !the_globals->haveEST() ){ |
836 | < | sprintf( painCave.errMsg, |
837 | < | "SimSetup Warning: using default value of 5%% of the " |
838 | < | "electrostaticCutoffRadius for the " |
839 | < | "electrostaticSkinThickness\n" |
840 | < | ); |
841 | < | painCave.isFatal = 0; |
842 | < | simError(); |
843 | < | info->est = 0.05 * info->ecr; |
844 | < | } else { |
1055 | < | info->est = the_globals->getEST(); |
835 | > | if( !globals->haveEST() ){ |
836 | > | sprintf( painCave.errMsg, |
837 | > | "SimSetup Warning: using default value of 0.05 * the " |
838 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
839 | > | ); |
840 | > | painCave.isFatal = 0; |
841 | > | simError(); |
842 | > | theEst = 0.05 * theEcr; |
843 | > | } else { |
844 | > | theEst= globals->getEST(); |
845 | } | |
846 | < | } |
847 | < | } |
846 | > | |
847 | > | info[i].setEcr( theEcr, theEst ); |
848 | > | |
849 | > | if(!globals->haveDielectric() ){ |
850 | > | sprintf( painCave.errMsg, |
851 | > | "SimSetup Error: You are trying to use Reaction Field without" |
852 | > | "setting a dielectric constant!\n" |
853 | > | ); |
854 | > | painCave.isFatal = 1; |
855 | > | simError(); |
856 | > | } |
857 | > | info[i].dielectric = globals->getDielectric(); |
858 | > | } |
859 | > | else { |
860 | > | if (usesDipoles) { |
861 | > | |
862 | > | if( !globals->haveECR() ){ |
863 | > | sprintf( painCave.errMsg, |
864 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
865 | > | "box length for the electrostaticCutoffRadius.\n" |
866 | > | "I hope you have a very fast processor!\n"); |
867 | > | painCave.isFatal = 0; |
868 | > | simError(); |
869 | > | double smallest; |
870 | > | smallest = info[i].boxL[0]; |
871 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
872 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
873 | > | theEcr = 0.5 * smallest; |
874 | > | } else { |
875 | > | theEcr = globals->getECR(); |
876 | > | } |
877 | > | |
878 | > | if( !globals->haveEST() ){ |
879 | > | sprintf( painCave.errMsg, |
880 | > | "SimSetup Warning: using default value of 0.05 * the " |
881 | > | "electrostaticCutoffRadius for the " |
882 | > | "electrostaticSkinThickness\n" |
883 | > | ); |
884 | > | painCave.isFatal = 0; |
885 | > | simError(); |
886 | > | theEst = 0.05 * theEcr; |
887 | > | } else { |
888 | > | theEst= globals->getEST(); |
889 | > | } |
890 | > | |
891 | > | info[i].setEcr( theEcr, theEst ); |
892 | > | } |
893 | > | } |
894 | > | } |
895 | ||
896 | #ifdef IS_MPI | |
897 | strcpy( checkPointMsg, "post processing checks out" ); | |
# | Line 1065 | Line 901 | void SimSetup::initSystemCoords( void ){ | |
901 | } | |
902 | ||
903 | void SimSetup::initSystemCoords( void ){ | |
904 | + | int i; |
905 | + | |
906 | + | std::cerr << "Setting atom Coords\n"; |
907 | ||
908 | < | if( the_globals->haveInitialConfig() ){ |
909 | < | |
910 | < | InitializeFromFile* fileInit; |
908 | > | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
909 | > | |
910 | > | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
911 | > | |
912 | > | if( globals->haveInitialConfig() ){ |
913 | > | |
914 | > | InitializeFromFile* fileInit; |
915 | #ifdef IS_MPI // is_mpi | |
916 | < | if( worldRank == 0 ){ |
916 | > | if( worldRank == 0 ){ |
917 | #endif //is_mpi | |
918 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
918 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
919 | #ifdef IS_MPI | |
920 | < | }else fileInit = new InitializeFromFile( NULL ); |
920 | > | }else fileInit = new InitializeFromFile( NULL ); |
921 | #endif | |
922 | < | fileInit->read_xyz( info ); // default velocities on |
923 | < | |
924 | < | delete fileInit; |
925 | < | } |
926 | < | else{ |
927 | < | |
922 | > | fileInit->readInit( info ); // default velocities on |
923 | > | |
924 | > | delete fileInit; |
925 | > | } |
926 | > | else{ |
927 | > | |
928 | #ifdef IS_MPI | |
929 | < | |
930 | < | // no init from bass |
931 | < | |
932 | < | sprintf( painCave.errMsg, |
933 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
934 | < | painCave.isFatal; |
935 | < | simError(); |
936 | < | |
929 | > | |
930 | > | // no init from bass |
931 | > | |
932 | > | sprintf( painCave.errMsg, |
933 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
934 | > | painCave.isFatal; |
935 | > | simError(); |
936 | > | |
937 | #else | |
938 | < | |
939 | < | initFromBass(); |
940 | < | |
941 | < | |
938 | > | |
939 | > | initFromBass(); |
940 | > | |
941 | > | |
942 | #endif | |
943 | < | } |
944 | < | |
943 | > | } |
944 | > | |
945 | #ifdef IS_MPI | |
946 | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); | |
947 | MPIcheckPoint(); | |
948 | #endif // is_mpi | |
949 | < | |
