# | Line 1 | Line 1 | |
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1 | #include <algorithm> | |
2 | < | #include <cstdlib> |
2 | > | #include <stdlib.h> |
3 | #include <iostream> | |
4 | < | #include <cmath> |
4 | > | #include <math.h> |
5 | #include <string> | |
6 | #include <sprng.h> | |
7 | – | |
7 | #include "SimSetup.hpp" | |
8 | #include "ReadWrite.hpp" | |
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 22 | Line 24 | |
24 | #define NVT_ENS 1 | |
25 | #define NPTi_ENS 2 | |
26 | #define NPTf_ENS 3 | |
27 | + | #define NPTxyz_ENS 4 |
28 | ||
26 | – | #define FF_DUFF 0 |
27 | – | #define FF_LJ 1 |
28 | – | #define FF_EAM 2 |
29 | ||
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; |
64 | isInfoArray = 0; | |
65 | nInfo = 1; | |
66 | ||
# | Line 52 | Line 83 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi | |
83 | info = the_info; | |
84 | nInfo = theNinfo; | |
85 | isInfoArray = 1; | |
86 | + | initSuspend = true; |
87 | } | |
88 | ||
89 | ||
# | Line 90 | Line 122 | void SimSetup::createSim(void){ | |
122 | #endif // is_mpi | |
123 | ||
124 | void SimSetup::createSim(void){ | |
93 | – | int i, j, k, globalAtomIndex; |
125 | ||
126 | // gather all of the information from the Bass file | |
127 | ||
# | Line 106 | Line 137 | void SimSetup::createSim(void){ | |
137 | ||
138 | // initialize the system coordinates | |
139 | ||
140 | < | if (!isInfoArray){ |
140 | > | if ( !initSuspend ){ |
141 | initSystemCoords(); | |
142 | + | |
143 | + | if( !(globals->getUseInitTime()) ) |
144 | + | info[0].currentTime = 0.0; |
145 | } | |
146 | ||
147 | // make the output filenames | |
148 | ||
149 | makeOutNames(); | |
150 | < | |
117 | < | // make the integrator |
118 | < | |
119 | < | makeIntegrator(); |
120 | < | |
150 | > | |
151 | #ifdef IS_MPI | |
152 | mpiSim->mpiRefresh(); | |
153 | #endif | |
# | Line 125 | 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, l; |
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 | < | |
185 | > | RigidBodyStamp* currentRigidBody; |
186 | > | CutoffGroupStamp* currentCutoffGroup; |
187 | > | CutoffGroup* myCutoffGroup; |
188 | > | |
189 | bond_pair* theBonds; | |
190 | bend_set* theBends; | |
191 | torsion_set* theTorsions; | |
192 | ||
193 | + | set<int> skipList; |
194 | ||
195 | + | double phi, theta, psi; |
196 | + | char* molName; |
197 | + | char rbName[100]; |
198 | + | |
199 | //init the forceField paramters | |
200 | ||
201 | the_ff->readParams(); | |
202 | ||
152 | – | |
203 | // init the atoms | |
204 | ||
205 | < | double ux, uy, uz, u, uSqr; |
205 | > | int nMembers, nNew, rb1, rb2; |
206 | ||
207 | for (k = 0; k < nInfo; k++){ | |
208 | the_ff->setSimInfo(&(info[k])); | |
209 | ||
210 | atomOffset = 0; | |
211 | < | excludeOffset = 0; |
211 | > | |
212 | for (i = 0; i < info[k].n_mol; i++){ | |
213 | stampID = info[k].molecules[i].getStampID(); | |
214 | + | molName = comp_stamps[stampID]->getID(); |
215 | ||
216 | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); | |
217 | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); | |
218 | molInfo.nBends = comp_stamps[stampID]->getNBends(); | |
219 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
220 | < | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
221 | < | |
220 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
221 | > | molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
222 | > | |
223 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
172 | – | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
173 | – | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
174 | – | molInfo.myBends = new Bend * [molInfo.nBends]; |
175 | – | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
224 | ||
225 | + | if (molInfo.nBonds > 0) |
226 | + | molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
227 | + | else |
228 | + | molInfo.myBonds = NULL; |
229 | + | |
230 | + | if (molInfo.nBends > 0) |
231 | + | molInfo.myBends = new (Bend *) [molInfo.nBends]; |
232 | + | else |
233 | + | molInfo.myBends = NULL; |
234 | + | |
235 | + | if (molInfo.nTorsions > 0) |
236 | + | molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
237 | + | else |
238 | + | molInfo.myTorsions = NULL; |
239 | + | |
240 | theBonds = new bond_pair[molInfo.nBonds]; | |
241 | theBends = new bend_set[molInfo.nBends]; | |
242 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
243 | < | |
243 | > | |
244 | // make the Atoms | |
245 | ||
246 | for (j = 0; j < molInfo.nAtoms; j++){ | |
247 | currentAtom = comp_stamps[stampID]->getAtom(j); | |
248 | + | |
249 | if (currentAtom->haveOrientation()){ | |
250 | dAtom = new DirectionalAtom((j + atomOffset), | |
251 | info[k].getConfiguration()); | |
252 | info[k].n_oriented++; | |
253 | molInfo.myAtoms[j] = dAtom; | |
254 | ||
255 | < | ux = currentAtom->getOrntX(); |
256 | < | uy = currentAtom->getOrntY(); |
257 | < | uz = currentAtom->getOrntZ(); |
255 | > | // Directional Atoms have standard unit vectors which are oriented |
256 | > | // in space using the three Euler angles. We assume the standard |
257 | > | // unit vector was originally along the z axis below. |
258 | ||
259 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
259 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
260 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
261 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
262 | ||
263 | < | u = sqrt(uSqr); |
264 | < | ux = ux / u; |
199 | < | uy = uy / u; |
200 | < | uz = uz / u; |
201 | < | |
202 | < | dAtom->setSUx(ux); |
203 | < | dAtom->setSUy(uy); |
204 | < | dAtom->setSUz(uz); |
263 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
264 | > | |
265 | } | |
266 | else{ | |
267 | < | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
268 | < | info[k].getConfiguration()); |
267 | > | |
268 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
269 | > | |
270 | } | |
210 | – | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
271 | ||
272 | + | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
273 | #ifdef IS_MPI | |
274 | ||
275 | < | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
275 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
