1 |
/* |
2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
* |
4 |
* The University of Notre Dame grants you ("Licensee") a |
5 |
* non-exclusive, royalty free, license to use, modify and |
6 |
* redistribute this software in source and binary code form, provided |
7 |
* that the following conditions are met: |
8 |
* |
9 |
* 1. Acknowledgement of the program authors must be made in any |
10 |
* publication of scientific results based in part on use of the |
11 |
* program. An acceptable form of acknowledgement is citation of |
12 |
* the article in which the program was described (Matthew |
13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 |
* Parallel Simulation Engine for Molecular Dynamics," |
16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
* |
18 |
* 2. Redistributions of source code must retain the above copyright |
19 |
* notice, this list of conditions and the following disclaimer. |
20 |
* |
21 |
* 3. Redistributions in binary form must reproduce the above copyright |
22 |
* notice, this list of conditions and the following disclaimer in the |
23 |
* documentation and/or other materials provided with the |
24 |
* distribution. |
25 |
* |
26 |
* This software is provided "AS IS," without a warranty of any |
27 |
* kind. All express or implied conditions, representations and |
28 |
* warranties, including any implied warranty of merchantability, |
29 |
* fitness for a particular purpose or non-infringement, are hereby |
30 |
* excluded. The University of Notre Dame and its licensors shall not |
31 |
* be liable for any damages suffered by licensee as a result of |
32 |
* using, modifying or distributing the software or its |
33 |
* derivatives. In no event will the University of Notre Dame or its |
34 |
* licensors be liable for any lost revenue, profit or data, or for |
35 |
* direct, indirect, special, consequential, incidental or punitive |
36 |
* damages, however caused and regardless of the theory of liability, |
37 |
* arising out of the use of or inability to use software, even if the |
38 |
* University of Notre Dame has been advised of the possibility of |
39 |
* such damages. |
40 |
*/ |
41 |
|
42 |
/** |
43 |
* @file SimInfo.cpp |
44 |
* @author tlin |
45 |
* @date 11/02/2004 |
46 |
* @version 1.0 |
47 |
*/ |
48 |
|
49 |
#include <algorithm> |
50 |
#include <set> |
51 |
|
52 |
#include "brains/SimInfo.hpp" |
53 |
#include "math/Vector3.hpp" |
54 |
#include "primitives/Molecule.hpp" |
55 |
#include "UseTheForce/doForces_interface.h" |
56 |
#include "UseTheForce/notifyCutoffs_interface.h" |
57 |
#include "utils/MemoryUtils.hpp" |
58 |
#include "utils/simError.h" |
59 |
#include "selection/SelectionManager.hpp" |
60 |
|
61 |
#ifdef IS_MPI |
62 |
#include "UseTheForce/mpiComponentPlan.h" |
63 |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
64 |
#endif |
65 |
|
66 |
namespace oopse { |
67 |
|
68 |
SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
69 |
ForceField* ff, Globals* simParams) : |
70 |
forceField_(ff), simParams_(simParams), |
71 |
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
72 |
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
73 |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
74 |
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
75 |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
76 |
sman_(NULL), fortranInitialized_(false) { |
77 |
|
78 |
|
79 |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
80 |
MoleculeStamp* molStamp; |
81 |
int nMolWithSameStamp; |
82 |
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
83 |
int nGroups = 0; //total cutoff groups defined in meta-data file |
84 |
CutoffGroupStamp* cgStamp; |
85 |
RigidBodyStamp* rbStamp; |
86 |
int nRigidAtoms = 0; |
87 |
|
88 |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
89 |
