# | Line 5 | Line 5 | |
---|---|---|
5 | #include <string> | |
6 | ||
7 | #include "SimSetup.hpp" | |
8 | + | #include "ReadWrite.hpp" |
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
# | Line 16 | Line 17 | |
17 | ||
18 | // some defines for ensemble and Forcefield cases | |
19 | ||
20 | < | #define NVE_ENS 0 |
21 | < | #define NVT_ENS 1 |
22 | < | #define NPTi_ENS 2 |
23 | < | #define NPTf_ENS 3 |
24 | < | #define NPTim_ENS 4 |
25 | < | #define NPTfm_ENS 5 |
25 | < | #define NVEZCONS_ENS 6 |
20 | > | #define NVE_ENS 0 |
21 | > | #define NVT_ENS 1 |
22 | > | #define NPTi_ENS 2 |
23 | > | #define NPTf_ENS 3 |
24 | > | #define NPTim_ENS 4 |
25 | > | #define NPTfm_ENS 5 |
26 | ||
27 | – | |
27 | #define FF_DUFF 0 | |
28 | #define FF_LJ 1 | |
29 | #define FF_EAM 2 | |
# | Line 55 | Line 54 | void SimSetup::setSimInfo( SimInfo* the_info, int theN | |
54 | info = the_info; | |
55 | nInfo = theNinfo; | |
56 | isInfoArray = 1; | |
57 | < | } |
57 | > | } |
58 | ||
59 | ||
60 | void SimSetup::parseFile( char* fileName ){ | |
# | Line 93 | Line 92 | void SimSetup::receiveParse(void){ | |
92 | ||
93 | #endif // is_mpi | |
94 | ||
95 | < | void SimSetup::createSim( void ){ |
95 | > | void SimSetup::createSim(void){ |
96 | ||
97 | int i, j, k, globalAtomIndex; | |
98 | ||
99 | // gather all of the information from the Bass file | |
100 | < | |
100 | > | |
101 | > | std::cerr << "gathering info\n"; |
102 | > | |
103 | gatherInfo(); | |
104 | ||
105 | // creation of complex system objects | |
106 | ||
107 | + | std::cerr << "creating system objects\n"; |
108 | + | |
109 | sysObjectsCreation(); | |
110 | ||
111 | // check on the post processing info | |
112 | ||
113 | + | std::cerr << "performing final info check.\n"; |
114 | + | |
115 | finalInfoCheck(); | |
116 | ||
117 | // initialize the system coordinates | |
118 | ||
119 | < | initSystemCoords(); |
115 | < | |
119 | > | std::cerr << "about to init coords\n"; |
120 | ||
121 | + | if( !isInfoArray ) initSystemCoords(); |
122 | + | |
123 | // make the output filenames | |
124 | ||
125 | makeOutNames(); | |
# | Line 137 | Line 143 | void SimSetup::makeMolecules( void ){ | |
143 | ||
144 | void SimSetup::makeMolecules( void ){ | |
145 | ||
146 | + | int k,l; |
147 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
148 | molInit molInfo; | |
149 | DirectionalAtom* dAtom; | |
# | Line 161 | Line 168 | void SimSetup::makeMolecules( void ){ | |
168 | ||
169 | double ux, uy, uz, u, uSqr; | |
170 | ||
171 | < | atomOffset = 0; |
165 | < | excludeOffset = 0; |
166 | < | for(i=0; i<info->n_mol; i++){ |
171 | > | for(k=0; k<nInfo; k++){ |
172 | ||
173 | < | stampID = the_molecules[i].getStampID(); |
173 | > | the_ff->setSimInfo( &(info[k]) ); |
174 | ||
175 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
176 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
177 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
178 | < | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
179 | < | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
175 | > | atomOffset = 0; |
176 | > | excludeOffset = 0; |
177 | > | for(i=0; i<info[k].n_mol; i++){ |
178 | > | |
179 | > | stampID = info[k].molecules[i].getStampID(); |
180 | ||
181 | < | molInfo.myAtoms = &the_atoms[atomOffset]; |
182 | < | molInfo.myExcludes = &the_excludes[excludeOffset]; |
183 | < | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
184 | < | molInfo.myBends = new Bend*[molInfo.nBends]; |
185 | < | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
181 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
182 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
183 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
184 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
185 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
186 | > | |
187 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
188 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
189 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
190 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
191 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
192 | ||
193 | < | theBonds = new bond_pair[molInfo.nBonds]; |
194 | < | theBends = new bend_set[molInfo.nBends]; |
195 | < | theTorsions = new torsion_set[molInfo.nTorsions]; |
193 | > | theBonds = new bond_pair[molInfo.nBonds]; |
194 | > | theBends = new bend_set[molInfo.nBends]; |
195 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
196 | ||
197 | < | // make the Atoms |
197 | > | // make the Atoms |
198 | ||
199 | < | for(j=0; j<molInfo.nAtoms; j++){ |
189 | < | |
190 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
191 | < | if( currentAtom->haveOrientation() ){ |
199 | > | for(j=0; j<molInfo.nAtoms; j++){ |
200 | ||
201 | < | dAtom = new DirectionalAtom(j + atomOffset); |
202 | < | info->n_oriented++; |
203 | < | molInfo.myAtoms[j] = dAtom; |
204 | < | |
205 | < | ux = currentAtom->getOrntX(); |
206 | < | uy = currentAtom->getOrntY(); |
207 | < | uz = currentAtom->getOrntZ(); |
208 | < | |
209 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
210 | < | |
211 | < | u = sqrt( uSqr ); |
212 | < | ux = ux / u; |
213 | < | uy = uy / u; |
214 | < | uz = uz / u; |
215 | < | |
216 | < | dAtom->setSUx( ux ); |
217 | < | dAtom->setSUy( uy ); |
218 | < | dAtom->setSUz( uz ); |
219 | < | } |
220 | < | else{ |
221 | < | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
222 | < | } |
223 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
201 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
202 | > | if( currentAtom->haveOrientation() ){ |
203 | > | |
204 | > | dAtom = new DirectionalAtom( (j + atomOffset), |
205 | > | info[k].getConfiguration() ); |
206 | > | info[k].n_oriented++; |
207 | > | molInfo.myAtoms[j] = dAtom; |
208 | > | |
209 | > | ux = currentAtom->getOrntX(); |
210 | > | uy = currentAtom->getOrntY(); |
211 | > | uz = currentAtom->getOrntZ(); |
212 | > | |
213 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
214 | > | |
215 | > | u = sqrt( uSqr ); |
216 | > | ux = ux / u; |
217 | > | uy = uy / u; |
218 | > | uz = uz / u; |
219 | > | |
220 | > | dAtom->setSUx( ux ); |
221 | > | dAtom->setSUy( uy ); |
222 | > | dAtom->setSUz( uz ); |
223 | > | } |
224 | > | else{ |
225 | > | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
226 | > | info[k].getConfiguration() ); |
227 | > | } |
228 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
229 | ||
230 | #ifdef IS_MPI | |
231 | ||
232 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
232 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
233 | ||
234 | #endif // is_mpi | |
235 | < | } |
235 | > | } |
236 | ||
237 | // make the bonds | |
238 | < | for(j=0; j<molInfo.nBonds; j++){ |
238 | > | for(j=0; j<molInfo.nBonds; j++){ |
239 | ||
240 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
241 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
242 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
243 | < | |
244 | < | exI = theBonds[j].a; |
245 | < | exJ = theBonds[j].b; |
246 | < | |
247 | < | // exclude_I must always be the smaller of the pair |
248 | < | if( exI > exJ ){ |
249 | < | tempEx = exI; |
250 | < | exI = exJ; |
251 | < | exJ = tempEx; |
252 | < | } |
240 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
241 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
242 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
243 | > | |
244 | > | exI = theBonds[j].a; |
245 | > | exJ = theBonds[j].b; |
246 | > | |
247 | > | // exclude_I must always be the smaller of the pair |
248 | > | if( exI > exJ ){ |
249 | > | tempEx = exI; |
250 | > | exI = exJ; |
251 | > | exJ = tempEx; |
252 | > | } |
253 | #ifdef IS_MPI | |
254 | < | tempEx = exI; |
255 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
256 | < | tempEx = exJ; |
257 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
258 | < | |
259 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
254 | > | tempEx = exI; |
255 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
256 | > | tempEx = exJ; |
257 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
258 | > | |
259 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
260 | #else // isn't MPI | |
261 | < | |
262 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
261 | > | |
262 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
263 | #endif //is_mpi | |
264 | < | } |
265 | < | excludeOffset += molInfo.nBonds; |
253 | < | |
254 | < | //make the bends |
255 | < | for(j=0; j<molInfo.nBends; j++){ |
264 | > | } |
265 | > | excludeOffset += molInfo.nBonds; |
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; |
267 | > | //make the bends |
268 | > | for(j=0; j<molInfo.nBends; j++){ |
269 | > | |
270 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
