# | 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 12 | Line 14 | |
14 | #include "mpiSimulation.hpp" | |
15 | #endif | |
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 |
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 | + | |
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 27 | 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 62 | Line 97 | void SimSetup::receiveParse(void){ | |
97 | ||
98 | #endif // is_mpi | |
99 | ||
100 | < | void SimSetup::createSim( void ){ |
100 | > | void SimSetup::createSim(void){ |
101 | ||
67 | – | MakeStamps *the_stamps; |
68 | – | Globals* the_globals; |
69 | – | ExtendedSystem* the_extendedsystem; |
102 | int i, j, k, globalAtomIndex; | |
103 | + | |
104 | + | // gather all of the information from the Bass file |
105 | + | |
106 | + | gatherInfo(); |
107 | ||
108 | < | // get the stamps and globals; |
73 | < | the_stamps = stamps; |
74 | < | the_globals = globals; |
108 | > | // creation of complex system objects |
109 | ||
110 | < | // set the easy ones first |
77 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
78 | < | simnfo->dt = the_globals->getDt(); |
79 | < | simnfo->run_time = the_globals->getRunTime(); |
110 | > | sysObjectsCreation(); |
111 | ||
112 | < | // get the ones we know are there, yet still may need some work. |
113 | < | n_components = the_globals->getNComponents(); |
114 | < | strcpy( force_field, the_globals->getForceField() ); |
112 | > | // check on the post processing info |
113 | > | |
114 | > | finalInfoCheck(); |
115 | ||
116 | < | // get the ensemble and set up an extended system if we need it: |
86 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
87 | < | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 | < | if (the_globals->haveTargetPressure()) |
91 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 | < | else { |
93 | < | sprintf( painCave.errMsg, |
94 | < | "SimSetup error: If you use the constant pressure\n" |
95 | < | " ensemble, you must set targetPressure.\n" |
96 | < | " This was found in the BASS file.\n"); |
97 | < | painCave.isFatal = 1; |
98 | < | simError(); |
99 | < | } |
116 | > | // initialize the system coordinates |
117 | ||
118 | < | if (the_globals->haveTauThermostat()) |
102 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 | < | else if (the_globals->haveQmass()) |
104 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
105 | < | else { |
106 | < | sprintf( painCave.errMsg, |
107 | < | "SimSetup error: If you use one of the constant temperature\n" |
108 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
109 | < | " Neither of these was found in the BASS file.\n"); |
110 | < | painCave.isFatal = 1; |
111 | < | simError(); |
112 | < | } |
118 | > | if( !isInfoArray ) initSystemCoords(); |
119 | ||
120 | < | if (the_globals->haveTauBarostat()) |
121 | < | the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
122 | < | else { |
120 | > | // make the output filenames |
121 | > | |
122 | > | makeOutNames(); |
123 | > | |
124 | > | // make the integrator |
125 | > | |
126 | > | makeIntegrator(); |
127 | > | |
128 | > | #ifdef IS_MPI |
129 | > | mpiSim->mpiRefresh(); |
130 | > | #endif |
131 | > | |
132 | > | // initialize the Fortran |
133 | > | |
134 | > | initFortran(); |
135 | > | |
136 | > | |
137 | > | |
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 molInfo; |
146 | > | DirectionalAtom* dAtom; |
147 | > | LinkedAssign* extras; |
148 | > | LinkedAssign* current_extra; |
149 | > | AtomStamp* currentAtom; |
150 | > | BondStamp* currentBond; |
151 | > | BendStamp* currentBend; |
152 | > | TorsionStamp* currentTorsion; |
153 | > | |
154 | > | bond_pair* theBonds; |
155 | > | bend_set* theBends; |
156 | > | torsion_set* theTorsions; |
157 | > | |
158 | > | |
159 | > | //init the forceField paramters |
160 | > | |
161 | > | the_ff->readParams(); |
162 | > | |
163 | > | |
164 | > | // init the atoms |
165 | > | |
166 | > | double ux, uy, uz, u, uSqr; |
167 | > | |
168 | > | for(k=0; k<nInfo; k++){ |
169 | > | |
170 | > | the_ff->setSimInfo( &(info[k]) ); |
171 | > | |
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 | > | 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[molInfo.nBonds]; |
191 | > | theBends = new bend_set[molInfo.nBends]; |
192 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
193 | > | |
194 | > | // make the Atoms |
195 | > | |
196 | > | for(j=0; j<molInfo.nAtoms; j++){ |
197 | > | |
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 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
230 | > | |
231 | > | #endif // is_mpi |
232 | > | } |
233 | > | |
234 | > | // make the bonds |
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 | > | } |
250 | > | #ifdef IS_MPI |
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 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
260 | > | #endif //is_mpi |
261 | > | } |
262 | > | excludeOffset += molInfo.nBonds; |
263 | > | |
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 | > | 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 | > | 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 | > | |
307 | > | sprintf( painCave.errMsg, |
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 | > | } |
315 | > | |
316 | > | current_extra = current_extra->getNext(); |
317 | > | } |
318 | > | } |
319 | > | |
320 | > | if( !theBends[j].isGhost ){ |
321 | > | |
322 | > | exI = theBends[j].a; |
323 | > | exJ = theBends[j].c; |
324 | > | } |
325 | > | else{ |
326 | > | |
327 | > | exI = theBends[j].a; |
328 | > | exJ = theBends[j].b; |
329 | > | } |
330 | > | |
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 = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
340 | > | tempEx = exJ; |
341 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
342 | > | |
343 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
344 | > | #else // isn't MPI |
345 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
346 | > | #endif //is_mpi |
347 | > | } |
348 | > | excludeOffset += molInfo.nBends; |
349 | > | |
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 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
376 | > | #endif //is_mpi |
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 | > | atomOffset += molInfo.nAtoms; |
393 | > | delete[] theBonds; |
394 | > | delete[] theBends; |
395 | > | delete[] theTorsions; |
396 | > | } |
397 | > | } |
398 | > | |
399 | > | #ifdef IS_MPI |
400 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
401 | > | MPIcheckPoint(); |
402 | > | #endif // is_mpi |
403 | > | |
404 | > | // clean up the forcefield |
405 | > | |
406 | > | the_ff->calcRcut(); |
407 | > | the_ff->cleanMe(); |
408 | > | |
409 | > | } |
410 | > | |
411 | > | void SimSetup::initFromBass( void ){ |
412 | > | |
413 | > | int i, j, k; |
414 | > | int n_cells; |
415 | > | double cellx, celly, cellz; |
416 | > | double temp1, temp2, temp3; |
417 | > | int n_per_extra; |
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 ); |
429 | > | |
430 | > | have_extra =0; |
431 | > | if( temp2 < temp3 ){ // we have a non-complete lattice |
432 | > | have_extra =1; |
433 | > | |
434 | > | n_cells = (int)temp3 - 1; |
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 ); |
441 | > | |
442 | > | if( n_per_extra > 4){ |
