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.hpp |
44 |
* @author tlin |
45 |
* @date 11/02/2004 |
46 |
* @version 1.0 |
47 |
*/ |
48 |
|
49 |
#ifndef BRAINS_SIMMODEL_HPP |
50 |
#define BRAINS_SIMMODEL_HPP |
51 |
|
52 |
#include <iostream> |
53 |
#include <set> |
54 |
#include <utility> |
55 |
#include <vector> |
56 |
|
57 |
#include "brains/Exclude.hpp" |
58 |
#include "io/Globals.hpp" |
59 |
#include "math/Vector3.hpp" |
60 |
#include "math/SquareMatrix3.hpp" |
61 |
#include "types/MoleculeStamp.hpp" |
62 |
#include "UseTheForce/ForceField.hpp" |
63 |
#include "utils/PropertyMap.hpp" |
64 |
#include "utils/LocalIndexManager.hpp" |
65 |
|
66 |
//another nonsense macro declaration |
67 |
#define __C |
68 |
#include "brains/fSimulation.h" |
69 |
|
70 |
namespace oopse{ |
71 |
|
72 |
//forward decalration |
73 |
class SnapshotManager; |
74 |
class Molecule; |
75 |
class SelectionManager; |
76 |
/** |
77 |
* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
78 |
* @brief As one of the heavy weight class of OOPSE, SimInfo |
79 |
* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
80 |
* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
81 |
* cutoff groups, constrains). |
82 |
* Another major change is the index. No matter single version or parallel version, atoms and |
83 |
* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
84 |
* cutoff group. |
85 |
*/ |
86 |
class SimInfo { |
87 |
public: |
88 |
typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
89 |
|
90 |
/** |
91 |
* Constructor of SimInfo |
92 |
* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
93 |
* second element is the total number of molecules with the same molecule stamp in the system |
94 |
* @param ff pointer of a concrete ForceField instance |
95 |
* @param simParams |
96 |
* @note |
97 |
*/ |
98 |
SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
99 |
virtual ~SimInfo(); |
100 |
|
101 |
/** |
102 |
* Adds a molecule |
103 |
* @return return true if adding successfully, return false if the molecule is already in SimInfo |
104 |
* @param mol molecule to be added |
105 |
*/ |
106 |
bool addMolecule(Molecule* mol); |
107 |
|
108 |
/** |
109 |
* Removes a molecule from SimInfo |
110 |
* @return true if removing successfully, return false if molecule is not in this SimInfo |
111 |
*/ |
112 |
bool removeMolecule(Molecule* mol); |
113 |
|
114 |
/** Returns the total number of molecules in the system. */ |
115 |
int getNGlobalMolecules() { |
116 |
return nGlobalMols_; |
117 |
} |
118 |
|
119 |
/** Returns the total number of atoms in the system. */ |
120 |
int getNGlobalAtoms() { |
121 |
return nGlobalAtoms_; |
122 |
} |
123 |
|
124 |
/** Returns the total number of cutoff groups in the system. */ |
125 |
int getNGlobalCutoffGroups() { |
126 |
return nGlobalCutoffGroups_; |
127 |
} |
128 |
|
129 |
/** |
130 |
* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
131 |
* of atoms which do not belong to the rigid bodies) in the system |
132 |
*/ |
133 |
int getNGlobalIntegrableObjects() { |
134 |
return nGlobalIntegrableObjects_; |
135 |
} |
136 |
|
137 |
/** |
138 |
* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
139 |
* of atoms which do not belong to the rigid bodies) in the system |
140 |
*/ |
141 |
int getNGlobalRigidBodies() { |
142 |
return nGlobalRigidBodies_; |
143 |
} |
144 |
|
145 |
int getNGlobalConstraints(); |
146 |
/** |
147 |
* Returns the number of local molecules. |
148 |
* @return the number of local molecules |
149 |
*/ |
150 |
int getNMolecules() { |
151 |
return molecules_.size(); |
152 |
} |
153 |
|
154 |
/** Returns the number of local atoms */ |
155 |
unsigned int getNAtoms() { |
156 |
return nAtoms_; |
157 |
} |
158 |
|
159 |
/** Returns the number of local bonds */ |
160 |
unsigned int getNBonds(){ |
161 |
return nBonds_; |
162 |
} |
163 |
|
164 |
/** Returns the number of local bends */ |
165 |
unsigned int getNBends() { |
166 |
return nBends_; |
167 |
} |
168 |
|
169 |
/** Returns the number of local torsions */ |
170 |
unsigned int getNTorsions() { |
171 |
return nTorsions_; |
172 |
} |
173 |
|
174 |
/** Returns the number of local rigid bodies */ |
175 |
unsigned int getNRigidBodies() { |
