# | Line 9 | Line 9 | |
---|---|---|
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
12 | + | #include "RigidBody.hpp" |
13 | + | //#include "ConjugateMinimizer.hpp" |
14 | + | #include "OOPSEMinimizer.hpp" |
15 | ||
16 | #ifdef IS_MPI | |
17 | #include "mpiBASS.h" | |
# | Line 24 | Line 27 | |
27 | #define NPTxyz_ENS 4 | |
28 | ||
29 | ||
30 | < | #define FF_DUFF 0 |
31 | < | #define FF_LJ 1 |
32 | < | #define FF_EAM 2 |
30 | > | #define FF_DUFF 0 |
31 | > | #define FF_LJ 1 |
32 | > | #define FF_EAM 2 |
33 | > | #define FF_H2O 3 |
34 | ||
35 | using namespace std; | |
36 | ||
37 | + | /** |
38 | + | * Check whether dividend is divisble by divisor or not |
39 | + | */ |
40 | + | bool isDivisible(double dividend, double divisor){ |
41 | + | double tolerance = 0.000001; |
42 | + | double quotient; |
43 | + | double diff; |
44 | + | int intQuotient; |
45 | + | |
46 | + | quotient = dividend / divisor; |
47 | + | |
48 | + | if (quotient < 0) |
49 | + | quotient = -quotient; |
50 | + | |
51 | + | intQuotient = int (quotient + tolerance); |
52 | + | |
53 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
54 | + | |
55 | + | if (diff <= tolerance) |
56 | + | return true; |
57 | + | else |
58 | + | return false; |
59 | + | } |
60 | + | |
61 | SimSetup::SimSetup(){ | |
62 | ||
63 | initSuspend = false; | |
# | Line 103 | Line 131 | void SimSetup::createSim(void){ | |
131 | ||
132 | sysObjectsCreation(); | |
133 | ||
134 | + | // check on the post processing info |
135 | + | |
136 | + | finalInfoCheck(); |
137 | + | |
138 | // initialize the system coordinates | |
139 | ||
140 | if ( !initSuspend ){ | |
# | Line 112 | Line 144 | void SimSetup::createSim(void){ | |
144 | info[0].currentTime = 0.0; | |
145 | } | |
146 | ||
115 | – | // check on the post processing info |
116 | – | |
117 | – | finalInfoCheck(); |
118 | – | |
147 | // make the output filenames | |
148 | ||
149 | makeOutNames(); | |
150 | < | |
123 | < | // make the integrator |
124 | < | |
125 | < | makeIntegrator(); |
126 | < | |
150 | > | |
151 | #ifdef IS_MPI | |
152 | mpiSim->mpiRefresh(); | |
153 | #endif | |
# | Line 131 | Line 155 | void SimSetup::createSim(void){ | |
155 | // initialize the Fortran | |
156 | ||
157 | initFortran(); | |
158 | + | |
159 | + | if (globals->haveMinimizer()) |
160 | + | // make minimizer |
161 | + | makeMinimizer(); |
162 | + | else |
163 | + | // make the integrator |
164 | + | makeIntegrator(); |
165 | + | |
166 | } | |
167 | ||
168 | ||
169 | void SimSetup::makeMolecules(void){ | |
170 | < | int k; |
171 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
170 | > | int i, j, k; |
171 | > | int exI, exJ, exK, exL, slI, slJ; |
172 | > | int tempI, tempJ, tempK, tempL; |
173 | > | int molI; |
174 | > | int stampID, atomOffset, rbOffset; |
175 | molInit molInfo; | |
176 | DirectionalAtom* dAtom; | |
177 | + | RigidBody* myRB; |
178 | + | StuntDouble* mySD; |
179 | LinkedAssign* extras; | |
180 | LinkedAssign* current_extra; | |
181 | AtomStamp* currentAtom; | |
182 | BondStamp* currentBond; | |
183 | BendStamp* currentBend; | |
184 | TorsionStamp* currentTorsion; | |
185 | + | RigidBodyStamp* currentRigidBody; |
186 | + | CutoffGroupStamp* currentCutoffGroup; |
187 | + | CutoffGroup* myCutoffGroup; |
188 | + | int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file |
189 | + | set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file |
190 | ||
191 | bond_pair* theBonds; | |
192 | bend_set* theBends; | |
193 | torsion_set* theTorsions; | |
194 | ||
195 | + | set<int> skipList; |
196 | ||
197 | + | double phi, theta, psi; |
198 | + | char* molName; |
199 | + | char rbName[100]; |
200 | + | |
201 | //init the forceField paramters | |
202 | ||
203 | the_ff->readParams(); | |
204 | ||
158 | – | |
205 | // init the atoms | |
206 | ||
207 | < | double ux, uy, uz, u, uSqr; |
207 | > | int nMembers, nNew, rb1, rb2; |
208 | ||
209 | for (k = 0; k < nInfo; k++){ | |
210 | the_ff->setSimInfo(&(info[k])); | |
211 | ||
212 | atomOffset = 0; | |
213 | < | excludeOffset = 0; |
213 | > | |
214 | for (i = 0; i < info[k].n_mol; i++){ | |
215 | stampID = info[k].molecules[i].getStampID(); | |
216 | + | molName = comp_stamps[stampID]->getID(); |
217 | ||
218 | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); | |
219 | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); | |
220 | molInfo.nBends = comp_stamps[stampID]->getNBends(); | |
221 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
222 | < | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
222 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
223 | ||
224 | + | nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
225 | + | |
226 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
178 | – | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
179 | – | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
180 | – | molInfo.myBends = new Bend * [molInfo.nBends]; |
181 | – | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
227 | ||
228 | + | if (molInfo.nBonds > 0) |
229 | + | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
230 | + | else |
231 | + | molInfo.myBonds = NULL; |
232 | + | |
233 | + | if (molInfo.nBends > 0) |
234 | + | molInfo.myBends = new Bend*[molInfo.nBends]; |
235 | + | else |
236 | + | molInfo.myBends = NULL; |
237 | + | |
238 | + | if (molInfo.nTorsions > 0) |
239 | + | molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
240 | + | else |
241 | + | molInfo.myTorsions = NULL; |
242 | + | |
243 | theBonds = new bond_pair[molInfo.nBonds]; | |
244 | theBends = new bend_set[molInfo.nBends]; | |
245 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
246 | < | |
246 | > | |
247 | // make the Atoms | |
248 | ||
249 | for (j = 0; j < molInfo.nAtoms; j++){ | |
250 | currentAtom = comp_stamps[stampID]->getAtom(j); | |
251 | + | |
252 | if (currentAtom->haveOrientation()){ | |
253 | dAtom = new DirectionalAtom((j + atomOffset), | |
254 | info[k].getConfiguration()); | |
255 | info[k].n_oriented++; | |
256 | molInfo.myAtoms[j] = dAtom; | |
257 | ||
258 | < | ux = currentAtom->getOrntX(); |
259 | < | uy = currentAtom->getOrntY(); |
260 | < | uz = currentAtom->getOrntZ(); |
258 | > | // Directional Atoms have standard unit vectors which are oriented |
259 | > | // in space using the three Euler angles. We assume the standard |
260 | > | // unit vector was originally along the z axis below. |
261 | ||
262 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
262 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