443 | sprintf( painCave.errMsg, | |
444 | < | "SimSetup error: If you use the constant pressure\n" |
445 | < | " ensemble, you must set tauBarostat.\n" |
120 | < | " This was found in the BASS file.\n"); |
444 | > | "SimSetup error. There has been an error in constructing" |
445 | > | " the non-complete lattice.\n" ); |
446 | painCave.isFatal = 1; | |
447 | simError(); | |
448 | } | |
449 | + | } |
450 | + | else{ |
451 | + | n_cells = (int)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 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
458 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
459 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
457 | > | current_mol = 0; |
458 | > | current_comp_mol = 0; |
459 | > | current_comp = 0; |
460 | > | current_atom_ndx = 0; |
461 | ||
462 | < | if (the_globals->haveTauThermostat()) |
463 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
464 | < | else if (the_globals->haveQmass()) |
465 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
466 | < | else { |
462 | > | for( i=0; i < n_cells ; i++ ){ |
463 | > | for( j=0; j < n_cells; j++ ){ |
464 | > | for( k=0; k < n_cells; k++ ){ |
465 | > | |
466 | > | makeElement( i * cellx, |
467 | > | j * celly, |
468 | > | k * cellz ); |
469 | > | |
470 | > | makeElement( i * cellx + 0.5 * cellx, |
471 | > | j * celly + 0.5 * celly, |
472 | > | k * cellz ); |
473 | > | |
474 | > | makeElement( i * cellx, |
475 | > | j * celly + 0.5 * celly, |
476 | > | k * cellz + 0.5 * cellz ); |
477 | > | |
478 | > | makeElement( i * cellx + 0.5 * cellx, |
479 | > | j * celly, |
480 | > | k * cellz + 0.5 * cellz ); |
481 | > | } |
482 | > | } |
483 | > | } |
484 | > | |
485 | > | if( have_extra ){ |
486 | > | done = 0; |
487 | > | |
488 | > | int start_ndx; |
489 | > | for( i=0; i < (n_cells+1) && !done; i++ ){ |
490 | > | for( j=0; j < (n_cells+1) && !done; j++ ){ |
491 | > | |
492 | > | if( i < n_cells ){ |
493 | > | |
494 | > | if( j < n_cells ){ |
495 | > | start_ndx = n_cells; |
496 | > | } |
497 | > | else start_ndx = 0; |
498 | > | } |
499 | > | else start_ndx = 0; |
500 | > | |
501 | > | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
502 | > | |
503 | > | makeElement( i * cellx, |
504 | > | j * celly, |
505 | > | k * cellz ); |
506 | > | done = ( current_mol >= tot_nmol ); |
507 | > | |
508 | > | if( !done && n_per_extra > 1 ){ |
509 | > | makeElement( i * cellx + 0.5 * cellx, |
510 | > | j * celly + 0.5 * celly, |
511 | > | k * cellz ); |
512 | > | done = ( current_mol >= tot_nmol ); |
513 | > | } |
514 | > | |
515 | > | if( !done && n_per_extra > 2){ |
516 | > | makeElement( i * cellx, |
517 | > | j * celly + 0.5 * celly, |
518 | > | k * cellz + 0.5 * cellz ); |
519 | > | done = ( current_mol >= tot_nmol ); |
520 | > | } |
521 | > | |
522 | > | if( !done && n_per_extra > 3){ |
523 | > | makeElement( i * cellx + 0.5 * cellx, |
524 | > | j * celly, |
525 | > | k * cellz + 0.5 * cellz ); |
526 | > | done = ( current_mol >= tot_nmol ); |
527 | > | } |
528 | > | } |
529 | > | } |
530 | > | } |
531 | > | } |
532 | > | |
533 | > | for( i=0; i<info[0].n_atoms; i++ ){ |
534 | > | info[0].atoms[i]->setVel( vel ); |
535 | > | } |
536 | > | } |
537 | > | |
538 | > | void SimSetup::makeElement( double x, double y, double z ){ |
539 | > | |
540 | > | int k; |
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 | > | |
548 | > | current_atom = comp_stamps[current_comp]->getAtom( k ); |
549 | > | if( !current_atom->havePosition() ){ |
550 | sprintf( painCave.errMsg, | |
551 | < | "SimSetup error: If you use one of the constant temperature\n" |
552 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
553 | < | " Neither of these was found in the BASS file.\n"); |
551 | > | "SimSetup:initFromBass error.\n" |
552 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
553 | > | "\tThe initialization routine is unable to give a start" |
554 | > | " position.\n", |
555 | > | comp_stamps[current_comp]->getID(), |
556 | > | current_atom->getType() ); |
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 | < | } else if ( !strcasecmp( ensemble, "NVE") ) { |
143 | < | } else { |
144 | < | sprintf( painCave.errMsg, |
145 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 | < | "reverting to NVE for this simulation.\n", |
147 | < | ensemble ); |
148 | < | painCave.isFatal = 0; |
149 | < | simError(); |
150 | < | strcpy( ensemble, "NVE" ); |
151 | < | } |
152 | < | strcpy( simnfo->ensemble, ensemble ); |
567 | > | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
568 | ||
569 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
570 | < | simnfo->usePBC = the_globals->getPBC(); |
571 | < | |
572 | < | int usesDipoles = 0; |
573 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
574 | < | the_ff = new TraPPE_ExFF(); |
575 | < | usesDipoles = 1; |
569 | > | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
570 | > | |
571 | > | rotMat[0][0] = 1.0; |
572 | > | rotMat[0][1] = 0.0; |
573 | > | rotMat[0][2] = 0.0; |
574 | > | |
575 | > | rotMat[1][0] = 0.0; |
576 | > | rotMat[1][1] = 1.0; |
577 | > | rotMat[1][2] = 0.0; |
578 | > | |
579 | > | rotMat[2][0] = 0.0; |
580 | > | rotMat[2][1] = 0.0; |
581 | > | rotMat[2][2] = 1.0; |
582 | > | |
583 | > | dAtom->setA( rotMat ); |
584 | > | } |
585 | > | |
586 | > | current_atom_ndx++; |
587 | } | |
588 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
588 | > | |
589 | > | current_mol++; |
590 | > | current_comp_mol++; |
591 | > | |
592 | > | if( current_comp_mol >= components_nmol[current_comp] ){ |
593 | > | |
594 | > | current_comp_mol = 0; |
595 | > | current_comp++; |
596 | > | } |
597 | > | } |
598 | > | |
599 | > | |
600 | > | void SimSetup::gatherInfo( void ){ |
601 | > | int i,j,k; |
602 | > | |
603 | > | ensembleCase = -1; |
604 | > | ffCase = -1; |
605 | > | |
606 | > | // set the easy ones first |
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, 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 168 | Line 628 | void SimSetup::createSim( void ){ | |
628 | simError(); | |
629 | } | |
630 | ||
631 | < | #ifdef IS_MPI |
172 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
173 | < | MPIcheckPoint(); |
174 | < | #endif // is_mpi |
631 | > | // get the ensemble |
632 | ||
633 | + | strcpy( ensemble, globals->getEnsemble() ); |
634 | + | |
635 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
636 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
637 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
638 | + | ensembleCase = NPTi_ENS; |
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, " |
654 | + | "reverting to NVE for this simulation.\n", |
655 | + | ensemble ); |
656 | + | painCave.isFatal = 0; |
657 | + | simError(); |
658 | + | strcpy( ensemble, "NVE" ); |
659 | + | ensembleCase = NVE_ENS; |
660 | + | } |
661 | + | |
662 | + | for(i=0; i<nInfo; i++){ |
663 | + | |
664 | + | strcpy( info[i].ensemble, ensemble ); |
665 | ||
666 | + | // get the mixing rule |
667 | + | |
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 | < | the_components = the_globals->getComponents(); |
673 | > | |
674 | > | the_components = globals->getComponents(); |
675 | components_nmol = new int[n_components]; | |
181 | – | comp_stamps = new MoleculeStamp*[n_components]; |
676 | ||
677 | < | if( !the_globals->haveNMol() ){ |
