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 |
#include <map> |
52 |
|
53 |
#include "brains/SimInfo.hpp" |
54 |
#include "math/Vector3.hpp" |
55 |
#include "primitives/Molecule.hpp" |
56 |
#include "UseTheForce/fCutoffPolicy.h" |
57 |
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
58 |
#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
59 |
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
60 |
#include "UseTheForce/doForces_interface.h" |
61 |
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
62 |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
63 |
#include "utils/MemoryUtils.hpp" |
64 |
#include "utils/simError.h" |
65 |
#include "selection/SelectionManager.hpp" |
66 |
|
67 |
#ifdef IS_MPI |
68 |
#include "UseTheForce/mpiComponentPlan.h" |
69 |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
70 |
#endif |
71 |
|
72 |
namespace oopse { |
73 |
std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
74 |
std::map<int, std::set<int> >::iterator i = container.find(index); |
75 |
std::set<int> result; |
76 |
if (i != container.end()) { |
77 |
result = i->second; |
78 |
} |
79 |
|
80 |
return result; |
81 |
} |
82 |
|
83 |
SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
84 |
forceField_(ff), simParams_(simParams), |
85 |
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
86 |
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
87 |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
88 |
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
89 |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
90 |
sman_(NULL), fortranInitialized_(false) { |
91 |
|
92 |
MoleculeStamp* molStamp; |
93 |
int nMolWithSameStamp; |
94 |
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
95 |
int nGroups = 0; //total cutoff groups defined in meta-data file |
96 |
CutoffGroupStamp* cgStamp; |
97 |
RigidBodyStamp* rbStamp; |
98 |
int nRigidAtoms = 0; |
99 |
std::vector<Component*> components = simParams->getComponents(); |
100 |
|
101 |
for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
102 |
molStamp = (*i)->getMoleculeStamp(); |
103 |
nMolWithSameStamp = (*i)->getNMol(); |
104 |
|
105 |
addMoleculeStamp(molStamp, nMolWithSameStamp); |
106 |
|
107 |
//calculate atoms in molecules |
108 |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
109 |
|
110 |
//calculate atoms in cutoff groups |
111 |
int nAtomsInGroups = 0; |
112 |
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
113 |
|
114 |
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
115 |
cgStamp = molStamp->getCutoffGroupStamp(j); |
116 |
nAtomsInGroups += cgStamp->getNMembers(); |
117 |
} |
118 |
|
119 |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
120 |
|
121 |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
122 |
|
123 |
//calculate atoms in rigid bodies |
124 |
int nAtomsInRigidBodies = 0; |
125 |
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
126 |
|
127 |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
128 |
rbStamp = molStamp->getRigidBodyStamp(j); |
129 |
nAtomsInRigidBodies += rbStamp->getNMembers(); |
130 |
} |
131 |
|
132 |
nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
133 |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
134 |
|
135 |
} |
136 |
|
137 |
//every free atom (atom does not belong to cutoff groups) is a cutoff |
138 |
//group therefore the total number of cutoff groups in the system is |
139 |
//equal to the total number of atoms minus number of atoms belong to |
140 |
//cutoff group defined in meta-data file plus the number of cutoff |
141 |
//groups defined in meta-data file |
142 |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
143 |
|
144 |
//every free atom (atom does not belong to rigid bodies) is an |
145 |
//integrable object therefore the total number of integrable objects |
146 |
//in the system is equal to the total number of atoms minus number of |
147 |
//atoms belong to rigid body defined in meta-data file plus the number |
148 |
//of rigid bodies defined in meta-data file |
149 |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
150 |
+ nGlobalRigidBodies_; |
151 |
|
152 |
nGlobalMols_ = molStampIds_.size(); |
153 |
|
154 |
#ifdef IS_MPI |
155 |
molToProcMap_.resize(nGlobalMols_); |
156 |
#endif |
157 |
|
158 |
} |
159 |
|
160 |
SimInfo::~SimInfo() { |
161 |
std::map<int, Molecule*>::iterator i; |
162 |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
163 |
delete i->second; |
164 |
} |
165 |
molecules_.clear(); |
166 |
|
167 |
delete sman_; |
168 |
delete simParams_; |
169 |
delete forceField_; |
170 |
} |
171 |
|
172 |
int SimInfo::getNGlobalConstraints() { |
173 |
int nGlobalConstraints; |
174 |
#ifdef IS_MPI |
175 |
MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
176 |
MPI_COMM_WORLD); |
177 |
#else |
178 |
nGlobalConstraints = nConstraints_; |
179 |
#endif |
180 |
return nGlobalConstraints; |
181 |
} |
182 |
|
183 |
bool SimInfo::addMolecule(Molecule* mol) { |
184 |
MoleculeIterator i; |
185 |
|
186 |
i = molecules_.find(mol->getGlobalIndex()); |
187 |
if (i == molecules_.end() ) { |
188 |
|
189 |
molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
190 |
|
191 |
nAtoms_ += mol->getNAtoms(); |
