# | 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 NPTim_ENS 4 |
26 | < | #define NPTfm_ENS 5 |
27 | > | #define NPTxyz_ENS 4 |
28 | ||
28 | – | #define FF_DUFF 0 |
29 | – | #define FF_LJ 1 |
30 | – | #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 54 | 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 92 | Line 122 | void SimSetup::createSim(void){ | |
122 | #endif // is_mpi | |
123 | ||
124 | void SimSetup::createSim(void){ | |
95 | – | int i, j, k, globalAtomIndex; |
125 | ||
126 | // gather all of the information from the Bass file | |
127 | ||
# | Line 108 | 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 | < | |
119 | < | // make the integrator |
120 | < | |
121 | < | makeIntegrator(); |
122 | < | |
150 | > | |
151 | #ifdef IS_MPI | |
152 | mpiSim->mpiRefresh(); | |
153 | #endif | |
# | Line 127 | 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 | + | RigidBodyStamp* currentRigidBody; |
186 | ||
187 | bond_pair* theBonds; | |
188 | bend_set* theBends; | |
189 | torsion_set* theTorsions; | |
190 | ||
191 | + | set<int> skipList; |
192 | ||
193 | + | double phi, theta, psi; |
194 | + | char* molName; |
195 | + | char rbName[100]; |
196 | + | |
197 | //init the forceField paramters | |
198 | ||
199 | the_ff->readParams(); | |
200 | ||
154 | – | |
201 | // init the atoms | |
202 | ||
203 | < | double ux, uy, uz, u, uSqr; |
203 | > | int nMembers, nNew, rb1, rb2; |
204 | ||
205 | for (k = 0; k < nInfo; k++){ | |
206 | the_ff->setSimInfo(&(info[k])); | |
207 | ||
208 | atomOffset = 0; | |
209 | < | excludeOffset = 0; |
209 | > | |
210 | for (i = 0; i < info[k].n_mol; i++){ | |
211 | stampID = info[k].molecules[i].getStampID(); | |
212 | + | molName = comp_stamps[stampID]->getID(); |
213 | ||
214 | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); | |
215 | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); | |
216 | molInfo.nBends = comp_stamps[stampID]->getNBends(); | |
217 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
218 | < | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
219 | < | |
218 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
219 | > | |
220 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
174 | – | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
175 | – | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
176 | – | molInfo.myBends = new Bend * [molInfo.nBends]; |
177 | – | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
221 | ||
222 | + | if (molInfo.nBonds > 0) |
223 | + | molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
224 | + | else |
225 | + | molInfo.myBonds = NULL; |
226 | + | |
227 | + | if (molInfo.nBends > 0) |
228 | + | molInfo.myBends = new (Bend *) [molInfo.nBends]; |
229 | + | else |
230 | + | molInfo.myBends = NULL; |
231 | + | |
232 | + | if (molInfo.nTorsions > 0) |
233 | + | molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
234 | + | else |
235 | + | molInfo.myTorsions = NULL; |
236 | + | |
237 | theBonds = new bond_pair[molInfo.nBonds]; | |
238 | theBends = new bend_set[molInfo.nBends]; | |
239 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
240 | < | |
240 | > | |
241 | // make the Atoms | |
242 | ||
243 | for (j = 0; j < molInfo.nAtoms; j++){ | |
244 | currentAtom = comp_stamps[stampID]->getAtom(j); | |
245 | + | |
246 | if (currentAtom->haveOrientation()){ | |
247 | dAtom = new DirectionalAtom((j + atomOffset), | |
248 | info[k].getConfiguration()); | |
249 | info[k].n_oriented++; | |
250 | molInfo.myAtoms[j] = dAtom; | |
251 | ||
252 | < | ux = currentAtom->getOrntX(); |
253 | < | uy = currentAtom->getOrntY(); |
254 | < | uz = currentAtom->getOrntZ(); |
252 | > | // Directional Atoms have standard unit vectors which are oriented |
253 | > | // in space using the three Euler angles. We assume the standard |
254 | > | // unit vector was originally along the z axis below. |
255 | ||
256 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
256 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
257 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
258 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
259 | ||
260 | < | u = sqrt(uSqr); |
261 | < | ux = ux / u; |
201 | < | uy = uy / u; |
202 | < | uz = uz / u; |
203 | < | |
204 | < | dAtom->setSUx(ux); |
205 | < | dAtom->setSUy(uy); |
206 | < | dAtom->setSUz(uz); |
260 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
261 | > | |
262 | } | |
263 | else{ | |
264 | < | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
265 | < | info[k].getConfiguration()); |
264 | > | |
265 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
266 | > | |
267 | } | |
212 | – | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
268 | ||
269 | + | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
270 | #ifdef IS_MPI | |
271 | ||
272 | < | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
272 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
273 | ||
274 | #endif // is_mpi | |
275 | } | |
# | Line 224 | Line 280 | void SimSetup::makeMolecules(void){ | |
280 | theBonds[j].a = currentBond->getA() + atomOffset; | |
281 | theBonds[j].b = currentBond->getB() + atomOffset; | |
282 | ||
283 | < | exI = theBonds[j].a; |
284 | < | exJ = theBonds[j].b; |
283 | > | tempI = theBonds[j].a; |
284 | > | tempJ = theBonds[j].b; |
285 | ||
230 | – | // exclude_I must always be the smaller of the pair |
231 | – | if (exI > exJ){ |
232 | – | tempEx = exI; |
233 | – | exI = exJ; |
234 | – | exJ = tempEx; |
235 | – | } |
286 | #ifdef IS_MPI | |
287 | < | tempEx = exI; |
288 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
289 | < | tempEx = exJ; |
290 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
287 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
288 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
289 | > | #else |
290 | > | exI = tempI + 1; |
291 | > | exJ = tempJ + 1; |
292 | > | #endif |
293 | ||
294 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
243 | < | #else // isn't MPI |
244 | < | |
245 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
246 | < | #endif //is_mpi |
294 | > | info[k].excludes->addPair(exI, exJ); |
295 | } | |
248 | – | excludeOffset += molInfo.nBonds; |
296 | ||
297 | //make the bends | |