263 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
264 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
265 | ||
266 | < | u = sqrt(uSqr); |
267 | < | ux = ux / u; |
205 | < | uy = uy / u; |
206 | < | uz = uz / u; |
207 | < | |
208 | < | dAtom->setSUx(ux); |
209 | < | dAtom->setSUy(uy); |
210 | < | dAtom->setSUz(uz); |
266 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
267 | > | |
268 | } | |
269 | else{ | |
270 | < | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
271 | < | info[k].getConfiguration()); |
270 | > | |
271 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
272 | > | |
273 | } | |
216 | – | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
274 | ||
275 | + | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
276 | #ifdef IS_MPI | |
277 | ||
278 | < | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
278 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
279 | ||
280 | #endif // is_mpi | |
281 | } | |
# | Line 228 | Line 286 | void SimSetup::makeMolecules(void){ | |
286 | theBonds[j].a = currentBond->getA() + atomOffset; | |
287 | theBonds[j].b = currentBond->getB() + atomOffset; | |
288 | ||
289 | < | exI = theBonds[j].a; |
290 | < | exJ = theBonds[j].b; |
289 | > | tempI = theBonds[j].a; |
290 | > | tempJ = theBonds[j].b; |
291 | ||
234 | – | // exclude_I must always be the smaller of the pair |
235 | – | if (exI > exJ){ |
236 | – | tempEx = exI; |
237 | – | exI = exJ; |
238 | – | exJ = tempEx; |
239 | – | } |
292 | #ifdef IS_MPI | |
293 | < | tempEx = exI; |
294 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
295 | < | tempEx = exJ; |
296 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
293 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
294 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
295 | > | #else |
296 | > | exI = tempI + 1; |
297 | > | exJ = tempJ + 1; |
298 | > | #endif |
299 | ||
300 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
247 | < | #else // isn't MPI |
248 | < | |
249 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
250 | < | #endif //is_mpi |
300 | > | info[k].excludes->addPair(exI, exJ); |
301 | } | |
252 | – | excludeOffset += molInfo.nBonds; |
302 | ||
303 | //make the bends | |
304 | for (j = 0; j < molInfo.nBends; j++){ | |
# | Line 299 | Line 348 | void SimSetup::makeMolecules(void){ | |
348 | } | |
349 | } | |
350 | ||
351 | < | if (!theBends[j].isGhost){ |
352 | < | exI = theBends[j].a; |
353 | < | exJ = theBends[j].c; |
354 | < | } |
355 | < | else{ |
307 | < | exI = theBends[j].a; |
308 | < | exJ = theBends[j].b; |
309 | < | } |
310 | < | |
311 | < | // exclude_I must always be the smaller of the pair |
312 | < | if (exI > exJ){ |
313 | < | tempEx = exI; |
314 | < | exI = exJ; |
315 | < | exJ = tempEx; |
316 | < | } |
351 | > | if (theBends[j].isGhost) { |
352 | > | |
353 | > | tempI = theBends[j].a; |
354 | > | tempJ = theBends[j].b; |
355 | > | |
356 | #ifdef IS_MPI | |
357 | < | tempEx = exI; |
358 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
359 | < | tempEx = exJ; |
360 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
357 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
358 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
359 | > | #else |
360 | > | exI = tempI + 1; |
361 | > | exJ = tempJ + 1; |
362 | > | #endif |
363 | > | info[k].excludes->addPair(exI, exJ); |
364 | ||
365 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
366 | < | #else // isn't MPI |
367 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
368 | < | #endif //is_mpi |
365 | > | } else { |
366 | > | |
367 | > | tempI = theBends[j].a; |
368 | > | tempJ = theBends[j].b; |
369 | > | tempK = theBends[j].c; |
370 | > | |
371 | > | #ifdef IS_MPI |
372 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
373 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
374 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
375 | > | #else |
376 | > | exI = tempI + 1; |
377 | > | exJ = tempJ + 1; |
378 | > | exK = tempK + 1; |
379 | > | #endif |
380 | > | |
381 | > | info[k].excludes->addPair(exI, exK); |
382 | > | info[k].excludes->addPair(exI, exJ); |
383 | > | info[k].excludes->addPair(exJ, exK); |
384 | > | } |
385 | } | |
328 | – | excludeOffset += molInfo.nBends; |
386 | ||
387 | for (j = 0; j < molInfo.nTorsions; j++){ | |
388 | currentTorsion = comp_stamps[stampID]->getTorsion(j); | |
# | Line 334 | Line 391 | void SimSetup::makeMolecules(void){ | |
391 | theTorsions[j].c = currentTorsion->getC() + atomOffset; | |
392 | theTorsions[j].d = currentTorsion->getD() + atomOffset; | |
393 | ||
394 | < | exI = theTorsions[j].a; |
395 | < | exJ = theTorsions[j].d; |
396 | < | |
397 | < | // exclude_I must always be the smaller of the pair |
341 | < | if (exI > exJ){ |
342 | < | tempEx = exI; |
343 | < | exI = exJ; |
344 | < | exJ = tempEx; |
345 | < | } |
346 | < | #ifdef IS_MPI |
347 | < | tempEx = exI; |
348 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
349 | < | tempEx = exJ; |
350 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
351 | < | |
352 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
353 | < | #else // isn't MPI |
354 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
355 | < | #endif //is_mpi |
356 | < | } |
357 | < | excludeOffset += molInfo.nTorsions; |
394 | > | tempI = theTorsions[j].a; |
395 | > | tempJ = theTorsions[j].b; |
396 | > | tempK = theTorsions[j].c; |
397 | > | tempL = theTorsions[j].d; |
398 | ||
399 | + | #ifdef IS_MPI |
400 | + | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
401 | + | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
402 | + | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
403 | + | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
404 | + | #else |
405 | + | exI = tempI + 1; |
406 | + | exJ = tempJ + 1; |
407 | + | exK = tempK + 1; |
408 | + | exL = tempL + 1; |
409 | + | #endif |
410 | ||
411 | < | // send the arrays off to the forceField for init. |
411 | > | info[k].excludes->addPair(exI, exJ); |
412 | > | info[k].excludes->addPair(exI, exK); |
413 | > | info[k].excludes->addPair(exI, exL); |
414 | > | info[k].excludes->addPair(exJ, exK); |
415 | > | info[k].excludes->addPair(exJ, exL); |
416 | > | info[k].excludes->addPair(exK, exL); |
417 | > | } |
418 | ||
419 | + | |
420 | + | molInfo.myRigidBodies.clear(); |
421 | + | |
422 | + | for (j = 0; j < molInfo.nRigidBodies; j++){ |
423 | + | |
424 | + | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