271 | > | theBends[j].a = currentBend->getA() + atomOffset; |
272 | > | theBends[j].b = currentBend->getB() + atomOffset; |
273 | > | theBends[j].c = currentBend->getC() + atomOffset; |
274 | > | |
275 | > | if( currentBend->haveExtras() ){ |
276 | ||
277 | < | if( currentBend->haveExtras() ){ |
278 | < | |
279 | < | extras = currentBend->getExtras(); |
280 | < | current_extra = extras; |
281 | < | |
267 | < | while( current_extra != NULL ){ |
268 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
269 | < | |
270 | < | switch( current_extra->getType() ){ |
277 | > | extras = currentBend->getExtras(); |
278 | > | current_extra = extras; |
279 | > | |
280 | > | while( current_extra != NULL ){ |
281 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
282 | ||
283 | < | case 0: |
284 | < | theBends[j].ghost = |
285 | < | current_extra->getInt() + atomOffset; |
286 | < | theBends[j].isGhost = 1; |
287 | < | break; |
288 | < | |
289 | < | case 1: |
290 | < | theBends[j].ghost = |
291 | < | (int)current_extra->getDouble() + atomOffset; |
292 | < | theBends[j].isGhost = 1; |
293 | < | break; |
294 | < | |
295 | < | default: |
283 | > | switch( current_extra->getType() ){ |
284 | > | |
285 | > | case 0: |
286 | > | theBends[j].ghost = |
287 | > | current_extra->getInt() + atomOffset; |
288 | > | theBends[j].isGhost = 1; |
289 | > | break; |
290 | > | |
291 | > | case 1: |
292 | > | theBends[j].ghost = |
293 | > | (int)current_extra->getDouble() + atomOffset; |
294 | > | theBends[j].isGhost = 1; |
295 | > | break; |
296 | > | |
297 | > | default: |
298 | > | sprintf( painCave.errMsg, |
299 | > | "SimSetup Error: ghostVectorSource was neither a " |
300 | > | "double nor an int.\n" |
301 | > | "-->Bend[%d] in %s\n", |
302 | > | j, comp_stamps[stampID]->getID() ); |
303 | > | painCave.isFatal = 1; |
304 | > | simError(); |
305 | > | } |
306 | > | } |
307 | > | |
308 | > | else{ |
309 | > | |
310 | sprintf( painCave.errMsg, | |
311 | < | "SimSetup Error: ghostVectorSource was neither a " |
312 | < | "double nor an int.\n" |
313 | < | "-->Bend[%d] in %s\n", |
311 | > | "SimSetup Error: unhandled bend assignment:\n" |
312 | > | " -->%s in Bend[%d] in %s\n", |
313 | > | current_extra->getlhs(), |
314 | j, comp_stamps[stampID]->getID() ); | |
315 | painCave.isFatal = 1; | |
316 | simError(); | |
317 | } | |
293 | – | } |
294 | – | |
295 | – | else{ |
318 | ||
319 | < | sprintf( painCave.errMsg, |
298 | < | "SimSetup Error: unhandled bend assignment:\n" |
299 | < | " -->%s in Bend[%d] in %s\n", |
300 | < | current_extra->getlhs(), |
301 | < | j, comp_stamps[stampID]->getID() ); |
302 | < | painCave.isFatal = 1; |
303 | < | simError(); |
319 | > | current_extra = current_extra->getNext(); |
320 | } | |
321 | + | } |
322 | + | |
323 | + | if( !theBends[j].isGhost ){ |
324 | ||
325 | < | current_extra = current_extra->getNext(); |
325 | > | exI = theBends[j].a; |
326 | > | exJ = theBends[j].c; |
327 | } | |
328 | < | } |
328 | > | else{ |
329 | ||
330 | < | if( !theBends[j].isGhost ){ |
331 | < | |
332 | < | exI = theBends[j].a; |
313 | < | exJ = theBends[j].c; |
314 | < | } |
315 | < | else{ |
330 | > | exI = theBends[j].a; |
331 | > | exJ = theBends[j].b; |
332 | > | } |
333 | ||
334 | < | exI = theBends[j].a; |
335 | < | exJ = theBends[j].b; |
336 | < | } |
337 | < | |
338 | < | // exclude_I must always be the smaller of the pair |
339 | < | if( exI > exJ ){ |
323 | < | tempEx = exI; |
324 | < | exI = exJ; |
325 | < | exJ = tempEx; |
326 | < | } |
334 | > | // exclude_I must always be the smaller of the pair |
335 | > | if( exI > exJ ){ |
336 | > | tempEx = exI; |
337 | > | exI = exJ; |
338 | > | exJ = tempEx; |
339 | > | } |
340 | #ifdef IS_MPI | |
341 | < | tempEx = exI; |
342 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 | < | tempEx = exJ; |
344 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
341 | > | tempEx = exI; |
342 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
343 | > | tempEx = exJ; |
344 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 | ||
346 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
346 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 | #else // isn't MPI | |
348 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
348 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 | #endif //is_mpi | |
337 | – | } |
338 | – | excludeOffset += molInfo.nBends; |
339 | – | |
340 | – | for(j=0; j<molInfo.nTorsions; j++){ |
341 | – | |
342 | – | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
343 | – | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
344 | – | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
345 | – | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
346 | – | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
347 | – | |
348 | – | exI = theTorsions[j].a; |
349 | – | exJ = theTorsions[j].d; |
350 | – | |
351 | – | // exclude_I must always be the smaller of the pair |
352 | – | if( exI > exJ ){ |
353 | – | tempEx = exI; |
354 | – | exI = exJ; |
355 | – | exJ = tempEx; |
350 | } | |
351 | < | #ifdef IS_MPI |
358 | < | tempEx = exI; |
359 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
360 | < | tempEx = exJ; |
361 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
351 | > | excludeOffset += molInfo.nBends; |
352 | ||
353 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
353 | > | for(j=0; j<molInfo.nTorsions; j++){ |
354 | > | |
355 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
356 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
357 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
358 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
359 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
360 | > | |
361 | > | exI = theTorsions[j].a; |
362 | > | exJ = theTorsions[j].d; |
363 | > | |
364 | > | // exclude_I must always be the smaller of the pair |
365 | > | if( exI > exJ ){ |
366 | > | tempEx = exI; |
367 | > | exI = exJ; |
368 | > | exJ = tempEx; |
369 | > | } |
370 | > | #ifdef IS_MPI |
371 | > | tempEx = exI; |
372 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
373 | > | tempEx = exJ; |
374 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 | > | |
376 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
377 | #else // isn't MPI | |
378 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
378 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
379 | #endif //is_mpi | |
380 | < | } |
381 | < | excludeOffset += molInfo.nTorsions; |
380 | > | } |
381 | > | excludeOffset += molInfo.nTorsions; |
382 | > | |
383 | > | |
384 | > | // send the arrays off to the forceField for init. |
385 | > | |
386 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
387 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
388 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
389 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
390 | > | |
391 | > | |
392 | > | info[k].molecules[i].initialize( molInfo ); |
393 | ||
394 | < | |
395 | < | // send the arrays off to the forceField for init. |
396 | < | |
397 | < | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
398 | < | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
399 | < | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
376 | < | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
377 | < | |
378 | < | |
379 | < | the_molecules[i].initialize( molInfo ); |
380 | < | |
381 | < | |
382 | < | atomOffset += molInfo.nAtoms; |
383 | < | delete[] theBonds; |
384 | < | delete[] theBends; |
385 | < | delete[] theTorsions; |
394 | > | |
395 | > | atomOffset += molInfo.nAtoms; |
396 | > | delete[] theBonds; |
397 | > | delete[] theBends; |
398 | > | delete[] theTorsions; |
399 | > | } |
400 | } | |
401 | < | |
401 | > | |
402 | #ifdef IS_MPI | |
403 | sprintf( checkPointMsg, "all molecules initialized succesfully" ); | |
404 | MPIcheckPoint(); | |
405 | #endif // is_mpi | |
406 | < | |
406 | > | |
407 | // clean up the forcefield | |
408 | + | |
409 | the_ff->calcRcut(); | |
410 | the_ff->cleanMe(); | |
411 | < | |
411 | > | |
412 | } | |
413 | ||
414 | void SimSetup::initFromBass( void ){ | |
# | Line 406 | Line 421 | void SimSetup::initFromBass( void ){ | |
421 | int n_extra; | |
422 | int have_extra, done; | |
423 | ||
424 | + | double vel[3]; |
425 | + | vel[0] = 0.0; |
426 | + | vel[1] = 0.0; |
427 | + | vel[2] = 0.0; |
428 | + | |
429 | temp1 = (double)tot_nmol / 4.0; | |
430 | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); | |
431 | temp3 = ceil( temp2 ); | |
# | Line 415 | Line 435 | void SimSetup::initFromBass( void ){ | |
435 | have_extra =1; | |
436 | ||
437 | n_cells = (int)temp3 - 1; | |
438 | < | cellx = info->boxL[0] / temp3; |
439 | < | celly = info->boxL[1] / temp3; |
440 | < | cellz = info->boxL[2] / temp3; |