192 |
nBonds_ += mol->getNBonds(); |
193 |
nBends_ += mol->getNBends(); |
194 |
nTorsions_ += mol->getNTorsions(); |
195 |
nRigidBodies_ += mol->getNRigidBodies(); |
196 |
nIntegrableObjects_ += mol->getNIntegrableObjects(); |
197 |
nCutoffGroups_ += mol->getNCutoffGroups(); |
198 |
nConstraints_ += mol->getNConstraintPairs(); |
199 |
|
200 |
addExcludePairs(mol); |
201 |
|
202 |
return true; |
203 |
} else { |
204 |
return false; |
205 |
} |
206 |
} |
207 |
|
208 |
bool SimInfo::removeMolecule(Molecule* mol) { |
209 |
MoleculeIterator i; |
210 |
i = molecules_.find(mol->getGlobalIndex()); |
211 |
|
212 |
if (i != molecules_.end() ) { |
213 |
|
214 |
assert(mol == i->second); |
215 |
|
216 |
nAtoms_ -= mol->getNAtoms(); |
217 |
nBonds_ -= mol->getNBonds(); |
218 |
nBends_ -= mol->getNBends(); |
219 |
nTorsions_ -= mol->getNTorsions(); |
220 |
nRigidBodies_ -= mol->getNRigidBodies(); |
221 |
nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
222 |
nCutoffGroups_ -= mol->getNCutoffGroups(); |
223 |
nConstraints_ -= mol->getNConstraintPairs(); |
224 |
|
225 |
removeExcludePairs(mol); |
226 |
molecules_.erase(mol->getGlobalIndex()); |
227 |
|
228 |
delete mol; |
229 |
|
230 |
return true; |
231 |
} else { |
232 |
return false; |
233 |
} |
234 |
|
235 |
|
236 |
} |
237 |
|
238 |
|
239 |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
240 |
i = molecules_.begin(); |
241 |
return i == molecules_.end() ? NULL : i->second; |
242 |
} |
243 |
|
244 |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
245 |
++i; |
246 |
return i == molecules_.end() ? NULL : i->second; |
247 |
} |
248 |
|
249 |
|
250 |
void SimInfo::calcNdf() { |
251 |
int ndf_local; |
252 |
MoleculeIterator i; |
253 |
std::vector<StuntDouble*>::iterator j; |
254 |
Molecule* mol; |
255 |
StuntDouble* integrableObject; |
256 |
|
257 |
ndf_local = 0; |
258 |
|
259 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
260 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
261 |
integrableObject = mol->nextIntegrableObject(j)) { |
262 |
|
263 |
ndf_local += 3; |
264 |
|
265 |
if (integrableObject->isDirectional()) { |
266 |
if (integrableObject->isLinear()) { |
267 |
ndf_local += 2; |
268 |
} else { |
269 |
ndf_local += 3; |
270 |
} |
271 |
} |
272 |
|
273 |
} |
274 |
} |
275 |
|
276 |
// n_constraints is local, so subtract them on each processor |
277 |
ndf_local -= nConstraints_; |
278 |
|
279 |
#ifdef IS_MPI |
280 |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
281 |
#else |
282 |
ndf_ = ndf_local; |
283 |
#endif |
284 |
|
285 |
// nZconstraints_ is global, as are the 3 COM translations for the |
286 |
// entire system: |
287 |
ndf_ = ndf_ - 3 - nZconstraint_; |
288 |
|
289 |
} |
290 |
|
291 |
void SimInfo::calcNdfRaw() { |
292 |
int ndfRaw_local; |
293 |
|
294 |
MoleculeIterator i; |
295 |
std::vector<StuntDouble*>::iterator j; |
296 |
Molecule* mol; |
297 |
StuntDouble* integrableObject; |
298 |
|
299 |
// Raw degrees of freedom that we have to set |
300 |
ndfRaw_local = 0; |
301 |
|
302 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
303 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
304 |
integrableObject = mol->nextIntegrableObject(j)) { |
305 |
|
306 |
ndfRaw_local += 3; |
307 |
|
308 |
if (integrableObject->isDirectional()) { |
309 |
if (integrableObject->isLinear()) { |
310 |
ndfRaw_local += 2; |
311 |
} else { |
312 |
ndfRaw_local += 3; |
313 |
} |
314 |
} |
315 |
|
316 |
} |
317 |
} |
318 |
|
319 |
#ifdef IS_MPI |
320 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
321 |
#else |
322 |
ndfRaw_ = ndfRaw_local; |
323 |
#endif |
324 |
} |
325 |
|
326 |
void SimInfo::calcNdfTrans() { |
327 |
int ndfTrans_local; |
328 |
|
329 |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
330 |
|
331 |
|
332 |
#ifdef IS_MPI |
333 |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
334 |
#else |
335 |
ndfTrans_ = ndfTrans_local; |
336 |
#endif |
337 |
|
338 |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
339 |
|
340 |
} |
341 |
|
342 |
void SimInfo::addExcludePairs(Molecule* mol) { |
343 |
std::vector<Bond*>::iterator bondIter; |
344 |
std::vector<Bend*>::iterator bendIter; |
345 |
std::vector<Torsion*>::iterator torsionIter; |
346 |
Bond* bond; |
347 |
Bend* bend; |
348 |
Torsion* torsion; |
349 |
int a; |
350 |
int b; |
351 |
int c; |
352 |
int d; |
353 |
|
354 |
std::map<int, std::set<int> > atomGroups; |
355 |
|
356 |
Molecule::RigidBodyIterator rbIter; |
357 |
RigidBody* rb; |
358 |
Molecule::IntegrableObjectIterator ii; |
359 |
StuntDouble* integrableObject; |
360 |
|
361 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
362 |
integrableObject = mol->nextIntegrableObject(ii)) { |
363 |
|
364 |
if (integrableObject->isRigidBody()) { |
365 |
rb = static_cast<RigidBody*>(integrableObject); |
366 |
std::vector<Atom*> atoms = rb->getAtoms(); |
367 |
std::set<int> rigidAtoms; |
368 |
for (int i = 0; i < atoms.size(); ++i) { |
369 |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
370 |
} |
371 |
for (int i = 0; i < atoms.size(); ++i) { |
372 |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
373 |
} |
374 |
} else { |
375 |
std::set<int> oneAtomSet; |
376 |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