425 | + | nMembers = currentRigidBody->getNMembers(); |
426 | + | |
427 | + | // Create the Rigid Body: |
428 | + | |
429 | + | myRB = new RigidBody(); |
430 | + | |
431 | + | sprintf(rbName,"%s_RB_%d", molName, j); |
432 | + | myRB->setType(rbName); |
433 | + | |
434 | + | for (rb1 = 0; rb1 < nMembers; rb1++) { |
435 | + | |
436 | + | // molI is atom numbering inside this molecule |
437 | + | molI = currentRigidBody->getMember(rb1); |
438 | + | |
439 | + | // tempI is atom numbering on local processor |
440 | + | tempI = molI + atomOffset; |
441 | + | |
442 | + | // currentAtom is the AtomStamp (which we need for |
443 | + | // rigid body reference positions) |
444 | + | currentAtom = comp_stamps[stampID]->getAtom(molI); |
445 | + | |
446 | + | // When we add to the rigid body, add the atom itself and |
447 | + | // the stamp info: |
448 | + | |
449 | + | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
450 | + | |
451 | + | // Add this atom to the Skip List for the integrators |
452 | + | #ifdef IS_MPI |
453 | + | slI = info[k].atoms[tempI]->getGlobalIndex(); |
454 | + | #else |
455 | + | slI = tempI; |
456 | + | #endif |
457 | + | skipList.insert(slI); |
458 | + | |
459 | + | } |
460 | + | |
461 | + | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
462 | + | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
463 | + | |
464 | + | tempI = currentRigidBody->getMember(rb1); |
465 | + | tempJ = currentRigidBody->getMember(rb2); |
466 | + | |
467 | + | // Some explanation is required here. |
468 | + | // Fortran indexing starts at 1, while c indexing starts at 0 |
469 | + | // Also, in parallel computations, the GlobalIndex is |
470 | + | // used for the exclude list: |
471 | + | |
472 | + | #ifdef IS_MPI |
473 | + | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
474 | + | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
475 | + | #else |
476 | + | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
477 | + | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
478 | + | #endif |
479 | + | |
480 | + | info[k].excludes->addPair(exI, exJ); |
481 | + | |
482 | + | } |
483 | + | } |
484 | + | |
485 | + | molInfo.myRigidBodies.push_back(myRB); |
486 | + | info[k].rigidBodies.push_back(myRB); |
487 | + | } |
488 | + | |
489 | + | |
490 | + | //create cutoff group for molecule |
491 | + | |
492 | + | cutoffAtomSet.clear(); |
493 | + | molInfo.myCutoffGroups.clear(); |
494 | + | |
495 | + | for (j = 0; j < nCutoffGroups; j++){ |
496 | + | |
497 | + | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
498 | + | nMembers = currentCutoffGroup->getNMembers(); |
499 | + | |
500 | + | myCutoffGroup = new CutoffGroup(); |
501 | + | |
502 | + | for (int cg = 0; cg < nMembers; cg++) { |
503 | + | |
504 | + | // molI is atom numbering inside this molecule |
505 | + | molI = currentCutoffGroup->getMember(cg); |
506 | + | |
507 | + | // tempI is atom numbering on local processor |
508 | + | tempI = molI + atomOffset; |
509 | + | |
510 | + | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
511 | + | |
512 | + | cutoffAtomSet.insert(tempI); |
513 | + | } |
514 | + | |
515 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
516 | + | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
517 | + | |
518 | + | //creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
519 | + | |
520 | + | for(j = 0; j < molInfo.nAtoms; j++){ |
521 | + | |
522 | + | if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
523 | + | myCutoffGroup = new CutoffGroup(); |
524 | + | myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
525 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
526 | + | } |
527 | + | |
528 | + | } |
529 | + | |
530 | + | |
531 | + | |
532 | + | |
533 | + | // After this is all set up, scan through the atoms to |
534 | + | // see if they can be added to the integrableObjects: |
535 | + | |
536 | + | molInfo.myIntegrableObjects.clear(); |
537 | + | |
538 | + | |
539 | + | for (j = 0; j < molInfo.nAtoms; j++){ |
540 | + | |
541 | + | #ifdef IS_MPI |
542 | + | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
543 | + | #else |
544 | + | slJ = j+atomOffset; |
545 | + | #endif |
546 | + | |
547 | + | // if they aren't on the skip list, then they can be integrated |
548 | + | |
549 | + | if (skipList.find(slJ) == skipList.end()) { |
550 | + | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
551 | + | info[k].integrableObjects.push_back(mySD); |
552 | + | molInfo.myIntegrableObjects.push_back(mySD); |
553 | + | } |
554 | + | } |
555 | + | |
556 | + | // all rigid bodies are integrated: |
557 | + | |
558 | + | for (j = 0; j < molInfo.nRigidBodies; j++) { |
559 | + | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
560 | + | info[k].integrableObjects.push_back(mySD); |
561 | + | molInfo.myIntegrableObjects.push_back(mySD); |
562 | + | } |
563 | + | |
564 | + | |
565 | + | // send the arrays off to the forceField for init. |
566 | + | |
567 | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); | |
568 | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); | |
569 | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); | |
570 | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, | |
571 | theTorsions); | |
572 | ||
368 | – | |
573 | info[k].molecules[i].initialize(molInfo); | |
574 | ||
575 | ||
# | Line 373 | Line 577 | void SimSetup::makeMolecules(void){ | |
577 | delete[] theBonds; | |
578 | delete[] theBends; | |
579 | delete[] theTorsions; | |
580 | < | } |
580 | > | } |
581 | } | |
582 | ||
583 | #ifdef IS_MPI | |
# | Line 381 | Line 585 | void SimSetup::makeMolecules(void){ | |
585 | MPIcheckPoint(); | |
586 | #endif // is_mpi | |
587 | ||
384 | – | // clean up the forcefield |
385 | – | |
386 | – | the_ff->calcRcut(); |
387 | – | the_ff->cleanMe(); |
588 | } | |
589 | ||
590 | void SimSetup::initFromBass(void){ | |
# | Line 585 | Line 785 | void SimSetup::gatherInfo(void){ | |
785 | else if (!strcasecmp(force_field, "EAM")){ | |
786 | ffCase = FF_EAM; | |
787 | } | |
788 | + | else if (!strcasecmp(force_field, "WATER")){ |
789 | + | ffCase = FF_H2O; |
790 | + | } |
791 | else{ | |
792 | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", | |
793 | force_field); | |
# | Line 613 | Line 816 | void SimSetup::gatherInfo(void){ | |
816 | } | |
817 | else{ | |
818 | sprintf(painCave.errMsg, | |
819 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
820 | < | "reverting to NVE for this simulation.\n", |
819 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