677 | > | |
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 209 | Line 704 | void SimSetup::createSim( void ){ | |
704 | " Please give nMol in the components.\n" ); | |
705 | painCave.isFatal = 1; | |
706 | simError(); | |
212 | – | |
213 | – | |
214 | – | // tot_nmol = the_globals->getNMol(); |
215 | – | |
216 | – | // //we have the total number of molecules, now we check for molfractions |
217 | – | // for( i=0; i<n_components; i++ ){ |
218 | – | |
219 | – | // if( !the_components[i]->haveMolFraction() ){ |
220 | – | |
221 | – | // if( !the_components[i]->haveNMol() ){ |
222 | – | // //we have a problem |
223 | – | // std::cerr << "SimSetup error. Neither molFraction nor " |
224 | – | // << " nMol was given in component |
225 | – | |
707 | } | |
708 | ||
709 | < | #ifdef IS_MPI |
229 | < | strcpy( checkPointMsg, "Have the number of components" ); |
230 | < | MPIcheckPoint(); |
231 | < | #endif // is_mpi |
232 | < | |
233 | < | // make an array of molecule stamps that match the components used. |
234 | < | // also extract the used stamps out into a separate linked list |
235 | < | |
236 | < | simnfo->nComponents = n_components; |
237 | < | simnfo->componentsNmol = components_nmol; |
238 | < | simnfo->compStamps = comp_stamps; |
239 | < | simnfo->headStamp = new LinkedMolStamp(); |
709 | > | // set the status, sample, and thermal kick times |
710 | ||
711 | < | char* id; |
242 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
243 | < | LinkedMolStamp* currentStamp = NULL; |
244 | < | for( i=0; i<n_components; i++ ){ |
711 | > | for(i=0; i<nInfo; i++){ |
712 | ||
713 | < | id = the_components[i]->getType(); |
714 | < | comp_stamps[i] = NULL; |
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 | < | // check to make sure the component isn't already in the list |
724 | > | if( globals->haveStatusTime() ){ |
725 | > | info[i].statusTime = globals->getStatusTime(); |
726 | > | } |
727 | > | |
728 | > | if( globals->haveThermalTime() ){ |
729 | > | info[i].thermalTime = globals->getThermalTime(); |
730 | > | } |
731 | ||
732 | < | comp_stamps[i] = headStamp->match( id ); |
733 | < | if( comp_stamps[i] == NULL ){ |
732 | > | // check for the temperature set flag |
733 | > | |
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 | < | // extract the component from the list; |
744 | > | info[i].setBox( boxVector ); |
745 | > | } |
746 | > | else if( globals->haveDensity() ){ |
747 | ||
748 | < | currentStamp = the_stamps->extractMolStamp( id ); |
749 | < | if( currentStamp == NULL ){ |
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: Component \"%s\" was not found in the " |
260 | < | "list of declared molecules\n", |
261 | < | id ); |
759 | > | "SimSetup error, no periodic BoxX size given.\n" ); |
760 | painCave.isFatal = 1; | |
761 | simError(); | |
762 | } | |
763 | + | boxVector[0] = globals->getBoxX(); |
764 | ||
765 | < | headStamp->add( currentStamp ); |
766 | < | comp_stamps[i] = headStamp->match( id ); |
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 | } | |
269 | – | } |
783 | ||
784 | + | } |
785 | + | |
786 | #ifdef IS_MPI | |
787 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
787 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
788 | MPIcheckPoint(); | |
789 | #endif // is_mpi | |
275 | – | |
790 | ||
791 | + | } |
792 | ||
793 | ||
794 | < | // caclulate the number of atoms, bonds, bends and torsions |
794 | > | void SimSetup::finalInfoCheck( void ){ |
795 | > | int index; |
796 | > | int usesDipoles; |
797 | > | int i; |
798 | ||
799 | < | tot_atoms = 0; |
800 | < | tot_bonds = 0; |
283 | < | tot_bends = 0; |
284 | < | tot_torsions = 0; |
285 | < | for( i=0; i<n_components; i++ ){ |
799 | > | for(i=0; i<nInfo; i++){ |
800 | > | // check electrostatic parameters |
801 | ||
802 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
803 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
804 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
805 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
806 | < | } |
807 | < | |
808 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
809 | < | |
810 | < | simnfo->n_atoms = tot_atoms; |
811 | < | simnfo->n_bonds = tot_bonds; |
812 | < | simnfo->n_bends = tot_bends; |
813 | < | simnfo->n_torsions = tot_torsions; |
814 | < | simnfo->n_SRI = tot_SRI; |
300 | < | simnfo->n_mol = tot_nmol; |
802 | > | index = 0; |
803 | > | usesDipoles = 0; |
804 | > | while( (index < info[i].n_atoms) && !usesDipoles ){ |
805 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
806 | > | index++; |
807 | > | } |
808 | > | |
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 | < | simnfo->molMembershipArray = new int[tot_atoms]; |
816 | > | if (globals->getUseRF() ) { |
817 | > | info[i].useReactionField = 1; |
818 | > | |
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 | > | theEcr = globals->getECR(); |
833 | > | } |
834 | > | |
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 | > | 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" ); |
898 | + | MPIcheckPoint(); |
899 | + | #endif // is_mpi |
900 | ||
901 | < | // divide the molecules among processors here. |
307 | < | |
308 | < | mpiSim = new mpiSimulation( simnfo ); |
309 | < | |
310 | < | globalIndex = mpiSim->divideLabor(); |
901 | > | } |
902 | ||
903 | < | // set up the local variables |
903 | > | void SimSetup::initSystemCoords( void ){ |
904 | > | int i; |
905 | ||
906 | < | int localMol, allMol; |
315 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
906 | > | std::cerr << "Setting atom Coords\n"; |
907 | ||
908 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
318 | < | int* molCompType = mpiSim->getMolComponentType(); |
908 | > | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
909 | ||
910 | < | allMol = 0; |
321 | < | localMol = 0; |
322 | < | local_atoms = 0; |
323 | < | local_bonds = 0; |
324 | < | local_bends = 0; |
325 | < | local_torsions = 0; |
326 | < | globalAtomIndex = 0; |
327 | < | |
328 | < | |
329 | < | for( i=0; i<n_components; i++ ){ |
330 | < | |
331 | < | for( j=0; j<components_nmol[i]; j++ ){ |
332 | < | |
333 | < | if( mol2proc[allMol] == worldRank ){ |
334 | < | |
335 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
336 | < | local_bonds += comp_stamps[i]->getNBonds(); |
337 | < | local_bends += comp_stamps[i]->getNBends(); |
338 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
339 | < | localMol++; |
340 | < | } |
341 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
342 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
343 | < | globalAtomIndex++; |
344 | < | } |
345 | < | |
346 | < | allMol++; |
347 | < | } |
348 | < | } |
349 | < | local_SRI = local_bonds + local_bends + local_torsions; |
910 | > | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
911 | ||
912 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
913 | < | |
914 | < | if( local_atoms != simnfo->n_atoms ){ |
912 | > | if( globals->haveInitialConfig() ){ |
913 | > | |
914 | > | InitializeFromFile* fileInit; |
915 | > | #ifdef IS_MPI // is_mpi |
916 | > | if( worldRank == 0 ){ |
917 | > | #endif //is_mpi |
918 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
919 | > | #ifdef IS_MPI |
920 | > | }else fileInit = new InitializeFromFile( NULL ); |