377 |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
378 |
} |
379 |
} |
380 |
|
381 |
|
382 |
|
383 |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
384 |
a = bond->getAtomA()->getGlobalIndex(); |
385 |
b = bond->getAtomB()->getGlobalIndex(); |
386 |
exclude_.addPair(a, b); |
387 |
} |
388 |
|
389 |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
390 |
a = bend->getAtomA()->getGlobalIndex(); |
391 |
b = bend->getAtomB()->getGlobalIndex(); |
392 |
c = bend->getAtomC()->getGlobalIndex(); |
393 |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
394 |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
395 |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
396 |
|
397 |
exclude_.addPairs(rigidSetA, rigidSetB); |
398 |
exclude_.addPairs(rigidSetA, rigidSetC); |
399 |
exclude_.addPairs(rigidSetB, rigidSetC); |
400 |
|
401 |
//exclude_.addPair(a, b); |
402 |
//exclude_.addPair(a, c); |
403 |
//exclude_.addPair(b, c); |
404 |
} |
405 |
|
406 |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
407 |
a = torsion->getAtomA()->getGlobalIndex(); |
408 |
b = torsion->getAtomB()->getGlobalIndex(); |
409 |
c = torsion->getAtomC()->getGlobalIndex(); |
410 |
d = torsion->getAtomD()->getGlobalIndex(); |
411 |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
412 |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
413 |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
414 |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
415 |
|
416 |
exclude_.addPairs(rigidSetA, rigidSetB); |
417 |
exclude_.addPairs(rigidSetA, rigidSetC); |
418 |
exclude_.addPairs(rigidSetA, rigidSetD); |
419 |
exclude_.addPairs(rigidSetB, rigidSetC); |
420 |
exclude_.addPairs(rigidSetB, rigidSetD); |
421 |
exclude_.addPairs(rigidSetC, rigidSetD); |
422 |
|
423 |
/* |
424 |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
425 |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
426 |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
427 |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
428 |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
429 |
exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
430 |
|
431 |
|
432 |
exclude_.addPair(a, b); |
433 |
exclude_.addPair(a, c); |
434 |
exclude_.addPair(a, d); |
435 |
exclude_.addPair(b, c); |
436 |
exclude_.addPair(b, d); |
437 |
exclude_.addPair(c, d); |
438 |
*/ |
439 |
} |
440 |
|
441 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
442 |
std::vector<Atom*> atoms = rb->getAtoms(); |
443 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
444 |
for (int j = i + 1; j < atoms.size(); ++j) { |
445 |
a = atoms[i]->getGlobalIndex(); |
446 |
b = atoms[j]->getGlobalIndex(); |
447 |
exclude_.addPair(a, b); |
448 |
} |
449 |
} |
450 |
} |
451 |
|
452 |
} |
453 |
|
454 |
void SimInfo::removeExcludePairs(Molecule* mol) { |
455 |
std::vector<Bond*>::iterator bondIter; |
456 |
std::vector<Bend*>::iterator bendIter; |
457 |
std::vector<Torsion*>::iterator torsionIter; |
458 |
Bond* bond; |
459 |
Bend* bend; |
460 |
Torsion* torsion; |
461 |
int a; |
462 |
int b; |
463 |
int c; |
464 |
int d; |
465 |
|
466 |
std::map<int, std::set<int> > atomGroups; |
467 |
|
468 |
Molecule::RigidBodyIterator rbIter; |
469 |
RigidBody* rb; |
470 |
Molecule::IntegrableObjectIterator ii; |
471 |
StuntDouble* integrableObject; |
472 |
|
473 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
474 |
integrableObject = mol->nextIntegrableObject(ii)) { |
475 |
|
476 |
if (integrableObject->isRigidBody()) { |
477 |
rb = static_cast<RigidBody*>(integrableObject); |
478 |
std::vector<Atom*> atoms = rb->getAtoms(); |
479 |
std::set<int> rigidAtoms; |
480 |
for (int i = 0; i < atoms.size(); ++i) { |
481 |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
482 |
} |
483 |
for (int i = 0; i < atoms.size(); ++i) { |
484 |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
485 |
} |
486 |
} else { |
487 |
std::set<int> oneAtomSet; |
488 |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
489 |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
490 |
} |
491 |
} |
492 |
|
493 |
|
494 |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
495 |
a = bond->getAtomA()->getGlobalIndex(); |
496 |
b = bond->getAtomB()->getGlobalIndex(); |
497 |
exclude_.removePair(a, b); |
498 |
} |
499 |
|
500 |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
501 |
a = bend->getAtomA()->getGlobalIndex(); |
502 |
b = bend->getAtomB()->getGlobalIndex(); |
503 |
c = bend->getAtomC()->getGlobalIndex(); |
504 |
|
505 |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
506 |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
507 |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
508 |
|
509 |
exclude_.removePairs(rigidSetA, rigidSetB); |
510 |
exclude_.removePairs(rigidSetA, rigidSetC); |
511 |
exclude_.removePairs(rigidSetB, rigidSetC); |
512 |
|
513 |
//exclude_.removePair(a, b); |
514 |
//exclude_.removePair(a, c); |
515 |
//exclude_.removePair(b, c); |
516 |
} |
517 |
|
518 |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
519 |
a = torsion->getAtomA()->getGlobalIndex(); |
520 |
b = torsion->getAtomB()->getGlobalIndex(); |
521 |
c = torsion->getAtomC()->getGlobalIndex(); |