949 | > | |
950 | } | |
951 | ||
952 | ||
953 | void SimSetup::makeOutNames( void ){ | |
954 | + | |
955 | + | int k; |
956 | ||
957 | + | |
958 | + | for(k=0; k<nInfo; k++){ |
959 | + | |
960 | #ifdef IS_MPI | |
961 | < | if( worldRank == 0 ){ |
961 | > | if( worldRank == 0 ){ |
962 | #endif // is_mpi | |
963 | < | |
964 | < | if( the_globals->haveFinalConfig() ){ |
965 | < | strcpy( info->finalName, the_globals->getFinalConfig() ); |
1118 | < | } |
1119 | < | else{ |
1120 | < | strcpy( info->finalName, inFileName ); |
1121 | < | char* endTest; |
1122 | < | int nameLength = strlen( info->finalName ); |
1123 | < | endTest = &(info->finalName[nameLength - 5]); |
1124 | < | if( !strcmp( endTest, ".bass" ) ){ |
1125 | < | strcpy( endTest, ".eor" ); |
963 | > | |
964 | > | if( globals->haveFinalConfig() ){ |
965 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
966 | } | |
1127 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
1128 | – | strcpy( endTest, ".eor" ); |
1129 | – | } |
967 | else{ | |
968 | < | endTest = &(info->finalName[nameLength - 4]); |
969 | < | if( !strcmp( endTest, ".bss" ) ){ |
968 | > | strcpy( info[k].finalName, inFileName ); |
969 | > | char* endTest; |
970 | > | int nameLength = strlen( info[k].finalName ); |
971 | > | endTest = &(info[k].finalName[nameLength - 5]); |
972 | > | if( !strcmp( endTest, ".bass" ) ){ |
973 | strcpy( endTest, ".eor" ); | |
974 | } | |
975 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
975 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
976 | strcpy( endTest, ".eor" ); | |
977 | } | |
978 | else{ | |
979 | < | strcat( info->finalName, ".eor" ); |
979 | > | endTest = &(info[k].finalName[nameLength - 4]); |
980 | > | if( !strcmp( endTest, ".bss" ) ){ |
981 | > | strcpy( endTest, ".eor" ); |
982 | > | } |
983 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
984 | > | strcpy( endTest, ".eor" ); |
985 | > | } |
986 | > | else{ |
987 | > | strcat( info[k].finalName, ".eor" ); |
988 | > | } |
989 | } | |
990 | } | |
991 | < | } |
992 | < | |
993 | < | // make the sample and status out names |
994 | < | |
995 | < | strcpy( info->sampleName, inFileName ); |
996 | < | char* endTest; |
997 | < | int nameLength = strlen( info->sampleName ); |
998 | < | endTest = &(info->sampleName[nameLength - 5]); |
1150 | < | if( !strcmp( endTest, ".bass" ) ){ |
1151 | < | strcpy( endTest, ".dump" ); |
1152 | < | } |
1153 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1154 | < | strcpy( endTest, ".dump" ); |
1155 | < | } |
1156 | < | else{ |
1157 | < | endTest = &(info->sampleName[nameLength - 4]); |
1158 | < | if( !strcmp( endTest, ".bss" ) ){ |
991 | > | |
992 | > | // make the sample and status out names |
993 | > | |
994 | > | strcpy( info[k].sampleName, inFileName ); |
995 | > | char* endTest; |
996 | > | int nameLength = strlen( info[k].sampleName ); |
997 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
998 | > | if( !strcmp( endTest, ".bass" ) ){ |
999 | strcpy( endTest, ".dump" ); | |
1000 | } | |
1001 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1001 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
1002 | strcpy( endTest, ".dump" ); | |
1003 | } | |
1004 | else{ | |
1005 | < | strcat( info->sampleName, ".dump" ); |
1005 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1006 | > | if( !strcmp( endTest, ".bss" ) ){ |
1007 | > | strcpy( endTest, ".dump" ); |
1008 | > | } |
1009 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1010 | > | strcpy( endTest, ".dump" ); |
1011 | > | } |
1012 | > | else{ |
1013 | > | strcat( info[k].sampleName, ".dump" ); |
1014 | > | } |
1015 | } | |
1016 | < | } |
1017 | < | |
1018 | < | strcpy( info->statusName, inFileName ); |
1019 | < | nameLength = strlen( info->statusName ); |
1020 | < | endTest = &(info->statusName[nameLength - 5]); |
1172 | < | if( !strcmp( endTest, ".bass" ) ){ |
1173 | < | strcpy( endTest, ".stat" ); |
1174 | < | } |
1175 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1176 | < | strcpy( endTest, ".stat" ); |
1177 | < | } |
1178 | < | else{ |
1179 | < | endTest = &(info->statusName[nameLength - 4]); |
1180 | < | if( !strcmp( endTest, ".bss" ) ){ |
1016 | > | |
1017 | > | strcpy( info[k].statusName, inFileName ); |
1018 | > | nameLength = strlen( info[k].statusName ); |
1019 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1020 | > | if( !strcmp( endTest, ".bass" ) ){ |
1021 | strcpy( endTest, ".stat" ); | |
1022 | } | |
1023 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1023 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
1024 | strcpy( endTest, ".stat" ); | |
1025 | } | |
1026 | else{ | |
1027 | < | strcat( info->statusName, ".stat" ); |