438 | > | cellx = info[0].boxL[0] / temp3; |
439 | > | celly = info[0].boxL[1] / temp3; |
440 | > | cellz = info[0].boxL[2] / temp3; |
441 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
442 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
443 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 432 | Line 452 | void SimSetup::initFromBass( void ){ | |
452 | } | |
453 | else{ | |
454 | n_cells = (int)temp3; | |
455 | < | cellx = info->boxL[0] / temp3; |
456 | < | celly = info->boxL[1] / temp3; |
457 | < | cellz = info->boxL[2] / temp3; |
455 | > | cellx = info[0].boxL[0] / temp3; |
456 | > | celly = info[0].boxL[1] / temp3; |
457 | > | cellz = info[0].boxL[2] / temp3; |
458 | } | |
459 | ||
460 | current_mol = 0; | |
# | Line 513 | Line 533 | void SimSetup::initFromBass( void ){ | |
533 | } | |
534 | } | |
535 | ||
536 | < | |
537 | < | for( i=0; i<info->n_atoms; i++ ){ |
518 | < | info->atoms[i]->set_vx( 0.0 ); |
519 | < | info->atoms[i]->set_vy( 0.0 ); |
520 | < | info->atoms[i]->set_vz( 0.0 ); |
536 | > | for( i=0; i<info[0].n_atoms; i++ ){ |
537 | > | info[0].atoms[i]->setVel( vel ); |
538 | } | |
539 | } | |
540 | ||
# | Line 527 | Line 544 | void SimSetup::makeElement( double x, double y, double | |
544 | AtomStamp* current_atom; | |
545 | DirectionalAtom* dAtom; | |
546 | double rotMat[3][3]; | |
547 | + | double pos[3]; |
548 | ||
549 | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ | |
550 | ||
# | Line 542 | Line 560 | void SimSetup::makeElement( double x, double y, double | |
560 | painCave.isFatal = 1; | |
561 | simError(); | |
562 | } | |
563 | + | |
564 | + | pos[0] = x + current_atom->getPosX(); |
565 | + | pos[1] = y + current_atom->getPosY(); |
566 | + | pos[2] = z + current_atom->getPosZ(); |
567 | + | |
568 | + | info[0].atoms[current_atom_ndx]->setPos( pos ); |
569 | ||
570 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
547 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
548 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
570 | > | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
571 | ||
572 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
572 | > | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
573 | ||
552 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
553 | – | |
574 | rotMat[0][0] = 1.0; | |
575 | rotMat[0][1] = 0.0; | |
576 | rotMat[0][2] = 0.0; | |
# | Line 586 | Line 606 | void SimSetup::gatherInfo( void ){ | |
606 | ensembleCase = -1; | |
607 | ffCase = -1; | |
608 | ||
589 | – | // get the stamps and globals; |
590 | – | stamps = stamps; |
591 | – | globals = globals; |
592 | – | |
609 | // set the easy ones first | |
610 | < | info->target_temp = globals->getTargetTemp(); |
611 | < | info->dt = globals->getDt(); |
612 | < | info->run_time = globals->getRunTime(); |
610 | > | |
611 | > | for( i=0; i<nInfo; i++){ |
612 | > | info[i].target_temp = globals->getTargetTemp(); |
613 | > | info[i].dt = globals->getDt(); |
614 | > | info[i].run_time = globals->getRunTime(); |
615 | > | } |
616 | n_components = globals->getNComponents(); | |
617 | ||
618 | ||
# | Line 623 | Line 642 | void SimSetup::gatherInfo( void ){ | |
642 | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; | |
643 | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; | |
644 | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; | |
626 | – | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
645 | else{ | |
646 | sprintf( painCave.errMsg, | |
647 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 634 | Line 652 | void SimSetup::gatherInfo( void ){ | |
652 | strcpy( ensemble, "NVE" ); | |
653 | ensembleCase = NVE_ENS; | |
654 | } | |
655 | < | strcpy( info->ensemble, ensemble ); |
655 | > | |
656 | > | for(i=0; i<nInfo; i++){ |
657 | > | |
658 | > | strcpy( info[i].ensemble, ensemble ); |
659 | ||
660 | < | // get the mixing rule |
660 | > | // get the mixing rule |
661 | ||
662 | < | strcpy( info->mixingRule, globals->getMixingRule() ); |
663 | < | info->usePBC = globals->getPBC(); |
664 | < | |
662 | > | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
663 | > | info[i].usePBC = globals->getPBC(); |
664 | > | } |
665 | ||
666 | // get the components and calculate the tot_nMol and indvidual n_mol | |
667 | ||
# | Line 681 | Line 702 | void SimSetup::gatherInfo( void ){ | |
702 | ||
703 | // set the status, sample, and thermal kick times | |
704 | ||
705 | < | if( globals->haveSampleTime() ){ |
685 | < | info->sampleTime = globals->getSampleTime(); |
686 | < | info->statusTime = info->sampleTime; |
687 | < | info->thermalTime = info->sampleTime; |
688 | < | } |
689 | < | else{ |
690 | < | info->sampleTime = globals->getRunTime(); |
691 | < | info->statusTime = info->sampleTime; |
692 | < | info->thermalTime = info->sampleTime; |
693 | < | } |
705 | > | for(i=0; i<nInfo; i++){ |
706 | ||
707 | < | if( globals->haveStatusTime() ){ |
708 | < | info->statusTime = globals->getStatusTime(); |
709 | < | } |
710 | < | |
711 | < | if( globals->haveThermalTime() ){ |
712 | < | info->thermalTime = globals->getThermalTime(); |
713 | < | } |
714 | < | |
715 | < | // check for the temperature set flag |
716 | < | |
705 | < | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
706 | < | |
707 | < | // get some of the tricky things that may still be in the globals |
708 | < | |
709 | < | double boxVector[3]; |
710 | < | if( globals->haveBox() ){ |
711 | < | boxVector[0] = globals->getBox(); |
712 | < | boxVector[1] = globals->getBox(); |
713 | < | boxVector[2] = globals->getBox(); |
707 | > | if( globals->haveSampleTime() ){ |
708 | > | info[i].sampleTime = globals->getSampleTime(); |
709 | > | info[i].statusTime = info[i].sampleTime; |
710 | > | info[i].thermalTime = info[i].sampleTime; |
711 | > | } |
712 | > | else{ |
713 | > | info[i].sampleTime = globals->getRunTime(); |
714 | > | info[i].statusTime = info[i].sampleTime; |
715 | > | info[i].thermalTime = info[i].sampleTime; |
716 | > | } |
717 | ||
718 | < | info->setBox( boxVector ); |
719 | < | } |
717 | < | else if( globals->haveDensity() ){ |
718 | < | |
719 | < | double vol; |
720 | < | vol = (double)tot_nmol / globals->getDensity(); |
721 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
722 | < | boxVector[1] = boxVector[0]; |
723 | < | boxVector[2] = boxVector[0]; |
724 | < | |
725 | < | info->setBox( boxVector ); |
726 | < | } |
727 | < | else{ |
728 | < | if( !globals->haveBoxX() ){ |
729 | < | sprintf( painCave.errMsg, |
730 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
731 | < | painCave.isFatal = 1; |
732 | < | simError(); |
718 | > | if( globals->haveStatusTime() ){ |
719 | > | info[i].statusTime = globals->getStatusTime(); |
720 | } | |
721 | < | boxVector[0] = globals->getBoxX(); |
722 | < | |
723 | < | if( !globals->haveBoxY() ){ |
737 | < | sprintf( painCave.errMsg, |
738 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
739 | < | painCave.isFatal = 1; |
740 | < | simError(); |
721 | > | |
722 | > | if( globals->haveThermalTime() ){ |
723 | > | info[i].thermalTime = globals->getThermalTime(); |
724 | } | |
742 | – | boxVector[1] = globals->getBoxY(); |
725 | ||
726 | < | if( !globals->haveBoxZ() ){ |
745 | < | sprintf( painCave.errMsg, |
746 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
747 | < | painCave.isFatal = 1; |
748 | < | simError(); |
749 | < | } |
750 | < | boxVector[2] = globals->getBoxZ(); |
726 | > | // check for the temperature set flag |
727 | ||
728 | < | info->setBox( boxVector ); |
728 | > | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
729 | > | |
730 | > | // get some of the tricky things that may still be in the globals |
731 | > | |
732 | > | double boxVector[3]; |
733 | > | if( globals->haveBox() ){ |
734 | > | boxVector[0] = globals->getBox(); |
735 | > | boxVector[1] = globals->getBox(); |
736 | > | boxVector[2] = globals->getBox(); |
737 | > | |
738 | > | info[i].setBox( boxVector ); |
739 | > | } |
740 | > | else if( globals->haveDensity() ){ |
741 | > | |
742 | > | double vol; |
743 | > | vol = (double)tot_nmol / globals->getDensity(); |
744 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
745 | > | boxVector[1] = boxVector[0]; |
746 | > | boxVector[2] = boxVector[0]; |
747 | > | |
748 | > | info[i].setBox( boxVector ); |
749 | } | |
750 | + | else{ |
751 | + | if( !globals->haveBoxX() ){ |
752 | + | sprintf( painCave.errMsg, |
753 | + | "SimSetup error, no periodic BoxX size given.\n" ); |
754 | + | painCave.isFatal = 1; |
755 | + | simError(); |
756 | + | } |
757 | + | boxVector[0] = globals->getBoxX(); |
758 | + | |
759 | + | if( !globals->haveBoxY() ){ |
760 | + | sprintf( painCave.errMsg, |
761 | + | "SimSetup error, no periodic BoxY size given.\n" ); |
762 | + | painCave.isFatal = 1; |
763 | + | simError(); |
764 | + | } |