276 | ||
277 | #endif // is_mpi | |
278 | } | |
# | Line 222 | Line 283 | void SimSetup::makeMolecules(void){ | |
283 | theBonds[j].a = currentBond->getA() + atomOffset; | |
284 | theBonds[j].b = currentBond->getB() + atomOffset; | |
285 | ||
286 | < | exI = theBonds[j].a; |
287 | < | exJ = theBonds[j].b; |
286 | > | tempI = theBonds[j].a; |
287 | > | tempJ = theBonds[j].b; |
288 | ||
228 | – | // exclude_I must always be the smaller of the pair |
229 | – | if (exI > exJ){ |
230 | – | tempEx = exI; |
231 | – | exI = exJ; |
232 | – | exJ = tempEx; |
233 | – | } |
289 | #ifdef IS_MPI | |
290 | < | tempEx = exI; |
291 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
292 | < | tempEx = exJ; |
293 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
290 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
291 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
292 | > | #else |
293 | > | exI = tempI + 1; |
294 | > | exJ = tempJ + 1; |
295 | > | #endif |
296 | ||
297 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
241 | < | #else // isn't MPI |
242 | < | |
243 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
244 | < | #endif //is_mpi |
297 | > | info[k].excludes->addPair(exI, exJ); |
298 | } | |
246 | – | excludeOffset += molInfo.nBonds; |
299 | ||
300 | //make the bends | |
301 | for (j = 0; j < molInfo.nBends; j++){ | |
# | Line 293 | Line 345 | void SimSetup::makeMolecules(void){ | |
345 | } | |
346 | } | |
347 | ||
348 | < | if (!theBends[j].isGhost){ |
349 | < | exI = theBends[j].a; |
350 | < | exJ = theBends[j].c; |
351 | < | } |
352 | < | else{ |
301 | < | exI = theBends[j].a; |
302 | < | exJ = theBends[j].b; |
303 | < | } |
304 | < | |
305 | < | // exclude_I must always be the smaller of the pair |
306 | < | if (exI > exJ){ |
307 | < | tempEx = exI; |
308 | < | exI = exJ; |
309 | < | exJ = tempEx; |
310 | < | } |
348 | > | if (theBends[j].isGhost) { |
349 | > | |
350 | > | tempI = theBends[j].a; |
351 | > | tempJ = theBends[j].b; |
352 | > | |
353 | #ifdef IS_MPI | |
354 | < | tempEx = exI; |
355 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
356 | < | tempEx = exJ; |
357 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
354 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
355 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
356 | > | #else |
357 | > | exI = tempI + 1; |
358 | > | exJ = tempJ + 1; |
359 | > | #endif |
360 | > | info[k].excludes->addPair(exI, exJ); |
361 | ||
362 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
363 | < | #else // isn't MPI |
364 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
365 | < | #endif //is_mpi |
362 | > | } else { |
363 | > | |
364 | > | tempI = theBends[j].a; |
365 | > | tempJ = theBends[j].b; |
366 | > | tempK = theBends[j].c; |
367 | > | |
368 | > | #ifdef IS_MPI |
369 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
370 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
371 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
372 | > | #else |
373 | > | exI = tempI + 1; |
374 | > | exJ = tempJ + 1; |
375 | > | exK = tempK + 1; |
376 | > | #endif |
377 | > | |
378 | > | info[k].excludes->addPair(exI, exK); |
379 | > | info[k].excludes->addPair(exI, exJ); |
380 | > | info[k].excludes->addPair(exJ, exK); |
381 | > | } |
382 | } | |
322 | – | excludeOffset += molInfo.nBends; |
383 | ||
384 | for (j = 0; j < molInfo.nTorsions; j++){ | |
385 | currentTorsion = comp_stamps[stampID]->getTorsion(j); | |
# | Line 328 | Line 388 | void SimSetup::makeMolecules(void){ | |
388 | theTorsions[j].c = currentTorsion->getC() + atomOffset; | |
389 | theTorsions[j].d = currentTorsion->getD() + atomOffset; | |
390 | ||
391 | < | exI = theTorsions[j].a; |
392 | < | exJ = theTorsions[j].d; |
391 | > | tempI = theTorsions[j].a; |
392 | > | tempJ = theTorsions[j].b; |
393 | > | tempK = theTorsions[j].c; |
394 | > | tempL = theTorsions[j].d; |
395 | ||
396 | < | // exclude_I must always be the smaller of the pair |
397 | < | if (exI > exJ){ |
398 | < | tempEx = exI; |
399 | < | exI = exJ; |
400 | < | exJ = tempEx; |
396 | > | #ifdef IS_MPI |
397 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
398 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
399 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
400 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
401 | > | #else |
402 | > | exI = tempI + 1; |
403 | > | exJ = tempJ + 1; |
404 | > | exK = tempK + 1; |
405 | > | exL = tempL + 1; |
406 | > | #endif |
407 | > | |
408 | > | info[k].excludes->addPair(exI, exJ); |
409 | > | info[k].excludes->addPair(exI, exK); |
410 | > | info[k].excludes->addPair(exI, exL); |
411 | > | info[k].excludes->addPair(exJ, exK); |
412 | > | info[k].excludes->addPair(exJ, exL); |
413 | > | info[k].excludes->addPair(exK, exL); |
414 | > | } |
415 | > | |
416 | > | |
417 | > | molInfo.myRigidBodies.clear(); |
418 | > | |
419 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
420 | > | |
421 | > | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
422 | > | nMembers = currentRigidBody->getNMembers(); |
423 | > | |
424 | > | // Create the Rigid Body: |
425 | > | |
426 | > | myRB = new RigidBody(); |
427 | > | |
428 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
429 | > | myRB->setType(rbName); |
430 | > | |
431 | > | for (rb1 = 0; rb1 < nMembers; rb1++) { |
432 | > | |
433 | > | // molI is atom numbering inside this molecule |
434 | > | molI = currentRigidBody->getMember(rb1); |
435 | > | |
436 | > | // tempI is atom numbering on local processor |
437 | > | tempI = molI + atomOffset; |
438 | > | |
439 | > | // currentAtom is the AtomStamp (which we need for |
440 | > | // rigid body reference positions) |
441 | > | currentAtom = comp_stamps[stampID]->getAtom(molI); |
442 | > | |
443 | > | // When we add to the rigid body, add the atom itself and |
444 | > | // the stamp info: |
445 | > | |
446 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
447 | > | |
448 | > | // Add this atom to the Skip List for the integrators |
449 | > | #ifdef IS_MPI |
450 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
451 | > | #else |
452 | > | slI = tempI; |
453 | > | #endif |