298 | for (j = 0; j < molInfo.nBends; j++){ | |
# | Line 295 | Line 342 | void SimSetup::makeMolecules(void){ | |
342 | } | |
343 | } | |
344 | ||
345 | < | if (!theBends[j].isGhost){ |
346 | < | exI = theBends[j].a; |
347 | < | exJ = theBends[j].c; |
348 | < | } |
349 | < | else{ |
303 | < | exI = theBends[j].a; |
304 | < | exJ = theBends[j].b; |
305 | < | } |
306 | < | |
307 | < | // exclude_I must always be the smaller of the pair |
308 | < | if (exI > exJ){ |
309 | < | tempEx = exI; |
310 | < | exI = exJ; |
311 | < | exJ = tempEx; |
312 | < | } |
345 | > | if (theBends[j].isGhost) { |
346 | > | |
347 | > | tempI = theBends[j].a; |
348 | > | tempJ = theBends[j].b; |
349 | > | |
350 | #ifdef IS_MPI | |
351 | < | tempEx = exI; |
352 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
353 | < | tempEx = exJ; |
354 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
351 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
352 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
353 | > | #else |
354 | > | exI = tempI + 1; |
355 | > | exJ = tempJ + 1; |
356 | > | #endif |
357 | > | info[k].excludes->addPair(exI, exJ); |
358 | ||
359 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
360 | < | #else // isn't MPI |
361 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
362 | < | #endif //is_mpi |
359 | > | } else { |
360 | > | |
361 | > | tempI = theBends[j].a; |
362 | > | tempJ = theBends[j].b; |
363 | > | tempK = theBends[j].c; |
364 | > | |
365 | > | #ifdef IS_MPI |
366 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
367 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
368 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
369 | > | #else |
370 | > | exI = tempI + 1; |
371 | > | exJ = tempJ + 1; |
372 | > | exK = tempK + 1; |
373 | > | #endif |
374 | > | |
375 | > | info[k].excludes->addPair(exI, exK); |
376 | > | info[k].excludes->addPair(exI, exJ); |
377 | > | info[k].excludes->addPair(exJ, exK); |
378 | > | } |
379 | } | |
324 | – | excludeOffset += molInfo.nBends; |
380 | ||
381 | for (j = 0; j < molInfo.nTorsions; j++){ | |
382 | currentTorsion = comp_stamps[stampID]->getTorsion(j); | |
# | Line 330 | Line 385 | void SimSetup::makeMolecules(void){ | |
385 | theTorsions[j].c = currentTorsion->getC() + atomOffset; | |
386 | theTorsions[j].d = currentTorsion->getD() + atomOffset; | |
387 | ||
388 | < | exI = theTorsions[j].a; |
389 | < | exJ = theTorsions[j].d; |
390 | < | |
391 | < | // exclude_I must always be the smaller of the pair |
392 | < | if (exI > exJ){ |
393 | < | tempEx = exI; |
394 | < | exI = exJ; |
395 | < | exJ = tempEx; |
388 | > | tempI = theTorsions[j].a; |
389 | > | tempJ = theTorsions[j].b; |
390 | > | tempK = theTorsions[j].c; |
391 | > | tempL = theTorsions[j].d; |
392 | > | |
393 | > | #ifdef IS_MPI |
394 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
395 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
396 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
397 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
398 | > | #else |
399 | > | exI = tempI + 1; |
400 | > | exJ = tempJ + 1; |
401 | > | exK = tempK + 1; |
402 | > | exL = tempL + 1; |
403 | > | #endif |
404 | > | |
405 | > | info[k].excludes->addPair(exI, exJ); |
406 | > | info[k].excludes->addPair(exI, exK); |
407 | > | info[k].excludes->addPair(exI, exL); |
408 | > | info[k].excludes->addPair(exJ, exK); |
409 | > | info[k].excludes->addPair(exJ, exL); |
410 | > | info[k].excludes->addPair(exK, exL); |
411 | > | } |
412 | > | |
413 | > | |
414 | > | molInfo.myRigidBodies.clear(); |
415 | > | |
416 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
417 | > | |
418 | > | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
419 | > | nMembers = currentRigidBody->getNMembers(); |
420 | > | |
421 | > | // Create the Rigid Body: |
422 | > | |
423 | > | myRB = new RigidBody(); |
424 | > | |
425 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
426 | > | myRB->setType(rbName); |
427 | > | |
428 | > | for (rb1 = 0; rb1 < nMembers; rb1++) { |
429 | > | |
430 | > | // molI is atom numbering inside this molecule |
431 | > | molI = currentRigidBody->getMember(rb1); |
432 | > | |
433 | > | // tempI is atom numbering on local processor |
434 | > | tempI = molI + atomOffset; |
435 | > | |
436 | > | // currentAtom is the AtomStamp (which we need for |
437 | > | // rigid body reference positions) |
438 | > | currentAtom = comp_stamps[stampID]->getAtom(molI); |
439 | > | |
440 | > | // When we add to the rigid body, add the atom itself and |
441 | > | // the stamp info: |
442 | > | |
443 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
444 | > | |
445 | > | // Add this atom to the Skip List for the integrators |
446 | > | #ifdef IS_MPI |
447 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
448 | > | #else |
449 | > | slI = tempI; |
450 | > | #endif |
451 | > | skipList.insert(slI); |
452 | > | |
453 | } | |
454 | + | |
455 | + | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
456 | + | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
457 | + | |
458 | + | tempI = currentRigidBody->getMember(rb1); |
459 | + | tempJ = currentRigidBody->getMember(rb2); |
460 | + | |
461 | + | // Some explanation is required here. |
462 | + | // Fortran indexing starts at 1, while c indexing starts at 0 |
463 | + | // Also, in parallel computations, the GlobalIndex is |
464 | + | // used for the exclude list: |
465 | + | |
466 | #ifdef IS_MPI | |
467 | < | tempEx = exI; |
468 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
469 | < | tempEx = exJ; |
470 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
467 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
468 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
469 | > | #else |
470 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
471 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
472 | > | #endif |
473 | > | |
474 | > | info[k].excludes->addPair(exI, exJ); |
475 | > | |
476 | > | } |
477 | > | } |
478 | ||
479 | < | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
480 | < | #else // isn't MPI |
350 | < | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
351 | < | #endif //is_mpi |
479 | > | molInfo.myRigidBodies.push_back(myRB); |