522 |
d = torsion->getAtomD()->getGlobalIndex(); |
523 |
|
524 |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
525 |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
526 |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
527 |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
528 |
|
529 |
exclude_.removePairs(rigidSetA, rigidSetB); |
530 |
exclude_.removePairs(rigidSetA, rigidSetC); |
531 |
exclude_.removePairs(rigidSetA, rigidSetD); |
532 |
exclude_.removePairs(rigidSetB, rigidSetC); |
533 |
exclude_.removePairs(rigidSetB, rigidSetD); |
534 |
exclude_.removePairs(rigidSetC, rigidSetD); |
535 |
|
536 |
/* |
537 |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
538 |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
539 |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
540 |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
541 |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
542 |
exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
543 |
|
544 |
|
545 |
exclude_.removePair(a, b); |
546 |
exclude_.removePair(a, c); |
547 |
exclude_.removePair(a, d); |
548 |
exclude_.removePair(b, c); |
549 |
exclude_.removePair(b, d); |
550 |
exclude_.removePair(c, d); |
551 |
*/ |
552 |
} |
553 |
|
554 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
555 |
std::vector<Atom*> atoms = rb->getAtoms(); |
556 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
557 |
for (int j = i + 1; j < atoms.size(); ++j) { |
558 |
a = atoms[i]->getGlobalIndex(); |
559 |
b = atoms[j]->getGlobalIndex(); |
560 |
exclude_.removePair(a, b); |
561 |
} |
562 |
} |
563 |
} |
564 |
|
565 |
} |
566 |
|
567 |
|
568 |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
569 |
int curStampId; |
570 |
|
571 |
//index from 0 |
572 |
curStampId = moleculeStamps_.size(); |
573 |
|
574 |
moleculeStamps_.push_back(molStamp); |
575 |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
576 |
} |
577 |
|
578 |
void SimInfo::update() { |
579 |
|
580 |
setupSimType(); |
581 |
|
582 |
#ifdef IS_MPI |
583 |
setupFortranParallel(); |
584 |
#endif |
585 |
|
586 |
setupFortranSim(); |
587 |
|
588 |
//setup fortran force field |
589 |
/** @deprecate */ |
590 |
int isError = 0; |
591 |
|
592 |
setupElectrostaticSummationMethod( isError ); |
593 |
setupSwitchingFunction(); |
594 |
|
595 |
if(isError){ |
596 |
sprintf( painCave.errMsg, |
597 |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
598 |
painCave.isFatal = 1; |
599 |
simError(); |
600 |
} |
601 |
|
602 |
|
603 |
setupCutoff(); |
604 |
|
605 |
calcNdf(); |
606 |
calcNdfRaw(); |
607 |
calcNdfTrans(); |
608 |
|
609 |
fortranInitialized_ = true; |
610 |
} |
611 |
|
612 |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
613 |
SimInfo::MoleculeIterator mi; |
614 |
Molecule* mol; |
615 |
Molecule::AtomIterator ai; |
616 |
Atom* atom; |
617 |
std::set<AtomType*> atomTypes; |
618 |
|
619 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
620 |
|
621 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
622 |
atomTypes.insert(atom->getAtomType()); |
623 |
} |
624 |
|
625 |
} |
626 |
|
627 |
return atomTypes; |
628 |
} |
629 |
|
630 |
void SimInfo::setupSimType() { |
631 |
std::set<AtomType*>::iterator i; |
632 |
std::set<AtomType*> atomTypes; |
633 |
atomTypes = getUniqueAtomTypes(); |
634 |
|
635 |
int useLennardJones = 0; |
636 |
int useElectrostatic = 0; |
637 |
int useEAM = 0; |
638 |
int useSC = 0; |
639 |
int useCharge = 0; |
640 |
int useDirectional = 0; |
641 |
int useDipole = 0; |
642 |
int useGayBerne = 0; |
643 |
int useSticky = 0; |
644 |
int useStickyPower = 0; |
645 |
int useShape = 0; |
646 |
int useFLARB = 0; //it is not in AtomType yet |
647 |
int useDirectionalAtom = 0; |
648 |
int useElectrostatics = 0; |
649 |
//usePBC and useRF are from simParams |
650 |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
651 |
int useRF; |
652 |
int useSF; |
653 |
std::string myMethod; |
654 |
|
655 |
// set the useRF logical |
656 |
useRF = 0; |
657 |
useSF = 0; |
658 |
|
659 |
|
660 |
if (simParams_->haveElectrostaticSummationMethod()) { |
661 |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
662 |
toUpper(myMethod); |
663 |
if (myMethod == "REACTION_FIELD") { |
664 |
useRF=1; |
665 |
} else { |
666 |
if (myMethod == "SHIFTED_FORCE") { |
667 |
useSF = 1; |
668 |
} |
669 |
} |
670 |
} |
671 |
|
672 |
//loop over all of the atom types |
673 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
674 |
useLennardJones |= (*i)->isLennardJones(); |
675 |
useElectrostatic |= (*i)->isElectrostatic(); |
676 |
useEAM |= (*i)->isEAM(); |
677 |
useSC |= (*i)->isSC(); |
678 |
useCharge |= (*i)->isCharge(); |
679 |
useDirectional |= (*i)->isDirectional(); |
680 |
useDipole |= (*i)->isDipole(); |
681 |
useGayBerne |= (*i)->isGayBerne(); |
682 |
useSticky |= (*i)->isSticky(); |
683 |
useStickyPower |= (*i)->isStickyPower(); |
684 |
useShape |= (*i)->isShape(); |
685 |
} |
686 |
|
687 |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
688 |
useDirectionalAtom = 1; |
689 |
} |
690 |
|
691 |
if (useCharge || useDipole) { |
692 |
useElectrostatics = 1; |
693 |
} |
694 |
|
695 |
#ifdef IS_MPI |
696 |
int temp; |
697 |
|
698 |
temp = usePBC; |