454 | > | skipList.insert(slI); |
455 | > | |
456 | } | |
457 | + | |
458 | + | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
459 | + | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
460 | + | |
461 | + | tempI = currentRigidBody->getMember(rb1); |
462 | + | tempJ = currentRigidBody->getMember(rb2); |
463 | + | |
464 | + | // Some explanation is required here. |
465 | + | // Fortran indexing starts at 1, while c indexing starts at 0 |
466 | + | // Also, in parallel computations, the GlobalIndex is |
467 | + | // used for the exclude list: |
468 | + | |
469 | #ifdef IS_MPI | |
470 | < | tempEx = exI; |
471 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
472 | < | tempEx = exJ; |
473 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
470 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
471 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
472 | > | #else |
473 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
474 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
475 | > | #endif |
476 | > | |
477 | > | info[k].excludes->addPair(exI, exJ); |
478 | > | |
479 | > | } |
480 | > | } |
481 | ||
482 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
483 | < | #else // isn't MPI |
348 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
349 | < | #endif //is_mpi |
482 | > | molInfo.myRigidBodies.push_back(myRB); |
483 | > | info[k].rigidBodies.push_back(myRB); |
484 | } | |
485 | < | excludeOffset += molInfo.nTorsions; |
485 | > | |
486 | ||
487 | + | //create cutoff group for molecule |
488 | + | molInfo.myCutoffGroups.clear(); |
489 | + | for (j = 0; j < molInfo.nCutoffGroups; j++){ |
490 | ||
491 | < | // send the arrays off to the forceField for init. |
491 | > | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
492 | > | nMembers = currentCutoffGroup->getNMembers(); |
493 | ||
494 | + | myCutoffGroup = new CutoffGroup(); |
495 | + | |
496 | + | for (int cg = 0; cg < nMembers; cg++) { |
497 | + | |
498 | + | // molI is atom numbering inside this molecule |
499 | + | molI = currentCutoffGroup->getMember(cg); |
500 | + | |
501 | + | // tempI is atom numbering on local processor |
502 | + | tempI = molI + atomOffset; |
503 | + | |
504 | + | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
505 | + | } |
506 | + | |
507 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
508 | + | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
509 | + | |
510 | + | |
511 | + | |
512 | + | // After this is all set up, scan through the atoms to |
513 | + | // see if they can be added to the integrableObjects: |
514 | + | |
515 | + | molInfo.myIntegrableObjects.clear(); |
516 | + | |
517 | + | |
518 | + | for (j = 0; j < molInfo.nAtoms; j++){ |
519 | + | |
520 | + | #ifdef IS_MPI |
521 | + | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
522 | + | #else |
523 | + | slJ = j+atomOffset; |
524 | + | #endif |
525 | + | |
526 | + | // if they aren't on the skip list, then they can be integrated |
527 | + | |
528 | + | if (skipList.find(slJ) == skipList.end()) { |
529 | + | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
530 | + | info[k].integrableObjects.push_back(mySD); |
531 | + | molInfo.myIntegrableObjects.push_back(mySD); |
532 | + | } |
533 | + | } |
534 | + | |
535 | + | // all rigid bodies are integrated: |
536 | + | |
537 | + | for (j = 0; j < molInfo.nRigidBodies; j++) { |
538 | + | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
539 | + | info[k].integrableObjects.push_back(mySD); |
540 | + | molInfo.myIntegrableObjects.push_back(mySD); |
541 | + | } |
542 | + | |
543 | + | |
544 | + | // send the arrays off to the forceField for init. |
545 | + | |
546 | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); | |
547 | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); | |
548 | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); | |
549 | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, | |
550 | theTorsions); | |
551 | ||
362 | – | |
552 | info[k].molecules[i].initialize(molInfo); | |
553 | ||
554 | ||
# | Line 367 | Line 556 | void SimSetup::makeMolecules(void){ | |
556 | delete[] theBonds; | |
557 | delete[] theBends; | |
558 | delete[] theTorsions; | |
559 | < | } |
559 | > | } |
560 | } | |
561 | ||
562 | #ifdef IS_MPI | |
# | Line 375 | Line 564 | void SimSetup::makeMolecules(void){ | |
564 | MPIcheckPoint(); | |
565 | #endif // is_mpi | |
566 | ||
378 | – | // clean up the forcefield |
379 | – | |
380 | – | the_ff->calcRcut(); |
381 | – | the_ff->cleanMe(); |
567 | } | |
568 | ||
569 | void SimSetup::initFromBass(void){ | |
# | Line 551 | Line 736 | void SimSetup::gatherInfo(void){ | |
736 | ||
737 | ||
738 | void SimSetup::gatherInfo(void){ | |
739 | < | int i, j, k; |
739 | > | int i; |
740 | ||
741 | ensembleCase = -1; | |
742 | ffCase = -1; | |
# | Line 579 | Line 764 | void SimSetup::gatherInfo(void){ | |
764 | else if (!strcasecmp(force_field, "EAM")){ | |
765 | ffCase = FF_EAM; | |
766 | } | |
767 | + | else if (!strcasecmp(force_field, "WATER")){ |
768 | + | ffCase = FF_H2O; |
769 | + | } |
770 | else{ | |
771 | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", | |
772 | force_field); | |
# | Line 602 | Line 790 | void SimSetup::gatherInfo(void){ | |
790 | else if (!strcasecmp(ensemble, "NPTf")){ | |
791 | ensembleCase = NPTf_ENS; | |
792 | } | |
793 | + | else if (!strcasecmp(ensemble, "NPTxyz")){ |
794 | + | ensembleCase = NPTxyz_ENS; |
795 | + | } |
796 | else{ | |
797 | sprintf(painCave.errMsg, | |
798 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
799 | < | "reverting to NVE for this simulation.\n", |
798 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
799 | > | "\treverting to NVE for this simulation.\n", |
800 | ensemble); | |
801 | painCave.isFatal = 0; | |
802 | simError(); | |
# | Line 637 | Line 828 | void SimSetup::gatherInfo(void){ | |
828 | if (!the_components[i]->haveNMol()){ | |
829 | // we have a problem | |
830 | sprintf(painCave.errMsg, | |
831 | < | "SimSetup Error. No global NMol or component NMol" |
832 | < | " given. Cannot calculate the number of atoms.\n"); |
831 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