176 |
return nRigidBodies_; |
177 |
} |
178 |
|
179 |
/** Returns the number of local integrable objects */ |
180 |
unsigned int getNIntegrableObjects() { |
181 |
return nIntegrableObjects_; |
182 |
} |
183 |
|
184 |
/** Returns the number of local cutoff groups */ |
185 |
unsigned int getNCutoffGroups() { |
186 |
return nCutoffGroups_; |
187 |
} |
188 |
|
189 |
/** Returns the total number of constraints in this SimInfo */ |
190 |
unsigned int getNConstraints() { |
191 |
return nConstraints_; |
192 |
} |
193 |
|
194 |
/** |
195 |
* Returns the first molecule in this SimInfo and intialize the iterator. |
196 |
* @return the first molecule, return NULL if there is not molecule in this SimInfo |
197 |
* @param i the iterator of molecule array (user shouldn't change it) |
198 |
*/ |
199 |
Molecule* beginMolecule(MoleculeIterator& i); |
200 |
|
201 |
/** |
202 |
* Returns the next avaliable Molecule based on the iterator. |
203 |
* @return the next avaliable molecule, return NULL if reaching the end of the array |
204 |
* @param i the iterator of molecule array |
205 |
*/ |
206 |
Molecule* nextMolecule(MoleculeIterator& i); |
207 |
|
208 |
/** Returns the number of degrees of freedom */ |
209 |
int getNdf() { |
210 |
return ndf_; |
211 |
} |
212 |
|
213 |
/** Returns the number of raw degrees of freedom */ |
214 |
int getNdfRaw() { |
215 |
return ndfRaw_; |
216 |
} |
217 |
|
218 |
/** Returns the number of translational degrees of freedom */ |
219 |
int getNdfTrans() { |
220 |
return ndfTrans_; |
221 |
} |
222 |
|
223 |
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
224 |
|
225 |
/** Returns the total number of z-constraint molecules in the system */ |
226 |
int getNZconstraint() { |
227 |
return nZconstraint_; |
228 |
} |
229 |
|
230 |
/** |
231 |
* Sets the number of z-constraint molecules in the system. |
232 |
*/ |
233 |
void setNZconstraint(int nZconstraint) { |
234 |
nZconstraint_ = nZconstraint; |
235 |
} |
236 |
|
237 |
/** Returns the snapshot manager. */ |
238 |
SnapshotManager* getSnapshotManager() { |
239 |
return sman_; |
240 |
} |
241 |
|
242 |
/** Sets the snapshot manager. */ |
243 |
void setSnapshotManager(SnapshotManager* sman); |
244 |
|
245 |
/** Returns the force field */ |
246 |
ForceField* getForceField() { |
247 |
return forceField_; |
248 |
} |
249 |
|
250 |
Globals* getSimParams() { |
251 |
return simParams_; |
252 |
} |
253 |
|
254 |
/** Returns the velocity of center of mass of the whole system.*/ |
255 |
Vector3d getComVel(); |
256 |
|
257 |
/** Returns the center of the mass of the whole system.*/ |
258 |
Vector3d getCom(); |
259 |
/** Returns the center of the mass and Center of Mass velocity of the whole system.*/ |
260 |
void getComAll(Vector3d& com,Vector3d& comVel); |
261 |
|
262 |
/** Returns intertia tensor for the entire system and system Angular Momentum.*/ |
263 |
void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum); |
264 |
|
265 |
/** Returns system angular momentum */ |
266 |
Vector3d getAngularMomentum(); |
267 |
|
268 |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
269 |
void update(); |
270 |
|
271 |
/** Returns the local index manager */ |
272 |
LocalIndexManager* getLocalIndexManager() { |
273 |
return &localIndexMan_; |
274 |
} |
275 |
|
276 |
int getMoleculeStampId(int globalIndex) { |
277 |
//assert(globalIndex < molStampIds_.size()) |
278 |
return molStampIds_[globalIndex]; |
279 |
} |
280 |
|
281 |
/** Returns the molecule stamp */ |
282 |
MoleculeStamp* getMoleculeStamp(int id) { |
283 |
return moleculeStamps_[id]; |
284 |
} |
285 |
|
286 |
/** Return the total number of the molecule stamps */ |
287 |
int getNMoleculeStamp() { |
288 |
return moleculeStamps_.size(); |
289 |
} |
290 |
/** |
291 |
* Finds a molecule with a specified global index |
292 |
* @return a pointer point to found molecule |
293 |
* @param index |
294 |
*/ |
295 |
Molecule* getMoleculeByGlobalIndex(int index) { |
296 |
MoleculeIterator i; |
297 |
i = molecules_.find(index); |
298 |
|
299 |
return i != molecules_.end() ? i->second : NULL; |
300 |
} |
301 |
|
302 |
/** Calculate the maximum cutoff radius based on the atom types */ |
303 |
double calcMaxCutoffRadius(); |
304 |