480 | > | info[k].rigidBodies.push_back(myRB); |
481 | } | |
482 | < | excludeOffset += molInfo.nTorsions; |
482 | > | |
483 | ||
484 | + | // After this is all set up, scan through the atoms to |
485 | + | // see if they can be added to the integrableObjects: |
486 | ||
487 | < | // send the arrays off to the forceField for init. |
487 | > | molInfo.myIntegrableObjects.clear(); |
488 | > | |
489 | > | |
490 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
491 | > | |
492 | > | #ifdef IS_MPI |
493 | > | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
494 | > | #else |
495 | > | slJ = j+atomOffset; |
496 | > | #endif |
497 | > | |
498 | > | // if they aren't on the skip list, then they can be integrated |
499 | > | |
500 | > | if (skipList.find(slJ) == skipList.end()) { |
501 | > | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
502 | > | info[k].integrableObjects.push_back(mySD); |
503 | > | molInfo.myIntegrableObjects.push_back(mySD); |
504 | > | } |
505 | > | } |
506 | ||
507 | + | // all rigid bodies are integrated: |
508 | + | |
509 | + | for (j = 0; j < molInfo.nRigidBodies; j++) { |
510 | + | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
511 | + | info[k].integrableObjects.push_back(mySD); |
512 | + | molInfo.myIntegrableObjects.push_back(mySD); |
513 | + | } |
514 | + | |
515 | + | |
516 | + | // send the arrays off to the forceField for init. |
517 | + | |
518 | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); | |
519 | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); | |
520 | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); | |
521 | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, | |
522 | theTorsions); | |
523 | ||
364 | – | |
524 | info[k].molecules[i].initialize(molInfo); | |
525 | ||
526 | ||
# | Line 369 | Line 528 | void SimSetup::makeMolecules(void){ | |
528 | delete[] theBonds; | |
529 | delete[] theBends; | |
530 | delete[] theTorsions; | |
531 | < | } |
531 | > | } |
532 | } | |
533 | ||
534 | #ifdef IS_MPI | |
# | Line 379 | Line 538 | void SimSetup::makeMolecules(void){ | |
538 | ||
539 | // clean up the forcefield | |
540 | ||
541 | < | the_ff->calcRcut(); |
541 | > | if (!globals->haveLJrcut()){ |
542 | > | |
543 | > | the_ff->calcRcut(); |
544 | > | |
545 | > | } else { |
546 | > | |
547 | > | the_ff->setRcut( globals->getLJrcut() ); |
548 | > | } |
549 | > | |
550 | the_ff->cleanMe(); | |
551 | } | |
552 | ||
# | Line 553 | Line 720 | void SimSetup::gatherInfo(void){ | |
720 | ||
721 | ||
722 | void SimSetup::gatherInfo(void){ | |
723 | < | int i, j, k; |
723 | > | int i; |
724 | ||
725 | ensembleCase = -1; | |
726 | ffCase = -1; | |
# | Line 581 | Line 748 | void SimSetup::gatherInfo(void){ | |
748 | else if (!strcasecmp(force_field, "EAM")){ | |
749 | ffCase = FF_EAM; | |
750 | } | |
751 | + | else if (!strcasecmp(force_field, "WATER")){ |
752 | + | ffCase = FF_H2O; |
753 | + | } |
754 | else{ | |
755 | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", | |
756 | force_field); | |
# | Line 604 | Line 774 | void SimSetup::gatherInfo(void){ | |
774 | else if (!strcasecmp(ensemble, "NPTf")){ | |
775 | ensembleCase = NPTf_ENS; | |
776 | } | |
777 | < | else if (!strcasecmp(ensemble, "NPTim")){ |
778 | < | ensembleCase = NPTim_ENS; |
777 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
778 | > | ensembleCase = NPTxyz_ENS; |
779 | } | |
610 | – | else if (!strcasecmp(ensemble, "NPTfm")){ |
611 | – | ensembleCase = NPTfm_ENS; |
612 | – | } |
780 | else{ | |
781 | sprintf(painCave.errMsg, | |
782 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
783 | < | "reverting to NVE for this simulation.\n", |
782 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
783 | > | "\treverting to NVE for this simulation.\n", |
784 | ensemble); | |
785 | painCave.isFatal = 0; | |
786 | simError(); | |
# | Line 645 | Line 812 | void SimSetup::gatherInfo(void){ | |
812 | if (!the_components[i]->haveNMol()){ | |
813 | // we have a problem | |
814 | sprintf(painCave.errMsg, | |
815 | < | "SimSetup Error. No global NMol or component NMol" |
816 | < | " given. Cannot calculate the number of atoms.\n"); |
815 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
816 | > | "\tCannot calculate the number of atoms.\n"); |
817 | painCave.isFatal = 1; | |
818 | simError(); | |
819 | } | |
# | Line 666 | Line 833 | void SimSetup::gatherInfo(void){ | |
833 | simError(); | |
834 | } | |
835 | ||
836 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
837 | + | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
838 | + | sprintf(painCave.errMsg, |
839 | + | "Sample time is not divisible by dt.\n" |
840 | + | "\tThis will result in samples that are not uniformly\n" |
841 | + | "\tdistributed in time. If this is a problem, change\n" |
842 | + | "\tyour sampleTime variable.\n"); |
843 | + | painCave.isFatal = 0; |
844 | + | simError(); |
845 | + | } |
846 | + | |
847 | + | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
848 | + | sprintf(painCave.errMsg, |
849 | + | "Status time is not divisible by dt.\n" |
850 | + | "\tThis will result in status reports that are not uniformly\n" |
851 | + | "\tdistributed in time. If this is a problem, change \n" |
852 | + | "\tyour statusTime variable.\n"); |
853 | + | painCave.isFatal = 0; |
854 | + | simError(); |
855 | + | } |
856 | + | |
857 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
858 | + | sprintf(painCave.errMsg, |
859 | + | "Thermal time is not divisible by dt.\n" |
860 | + | "\tThis will result in thermalizations that are not uniformly\n" |
861 | + | "\tdistributed in time. If this is a problem, change \n" |
862 | + | "\tyour thermalTime variable.\n"); |
863 | + | painCave.isFatal = 0; |
864 | + | simError(); |
865 | + | } |
866 | + | |
867 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
868 | + | sprintf(painCave.errMsg, |
869 | + | "Reset time is not divisible by dt.\n" |
870 | + | "\tThis will result in integrator resets that are not uniformly\n" |
871 | + | "\tdistributed in time. If this is a problem, change\n" |
872 | + | "\tyour resetTime variable.\n"); |
873 | + | painCave.isFatal = 0; |
874 | + | simError(); |
875 | + | } |
876 | + | |