molStamp = i->first; |
90 |
nMolWithSameStamp = i->second; |
91 |
|
92 |
addMoleculeStamp(molStamp, nMolWithSameStamp); |
93 |
|
94 |
//calculate atoms in molecules |
95 |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
96 |
|
97 |
|
98 |
//calculate atoms in cutoff groups |
99 |
int nAtomsInGroups = 0; |
100 |
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
101 |
|
102 |
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
103 |
cgStamp = molStamp->getCutoffGroup(j); |
104 |
nAtomsInGroups += cgStamp->getNMembers(); |
105 |
} |
106 |
|
107 |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
108 |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
109 |
|
110 |
//calculate atoms in rigid bodies |
111 |
int nAtomsInRigidBodies = 0; |
112 |
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
113 |
|
114 |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
115 |
rbStamp = molStamp->getRigidBody(j); |
116 |
nAtomsInRigidBodies += rbStamp->getNMembers(); |
117 |
} |
118 |
|
119 |
nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
120 |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
121 |
|
122 |
} |
123 |
|
124 |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
125 |
//therefore the total number of cutoff groups in the system is equal to |
126 |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
127 |
//file plus the number of cutoff groups defined in meta-data file |
128 |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
129 |
|
130 |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
131 |
//therefore the total number of integrable objects in the system is equal to |
132 |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
133 |
//file plus the number of rigid bodies defined in meta-data file |
134 |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
135 |
|
136 |
nGlobalMols_ = molStampIds_.size(); |
137 |
|
138 |
#ifdef IS_MPI |
139 |
molToProcMap_.resize(nGlobalMols_); |
140 |
#endif |
141 |
|
142 |
} |
143 |
|
144 |
SimInfo::~SimInfo() { |
145 |
std::map<int, Molecule*>::iterator i; |
146 |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
147 |
delete i->second; |
148 |
} |
149 |
molecules_.clear(); |
150 |
|
151 |
MemoryUtils::deletePointers(moleculeStamps_); |
152 |
|
153 |
delete sman_; |
154 |
delete simParams_; |
155 |
delete forceField_; |
156 |
} |
157 |
|
158 |
int SimInfo::getNGlobalConstraints() { |
159 |
int nGlobalConstraints; |
160 |
#ifdef IS_MPI |
161 |
MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
162 |
MPI_COMM_WORLD); |
163 |
#else |
164 |
nGlobalConstraints = nConstraints_; |
165 |
#endif |
166 |
return nGlobalConstraints; |
167 |
} |
168 |
|
169 |
bool SimInfo::addMolecule(Molecule* mol) { |
170 |
MoleculeIterator i; |
171 |
|
172 |
i = molecules_.find(mol->getGlobalIndex()); |
173 |
if (i == molecules_.end() ) { |
174 |
|
175 |
molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
176 |
|
177 |
nAtoms_ += mol->getNAtoms(); |
178 |
nBonds_ += mol->getNBonds(); |
179 |
nBends_ += mol->getNBends(); |
180 |
nTorsions_ += mol->getNTorsions(); |
181 |
nRigidBodies_ += mol->getNRigidBodies(); |
182 |
nIntegrableObjects_ += mol->getNIntegrableObjects(); |
183 |
nCutoffGroups_ += mol->getNCutoffGroups(); |
184 |
nConstraints_ += mol->getNConstraintPairs(); |
185 |
|
186 |
addExcludePairs(mol); |
187 |
|
188 |
return true; |
189 |
} else { |
190 |
return false; |
191 |
} |
192 |
} |
193 |
|
194 |
bool SimInfo::removeMolecule(Molecule* mol) { |
195 |
MoleculeIterator i; |
196 |
i = molecules_.find(mol->getGlobalIndex()); |
197 |
|
198 |
if (i != molecules_.end() ) { |
199 |
|
200 |
assert(mol == i->second); |
201 |
|
202 |
nAtoms_ -= mol->getNAtoms(); |
203 |
nBonds_ -= mol->getNBonds(); |
204 |
nBends_ -= mol->getNBends(); |
205 |
nTorsions_ -= mol->getNTorsions(); |