921 | > | #endif |
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 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
934 | < | " localAtom (%d) are not equal.\n", |
357 | < | simnfo->n_atoms, |
358 | < | local_atoms ); |
359 | < | painCave.isFatal = 1; |
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 | + | |
942 | + | #endif |
943 | } | |
362 | – | |
363 | – | simnfo->n_bonds = local_bonds; |
364 | – | simnfo->n_bends = local_bends; |
365 | – | simnfo->n_torsions = local_torsions; |
366 | – | simnfo->n_SRI = local_SRI; |
367 | – | simnfo->n_mol = localMol; |
368 | – | |
369 | – | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
370 | – | MPIcheckPoint(); |
944 | ||
945 | < | |
945 | > | #ifdef IS_MPI |
946 | > | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
947 | > | MPIcheckPoint(); |
948 | #endif // is_mpi | |
949 | ||
950 | + | } |
951 | ||
376 | – | // create the atom and short range interaction arrays |
952 | ||
953 | < | Atom::createArrays(simnfo->n_atoms); |
379 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
380 | < | the_molecules = new Molecule[simnfo->n_mol]; |
381 | < | int molIndex; |
382 | < | |
383 | < | // initialize the molecule's stampID's |
384 | < | |
385 | < | #ifdef IS_MPI |
953 | > | void SimSetup::makeOutNames( void ){ |
954 | ||
955 | + | int k; |
956 | ||
388 | – | molIndex = 0; |
389 | – | for(i=0; i<mpiSim->getTotNmol(); i++){ |
390 | – | |
391 | – | if(mol2proc[i] == worldRank ){ |
392 | – | the_molecules[molIndex].setStampID( molCompType[i] ); |
393 | – | the_molecules[molIndex].setMyIndex( molIndex ); |
394 | – | the_molecules[molIndex].setGlobalIndex( i ); |
395 | – | molIndex++; |
396 | – | } |
397 | – | } |
398 | – | |
399 | – | #else // is_mpi |
957 | ||
958 | < | molIndex = 0; |
959 | < | globalAtomIndex = 0; |
960 | < | for(i=0; i<n_components; i++){ |
961 | < | for(j=0; j<components_nmol[i]; j++ ){ |
962 | < | the_molecules[molIndex].setStampID( i ); |
963 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
964 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
965 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
966 | < | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
967 | < | globalAtomIndex++; |
968 | < | } |
969 | < | molIndex++; |
958 | > | for(k=0; k<nInfo; k++){ |
959 | > | |
960 | > | #ifdef IS_MPI |
961 | > | if( worldRank == 0 ){ |
962 | > | #endif // is_mpi |
963 | > | |
964 | > | if( globals->haveFinalConfig() ){ |
965 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
966 | > | } |
967 | > | else{ |
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, ".BASS" ) ){ |
976 | > | strcpy( endTest, ".eor" ); |
977 | > | } |
978 | > | else{ |
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 | > | // 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, ".BASS" ) ){ |
1002 | > | strcpy( endTest, ".dump" ); |
1003 | > | } |
1004 | > | else{ |
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 | > | 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, ".BASS" ) ){ |
1024 | > | strcpy( endTest, ".stat" ); |
1025 | > | } |
1026 | > | else{ |
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 | > | |
1039 | > | #ifdef IS_MPI |
1040 | } | |
1041 | + | #endif // is_mpi |
1042 | } | |
1043 | < | |
1043 | > | } |
1044 | ||
417 | – | #endif // is_mpi |
1045 | ||
1046 | + | void SimSetup::sysObjectsCreation( void ){ |
1047 | + | |
1048 | + | int i,k; |
1049 | + | |
1050 | + | // create the forceField |
1051 | + | |
1052 | + | createFF(); |
1053 | ||
1054 | < | if( simnfo->n_SRI ){ |
421 | < | |
422 | < | Exclude::createArray(simnfo->n_SRI); |
423 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
424 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
425 | < | simnfo->globalExcludes = new int; |
426 | < | simnfo->n_exclude = simnfo->n_SRI; |
427 | < | } |
428 | < | else{ |
429 | < | |
430 | < | Exclude::createArray( 1 ); |
431 | < | the_excludes = new Exclude*; |
432 | < | the_excludes[0] = new Exclude(0); |
433 | < | the_excludes[0]->setPair( 0,0 ); |
434 | < | simnfo->globalExcludes = new int; |
435 | < | simnfo->globalExcludes[0] = 0; |
436 | < | simnfo->n_exclude = 0; |
437 | < | } |
1054 | > | // extract componentList |
1055 | ||
1056 | < | // set the arrays into the SimInfo object |
1056 | > | compList(); |
1057 | ||
1058 | < | simnfo->atoms = the_atoms; |
442 | < | simnfo->molecules = the_molecules; |
443 | < | simnfo->nGlobalExcludes = 0; |
444 | < | simnfo->excludes = the_excludes; |
1058 | > | // calc the number of atoms, bond, bends, and torsions |
1059 | ||
1060 | + | calcSysValues(); |
1061 | ||
1062 | < | // get some of the tricky things that may still be in the globals |
1062 | > | #ifdef IS_MPI |
1063 | > | // divide the molecules among the processors |
1064 | > | |
1065 | > | mpiMolDivide(); |
1066 | > | #endif //is_mpi |
1067 | > | |
1068 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1069 | > | |
1070 | > | makeSysArrays(); |
1071 | ||
1072 | + | // make and initialize the molecules (all but atomic coordinates) |
1073 | ||
1074 | < | if( the_globals->haveBox() ){ |
1075 | < | simnfo->box_x = the_globals->getBox(); |
1076 | < | simnfo->box_y = the_globals->getBox(); |
1077 | < | simnfo->box_z = the_globals->getBox(); |
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 | < | else if( the_globals->haveDensity() ){ |
1082 | > | } |
1083 | ||
457 | – | double vol; |
458 | – | vol = (double)tot_nmol / the_globals->getDensity(); |
459 | – | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
460 | – | simnfo->box_y = simnfo->box_x; |
461 | – | simnfo->box_z = simnfo->box_x; |
462 | – | } |
463 | – | else{ |
464 | – | if( !the_globals->haveBoxX() ){ |
465 | – | sprintf( painCave.errMsg, |
466 | – | "SimSetup error, no periodic BoxX size given.\n" ); |
467 | – | painCave.isFatal = 1; |
468 | – | simError(); |
469 | – | } |
470 | – | simnfo->box_x = the_globals->getBoxX(); |
1084 | ||
1085 | < | if( !the_globals->haveBoxY() ){ |
473 | < | sprintf( painCave.errMsg, |
474 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
475 | < | painCave.isFatal = 1; |
476 | < | simError(); |
477 | < | } |
478 | < | simnfo->box_y = the_globals->getBoxY(); |
1085 | > | void SimSetup::createFF( void ){ |
1086 | ||
1087 | < | if( !the_globals->haveBoxZ() ){ |
1088 | < | sprintf( painCave.errMsg, |
1089 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
1090 | < | painCave.isFatal = 1; |
1091 | < | simError(); |
1092 | < | } |
1093 | < | simnfo->box_z = the_globals->getBoxZ(); |
1087 | > | switch( ffCase ){ |
1088 | > | |
1089 | > | case FF_DUFF: |
1090 | > | the_ff = new DUFF(); |
1091 | > | break; |
1092 | > | |
1093 | > | case FF_LJ: |
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"); |
1104 | > | painCave.isFatal = 1; |
1105 | > | simError(); |
1106 | } | |
1107 | ||
1108 | #ifdef IS_MPI | |
1109 | < | strcpy( checkPointMsg, "Box size set up" ); |
1109 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1110 | MPIcheckPoint(); | |
1111 | #endif // is_mpi | |
1112 | ||
1113 | + | } |
1114 | ||
495 | – | // initialize the arrays |
1115 | ||
1116 | < | the_ff->setSimInfo( simnfo ); |
1116 | > | void SimSetup::compList( void ){ |
1117 | ||
1118 | < | makeMolecules(); |
1119 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