832 | > | "\tCannot calculate the number of atoms.\n"); |
833 | painCave.isFatal = 1; | |
834 | simError(); | |
835 | } | |
# | Line 658 | Line 849 | void SimSetup::gatherInfo(void){ | |
849 | simError(); | |
850 | } | |
851 | ||
852 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
853 | + | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
854 | + | sprintf(painCave.errMsg, |
855 | + | "Sample time is not divisible by dt.\n" |
856 | + | "\tThis will result in samples that are not uniformly\n" |
857 | + | "\tdistributed in time. If this is a problem, change\n" |
858 | + | "\tyour sampleTime variable.\n"); |
859 | + | painCave.isFatal = 0; |
860 | + | simError(); |
861 | + | } |
862 | + | |
863 | + | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
864 | + | sprintf(painCave.errMsg, |
865 | + | "Status time is not divisible by dt.\n" |
866 | + | "\tThis will result in status reports that are not uniformly\n" |
867 | + | "\tdistributed in time. If this is a problem, change \n" |
868 | + | "\tyour statusTime variable.\n"); |
869 | + | painCave.isFatal = 0; |
870 | + | simError(); |
871 | + | } |
872 | + | |
873 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
874 | + | sprintf(painCave.errMsg, |
875 | + | "Thermal time is not divisible by dt.\n" |
876 | + | "\tThis will result in thermalizations that are not uniformly\n" |
877 | + | "\tdistributed in time. If this is a problem, change \n" |
878 | + | "\tyour thermalTime variable.\n"); |
879 | + | painCave.isFatal = 0; |
880 | + | simError(); |
881 | + | } |
882 | + | |
883 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
884 | + | sprintf(painCave.errMsg, |
885 | + | "Reset time is not divisible by dt.\n" |
886 | + | "\tThis will result in integrator resets that are not uniformly\n" |
887 | + | "\tdistributed in time. If this is a problem, change\n" |
888 | + | "\tyour resetTime variable.\n"); |
889 | + | painCave.isFatal = 0; |
890 | + | simError(); |
891 | + | } |
892 | + | |
893 | // set the status, sample, and thermal kick times | |
894 | ||
895 | for (i = 0; i < nInfo; i++){ | |
896 | if (globals->haveSampleTime()){ | |
897 | info[i].sampleTime = globals->getSampleTime(); | |
898 | info[i].statusTime = info[i].sampleTime; | |
667 | – | info[i].thermalTime = info[i].sampleTime; |
899 | } | |
900 | else{ | |
901 | info[i].sampleTime = globals->getRunTime(); | |
902 | info[i].statusTime = info[i].sampleTime; | |
672 | – | info[i].thermalTime = info[i].sampleTime; |
903 | } | |
904 | ||
905 | if (globals->haveStatusTime()){ | |
# | Line 678 | Line 908 | void SimSetup::gatherInfo(void){ | |
908 | ||
909 | if (globals->haveThermalTime()){ | |
910 | info[i].thermalTime = globals->getThermalTime(); | |
911 | + | } else { |
912 | + | info[i].thermalTime = globals->getRunTime(); |
913 | } | |
914 | ||
915 | info[i].resetIntegrator = 0; | |
# | Line 687 | Line 919 | void SimSetup::gatherInfo(void){ | |
919 | } | |
920 | ||
921 | // check for the temperature set flag | |
922 | < | |
922 | > | |
923 | if (globals->haveTempSet()) | |
924 | info[i].setTemp = globals->getTempSet(); | |
925 | ||
926 | < | // get some of the tricky things that may still be in the globals |
926 | > | // check for the extended State init |
927 | ||
928 | < | double boxVector[3]; |
929 | < | if (globals->haveBox()){ |
930 | < | boxVector[0] = globals->getBox(); |
699 | < | boxVector[1] = globals->getBox(); |
700 | < | boxVector[2] = globals->getBox(); |
701 | < | |
702 | < | info[i].setBox(boxVector); |
703 | < | } |
704 | < | else if (globals->haveDensity()){ |
705 | < | double vol; |
706 | < | vol = (double) tot_nmol / globals->getDensity(); |
707 | < | boxVector[0] = pow(vol, (1.0 / 3.0)); |
708 | < | boxVector[1] = boxVector[0]; |
709 | < | boxVector[2] = boxVector[0]; |
710 | < | |
711 | < | info[i].setBox(boxVector); |
712 | < | } |
713 | < | else{ |
714 | < | if (!globals->haveBoxX()){ |
715 | < | sprintf(painCave.errMsg, |
716 | < | "SimSetup error, no periodic BoxX size given.\n"); |
717 | < | painCave.isFatal = 1; |
718 | < | simError(); |
719 | < | } |
720 | < | boxVector[0] = globals->getBoxX(); |
721 | < | |
722 | < | if (!globals->haveBoxY()){ |
723 | < | sprintf(painCave.errMsg, |
724 | < | "SimSetup error, no periodic BoxY size given.\n"); |
725 | < | painCave.isFatal = 1; |
726 | < | simError(); |
727 | < | } |
728 | < | boxVector[1] = globals->getBoxY(); |
729 | < | |
730 | < | if (!globals->haveBoxZ()){ |
731 | < | sprintf(painCave.errMsg, |
732 | < | "SimSetup error, no periodic BoxZ size given.\n"); |
733 | < | painCave.isFatal = 1; |
734 | < | simError(); |
735 | < | } |
736 | < | boxVector[2] = globals->getBoxZ(); |
737 | < | |
738 | < | info[i].setBox(boxVector); |
739 | < | } |
928 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
929 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
930 | > | |
931 | } | |
932 | < | |
932 | > | |
933 | //setup seed for random number generator | |
934 | int seedValue; | |
935 | ||
# | Line 778 | Line 969 | void SimSetup::gatherInfo(void){ | |
969 | for (int i = 0; i < nInfo; i++){ | |
970 | info[i].setSeed(seedValue); | |
971 | } | |
972 | < | |
972 | > | |
973 | #ifdef IS_MPI | |
974 | < | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
974 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
975 | MPIcheckPoint(); | |
976 | #endif // is_mpi | |
977 | } | |
# | Line 789 | Line 980 | void SimSetup::finalInfoCheck(void){ | |
980 | void SimSetup::finalInfoCheck(void){ | |
981 | int index; | |
982 | int usesDipoles; | |
983 | + | int usesCharges; |
984 | int i; | |
985 | ||
986 | for (i = 0; i < nInfo; i++){ | |
# | Line 800 | Line 992 | void SimSetup::finalInfoCheck(void){ | |
992 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
993 | index++; | |
994 | } | |
995 | < | |
995 | > | index = 0; |
996 | > | usesCharges = 0; |
997 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
998 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
999 | > | index++; |
1000 | > | } |
1001 | #ifdef IS_MPI | |
1002 | int myUse = usesDipoles; | |
1003 | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
1004 | #endif //is_mpi | |
1005 | ||
1006 | < | double theEcr, theEst; |