1027 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1028 | > | if( !strcmp( endTest, ".bss" ) ){ |
1029 | > | strcpy( endTest, ".stat" ); |
1030 | > | } |
1031 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1032 | > | strcpy( endTest, ".stat" ); |
1033 | > | } |
1034 | > | else{ |
1035 | > | strcat( info[k].statusName, ".stat" ); |
1036 | > | } |
1037 | } | |
1038 | < | } |
1190 | < | |
1038 | > | |
1039 | #ifdef IS_MPI | |
1040 | < | } |
1040 | > | } |
1041 | #endif // is_mpi | |
1042 | < | |
1042 | > | } |
1043 | } | |
1044 | ||
1045 | ||
1046 | void SimSetup::sysObjectsCreation( void ){ | |
1047 | < | |
1047 | > | |
1048 | > | int i,k; |
1049 | > | |
1050 | // create the forceField | |
1051 | < | |
1051 | > | |
1052 | createFF(); | |
1053 | ||
1054 | // extract componentList | |
# | Line 1219 | Line 1069 | void SimSetup::sysObjectsCreation( void ){ | |
1069 | ||
1070 | makeSysArrays(); | |
1071 | ||
1072 | + | // make and initialize the molecules (all but atomic coordinates) |
1073 | ||
1074 | < | |
1075 | < | |
1074 | > | makeMolecules(); |
1075 | > | |
1076 | > | for(k=0; k<nInfo; k++){ |
1077 | > | info[k].identArray = new int[info[k].n_atoms]; |
1078 | > | for(i=0; i<info[k].n_atoms; i++){ |
1079 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1080 | > | } |
1081 | > | } |
1082 | } | |
1083 | ||
1084 | ||
# | Line 1237 | Line 1094 | void SimSetup::createFF( void ){ | |
1094 | the_ff = new LJFF(); | |
1095 | break; | |
1096 | ||
1097 | + | case FF_EAM: |
1098 | + | the_ff = new EAM_FF(); |
1099 | + | break; |
1100 | + | |
1101 | default: | |
1102 | sprintf( painCave.errMsg, | |
1103 | "SimSetup Error. Unrecognized force field in case statement.\n"); | |
# | Line 1254 | Line 1115 | void SimSetup::compList( void ){ | |
1115 | ||
1116 | void SimSetup::compList( void ){ | |
1117 | ||
1118 | + | int i; |
1119 | + | char* id; |
1120 | + | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1121 | + | LinkedMolStamp* currentStamp = NULL; |
1122 | comp_stamps = new MoleculeStamp*[n_components]; | |
1123 | < | |
1123 | > | |
1124 | // make an array of molecule stamps that match the components used. | |
1125 | // also extract the used stamps out into a separate linked list | |
1261 | – | |
1262 | – | info->nComponents = n_components; |
1263 | – | info->componentsNmol = components_nmol; |
1264 | – | info->compStamps = comp_stamps; |
1265 | – | info->headStamp = new LinkedMolStamp(); |
1126 | ||
1127 | < | char* id; |
1128 | < | LinkedMolStamp* headStamp = info->headStamp; |
1129 | < | LinkedMolStamp* currentStamp = NULL; |
1127 | > | for(i=0; i<nInfo; i++){ |
1128 | > | info[i].nComponents = n_components; |
1129 | > | info[i].componentsNmol = components_nmol; |
1130 | > | info[i].compStamps = comp_stamps; |
1131 | > | info[i].headStamp = headStamp; |
1132 | > | } |
1133 | > | |
1134 | > | |
1135 | for( i=0; i<n_components; i++ ){ | |
1136 | ||
1137 | id = the_components[i]->getType(); | |
# | Line 1279 | Line 1144 | void SimSetup::compList( void ){ | |
1144 | ||
1145 | // extract the component from the list; | |
1146 | ||
1147 | < | currentStamp = the_stamps->extractMolStamp( id ); |
1147 | > | currentStamp = stamps->extractMolStamp( id ); |
1148 | if( currentStamp == NULL ){ | |
1149 | sprintf( painCave.errMsg, | |
1150 | "SimSetup error: Component \"%s\" was not found in the " | |
# | Line 1303 | Line 1168 | void SimSetup::calcSysValues( void ){ | |
1168 | } | |
1169 | ||
1170 | void SimSetup::calcSysValues( void ){ | |
1171 | < | |
1171 | > | int i, j, k; |
1172 | > | |
1173 | > | int *molMembershipArray; |
1174 | > | |
1175 | tot_atoms = 0; | |
1176 | tot_bonds = 0; | |
1177 | tot_bends = 0; | |
# | Line 1315 | Line 1183 | void SimSetup::calcSysValues( void ){ | |
1183 | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); | |
1184 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1185 | } | |
1186 | < | |
1186 | > | |
1187 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1188 | < | |
1321 | < | info->n_atoms = tot_atoms; |
1322 | < | info->n_bonds = tot_bonds; |
1323 | < | info->n_bends = tot_bends; |
1324 | < | info->n_torsions = tot_torsions; |
1325 | < | info->n_SRI = tot_SRI; |
1326 | < | info->n_mol = tot_nmol; |
1188 | > | molMembershipArray = new int[tot_atoms]; |
1189 | ||
1190 | < | info->molMembershipArray = new int[tot_atoms]; |
1190 | > | for(i=0; i<nInfo; i++){ |
1191 | > | info[i].n_atoms = tot_atoms; |
1192 | > | info[i].n_bonds = tot_bonds; |
1193 | > | info[i].n_bends = tot_bends; |
1194 | > | info[i].n_torsions = tot_torsions; |
1195 | > | info[i].n_SRI = tot_SRI; |
1196 | > | info[i].n_mol = tot_nmol; |
1197 | > | |
1198 | > | info[i].molMembershipArray = molMembershipArray; |