820 | > | "\treverting to NVE for this simulation.\n", |
821 | ensemble); | |
822 | painCave.isFatal = 0; | |
823 | simError(); | |
# | Line 646 | Line 849 | void SimSetup::gatherInfo(void){ | |
849 | if (!the_components[i]->haveNMol()){ | |
850 | // we have a problem | |
851 | sprintf(painCave.errMsg, | |
852 | < | "SimSetup Error. No global NMol or component NMol" |
853 | < | " given. Cannot calculate the number of atoms.\n"); |
852 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
853 | > | "\tCannot calculate the number of atoms.\n"); |
854 | painCave.isFatal = 1; | |
855 | simError(); | |
856 | } | |
# | Line 667 | Line 870 | void SimSetup::gatherInfo(void){ | |
870 | simError(); | |
871 | } | |
872 | ||
873 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
874 | + | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
875 | + | sprintf(painCave.errMsg, |
876 | + | "Sample time is not divisible by dt.\n" |
877 | + | "\tThis will result in samples that are not uniformly\n" |
878 | + | "\tdistributed in time. If this is a problem, change\n" |
879 | + | "\tyour sampleTime variable.\n"); |
880 | + | painCave.isFatal = 0; |
881 | + | simError(); |
882 | + | } |
883 | + | |
884 | + | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
885 | + | sprintf(painCave.errMsg, |
886 | + | "Status time is not divisible by dt.\n" |
887 | + | "\tThis will result in status reports that are not uniformly\n" |
888 | + | "\tdistributed in time. If this is a problem, change \n" |
889 | + | "\tyour statusTime variable.\n"); |
890 | + | painCave.isFatal = 0; |
891 | + | simError(); |
892 | + | } |
893 | + | |
894 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
895 | + | sprintf(painCave.errMsg, |
896 | + | "Thermal time is not divisible by dt.\n" |
897 | + | "\tThis will result in thermalizations that are not uniformly\n" |
898 | + | "\tdistributed in time. If this is a problem, change \n" |
899 | + | "\tyour thermalTime variable.\n"); |
900 | + | painCave.isFatal = 0; |
901 | + | simError(); |
902 | + | } |
903 | + | |
904 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
905 | + | sprintf(painCave.errMsg, |
906 | + | "Reset time is not divisible by dt.\n" |
907 | + | "\tThis will result in integrator resets that are not uniformly\n" |
908 | + | "\tdistributed in time. If this is a problem, change\n" |
909 | + | "\tyour resetTime variable.\n"); |
910 | + | painCave.isFatal = 0; |
911 | + | simError(); |
912 | + | } |
913 | + | |
914 | // set the status, sample, and thermal kick times | |
915 | ||
916 | for (i = 0; i < nInfo; i++){ | |
917 | if (globals->haveSampleTime()){ | |
918 | info[i].sampleTime = globals->getSampleTime(); | |
919 | info[i].statusTime = info[i].sampleTime; | |
676 | – | info[i].thermalTime = info[i].sampleTime; |
920 | } | |
921 | else{ | |
922 | info[i].sampleTime = globals->getRunTime(); | |
923 | info[i].statusTime = info[i].sampleTime; | |
681 | – | info[i].thermalTime = info[i].sampleTime; |
924 | } | |
925 | ||
926 | if (globals->haveStatusTime()){ | |
# | Line 687 | Line 929 | void SimSetup::gatherInfo(void){ | |
929 | ||
930 | if (globals->haveThermalTime()){ | |
931 | info[i].thermalTime = globals->getThermalTime(); | |
932 | + | } else { |
933 | + | info[i].thermalTime = globals->getRunTime(); |
934 | } | |
935 | ||
936 | info[i].resetIntegrator = 0; | |
# | Line 704 | Line 948 | void SimSetup::gatherInfo(void){ | |
948 | ||
949 | info[i].useInitXSstate = globals->getUseInitXSstate(); | |
950 | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); | |
951 | < | |
951 | > | |
952 | > | // check for thermodynamic integration |
953 | > | if (globals->getUseThermInt()) { |
954 | > | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
955 | > | info[i].useThermInt = globals->getUseThermInt(); |
956 | > | info[i].thermIntLambda = globals->getThermIntLambda(); |
957 | > | info[i].thermIntK = globals->getThermIntK(); |
958 | > | |
959 | > | Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
960 | > | info[i].restraint = myRestraint; |
961 | > | } |
962 | > | else { |
963 | > | sprintf(painCave.errMsg, |
964 | > | "SimSetup Error:\n" |
965 | > | "\tKeyword useThermInt was set to 'true' but\n" |
966 | > | "\tthermodynamicIntegrationLambda (and/or\n" |
967 | > | "\tthermodynamicIntegrationK) was not specified.\n" |
968 | > | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
969 | > | painCave.isFatal = 1; |
970 | > | simError(); |
971 | > | } |
972 | > | } |
973 | > | else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
974 | > | sprintf(painCave.errMsg, |
975 | > | "SimSetup Warning: If you want to use Thermodynamic\n" |
976 | > | "\tIntegration, set useThermInt to 'true' in your .bass file.\n" |
977 | > | "\tThe useThermInt keyword is 'false' by default, so your\n" |
978 | > | "\tlambda and/or k values are being ignored.\n"); |
979 | > | painCave.isFatal = 0; |
980 | > | simError(); |
981 | > | } |
982 | } | |
983 | ||
984 | //setup seed for random number generator | |
# | Line 746 | Line 1020 | void SimSetup::gatherInfo(void){ | |
1020 | for (int i = 0; i < nInfo; i++){ | |
1021 | info[i].setSeed(seedValue); | |
1022 | } | |
1023 | < | |
1023 | > | |
1024 | #ifdef IS_MPI | |
1025 | < | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
1025 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
1026 | MPIcheckPoint(); | |
1027 | #endif // is_mpi | |
1028 | } | |
# | Line 757 | Line 1031 | void SimSetup::finalInfoCheck(void){ | |
1031 | void SimSetup::finalInfoCheck(void){ | |
1032 | int index; | |
1033 | int usesDipoles; | |
1034 | + | int usesCharges; |
1035 | int i; | |
1036 | ||
1037 | for (i = 0; i < nInfo; i++){ | |
# | Line 768 | Line 1043 | void SimSetup::finalInfoCheck(void){ | |
1043 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
1044 | index++; | |
1045 | } | |
1046 | < | |
1046 | > | index = 0; |
1047 | > | usesCharges = 0; |
1048 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
1049 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
1050 | > | index++; |
1051 | > | } |
1052 | #ifdef IS_MPI | |
1053 | int myUse = usesDipoles; | |
1054 | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
1055 | #endif //is_mpi | |
1056 | ||
1057 | < | double theEcr, theEst; |
1057 | > | double theRcut, theRsw; |
1058 | ||
1059 | + | if (globals->haveRcut()) { |
1060 | + | theRcut = globals->getRcut(); |
1061 | + | |
1062 | + | if (globals->haveRsw()) |
1063 | + | theRsw = globals->getRsw(); |
1064 | + | else |
1065 | + | theRsw = theRcut; |
1066 | + | |