765 | + | boxVector[1] = globals->getBoxY(); |
766 | + | |
767 | + | if( !globals->haveBoxZ() ){ |
768 | + | sprintf( painCave.errMsg, |
769 | + | "SimSetup error, no periodic BoxZ size given.\n" ); |
770 | + | painCave.isFatal = 1; |
771 | + | simError(); |
772 | + | } |
773 | + | boxVector[2] = globals->getBoxZ(); |
774 | + | |
775 | + | info[i].setBox( boxVector ); |
776 | + | } |
777 | ||
778 | < | |
778 | > | } |
779 | ||
780 | #ifdef IS_MPI | |
781 | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); | |
# | Line 765 | Line 788 | void SimSetup::finalInfoCheck( void ){ | |
788 | void SimSetup::finalInfoCheck( void ){ | |
789 | int index; | |
790 | int usesDipoles; | |
791 | < | |
791 | > | int i; |
792 | ||
793 | < | // check electrostatic parameters |
794 | < | |
795 | < | index = 0; |
796 | < | usesDipoles = 0; |
797 | < | while( (index < info->n_atoms) && !usesDipoles ){ |
798 | < | usesDipoles = ((info->atoms)[index])->hasDipole(); |
799 | < | index++; |
800 | < | } |
801 | < | |
793 | > | for(i=0; i<nInfo; i++){ |
794 | > | // check electrostatic parameters |
795 | > | |
796 | > | index = 0; |
797 | > | usesDipoles = 0; |
798 | > | while( (index < info[i].n_atoms) && !usesDipoles ){ |
799 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
800 | > | index++; |
801 | > | } |
802 | > | |
803 | #ifdef IS_MPI | |
804 | < | int myUse = usesDipoles; |
805 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
804 | > | int myUse = usesDipoles; |
805 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
806 | #endif //is_mpi | |
783 | – | |
784 | – | double theEcr, theEst; |
785 | – | |
786 | – | if (globals->getUseRF() ) { |
787 | – | info->useReactionField = 1; |
807 | ||
808 | < | if( !globals->haveECR() ){ |
809 | < | sprintf( painCave.errMsg, |
810 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
811 | < | "box length for the electrostaticCutoffRadius.\n" |
793 | < | "I hope you have a very fast processor!\n"); |
794 | < | painCave.isFatal = 0; |
795 | < | simError(); |
796 | < | double smallest; |
797 | < | smallest = info->boxL[0]; |
798 | < | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
799 | < | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
800 | < | theEcr = 0.5 * smallest; |
801 | < | } else { |
802 | < | theEcr = globals->getECR(); |
803 | < | } |
804 | < | |
805 | < | if( !globals->haveEST() ){ |
806 | < | sprintf( painCave.errMsg, |
807 | < | "SimSetup Warning: using default value of 0.05 * the " |
808 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
809 | < | ); |
810 | < | painCave.isFatal = 0; |
811 | < | simError(); |
812 | < | theEst = 0.05 * theEcr; |
813 | < | } else { |
814 | < | theEst= globals->getEST(); |
815 | < | } |
816 | < | |
817 | < | info->setEcr( theEcr, theEst ); |
818 | < | |
819 | < | if(!globals->haveDielectric() ){ |
820 | < | sprintf( painCave.errMsg, |
821 | < | "SimSetup Error: You are trying to use Reaction Field without" |
822 | < | "setting a dielectric constant!\n" |
823 | < | ); |
824 | < | painCave.isFatal = 1; |
825 | < | simError(); |
826 | < | } |
827 | < | info->dielectric = globals->getDielectric(); |
828 | < | } |
829 | < | else { |
830 | < | if (usesDipoles) { |
808 | > | double theEcr, theEst; |
809 | > | |
810 | > | if (globals->getUseRF() ) { |
811 | > | info[i].useReactionField = 1; |
812 | ||
813 | if( !globals->haveECR() ){ | |
814 | sprintf( painCave.errMsg, | |
# | Line 837 | Line 818 | void SimSetup::finalInfoCheck( void ){ | |
818 | painCave.isFatal = 0; | |
819 | simError(); | |
820 | double smallest; | |
821 | < | smallest = info->boxL[0]; |
822 | < | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
823 | < | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
821 | > | smallest = info[i].boxL[0]; |
822 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
823 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
824 | theEcr = 0.5 * smallest; | |
825 | } else { | |
826 | theEcr = globals->getECR(); | |
# | Line 848 | Line 829 | void SimSetup::finalInfoCheck( void ){ | |
829 | if( !globals->haveEST() ){ | |
830 | sprintf( painCave.errMsg, | |
831 | "SimSetup Warning: using default value of 0.05 * the " | |
832 | < | "electrostaticCutoffRadius for the " |
852 | < | "electrostaticSkinThickness\n" |
832 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
833 | ); | |
834 | painCave.isFatal = 0; | |
835 | simError(); | |
# | Line 857 | Line 837 | void SimSetup::finalInfoCheck( void ){ | |
837 | } else { | |
838 | theEst= globals->getEST(); | |
839 | } | |
840 | + | |
841 | + | info[i].setEcr( theEcr, theEst ); |
842 | + | |
843 | + | if(!globals->haveDielectric() ){ |
844 | + | sprintf( painCave.errMsg, |
845 | + | "SimSetup Error: You are trying to use Reaction Field without" |
846 | + | "setting a dielectric constant!\n" |
847 | + | ); |
848 | + | painCave.isFatal = 1; |
849 | + | simError(); |
850 | + | } |
851 | + | info[i].dielectric = globals->getDielectric(); |
852 | + | } |
853 | + | else { |
854 | + | if (usesDipoles) { |
855 | + | |
856 | + | if( !globals->haveECR() ){ |
857 | + | sprintf( painCave.errMsg, |
858 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
859 | + | "box length for the electrostaticCutoffRadius.\n" |
860 | + | "I hope you have a very fast processor!\n"); |
861 | + | painCave.isFatal = 0; |
862 | + | simError(); |
863 | + | double smallest; |
864 | + | smallest = info[i].boxL[0]; |
865 | + | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
866 | + | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
867 | + | theEcr = 0.5 * smallest; |
868 | + | } else { |
869 | + | theEcr = globals->getECR(); |
870 | + | } |
871 | + | |
872 | + | if( !globals->haveEST() ){ |
873 | + | sprintf( painCave.errMsg, |
874 | + | "SimSetup Warning: using default value of 0.05 * the " |
875 | + | "electrostaticCutoffRadius for the " |
876 | + | "electrostaticSkinThickness\n" |
877 | + | ); |
878 | + | painCave.isFatal = 0; |
879 | + | simError(); |
880 | + | theEst = 0.05 * theEcr; |
881 | + | } else { |
882 | + | theEst= globals->getEST(); |
883 | + | } |
884 | + | |
885 | + | info[i].setEcr( theEcr, theEst ); |
886 | + | } |
887 | + | } |
888 | + | } |
889 | ||
861 | – | info->setEcr( theEcr, theEst ); |
862 | – | } |
863 | – | } |
864 | – | |
890 | #ifdef IS_MPI | |
891 | strcpy( checkPointMsg, "post processing checks out" ); | |
892 | MPIcheckPoint(); | |
# | Line 870 | Line 895 | void SimSetup::initSystemCoords( void ){ | |
895 | } | |
896 | ||
897 | void SimSetup::initSystemCoords( void ){ | |
898 | + | int i; |
899 | + | |
900 | + | char* inName; |
901 | ||
902 | < | if( globals->haveInitialConfig() ){ |
903 | < | |
904 | < | InitializeFromFile* fileInit; |
902 | > | std::cerr << "Setting atom Coords\n"; |
903 | > | |
904 | > | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
905 | > | |
906 | > | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
907 | > | |
908 | > | if( globals->haveInitialConfig() ){ |
909 | > | |
910 | > | InitializeFromFile* fileInit; |
911 | #ifdef IS_MPI // is_mpi | |
912 | < | if( worldRank == 0 ){ |
912 | > | if( worldRank == 0 ){ |
913 | #endif //is_mpi | |
914 | < | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
914 | > | inName = globals->getInitialConfig(); |
915 | > | fileInit = new InitializeFromFile( inName ); |
916 | #ifdef IS_MPI | |
917 | < | }else fileInit = new InitializeFromFile( NULL ); |
917 | > | }else fileInit = new InitializeFromFile( NULL ); |
918 | #endif | |
919 | < | fileInit->readInit( info ); // default velocities on |
920 | < | |
921 | < | delete fileInit; |
922 | < | } |
923 | < | else{ |
924 | < | |
919 | > | fileInit->readInit( info ); // default velocities on |
920 | > | |
921 | > | delete fileInit; |
922 | > | } |
923 | > | else{ |
924 | > | |
925 | #ifdef IS_MPI | |
926 | < | |
927 | < | // no init from bass |
928 | < | |
929 | < | sprintf( painCave.errMsg, |
930 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
931 | < | painCave.isFatal; |
932 | < | simError(); |
933 | < | |
926 | > | |
927 | > | // no init from bass |
928 | > | |
929 | > | sprintf( painCave.errMsg, |
930 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
931 | > | painCave.isFatal; |
932 | > | simError(); |
933 | > | |
934 | #else | |
935 | < | |
936 | < | initFromBass(); |
937 | < | |
938 | < | |
935 | > | |
936 | > | initFromBass(); |
937 | > | |
938 | > | |
939 | #endif | |
940 | < | } |
941 | < | |
940 | > | } |
941 | > | |
942 | #ifdef IS_MPI | |
943 | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); | |
944 | MPIcheckPoint(); | |
945 | #endif // is_mpi | |
946 | < | |
946 | > | |
947 | } | |
948 | ||
949 | ||
950 | void SimSetup::makeOutNames( void ){ | |
951 | + | |
952 | + | int k; |
953 | ||
954 | + | |
955 | + | for(k=0; k<nInfo; k++){ |