206 |
nRigidBodies_ -= mol->getNRigidBodies(); |
207 |
nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
208 |
nCutoffGroups_ -= mol->getNCutoffGroups(); |
209 |
nConstraints_ -= mol->getNConstraintPairs(); |
210 |
|
211 |
removeExcludePairs(mol); |
212 |
molecules_.erase(mol->getGlobalIndex()); |
213 |
|
214 |
delete mol; |
215 |
|
216 |
return true; |
217 |
} else { |
218 |
return false; |
219 |
} |
220 |
|
221 |
|
222 |
} |
223 |
|
224 |
|
225 |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
226 |
i = molecules_.begin(); |
227 |
return i == molecules_.end() ? NULL : i->second; |
228 |
} |
229 |
|
230 |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
231 |
++i; |
232 |
return i == molecules_.end() ? NULL : i->second; |
233 |
} |
234 |
|
235 |
|
236 |
void SimInfo::calcNdf() { |
237 |
int ndf_local; |
238 |
MoleculeIterator i; |
239 |
std::vector<StuntDouble*>::iterator j; |
240 |
Molecule* mol; |
241 |
StuntDouble* integrableObject; |
242 |
|
243 |
ndf_local = 0; |
244 |
|
245 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
246 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
247 |
integrableObject = mol->nextIntegrableObject(j)) { |
248 |
|
249 |
ndf_local += 3; |
250 |
|
251 |
if (integrableObject->isDirectional()) { |
252 |
if (integrableObject->isLinear()) { |
253 |
ndf_local += 2; |
254 |
} else { |
255 |
ndf_local += 3; |
256 |
} |
257 |
} |
258 |
|
259 |
}//end for (integrableObject) |
260 |
}// end for (mol) |
261 |
|
262 |
// n_constraints is local, so subtract them on each processor |
263 |
ndf_local -= nConstraints_; |
264 |
|
265 |
#ifdef IS_MPI |
266 |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
267 |
#else |
268 |
ndf_ = ndf_local; |
269 |
#endif |
270 |
|
271 |
// nZconstraints_ is global, as are the 3 COM translations for the |
272 |
// entire system: |
273 |
ndf_ = ndf_ - 3 - nZconstraint_; |
274 |
|
275 |
} |
276 |
|
277 |
void SimInfo::calcNdfRaw() { |
278 |
int ndfRaw_local; |
279 |
|
280 |
MoleculeIterator i; |
281 |
std::vector<StuntDouble*>::iterator j; |
282 |
Molecule* mol; |
283 |
StuntDouble* integrableObject; |
284 |
|
285 |
// Raw degrees of freedom that we have to set |
286 |
ndfRaw_local = 0; |
287 |
|
288 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
289 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
290 |
integrableObject = mol->nextIntegrableObject(j)) { |
291 |
|
292 |
ndfRaw_local += 3; |
293 |
|
294 |
if (integrableObject->isDirectional()) { |
295 |
if (integrableObject->isLinear()) { |
296 |
ndfRaw_local += 2; |
297 |
} else { |
298 |
ndfRaw_local += 3; |
299 |
} |
300 |
} |
301 |
|
302 |
} |
303 |
} |
304 |
|
305 |
#ifdef IS_MPI |
306 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
307 |
#else |
308 |
ndfRaw_ = ndfRaw_local; |
309 |
#endif |
310 |
} |
311 |
|
312 |
void SimInfo::calcNdfTrans() { |
313 |
int ndfTrans_local; |
314 |
|
315 |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
316 |
|
317 |
|
318 |
#ifdef IS_MPI |
319 |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
320 |
#else |
321 |
ndfTrans_ = ndfTrans_local; |
322 |
#endif |
323 |
|
324 |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
325 |
|
326 |
} |
327 |
|
328 |
void SimInfo::addExcludePairs(Molecule* mol) { |
329 |
std::vector<Bond*>::iterator bondIter; |
330 |
std::vector<Bend*>::iterator bendIter; |
331 |
std::vector<Torsion*>::iterator torsionIter; |
332 |
Bond* bond; |
333 |
Bend* bend; |
334 |
Torsion* torsion; |
335 |
int a; |
336 |
int b; |
337 |
int c; |
338 |
int d; |
339 |
|
340 |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
341 |
a = bond->getAtomA()->getGlobalIndex(); |
342 |
b = bond->getAtomB()->getGlobalIndex(); |
343 |
exclude_.addPair(a, b); |
344 |
} |
345 |
|
346 |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
347 |