699 |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
700 |
|
701 |
temp = useDirectionalAtom; |
702 |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
703 |
|
704 |
temp = useLennardJones; |
705 |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
706 |
|
707 |
temp = useElectrostatics; |
708 |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
709 |
|
710 |
temp = useCharge; |
711 |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
712 |
|
713 |
temp = useDipole; |
714 |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
715 |
|
716 |
temp = useSticky; |
717 |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
718 |
|
719 |
temp = useStickyPower; |
720 |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
721 |
|
722 |
temp = useGayBerne; |
723 |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
724 |
|
725 |
temp = useEAM; |
726 |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
727 |
|
728 |
temp = useSC; |
729 |
MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
730 |
|
731 |
temp = useShape; |
732 |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
733 |
|
734 |
temp = useFLARB; |
735 |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
736 |
|
737 |
temp = useRF; |
738 |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
739 |
|
740 |
temp = useSF; |
741 |
MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
742 |
|
743 |
#endif |
744 |
|
745 |
fInfo_.SIM_uses_PBC = usePBC; |
746 |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
747 |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
748 |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
749 |
fInfo_.SIM_uses_Charges = useCharge; |
750 |
fInfo_.SIM_uses_Dipoles = useDipole; |
751 |
fInfo_.SIM_uses_Sticky = useSticky; |
752 |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
753 |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
754 |
fInfo_.SIM_uses_EAM = useEAM; |
755 |
fInfo_.SIM_uses_SC = useSC; |
756 |
fInfo_.SIM_uses_Shapes = useShape; |
757 |
fInfo_.SIM_uses_FLARB = useFLARB; |
758 |
fInfo_.SIM_uses_RF = useRF; |
759 |
fInfo_.SIM_uses_SF = useSF; |
760 |
|
761 |
if( myMethod == "REACTION_FIELD") { |
762 |
|
763 |
if (simParams_->haveDielectric()) { |
764 |
fInfo_.dielect = simParams_->getDielectric(); |
765 |
} else { |
766 |
sprintf(painCave.errMsg, |
767 |
"SimSetup Error: No Dielectric constant was set.\n" |
768 |
"\tYou are trying to use Reaction Field without" |
769 |
"\tsetting a dielectric constant!\n"); |
770 |
painCave.isFatal = 1; |
771 |
simError(); |
772 |
} |
773 |
} |
774 |
|
775 |
} |
776 |
|
777 |
void SimInfo::setupFortranSim() { |
778 |
int isError; |
779 |
int nExclude; |
780 |
std::vector<int> fortranGlobalGroupMembership; |
781 |
|
782 |
nExclude = exclude_.getSize(); |
783 |
isError = 0; |
784 |
|
785 |
//globalGroupMembership_ is filled by SimCreator |
786 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
787 |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
788 |
} |
789 |
|
790 |
//calculate mass ratio of cutoff group |
791 |
std::vector<double> mfact; |
792 |
SimInfo::MoleculeIterator mi; |
793 |
Molecule* mol; |
794 |
Molecule::CutoffGroupIterator ci; |
795 |
CutoffGroup* cg; |
796 |
Molecule::AtomIterator ai; |
797 |
Atom* atom; |
798 |
double totalMass; |
799 |
|
800 |
//to avoid memory reallocation, reserve enough space for mfact |
801 |
mfact.reserve(getNCutoffGroups()); |
802 |
|
803 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
804 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
805 |
|
806 |
totalMass = cg->getMass(); |
807 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
808 |
// Check for massless groups - set mfact to 1 if true |
809 |
if (totalMass != 0) |
810 |
mfact.push_back(atom->getMass()/totalMass); |
811 |
else |
812 |
mfact.push_back( 1.0 ); |
813 |
} |
814 |
|
815 |
} |
816 |
} |
817 |
|
818 |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
819 |
std::vector<int> identArray; |
820 |
|
821 |
//to avoid memory reallocation, reserve enough space identArray |
822 |
identArray.reserve(getNAtoms()); |
823 |
|
824 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
825 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
826 |
identArray.push_back(atom->getIdent()); |
827 |
} |
828 |
} |
829 |
|
830 |
//fill molMembershipArray |
831 |
//molMembershipArray is filled by SimCreator |
832 |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
833 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
834 |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
835 |
} |
836 |
|
837 |
//setup fortran simulation |
838 |
int nGlobalExcludes = 0; |
839 |
int* globalExcludes = NULL; |
840 |
int* excludeList = exclude_.getExcludeList(); |
841 |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
842 |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
843 |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
844 |
|
845 |
if( isError ){ |
846 |
|
847 |
sprintf( painCave.errMsg, |
848 |
"There was an error setting the simulation information in fortran.\n" ); |
849 |
painCave.isFatal = 1; |
850 |
painCave.severity = OOPSE_ERROR; |
851 |
simError(); |
852 |
} |
853 |
|
854 |
#ifdef IS_MPI |
855 |
sprintf( checkPointMsg, |