1199 | > | } |
1200 | } | |
1201 | ||
1331 | – | |
1202 | #ifdef IS_MPI | |
1203 | ||
1204 | void SimSetup::mpiMolDivide( void ){ | |
1205 | ||
1206 | + | int i, j, k; |
1207 | int localMol, allMol; | |
1208 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1209 | ||
# | Line 1367 | Line 1238 | void SimSetup::mpiMolDivide( void ){ | |
1238 | localMol++; | |
1239 | } | |
1240 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { | |
1241 | < | info->molMembershipArray[globalAtomIndex] = allMol; |
1241 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1242 | globalAtomIndex++; | |
1243 | } | |
1244 | ||
# | Line 1376 | Line 1247 | void SimSetup::mpiMolDivide( void ){ | |
1247 | } | |
1248 | local_SRI = local_bonds + local_bends + local_torsions; | |
1249 | ||
1250 | < | info->n_atoms = mpiSim->getMyNlocal(); |
1250 | > | info[0].n_atoms = mpiSim->getMyNlocal(); |
1251 | ||
1252 | < | if( local_atoms != info->n_atoms ){ |
1252 | > | if( local_atoms != info[0].n_atoms ){ |
1253 | sprintf( painCave.errMsg, | |
1254 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
1255 | " localAtom (%d) are not equal.\n", | |
1256 | < | info->n_atoms, |
1256 | > | info[0].n_atoms, |
1257 | local_atoms ); | |
1258 | painCave.isFatal = 1; | |
1259 | simError(); | |
1260 | } | |
1261 | ||
1262 | < | info->n_bonds = local_bonds; |
1263 | < | info->n_bends = local_bends; |
1264 | < | info->n_torsions = local_torsions; |
1265 | < | info->n_SRI = local_SRI; |
1266 | < | info->n_mol = localMol; |
1262 | > | info[0].n_bonds = local_bonds; |
1263 | > | info[0].n_bends = local_bends; |
1264 | > | info[0].n_torsions = local_torsions; |
1265 | > | info[0].n_SRI = local_SRI; |
1266 | > | info[0].n_mol = localMol; |
1267 | ||
1268 | strcpy( checkPointMsg, "Passed nlocal consistency check." ); | |
1269 | MPIcheckPoint(); | |
1270 | } | |
1271 | < | |
1271 | > | |
1272 | #endif // is_mpi | |
1273 | ||
1274 | ||
1275 | void SimSetup::makeSysArrays( void ){ | |
1276 | + | int i, j, k, l; |
1277 | ||
1278 | < | // create the atom and short range interaction arrays |
1278 | > | Atom** the_atoms; |
1279 | > | Molecule* the_molecules; |
1280 | > | Exclude** the_excludes; |
1281 | ||
1408 | – | Atom::createArrays(info->n_atoms); |
1409 | – | the_atoms = new Atom*[info->n_atoms]; |
1410 | – | the_molecules = new Molecule[info->n_mol]; |
1411 | – | int molIndex; |
1412 | – | |
1413 | – | // initialize the molecule's stampID's |
1414 | – | |
1415 | – | #ifdef IS_MPI |
1282 | ||
1283 | + | for(l=0; l<nInfo; l++){ |
1284 | + | |
1285 | + | // create the atom and short range interaction arrays |
1286 | + | |
1287 | + | the_atoms = new Atom*[info[l].n_atoms]; |
1288 | + | the_molecules = new Molecule[info[l].n_mol]; |
1289 | + | int molIndex; |
1290 | ||
1291 | < | molIndex = 0; |
1419 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1291 | > | // initialize the molecule's stampID's |
1292 | ||
1293 | < | if(mol2proc[i] == worldRank ){ |
1294 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1295 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1296 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1297 | < | molIndex++; |
1293 | > | #ifdef IS_MPI |
1294 | > | |
1295 | > | |
1296 | > | molIndex = 0; |
1297 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1298 | > | |
1299 | > | if(mol2proc[i] == worldRank ){ |
1300 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1301 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1302 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1303 | > | molIndex++; |
1304 | > | } |
1305 | } | |
1306 | < | } |
1428 | < | |
1306 | > | |
1307 | #else // is_mpi | |
1308 | < | |
1309 | < | molIndex = 0; |
1310 | < | globalAtomIndex = 0; |
1311 | < | for(i=0; i<n_components; i++){ |
1312 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1313 | < | the_molecules[molIndex].setStampID( i ); |
1314 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1315 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1316 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1317 | < | info->molMembershipArray[globalAtomIndex] = molIndex; |
1318 | < | globalAtomIndex++; |
1308 | > | |
1309 | > | molIndex = 0; |
1310 | > | globalAtomIndex = 0; |
1311 | > | for(i=0; i<n_components; i++){ |
1312 | > | for(j=0; j<components_nmol[i]; j++ ){ |
1313 | > | the_molecules[molIndex].setStampID( i ); |
1314 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1315 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1316 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1317 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1318 | > | globalAtomIndex++; |
1319 | > | } |
1320 | > | molIndex++; |