956 | + | |
957 | #ifdef IS_MPI | |
958 | < | if( worldRank == 0 ){ |
958 | > | if( worldRank == 0 ){ |
959 | #endif // is_mpi | |
960 | < | |
961 | < | if( globals->haveFinalConfig() ){ |
962 | < | strcpy( info->finalName, globals->getFinalConfig() ); |
923 | < | } |
924 | < | else{ |
925 | < | strcpy( info->finalName, inFileName ); |
926 | < | char* endTest; |
927 | < | int nameLength = strlen( info->finalName ); |
928 | < | endTest = &(info->finalName[nameLength - 5]); |
929 | < | if( !strcmp( endTest, ".bass" ) ){ |
930 | < | strcpy( endTest, ".eor" ); |
960 | > | |
961 | > | if( globals->haveFinalConfig() ){ |
962 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
963 | } | |
932 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
933 | – | strcpy( endTest, ".eor" ); |
934 | – | } |
964 | else{ | |
965 | < | endTest = &(info->finalName[nameLength - 4]); |
966 | < | if( !strcmp( endTest, ".bss" ) ){ |
965 | > | strcpy( info[k].finalName, inFileName ); |
966 | > | char* endTest; |
967 | > | int nameLength = strlen( info[k].finalName ); |
968 | > | endTest = &(info[k].finalName[nameLength - 5]); |
969 | > | if( !strcmp( endTest, ".bass" ) ){ |
970 | strcpy( endTest, ".eor" ); | |
971 | } | |
972 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
972 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
973 | strcpy( endTest, ".eor" ); | |
974 | } | |
975 | else{ | |
976 | < | strcat( info->finalName, ".eor" ); |
976 | > | endTest = &(info[k].finalName[nameLength - 4]); |
977 | > | if( !strcmp( endTest, ".bss" ) ){ |
978 | > | strcpy( endTest, ".eor" ); |
979 | > | } |
980 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
981 | > | strcpy( endTest, ".eor" ); |
982 | > | } |
983 | > | else{ |
984 | > | strcat( info[k].finalName, ".eor" ); |
985 | > | } |
986 | } | |
987 | } | |
988 | < | } |
989 | < | |
990 | < | // make the sample and status out names |
991 | < | |
992 | < | strcpy( info->sampleName, inFileName ); |
993 | < | char* endTest; |
994 | < | int nameLength = strlen( info->sampleName ); |
995 | < | endTest = &(info->sampleName[nameLength - 5]); |
955 | < | if( !strcmp( endTest, ".bass" ) ){ |
956 | < | strcpy( endTest, ".dump" ); |
957 | < | } |
958 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
959 | < | strcpy( endTest, ".dump" ); |
960 | < | } |
961 | < | else{ |
962 | < | endTest = &(info->sampleName[nameLength - 4]); |
963 | < | if( !strcmp( endTest, ".bss" ) ){ |
988 | > | |
989 | > | // make the sample and status out names |
990 | > | |
991 | > | strcpy( info[k].sampleName, inFileName ); |
992 | > | char* endTest; |
993 | > | int nameLength = strlen( info[k].sampleName ); |
994 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
995 | > | if( !strcmp( endTest, ".bass" ) ){ |
996 | strcpy( endTest, ".dump" ); | |
997 | } | |
998 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
998 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
999 | strcpy( endTest, ".dump" ); | |
1000 | } | |
1001 | else{ | |
1002 | < | strcat( info->sampleName, ".dump" ); |
1002 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1003 | > | if( !strcmp( endTest, ".bss" ) ){ |
1004 | > | strcpy( endTest, ".dump" ); |
1005 | > | } |
1006 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1007 | > | strcpy( endTest, ".dump" ); |
1008 | > | } |
1009 | > | else{ |
1010 | > | strcat( info[k].sampleName, ".dump" ); |
1011 | > | } |
1012 | } | |
1013 | < | } |
1014 | < | |
1015 | < | strcpy( info->statusName, inFileName ); |
1016 | < | nameLength = strlen( info->statusName ); |
1017 | < | endTest = &(info->statusName[nameLength - 5]); |
977 | < | if( !strcmp( endTest, ".bass" ) ){ |
978 | < | strcpy( endTest, ".stat" ); |
979 | < | } |
980 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
981 | < | strcpy( endTest, ".stat" ); |
982 | < | } |
983 | < | else{ |
984 | < | endTest = &(info->statusName[nameLength - 4]); |
985 | < | if( !strcmp( endTest, ".bss" ) ){ |
1013 | > | |
1014 | > | strcpy( info[k].statusName, inFileName ); |
1015 | > | nameLength = strlen( info[k].statusName ); |
1016 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1017 | > | if( !strcmp( endTest, ".bass" ) ){ |
1018 | strcpy( endTest, ".stat" ); | |
1019 | } | |
1020 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1020 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
1021 | strcpy( endTest, ".stat" ); | |
1022 | } | |
1023 | else{ | |
1024 | < | strcat( info->statusName, ".stat" ); |
1024 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1025 | > | if( !strcmp( endTest, ".bss" ) ){ |
1026 | > | strcpy( endTest, ".stat" ); |
1027 | > | } |
1028 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1029 | > | strcpy( endTest, ".stat" ); |
1030 | > | } |
1031 | > | else{ |
1032 | > | strcat( info[k].statusName, ".stat" ); |
1033 | > | } |
1034 | } | |
1035 | < | } |
995 | < | |
1035 | > | |
1036 | #ifdef IS_MPI | |
1037 | < | } |
1037 | > | } |
1038 | #endif // is_mpi | |
1039 | < | |
1039 | > | } |
1040 | } | |
1041 | ||
1042 | ||
1043 | void SimSetup::sysObjectsCreation( void ){ | |
1044 | < | |
1045 | < | int i; |
1046 | < | |
1044 | > | |
1045 | > | int i,k; |
1046 | > | |
1047 | // create the forceField | |
1048 | ||
1049 | createFF(); | |
# | Line 1023 | Line 1063 | void SimSetup::sysObjectsCreation( void ){ | |
1063 | #endif //is_mpi | |
1064 | ||
1065 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1066 | < | |
1066 | > | |
1067 | makeSysArrays(); | |
1068 | ||
1069 | // make and initialize the molecules (all but atomic coordinates) | |
1070 | < | |
1070 | > | |
1071 | makeMolecules(); | |
1032 | – | info->identArray = new int[info->n_atoms]; |
1033 | – | for(i=0; i<info->n_atoms; i++){ |
1034 | – | info->identArray[i] = the_atoms[i]->getIdent(); |
1035 | – | } |
1072 | ||
1073 | < | |
1074 | < | |
1073 | > | for(k=0; k<nInfo; k++){ |
1074 | > | info[k].identArray = new int[info[k].n_atoms]; |
1075 | > | for(i=0; i<info[k].n_atoms; i++){ |
1076 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1077 | > | } |
1078 | > | } |
1079 | } | |
1080 | ||
1081 | ||
# | Line 1073 | Line 1113 | void SimSetup::compList( void ){ | |
1113 | void SimSetup::compList( void ){ | |
1114 | ||
1115 | int i; | |
1116 | < | |
1116 | > | char* id; |
1117 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1118 | > | LinkedMolStamp* currentStamp = NULL; |
1119 | comp_stamps = new MoleculeStamp*[n_components]; | |
1120 | < | |
1120 | > | |
1121 | // make an array of molecule stamps that match the components used. | |
1122 | // also extract the used stamps out into a separate linked list | |
1123 | < | |
1124 | < | info->nComponents = n_components; |
1125 | < | info->componentsNmol = components_nmol; |
1126 | < | info->compStamps = comp_stamps; |
1127 | < | info->headStamp = new LinkedMolStamp(); |
1123 | > | |
1124 | > | for(i=0; i<nInfo; i++){ |
1125 | > | info[i].nComponents = n_components; |
1126 | > | info[i].componentsNmol = components_nmol; |
1127 | > | info[i].compStamps = comp_stamps; |
1128 | > | info[i].headStamp = headStamp; |
1129 | > | } |
1130 | ||
1131 | < | char* id; |
1088 | < | LinkedMolStamp* headStamp = info->headStamp; |
1089 | < | LinkedMolStamp* currentStamp = NULL; |
1131 | > | |
1132 | for( i=0; i<n_components; i++ ){ | |
1133 | ||
1134 | id = the_components[i]->getType(); | |
# | Line 1124 | Line 1166 | void SimSetup::calcSysValues( void ){ | |
1166 | ||
1167 | void SimSetup::calcSysValues( void ){ | |
1168 | int i, j, k; | |
1169 | < | |
1170 | < | |
1169 | > | |
1170 | > | int *molMembershipArray; |
1171 | > | |
1172 | tot_atoms = 0; | |
1173 | tot_bonds = 0; | |
1174 | tot_bends = 0; | |
# | Line 1137 | Line 1180 | void SimSetup::calcSysValues( void ){ | |
1180 | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); | |
1181 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1182 | } | |
1183 | < | |
1183 | > | |
1184 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1185 | < | |
1143 | < | info->n_atoms = tot_atoms; |
1144 | < | info->n_bonds = tot_bonds; |
1145 | < | info->n_bends = tot_bends; |
1146 | < | info->n_torsions = tot_torsions; |
1147 | < | info->n_SRI = tot_SRI; |
1148 | < | info->n_mol = tot_nmol; |
1185 | > | molMembershipArray = new int[tot_atoms]; |
1186 | ||
1187 | < | info->molMembershipArray = new int[tot_atoms]; |
1187 | > | for(i=0; i<nInfo; i++){ |
1188 | > | info[i].n_atoms = tot_atoms; |
1189 | > | info[i].n_bonds = tot_bonds; |
1190 | > | info[i].n_bends = tot_bends; |
1191 | > | info[i].n_torsions = tot_torsions; |
1192 | > | info[i].n_SRI = tot_SRI; |
1193 | > | info[i].n_mol = tot_nmol; |
1194 | > | |
1195 | > | info[i].molMembershipArray = molMembershipArray; |
1196 | > | } |
1197 | } | |
1198 | ||
1153 | – | |
1199 | #ifdef IS_MPI | |
1200 | ||