856 |
"succesfully sent the simulation information to fortran.\n"); |
857 |
MPIcheckPoint(); |
858 |
#endif // is_mpi |
859 |
} |
860 |
|
861 |
|
862 |
#ifdef IS_MPI |
863 |
void SimInfo::setupFortranParallel() { |
864 |
|
865 |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
866 |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
867 |
std::vector<int> localToGlobalCutoffGroupIndex; |
868 |
SimInfo::MoleculeIterator mi; |
869 |
Molecule::AtomIterator ai; |
870 |
Molecule::CutoffGroupIterator ci; |
871 |
Molecule* mol; |
872 |
Atom* atom; |
873 |
CutoffGroup* cg; |
874 |
mpiSimData parallelData; |
875 |
int isError; |
876 |
|
877 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
878 |
|
879 |
//local index(index in DataStorge) of atom is important |
880 |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
881 |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
882 |
} |
883 |
|
884 |
//local index of cutoff group is trivial, it only depends on the order of travesing |
885 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
886 |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
887 |
} |
888 |
|
889 |
} |
890 |
|
891 |
//fill up mpiSimData struct |
892 |
parallelData.nMolGlobal = getNGlobalMolecules(); |
893 |
parallelData.nMolLocal = getNMolecules(); |
894 |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
895 |
parallelData.nAtomsLocal = getNAtoms(); |
896 |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
897 |
parallelData.nGroupsLocal = getNCutoffGroups(); |
898 |
parallelData.myNode = worldRank; |
899 |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
900 |
|
901 |
//pass mpiSimData struct and index arrays to fortran |
902 |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
903 |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
904 |
&localToGlobalCutoffGroupIndex[0], &isError); |
905 |
|
906 |
if (isError) { |
907 |
sprintf(painCave.errMsg, |
908 |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
909 |
painCave.isFatal = 1; |
910 |
simError(); |
911 |
} |
912 |
|
913 |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
914 |
MPIcheckPoint(); |
915 |
|
916 |
|
917 |
} |
918 |
|
919 |
#endif |
920 |
|
921 |
void SimInfo::setupCutoff() { |
922 |
|
923 |
// Check the cutoff policy |
924 |
int cp = TRADITIONAL_CUTOFF_POLICY; |
925 |
if (simParams_->haveCutoffPolicy()) { |
926 |
std::string myPolicy = simParams_->getCutoffPolicy(); |
927 |
toUpper(myPolicy); |
928 |
if (myPolicy == "MIX") { |
929 |
cp = MIX_CUTOFF_POLICY; |
930 |
} else { |
931 |
if (myPolicy == "MAX") { |
932 |
cp = MAX_CUTOFF_POLICY; |
933 |
} else { |
934 |
if (myPolicy == "TRADITIONAL") { |
935 |
cp = TRADITIONAL_CUTOFF_POLICY; |
936 |
} else { |
937 |
// throw error |
938 |
sprintf( painCave.errMsg, |
939 |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
940 |
painCave.isFatal = 1; |
941 |
simError(); |
942 |
} |
943 |
} |
944 |
} |
945 |
} |
946 |
notifyFortranCutoffPolicy(&cp); |
947 |
|
948 |
// Check the Skin Thickness for neighborlists |
949 |
double skin; |
950 |
if (simParams_->haveSkinThickness()) { |
951 |
skin = simParams_->getSkinThickness(); |
952 |
notifyFortranSkinThickness(&skin); |
953 |
} |
954 |
|
955 |
// Check if the cutoff was set explicitly: |
956 |
if (simParams_->haveCutoffRadius()) { |
957 |
rcut_ = simParams_->getCutoffRadius(); |
958 |
if (simParams_->haveSwitchingRadius()) { |
959 |
rsw_ = simParams_->getSwitchingRadius(); |
960 |
} else { |
961 |
rsw_ = rcut_; |
962 |
} |
963 |
notifyFortranCutoffs(&rcut_, &rsw_); |
964 |
|
965 |
} else { |
966 |
|
967 |
// For electrostatic atoms, we'll assume a large safe value: |
968 |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
969 |
sprintf(painCave.errMsg, |
970 |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
971 |
"\tOOPSE will use a default value of 15.0 angstroms" |
972 |
"\tfor the cutoffRadius.\n"); |
973 |
painCave.isFatal = 0; |
974 |
simError(); |
975 |
rcut_ = 15.0; |
976 |
|
977 |
if (simParams_->haveElectrostaticSummationMethod()) { |
978 |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
979 |
toUpper(myMethod); |
980 |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
981 |
if (simParams_->haveSwitchingRadius()){ |
982 |
sprintf(painCave.errMsg, |
983 |
"SimInfo Warning: A value was set for the switchingRadius\n" |
984 |
"\teven though the electrostaticSummationMethod was\n" |
985 |
"\tset to %s\n", myMethod.c_str()); |
986 |
painCave.isFatal = 1; |
987 |
simError(); |
988 |
} |
989 |
} |
990 |
} |
991 |
|
992 |
if (simParams_->haveSwitchingRadius()){ |
993 |
rsw_ = simParams_->getSwitchingRadius(); |
994 |
} else { |
995 |
sprintf(painCave.errMsg, |
996 |
"SimCreator Warning: No value was set for switchingRadius.\n" |
997 |
"\tOOPSE will use a default value of\n" |
998 |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
999 |
painCave.isFatal = 0; |
1000 |
simError(); |
1001 |
rsw_ = 0.85 * rcut_; |
1002 |
} |
1003 |
notifyFortranCutoffs(&rcut_, &rsw_); |
1004 |
} else { |
1005 |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1006 |
// We'll punt and let fortran figure out the cutoffs later. |
1007 |
|
1008 |
notifyFortranYouAreOnYourOwn(); |
1009 |
|
1010 |
} |