a = bend->getAtomA()->getGlobalIndex(); |
348 |
b = bend->getAtomB()->getGlobalIndex(); |
349 |
c = bend->getAtomC()->getGlobalIndex(); |
350 |
|
351 |
exclude_.addPair(a, b); |
352 |
exclude_.addPair(a, c); |
353 |
exclude_.addPair(b, c); |
354 |
} |
355 |
|
356 |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
357 |
a = torsion->getAtomA()->getGlobalIndex(); |
358 |
b = torsion->getAtomB()->getGlobalIndex(); |
359 |
c = torsion->getAtomC()->getGlobalIndex(); |
360 |
d = torsion->getAtomD()->getGlobalIndex(); |
361 |
|
362 |
exclude_.addPair(a, b); |
363 |
exclude_.addPair(a, c); |
364 |
exclude_.addPair(a, d); |
365 |
exclude_.addPair(b, c); |
366 |
exclude_.addPair(b, d); |
367 |
exclude_.addPair(c, d); |
368 |
} |
369 |
|
370 |
Molecule::RigidBodyIterator rbIter; |
371 |
RigidBody* rb; |
372 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
373 |
std::vector<Atom*> atoms = rb->getAtoms(); |
374 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
375 |
for (int j = i + 1; j < atoms.size(); ++j) { |
376 |
a = atoms[i]->getGlobalIndex(); |
377 |
b = atoms[j]->getGlobalIndex(); |
378 |
exclude_.addPair(a, b); |
379 |
} |
380 |
} |
381 |
} |
382 |
|
383 |
Molecule::CutoffGroupIterator cgIter; |
384 |
CutoffGroup* cg; |
385 |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
386 |
std::vector<Atom*> atoms = cg->getAtoms(); |
387 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
388 |
for (int j = i + 1; j < atoms.size(); ++j) { |
389 |
a = atoms[i]->getGlobalIndex(); |
390 |
b = atoms[j]->getGlobalIndex(); |
391 |
exclude_.addPair(a, b); |
392 |
} |
393 |
} |
394 |
} |
395 |
|
396 |
} |
397 |
|
398 |
void SimInfo::removeExcludePairs(Molecule* mol) { |
399 |
std::vector<Bond*>::iterator bondIter; |
400 |
std::vector<Bend*>::iterator bendIter; |
401 |
std::vector<Torsion*>::iterator torsionIter; |
402 |
Bond* bond; |
403 |
Bend* bend; |
404 |
Torsion* torsion; |
405 |
int a; |
406 |
int b; |
407 |
int c; |
408 |
int d; |
409 |
|
410 |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
411 |
a = bond->getAtomA()->getGlobalIndex(); |
412 |
b = bond->getAtomB()->getGlobalIndex(); |
413 |
exclude_.removePair(a, b); |
414 |
} |
415 |
|
416 |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
417 |
a = bend->getAtomA()->getGlobalIndex(); |
418 |
b = bend->getAtomB()->getGlobalIndex(); |
419 |
c = bend->getAtomC()->getGlobalIndex(); |
420 |
|
421 |
exclude_.removePair(a, b); |
422 |
exclude_.removePair(a, c); |
423 |
exclude_.removePair(b, c); |
424 |
} |
425 |
|
426 |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
427 |
a = torsion->getAtomA()->getGlobalIndex(); |
428 |
b = torsion->getAtomB()->getGlobalIndex(); |
429 |
c = torsion->getAtomC()->getGlobalIndex(); |
430 |
d = torsion->getAtomD()->getGlobalIndex(); |
431 |
|
432 |
exclude_.removePair(a, b); |
433 |
exclude_.removePair(a, c); |
434 |
exclude_.removePair(a, d); |
435 |
exclude_.removePair(b, c); |
436 |
exclude_.removePair(b, d); |
437 |
exclude_.removePair(c, d); |
438 |
} |
439 |
|
440 |
Molecule::RigidBodyIterator rbIter; |
441 |
RigidBody* rb; |
442 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
443 |
std::vector<Atom*> atoms = rb->getAtoms(); |
444 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
445 |
for (int j = i + 1; j < atoms.size(); ++j) { |
446 |
a = atoms[i]->getGlobalIndex(); |
447 |
b = atoms[j]->getGlobalIndex(); |
448 |
exclude_.removePair(a, b); |
449 |
} |
450 |
} |
451 |
} |
452 |
|
453 |
Molecule::CutoffGroupIterator cgIter; |
454 |
CutoffGroup* cg; |
455 |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
456 |
std::vector<Atom*> atoms = cg->getAtoms(); |
457 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
458 |
for (int j = i + 1; j < atoms.size(); ++j) { |
459 |
a = atoms[i]->getGlobalIndex(); |
460 |