1120 | < | for(i=0; i<simnfo->n_atoms; i++){ |
1121 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
1122 | < | } |
1118 | > | int i; |
1119 | > | char* id; |
1120 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1121 | > | LinkedMolStamp* currentStamp = NULL; |
1122 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1123 | ||
1124 | < | if (the_globals->getUseRF() ) { |
1125 | < | simnfo->useReactionField = 1; |
1124 | > | // make an array of molecule stamps that match the components used. |
1125 | > | // also extract the used stamps out into a separate linked list |
1126 | ||
1127 | < | if( !the_globals->haveECR() ){ |
1128 | < | sprintf( painCave.errMsg, |
1129 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1130 | < | "box length for the electrostaticCutoffRadius.\n" |
1131 | < | "I hope you have a very fast processor!\n"); |
1132 | < | painCave.isFatal = 0; |
1133 | < | simError(); |
515 | < | double smallest; |
516 | < | smallest = simnfo->box_x; |
517 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
518 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
519 | < | simnfo->ecr = 0.5 * smallest; |
520 | < | } else { |
521 | < | simnfo->ecr = the_globals->getECR(); |
522 | < | } |
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 | < | if( !the_globals->haveEST() ){ |
1136 | < | sprintf( painCave.errMsg, |
1137 | < | "SimSetup Warning: using default value of 0.05 * the " |
1138 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
528 | < | ); |
529 | < | painCave.isFatal = 0; |
530 | < | simError(); |
531 | < | simnfo->est = 0.05 * simnfo->ecr; |
532 | < | } else { |
533 | < | simnfo->est = the_globals->getEST(); |
534 | < | } |
1135 | > | for( i=0; i<n_components; i++ ){ |
1136 | > | |
1137 | > | id = the_components[i]->getType(); |
1138 | > | comp_stamps[i] = NULL; |
1139 | ||
1140 | < | if(!the_globals->haveDielectric() ){ |
1141 | < | sprintf( painCave.errMsg, |
1142 | < | "SimSetup Error: You are trying to use Reaction Field without" |
1143 | < | "setting a dielectric constant!\n" |
540 | < | ); |
541 | < | painCave.isFatal = 1; |
542 | < | simError(); |
543 | < | } |
544 | < | simnfo->dielectric = the_globals->getDielectric(); |
545 | < | } else { |
546 | < | if (usesDipoles) { |
1140 | > | // check to make sure the component isn't already in the list |
1141 | > | |
1142 | > | comp_stamps[i] = headStamp->match( id ); |
1143 | > | if( comp_stamps[i] == NULL ){ |
1144 | ||
1145 | < | if( !the_globals->haveECR() ){ |
549 | < | sprintf( painCave.errMsg, |
550 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
551 | < | "box length for the electrostaticCutoffRadius.\n" |
552 | < | "I hope you have a very fast processor!\n"); |
553 | < | painCave.isFatal = 0; |
554 | < | simError(); |
555 | < | double smallest; |
556 | < | smallest = simnfo->box_x; |
557 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
558 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 | < | simnfo->ecr = 0.5 * smallest; |
560 | < | } else { |
561 | < | simnfo->ecr = the_globals->getECR(); |
562 | < | } |
1145 | > | // extract the component from the list; |
1146 | ||
1147 | < | if( !the_globals->haveEST() ){ |
1148 | < | sprintf( painCave.errMsg, |
1149 | < | "SimSetup Warning: using default value of 5%% of the " |
1150 | < | "electrostaticCutoffRadius for the " |
1151 | < | "electrostaticSkinThickness\n" |
1152 | < | ); |
1153 | < | painCave.isFatal = 0; |
1154 | < | simError(); |
572 | < | simnfo->est = 0.05 * simnfo->ecr; |
573 | < | } else { |
574 | < | simnfo->est = the_globals->getEST(); |
1147 | > | currentStamp = stamps->extractMolStamp( id ); |
1148 | > | if( currentStamp == NULL ){ |
1149 | > | sprintf( painCave.errMsg, |
1150 | > | "SimSetup error: Component \"%s\" was not found in the " |
1151 | > | "list of declared molecules\n", |
1152 | > | id ); |
1153 | > | painCave.isFatal = 1; |
1154 | > | simError(); |
1155 | } | |
1156 | + | |
1157 | + | headStamp->add( currentStamp ); |
1158 | + | comp_stamps[i] = headStamp->match( id ); |
1159 | } | |
1160 | < | } |
1160 | > | } |
1161 | ||
1162 | #ifdef IS_MPI | |
1163 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
1163 | > | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1164 | MPIcheckPoint(); | |
1165 | #endif // is_mpi | |
1166 | ||
584 | – | if( the_globals->haveInitialConfig() ){ |
585 | – | |
586 | – | InitializeFromFile* fileInit; |
587 | – | #ifdef IS_MPI // is_mpi |
588 | – | if( worldRank == 0 ){ |
589 | – | #endif //is_mpi |
590 | – | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
591 | – | #ifdef IS_MPI |
592 | – | }else fileInit = new InitializeFromFile( NULL ); |
593 | – | #endif |
594 | – | fileInit->read_xyz( simnfo ); // default velocities on |
1167 | ||
1168 | < | delete fileInit; |
597 | < | } |
598 | < | else{ |
1168 | > | } |
1169 | ||
1170 | < | #ifdef IS_MPI |
1171 | < | |
602 | < | // no init from bass |
1170 | > | void SimSetup::calcSysValues( void ){ |
1171 | > | int i, j, k; |
1172 | ||
1173 | < | sprintf( painCave.errMsg, |
605 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
606 | < | painCave.isFatal; |
607 | < | simError(); |
1173 | > | int *molMembershipArray; |
1174 | ||
1175 | < | #else |
1175 | > | tot_atoms = 0; |
1176 | > | tot_bonds = 0; |
1177 | > | tot_bends = 0; |
1178 | > | tot_torsions = 0; |
1179 | > | for( i=0; i<n_components; i++ ){ |
1180 | > | |
1181 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1182 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1183 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1184 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1185 | > | } |
1186 | > | |
1187 | > | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1188 | > | molMembershipArray = new int[tot_atoms]; |
1189 | > | |
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 | ||
611 | – | initFromBass(); |
612 | – | |
613 | – | |
614 | – | #endif |
615 | – | } |
616 | – | |
1202 | #ifdef IS_MPI | |
618 | – | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
619 | – | MPIcheckPoint(); |
620 | – | #endif // 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 | ||
1210 | < | |
624 | < | |
1210 | > | mpiSim = new mpiSimulation( info ); |
1211 | ||
1212 | + | globalIndex = mpiSim->divideLabor(); |
1213 | ||
1214 | + | // set up the local variables |
1215 | ||
1216 | < | #ifdef IS_MPI |
1217 | < | if( worldRank == 0 ){ |
630 | < | #endif // is_mpi |
631 | < | |
632 | < | if( the_globals->haveFinalConfig() ){ |
633 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
634 | < | } |
635 | < | else{ |
636 | < | strcpy( simnfo->finalName, inFileName ); |
637 | < | char* endTest; |
638 | < | int nameLength = strlen( simnfo->finalName ); |
639 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
640 | < | if( !strcmp( endTest, ".bass" ) ){ |
641 | < | strcpy( endTest, ".eor" ); |
642 | < | } |
643 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
644 | < | strcpy( endTest, ".eor" ); |
645 | < | } |
646 | < | else{ |
647 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
648 | < | if( !strcmp( endTest, ".bss" ) ){ |
649 | < | strcpy( endTest, ".eor" ); |
650 | < | } |
651 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
652 | < | strcpy( endTest, ".eor" ); |
653 | < | } |
654 | < | else{ |