877 | // set the status, sample, and thermal kick times | |
878 | ||
879 | for (i = 0; i < nInfo; i++){ | |
880 | if (globals->haveSampleTime()){ | |
881 | info[i].sampleTime = globals->getSampleTime(); | |
882 | info[i].statusTime = info[i].sampleTime; | |
675 | – | info[i].thermalTime = info[i].sampleTime; |
883 | } | |
884 | else{ | |
885 | info[i].sampleTime = globals->getRunTime(); | |
886 | info[i].statusTime = info[i].sampleTime; | |
680 | – | info[i].thermalTime = info[i].sampleTime; |
887 | } | |
888 | ||
889 | if (globals->haveStatusTime()){ | |
# | Line 686 | Line 892 | void SimSetup::gatherInfo(void){ | |
892 | ||
893 | if (globals->haveThermalTime()){ | |
894 | info[i].thermalTime = globals->getThermalTime(); | |
895 | + | } else { |
896 | + | info[i].thermalTime = globals->getRunTime(); |
897 | } | |
898 | ||
899 | < | // check for the temperature set flag |
899 | > | info[i].resetIntegrator = 0; |
900 | > | if( globals->haveResetTime() ){ |
901 | > | info[i].resetTime = globals->getResetTime(); |
902 | > | info[i].resetIntegrator = 1; |
903 | > | } |
904 | ||
905 | + | // check for the temperature set flag |
906 | + | |
907 | if (globals->haveTempSet()) | |
908 | info[i].setTemp = globals->getTempSet(); | |
909 | ||
910 | < | // get some of the tricky things that may still be in the globals |
697 | < | |
698 | < | double boxVector[3]; |
699 | < | if (globals->haveBox()){ |
700 | < | boxVector[0] = globals->getBox(); |
701 | < | boxVector[1] = globals->getBox(); |
702 | < | boxVector[2] = globals->getBox(); |
910 | > | // check for the extended State init |
911 | ||
912 | < | info[i].setBox(boxVector); |
913 | < | } |
914 | < | else if (globals->haveDensity()){ |
707 | < | double vol; |
708 | < | vol = (double) tot_nmol / globals->getDensity(); |
709 | < | boxVector[0] = pow(vol, (1.0 / 3.0)); |
710 | < | boxVector[1] = boxVector[0]; |
711 | < | boxVector[2] = boxVector[0]; |
712 | < | |
713 | < | info[i].setBox(boxVector); |
714 | < | } |
715 | < | else{ |
716 | < | if (!globals->haveBoxX()){ |
717 | < | sprintf(painCave.errMsg, |
718 | < | "SimSetup error, no periodic BoxX size given.\n"); |
719 | < | painCave.isFatal = 1; |
720 | < | simError(); |
721 | < | } |
722 | < | boxVector[0] = globals->getBoxX(); |
723 | < | |
724 | < | if (!globals->haveBoxY()){ |
725 | < | sprintf(painCave.errMsg, |
726 | < | "SimSetup error, no periodic BoxY size given.\n"); |
727 | < | painCave.isFatal = 1; |
728 | < | simError(); |
729 | < | } |
730 | < | boxVector[1] = globals->getBoxY(); |
731 | < | |
732 | < | if (!globals->haveBoxZ()){ |
733 | < | sprintf(painCave.errMsg, |
734 | < | "SimSetup error, no periodic BoxZ size given.\n"); |
735 | < | painCave.isFatal = 1; |
736 | < | simError(); |
737 | < | } |
738 | < | boxVector[2] = globals->getBoxZ(); |
739 | < | |
740 | < | info[i].setBox(boxVector); |
741 | < | } |
912 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
913 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
914 | > | |
915 | } | |
916 | < | |
916 | > | |
917 | //setup seed for random number generator | |
918 | int seedValue; | |
919 | ||
# | Line 780 | Line 953 | void SimSetup::gatherInfo(void){ | |
953 | for (int i = 0; i < nInfo; i++){ | |
954 | info[i].setSeed(seedValue); | |
955 | } | |
956 | < | |
956 | > | |
957 | #ifdef IS_MPI | |
958 | < | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
958 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
959 | MPIcheckPoint(); | |
960 | #endif // is_mpi | |
961 | } | |
# | Line 791 | Line 964 | void SimSetup::finalInfoCheck(void){ | |
964 | void SimSetup::finalInfoCheck(void){ | |
965 | int index; | |
966 | int usesDipoles; | |
967 | + | int usesCharges; |
968 | int i; | |
969 | ||
970 | for (i = 0; i < nInfo; i++){ | |
# | Line 802 | Line 976 | void SimSetup::finalInfoCheck(void){ | |
976 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
977 | index++; | |
978 | } | |
979 | < | |
979 | > | index = 0; |
980 | > | usesCharges = 0; |
981 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
982 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
983 | > | index++; |
984 | > | } |
985 | #ifdef IS_MPI | |
986 | int myUse = usesDipoles; | |
987 | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
# | Line 815 | Line 994 | void SimSetup::finalInfoCheck(void){ | |
994 | ||
995 | if (!globals->haveECR()){ | |
996 | sprintf(painCave.errMsg, | |
997 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
998 | < | "box length for the electrostaticCutoffRadius.\n" |
999 | < | "I hope you have a very fast processor!\n"); |
997 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
998 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
999 | > | "\tfor the electrostaticCutoffRadius.\n"); |
1000 | painCave.isFatal = 0; | |
1001 | simError(); | |
1002 | < | double smallest; |
824 | < | smallest = info[i].boxL[0]; |
825 | < | if (info[i].boxL[1] <= smallest) |
826 | < | smallest = info[i].boxL[1]; |
827 | < | if (info[i].boxL[2] <= smallest) |
828 | < | smallest = info[i].boxL[2]; |
829 | < | theEcr = 0.5 * smallest; |
1002 | > | theEcr = 15.0; |
1003 | } | |
1004 | else{ | |
1005 | theEcr = globals->getECR(); | |
# | Line 834 | Line 1007 | void SimSetup::finalInfoCheck(void){ | |
1007 | ||
1008 | if (!globals->haveEST()){ | |
1009 | sprintf(painCave.errMsg, | |
1010 | < | "SimSetup Warning: using default value of 0.05 * the " |
1011 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
1010 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1011 | > | "\tOOPSE will use a default value of\n" |
1012 | > | "\t0.05 * electrostaticCutoffRadius\n" |
1013 | > | "\tfor the electrostaticSkinThickness\n"); |
1014 | painCave.isFatal = 0; | |
1015 | simError(); | |
1016 | theEst = 0.05 * theEcr; | |
# | Line 844 | Line 1019 | void SimSetup::finalInfoCheck(void){ | |
1019 | theEst = globals->getEST(); | |
1020 | } | |
1021 | ||
1022 | < | info[i].setEcr(theEcr, theEst); |
1022 | > | info[i].setDefaultEcr(theEcr, theEst); |
1023 | ||
1024 | if (!globals->haveDielectric()){ | |
1025 | sprintf(painCave.errMsg, | |
1026 | < | "SimSetup Error: You are trying to use Reaction Field without" |
1027 | < | "setting a dielectric constant!\n"); |
1026 | > | "SimSetup Error: No Dielectric constant was set.\n" |