1006 | > | double theRcut, theRsw; |
1007 | ||
1008 | + | if (globals->haveRcut()) { |
1009 | + | theRcut = globals->getRcut(); |
1010 | + | |
1011 | + | if (globals->haveRsw()) |
1012 | + | theRsw = globals->getRsw(); |
1013 | + | else |
1014 | + | theRsw = theRcut; |
1015 | + | |
1016 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1017 | + | |
1018 | + | } else { |
1019 | + | |
1020 | + | the_ff->calcRcut(); |
1021 | + | theRcut = info[i].getRcut(); |
1022 | + | |
1023 | + | if (globals->haveRsw()) |
1024 | + | theRsw = globals->getRsw(); |
1025 | + | else |
1026 | + | theRsw = theRcut; |
1027 | + | |
1028 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1029 | + | } |
1030 | + | |
1031 | if (globals->getUseRF()){ | |
1032 | info[i].useReactionField = 1; | |
1033 | < | |
1034 | < | if (!globals->haveECR()){ |
1033 | > | |
1034 | > | if (!globals->haveRcut()){ |
1035 | sprintf(painCave.errMsg, | |
1036 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1037 | < | "box length for the electrostaticCutoffRadius.\n" |
1038 | < | "I hope you have a very fast processor!\n"); |
1036 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1037 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1038 | > | "\tfor the cutoffRadius.\n"); |
1039 | painCave.isFatal = 0; | |
1040 | simError(); | |
1041 | < | double smallest; |
822 | < | smallest = info[i].boxL[0]; |
823 | < | if (info[i].boxL[1] <= smallest) |
824 | < | smallest = info[i].boxL[1]; |
825 | < | if (info[i].boxL[2] <= smallest) |
826 | < | smallest = info[i].boxL[2]; |
827 | < | theEcr = 0.5 * smallest; |
1041 | > | theRcut = 15.0; |
1042 | } | |
1043 | else{ | |
1044 | < | theEcr = globals->getECR(); |
1044 | > | theRcut = globals->getRcut(); |
1045 | } | |
1046 | ||
1047 | < | if (!globals->haveEST()){ |
1047 | > | if (!globals->haveRsw()){ |
1048 | sprintf(painCave.errMsg, | |
1049 | < | "SimSetup Warning: using default value of 0.05 * the " |
1050 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
1049 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1050 | > | "\tOOPSE will use a default value of\n" |
1051 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1052 | painCave.isFatal = 0; | |
1053 | simError(); | |
1054 | < | theEst = 0.05 * theEcr; |
1054 | > | theRsw = 0.95 * theRcut; |
1055 | } | |
1056 | else{ | |
1057 | < | theEst = globals->getEST(); |
1057 | > | theRsw = globals->getRsw(); |
1058 | } | |
1059 | ||
1060 | < | info[i].setEcr(theEcr, theEst); |
1060 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1061 | ||
1062 | if (!globals->haveDielectric()){ | |
1063 | sprintf(painCave.errMsg, | |
1064 | < | "SimSetup Error: You are trying to use Reaction Field without" |
1065 | < | "setting a dielectric constant!\n"); |
1064 | > | "SimSetup Error: No Dielectric constant was set.\n" |
1065 | > | "\tYou are trying to use Reaction Field without" |
1066 | > | "\tsetting a dielectric constant!\n"); |
1067 | painCave.isFatal = 1; | |
1068 | simError(); | |
1069 | } | |
1070 | info[i].dielectric = globals->getDielectric(); | |
1071 | } | |
1072 | else{ | |
1073 | < | if (usesDipoles){ |
1074 | < | if (!globals->haveECR()){ |
1073 | > | if (usesDipoles || usesCharges){ |
1074 | > | |
1075 | > | if (!globals->haveRcut()){ |
1076 | sprintf(painCave.errMsg, | |
1077 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1078 | < | "box length for the electrostaticCutoffRadius.\n" |
1079 | < | "I hope you have a very fast processor!\n"); |
1077 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1078 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1079 | > | "\tfor the cutoffRadius.\n"); |
1080 | painCave.isFatal = 0; | |
1081 | simError(); | |
1082 | < | double smallest; |
1083 | < | smallest = info[i].boxL[0]; |
867 | < | if (info[i].boxL[1] <= smallest) |
868 | < | smallest = info[i].boxL[1]; |
869 | < | if (info[i].boxL[2] <= smallest) |
870 | < | smallest = info[i].boxL[2]; |
871 | < | theEcr = 0.5 * smallest; |
872 | < | } |
1082 | > | theRcut = 15.0; |
1083 | > | } |
1084 | else{ | |
1085 | < | theEcr = globals->getECR(); |
1085 | > | theRcut = globals->getRcut(); |
1086 | } | |
1087 | < | |
1088 | < | if (!globals->haveEST()){ |
1087 | > | |
1088 | > | if (!globals->haveRsw()){ |
1089 | sprintf(painCave.errMsg, | |
1090 | < | "SimSetup Warning: using default value of 0.05 * the " |
1091 | < | "electrostaticCutoffRadius for the " |
1092 | < | "electrostaticSkinThickness\n"); |
1090 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1091 | > | "\tOOPSE will use a default value of\n" |
1092 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1093 | painCave.isFatal = 0; | |
1094 | simError(); | |
1095 | < | theEst = 0.05 * theEcr; |
1095 | > | theRsw = 0.95 * theRcut; |
1096 | } | |
1097 | else{ | |
1098 | < | theEst = globals->getEST(); |
1098 | > | theRsw = globals->getRsw(); |
1099 | } | |
1100 | < | |
1101 | < | info[i].setEcr(theEcr, theEst); |
1100 | > | |
1101 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1102 | > | |
1103 | } | |
1104 | } | |
1105 | } | |
894 | – | |
1106 | #ifdef IS_MPI | |
1107 | strcpy(checkPointMsg, "post processing checks out"); | |
1108 | MPIcheckPoint(); | |
1109 | #endif // is_mpi | |
899 | – | } |
1110 | ||
1111 | + | // clean up the forcefield |
1112 | + | the_ff->cleanMe(); |
1113 | + | } |
1114 | + | |
1115 | void SimSetup::initSystemCoords(void){ | |
1116 | int i; | |
1117 | ||
# | Line 914 | Line 1128 | void SimSetup::initSystemCoords(void){ | |
1128 | if (worldRank == 0){ | |
1129 | #endif //is_mpi | |
1130 | inName = globals->getInitialConfig(); | |
917 | – | double* tempDouble = new double[1000000]; |
1131 | fileInit = new InitializeFromFile(inName); | |
1132 | #ifdef IS_MPI | |
1133 | } | |
# | Line 926 | Line 1139 | void SimSetup::initSystemCoords(void){ | |
1139 | delete fileInit; | |
1140 | } | |
1141 | else{ | |
1142 | < | #ifdef IS_MPI |
930 | < | |
1142 | > | |
1143 | // no init from bass | |
1144 | < | |
1144 | > | |
1145 | sprintf(painCave.errMsg, | |
1146 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
1147 | < | painCave.isFatal; |
1146 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