1011 |
} |
1012 |
} |
1013 |
|
1014 |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1015 |
|
1016 |
int errorOut; |
1017 |
int esm = NONE; |
1018 |
int sm = UNDAMPED; |
1019 |
double alphaVal; |
1020 |
double dielectric; |
1021 |
|
1022 |
errorOut = isError; |
1023 |
alphaVal = simParams_->getDampingAlpha(); |
1024 |
dielectric = simParams_->getDielectric(); |
1025 |
|
1026 |
if (simParams_->haveElectrostaticSummationMethod()) { |
1027 |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
1028 |
toUpper(myMethod); |
1029 |
if (myMethod == "NONE") { |
1030 |
esm = NONE; |
1031 |
} else { |
1032 |
if (myMethod == "SWITCHING_FUNCTION") { |
1033 |
esm = SWITCHING_FUNCTION; |
1034 |
} else { |
1035 |
if (myMethod == "SHIFTED_POTENTIAL") { |
1036 |
esm = SHIFTED_POTENTIAL; |
1037 |
} else { |
1038 |
if (myMethod == "SHIFTED_FORCE") { |
1039 |
esm = SHIFTED_FORCE; |
1040 |
} else { |
1041 |
if (myMethod == "REACTION_FIELD") { |
1042 |
esm = REACTION_FIELD; |
1043 |
} else { |
1044 |
// throw error |
1045 |
sprintf( painCave.errMsg, |
1046 |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1047 |
"\t(Input file specified %s .)\n" |
1048 |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1049 |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1050 |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1051 |
painCave.isFatal = 1; |
1052 |
simError(); |
1053 |
} |
1054 |
} |
1055 |
} |
1056 |
} |
1057 |
} |
1058 |
} |
1059 |
|
1060 |
if (simParams_->haveElectrostaticScreeningMethod()) { |
1061 |
std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
1062 |
toUpper(myScreen); |
1063 |
if (myScreen == "UNDAMPED") { |
1064 |
sm = UNDAMPED; |
1065 |
} else { |
1066 |
if (myScreen == "DAMPED") { |
1067 |
sm = DAMPED; |
1068 |
if (!simParams_->haveDampingAlpha()) { |
1069 |
//throw error |
1070 |
sprintf( painCave.errMsg, |
1071 |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1072 |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1073 |
painCave.isFatal = 0; |
1074 |
simError(); |
1075 |
} |
1076 |
} else { |
1077 |
// throw error |
1078 |
sprintf( painCave.errMsg, |
1079 |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1080 |
"\t(Input file specified %s .)\n" |
1081 |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1082 |
"or \"damped\".\n", myScreen.c_str() ); |
1083 |
painCave.isFatal = 1; |
1084 |
simError(); |
1085 |
} |
1086 |
} |
1087 |
} |
1088 |
|
1089 |
// let's pass some summation method variables to fortran |
1090 |
setElectrostaticSumMethod( &esm ); |
1091 |
setFortranElectrostaticMethod( &esm ); |
1092 |
setScreeningMethod( &sm ); |
1093 |
setDampingAlpha( &alphaVal ); |
1094 |
setReactionFieldDielectric( &dielectric ); |
1095 |
initFortranFF( &errorOut ); |
1096 |
} |
1097 |
|
1098 |
void SimInfo::setupSwitchingFunction() { |
1099 |
int ft = CUBIC; |
1100 |
|
1101 |
if (simParams_->haveSwitchingFunctionType()) { |
1102 |
std::string funcType = simParams_->getSwitchingFunctionType(); |
1103 |
toUpper(funcType); |
1104 |
if (funcType == "CUBIC") { |
1105 |
ft = CUBIC; |
1106 |
} else { |
1107 |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
1108 |
ft = FIFTH_ORDER_POLY; |
1109 |
} else { |
1110 |
// throw error |
1111 |
sprintf( painCave.errMsg, |
1112 |
"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
1113 |
painCave.isFatal = 1; |
1114 |
simError(); |
1115 |
} |
1116 |
} |
1117 |
} |
1118 |
|
1119 |
// send switching function notification to switcheroo |
1120 |
setFunctionType(&ft); |
1121 |
|
1122 |
} |
1123 |
|
1124 |
void SimInfo::addProperty(GenericData* genData) { |
1125 |
properties_.addProperty(genData); |
1126 |
} |
1127 |
|
1128 |
void SimInfo::removeProperty(const std::string& propName) { |
1129 |
properties_.removeProperty(propName); |
1130 |
} |
1131 |
|
1132 |
void SimInfo::clearProperties() { |
1133 |
properties_.clearProperties(); |
1134 |
} |
1135 |
|
1136 |
std::vector<std::string> SimInfo::getPropertyNames() { |
1137 |
return properties_.getPropertyNames(); |
1138 |
} |
1139 |
|
1140 |
std::vector<GenericData*> SimInfo::getProperties() { |
1141 |
return properties_.getProperties(); |
1142 |
} |
1143 |
|
1144 |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
1145 |
return properties_.getPropertyByName(propName); |
1146 |
} |
1147 |
|
1148 |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
1149 |
if (sman_ == sman) { |
1150 |
return; |
1151 |
} |
1152 |
delete sman_; |
1153 |
sman_ = sman; |
1154 |
|
1155 |
Molecule* mol; |
1156 |
RigidBody* rb; |
1157 |
Atom* atom; |
1158 |
SimInfo::MoleculeIterator mi; |
1159 |
Molecule::RigidBodyIterator rbIter; |
1160 |
Molecule::AtomIterator atomIter;; |
1161 |
|
1162 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
1163 |
|
1164 |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1165 |
atom->setSnapshotManager(sman_); |
1166 |
} |
1167 |
|
1168 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1169 |
rb->setSnapshotManager(sman_); |
1170 |
} |
1171 |
} |
1172 |
|
1173 |
} |
1174 |
|
1175 |
Vector3d SimInfo::getComVel(){ |
1176 |
SimInfo::MoleculeIterator i; |
1177 |
Molecule* mol; |
1178 |
|
1179 |
Vector3d comVel(0.0); |
1180 |
double totalMass = 0.0; |
1181 |
|
1182 |
|