1321 | } | |
1442 | – | molIndex++; |
1322 | } | |
1444 | – | } |
1323 | ||
1324 | < | |
1324 | > | |
1325 | #endif // is_mpi | |
1326 | ||
1327 | ||
1328 | < | if( info->n_SRI ){ |
1328 | > | if( info[l].n_SRI ){ |
1329 | ||
1330 | < | Exclude::createArray(info->n_SRI); |
1331 | < | the_excludes = new Exclude*[info->n_SRI]; |
1332 | < | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1333 | < | info->globalExcludes = new int; |
1334 | < | info->n_exclude = info->n_SRI; |
1335 | < | } |
1336 | < | else{ |
1330 | > | Exclude::createArray(info[l].n_SRI); |
1331 | > | the_excludes = new Exclude*[info[l].n_SRI]; |
1332 | > | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1333 | > | the_excludes[ex] = new Exclude(ex); |
1334 | > | } |
1335 | > | info[l].globalExcludes = new int; |
1336 | > | info[l].n_exclude = info[l].n_SRI; |
1337 | > | } |
1338 | > | else{ |
1339 | ||
1340 | < | Exclude::createArray( 1 ); |
1341 | < | the_excludes = new Exclude*; |
1342 | < | the_excludes[0] = new Exclude(0); |
1343 | < | the_excludes[0]->setPair( 0,0 ); |
1344 | < | info->globalExcludes = new int; |
1345 | < | info->globalExcludes[0] = 0; |
1346 | < | info->n_exclude = 0; |
1340 | > | Exclude::createArray( 1 ); |
1341 | > | the_excludes = new Exclude*; |
1342 | > | the_excludes[0] = new Exclude(0); |
1343 | > | the_excludes[0]->setPair( 0,0 ); |
1344 | > | info[l].globalExcludes = new int; |
1345 | > | info[l].globalExcludes[0] = 0; |
1346 | > | info[l].n_exclude = 0; |
1347 | > | } |
1348 | > | |
1349 | > | // set the arrays into the SimInfo object |
1350 | > | |
1351 | > | info[l].atoms = the_atoms; |
1352 | > | info[l].molecules = the_molecules; |
1353 | > | info[l].nGlobalExcludes = 0; |
1354 | > | info[l].excludes = the_excludes; |
1355 | > | |
1356 | > | the_ff->setSimInfo( info ); |
1357 | > | |
1358 | } | |
1359 | + | } |
1360 | ||
1361 | < | // set the arrays into the SimInfo object |
1361 | > | void SimSetup::makeIntegrator( void ){ |
1362 | ||
1363 | < | info->atoms = the_atoms; |
1472 | < | info->molecules = the_molecules; |
1473 | < | info->nGlobalExcludes = 0; |
1474 | < | info->excludes = the_excludes; |
1363 | > | int k; |
1364 | ||
1365 | < | the_ff->setSimInfo( info ); |
1365 | > | NVT<RealIntegrator>* myNVT = NULL; |
1366 | > | NPTi<RealIntegrator>* myNPTi = NULL; |
1367 | > | NPTf<RealIntegrator>* myNPTf = NULL; |
1368 | > | NPTim<RealIntegrator>* myNPTim = NULL; |
1369 | > | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1370 | > | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1371 | > | ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1372 | > | ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1373 | > | ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1374 | > | ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1375 | > | ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1376 | > | |
1377 | > | for(k=0; k<nInfo; k++){ |
1378 | > | |
1379 | > | switch( ensembleCase ){ |
1380 | > | |
1381 | > | case NVE_ENS: |
1382 | > | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1383 | > | break; |
1384 | > | |
1385 | > | case NVT_ENS: |
1386 | > | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1387 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1388 | > | |
1389 | > | if (globals->haveTauThermostat()) |
1390 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1391 | > | |
1392 | > | else { |
1393 | > | sprintf( painCave.errMsg, |
1394 | > | "SimSetup error: If you use the NVT\n" |
1395 | > | " ensemble, you must set tauThermostat.\n"); |
1396 | > | painCave.isFatal = 1; |
1397 | > | simError(); |
1398 | > | } |
1399 | > | break; |
1400 | > | |
1401 | > | case NPTi_ENS: |
1402 | > | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1403 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 | > | |
1405 | > | if (globals->haveTargetPressure()) |
1406 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 | > | else { |
1408 | > | sprintf( painCave.errMsg, |
1409 | > | "SimSetup error: If you use a constant pressure\n" |
1410 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1411 | > | painCave.isFatal = 1; |
1412 | > | simError(); |
1413 | > | } |
1414 | > | |
1415 | > | if( globals->haveTauThermostat() ) |
1416 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 | > | else{ |
1418 | > | sprintf( painCave.errMsg, |
1419 | > | "SimSetup error: If you use an NPT\n" |
1420 | > | " ensemble, you must set tauThermostat.\n"); |
1421 | > | painCave.isFatal = 1; |
1422 | > | simError(); |
1423 | > | } |
1424 | > | |
1425 | > | if( globals->haveTauBarostat() ) |
1426 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 | > | else{ |
1428 | > | sprintf( painCave.errMsg, |