b = atoms[j]->getGlobalIndex(); |
461 |
exclude_.removePair(a, b); |
462 |
} |
463 |
} |
464 |
} |
465 |
|
466 |
} |
467 |
|
468 |
|
469 |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
470 |
int curStampId; |
471 |
|
472 |
//index from 0 |
473 |
curStampId = moleculeStamps_.size(); |
474 |
|
475 |
moleculeStamps_.push_back(molStamp); |
476 |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
477 |
} |
478 |
|
479 |
void SimInfo::update() { |
480 |
|
481 |
setupSimType(); |
482 |
|
483 |
#ifdef IS_MPI |
484 |
setupFortranParallel(); |
485 |
#endif |
486 |
|
487 |
setupFortranSim(); |
488 |
|
489 |
//setup fortran force field |
490 |
/** @deprecate */ |
491 |
int isError = 0; |
492 |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
493 |
if(isError){ |
494 |
sprintf( painCave.errMsg, |
495 |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
496 |
painCave.isFatal = 1; |
497 |
simError(); |
498 |
} |
499 |
|
500 |
|
501 |
setupCutoff(); |
502 |
|
503 |
calcNdf(); |
504 |
calcNdfRaw(); |
505 |
calcNdfTrans(); |
506 |
|
507 |
fortranInitialized_ = true; |
508 |
} |
509 |
|
510 |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
511 |
SimInfo::MoleculeIterator mi; |
512 |
Molecule* mol; |
513 |
Molecule::AtomIterator ai; |
514 |
Atom* atom; |
515 |
std::set<AtomType*> atomTypes; |
516 |
|
517 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
518 |
|
519 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
520 |
atomTypes.insert(atom->getAtomType()); |
521 |
} |
522 |
|
523 |
} |
524 |
|
525 |
return atomTypes; |
526 |
} |
527 |
|
528 |
void SimInfo::setupSimType() { |
529 |
std::set<AtomType*>::iterator i; |
530 |
std::set<AtomType*> atomTypes; |
531 |
atomTypes = getUniqueAtomTypes(); |
532 |
|
533 |
int useLennardJones = 0; |
534 |
int useElectrostatic = 0; |
535 |
int useEAM = 0; |
536 |
int useCharge = 0; |
537 |
int useDirectional = 0; |
538 |
int useDipole = 0; |
539 |
int useGayBerne = 0; |
540 |
int useSticky = 0; |
541 |
int useShape = 0; |
542 |
int useFLARB = 0; //it is not in AtomType yet |
543 |
int useDirectionalAtom = 0; |
544 |
int useElectrostatics = 0; |
545 |
//usePBC and useRF are from simParams |
546 |
int usePBC = simParams_->getPBC(); |
547 |
int useRF = simParams_->getUseRF(); |
548 |
|
549 |
//loop over all of the atom types |
550 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
551 |
useLennardJones |= (*i)->isLennardJones(); |
552 |
useElectrostatic |= (*i)->isElectrostatic(); |
553 |
useEAM |= (*i)->isEAM(); |
554 |
useCharge |= (*i)->isCharge(); |
555 |
useDirectional |= (*i)->isDirectional(); |
556 |
useDipole |= (*i)->isDipole(); |
557 |
useGayBerne |= (*i)->isGayBerne(); |
558 |
useSticky |= (*i)->isSticky(); |
559 |
useShape |= (*i)->isShape(); |
560 |
} |
561 |
|
562 |
if (useSticky || useDipole || useGayBerne || useShape) { |
563 |
useDirectionalAtom = 1; |
564 |
} |
565 |
|
566 |
if (useCharge || useDipole) { |
567 |
useElectrostatics = 1; |
568 |
} |
569 |
|
570 |
#ifdef IS_MPI |
571 |
int temp; |
572 |
|
573 |
temp = usePBC; |
574 |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
575 |
|
576 |
temp = useDirectionalAtom; |
577 |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
578 |
|
579 |
temp = useLennardJones; |
580 |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
581 |
|
582 |
temp = useElectrostatics; |
583 |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
584 |
|
585 |
temp = useCharge; |
586 |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
587 |
|
588 |
temp = useDipole; |
589 |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
590 |
|
591 |
temp = useSticky; |
592 |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
593 |
|
594 |
temp = useGayBerne; |
595 |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
596 |
|
597 |
temp = useEAM; |