|
305 |
double getRcut() { |
306 |
return rcut_; |
307 |
} |
308 |
|
309 |
double getRsw() { |
310 |
return rsw_; |
311 |
} |
312 |
|
313 |
std::string getFinalConfigFileName() { |
314 |
return finalConfigFileName_; |
315 |
} |
316 |
|
317 |
void setFinalConfigFileName(const std::string& fileName) { |
318 |
finalConfigFileName_ = fileName; |
319 |
} |
320 |
|
321 |
std::string getDumpFileName() { |
322 |
return dumpFileName_; |
323 |
} |
324 |
|
325 |
void setDumpFileName(const std::string& fileName) { |
326 |
dumpFileName_ = fileName; |
327 |
} |
328 |
|
329 |
std::string getStatFileName() { |
330 |
return statFileName_; |
331 |
} |
332 |
|
333 |
void setStatFileName(const std::string& fileName) { |
334 |
statFileName_ = fileName; |
335 |
} |
336 |
|
337 |
std::string getRestFileName() { |
338 |
return restFileName_; |
339 |
} |
340 |
|
341 |
void setRestFileName(const std::string& fileName) { |
342 |
restFileName_ = fileName; |
343 |
} |
344 |
|
345 |
/** |
346 |
* Sets GlobalGroupMembership |
347 |
* @see #SimCreator::setGlobalIndex |
348 |
*/ |
349 |
void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
350 |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
351 |
globalGroupMembership_ = globalGroupMembership; |
352 |
} |
353 |
|
354 |
/** |
355 |
* Sets GlobalMolMembership |
356 |
* @see #SimCreator::setGlobalIndex |
357 |
*/ |
358 |
void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
359 |
assert(globalMolMembership.size() == nGlobalAtoms_); |
360 |
globalMolMembership_ = globalMolMembership; |
361 |
} |
362 |
|
363 |
|
364 |
bool isFortranInitialized() { |
365 |
return fortranInitialized_; |
366 |
} |
367 |
|
368 |
//below functions are just forward functions |
369 |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
370 |
//the other hand, has-a relation need composing. |
371 |
/** |
372 |
* Adds property into property map |
373 |
* @param genData GenericData to be added into PropertyMap |
374 |
*/ |
375 |
void addProperty(GenericData* genData); |
376 |
|
377 |
/** |
378 |
* Removes property from PropertyMap by name |
379 |
* @param propName the name of property to be removed |
380 |
*/ |
381 |
void removeProperty(const std::string& propName); |
382 |
|
383 |
/** |
384 |
* clear all of the properties |
385 |
*/ |
386 |
void clearProperties(); |
387 |
|
388 |
/** |
389 |
* Returns all names of properties |
390 |
* @return all names of properties |
391 |
*/ |
392 |
std::vector<std::string> getPropertyNames(); |
393 |
|
394 |
/** |
395 |
* Returns all of the properties in PropertyMap |
396 |
* @return all of the properties in PropertyMap |
397 |
*/ |
398 |
std::vector<GenericData*> getProperties(); |
399 |
|
400 |
/** |
401 |
* Returns property |
402 |
* @param propName name of property |
403 |
* @return a pointer point to property with propName. If no property named propName |
404 |
* exists, return NULL |
405 |
*/ |
406 |
GenericData* getPropertyByName(const std::string& propName); |
407 |
|
408 |
/** |
409 |
* add all exclude pairs of a molecule into exclude list. |
410 |
*/ |
411 |
void addExcludePairs(Molecule* mol); |
412 |
|
413 |
/** |
414 |
* remove all exclude pairs which belong to a molecule from exclude list |
415 |
*/ |
416 |
|
417 |
void removeExcludePairs(Molecule* mol); |
418 |
|
419 |
|
420 |
/** Returns the unique atom types of local processor in an array */ |
421 |
std::set<AtomType*> getUniqueAtomTypes(); |
422 |
|
423 |
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
424 |
|
425 |
void getCutoff(double& rcut, double& rsw); |
426 |
|
427 |
private: |
428 |
|
429 |
/** fill up the simtype struct*/ |
430 |
void setupSimType(); |
431 |
|
432 |
/** |
433 |
* Setup Fortran Simulation |
434 |
* @see #setupFortranParallel |
435 |
*/ |
436 |
void setupFortranSim(); |
437 |
|
438 |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
439 |
void setupCutoff(); |
440 |
|
441 |
/** Figure out which coulombic correction method to use and pass to fortran */ |
442 |
void setupCoulombicCorrection( int isError ); |
443 |
|
444 |
/** Calculates the number of degress of freedom in the whole system */ |
445 |
void calcNdf(); |
446 |
void calcNdfRaw(); |
447 |
void calcNdfTrans(); |
448 |