1429 | > | "SimSetup error: If you use an NPT\n" |
1430 | > | " ensemble, you must set tauBarostat.\n"); |
1431 | > | painCave.isFatal = 1; |
1432 | > | simError(); |
1433 | > | } |
1434 | > | break; |
1435 | > | |
1436 | > | case NPTf_ENS: |
1437 | > | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1438 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1439 | > | |
1440 | > | if (globals->haveTargetPressure()) |
1441 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1442 | > | else { |
1443 | > | sprintf( painCave.errMsg, |
1444 | > | "SimSetup error: If you use a constant pressure\n" |
1445 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1446 | > | painCave.isFatal = 1; |
1447 | > | simError(); |
1448 | > | } |
1449 | > | |
1450 | > | if( globals->haveTauThermostat() ) |
1451 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1452 | > | else{ |
1453 | > | sprintf( painCave.errMsg, |
1454 | > | "SimSetup error: If you use an NPT\n" |
1455 | > | " ensemble, you must set tauThermostat.\n"); |
1456 | > | painCave.isFatal = 1; |
1457 | > | simError(); |
1458 | > | } |
1459 | > | |
1460 | > | if( globals->haveTauBarostat() ) |
1461 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1462 | > | else{ |
1463 | > | sprintf( painCave.errMsg, |
1464 | > | "SimSetup error: If you use an NPT\n" |
1465 | > | " ensemble, you must set tauBarostat.\n"); |
1466 | > | painCave.isFatal = 1; |
1467 | > | simError(); |
1468 | > | } |
1469 | > | break; |
1470 | > | |
1471 | > | case NPTim_ENS: |
1472 | > | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1473 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1474 | > | |
1475 | > | if (globals->haveTargetPressure()) |
1476 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1477 | > | else { |
1478 | > | sprintf( painCave.errMsg, |
1479 | > | "SimSetup error: If you use a constant pressure\n" |
1480 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1481 | > | painCave.isFatal = 1; |
1482 | > | simError(); |
1483 | > | } |
1484 | > | |
1485 | > | if( globals->haveTauThermostat() ) |
1486 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1487 | > | else{ |
1488 | > | sprintf( painCave.errMsg, |
1489 | > | "SimSetup error: If you use an NPT\n" |
1490 | > | " ensemble, you must set tauThermostat.\n"); |
1491 | > | painCave.isFatal = 1; |
1492 | > | simError(); |
1493 | > | } |
1494 | > | |
1495 | > | if( globals->haveTauBarostat() ) |
1496 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1497 | > | else{ |
1498 | > | sprintf( painCave.errMsg, |
1499 | > | "SimSetup error: If you use an NPT\n" |
1500 | > | " ensemble, you must set tauBarostat.\n"); |
1501 | > | painCave.isFatal = 1; |
1502 | > | simError(); |
1503 | > | } |
1504 | > | break; |
1505 | > | |
1506 | > | case NPTfm_ENS: |
1507 | > | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1508 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1509 | > | |
1510 | > | if (globals->haveTargetPressure()) |
1511 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1512 | > | else { |
1513 | > | sprintf( painCave.errMsg, |
1514 | > | "SimSetup error: If you use a constant pressure\n" |
1515 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1516 | > | painCave.isFatal = 1; |
1517 | > | simError(); |
1518 | > | } |
1519 | > | |
1520 | > | if( globals->haveTauThermostat() ) |
1521 | > | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1522 | > | else{ |
1523 | > | sprintf( painCave.errMsg, |
1524 | > | "SimSetup error: If you use an NPT\n" |
1525 | > | " ensemble, you must set tauThermostat.\n"); |
1526 | > | painCave.isFatal = 1; |
1527 | > | simError(); |
1528 | > | } |
1529 | > | |
1530 | > | if( globals->haveTauBarostat() ) |
1531 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1532 | > | else{ |
1533 | > | sprintf( painCave.errMsg, |
1534 | > | "SimSetup error: If you use an NPT\n" |
1535 | > | " ensemble, you must set tauBarostat.\n"); |
1536 | > | painCave.isFatal = 1; |
1537 | > | simError(); |
1538 | > | } |
1539 | > | break; |
1540 | > | |
1541 | > | case NVEZCONS_ENS: |
1542 | > | |
1543 | > | |
1544 | > | //setup index of z-constraint molecules, z-constraint sampel time |
1545 | > | //and z-constraint force output name. These parameter should be known |
1546 | > | //before constructing the z-constraint integrator |
1547 | > | setupZConstraint(); |
1548 | > | |
1549 | > | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1550 | > | |
1551 | > | break; |
1552 | > | |
1553 | > | |
1554 | > | case NVTZCONS_ENS: |
1555 | > | |
1556 | > | setupZConstraint(); |
1557 | > | |
1558 | > | myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1559 | > | myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1560 | > | |