1147 | > | painCave.isFatal = 1;; |
1148 | simError(); | |
1149 | < | |
938 | < | #else |
939 | < | |
940 | < | initFromBass(); |
941 | < | |
942 | < | |
943 | < | #endif |
1149 | > | |
1150 | } | |
1151 | ||
1152 | #ifdef IS_MPI | |
# | Line 1094 | Line 1300 | void SimSetup::createFF(void){ | |
1300 | the_ff = new EAM_FF(); | |
1301 | break; | |
1302 | ||
1303 | + | case FF_H2O: |
1304 | + | the_ff = new WATER(); |
1305 | + | break; |
1306 | + | |
1307 | default: | |
1308 | sprintf(painCave.errMsg, | |
1309 | "SimSetup Error. Unrecognized force field in case statement.\n"); | |
# | Line 1114 | Line 1324 | void SimSetup::compList(void){ | |
1324 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1325 | LinkedMolStamp* currentStamp = NULL; | |
1326 | comp_stamps = new MoleculeStamp * [n_components]; | |
1327 | + | bool haveCutoffGroups; |
1328 | ||
1329 | + | haveCutoffGroups = false; |
1330 | + | |
1331 | // make an array of molecule stamps that match the components used. | |
1332 | // also extract the used stamps out into a separate linked list | |
1333 | ||
# | Line 1149 | Line 1362 | void SimSetup::compList(void){ | |
1362 | headStamp->add(currentStamp); | |
1363 | comp_stamps[i] = headStamp->match(id); | |
1364 | } | |
1365 | + | |
1366 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1367 | + | haveCutoffGroups = true; |
1368 | } | |
1369 | + | |
1370 | + | for (i = 0; i < nInfo; i++) |
1371 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1372 | ||
1373 | #ifdef IS_MPI | |
1374 | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); | |
# | Line 1158 | Line 1377 | void SimSetup::calcSysValues(void){ | |
1377 | } | |
1378 | ||
1379 | void SimSetup::calcSysValues(void){ | |
1380 | < | int i, j, k; |
1380 | > | int i; |
1381 | ||
1382 | int* molMembershipArray; | |
1383 | ||
# | Line 1166 | Line 1385 | void SimSetup::calcSysValues(void){ | |
1385 | tot_bonds = 0; | |
1386 | tot_bends = 0; | |
1387 | tot_torsions = 0; | |
1388 | + | tot_rigid = 0; |
1389 | for (i = 0; i < n_components; i++){ | |
1390 | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); | |
1391 | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); | |
1392 | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); | |
1393 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1394 | + | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1395 | } | |
1396 | < | |
1396 | > | |
1397 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1398 | molMembershipArray = new int[tot_atoms]; | |
1399 | ||
# | Line 1194 | Line 1415 | void SimSetup::mpiMolDivide(void){ | |
1415 | int i, j, k; | |
1416 | int localMol, allMol; | |
1417 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1418 | + | int local_rigid; |
1419 | + | vector<int> globalMolIndex; |
1420 | ||
1421 | mpiSim = new mpiSimulation(info); | |
1422 | ||
1423 | < | globalIndex = mpiSim->divideLabor(); |
1423 | > | mpiSim->divideLabor(); |
1424 | > | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1425 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1426 | ||
1427 | // set up the local variables | |
1428 | ||
# | Line 1210 | Line 1435 | void SimSetup::mpiMolDivide(void){ | |
1435 | local_bonds = 0; | |
1436 | local_bends = 0; | |
1437 | local_torsions = 0; | |
1438 | < | globalAtomIndex = 0; |
1438 | > | local_rigid = 0; |
1439 | > | globalAtomCounter = 0; |
1440 | ||
1215 | – | |
1441 | for (i = 0; i < n_components; i++){ | |
1442 | for (j = 0; j < components_nmol[i]; j++){ | |
1443 | if (mol2proc[allMol] == worldRank){ | |
# | Line 1220 | Line 1445 | void SimSetup::mpiMolDivide(void){ | |
1445 | local_bonds += comp_stamps[i]->getNBonds(); | |
1446 | local_bends += comp_stamps[i]->getNBends(); | |
1447 | local_torsions += comp_stamps[i]->getNTorsions(); | |
1448 | + | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1449 | localMol++; | |
1450 | } | |
1451 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1452 | < | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1453 | < | globalAtomIndex++; |
1452 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1453 | > | globalAtomCounter++; |
1454 | } | |
1455 | ||
1456 | allMol++; | |
# | Line 1233 | Line 1459 | void SimSetup::mpiMolDivide(void){ | |
1459 | local_SRI = local_bonds + local_bends + local_torsions; | |
1460 | ||
1461 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1462 | + | |
1463 | ||
1464 | if (local_atoms != info[0].n_atoms){ | |
1465 | sprintf(painCave.errMsg, | |
1466 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1467 | < | " localAtom (%d) are not equal.\n", |
1466 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1467 | > | "\tlocalAtom (%d) are not equal.\n", |
1468 | info[0].n_atoms, local_atoms); | |
1469 | painCave.isFatal = 1; | |
1470 | simError(); | |
# | Line 1257 | Line 1484 | void SimSetup::makeSysArrays(void){ | |
1484 | ||
1485 | ||
1486 | void SimSetup::makeSysArrays(void){ | |
1487 | < | int i, j, k, l; |
1487 | > | |
1488 | > | #ifndef IS_MPI |
1489 | > | int k, j; |
1490 | > | #endif // is_mpi |
1491 | > | int i, l; |
1492 | ||
1493 | Atom** the_atoms; | |
1494 | Molecule* the_molecules; | |
1264 | – | Exclude** the_excludes; |
1495 | ||
1266 | – | |
1496 | for (l = 0; l < nInfo; l++){ | |
1497 | // create the atom and short range interaction arrays | |
1498 | ||
# | Line 1289 | Line 1518 | void SimSetup::makeSysArrays(void){ | |
1518 | #else // is_mpi | |
1519 | ||
1520 | molIndex = 0; | |
1521 | < | globalAtomIndex = 0; |
1521 | > | globalAtomCounter = 0; |
1522 | for (i = 0; i < n_components; i++){ | |
1523 | for (j = 0; j < components_nmol[i]; j++){ | |
1524 | the_molecules[molIndex].setStampID(i); | |
1525 | the_molecules[molIndex].setMyIndex(molIndex); | |
1526 | the_molecules[molIndex].setGlobalIndex(molIndex); | |
1527 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1528 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1529 | < | globalAtomIndex++; |
1528 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1529 | > | globalAtomCounter++; |
1530 | } | |
1531 | molIndex++; | |
1532 | } | |
# | Line 1306 | Line 1535 | void SimSetup::makeSysArrays(void){ | |
1535 | ||
1536 | #endif // is_mpi | |