1201 | void SimSetup::mpiMolDivide( void ){ | |
# | Line 1190 | Line 1235 | void SimSetup::mpiMolDivide( void ){ | |
1235 | localMol++; | |
1236 | } | |
1237 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { | |
1238 | < | info->molMembershipArray[globalAtomIndex] = allMol; |
1238 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1239 | globalAtomIndex++; | |
1240 | } | |
1241 | ||
# | Line 1199 | Line 1244 | void SimSetup::mpiMolDivide( void ){ | |
1244 | } | |
1245 | local_SRI = local_bonds + local_bends + local_torsions; | |
1246 | ||
1247 | < | info->n_atoms = mpiSim->getMyNlocal(); |
1247 | > | info[0].n_atoms = mpiSim->getMyNlocal(); |
1248 | ||
1249 | < | if( local_atoms != info->n_atoms ){ |
1249 | > | if( local_atoms != info[0].n_atoms ){ |
1250 | sprintf( painCave.errMsg, | |
1251 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
1252 | " localAtom (%d) are not equal.\n", | |
1253 | < | info->n_atoms, |
1253 | > | info[0].n_atoms, |
1254 | local_atoms ); | |
1255 | painCave.isFatal = 1; | |
1256 | simError(); | |
1257 | } | |
1258 | ||
1259 | < | info->n_bonds = local_bonds; |
1260 | < | info->n_bends = local_bends; |
1261 | < | info->n_torsions = local_torsions; |
1262 | < | info->n_SRI = local_SRI; |
1263 | < | info->n_mol = localMol; |
1259 | > | info[0].n_bonds = local_bonds; |
1260 | > | info[0].n_bends = local_bends; |
1261 | > | info[0].n_torsions = local_torsions; |
1262 | > | info[0].n_SRI = local_SRI; |
1263 | > | info[0].n_mol = localMol; |
1264 | ||
1265 | strcpy( checkPointMsg, "Passed nlocal consistency check." ); | |
1266 | MPIcheckPoint(); | |
1267 | } | |
1268 | < | |
1268 | > | |
1269 | #endif // is_mpi | |
1270 | ||
1271 | ||
1272 | void SimSetup::makeSysArrays( void ){ | |
1273 | < | int i, j, k; |
1273 | > | int i, j, k, l; |
1274 | ||
1275 | < | |
1276 | < | // create the atom and short range interaction arrays |
1277 | < | |
1278 | < | Atom::createArrays(info->n_atoms); |
1279 | < | the_atoms = new Atom*[info->n_atoms]; |
1280 | < | the_molecules = new Molecule[info->n_mol]; |
1236 | < | int molIndex; |
1237 | < | |
1238 | < | // initialize the molecule's stampID's |
1239 | < | |
1240 | < | #ifdef IS_MPI |
1241 | < | |
1242 | < | |
1243 | < | molIndex = 0; |
1244 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1245 | < | |
1246 | < | if(mol2proc[i] == worldRank ){ |
1247 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1248 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1249 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1250 | < | molIndex++; |
1251 | < | } |
1252 | < | } |
1253 | < | |
1254 | < | #else // is_mpi |
1255 | < | |
1256 | < | molIndex = 0; |
1257 | < | globalAtomIndex = 0; |
1258 | < | for(i=0; i<n_components; i++){ |
1259 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1260 | < | the_molecules[molIndex].setStampID( i ); |
1261 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1262 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1263 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1264 | < | info->molMembershipArray[globalAtomIndex] = molIndex; |
1265 | < | globalAtomIndex++; |
1266 | < | } |
1267 | < | molIndex++; |
1268 | < | } |
1269 | < | } |
1275 | > | Atom** the_atoms; |
1276 | > | Molecule* the_molecules; |
1277 | > | Exclude** the_excludes; |
1278 | > | |
1279 | > | |
1280 | > | for(l=0; l<nInfo; l++){ |
1281 | ||
1282 | + | // create the atom and short range interaction arrays |
1283 | + | |
1284 | + | the_atoms = new Atom*[info[l].n_atoms]; |
1285 | + | the_molecules = new Molecule[info[l].n_mol]; |
1286 | + | int molIndex; |
1287 | ||
1288 | + | // initialize the molecule's stampID's |
1289 | + | |
1290 | + | #ifdef IS_MPI |
1291 | + | |
1292 | + | |
1293 | + | molIndex = 0; |
1294 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1295 | + | |
1296 | + | if(mol2proc[i] == worldRank ){ |
1297 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
1298 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1299 | + | the_molecules[molIndex].setGlobalIndex( i ); |
1300 | + | molIndex++; |
1301 | + | } |
1302 | + | } |
1303 | + | |
1304 | + | #else // is_mpi |
1305 | + | |
1306 | + | molIndex = 0; |
1307 | + | globalAtomIndex = 0; |
1308 | + | for(i=0; i<n_components; i++){ |
1309 | + | for(j=0; j<components_nmol[i]; j++ ){ |
1310 | + | the_molecules[molIndex].setStampID( i ); |
1311 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1312 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1313 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1314 | + | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1315 | + | globalAtomIndex++; |
1316 | + | } |
1317 | + | molIndex++; |
1318 | + | } |
1319 | + | } |
1320 | + | |
1321 | + | |
1322 | #endif // is_mpi | |
1323 | ||
1324 | ||
1325 | < | if( info->n_SRI ){ |
1325 | > | if( info[l].n_SRI ){ |
1326 | ||
1327 | < | Exclude::createArray(info->n_SRI); |
1328 | < | the_excludes = new Exclude*[info->n_SRI]; |
1329 | < | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1330 | < | info->globalExcludes = new int; |
1331 | < | info->n_exclude = info->n_SRI; |
1332 | < | } |
1333 | < | else{ |
1327 | > | Exclude::createArray(info[l].n_SRI); |
1328 | > | the_excludes = new Exclude*[info[l].n_SRI]; |
1329 | > | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1330 | > | the_excludes[ex] = new Exclude(ex); |
1331 | > | } |
1332 | > | info[l].globalExcludes = new int; |
1333 | > | info[l].n_exclude = info[l].n_SRI; |
1334 | > | } |
1335 | > | else{ |
1336 | ||
1337 | < | Exclude::createArray( 1 ); |
1338 | < | the_excludes = new Exclude*; |
1339 | < | the_excludes[0] = new Exclude(0); |
1340 | < | the_excludes[0]->setPair( 0,0 ); |
1341 | < | info->globalExcludes = new int; |
1342 | < | info->globalExcludes[0] = 0; |
1343 | < | info->n_exclude = 0; |
1344 | < | } |
1337 | > | Exclude::createArray( 1 ); |
1338 | > | the_excludes = new Exclude*; |
1339 | > | the_excludes[0] = new Exclude(0); |
1340 | > | the_excludes[0]->setPair( 0,0 ); |
1341 | > | info[l].globalExcludes = new int; |
1342 | > | info[l].globalExcludes[0] = 0; |
1343 | > | info[l].n_exclude = 0; |
1344 | > | } |
1345 | ||
1346 | < | // set the arrays into the SimInfo object |
1346 | > | // set the arrays into the SimInfo object |
1347 | ||
1348 | < | info->atoms = the_atoms; |
1349 | < | info->molecules = the_molecules; |
1350 | < | info->nGlobalExcludes = 0; |
1351 | < | info->excludes = the_excludes; |
1348 | > | info[l].atoms = the_atoms; |
1349 | > | info[l].molecules = the_molecules; |
1350 | > | info[l].nGlobalExcludes = 0; |
1351 | > | info[l].excludes = the_excludes; |
1352 | ||
1353 | < | the_ff->setSimInfo( info ); |
1354 | < | |
1353 | > | the_ff->setSimInfo( info ); |
1354 | > | |
1355 | > | } |
1356 | } | |
1357 | ||
1358 | void SimSetup::makeIntegrator( void ){ | |
1359 | ||
1360 | + | int k; |
1361 | + | |
1362 | NVT<RealIntegrator>* myNVT = NULL; | |
1363 | NPTi<RealIntegrator>* myNPTi = NULL; | |
1364 | NPTf<RealIntegrator>* myNPTf = NULL; | |
1365 | NPTim<RealIntegrator>* myNPTim = NULL; | |
1366 | NPTfm<RealIntegrator>* myNPTfm = NULL; | |
1367 | < | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1367 | > | |
1368 | > | for(k=0; k<nInfo; k++){ |
1369 | > | |
1370 | > | switch( ensembleCase ){ |
1371 | ||
1372 | < | cerr << "setting integrator" <<endl; |
1373 | < | |
1374 | < | switch( ensembleCase ){ |
1372 | > | case NVE_ENS: |
1373 | > | if (globals->haveZconstraints()){ |
1374 | > | setupZConstraint(info[k]); |
1375 | > | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1376 | > | } |
1377 | ||
1378 | < | case NVE_ENS: |
1379 | < | new NVE<RealIntegrator>( info, the_ff ); |
1380 | < | break; |
1378 | > | else |
1379 | > | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1380 | > | break; |
1381 | > | |
1382 | > | case NVT_ENS: |
1383 | > | if (globals->haveZconstraints()){ |
1384 | > | setupZConstraint(info[k]); |
1385 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1386 | > | } |
1387 | > | else |
1388 | > | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1389 | ||
1390 | < | case NVT_ENS: |
1391 | < | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1392 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1390 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1391 | > | |
1392 | > | if (globals->haveTauThermostat()) |
1393 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1394 | > | |
1395 | > | else { |
1396 | > | sprintf( painCave.errMsg, |
1397 | > | "SimSetup error: If you use the NVT\n" |
1398 | > | " ensemble, you must set tauThermostat.\n"); |
1399 | > | painCave.isFatal = 1; |
1400 | > | simError(); |
1401 | > | } |
1402 | > | break; |
1403 | > | |
1404 | > | case NPTi_ENS: |
1405 | > | if (globals->haveZconstraints()){ |