1561 | > | if (globals->haveTauThermostat()) |
1562 | > | myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1563 | > | |
1564 | > | else { |
1565 | > | sprintf( painCave.errMsg, |
1566 | > | "SimSetup error: If you use the NVT\n" |
1567 | > | " ensemble, you must set tauThermostat.\n"); |
1568 | > | painCave.isFatal = 1; |
1569 | > | simError(); |
1570 | > | } |
1571 | > | break; |
1572 | > | |
1573 | > | case NPTiZCONS_ENS: |
1574 | > | |
1575 | > | setupZConstraint(); |
1576 | > | |
1577 | > | myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1578 | > | myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1579 | > | |
1580 | > | if (globals->haveTargetPressure()) |
1581 | > | myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1582 | > | else { |
1583 | > | sprintf( painCave.errMsg, |
1584 | > | "SimSetup error: If you use a constant pressure\n" |
1585 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1586 | > | painCave.isFatal = 1; |
1587 | > | simError(); |
1588 | > | } |
1589 | > | |
1590 | > | if( globals->haveTauThermostat() ) |
1591 | > | myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1592 | > | else{ |
1593 | > | sprintf( painCave.errMsg, |
1594 | > | "SimSetup error: If you use an NPT\n" |
1595 | > | " ensemble, you must set tauThermostat.\n"); |
1596 | > | painCave.isFatal = 1; |
1597 | > | simError(); |
1598 | > | } |
1599 | > | |
1600 | > | if( globals->haveTauBarostat() ) |
1601 | > | myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1602 | > | else{ |
1603 | > | sprintf( painCave.errMsg, |
1604 | > | "SimSetup error: If you use an NPT\n" |
1605 | > | " ensemble, you must set tauBarostat.\n"); |
1606 | > | painCave.isFatal = 1; |
1607 | > | simError(); |
1608 | > | } |
1609 | > | |
1610 | > | break; |
1611 | > | |
1612 | > | case NPTfZCONS_ENS: |
1613 | > | |
1614 | > | setupZConstraint(); |
1615 | > | |
1616 | > | myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1617 | > | myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1618 | > | |
1619 | > | if (globals->haveTargetPressure()) |
1620 | > | myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1621 | > | else { |
1622 | > | sprintf( painCave.errMsg, |
1623 | > | "SimSetup error: If you use a constant pressure\n" |
1624 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1625 | > | painCave.isFatal = 1; |
1626 | > | simError(); |
1627 | > | } |
1628 | > | |
1629 | > | if( globals->haveTauThermostat() ) |
1630 | > | myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1631 | > | else{ |
1632 | > | sprintf( painCave.errMsg, |
1633 | > | "SimSetup error: If you use an NPT\n" |
1634 | > | " ensemble, you must set tauThermostat.\n"); |
1635 | > | painCave.isFatal = 1; |
1636 | > | simError(); |
1637 | > | } |
1638 | > | |
1639 | > | if( globals->haveTauBarostat() ) |
1640 | > | myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1641 | > | else{ |
1642 | > | sprintf( painCave.errMsg, |
1643 | > | "SimSetup error: If you use an NPT\n" |
1644 | > | " ensemble, you must set tauBarostat.\n"); |
1645 | > | painCave.isFatal = 1; |
1646 | > | simError(); |
1647 | > | } |
1648 | > | |
1649 | > | break; |
1650 | > | |
1651 | > | case NPTimZCONS_ENS: |
1652 | > | |
1653 | > | setupZConstraint(); |
1654 | > | |
1655 | > | myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1656 | > | myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1657 | > | |
1658 | > | if (globals->haveTargetPressure()) |
1659 | > | myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1660 | > | else { |
1661 | > | sprintf( painCave.errMsg, |
1662 | > | "SimSetup error: If you use a constant pressure\n" |
1663 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1664 | > | painCave.isFatal = 1; |
1665 | > | simError(); |
1666 | > | } |
1667 | > | |
1668 | > | if( globals->haveTauThermostat() ) |
1669 | > | myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1670 | > | else{ |
1671 | > | sprintf( painCave.errMsg, |
1672 | > | "SimSetup error: If you use an NPT\n" |
1673 | > | " ensemble, you must set tauThermostat.\n"); |
1674 | > | painCave.isFatal = 1; |
1675 | > | simError(); |
1676 | > | } |
1677 | > | |
1678 | > | if( globals->haveTauBarostat() ) |
1679 | > | myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1680 | > | else{ |
1681 | > | sprintf( painCave.errMsg, |
1682 | > | "SimSetup error: If you use an NPT\n" |
1683 | > | " ensemble, you must set tauBarostat.\n"); |
1684 | > | painCave.isFatal = 1; |
1685 | > | simError(); |
1686 | > | } |
1687 | > | |
1688 | > | break; |
1689 | > | |
1690 | > | case NPTfmZCONS_ENS: |
1691 | > | |
1692 | > | setupZConstraint(); |