1537 | ||
1538 | < | |
1539 | < | if (info[l].n_SRI){ |
1540 | < | Exclude::createArray(info[l].n_SRI); |
1312 | < | the_excludes = new Exclude * [info[l].n_SRI]; |
1313 | < | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1314 | < | the_excludes[ex] = new Exclude(ex); |
1315 | < | } |
1316 | < | info[l].globalExcludes = new int; |
1317 | < | info[l].n_exclude = info[l].n_SRI; |
1318 | < | } |
1319 | < | else{ |
1320 | < | Exclude::createArray(1); |
1321 | < | the_excludes = new Exclude * ; |
1322 | < | the_excludes[0] = new Exclude(0); |
1323 | < | the_excludes[0]->setPair(0, 0); |
1324 | < | info[l].globalExcludes = new int; |
1325 | < | info[l].globalExcludes[0] = 0; |
1326 | < | info[l].n_exclude = 0; |
1327 | < | } |
1328 | < | |
1538 | > | info[l].globalExcludes = new int; |
1539 | > | info[l].globalExcludes[0] = 0; |
1540 | > | |
1541 | // set the arrays into the SimInfo object | |
1542 | ||
1543 | info[l].atoms = the_atoms; | |
1544 | info[l].molecules = the_molecules; | |
1545 | info[l].nGlobalExcludes = 0; | |
1546 | < | info[l].excludes = the_excludes; |
1335 | < | |
1546 | > | |
1547 | the_ff->setSimInfo(info); | |
1548 | } | |
1549 | } | |
# | Line 1344 | Line 1555 | void SimSetup::makeIntegrator(void){ | |
1555 | NVT<RealIntegrator>* myNVT = NULL; | |
1556 | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; | |
1557 | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; | |
1558 | + | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1559 | ||
1560 | for (k = 0; k < nInfo; k++){ | |
1561 | switch (ensembleCase){ | |
# | Line 1374 | Line 1586 | void SimSetup::makeIntegrator(void){ | |
1586 | else{ | |
1587 | sprintf(painCave.errMsg, | |
1588 | "SimSetup error: If you use the NVT\n" | |
1589 | < | " ensemble, you must set tauThermostat.\n"); |
1589 | > | "\tensemble, you must set tauThermostat.\n"); |
1590 | painCave.isFatal = 1; | |
1591 | simError(); | |
1592 | } | |
# | Line 1397 | Line 1609 | void SimSetup::makeIntegrator(void){ | |
1609 | else{ | |
1610 | sprintf(painCave.errMsg, | |
1611 | "SimSetup error: If you use a constant pressure\n" | |
1612 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1612 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1613 | painCave.isFatal = 1; | |
1614 | simError(); | |
1615 | } | |
# | Line 1407 | Line 1619 | void SimSetup::makeIntegrator(void){ | |
1619 | else{ | |
1620 | sprintf(painCave.errMsg, | |
1621 | "SimSetup error: If you use an NPT\n" | |
1622 | < | " ensemble, you must set tauThermostat.\n"); |
1622 | > | "\tensemble, you must set tauThermostat.\n"); |
1623 | painCave.isFatal = 1; | |
1624 | simError(); | |
1625 | } | |
# | Line 1417 | Line 1629 | void SimSetup::makeIntegrator(void){ | |
1629 | else{ | |
1630 | sprintf(painCave.errMsg, | |
1631 | "SimSetup error: If you use an NPT\n" | |
1632 | < | " ensemble, you must set tauBarostat.\n"); |
1632 | > | "\tensemble, you must set tauBarostat.\n"); |
1633 | painCave.isFatal = 1; | |
1634 | simError(); | |
1635 | } | |
# | Line 1440 | Line 1652 | void SimSetup::makeIntegrator(void){ | |
1652 | else{ | |
1653 | sprintf(painCave.errMsg, | |
1654 | "SimSetup error: If you use a constant pressure\n" | |
1655 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1655 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1656 | painCave.isFatal = 1; | |
1657 | simError(); | |
1658 | } | |
1659 | ||
1660 | if (globals->haveTauThermostat()) | |
1661 | myNPTf->setTauThermostat(globals->getTauThermostat()); | |
1662 | + | |
1663 | else{ | |
1664 | sprintf(painCave.errMsg, | |
1665 | "SimSetup error: If you use an NPT\n" | |
1666 | < | " ensemble, you must set tauThermostat.\n"); |
1666 | > | "\tensemble, you must set tauThermostat.\n"); |
1667 | painCave.isFatal = 1; | |
1668 | simError(); | |
1669 | } | |
1670 | ||
1671 | if (globals->haveTauBarostat()) | |
1672 | myNPTf->setTauBarostat(globals->getTauBarostat()); | |
1673 | + | |
1674 | else{ | |
1675 | sprintf(painCave.errMsg, | |
1676 | "SimSetup error: If you use an NPT\n" | |
1677 | < | " ensemble, you must set tauBarostat.\n"); |
1677 | > | "\tensemble, you must set tauBarostat.\n"); |
1678 | painCave.isFatal = 1; | |
1679 | simError(); | |
1680 | } | |
# | Line 1468 | Line 1682 | void SimSetup::makeIntegrator(void){ | |
1682 | info->the_integrator = myNPTf; | |
1683 | break; | |
1684 | ||
1685 | + | case NPTxyz_ENS: |
1686 | + | if (globals->haveZconstraints()){ |
1687 | + | setupZConstraint(info[k]); |
1688 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1689 | + | } |
1690 | + | else |
1691 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1692 | + | |
1693 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1694 | + | |
1695 | + | if (globals->haveTargetPressure()) |
1696 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1697 | + | else{ |
1698 | + | sprintf(painCave.errMsg, |
1699 | + | "SimSetup error: If you use a constant pressure\n" |
1700 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1701 | + | painCave.isFatal = 1; |
1702 | + | simError(); |
1703 | + | } |
1704 | + | |
1705 | + | if (globals->haveTauThermostat()) |
1706 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1707 | + | else{ |
1708 | + | sprintf(painCave.errMsg, |
1709 | + | "SimSetup error: If you use an NPT\n" |
1710 | + | "\tensemble, you must set tauThermostat.\n"); |
1711 | + | painCave.isFatal = 1; |
1712 | + | simError(); |
1713 | + | } |
1714 | + | |
1715 | + | if (globals->haveTauBarostat()) |
1716 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1717 | + | else{ |
1718 | + | sprintf(painCave.errMsg, |
1719 | + | "SimSetup error: If you use an NPT\n" |
1720 | + | "\tensemble, you must set tauBarostat.\n"); |
1721 | + | painCave.isFatal = 1; |
1722 | + | simError(); |
1723 | + | } |
1724 | + | |
1725 | + | info->the_integrator = myNPTxyz; |
1726 | + | break; |
1727 | + | |
1728 | default: | |
1729 | sprintf(painCave.errMsg, | |
1730 | "SimSetup Error. Unrecognized ensemble in case statement.\n"); | |
# | Line 1513 | Line 1770 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1770 | } | |
1771 | else{ | |
1772 | sprintf(painCave.errMsg, | |