1067 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1068 | + | |
1069 | + | } else { |
1070 | + | |
1071 | + | the_ff->calcRcut(); |
1072 | + | theRcut = info[i].getRcut(); |
1073 | + | |
1074 | + | if (globals->haveRsw()) |
1075 | + | theRsw = globals->getRsw(); |
1076 | + | else |
1077 | + | theRsw = theRcut; |
1078 | + | |
1079 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1080 | + | } |
1081 | + | |
1082 | if (globals->getUseRF()){ | |
1083 | info[i].useReactionField = 1; | |
1084 | < | |
1085 | < | if (!globals->haveECR()){ |
1084 | > | |
1085 | > | if (!globals->haveRcut()){ |
1086 | sprintf(painCave.errMsg, | |
1087 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1088 | < | "box length for the electrostaticCutoffRadius.\n" |
1089 | < | "I hope you have a very fast processor!\n"); |
1087 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1088 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1089 | > | "\tfor the cutoffRadius.\n"); |
1090 | painCave.isFatal = 0; | |
1091 | simError(); | |
1092 | < | double smallest; |
790 | < | smallest = info[i].boxL[0]; |
791 | < | if (info[i].boxL[1] <= smallest) |
792 | < | smallest = info[i].boxL[1]; |
793 | < | if (info[i].boxL[2] <= smallest) |
794 | < | smallest = info[i].boxL[2]; |
795 | < | theEcr = 0.5 * smallest; |
1092 | > | theRcut = 15.0; |
1093 | } | |
1094 | else{ | |
1095 | < | theEcr = globals->getECR(); |
1095 | > | theRcut = globals->getRcut(); |
1096 | } | |
1097 | ||
1098 | < | if (!globals->haveEST()){ |
1098 | > | if (!globals->haveRsw()){ |
1099 | sprintf(painCave.errMsg, | |
1100 | < | "SimSetup Warning: using default value of 0.05 * the " |
1101 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
1100 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1101 | > | "\tOOPSE will use a default value of\n" |
1102 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1103 | painCave.isFatal = 0; | |
1104 | simError(); | |
1105 | < | theEst = 0.05 * theEcr; |
1105 | > | theRsw = 0.95 * theRcut; |
1106 | } | |
1107 | else{ | |
1108 | < | theEst = globals->getEST(); |
1108 | > | theRsw = globals->getRsw(); |
1109 | } | |
1110 | ||
1111 | < | info[i].setDefaultEcr(theEcr, theEst); |
1111 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1112 | ||
1113 | if (!globals->haveDielectric()){ | |
1114 | sprintf(painCave.errMsg, | |
1115 | < | "SimSetup Error: You are trying to use Reaction Field without" |
1116 | < | "setting a dielectric constant!\n"); |
1115 | > | "SimSetup Error: No Dielectric constant was set.\n" |
1116 | > | "\tYou are trying to use Reaction Field without" |
1117 | > | "\tsetting a dielectric constant!\n"); |
1118 | painCave.isFatal = 1; | |
1119 | simError(); | |
1120 | } | |
1121 | info[i].dielectric = globals->getDielectric(); | |
1122 | } | |
1123 | else{ | |
1124 | < | if (usesDipoles){ |
1125 | < | if (!globals->haveECR()){ |
1124 | > | if (usesDipoles || usesCharges){ |
1125 | > | |
1126 | > | if (!globals->haveRcut()){ |
1127 | sprintf(painCave.errMsg, | |
1128 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1129 | < | "box length for the electrostaticCutoffRadius.\n" |
1130 | < | "I hope you have a very fast processor!\n"); |
1128 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1129 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1130 | > | "\tfor the cutoffRadius.\n"); |
1131 | painCave.isFatal = 0; | |
1132 | simError(); | |
1133 | < | double smallest; |
1134 | < | smallest = info[i].boxL[0]; |
835 | < | if (info[i].boxL[1] <= smallest) |
836 | < | smallest = info[i].boxL[1]; |
837 | < | if (info[i].boxL[2] <= smallest) |
838 | < | smallest = info[i].boxL[2]; |
839 | < | theEcr = 0.5 * smallest; |
840 | < | } |
1133 | > | theRcut = 15.0; |
1134 | > | } |
1135 | else{ | |
1136 | < | theEcr = globals->getECR(); |
1136 | > | theRcut = globals->getRcut(); |
1137 | } | |
1138 | < | |
1139 | < | if (!globals->haveEST()){ |
1138 | > | |
1139 | > | if (!globals->haveRsw()){ |
1140 | sprintf(painCave.errMsg, | |
1141 | < | "SimSetup Warning: using default value of 0.05 * the " |
1142 | < | "electrostaticCutoffRadius for the " |
1143 | < | "electrostaticSkinThickness\n"); |
1141 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1142 | > | "\tOOPSE will use a default value of\n" |
1143 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1144 | painCave.isFatal = 0; | |
1145 | simError(); | |
1146 | < | theEst = 0.05 * theEcr; |
1146 | > | theRsw = 0.95 * theRcut; |
1147 | } | |
1148 | else{ | |
1149 | < | theEst = globals->getEST(); |
1149 | > | theRsw = globals->getRsw(); |
1150 | } | |
1151 | < | |
1152 | < | info[i].setDefaultEcr(theEcr, theEst); |
1151 | > | |
1152 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1153 | > | |
1154 | } | |
1155 | } | |
861 | – | |
862 | – | if( !initSuspend ) |
863 | – | info[i].checkCutOffs(); |
1156 | } | |
865 | – | |
1157 | #ifdef IS_MPI | |
1158 | strcpy(checkPointMsg, "post processing checks out"); | |
1159 | MPIcheckPoint(); | |
1160 | #endif // is_mpi | |
870 | – | } |
1161 | ||
1162 | + | // clean up the forcefield |
1163 | + | the_ff->cleanMe(); |
1164 | + | } |
1165 | + | |
1166 | void SimSetup::initSystemCoords(void){ | |
1167 | int i; | |
1168 | ||
# | Line 896 | Line 1190 | void SimSetup::initSystemCoords(void){ | |
1190 | delete fileInit; | |
1191 | } | |
1192 | else{ | |
1193 | < | #ifdef IS_MPI |
900 | < | |
1193 | > | |
1194 | // no init from bass | |
1195 | < | |
1195 | > | |
1196 | sprintf(painCave.errMsg, | |
1197 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
1197 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
1198 | painCave.isFatal = 1;; | |
1199 | simError(); | |
1200 | < | |
908 | < | #else |
909 | < | |
910 | < | initFromBass(); |
911 | < | |
912 | < | |
913 | < | #endif |
1200 | > | |
1201 | } | |
1202 | ||
1203 | #ifdef IS_MPI | |
# | Line 1001 | Line 1288 | void SimSetup::makeOutNames(void){ | |
1288 | } | |
1289 | else{ | |
1290 | strcat(info[k].statusName, ".stat"); | |
1291 | + | } |
1292 | + | } |
1293 | + | |
1294 | + | strcpy(info[k].rawPotName, inFileName); |
1295 | + | nameLength = strlen(info[k].rawPotName); |
1296 | + | endTest = &(info[k].rawPotName[nameLength - 5]); |
1297 | + | if (!strcmp(endTest, ".bass")){ |
1298 | + | strcpy(endTest, ".raw"); |
1299 | + | } |
1300 | + | else if (!strcmp(endTest, ".BASS")){ |
1301 | + | strcpy(endTest, ".raw"); |
1302 | + | } |
1303 | + | else{ |
1304 | + | endTest = &(info[k].rawPotName[nameLength - 4]); |
1305 | + | if (!strcmp(endTest, ".bss")){ |