1693 | > | |
1694 | > | myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1695 | > | myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1696 | > | |
1697 | > | if (globals->haveTargetPressure()) |
1698 | > | myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1699 | > | else { |
1700 | > | sprintf( painCave.errMsg, |
1701 | > | "SimSetup error: If you use a constant pressure\n" |
1702 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1703 | > | painCave.isFatal = 1; |
1704 | > | simError(); |
1705 | > | } |
1706 | > | |
1707 | > | if( globals->haveTauThermostat() ) |
1708 | > | myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1709 | > | else{ |
1710 | > | sprintf( painCave.errMsg, |
1711 | > | "SimSetup error: If you use an NPT\n" |
1712 | > | " ensemble, you must set tauThermostat.\n"); |
1713 | > | painCave.isFatal = 1; |
1714 | > | simError(); |
1715 | > | } |
1716 | > | |
1717 | > | if( globals->haveTauBarostat() ) |
1718 | > | myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1719 | > | else{ |
1720 | > | sprintf( painCave.errMsg, |
1721 | > | "SimSetup error: If you use an NPT\n" |
1722 | > | " ensemble, you must set tauBarostat.\n"); |
1723 | > | painCave.isFatal = 1; |
1724 | > | simError(); |
1725 | > | } |
1726 | > | break; |
1727 | > | |
1728 | > | |
1729 | > | |
1730 | > | default: |
1731 | > | sprintf( painCave.errMsg, |
1732 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1733 | > | painCave.isFatal = 1; |
1734 | > | simError(); |
1735 | > | } |
1736 | > | } |
1737 | > | } |
1738 | ||
1739 | + | void SimSetup::initFortran( void ){ |
1740 | + | |
1741 | + | info[0].refreshSim(); |
1742 | + | |
1743 | + | if( !strcmp( info[0].mixingRule, "standard") ){ |
1744 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1745 | + | } |
1746 | + | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1747 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1748 | + | } |
1749 | + | else{ |
1750 | + | sprintf( painCave.errMsg, |
1751 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1752 | + | info[0].mixingRule ); |
1753 | + | painCave.isFatal = 1; |
1754 | + | simError(); |
1755 | + | } |
1756 | + | |
1757 | + | |
1758 | + | #ifdef IS_MPI |
1759 | + | strcpy( checkPointMsg, |
1760 | + | "Successfully intialized the mixingRule for Fortran." ); |
1761 | + | MPIcheckPoint(); |
1762 | + | #endif // is_mpi |
1763 | + | |
1764 | } | |
1765 | + | |
1766 | + | void SimSetup::setupZConstraint() |
1767 | + | { |
1768 | + | int k; |
1769 | + | |
1770 | + | for(k=0; k<nInfo; k++){ |
1771 | + | |
1772 | + | if(globals->haveZConsTime()){ |
1773 | + | |
1774 | + | //add sample time of z-constraint into SimInfo's property list |
1775 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1776 | + | zconsTimeProp->setID("zconstime"); |
1777 | + | zconsTimeProp->setData(globals->getZConsTime()); |
1778 | + | info[k].addProperty(zconsTimeProp); |
1779 | + | } |
1780 | + | else{ |
1781 | + | sprintf( painCave.errMsg, |
1782 | + | "ZConstraint error: If you use an ZConstraint\n" |
1783 | + | " , you must set sample time.\n"); |
1784 | + | painCave.isFatal = 1; |
1785 | + | simError(); |
1786 | + | } |
1787 | + | |
1788 | + | if(globals->haveIndexOfAllZConsMols()){ |
1789 | + | |
1790 | + | //add index of z-constraint molecules into SimInfo's property list |
1791 | + | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1792 | + | |
1793 | + | //sort the index |
1794 | + | sort(tempIndex.begin(), tempIndex.end()); |
1795 | + | |
1796 | + | IndexData* zconsIndex = new IndexData(); |
1797 | + | zconsIndex->setID("zconsindex"); |
1798 | + | zconsIndex->setIndexData(tempIndex); |
1799 | + | info[k].addProperty(zconsIndex); |
1800 | + | } |
1801 | + | else{ |
1802 | + | sprintf( painCave.errMsg, |
1803 | + | "SimSetup error: If you use an ZConstraint\n" |
1804 | + | " , you must set index of z-constraint molecules.\n"); |
1805 | + | painCave.isFatal = 1; |
1806 | + | simError(); |
1807 | + | |
1808 | + | } |
1809 | + | |
1810 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1811 | + | //Be careful, do not use inFileName, since it is a pointer which |
1812 | + | //point to a string at master node, and slave nodes do not contain that string |
1813 | + | |
1814 | + | string zconsOutput(info[k].finalName); |
1815 | + | |
1816 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1817 | + | |
1818 | + | StringData* zconsFilename = new StringData(); |
1819 | + | zconsFilename->setID("zconsfilename"); |
1820 | + | zconsFilename->setData(zconsOutput); |
1821 | + | |
1822 | + | info[k].addProperty(zconsFilename); |
1823 | + | } |
1824 | + | } |
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