1773 | < | "ZConstraint error: If you use an ZConstraint\n" |
1774 | < | " , you must set sample time.\n"); |
1773 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1774 | > | "\tyou must set zconsTime.\n"); |
1775 | painCave.isFatal = 1; | |
1776 | simError(); | |
1777 | } | |
# | Line 1529 | Line 1786 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1786 | else{ | |
1787 | double defaultZConsTol = 0.01; | |
1788 | sprintf(painCave.errMsg, | |
1789 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1790 | < | " , default value %f is used.\n", |
1789 | > | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1790 | > | "\tOOPSE will use a default value of %f.\n" |
1791 | > | "\tTo set the tolerance, use the zconsTol variable.\n", |
1792 | defaultZConsTol); | |
1793 | painCave.isFatal = 0; | |
1794 | simError(); | |
# | Line 1548 | Line 1806 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1806 | } | |
1807 | else{ | |
1808 | sprintf(painCave.errMsg, | |
1809 | < | "ZConstraint Warning: User does not set force Subtraction policy, " |
1810 | < | "PolicyByMass is used\n"); |
1809 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
1810 | > | "\tOOPSE will use PolicyByMass.\n" |
1811 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1812 | painCave.isFatal = 0; | |
1813 | simError(); | |
1814 | zconsForcePolicy->setData("BYMASS"); | |
# | Line 1557 | Line 1816 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1816 | ||
1817 | theInfo.addProperty(zconsForcePolicy); | |
1818 | ||
1819 | + | //set zcons gap |
1820 | + | DoubleData* zconsGap = new DoubleData(); |
1821 | + | zconsGap->setID(ZCONSGAP_ID); |
1822 | + | |
1823 | + | if (globals->haveZConsGap()){ |
1824 | + | zconsGap->setData(globals->getZconsGap()); |
1825 | + | theInfo.addProperty(zconsGap); |
1826 | + | } |
1827 | + | |
1828 | + | //set zcons fixtime |
1829 | + | DoubleData* zconsFixtime = new DoubleData(); |
1830 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
1831 | + | |
1832 | + | if (globals->haveZConsFixTime()){ |
1833 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
1834 | + | theInfo.addProperty(zconsFixtime); |
1835 | + | } |
1836 | + | |
1837 | + | //set zconsUsingSMD |
1838 | + | IntData* zconsUsingSMD = new IntData(); |
1839 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
1840 | + | |
1841 | + | if (globals->haveZConsUsingSMD()){ |
1842 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
1843 | + | theInfo.addProperty(zconsUsingSMD); |
1844 | + | } |
1845 | + | |
1846 | //Determine the name of ouput file and add it into SimInfo's property list | |
1847 | //Be careful, do not use inFileName, since it is a pointer which | |
1848 | //point to a string at master node, and slave nodes do not contain that string | |
# | Line 1586 | Line 1872 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1872 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1873 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
1874 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
1875 | < | |
1875 | > | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
1876 | > | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
1877 | zconsParaData->addItem(tempParaItem); | |
1878 | } | |
1879 | ||
1880 | //check the uniqueness of index | |
1881 | if(!zconsParaData->isIndexUnique()){ | |
1882 | sprintf(painCave.errMsg, | |
1883 | < | "ZConstraint Error: molIndex is not unique\n"); |
1883 | > | "ZConstraint Error: molIndex is not unique!\n"); |
1884 | painCave.isFatal = 1; | |
1885 | simError(); | |
1886 | } | |
# | Line 1604 | Line 1891 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1891 | //push data into siminfo, therefore, we can retrieve later | |
1892 | theInfo.addProperty(zconsParaData); | |
1893 | } | |
1894 | + | |
1895 | + | void SimSetup::makeMinimizer(){ |
1896 | + | |
1897 | + | OOPSEMinimizer* myOOPSEMinimizer; |
1898 | + | MinimizerParameterSet* param; |
1899 | + | char minimizerName[100]; |
1900 | + | |
1901 | + | for (int i = 0; i < nInfo; i++){ |
1902 | + | |
1903 | + | //prepare parameter set for minimizer |
1904 | + | param = new MinimizerParameterSet(); |
1905 | + | param->setDefaultParameter(); |
1906 | + | |
1907 | + | if (globals->haveMinimizer()){ |
1908 | + | param->setFTol(globals->getMinFTol()); |
1909 | + | } |
1910 | + | |
1911 | + | if (globals->haveMinGTol()){ |
1912 | + | param->setGTol(globals->getMinGTol()); |
1913 | + | } |
1914 | + | |
1915 | + | if (globals->haveMinMaxIter()){ |
1916 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1917 | + | } |
1918 | + | |
1919 | + | if (globals->haveMinWriteFrq()){ |
1920 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1921 | + | } |
1922 | + | |
1923 | + | if (globals->haveMinWriteFrq()){ |
1924 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
1925 | + | } |
1926 | + | |
1927 | + | if (globals->haveMinStepSize()){ |
1928 | + | param->setStepSize(globals->getMinStepSize()); |
1929 | + | } |
1930 | + | |
1931 | + | if (globals->haveMinLSMaxIter()){ |
1932 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1933 | + | } |
1934 | + | |
1935 | + | if (globals->haveMinLSTol()){ |
1936 | + | param->setLineSearchTol(globals->getMinLSTol()); |
1937 | + | } |
1938 | + | |
1939 | + | strcpy(minimizerName, globals->getMinimizer()); |
1940 | + | |
1941 | + | if (!strcasecmp(minimizerName, "CG")){ |
1942 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1943 | + | } |
1944 | + | else if (!strcasecmp(minimizerName, "SD")){ |
1945 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
1946 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
1947 | + | } |
1948 | + | else{ |
1949 | + | sprintf(painCave.errMsg, |
1950 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
1951 | + | painCave.isFatal = 0; |
1952 | + | simError(); |
1953 | + | |
1954 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1955 | + | } |
1956 | + | info[i].the_integrator = myOOPSEMinimizer; |
1957 | + | |
1958 | + | //store the minimizer into simInfo |
1959 | + | info[i].the_minimizer = myOOPSEMinimizer; |
1960 | + | info[i].has_minimizer = true; |
1961 | + | } |
1962 | + | |
1963 | + | } |
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