1306 | + | strcpy(endTest, ".raw"); |
1307 | } | |
1308 | + | else if (!strcmp(endTest, ".mdl")){ |
1309 | + | strcpy(endTest, ".raw"); |
1310 | + | } |
1311 | + | else{ |
1312 | + | strcat(info[k].rawPotName, ".raw"); |
1313 | + | } |
1314 | } | |
1315 | ||
1316 | #ifdef IS_MPI | |
# | Line 1064 | Line 1373 | void SimSetup::createFF(void){ | |
1373 | the_ff = new EAM_FF(); | |
1374 | break; | |
1375 | ||
1376 | + | case FF_H2O: |
1377 | + | the_ff = new WATER(); |
1378 | + | break; |
1379 | + | |
1380 | default: | |
1381 | sprintf(painCave.errMsg, | |
1382 | "SimSetup Error. Unrecognized force field in case statement.\n"); | |
# | Line 1084 | Line 1397 | void SimSetup::compList(void){ | |
1397 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1398 | LinkedMolStamp* currentStamp = NULL; | |
1399 | comp_stamps = new MoleculeStamp * [n_components]; | |
1400 | + | bool haveCutoffGroups; |
1401 | ||
1402 | + | haveCutoffGroups = false; |
1403 | + | |
1404 | // make an array of molecule stamps that match the components used. | |
1405 | // also extract the used stamps out into a separate linked list | |
1406 | ||
# | Line 1119 | Line 1435 | void SimSetup::compList(void){ | |
1435 | headStamp->add(currentStamp); | |
1436 | comp_stamps[i] = headStamp->match(id); | |
1437 | } | |
1438 | + | |
1439 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1440 | + | haveCutoffGroups = true; |
1441 | } | |
1442 | + | |
1443 | + | for (i = 0; i < nInfo; i++) |
1444 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1445 | ||
1446 | #ifdef IS_MPI | |
1447 | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); | |
# | Line 1128 | Line 1450 | void SimSetup::calcSysValues(void){ | |
1450 | } | |
1451 | ||
1452 | void SimSetup::calcSysValues(void){ | |
1453 | < | int i; |
1453 | > | int i, j; |
1454 | > | int ncutgroups, atomsingroups, ngroupsinstamp; |
1455 | ||
1456 | int* molMembershipArray; | |
1457 | + | CutoffGroupStamp* cg; |
1458 | ||
1459 | tot_atoms = 0; | |
1460 | tot_bonds = 0; | |
1461 | tot_bends = 0; | |
1462 | tot_torsions = 0; | |
1463 | + | tot_rigid = 0; |
1464 | + | tot_groups = 0; |
1465 | for (i = 0; i < n_components; i++){ | |
1466 | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); | |
1467 | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); | |
1468 | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); | |
1469 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1470 | < | } |
1470 | > | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1471 | ||
1472 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1473 | + | atomsingroups = 0; |
1474 | + | for (j=0; j < ncutgroups; j++) { |
1475 | + | cg = comp_stamps[i]->getCutoffGroup(j); |
1476 | + | atomsingroups += cg->getNMembers(); |
1477 | + | } |
1478 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; |
1479 | + | tot_groups += components_nmol[i] * ngroupsinstamp; |
1480 | + | } |
1481 | + | |
1482 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1483 | molMembershipArray = new int[tot_atoms]; | |
1484 | ||
# | Line 1153 | Line 1489 | void SimSetup::calcSysValues(void){ | |
1489 | info[i].n_torsions = tot_torsions; | |
1490 | info[i].n_SRI = tot_SRI; | |
1491 | info[i].n_mol = tot_nmol; | |
1492 | < | |
1492 | > | info[i].ngroup = tot_groups; |
1493 | info[i].molMembershipArray = molMembershipArray; | |
1494 | } | |
1495 | } | |
# | Line 1164 | Line 1500 | void SimSetup::mpiMolDivide(void){ | |
1500 | int i, j, k; | |
1501 | int localMol, allMol; | |
1502 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1503 | + | int local_rigid, local_groups; |
1504 | + | vector<int> globalMolIndex; |
1505 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1506 | + | CutoffGroupStamp* cg; |
1507 | ||
1508 | mpiSim = new mpiSimulation(info); | |
1509 | ||
1510 | < | globalIndex = mpiSim->divideLabor(); |
1510 | > | mpiSim->divideLabor(); |
1511 | > | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1512 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1513 | ||
1514 | // set up the local variables | |
1515 | ||
# | Line 1180 | Line 1522 | void SimSetup::mpiMolDivide(void){ | |
1522 | local_bonds = 0; | |
1523 | local_bends = 0; | |
1524 | local_torsions = 0; | |
1525 | < | globalAtomIndex = 0; |
1525 | > | local_rigid = 0; |
1526 | > | local_groups = 0; |
1527 | > | globalAtomCounter = 0; |
1528 | ||
1185 | – | |
1529 | for (i = 0; i < n_components; i++){ | |
1530 | for (j = 0; j < components_nmol[i]; j++){ | |
1531 | if (mol2proc[allMol] == worldRank){ | |
# | Line 1190 | Line 1533 | void SimSetup::mpiMolDivide(void){ | |
1533 | local_bonds += comp_stamps[i]->getNBonds(); | |
1534 | local_bends += comp_stamps[i]->getNBends(); | |
1535 | local_torsions += comp_stamps[i]->getNTorsions(); | |
1536 | + | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1537 | + | |
1538 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1539 | + | atomsingroups = 0; |
1540 | + | for (k=0; k < ncutgroups; k++) { |
1541 | + | cg = comp_stamps[i]->getCutoffGroup(k); |
1542 | + | atomsingroups += cg->getNMembers(); |
1543 | + | } |
1544 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
1545 | + | ncutgroups; |
1546 | + | local_groups += ngroupsinstamp; |
1547 | + | |
1548 | localMol++; | |
1549 | } | |
1550 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1551 | < | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1552 | < | globalAtomIndex++; |
1551 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1552 | > | globalAtomCounter++; |
1553 | } | |
1554 | ||
1555 | allMol++; | |
# | Line 1202 | Line 1557 | void SimSetup::mpiMolDivide(void){ | |
1557 | } | |
1558 | local_SRI = local_bonds + local_bends + local_torsions; | |
1559 | ||
1560 | < | info[0].n_atoms = mpiSim->getMyNlocal(); |
1561 | < | |
1560 | > | info[0].n_atoms = mpiSim->getNAtomsLocal(); |
1561 | > | |
1562 | if (local_atoms != info[0].n_atoms){ | |
1563 | sprintf(painCave.errMsg, | |
1564 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1565 | < | " localAtom (%d) are not equal.\n", |
1564 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1565 | > | "\tlocalAtom (%d) are not equal.\n", |
1566 | info[0].n_atoms, local_atoms); | |
1567 | painCave.isFatal = 1; | |
1568 | simError(); | |
1569 | } | |
1570 | ||
1571 | + | info[0].ngroup = mpiSim->getNGroupsLocal(); |
1572 | + | if (local_groups != info[0].ngroup){ |
1573 | + | sprintf(painCave.errMsg, |
1574 | + | "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