655 | < | strcat( simnfo->finalName, ".eor" ); |
656 | < | } |
657 | < | } |
658 | < | } |
659 | < | |
660 | < | // make the sample and status out names |
661 | < | |
662 | < | strcpy( simnfo->sampleName, inFileName ); |
663 | < | char* endTest; |
664 | < | int nameLength = strlen( simnfo->sampleName ); |
665 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
666 | < | if( !strcmp( endTest, ".bass" ) ){ |
667 | < | strcpy( endTest, ".dump" ); |
668 | < | } |
669 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
670 | < | strcpy( endTest, ".dump" ); |
671 | < | } |
672 | < | else{ |
673 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
674 | < | if( !strcmp( endTest, ".bss" ) ){ |
675 | < | strcpy( endTest, ".dump" ); |
676 | < | } |
677 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
678 | < | strcpy( endTest, ".dump" ); |
679 | < | } |
680 | < | else{ |
681 | < | strcat( simnfo->sampleName, ".dump" ); |
682 | < | } |
683 | < | } |
684 | < | |
685 | < | strcpy( simnfo->statusName, inFileName ); |
686 | < | nameLength = strlen( simnfo->statusName ); |
687 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
688 | < | if( !strcmp( endTest, ".bass" ) ){ |
689 | < | strcpy( endTest, ".stat" ); |
690 | < | } |
691 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
692 | < | strcpy( endTest, ".stat" ); |
693 | < | } |
694 | < | else{ |
695 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
696 | < | if( !strcmp( endTest, ".bss" ) ){ |
697 | < | strcpy( endTest, ".stat" ); |
698 | < | } |
699 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
700 | < | strcpy( endTest, ".stat" ); |
701 | < | } |
702 | < | else{ |
703 | < | strcat( simnfo->statusName, ".stat" ); |
704 | < | } |
705 | < | } |
706 | < | |
707 | < | #ifdef IS_MPI |
708 | < | } |
709 | < | #endif // is_mpi |
1216 | > | mol2proc = mpiSim->getMolToProcMap(); |
1217 | > | molCompType = mpiSim->getMolComponentType(); |
1218 | ||
1219 | < | // set the status, sample, and themal kick times |
1220 | < | |
1221 | < | if( the_globals->haveSampleTime() ){ |
1222 | < | simnfo->sampleTime = the_globals->getSampleTime(); |
1223 | < | simnfo->statusTime = simnfo->sampleTime; |
1224 | < | simnfo->thermalTime = simnfo->sampleTime; |
1225 | < | } |
718 | < | else{ |
719 | < | simnfo->sampleTime = the_globals->getRunTime(); |
720 | < | simnfo->statusTime = simnfo->sampleTime; |
721 | < | simnfo->thermalTime = simnfo->sampleTime; |
722 | < | } |
1219 | > | allMol = 0; |
1220 | > | localMol = 0; |
1221 | > | local_atoms = 0; |
1222 | > | local_bonds = 0; |
1223 | > | local_bends = 0; |
1224 | > | local_torsions = 0; |
1225 | > | globalAtomIndex = 0; |
1226 | ||
724 | – | if( the_globals->haveStatusTime() ){ |
725 | – | simnfo->statusTime = the_globals->getStatusTime(); |
726 | – | } |
1227 | ||
1228 | < | if( the_globals->haveThermalTime() ){ |
729 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
730 | < | } |
1228 | > | for( i=0; i<n_components; i++ ){ |
1229 | ||
1230 | < | // check for the temperature set flag |
1230 | > | for( j=0; j<components_nmol[i]; j++ ){ |
1231 | > | |
1232 | > | if( mol2proc[allMol] == worldRank ){ |
1233 | > | |
1234 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1235 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1236 | > | local_bends += comp_stamps[i]->getNBends(); |
1237 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1238 | > | localMol++; |
1239 | > | } |
1240 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1241 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1242 | > | globalAtomIndex++; |
1243 | > | } |
1244 | ||
1245 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
1246 | < | |
736 | < | |
737 | < | // // make the longe range forces and the integrator |
738 | < | |
739 | < | // new AllLong( simnfo ); |
740 | < | |
741 | < | |
742 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
743 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
1245 | > | allMol++; |
1246 | > | } |
1247 | } | |
1248 | < | else if( !strcmp( force_field, "LJ" ) ){ |
746 | < | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
747 | < | } |
748 | < | |
749 | < | #ifdef IS_MPI |
750 | < | mpiSim->mpiRefresh(); |
751 | < | #endif |
752 | < | |
753 | < | // initialize the Fortran |
754 | < | |
755 | < | |
756 | < | simnfo->refreshSim(); |
1248 | > | local_SRI = local_bonds + local_bends + local_torsions; |
1249 | ||
1250 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
1251 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1252 | < | } |
761 | < | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
762 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
763 | < | } |
764 | < | else{ |
1250 | > | info[0].n_atoms = mpiSim->getMyNlocal(); |
1251 | > | |
1252 | > | if( local_atoms != info[0].n_atoms ){ |
1253 | sprintf( painCave.errMsg, | |
1254 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1255 | < | simnfo->mixingRule ); |
1254 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1255 | > | " localAtom (%d) are not equal.\n", |
1256 | > | info[0].n_atoms, |
1257 | > | local_atoms ); |
1258 | painCave.isFatal = 1; | |
1259 | simError(); | |
1260 | } | |
1261 | ||
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 | < | #ifdef IS_MPI |
774 | < | strcpy( checkPointMsg, |
775 | < | "Successfully intialized the mixingRule for Fortran." ); |
1268 | > | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1269 | MPIcheckPoint(); | |
777 | – | #endif // is_mpi |
1270 | } | |
1271 | + | |
1272 | + | #endif // is_mpi |
1273 | ||
1274 | ||
1275 | < | void SimSetup::makeMolecules( void ){ |
1275 | > | void SimSetup::makeSysArrays( void ){ |
1276 | > | int i, j, k, l; |
1277 | ||
1278 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
1279 | < | molInit info; |
1280 | < | DirectionalAtom* dAtom; |
786 | < | LinkedAssign* extras; |
787 | < | LinkedAssign* current_extra; |
788 | < | AtomStamp* currentAtom; |
789 | < | BondStamp* currentBond; |
790 | < | BendStamp* currentBend; |
791 | < | TorsionStamp* currentTorsion; |
1278 | > | Atom** the_atoms; |
1279 | > | Molecule* the_molecules; |
1280 | > | Exclude** the_excludes; |
1281 | ||
793 | – | bond_pair* theBonds; |
794 | – | bend_set* theBends; |
795 | – | torsion_set* theTorsions; |
796 | – | |
1282 | ||
1283 | < | //init the forceField paramters |
799 | < | |
800 | < | the_ff->readParams(); |
801 | < | |
802 | < | |
803 | < | // init the atoms |
804 | < | |
805 | < | double ux, uy, uz, u, uSqr; |
806 | < | |
807 | < | atomOffset = 0; |
808 | < | excludeOffset = 0; |
809 | < | for(i=0; i<simnfo->n_mol; i++){ |
1283 | > | for(l=0; l<nInfo; l++){ |
1284 | ||
1285 | < | stampID = the_molecules[i].getStampID(); |
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 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
814 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
815 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
816 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
817 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
818 | < | |
819 | < | info.myAtoms = &the_atoms[atomOffset]; |
820 | < | info.myExcludes = &the_excludes[excludeOffset]; |
821 | < | info.myBonds = new Bond*[info.nBonds]; |
822 | < | info.myBends = new Bend*[info.nBends]; |