1406 | > | setupZConstraint(info[k]); |
1407 | > | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1408 | > | } |
1409 | > | else |
1410 | > | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1411 | ||
1412 | < | if (globals->haveTauThermostat()) |
1413 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1412 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1413 | > | |
1414 | > | if (globals->haveTargetPressure()) |
1415 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1416 | > | else { |
1417 | > | sprintf( painCave.errMsg, |
1418 | > | "SimSetup error: If you use a constant pressure\n" |
1419 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1420 | > | painCave.isFatal = 1; |
1421 | > | simError(); |
1422 | > | } |
1423 | > | |
1424 | > | if( globals->haveTauThermostat() ) |
1425 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1426 | > | else{ |
1427 | > | sprintf( painCave.errMsg, |
1428 | > | "SimSetup error: If you use an NPT\n" |
1429 | > | " ensemble, you must set tauThermostat.\n"); |
1430 | > | painCave.isFatal = 1; |
1431 | > | simError(); |
1432 | > | } |
1433 | > | |
1434 | > | if( globals->haveTauBarostat() ) |
1435 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1436 | > | else{ |
1437 | > | sprintf( painCave.errMsg, |
1438 | > | "SimSetup error: If you use an NPT\n" |
1439 | > | " ensemble, you must set tauBarostat.\n"); |
1440 | > | painCave.isFatal = 1; |
1441 | > | simError(); |
1442 | > | } |
1443 | > | break; |
1444 | > | |
1445 | > | case NPTf_ENS: |
1446 | > | if (globals->haveZconstraints()){ |
1447 | > | setupZConstraint(info[k]); |
1448 | > | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1449 | > | } |
1450 | > | else |
1451 | > | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1452 | ||
1453 | < | else { |
1454 | < | sprintf( painCave.errMsg, |
1455 | < | "SimSetup error: If you use the NVT\n" |
1453 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1454 | > | |
1455 | > | if (globals->haveTargetPressure()) |
1456 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1457 | > | else { |
1458 | > | sprintf( painCave.errMsg, |
1459 | > | "SimSetup error: If you use a constant pressure\n" |
1460 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1461 | > | painCave.isFatal = 1; |
1462 | > | simError(); |
1463 | > | } |
1464 | > | |
1465 | > | if( globals->haveTauThermostat() ) |
1466 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1467 | > | else{ |
1468 | > | sprintf( painCave.errMsg, |
1469 | > | "SimSetup error: If you use an NPT\n" |
1470 | " ensemble, you must set tauThermostat.\n"); | |
1471 | < | painCave.isFatal = 1; |
1472 | < | simError(); |
1473 | < | } |
1474 | < | break; |
1471 | > | painCave.isFatal = 1; |
1472 | > | simError(); |
1473 | > | } |
1474 | > | |
1475 | > | if( globals->haveTauBarostat() ) |
1476 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1477 | > | else{ |
1478 | > | sprintf( painCave.errMsg, |
1479 | > | "SimSetup error: If you use an NPT\n" |
1480 | > | " ensemble, you must set tauBarostat.\n"); |
1481 | > | painCave.isFatal = 1; |
1482 | > | simError(); |
1483 | > | } |
1484 | > | break; |
1485 | > | |
1486 | > | case NPTim_ENS: |
1487 | > | if (globals->haveZconstraints()){ |
1488 | > | setupZConstraint(info[k]); |
1489 | > | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1490 | > | } |
1491 | > | else |
1492 | > | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1493 | ||
1494 | < | case NPTi_ENS: |
1495 | < | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1496 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1497 | < | |
1498 | < | if (globals->haveTargetPressure()) |
1499 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1500 | < | else { |
1494 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1495 | > | |
1496 | > | if (globals->haveTargetPressure()) |
1497 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1498 | > | else { |
1499 | > | sprintf( painCave.errMsg, |
1500 | > | "SimSetup error: If you use a constant pressure\n" |
1501 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1502 | > | painCave.isFatal = 1; |
1503 | > | simError(); |
1504 | > | } |
1505 | > | |
1506 | > | if( globals->haveTauThermostat() ) |
1507 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1508 | > | else{ |
1509 | > | sprintf( painCave.errMsg, |
1510 | > | "SimSetup error: If you use an NPT\n" |
1511 | > | " ensemble, you must set tauThermostat.\n"); |
1512 | > | painCave.isFatal = 1; |
1513 | > | simError(); |
1514 | > | } |
1515 | > | |
1516 | > | if( globals->haveTauBarostat() ) |
1517 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1518 | > | else{ |
1519 | sprintf( painCave.errMsg, | |
1346 | – | "SimSetup error: If you use a constant pressure\n" |
1347 | – | " ensemble, you must set targetPressure in the BASS file.\n"); |
1348 | – | painCave.isFatal = 1; |
1349 | – | simError(); |
1350 | – | } |
1351 | – | |
1352 | – | if( globals->haveTauThermostat() ) |
1353 | – | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1354 | – | else{ |
1355 | – | sprintf( painCave.errMsg, |
1520 | "SimSetup error: If you use an NPT\n" | |
1357 | – | " ensemble, you must set tauThermostat.\n"); |
1358 | – | painCave.isFatal = 1; |
1359 | – | simError(); |
1360 | – | } |
1361 | – | |
1362 | – | if( globals->haveTauBarostat() ) |
1363 | – | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1364 | – | else{ |
1365 | – | sprintf( painCave.errMsg, |
1366 | – | "SimSetup error: If you use an NPT\n" |
1521 | " ensemble, you must set tauBarostat.\n"); | |
1522 | painCave.isFatal = 1; | |
1523 | simError(); | |
1524 | < | } |
1525 | < | break; |
1524 | > | } |
1525 | > | break; |
1526 | > | |
1527 | > | case NPTfm_ENS: |
1528 | > | if (globals->haveZconstraints()){ |
1529 | > | setupZConstraint(info[k]); |
1530 | > | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1531 | > | } |
1532 | > | else |
1533 | > | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1534 | ||
1535 | < | case NPTf_ENS: |
1536 | < | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1537 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1538 | < | |
1539 | < | if (globals->haveTargetPressure()) |
1540 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1541 | < | else { |
1542 | < | sprintf( painCave.errMsg, |
1543 | < | "SimSetup error: If you use a constant pressure\n" |
1544 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1383 | < | painCave.isFatal = 1; |
1384 | < | simError(); |
1385 | < | } |
1386 | < | |
1387 | < | if( globals->haveTauThermostat() ) |
1388 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1389 | < | else{ |
1390 | < | sprintf( painCave.errMsg, |
1391 | < | "SimSetup error: If you use an NPT\n" |
1392 | < | " ensemble, you must set tauThermostat.\n"); |
1393 | < | painCave.isFatal = 1; |
1394 | < | simError(); |
1395 | < | } |
1396 | < | |
1397 | < | if( globals->haveTauBarostat() ) |
1398 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1399 | < | else{ |
1400 | < | sprintf( painCave.errMsg, |
1401 | < | "SimSetup error: If you use an NPT\n" |
1402 | < | " ensemble, you must set tauBarostat.\n"); |
1403 | < | painCave.isFatal = 1; |
1404 | < | simError(); |
1405 | < | } |
1406 | < | break; |
1407 | < | |
1408 | < | case NPTim_ENS: |
1409 | < | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1410 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1411 | < | |
1412 | < | if (globals->haveTargetPressure()) |
1413 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1414 | < | else { |
1415 | < | sprintf( painCave.errMsg, |
1416 | < | "SimSetup error: If you use a constant pressure\n" |
1417 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1418 | < | painCave.isFatal = 1; |
1419 | < | simError(); |
1420 | < | } |
1421 | < | |
1422 | < | if( globals->haveTauThermostat() ) |
1423 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1424 | < | else{ |
1425 | < | sprintf( painCave.errMsg, |
1426 | < | "SimSetup error: If you use an NPT\n" |
1427 | < | " ensemble, you must set tauThermostat.\n"); |
1428 | < | painCave.isFatal = 1; |
1429 | < | simError(); |
1430 | < | } |
1431 | < | |
1432 | < | if( globals->haveTauBarostat() ) |
1433 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1434 | < | else{ |
1435 | < | sprintf( painCave.errMsg, |
1436 | < | "SimSetup error: If you use an NPT\n" |
1437 | < | " ensemble, you must set tauBarostat.\n"); |
1438 | < | painCave.isFatal = 1; |
1439 | < | simError(); |
1440 | < | } |
1441 | < | break; |
1442 | < | |
1443 | < | case NPTfm_ENS: |
1444 | < | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1445 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 | < | |
1447 | < | if (globals->haveTargetPressure()) |