1575 | + | "\tlocalGroups (%d) are not equal.\n", |
1576 | + | info[0].ngroup, local_groups); |
1577 | + | painCave.isFatal = 1; |
1578 | + | simError(); |
1579 | + | } |
1580 | + | |
1581 | info[0].n_bonds = local_bonds; | |
1582 | info[0].n_bends = local_bends; | |
1583 | info[0].n_torsions = local_torsions; | |
# | Line 1235 | Line 1600 | void SimSetup::makeSysArrays(void){ | |
1600 | ||
1601 | Atom** the_atoms; | |
1602 | Molecule* the_molecules; | |
1238 | – | Exclude** the_excludes; |
1603 | ||
1240 | – | |
1604 | for (l = 0; l < nInfo; l++){ | |
1605 | // create the atom and short range interaction arrays | |
1606 | ||
# | Line 1251 | Line 1614 | void SimSetup::makeSysArrays(void){ | |
1614 | ||
1615 | ||
1616 | molIndex = 0; | |
1617 | < | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1617 | > | for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
1618 | if (mol2proc[i] == worldRank){ | |
1619 | the_molecules[molIndex].setStampID(molCompType[i]); | |
1620 | the_molecules[molIndex].setMyIndex(molIndex); | |
# | Line 1263 | Line 1626 | void SimSetup::makeSysArrays(void){ | |
1626 | #else // is_mpi | |
1627 | ||
1628 | molIndex = 0; | |
1629 | < | globalAtomIndex = 0; |
1629 | > | globalAtomCounter = 0; |
1630 | for (i = 0; i < n_components; i++){ | |
1631 | for (j = 0; j < components_nmol[i]; j++){ | |
1632 | the_molecules[molIndex].setStampID(i); | |
1633 | the_molecules[molIndex].setMyIndex(molIndex); | |
1634 | the_molecules[molIndex].setGlobalIndex(molIndex); | |
1635 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1636 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1637 | < | globalAtomIndex++; |
1636 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1637 | > | globalAtomCounter++; |
1638 | } | |
1639 | molIndex++; | |
1640 | } | |
# | Line 1280 | Line 1643 | void SimSetup::makeSysArrays(void){ | |
1643 | ||
1644 | #endif // is_mpi | |
1645 | ||
1646 | < | |
1647 | < | if (info[l].n_SRI){ |
1648 | < | Exclude::createArray(info[l].n_SRI); |
1286 | < | the_excludes = new Exclude * [info[l].n_SRI]; |
1287 | < | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1288 | < | the_excludes[ex] = new Exclude(ex); |
1289 | < | } |
1290 | < | info[l].globalExcludes = new int; |
1291 | < | info[l].n_exclude = info[l].n_SRI; |
1292 | < | } |
1293 | < | else{ |
1294 | < | Exclude::createArray(1); |
1295 | < | the_excludes = new Exclude * ; |
1296 | < | the_excludes[0] = new Exclude(0); |
1297 | < | the_excludes[0]->setPair(0, 0); |
1298 | < | info[l].globalExcludes = new int; |
1299 | < | info[l].globalExcludes[0] = 0; |
1300 | < | info[l].n_exclude = 0; |
1301 | < | } |
1302 | < | |
1646 | > | info[l].globalExcludes = new int; |
1647 | > | info[l].globalExcludes[0] = 0; |
1648 | > | |
1649 | // set the arrays into the SimInfo object | |
1650 | ||
1651 | info[l].atoms = the_atoms; | |
1652 | info[l].molecules = the_molecules; | |
1653 | info[l].nGlobalExcludes = 0; | |
1654 | < | info[l].excludes = the_excludes; |
1309 | < | |
1654 | > | |
1655 | the_ff->setSimInfo(info); | |
1656 | } | |
1657 | } | |
# | Line 1349 | Line 1694 | void SimSetup::makeIntegrator(void){ | |
1694 | else{ | |
1695 | sprintf(painCave.errMsg, | |
1696 | "SimSetup error: If you use the NVT\n" | |
1697 | < | " ensemble, you must set tauThermostat.\n"); |
1697 | > | "\tensemble, you must set tauThermostat.\n"); |
1698 | painCave.isFatal = 1; | |
1699 | simError(); | |
1700 | } | |
# | Line 1372 | Line 1717 | void SimSetup::makeIntegrator(void){ | |
1717 | else{ | |
1718 | sprintf(painCave.errMsg, | |
1719 | "SimSetup error: If you use a constant pressure\n" | |
1720 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1720 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1721 | painCave.isFatal = 1; | |
1722 | simError(); | |
1723 | } | |
# | Line 1382 | Line 1727 | void SimSetup::makeIntegrator(void){ | |
1727 | else{ | |
1728 | sprintf(painCave.errMsg, | |
1729 | "SimSetup error: If you use an NPT\n" | |
1730 | < | " ensemble, you must set tauThermostat.\n"); |
1730 | > | "\tensemble, you must set tauThermostat.\n"); |
1731 | painCave.isFatal = 1; | |
1732 | simError(); | |
1733 | } | |
# | Line 1392 | Line 1737 | void SimSetup::makeIntegrator(void){ | |
1737 | else{ | |
1738 | sprintf(painCave.errMsg, | |
1739 | "SimSetup error: If you use an NPT\n" | |
1740 | < | " ensemble, you must set tauBarostat.\n"); |
1740 | > | "\tensemble, you must set tauBarostat.\n"); |
1741 | painCave.isFatal = 1; | |
1742 | simError(); | |
1743 | } | |
# | Line 1415 | Line 1760 | void SimSetup::makeIntegrator(void){ | |
1760 | else{ | |
1761 | sprintf(painCave.errMsg, | |
1762 | "SimSetup error: If you use a constant pressure\n" | |
1763 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1763 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1764 | painCave.isFatal = 1; | |
1765 | simError(); | |
1766 | } | |
# | Line 1426 | Line 1771 | void SimSetup::makeIntegrator(void){ | |
1771 | else{ | |
1772 | sprintf(painCave.errMsg, | |
1773 | "SimSetup error: If you use an NPT\n" | |
1774 | < | " ensemble, you must set tauThermostat.\n"); |
1774 | > | "\tensemble, you must set tauThermostat.\n"); |
1775 | painCave.isFatal = 1; | |
1776 | simError(); | |
1777 | } | |
# | Line 1437 | Line 1782 | void SimSetup::makeIntegrator(void){ | |
1782 | else{ | |
1783 | sprintf(painCave.errMsg, | |
1784 | "SimSetup error: If you use an NPT\n" | |
1785 | < | " ensemble, you must set tauBarostat.\n"); |
1785 | > | "\tensemble, you must set tauBarostat.\n"); |
1786 | painCave.isFatal = 1; | |
1787 | simError(); | |
1788 | } | |
# | Line 1460 | Line 1805 | void SimSetup::makeIntegrator(void){ | |
1805 | else{ | |
1806 | sprintf(painCave.errMsg, | |
1807 | "SimSetup error: If you use a constant pressure\n" | |
1808 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1808 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1809 | painCave.isFatal = 1; | |
1810 | simError(); | |
1811 | } | |
# | Line 1470 | Line 1815 | void SimSetup::makeIntegrator(void){ | |
1815 | else{ | |
1816 | sprintf(painCave.errMsg, | |
1817 | "SimSetup error: If you use an NPT\n" | |
1818 | < | " ensemble, you must set tauThermostat.\n"); |
1818 | > | "\tensemble, you must set tauThermostat.\n"); |
1819 | painCave.isFatal = 1; | |
1820 | simError(); | |
1821 | } | |
# | Line 1480 | Line 1825 | void SimSetup::makeIntegrator(void){ | |
1825 | else{ | |
1826 | sprintf(painCave.errMsg, | |
1827 | "SimSetup error: If you use an NPT\n" | |