1027 | > | "\tYou are trying to use Reaction Field without" |
1028 | > | "\tsetting a dielectric constant!\n"); |
1029 | painCave.isFatal = 1; | |
1030 | simError(); | |
1031 | } | |
1032 | info[i].dielectric = globals->getDielectric(); | |
1033 | } | |
1034 | else{ | |
1035 | < | if (usesDipoles){ |
1035 | > | if (usesDipoles || usesCharges){ |
1036 | if (!globals->haveECR()){ | |
1037 | sprintf(painCave.errMsg, | |
1038 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1039 | < | "box length for the electrostaticCutoffRadius.\n" |
1040 | < | "I hope you have a very fast processor!\n"); |
1041 | < | painCave.isFatal = 0; |
1042 | < | simError(); |
1043 | < | double smallest; |
868 | < | smallest = info[i].boxL[0]; |
869 | < | if (info[i].boxL[1] <= smallest) |
870 | < | smallest = info[i].boxL[1]; |
871 | < | if (info[i].boxL[2] <= smallest) |
872 | < | smallest = info[i].boxL[2]; |
873 | < | theEcr = 0.5 * smallest; |
1038 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1039 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1040 | > | "\tfor the electrostaticCutoffRadius.\n"); |
1041 | > | painCave.isFatal = 0; |
1042 | > | simError(); |
1043 | > | theEcr = 15.0; |
1044 | } | |
1045 | else{ | |
1046 | theEcr = globals->getECR(); | |
1047 | } | |
1048 | < | |
1048 | > | |
1049 | if (!globals->haveEST()){ | |
1050 | sprintf(painCave.errMsg, | |
1051 | < | "SimSetup Warning: using default value of 0.05 * the " |
1052 | < | "electrostaticCutoffRadius for the " |
1053 | < | "electrostaticSkinThickness\n"); |
1051 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1052 | > | "\tOOPSE will use a default value of\n" |
1053 | > | "\t0.05 * electrostaticCutoffRadius\n" |
1054 | > | "\tfor the electrostaticSkinThickness\n"); |
1055 | painCave.isFatal = 0; | |
1056 | simError(); | |
1057 | theEst = 0.05 * theEcr; | |
# | Line 888 | Line 1059 | void SimSetup::finalInfoCheck(void){ | |
1059 | else{ | |
1060 | theEst = globals->getEST(); | |
1061 | } | |
1062 | < | |
1063 | < | info[i].setEcr(theEcr, theEst); |
1062 | > | |
1063 | > | info[i].setDefaultEcr(theEcr, theEst); |
1064 | } | |
1065 | } | |
1066 | } | |
896 | – | |
1067 | #ifdef IS_MPI | |
1068 | strcpy(checkPointMsg, "post processing checks out"); | |
1069 | MPIcheckPoint(); | |
1070 | #endif // is_mpi | |
1071 | } | |
1072 | < | |
1072 | > | |
1073 | void SimSetup::initSystemCoords(void){ | |
1074 | int i; | |
1075 | ||
# | Line 916 | Line 1086 | void SimSetup::initSystemCoords(void){ | |
1086 | if (worldRank == 0){ | |
1087 | #endif //is_mpi | |
1088 | inName = globals->getInitialConfig(); | |
919 | – | double* tempDouble = new double[1000000]; |
1089 | fileInit = new InitializeFromFile(inName); | |
1090 | #ifdef IS_MPI | |
1091 | } | |
# | Line 928 | Line 1097 | void SimSetup::initSystemCoords(void){ | |
1097 | delete fileInit; | |
1098 | } | |
1099 | else{ | |
1100 | < | #ifdef IS_MPI |
932 | < | |
1100 | > | |
1101 | // no init from bass | |
1102 | < | |
1102 | > | |
1103 | sprintf(painCave.errMsg, | |
1104 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
1105 | < | painCave.isFatal; |
1104 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
1105 | > | painCave.isFatal = 1;; |
1106 | simError(); | |
1107 | < | |
940 | < | #else |
941 | < | |
942 | < | initFromBass(); |
943 | < | |
944 | < | |
945 | < | #endif |
1107 | > | |
1108 | } | |
1109 | ||
1110 | #ifdef IS_MPI | |
# | Line 1096 | Line 1258 | void SimSetup::createFF(void){ | |
1258 | the_ff = new EAM_FF(); | |
1259 | break; | |
1260 | ||
1261 | + | case FF_H2O: |
1262 | + | the_ff = new WATER(); |
1263 | + | break; |
1264 | + | |
1265 | default: | |
1266 | sprintf(painCave.errMsg, | |
1267 | "SimSetup Error. Unrecognized force field in case statement.\n"); | |
# | Line 1160 | Line 1326 | void SimSetup::calcSysValues(void){ | |
1326 | } | |
1327 | ||
1328 | void SimSetup::calcSysValues(void){ | |
1329 | < | int i, j, k; |
1329 | > | int i; |
1330 | ||
1331 | int* molMembershipArray; | |
1332 | ||
# | Line 1168 | Line 1334 | void SimSetup::calcSysValues(void){ | |
1334 | tot_bonds = 0; | |
1335 | tot_bends = 0; | |
1336 | tot_torsions = 0; | |
1337 | + | tot_rigid = 0; |
1338 | for (i = 0; i < n_components; i++){ | |
1339 | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); | |
1340 | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); | |
1341 | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); | |
1342 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1343 | + | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1344 | } | |
1345 | < | |
1345 | > | |
1346 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1347 | molMembershipArray = new int[tot_atoms]; | |
1348 | ||
# | Line 1196 | Line 1364 | void SimSetup::mpiMolDivide(void){ | |
1364 | int i, j, k; | |
1365 | int localMol, allMol; | |
1366 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1367 | + | int local_rigid; |
1368 | + | vector<int> globalMolIndex; |
1369 | ||
1370 | mpiSim = new mpiSimulation(info); | |
1371 | ||
1372 | < | globalIndex = mpiSim->divideLabor(); |
1372 | > | mpiSim->divideLabor(); |
1373 | > | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1374 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1375 | ||
1376 | // set up the local variables | |
1377 | ||
# | Line 1212 | Line 1384 | void SimSetup::mpiMolDivide(void){ | |
1384 | local_bonds = 0; | |
1385 | local_bends = 0; | |
1386 | local_torsions = 0; | |
1387 | < | globalAtomIndex = 0; |
1387 | > | local_rigid = 0; |
1388 | > | globalAtomCounter = 0; |
1389 | ||
1217 | – | |
1390 | for (i = 0; i < n_components; i++){ | |
1391 | for (j = 0; j < components_nmol[i]; j++){ | |
1392 | if (mol2proc[allMol] == worldRank){ | |
# | Line 1222 | Line 1394 | void SimSetup::mpiMolDivide(void){ | |
1394 | local_bonds += comp_stamps[i]->getNBonds(); | |
1395 | local_bends += comp_stamps[i]->getNBends(); | |
1396 | local_torsions += comp_stamps[i]->getNTorsions(); | |
1397 | + | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1398 | localMol++; | |
1399 | } | |
1400 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1401 | < | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1402 | < | globalAtomIndex++; |