823 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
824 | < | |
825 | < | theBonds = new bond_pair[info.nBonds]; |
826 | < | theBends = new bend_set[info.nBends]; |
827 | < | theTorsions = new torsion_set[info.nTorsions]; |
1291 | > | // initialize the molecule's stampID's |
1292 | ||
1293 | < | // make the Atoms |
1293 | > | #ifdef IS_MPI |
1294 | ||
1295 | < | for(j=0; j<info.nAtoms; j++){ |
1296 | < | |
1297 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
1298 | < | if( currentAtom->haveOrientation() ){ |
1299 | < | |
1300 | < | dAtom = new DirectionalAtom(j + atomOffset); |
1301 | < | simnfo->n_oriented++; |
1302 | < | info.myAtoms[j] = dAtom; |
1303 | < | |
840 | < | ux = currentAtom->getOrntX(); |
841 | < | uy = currentAtom->getOrntY(); |
842 | < | uz = currentAtom->getOrntZ(); |
843 | < | |
844 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
845 | < | |
846 | < | u = sqrt( uSqr ); |
847 | < | ux = ux / u; |
848 | < | uy = uy / u; |
849 | < | uz = uz / u; |
850 | < | |
851 | < | dAtom->setSUx( ux ); |
852 | < | dAtom->setSUy( uy ); |
853 | < | dAtom->setSUz( uz ); |
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 | < | else{ |
1306 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1305 | > | } |
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[l].molMembershipArray[globalAtomIndex] = molIndex; |
1318 | > | globalAtomIndex++; |
1319 | > | } |
1320 | > | molIndex++; |
1321 | } | |
1322 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
1322 | > | } |
1323 | ||
860 | – | #ifdef IS_MPI |
861 | – | |
862 | – | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
863 | – | |
864 | – | #endif // is_mpi |
865 | – | } |
1324 | ||
1325 | < | // make the bonds |
868 | < | for(j=0; j<info.nBonds; j++){ |
869 | < | |
870 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
871 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
872 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
1325 | > | #endif // is_mpi |
1326 | ||
874 | – | exI = theBonds[j].a; |
875 | – | exJ = theBonds[j].b; |
1327 | ||
1328 | < | // exclude_I must always be the smaller of the pair |
1329 | < | if( exI > exJ ){ |
1330 | < | tempEx = exI; |
1331 | < | exI = exJ; |
1332 | < | exJ = tempEx; |
1328 | > | if( info[l].n_SRI ){ |
1329 | > | |
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 | < | #ifdef IS_MPI |
1336 | < | tempEx = exI; |
885 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
886 | < | tempEx = exJ; |
887 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
888 | < | |
889 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
890 | < | #else // isn't MPI |
891 | < | |
892 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
893 | < | #endif //is_mpi |
1335 | > | info[l].globalExcludes = new int; |
1336 | > | info[l].n_exclude = info[l].n_SRI; |
1337 | } | |
1338 | < | excludeOffset += info.nBonds; |
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[l].globalExcludes = new int; |
1345 | > | info[l].globalExcludes[0] = 0; |
1346 | > | info[l].n_exclude = 0; |
1347 | > | } |
1348 | ||
1349 | < | //make the bends |
1350 | < | for(j=0; j<info.nBends; j++){ |
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 | > | void SimSetup::makeIntegrator( void ){ |
1362 | > | |
1363 | > | int k; |
1364 | > | |
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 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
1382 | < | theBends[j].a = currentBend->getA() + atomOffset; |
1383 | < | theBends[j].b = currentBend->getB() + atomOffset; |
1384 | < | theBends[j].c = currentBend->getC() + atomOffset; |
1385 | < | |
1386 | < | if( currentBend->haveExtras() ){ |
1387 | < | |
1388 | < | extras = currentBend->getExtras(); |
1389 | < | current_extra = extras; |
1390 | < | |
1391 | < | while( current_extra != NULL ){ |
1392 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1393 | < | |
1394 | < | switch( current_extra->getType() ){ |
1395 | < | |
1396 | < | case 0: |
1397 | < | theBends[j].ghost = |
917 | < | current_extra->getInt() + atomOffset; |
918 | < | theBends[j].isGhost = 1; |
919 | < | break; |
920 | < | |
921 | < | case 1: |
922 | < | theBends[j].ghost = |
923 | < | (int)current_extra->getDouble() + atomOffset; |
924 | < | theBends[j].isGhost = 1; |
925 | < | break; |
926 | < | |
927 | < | default: |
928 | < | sprintf( painCave.errMsg, |
929 | < | "SimSetup Error: ghostVectorSource was neither a " |
930 | < | "double nor an int.\n" |
931 | < | "-->Bend[%d] in %s\n", |
932 | < | j, comp_stamps[stampID]->getID() ); |
933 | < | painCave.isFatal = 1; |
934 | < | simError(); |
935 | < | } |
936 | < | } |
937 | < | |
938 | < | else{ |
939 | < | |
940 | < | sprintf( painCave.errMsg, |
941 | < | "SimSetup Error: unhandled bend assignment:\n" |
942 | < | " -->%s in Bend[%d] in %s\n", |
943 | < | current_extra->getlhs(), |
944 | < | j, comp_stamps[stampID]->getID() ); |
945 | < | painCave.isFatal = 1; |
946 | < | simError(); |
947 | < | } |
948 | < | |
949 | < | current_extra = current_extra->getNext(); |
950 | < | } |
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 | < | |
1400 | < | if( !theBends[j].isGhost ){ |
1401 | < | |
1402 | < | exI = theBends[j].a; |
1403 | < | exJ = theBends[j].c; |
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 | < | |
1419 | < | exI = theBends[j].a; |
1420 | < | exJ = theBends[j].b; |
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 | < | // exclude_I must always be the smaller of the pair |
1426 | < | if( exI > exJ ){ |
1427 | < | tempEx = exI; |
1428 | < | exI = exJ; |
1429 | < | exJ = tempEx; |
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 | < | #ifdef IS_MPI |
971 | < | tempEx = exI; |
972 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
973 | < | tempEx = exJ; |
974 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1434 | > | break; |
1435 | ||
1436 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1437 | < | #else // isn't MPI |
1438 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
979 | < | #endif //is_mpi |
980 | < | } |
981 | < | excludeOffset += info.nBends; |
982 | < | |
983 | < | for(j=0; j<info.nTorsions; j++){ |
1436 | > | case NPTf_ENS: |
1437 | > | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1438 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1439 | ||
1440 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1441 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1442 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1443 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1444 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
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 | < | exI = theTorsions[j].a; |
1451 | < | exJ = theTorsions[j].d; |
1452 | < | |
1453 | < | // exclude_I must always be the smaller of the pair |
1454 | < | if( exI > exJ ){ |
1455 | < | tempEx = exI; |
1456 | < | exI = exJ; |
1457 | < | exJ = tempEx; |
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 | } | |
1000 | – | #ifdef IS_MPI |
1001 | – | tempEx = exI; |
1002 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1003 | – | tempEx = exJ; |
1004 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1459 | ||
1460 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1461 | < | #else // isn't MPI |
1462 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1463 | < | #endif //is_mpi |