1183 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1184 |
double mass = mol->getMass(); |
1185 |
totalMass += mass; |
1186 |
comVel += mass * mol->getComVel(); |
1187 |
} |
1188 |
|
1189 |
#ifdef IS_MPI |
1190 |
double tmpMass = totalMass; |
1191 |
Vector3d tmpComVel(comVel); |
1192 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1193 |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1194 |
#endif |
1195 |
|
1196 |
comVel /= totalMass; |
1197 |
|
1198 |
return comVel; |
1199 |
} |
1200 |
|
1201 |
Vector3d SimInfo::getCom(){ |
1202 |
SimInfo::MoleculeIterator i; |
1203 |
Molecule* mol; |
1204 |
|
1205 |
Vector3d com(0.0); |
1206 |
double totalMass = 0.0; |
1207 |
|
1208 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1209 |
double mass = mol->getMass(); |
1210 |
totalMass += mass; |
1211 |
com += mass * mol->getCom(); |
1212 |
} |
1213 |
|
1214 |
#ifdef IS_MPI |
1215 |
double tmpMass = totalMass; |
1216 |
Vector3d tmpCom(com); |
1217 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1218 |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1219 |
#endif |
1220 |
|
1221 |
com /= totalMass; |
1222 |
|
1223 |
return com; |
1224 |
|
1225 |
} |
1226 |
|
1227 |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1228 |
|
1229 |
return o; |
1230 |
} |
1231 |
|
1232 |
|
1233 |
/* |
1234 |
Returns center of mass and center of mass velocity in one function call. |
1235 |
*/ |
1236 |
|
1237 |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1238 |
SimInfo::MoleculeIterator i; |
1239 |
Molecule* mol; |
1240 |
|
1241 |
|
1242 |
double totalMass = 0.0; |
1243 |
|
1244 |
|
1245 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1246 |
double mass = mol->getMass(); |
1247 |
totalMass += mass; |
1248 |
com += mass * mol->getCom(); |
1249 |
comVel += mass * mol->getComVel(); |
1250 |
} |
1251 |
|
1252 |
#ifdef IS_MPI |
1253 |
double tmpMass = totalMass; |
1254 |
Vector3d tmpCom(com); |
1255 |
Vector3d tmpComVel(comVel); |
1256 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1257 |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1258 |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1259 |
#endif |
1260 |
|
1261 |
com /= totalMass; |
1262 |
comVel /= totalMass; |
1263 |
} |
1264 |
|
1265 |
/* |
1266 |
Return intertia tensor for entire system and angular momentum Vector. |
1267 |
|
1268 |
|
1269 |
[ Ixx -Ixy -Ixz ] |
1270 |
J =| -Iyx Iyy -Iyz | |
1271 |
[ -Izx -Iyz Izz ] |
1272 |
*/ |
1273 |
|
1274 |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1275 |
|
1276 |
|
1277 |
double xx = 0.0; |
1278 |
double yy = 0.0; |
1279 |
double zz = 0.0; |
1280 |
double xy = 0.0; |
1281 |
double xz = 0.0; |
1282 |
double yz = 0.0; |
1283 |
Vector3d com(0.0); |
1284 |
Vector3d comVel(0.0); |
1285 |
|
1286 |
getComAll(com, comVel); |
1287 |
|
1288 |
SimInfo::MoleculeIterator i; |
1289 |
Molecule* mol; |
1290 |
|
1291 |
Vector3d thisq(0.0); |
1292 |
Vector3d thisv(0.0); |
1293 |
|
1294 |
double thisMass = 0.0; |
1295 |
|
1296 |
|
1297 |
|
1298 |
|
1299 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1300 |
|
1301 |
thisq = mol->getCom()-com; |
1302 |
thisv = mol->getComVel()-comVel; |
1303 |
thisMass = mol->getMass(); |
1304 |
// Compute moment of intertia coefficients. |
1305 |
xx += thisq[0]*thisq[0]*thisMass; |
1306 |
yy += thisq[1]*thisq[1]*thisMass; |
1307 |
zz += thisq[2]*thisq[2]*thisMass; |
1308 |
|
1309 |
// compute products of intertia |
1310 |
xy += thisq[0]*thisq[1]*thisMass; |
1311 |
xz += thisq[0]*thisq[2]*thisMass; |
1312 |
yz += thisq[1]*thisq[2]*thisMass; |
1313 |
|
1314 |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1315 |
|
1316 |
} |
1317 |
|
1318 |
|
1319 |
inertiaTensor(0,0) = yy + zz; |
1320 |
inertiaTensor(0,1) = -xy; |
1321 |
inertiaTensor(0,2) = -xz; |
1322 |
inertiaTensor(1,0) = -xy; |
1323 |
inertiaTensor(1,1) = xx + zz; |
1324 |
inertiaTensor(1,2) = -yz; |
1325 |
inertiaTensor(2,0) = -xz; |
1326 |
inertiaTensor(2,1) = -yz; |
1327 |
inertiaTensor(2,2) = xx + yy; |
1328 |
|
1329 |
#ifdef IS_MPI |
1330 |
Mat3x3d tmpI(inertiaTensor); |
1331 |
Vector3d tmpAngMom; |
1332 |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1333 |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1334 |
#endif |
1335 |
|
1336 |
return; |
1337 |
} |
1338 |
|
1339 |
//Returns the angular momentum of the system |
1340 |
Vector3d SimInfo::getAngularMomentum(){ |
1341 |
|
1342 |
Vector3d com(0.0); |
1343 |
Vector3d comVel(0.0); |
1344 |
Vector3d angularMomentum(0.0); |
1345 |
|
1346 |
getComAll(com,comVel); |
1347 |
|
1348 |
SimInfo::MoleculeIterator i; |
1349 |
Molecule* mol; |
1350 |
|
1351 |
Vector3d thisr(0.0); |
1352 |
Vector3d thisp(0.0); |
1353 |
|
1354 |
double thisMass; |
1355 |
|
1356 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1357 |
thisMass = mol->getMass(); |
1358 |
thisr = mol->getCom()-com; |
1359 |
thisp = (mol->getComVel()-comVel)*thisMass; |
1360 |
|
1361 |
angularMomentum += cross( thisr, thisp ); |
1362 |
|
1363 |
} |
1364 |
|
1365 |
#ifdef IS_MPI |
1366 |
Vector3d tmpAngMom; |
1367 |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1368 |
#endif |
1369 |
|
1370 |
return angularMomentum; |
1371 |
} |
1372 |
|
1373 |
|
1374 |
}//end namespace oopse |
1375 |
|