1401 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1402 | > | globalAtomCounter++; |
1403 | } | |
1404 | ||
1405 | allMol++; | |
# | Line 1235 | Line 1408 | void SimSetup::mpiMolDivide(void){ | |
1408 | local_SRI = local_bonds + local_bends + local_torsions; | |
1409 | ||
1410 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1411 | + | |
1412 | ||
1413 | if (local_atoms != info[0].n_atoms){ | |
1414 | sprintf(painCave.errMsg, | |
1415 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1416 | < | " localAtom (%d) are not equal.\n", |
1415 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1416 | > | "\tlocalAtom (%d) are not equal.\n", |
1417 | info[0].n_atoms, local_atoms); | |
1418 | painCave.isFatal = 1; | |
1419 | simError(); | |
# | Line 1259 | Line 1433 | void SimSetup::makeSysArrays(void){ | |
1433 | ||
1434 | ||
1435 | void SimSetup::makeSysArrays(void){ | |
1436 | < | int i, j, k, l; |
1436 | > | |
1437 | > | #ifndef IS_MPI |
1438 | > | int k, j; |
1439 | > | #endif // is_mpi |
1440 | > | int i, l; |
1441 | ||
1442 | Atom** the_atoms; | |
1443 | Molecule* the_molecules; | |
1266 | – | Exclude** the_excludes; |
1444 | ||
1268 | – | |
1445 | for (l = 0; l < nInfo; l++){ | |
1446 | // create the atom and short range interaction arrays | |
1447 | ||
# | Line 1291 | Line 1467 | void SimSetup::makeSysArrays(void){ | |
1467 | #else // is_mpi | |
1468 | ||
1469 | molIndex = 0; | |
1470 | < | globalAtomIndex = 0; |
1470 | > | globalAtomCounter = 0; |
1471 | for (i = 0; i < n_components; i++){ | |
1472 | for (j = 0; j < components_nmol[i]; j++){ | |
1473 | the_molecules[molIndex].setStampID(i); | |
1474 | the_molecules[molIndex].setMyIndex(molIndex); | |
1475 | the_molecules[molIndex].setGlobalIndex(molIndex); | |
1476 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1477 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1478 | < | globalAtomIndex++; |
1477 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1478 | > | globalAtomCounter++; |
1479 | } | |
1480 | molIndex++; | |
1481 | } | |
# | Line 1308 | Line 1484 | void SimSetup::makeSysArrays(void){ | |
1484 | ||
1485 | #endif // is_mpi | |
1486 | ||
1487 | < | |
1488 | < | if (info[l].n_SRI){ |
1489 | < | Exclude::createArray(info[l].n_SRI); |
1314 | < | the_excludes = new Exclude * [info[l].n_SRI]; |
1315 | < | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1316 | < | the_excludes[ex] = new Exclude(ex); |
1317 | < | } |
1318 | < | info[l].globalExcludes = new int; |
1319 | < | info[l].n_exclude = info[l].n_SRI; |
1320 | < | } |
1321 | < | else{ |
1322 | < | Exclude::createArray(1); |
1323 | < | the_excludes = new Exclude * ; |
1324 | < | the_excludes[0] = new Exclude(0); |
1325 | < | the_excludes[0]->setPair(0, 0); |
1326 | < | info[l].globalExcludes = new int; |
1327 | < | info[l].globalExcludes[0] = 0; |
1328 | < | info[l].n_exclude = 0; |
1329 | < | } |
1330 | < | |
1487 | > | info[l].globalExcludes = new int; |
1488 | > | info[l].globalExcludes[0] = 0; |
1489 | > | |
1490 | // set the arrays into the SimInfo object | |
1491 | ||
1492 | info[l].atoms = the_atoms; | |
1493 | info[l].molecules = the_molecules; | |
1494 | info[l].nGlobalExcludes = 0; | |
1336 | – | info[l].excludes = the_excludes; |
1495 | ||
1496 | the_ff->setSimInfo(info); | |
1497 | } | |
# | Line 1342 | Line 1500 | void SimSetup::makeIntegrator(void){ | |
1500 | void SimSetup::makeIntegrator(void){ | |
1501 | int k; | |
1502 | ||
1503 | + | NVE<RealIntegrator>* myNVE = NULL; |
1504 | NVT<RealIntegrator>* myNVT = NULL; | |
1505 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1506 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1507 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1349 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1505 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1506 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1507 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1508 | ||
1509 | for (k = 0; k < nInfo; k++){ | |
1510 | switch (ensembleCase){ | |
1511 | case NVE_ENS: | |
1512 | if (globals->haveZconstraints()){ | |
1513 | setupZConstraint(info[k]); | |
1514 | < | new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1514 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1515 | } | |
1516 | < | else |
1517 | < | new NVE<RealIntegrator>(&(info[k]), the_ff); |
1516 | > | else{ |
1517 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1518 | > | } |
1519 | > | |
1520 | > | info->the_integrator = myNVE; |
1521 | break; | |
1522 | ||
1523 | case NVT_ENS: | |
# | Line 1374 | Line 1535 | void SimSetup::makeIntegrator(void){ | |
1535 | else{ | |
1536 | sprintf(painCave.errMsg, | |
1537 | "SimSetup error: If you use the NVT\n" | |
1538 | < | " ensemble, you must set tauThermostat.\n"); |
1538 | > | "\tensemble, you must set tauThermostat.\n"); |
1539 | painCave.isFatal = 1; | |
1540 | simError(); | |
1541 | } | |
1542 | + | |
1543 | + | info->the_integrator = myNVT; |
1544 | break; | |
1545 | ||
1546 | case NPTi_ENS: | |
1547 | if (globals->haveZconstraints()){ | |
1548 | setupZConstraint(info[k]); | |
1549 | < | myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff); |
1549 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1550 | } | |
1551 | else | |
1552 | < | myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff); |
1552 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1553 | ||
1554 | myNPTi->setTargetTemp(globals->getTargetTemp()); | |
1555 | ||
# | Line 1395 | Line 1558 | void SimSetup::makeIntegrator(void){ | |
1558 | else{ | |
1559 | sprintf(painCave.errMsg, | |
1560 | "SimSetup error: If you use a constant pressure\n" | |
1561 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1561 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1562 | painCave.isFatal = 1; | |
1563 | simError(); | |
1564 | } | |
# | Line 1405 | Line 1568 | void SimSetup::makeIntegrator(void){ | |
1568 | else{ | |
1569 | sprintf(painCave.errMsg, | |
1570 | "SimSetup error: If you use an NPT\n" | |
1571 | < | " ensemble, you must set tauThermostat.\n"); |
1571 | > | "\tensemble, you must set tauThermostat.\n"); |
1572 | painCave.isFatal = 1; | |
1573 | simError(); | |
1574 | } | |