598 |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
599 |
|
600 |
temp = useShape; |
601 |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
602 |
|
603 |
temp = useFLARB; |
604 |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
605 |
|
606 |
temp = useRF; |
607 |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
608 |
|
609 |
#endif |
610 |
|
611 |
fInfo_.SIM_uses_PBC = usePBC; |
612 |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
613 |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
614 |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
615 |
fInfo_.SIM_uses_Charges = useCharge; |
616 |
fInfo_.SIM_uses_Dipoles = useDipole; |
617 |
fInfo_.SIM_uses_Sticky = useSticky; |
618 |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
619 |
fInfo_.SIM_uses_EAM = useEAM; |
620 |
fInfo_.SIM_uses_Shapes = useShape; |
621 |
fInfo_.SIM_uses_FLARB = useFLARB; |
622 |
fInfo_.SIM_uses_RF = useRF; |
623 |
|
624 |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
625 |
|
626 |
if (simParams_->haveDielectric()) { |
627 |
fInfo_.dielect = simParams_->getDielectric(); |
628 |
} else { |
629 |
sprintf(painCave.errMsg, |
630 |
"SimSetup Error: No Dielectric constant was set.\n" |
631 |
"\tYou are trying to use Reaction Field without" |
632 |
"\tsetting a dielectric constant!\n"); |
633 |
painCave.isFatal = 1; |
634 |
simError(); |
635 |
} |
636 |
|
637 |
} else { |
638 |
fInfo_.dielect = 0.0; |
639 |
} |
640 |
|
641 |
} |
642 |
|
643 |
void SimInfo::setupFortranSim() { |
644 |
int isError; |
645 |
int nExclude; |
646 |
std::vector<int> fortranGlobalGroupMembership; |
647 |
|
648 |
nExclude = exclude_.getSize(); |
649 |
isError = 0; |
650 |
|
651 |
//globalGroupMembership_ is filled by SimCreator |
652 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
653 |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
654 |
} |
655 |
|
656 |
//calculate mass ratio of cutoff group |
657 |
std::vector<double> mfact; |
658 |
SimInfo::MoleculeIterator mi; |
659 |
Molecule* mol; |
660 |
Molecule::CutoffGroupIterator ci; |
661 |
CutoffGroup* cg; |
662 |
Molecule::AtomIterator ai; |
663 |
Atom* atom; |
664 |
double totalMass; |
665 |
|
666 |
//to avoid memory reallocation, reserve enough space for mfact |
667 |
mfact.reserve(getNCutoffGroups()); |
668 |
|
669 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
670 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
671 |
|
672 |
totalMass = cg->getMass(); |
673 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
674 |
mfact.push_back(atom->getMass()/totalMass); |
675 |
} |
676 |
|
677 |
} |
678 |
} |
679 |
|
680 |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
681 |
std::vector<int> identArray; |
682 |
|
683 |
//to avoid memory reallocation, reserve enough space identArray |
684 |
identArray.reserve(getNAtoms()); |
685 |
|
686 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
687 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
688 |
identArray.push_back(atom->getIdent()); |
689 |
} |
690 |
} |
691 |
|
692 |
//fill molMembershipArray |
693 |
//molMembershipArray is filled by SimCreator |
694 |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
695 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
696 |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
697 |
} |
698 |
|
699 |
//setup fortran simulation |
700 |
int nGlobalExcludes = 0; |
701 |
int* globalExcludes = NULL; |
702 |
int* excludeList = exclude_.getExcludeList(); |
703 |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
704 |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
705 |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
706 |
|
707 |
if( isError ){ |
708 |
|
709 |
sprintf( painCave.errMsg, |
710 |
"There was an error setting the simulation information in fortran.\n" ); |
711 |