1448 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1449 | < | else { |
1450 | < | sprintf( painCave.errMsg, |
1451 | < | "SimSetup error: If you use a constant pressure\n" |
1452 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1453 | < | painCave.isFatal = 1; |
1454 | < | simError(); |
1455 | < | } |
1456 | < | |
1457 | < | if( globals->haveTauThermostat() ) |
1458 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1459 | < | else{ |
1460 | < | sprintf( painCave.errMsg, |
1461 | < | "SimSetup error: If you use an NPT\n" |
1462 | < | " ensemble, you must set tauThermostat.\n"); |
1463 | < | painCave.isFatal = 1; |
1464 | < | simError(); |
1465 | < | } |
1466 | < | |
1467 | < | if( globals->haveTauBarostat() ) |
1468 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1469 | < | else{ |
1470 | < | sprintf( painCave.errMsg, |
1471 | < | "SimSetup error: If you use an NPT\n" |
1472 | < | " ensemble, you must set tauBarostat.\n"); |
1473 | < | painCave.isFatal = 1; |
1474 | < | simError(); |
1475 | < | } |
1476 | < | break; |
1477 | < | |
1478 | < | case NVEZCONS_ENS: |
1479 | < | { |
1480 | < | |
1481 | < | if(globals->haveZConsTime()){ |
1482 | < | |
1483 | < | //add sample time of z-constraint into SimInfo's property list |
1484 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1485 | < | zconsTimeProp->setID("zconstime"); |
1486 | < | zconsTimeProp->setData(globals->getZConsTime()); |
1487 | < | info->addProperty(zconsTimeProp); |
1535 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1536 | > | |
1537 | > | if (globals->haveTargetPressure()) |
1538 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1539 | > | else { |
1540 | > | sprintf( painCave.errMsg, |
1541 | > | "SimSetup error: If you use a constant pressure\n" |
1542 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1543 | > | painCave.isFatal = 1; |
1544 | > | simError(); |
1545 | } | |
1546 | + | |
1547 | + | if( globals->haveTauThermostat() ) |
1548 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1549 | else{ | |
1550 | < | sprintf( painCave.errMsg, |
1551 | < | "ZConstraint error: If you use an ZConstraint\n" |
1552 | < | " , you must set sample time.\n"); |
1553 | < | painCave.isFatal = 1; |
1554 | < | simError(); |
1550 | > | sprintf( painCave.errMsg, |
1551 | > | "SimSetup error: If you use an NPT\n" |
1552 | > | " ensemble, you must set tauThermostat.\n"); |
1553 | > | painCave.isFatal = 1; |
1554 | > | simError(); |
1555 | } | |
1556 | ||
1557 | < | if(globals->haveIndexOfAllZConsMols()){ |
1558 | < | |
1499 | < | //add index of z-constraint molecules into SimInfo's property list |
1500 | < | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1501 | < | sort(tempIndex.begin(), tempIndex.end()); |
1502 | < | |
1503 | < | IndexData* zconsIndex = new IndexData(); |
1504 | < | zconsIndex->setID("zconsindex"); |
1505 | < | zconsIndex->setIndexData(tempIndex); |
1506 | < | info->addProperty(zconsIndex); |
1507 | < | } |
1557 | > | if( globals->haveTauBarostat() ) |
1558 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1559 | else{ | |
1560 | < | sprintf( painCave.errMsg, |
1561 | < | "SimSetup error: If you use an ZConstraint\n" |
1562 | < | " , you must set index of z-constraint molecules.\n"); |
1563 | < | painCave.isFatal = 1; |
1564 | < | simError(); |
1514 | < | |
1560 | > | sprintf( painCave.errMsg, |
1561 | > | "SimSetup error: If you use an NPT\n" |
1562 | > | " ensemble, you must set tauBarostat.\n"); |
1563 | > | painCave.isFatal = 1; |
1564 | > | simError(); |
1565 | } | |
1566 | < | |
1517 | < | //Determine the name of ouput file and add it into SimInfo's property list |
1518 | < | //Be careful, do not use inFileName, since it is a pointer which |
1519 | < | //point to a string at master node, and slave nodes do not contain that string |
1520 | < | |
1521 | < | string zconsOutput(info->finalName); |
1522 | < | |
1523 | < | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1524 | < | |
1525 | < | StringData* zconsFilename = new StringData(); |
1526 | < | zconsFilename->setID("zconsfilename"); |
1527 | < | zconsFilename->setData(zconsOutput); |
1528 | < | |
1529 | < | info->addProperty(zconsFilename); |
1566 | > | break; |
1567 | ||
1568 | < | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1569 | < | |
1570 | < | break; |
1568 | > | default: |
1569 | > | sprintf( painCave.errMsg, |
1570 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1571 | > | painCave.isFatal = 1; |
1572 | > | simError(); |
1573 | } | |
1535 | – | |
1536 | – | default: |
1537 | – | sprintf( painCave.errMsg, |
1538 | – | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1539 | – | painCave.isFatal = 1; |
1540 | – | simError(); |
1574 | } | |
1542 | – | |
1575 | } | |
1576 | ||
1577 | void SimSetup::initFortran( void ){ | |
1578 | ||
1579 | < | info->refreshSim(); |
1579 | > | info[0].refreshSim(); |
1580 | ||
1581 | < | if( !strcmp( info->mixingRule, "standard") ){ |
1581 | > | if( !strcmp( info[0].mixingRule, "standard") ){ |
1582 | the_ff->initForceField( LB_MIXING_RULE ); | |
1583 | } | |
1584 | < | else if( !strcmp( info->mixingRule, "explicit") ){ |
1584 | > | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1585 | the_ff->initForceField( EXPLICIT_MIXING_RULE ); | |
1586 | } | |
1587 | else{ | |
1588 | sprintf( painCave.errMsg, | |
1589 | "SimSetup Error: unknown mixing rule -> \"%s\"\n", | |
1590 | < | info->mixingRule ); |
1590 | > | info[0].mixingRule ); |
1591 | painCave.isFatal = 1; | |
1592 | simError(); | |
1593 | } | |
# | Line 1568 | Line 1600 | void SimSetup::initFortran( void ){ | |
1600 | #endif // is_mpi | |
1601 | ||
1602 | } | |
1603 | + | |
1604 | + | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1605 | + | { |
1606 | + | int nZConstraints; |
1607 | + | ZconStamp** zconStamp; |
1608 | + | |
1609 | + | if(globals->haveZconstraintTime()){ |
1610 | + | |
1611 | + | //add sample time of z-constraint into SimInfo's property list |
1612 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1613 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1614 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1615 | + | theInfo.addProperty(zconsTimeProp); |
1616 | + | } |
1617 | + | else{ |
1618 | + | sprintf( painCave.errMsg, |
1619 | + | "ZConstraint error: If you use an ZConstraint\n" |
1620 | + | " , you must set sample time.\n"); |
1621 | + | painCave.isFatal = 1; |
1622 | + | simError(); |
1623 | + | } |
1624 | + | |
1625 | + | // |
1626 | + | nZConstraints = globals->getNzConstraints(); |
1627 | + | zconStamp = globals->getZconStamp(); |
1628 | + | ZConsParaItem tempParaItem; |
1629 | + | |
1630 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1631 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1632 | + | |
1633 | + | for(int i = 0; i < nZConstraints; i++){ |
1634 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1635 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1636 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1637 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1638 | + | |
1639 | + | zconsParaData->addItem(tempParaItem); |
1640 | + | } |
1641 | + | |
1642 | + | //sort the parameters by index of molecules |
1643 | + | zconsParaData->sortByIndex(); |
1644 | + | |
1645 | + | //push data into siminfo, therefore, we can retrieve later |
1646 | + | theInfo.addProperty(zconsParaData); |
1647 | + | |
1648 | + | //push zconsTol into siminfo, if user does not specify |
1649 | + | //value for zconsTol, a default value will be used |
1650 | + | DoubleData* zconsTol = new DoubleData(); |
1651 | + | zconsTol->setID(ZCONSTOL_ID); |
1652 | + | if(globals->haveZconsTol()){ |
1653 | + | zconsTol->setData(globals->getZconsTol()); |
1654 | + | } |
1655 | + | else{ |
1656 | + | double defaultZConsTol = 1E-6; |
1657 | + | sprintf( painCave.errMsg, |
1658 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1659 | + | " , default value %f is used.\n", defaultZConsTol); |
1660 | + | painCave.isFatal = 0; |
1661 | + | simError(); |
1662 | + | |
1663 | + | zconsTol->setData(defaultZConsTol); |
1664 | + | } |
1665 | + | theInfo.addProperty(zconsTol); |
1666 | + | |
1667 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1668 | + | //Be careful, do not use inFileName, since it is a pointer which |
1669 | + | //point to a string at master node, and slave nodes do not contain that string |
1670 | + | |
1671 | + | string zconsOutput(theInfo.finalName); |
1672 | + | |
1673 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1674 | + | |
1675 | + | StringData* zconsFilename = new StringData(); |
1676 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1677 | + | zconsFilename->setData(zconsOutput); |
1678 | + | |
1679 | + | theInfo.addProperty(zconsFilename); |
1680 | + | } |
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