# | Line 1415 | Line 1578 | void SimSetup::makeIntegrator(void){ | |
1578 | else{ | |
1579 | sprintf(painCave.errMsg, | |
1580 | "SimSetup error: If you use an NPT\n" | |
1581 | < | " ensemble, you must set tauBarostat.\n"); |
1581 | > | "\tensemble, you must set tauBarostat.\n"); |
1582 | painCave.isFatal = 1; | |
1583 | simError(); | |
1584 | } | |
1585 | + | |
1586 | + | info->the_integrator = myNPTi; |
1587 | break; | |
1588 | ||
1589 | case NPTf_ENS: | |
1590 | if (globals->haveZconstraints()){ | |
1591 | setupZConstraint(info[k]); | |
1592 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1592 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1593 | } | |
1594 | else | |
1595 | < | myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1595 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1596 | ||
1597 | myNPTf->setTargetTemp(globals->getTargetTemp()); | |
1598 | ||
# | Line 1436 | Line 1601 | void SimSetup::makeIntegrator(void){ | |
1601 | else{ | |
1602 | sprintf(painCave.errMsg, | |
1603 | "SimSetup error: If you use a constant pressure\n" | |
1604 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1604 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1605 | painCave.isFatal = 1; | |
1606 | simError(); | |
1607 | } | |
1608 | ||
1609 | if (globals->haveTauThermostat()) | |
1610 | myNPTf->setTauThermostat(globals->getTauThermostat()); | |
1611 | + | |
1612 | else{ | |
1613 | sprintf(painCave.errMsg, | |
1614 | "SimSetup error: If you use an NPT\n" | |
1615 | < | " ensemble, you must set tauThermostat.\n"); |
1615 | > | "\tensemble, you must set tauThermostat.\n"); |
1616 | painCave.isFatal = 1; | |
1617 | simError(); | |
1618 | } | |
1619 | ||
1620 | if (globals->haveTauBarostat()) | |
1621 | myNPTf->setTauBarostat(globals->getTauBarostat()); | |
1456 | – | else{ |
1457 | – | sprintf(painCave.errMsg, |
1458 | – | "SimSetup error: If you use an NPT\n" |
1459 | – | " ensemble, you must set tauBarostat.\n"); |
1460 | – | painCave.isFatal = 1; |
1461 | – | simError(); |
1462 | – | } |
1463 | – | break; |
1622 | ||
1465 | – | case NPTim_ENS: |
1466 | – | if (globals->haveZconstraints()){ |
1467 | – | setupZConstraint(info[k]); |
1468 | – | myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1469 | – | } |
1470 | – | else |
1471 | – | myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1472 | – | |
1473 | – | myNPTim->setTargetTemp(globals->getTargetTemp()); |
1474 | – | |
1475 | – | if (globals->haveTargetPressure()) |
1476 | – | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1623 | else{ | |
1624 | sprintf(painCave.errMsg, | |
1479 | – | "SimSetup error: If you use a constant pressure\n" |
1480 | – | " ensemble, you must set targetPressure in the BASS file.\n"); |
1481 | – | painCave.isFatal = 1; |
1482 | – | simError(); |
1483 | – | } |
1484 | – | |
1485 | – | if (globals->haveTauThermostat()) |
1486 | – | myNPTim->setTauThermostat(globals->getTauThermostat()); |
1487 | – | else{ |
1488 | – | sprintf(painCave.errMsg, |
1625 | "SimSetup error: If you use an NPT\n" | |
1626 | < | " ensemble, you must set tauThermostat.\n"); |
1626 | > | "\tensemble, you must set tauBarostat.\n"); |
1627 | painCave.isFatal = 1; | |
1628 | simError(); | |
1629 | } | |
1630 | ||
1631 | < | if (globals->haveTauBarostat()) |
1496 | < | myNPTim->setTauBarostat(globals->getTauBarostat()); |
1497 | < | else{ |
1498 | < | sprintf(painCave.errMsg, |
1499 | < | "SimSetup error: If you use an NPT\n" |
1500 | < | " ensemble, you must set tauBarostat.\n"); |
1501 | < | painCave.isFatal = 1; |
1502 | < | simError(); |
1503 | < | } |
1631 | > | info->the_integrator = myNPTf; |
1632 | break; | |
1633 | ||
1634 | < | case NPTfm_ENS: |
1634 | > | case NPTxyz_ENS: |
1635 | if (globals->haveZconstraints()){ | |
1636 | setupZConstraint(info[k]); | |
1637 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1637 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1638 | } | |
1639 | else | |
1640 | < | myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1640 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1641 | ||
1642 | < | myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1642 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1643 | ||
1644 | if (globals->haveTargetPressure()) | |
1645 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1645 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1646 | else{ | |
1647 | sprintf(painCave.errMsg, | |
1648 | "SimSetup error: If you use a constant pressure\n" | |
1649 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1649 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1650 | painCave.isFatal = 1; | |
1651 | simError(); | |
1652 | < | } |
1652 | > | } |
1653 | ||
1654 | if (globals->haveTauThermostat()) | |
1655 | < | myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1655 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1656 | else{ | |
1657 | sprintf(painCave.errMsg, | |
1658 | "SimSetup error: If you use an NPT\n" | |
1659 | < | " ensemble, you must set tauThermostat.\n"); |
1659 | > | "\tensemble, you must set tauThermostat.\n"); |
1660 | painCave.isFatal = 1; | |
1661 | simError(); | |
1662 | } | |
1663 | ||
1664 | if (globals->haveTauBarostat()) | |
1665 | < | myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1665 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1666 | else{ | |
1667 | sprintf(painCave.errMsg, | |
1668 | "SimSetup error: If you use an NPT\n" | |
1669 | < | " ensemble, you must set tauBarostat.\n"); |
1669 | > | "\tensemble, you must set tauBarostat.\n"); |
1670 | painCave.isFatal = 1; | |
1671 | simError(); | |
1672 | } | |
1673 | + | |
1674 | + | info->the_integrator = myNPTxyz; |
1675 | break; | |
1676 | ||
1677 | default: | |
# | Line 1589 | Line 1719 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1719 | } | |
1720 | else{ | |
1721 | sprintf(painCave.errMsg, | |
1722 | < | "ZConstraint error: If you use an ZConstraint\n" |
1723 | < | " , you must set sample time.\n"); |
1722 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1723 | > | "\tyou must set zconsTime.\n"); |
1724 | painCave.isFatal = 1; | |
1725 | simError(); | |
1726 | } | |
# | Line 1605 | Line 1735 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1735 | else{ | |
1736 | double defaultZConsTol = 0.01; | |