1464 | < | } |
1465 | < | excludeOffset += info.nTorsions; |
1466 | < | |
1467 | < | |
1468 | < | // send the arrays off to the forceField for init. |
1469 | < | |
1470 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1471 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1472 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1473 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1474 | < | |
1475 | < | |
1476 | < | the_molecules[i].initialize( info ); |
1477 | < | |
1478 | < | |
1479 | < | atomOffset += info.nAtoms; |
1480 | < | delete[] theBonds; |
1481 | < | delete[] theBends; |
1482 | < | delete[] theTorsions; |
1483 | < | } |
1484 | < | |
1485 | < | #ifdef IS_MPI |
1486 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1487 | < | MPIcheckPoint(); |
1488 | < | #endif // is_mpi |
1489 | < | |
1490 | < | // clean up the forcefield |
1491 | < | the_ff->calcRcut(); |
1492 | < | the_ff->cleanMe(); |
1493 | < | |
1494 | < | } |
1495 | < | |
1496 | < | void SimSetup::initFromBass( void ){ |
1497 | < | |
1044 | < | int i, j, k; |
1045 | < | int n_cells; |
1046 | < | double cellx, celly, cellz; |
1047 | < | double temp1, temp2, temp3; |
1048 | < | int n_per_extra; |
1049 | < | int n_extra; |
1050 | < | int have_extra, done; |
1051 | < | |
1052 | < | temp1 = (double)tot_nmol / 4.0; |
1053 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1054 | < | temp3 = ceil( temp2 ); |
1055 | < | |
1056 | < | have_extra =0; |
1057 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1058 | < | have_extra =1; |
1059 | < | |
1060 | < | n_cells = (int)temp3 - 1; |
1061 | < | cellx = simnfo->box_x / temp3; |
1062 | < | celly = simnfo->box_y / temp3; |
1063 | < | cellz = simnfo->box_z / temp3; |
1064 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1065 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1066 | < | n_per_extra = (int)ceil( temp1 ); |
1067 | < | |
1068 | < | if( n_per_extra > 4){ |
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. There has been an error in constructing" |
1500 | < | " the non-complete lattice.\n" ); |
1499 | > | "SimSetup error: If you use an NPT\n" |
1500 | > | " ensemble, you must set tauBarostat.\n"); |
1501 | painCave.isFatal = 1; | |
1502 | simError(); | |
1503 | < | } |
1504 | < | } |
1505 | < | else{ |
1506 | < | n_cells = (int)temp3; |
1507 | < | cellx = simnfo->box_x / temp3; |
1508 | < | celly = simnfo->box_y / temp3; |
1509 | < | cellz = simnfo->box_z / temp3; |
1510 | < | } |
1511 | < | |
1512 | < | current_mol = 0; |
1513 | < | current_comp_mol = 0; |
1514 | < | current_comp = 0; |
1515 | < | current_atom_ndx = 0; |
1516 | < | |
1517 | < | for( i=0; i < n_cells ; i++ ){ |
1518 | < | for( j=0; j < n_cells; j++ ){ |
1519 | < | for( k=0; k < n_cells; k++ ){ |
1520 | < | |
1521 | < | makeElement( i * cellx, |
1522 | < | j * celly, |
1523 | < | k * cellz ); |
1524 | < | |
1525 | < | makeElement( i * cellx + 0.5 * cellx, |
1526 | < | j * celly + 0.5 * celly, |
1527 | < | k * cellz ); |
1528 | < | |
1529 | < | makeElement( i * cellx, |
1530 | < | j * celly + 0.5 * celly, |
1531 | < | k * cellz + 0.5 * cellz ); |
1532 | < | |
1533 | < | makeElement( i * cellx + 0.5 * cellx, |
1534 | < | j * celly, |
1535 | < | k * cellz + 0.5 * cellz ); |
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 | < | if( have_extra ){ |
1112 | < | done = 0; |
1739 | > | void SimSetup::initFortran( void ){ |
1740 | ||
1741 | < | int start_ndx; |
1742 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1743 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1744 | < | |
1118 | < | if( i < n_cells ){ |
1119 | < | |
1120 | < | if( j < n_cells ){ |
1121 | < | start_ndx = n_cells; |
1122 | < | } |
1123 | < | else start_ndx = 0; |
1124 | < | } |
1125 | < | else start_ndx = 0; |
1126 | < | |
1127 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1128 | < | |
1129 | < | makeElement( i * cellx, |
1130 | < | j * celly, |
1131 | < | k * cellz ); |
1132 | < | done = ( current_mol >= tot_nmol ); |
1133 | < | |
1134 | < | if( !done && n_per_extra > 1 ){ |
1135 | < | makeElement( i * cellx + 0.5 * cellx, |
1136 | < | j * celly + 0.5 * celly, |
1137 | < | k * cellz ); |
1138 | < | done = ( current_mol >= tot_nmol ); |
1139 | < | } |
1140 | < | |
1141 | < | if( !done && n_per_extra > 2){ |
1142 | < | makeElement( i * cellx, |
1143 | < | j * celly + 0.5 * celly, |
1144 | < | k * cellz + 0.5 * cellz ); |
1145 | < | done = ( current_mol >= tot_nmol ); |
1146 | < | } |
1147 | < | |
1148 | < | if( !done && n_per_extra > 3){ |
1149 | < | makeElement( i * cellx + 0.5 * cellx, |
1150 | < | j * celly, |
1151 | < | k * cellz + 0.5 * cellz ); |
1152 | < | done = ( current_mol >= tot_nmol ); |
1153 | < | } |
1154 | < | } |
1155 | < | } |
1156 | < | } |
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 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1759 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1760 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1761 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1762 | < | } |
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::makeElement( double x, double y, double z ){ |
1767 | < | |
1766 | > | void SimSetup::setupZConstraint() |
1767 | > | { |
1768 | int k; | |
1170 | – | AtomStamp* current_atom; |
1171 | – | DirectionalAtom* dAtom; |
1172 | – | double rotMat[3][3]; |
1769 | ||
1770 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1771 | < | |
1772 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1773 | < | if( !current_atom->havePosition() ){ |
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 | < | "SimSetup:initFromBass error.\n" |
1783 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
1181 | < | "\tThe initialization routine is unable to give a start" |
1182 | < | " position.\n", |
1183 | < | comp_stamps[current_comp]->getID(), |
1184 | < | current_atom->getType() ); |
1782 | > | "ZConstraint error: If you use an ZConstraint\n" |
1783 | > | " , you must set sample time.\n"); |
1784 | painCave.isFatal = 1; | |
1785 | < | simError(); |
1785 | > | simError(); |
1786 | } | |
1787 | < | |
1788 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1789 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1790 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1791 | < | |
1792 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1793 | < | |
1794 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1795 | < | |
1796 | < | rotMat[0][0] = 1.0; |
1797 | < | rotMat[0][1] = 0.0; |
1798 | < | rotMat[0][2] = 0.0; |
1799 | < | |
1201 | < | rotMat[1][0] = 0.0; |
1202 | < | rotMat[1][1] = 1.0; |
1203 | < | rotMat[1][2] = 0.0; |
1204 | < | |
1205 | < | rotMat[2][0] = 0.0; |
1206 | < | rotMat[2][1] = 0.0; |
1207 | < | rotMat[2][2] = 1.0; |
1208 | < | |
1209 | < | dAtom->setA( rotMat ); |
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 | < | |
1802 | < | current_atom_ndx++; |
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 | } | |
1214 | – | |
1215 | – | current_mol++; |
1216 | – | current_comp_mol++; |
1217 | – | |
1218 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
1219 | – | |
1220 | – | current_comp_mol = 0; |
1221 | – | current_comp++; |
1222 | – | } |
1824 | } |
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