painCave.isFatal = 1; |
712 |
painCave.severity = OOPSE_ERROR; |
713 |
simError(); |
714 |
} |
715 |
|
716 |
#ifdef IS_MPI |
717 |
sprintf( checkPointMsg, |
718 |
"succesfully sent the simulation information to fortran.\n"); |
719 |
MPIcheckPoint(); |
720 |
#endif // is_mpi |
721 |
} |
722 |
|
723 |
|
724 |
#ifdef IS_MPI |
725 |
void SimInfo::setupFortranParallel() { |
726 |
|
727 |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
728 |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
729 |
std::vector<int> localToGlobalCutoffGroupIndex; |
730 |
SimInfo::MoleculeIterator mi; |
731 |
Molecule::AtomIterator ai; |
732 |
Molecule::CutoffGroupIterator ci; |
733 |
Molecule* mol; |
734 |
Atom* atom; |
735 |
CutoffGroup* cg; |
736 |
mpiSimData parallelData; |
737 |
int isError; |
738 |
|
739 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
740 |
|
741 |
//local index(index in DataStorge) of atom is important |
742 |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
743 |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
744 |
} |
745 |
|
746 |
//local index of cutoff group is trivial, it only depends on the order of travesing |
747 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
748 |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
749 |
} |
750 |
|
751 |
} |
752 |
|
753 |
//fill up mpiSimData struct |
754 |
parallelData.nMolGlobal = getNGlobalMolecules(); |
755 |
parallelData.nMolLocal = getNMolecules(); |
756 |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
757 |
parallelData.nAtomsLocal = getNAtoms(); |
758 |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
759 |
parallelData.nGroupsLocal = getNCutoffGroups(); |
760 |
parallelData.myNode = worldRank; |
761 |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
762 |
|
763 |
//pass mpiSimData struct and index arrays to fortran |
764 |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
765 |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
766 |
&localToGlobalCutoffGroupIndex[0], &isError); |
767 |
|
768 |
if (isError) { |
769 |
sprintf(painCave.errMsg, |
770 |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
771 |
painCave.isFatal = 1; |
772 |
simError(); |
773 |
} |
774 |
|
775 |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
776 |
MPIcheckPoint(); |
777 |
|
778 |
|
779 |
} |
780 |
|
781 |
#endif |
782 |
|
783 |
double SimInfo::calcMaxCutoffRadius() { |
784 |
|
785 |
|
786 |
std::set<AtomType*> atomTypes; |
787 |
std::set<AtomType*>::iterator i; |
788 |
std::vector<double> cutoffRadius; |
789 |
|
790 |
//get the unique atom types |
791 |
atomTypes = getUniqueAtomTypes(); |
792 |
|
793 |
//query the max cutoff radius among these atom types |
794 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
795 |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
796 |
} |
797 |
|
798 |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
799 |
#ifdef IS_MPI |
800 |
//pick the max cutoff radius among the processors |
801 |
#endif |
802 |
|
803 |
return maxCutoffRadius; |
804 |
} |
805 |
|
806 |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
807 |
|
808 |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
809 |
|
810 |
if (!simParams_->haveRcut()){ |
811 |
sprintf(painCave.errMsg, |
812 |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
813 |
"\tOOPSE will use a default value of 15.0 angstroms" |
814 |
"\tfor the cutoffRadius.\n"); |
815 |
painCave.isFatal = 0; |
816 |
simError(); |
817 |
rcut = 15.0; |
818 |
} else{ |
819 |
rcut = simParams_->getRcut(); |
820 |
} |
821 |
|
822 |
if (!simParams_->haveRsw()){ |
823 |
sprintf(painCave.errMsg, |
824 |
"SimCreator Warning: No value was set for switchingRadius.\n" |
825 |
"\tOOPSE will use a default value of\n" |
826 |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
827 |
painCave.isFatal = 0; |