1737 | sprintf(painCave.errMsg, | |
1738 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1739 | < | " , default value %f is used.\n", |
1738 | > | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1739 | > | "\tOOPSE will use a default value of %f.\n" |
1740 | > | "\tTo set the tolerance, use the zconsTol variable.\n", |
1741 | defaultZConsTol); | |
1742 | painCave.isFatal = 0; | |
1743 | simError(); | |
# | Line 1615 | Line 1746 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1746 | } | |
1747 | theInfo.addProperty(zconsTol); | |
1748 | ||
1749 | < | //set Force Substraction Policy |
1749 | > | //set Force Subtraction Policy |
1750 | StringData* zconsForcePolicy = new StringData(); | |
1751 | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); | |
1752 | ||
# | Line 1624 | Line 1755 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1755 | } | |
1756 | else{ | |
1757 | sprintf(painCave.errMsg, | |
1758 | < | "ZConstraint Warning: User does not set force substraction policy, " |
1759 | < | "average force substraction policy is used\n"); |
1758 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
1759 | > | "\tOOPSE will use PolicyByMass.\n" |
1760 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1761 | painCave.isFatal = 0; | |
1762 | simError(); | |
1763 | < | zconsForcePolicy->setData("BYNUMBER"); |
1763 | > | zconsForcePolicy->setData("BYMASS"); |
1764 | } | |
1765 | ||
1766 | theInfo.addProperty(zconsForcePolicy); | |
1767 | ||
1768 | + | //set zcons gap |
1769 | + | DoubleData* zconsGap = new DoubleData(); |
1770 | + | zconsGap->setID(ZCONSGAP_ID); |
1771 | + | |
1772 | + | if (globals->haveZConsGap()){ |
1773 | + | zconsGap->setData(globals->getZconsGap()); |
1774 | + | theInfo.addProperty(zconsGap); |
1775 | + | } |
1776 | + | |
1777 | + | //set zcons fixtime |
1778 | + | DoubleData* zconsFixtime = new DoubleData(); |
1779 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
1780 | + | |
1781 | + | if (globals->haveZConsFixTime()){ |
1782 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
1783 | + | theInfo.addProperty(zconsFixtime); |
1784 | + | } |
1785 | + | |
1786 | + | //set zconsUsingSMD |
1787 | + | IntData* zconsUsingSMD = new IntData(); |
1788 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
1789 | + | |
1790 | + | if (globals->haveZConsUsingSMD()){ |
1791 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
1792 | + | theInfo.addProperty(zconsUsingSMD); |
1793 | + | } |
1794 | + | |
1795 | //Determine the name of ouput file and add it into SimInfo's property list | |
1796 | //Be careful, do not use inFileName, since it is a pointer which | |
1797 | //point to a string at master node, and slave nodes do not contain that string | |
# | Line 1662 | Line 1821 | void SimSetup::setupZConstraint(SimInfo& theInfo){ | |
1821 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1822 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
1823 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
1824 | < | |
1824 | > | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
1825 | > | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
1826 | zconsParaData->addItem(tempParaItem); | |
1827 | } | |
1828 | ||
1829 | + | //check the uniqueness of index |
1830 | + | if(!zconsParaData->isIndexUnique()){ |
1831 | + | sprintf(painCave.errMsg, |
1832 | + | "ZConstraint Error: molIndex is not unique!\n"); |
1833 | + | painCave.isFatal = 1; |
1834 | + | simError(); |
1835 | + | } |
1836 | + | |
1837 | //sort the parameters by index of molecules | |
1838 | zconsParaData->sortByIndex(); | |
1839 | < | |
1839 | > | |
1840 | //push data into siminfo, therefore, we can retrieve later | |
1841 | theInfo.addProperty(zconsParaData); | |
1842 | } | |
1843 | + | |
1844 | + | void SimSetup::makeMinimizer(){ |
1845 | + | |
1846 | + | OOPSEMinimizer* myOOPSEMinimizer; |
1847 | + | MinimizerParameterSet* param; |
1848 | + | char minimizerName[100]; |
1849 | + | |
1850 | + | for (int i = 0; i < nInfo; i++){ |
1851 | + | |
1852 | + | //prepare parameter set for minimizer |
1853 | + | param = new MinimizerParameterSet(); |
1854 | + | param->setDefaultParameter(); |
1855 | + | |
1856 | + | if (globals->haveMinimizer()){ |
1857 | + | param->setFTol(globals->getMinFTol()); |
1858 | + | } |
1859 | + | |
1860 | + | if (globals->haveMinGTol()){ |
1861 | + | param->setGTol(globals->getMinGTol()); |
1862 | + | } |
1863 | + | |
1864 | + | if (globals->haveMinMaxIter()){ |
1865 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1866 | + | } |
1867 | + | |
1868 | + | if (globals->haveMinWriteFrq()){ |
1869 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1870 | + | } |
1871 | + | |
1872 | + | if (globals->haveMinWriteFrq()){ |
1873 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
1874 | + | } |
1875 | + | |
1876 | + | if (globals->haveMinStepSize()){ |
1877 | + | param->setStepSize(globals->getMinStepSize()); |
1878 | + | } |
1879 | + | |
1880 | + | if (globals->haveMinLSMaxIter()){ |
1881 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1882 | + | } |
1883 | + | |
1884 | + | if (globals->haveMinLSTol()){ |
1885 | + | param->setLineSearchTol(globals->getMinLSTol()); |
1886 | + | } |
1887 | + | |
1888 | + | strcpy(minimizerName, globals->getMinimizer()); |
1889 | + | |
1890 | + | if (!strcasecmp(minimizerName, "CG")){ |
1891 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1892 | + | } |
1893 | + | else if (!strcasecmp(minimizerName, "SD")){ |
1894 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
1895 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
1896 | + | } |
1897 | + | else{ |
1898 | + | sprintf(painCave.errMsg, |
1899 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
1900 | + | painCave.isFatal = 0; |
1901 | + | simError(); |
1902 | + | |
1903 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1904 | + | } |
1905 | + | info[i].the_integrator = myOOPSEMinimizer; |
1906 | + | |
1907 | + | //store the minimizer into simInfo |
1908 | + | info[i].the_minimizer = myOOPSEMinimizer; |
1909 | + | info[i].has_minimizer = true; |
1910 | + | } |
1911 | + | |
1912 | + | } |
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