|
449 |
/** |
450 |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
451 |
* system. |
452 |
*/ |
453 |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
454 |
|
455 |
MakeStamps* stamps_; |
456 |
ForceField* forceField_; |
457 |
Globals* simParams_; |
458 |
|
459 |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
460 |
|
461 |
//degress of freedom |
462 |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
463 |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
464 |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
465 |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
466 |
|
467 |
//number of global objects |
468 |
int nGlobalMols_; /**< number of molecules in the system */ |
469 |
int nGlobalAtoms_; /**< number of atoms in the system */ |
470 |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
471 |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
472 |
int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
473 |
/** |
474 |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
475 |
* corresponding content is the global index of cutoff group this atom belong to. |
476 |
* It is filled by SimCreator once and only once, since it never changed during the simulation. |
477 |
*/ |
478 |
std::vector<int> globalGroupMembership_; |
479 |
|
480 |
/** |
481 |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
482 |
* corresponding content is the global index of molecule this atom belong to. |
483 |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
484 |
*/ |
485 |
std::vector<int> globalMolMembership_; |
486 |
|
487 |
|
488 |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
489 |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
490 |
|
491 |
//number of local objects |
492 |
int nAtoms_; /**< number of atoms in local processor */ |
493 |
int nBonds_; /**< number of bonds in local processor */ |
494 |
int nBends_; /**< number of bends in local processor */ |
495 |
int nTorsions_; /**< number of torsions in local processor */ |
496 |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
497 |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
498 |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
499 |
int nConstraints_; /**< number of constraints in local processors */ |
500 |
|
501 |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
502 |
Exclude exclude_; |
503 |
PropertyMap properties_; /**< Generic Property */ |
504 |
SnapshotManager* sman_; /**< SnapshotManager */ |
505 |
|
506 |
/** |
507 |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
508 |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
509 |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
510 |
* to make a efficient data moving plan. |
511 |
*/ |
512 |
LocalIndexManager localIndexMan_; |
513 |
|
514 |
//file names |
515 |
std::string finalConfigFileName_; |
516 |
std::string dumpFileName_; |
517 |
std::string statFileName_; |
518 |
std::string restFileName_; |
519 |
|
520 |
double rcut_; /**< cutoff radius*/ |
521 |
double rsw_; /**< radius of switching function*/ |
522 |
|
523 |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
524 |
|
525 |
#ifdef IS_MPI |
526 |
//in Parallel version, we need MolToProc |
527 |
public: |
528 |
|
529 |
/** |
530 |
* Finds the processor where a molecule resides |
531 |
* @return the id of the processor which contains the molecule |
532 |
* @param globalIndex global Index of the molecule |
533 |
*/ |
534 |
int getMolToProc(int globalIndex) { |
535 |
//assert(globalIndex < molToProcMap_.size()); |
536 |
return molToProcMap_[globalIndex]; |
537 |
} |
538 |
|
539 |
/** |
540 |
* Set MolToProcMap array |
541 |
* @see #SimCreator::divideMolecules |
542 |
*/ |
543 |
void setMolToProcMap(const std::vector<int>& molToProcMap) { |
544 |
molToProcMap_ = molToProcMap; |
545 |
} |
546 |
|
547 |
private: |
548 |
|
549 |
void setupFortranParallel(); |
550 |
|
551 |
/** |
552 |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
553 |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
554 |
* once. |
555 |
*/ |
556 |
std::vector<int> molToProcMap_; |
557 |
|
558 |
#endif |
559 |
|
560 |
}; |
561 |
|
562 |
} //namespace oopse |
563 |
#endif //BRAINS_SIMMODEL_HPP |
564 |
|