828 |
simError(); |
829 |
rsw = 0.95 * rcut; |
830 |
} else{ |
831 |
rsw = simParams_->getRsw(); |
832 |
} |
833 |
|
834 |
} else { |
835 |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
836 |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
837 |
|
838 |
if (simParams_->haveRcut()) { |
839 |
rcut = simParams_->getRcut(); |
840 |
} else { |
841 |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
842 |
rcut = calcMaxCutoffRadius(); |
843 |
} |
844 |
|
845 |
if (simParams_->haveRsw()) { |
846 |
rsw = simParams_->getRsw(); |
847 |
} else { |
848 |
rsw = rcut; |
849 |
} |
850 |
|
851 |
} |
852 |
} |
853 |
|
854 |
void SimInfo::setupCutoff() { |
855 |
getCutoff(rcut_, rsw_); |
856 |
double rnblist = rcut_ + 1; // skin of neighbor list |
857 |
|
858 |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
859 |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
860 |
} |
861 |
|
862 |
void SimInfo::addProperty(GenericData* genData) { |
863 |
properties_.addProperty(genData); |
864 |
} |
865 |
|
866 |
void SimInfo::removeProperty(const std::string& propName) { |
867 |
properties_.removeProperty(propName); |
868 |
} |
869 |
|
870 |
void SimInfo::clearProperties() { |
871 |
properties_.clearProperties(); |
872 |
} |
873 |
|
874 |
std::vector<std::string> SimInfo::getPropertyNames() { |
875 |
return properties_.getPropertyNames(); |
876 |
} |
877 |
|
878 |
std::vector<GenericData*> SimInfo::getProperties() { |
879 |
return properties_.getProperties(); |
880 |
} |
881 |
|
882 |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
883 |
return properties_.getPropertyByName(propName); |
884 |
} |
885 |
|
886 |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
887 |
if (sman_ == sman) { |
888 |
return; |
889 |
} |
890 |
delete sman_; |
891 |
sman_ = sman; |
892 |
|
893 |
Molecule* mol; |
894 |
RigidBody* rb; |
895 |
Atom* atom; |
896 |
SimInfo::MoleculeIterator mi; |
897 |
Molecule::RigidBodyIterator rbIter; |
898 |
Molecule::AtomIterator atomIter;; |
899 |
|
900 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
901 |
|
902 |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
903 |
atom->setSnapshotManager(sman_); |
904 |
} |
905 |
|
906 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
907 |
rb->setSnapshotManager(sman_); |
908 |
} |
909 |
} |
910 |
|
911 |
} |
912 |
|
913 |
Vector3d SimInfo::getComVel(){ |
914 |
SimInfo::MoleculeIterator i; |
915 |
Molecule* mol; |
916 |
|
917 |
Vector3d comVel(0.0); |
918 |
double totalMass = 0.0; |
919 |
|
920 |
|
921 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
922 |
double mass = mol->getMass(); |
923 |
totalMass += mass; |
924 |
comVel += mass * mol->getComVel(); |
925 |
} |
926 |
|
927 |
#ifdef IS_MPI |
928 |
double tmpMass = totalMass; |
929 |
Vector3d tmpComVel(comVel); |
930 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
931 |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
932 |
#endif |
933 |
|
934 |
comVel /= totalMass; |
935 |
|
936 |
return comVel; |
937 |
} |
938 |
|
939 |
Vector3d SimInfo::getCom(){ |
940 |
SimInfo::MoleculeIterator i; |
941 |
Molecule* mol; |
942 |
|
943 |
Vector3d com(0.0); |
944 |
double totalMass = 0.0; |
945 |
|
946 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
947 |
double mass = mol->getMass(); |
948 |
totalMass += mass; |
949 |
com += mass * mol->getCom(); |
950 |
} |
951 |
|
952 |
#ifdef IS_MPI |
953 |
double tmpMass = totalMass; |
954 |
Vector3d tmpCom(com); |
955 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
956 |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
957 |
#endif |
958 |
|
959 |
com /= totalMass; |
960 |
|
961 |
return com; |
962 |
|
963 |
} |
964 |
|
965 |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
966 |
|
967 |
return o; |
968 |
} |
969 |
|
970 |
}//end namespace oopse |
971 |
|