1828 | < | " ensemble, you must set tauBarostat.\n"); |
1828 | > | "\tensemble, you must set tauBarostat.\n"); |
1829 | painCave.isFatal = 1; | |
1830 | simError(); | |
1831 | } | |
# | Line 1533 | Line 1878 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1878 | } | |
1879 | else{ | |
1880 | sprintf(painCave.errMsg, | |
1881 | < | "ZConstraint error: If you use an ZConstraint\n" |
1882 | < | " , you must set sample time.\n"); |
1881 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1882 | > | "\tyou must set zconsTime.\n"); |
1883 | painCave.isFatal = 1; | |
1884 | simError(); | |
1885 | } | |
# | Line 1549 | Line 1894 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1894 | else{ | |
1895 | double defaultZConsTol = 0.01; | |
1896 | sprintf(painCave.errMsg, | |
1897 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1898 | < | " , default value %f is used.\n", |
1897 | > | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1898 | > | "\tOOPSE will use a default value of %f.\n" |
1899 | > | "\tTo set the tolerance, use the zconsTol variable.\n", |
1900 | defaultZConsTol); | |
1901 | painCave.isFatal = 0; | |
1902 | simError(); | |
# | Line 1568 | Line 1914 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1914 | } | |
1915 | else{ | |
1916 | sprintf(painCave.errMsg, | |
1917 | < | "ZConstraint Warning: User does not set force Subtraction policy, " |
1918 | < | "PolicyByMass is used\n"); |
1917 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
1918 | > | "\tOOPSE will use PolicyByMass.\n" |
1919 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1920 | painCave.isFatal = 0; | |
1921 | simError(); | |
1922 | zconsForcePolicy->setData("BYMASS"); | |
# | Line 1577 | Line 1924 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1924 | ||
1925 | theInfo.addProperty(zconsForcePolicy); | |
1926 | ||
1927 | + | //set zcons gap |
1928 | + | DoubleData* zconsGap = new DoubleData(); |
1929 | + | zconsGap->setID(ZCONSGAP_ID); |
1930 | + | |
1931 | + | if (globals->haveZConsGap()){ |
1932 | + | zconsGap->setData(globals->getZconsGap()); |
1933 | + | theInfo.addProperty(zconsGap); |
1934 | + | } |
1935 | + | |
1936 | + | //set zcons fixtime |
1937 | + | DoubleData* zconsFixtime = new DoubleData(); |
1938 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
1939 | + | |
1940 | + | if (globals->haveZConsFixTime()){ |
1941 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
1942 | + | theInfo.addProperty(zconsFixtime); |
1943 | + | } |
1944 | + | |
1945 | + | //set zconsUsingSMD |
1946 | + | IntData* zconsUsingSMD = new IntData(); |
1947 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
1948 | + | |
1949 | + | if (globals->haveZConsUsingSMD()){ |
1950 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
1951 | + | theInfo.addProperty(zconsUsingSMD); |
1952 | + | } |
1953 | + | |
1954 | //Determine the name of ouput file and add it into SimInfo's property list | |
1955 | //Be careful, do not use inFileName, since it is a pointer which | |
1956 | //point to a string at master node, and slave nodes do not contain that string | |
# | Line 1606 | Line 1980 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1980 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1981 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
1982 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
1983 | < | |
1983 | > | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
1984 | > | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
1985 | zconsParaData->addItem(tempParaItem); | |
1986 | } | |
1987 | ||
1988 | //check the uniqueness of index | |
1989 | if(!zconsParaData->isIndexUnique()){ | |
1990 | sprintf(painCave.errMsg, | |
1991 | < | "ZConstraint Error: molIndex is not unique\n"); |
1991 | > | "ZConstraint Error: molIndex is not unique!\n"); |
1992 | painCave.isFatal = 1; | |
1993 | simError(); | |
1994 | } | |
# | Line 1624 | Line 1999 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1999 | //push data into siminfo, therefore, we can retrieve later | |
2000 | theInfo.addProperty(zconsParaData); | |
2001 | } | |
2002 | + | |
2003 | + | void SimSetup::makeMinimizer(){ |
2004 | + | |
2005 | + | OOPSEMinimizer* myOOPSEMinimizer; |
2006 | + | MinimizerParameterSet* param; |
2007 | + | char minimizerName[100]; |
2008 | + | |
2009 | + | for (int i = 0; i < nInfo; i++){ |
2010 | + | |
2011 | + | //prepare parameter set for minimizer |
2012 | + | param = new MinimizerParameterSet(); |
2013 | + | param->setDefaultParameter(); |
2014 | + | |
2015 | + | if (globals->haveMinimizer()){ |
2016 | + | param->setFTol(globals->getMinFTol()); |
2017 | + | } |
2018 | + | |
2019 | + | if (globals->haveMinGTol()){ |
2020 | + | param->setGTol(globals->getMinGTol()); |
2021 | + | } |
2022 | + | |
2023 | + | if (globals->haveMinMaxIter()){ |
2024 | + | param->setMaxIteration(globals->getMinMaxIter()); |
2025 | + | } |
2026 | + | |
2027 | + | if (globals->haveMinWriteFrq()){ |
2028 | + | param->setMaxIteration(globals->getMinMaxIter()); |
2029 | + | } |
2030 | + | |
2031 | + | if (globals->haveMinWriteFrq()){ |
2032 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
2033 | + | } |
2034 | + | |
2035 | + | if (globals->haveMinStepSize()){ |
2036 | + | param->setStepSize(globals->getMinStepSize()); |
2037 | + | } |
2038 | + | |
2039 | + | if (globals->haveMinLSMaxIter()){ |
2040 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
2041 | + | } |
2042 | + | |
2043 | + | if (globals->haveMinLSTol()){ |
2044 | + | param->setLineSearchTol(globals->getMinLSTol()); |
2045 | + | } |
2046 | + | |
2047 | + | strcpy(minimizerName, globals->getMinimizer()); |
2048 | + | |
2049 | + | if (!strcasecmp(minimizerName, "CG")){ |
2050 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2051 | + | } |
2052 | + | else if (!strcasecmp(minimizerName, "SD")){ |
2053 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
2054 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
2055 | + | } |
2056 | + | else{ |
2057 | + | sprintf(painCave.errMsg, |
2058 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
2059 | + | painCave.isFatal = 0; |
2060 | + | simError(); |
2061 | + | |
2062 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2063 | + | } |
2064 | + | info[i].the_integrator = myOOPSEMinimizer; |
2065 | + | |
2066 | + | //store the minimizer into simInfo |
2067 | + | info[i].the_minimizer = myOOPSEMinimizer; |
2068 | + | info[i].has_minimizer = true; |
2069 | + | } |
2070 | + | |
2071 | + | } |
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