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Comparing branches/new_design/OOPSE-3.0/src/brains/SimInfo.hpp (file contents):
Revision 1722 by tim, Tue Nov 9 23:11:39 2004 UTC vs.
Revision 1739 by tim, Mon Nov 15 18:02:15 2004 UTC

# Line 38 | Line 38
38   #include <utility>
39  
40   #include "brains/fSimulation.h"
41 + #include "brains/SimInfo.hpp"
42   #include "primitives/Molecule.hpp"
43   #include "types/MoleculeStamp.hpp"
44   #include "utils/PropertyMap.hpp"
# Line 47 | Line 48 | namespace oopse{
48  
49   /**
50   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
51 < * @brief
51 > * @brief As one of the heavy weight class of OOPSE, SimInfo
52 > * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
53 > * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
54 > * cutoff groups, constrains).
55 > * Another major change is the index. No matter single version or parallel version,  atoms and
56 > * rigid bodies have both global index and local index. Local index is not important to molecule as well as
57 > * cutoff group.
58   */
59   class SimInfo {
60      public:
61 <        SimInfo();
61 >        typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
62 >
63 >        /**
64 >         * Constructor of SimInfo
65 >         * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
66 >         * second element is the total number of molecules with the same molecule stamp in the system
67 >         * @param ff pointer of a concrete ForceField instance
68 >         * @param globals
69 >         * @note
70 >         */
71 >        SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals);
72          virtual ~SimInfo();
73  
74          /**
# Line 67 | Line 84 | class SimInfo {
84           */
85          bool removeMolecule(Molecule* mol);
86  
87 +        /** Returns the total number of molecules in the system. */
88 +        int getNGlobalMolecules() {
89 +            return nGlobalMols_;
90 +        }
91 +
92 +        /** Returns the total number of atoms in the system. */
93 +        int getNGlobalAtoms() {
94 +            return nGlobalAtoms_;
95 +        }
96 +
97 +        /** Returns the total number of cutoff groups in the system. */
98 +        int getNGlobalCutoffGroups() {
99 +            return nGlobalCutoffGroups_;
100 +        }
101 +
102 +        /**
103 +         * Returns the total number of integrable objects (total number of rigid bodies plus the total number
104 +         * of atoms which do not belong to the rigid bodies) in the system
105 +         */
106 +        int getNGlobalIntegrableObjects() {
107 +            return nGlobalIntegrableObjects_;
108 +        }
109 +        
110          /**
111 <         * Returns the number of molecules.
112 <         * @return the number of molecules in this SimInfo
111 >         * Returns the number of local molecules.
112 >         * @return the number of local molecules
113           */
114          int getNMolecules() {
115              return molecules_.size();
116          }
117  
118 <        /** Returns the total number of atoms in this SimInfo */
118 >        /** Returns the number of local atoms */
119          unsigned int getNAtoms() {
120              return nAtoms_;
121          }
122  
123 <        /** Returns the total number of bonds in this SimInfo */        
123 >        /** Returns the number of local bonds */        
124          unsigned int getNBonds(){
125              return nBonds_;
126          }
127  
128 <        /** Returns the total number of bends in this SimInfo */        
128 >        /** Returns the number of local bends */        
129          unsigned int getNBends() {
130              return nBends_;
131          }
132  
133 <        /** Returns the total number of torsions in this SimInfo */        
133 >        /** Returns the number of local torsions */        
134          unsigned int getNTorsions() {
135              return nTorsions_;
136          }
137  
138 <        /** Returns the total number of rigid bodies in this SimInfo */        
138 >        /** Returns the number of local rigid bodies */        
139          unsigned int getNRigidBodies() {
140              return nRigidBodies_;
141          }
142  
143 <        /** Returns the total number of integrable objects in this SimInfo */
143 >        /** Returns the number of local integrable objects */
144          unsigned int getNIntegrableObjects() {
145              return nIntegrableObjects_;
146          }
147  
148 <        /** Returns the total number of cutoff groups in this SimInfo */
148 >        /** Returns the number of local cutoff groups */
149          unsigned int getNCutoffGroups() {
150              return nCutoffGroups_;
151          }
# Line 120 | Line 160 | class SimInfo {
160           * @return the first molecule, return NULL if there is not molecule in this SimInfo
161           * @param i the iterator of molecule array (user shouldn't change it)
162           */
163 <        Molecule* beginMolecule(std::vector<Molecule*>::iterator& i);
163 >        Molecule* beginMolecule(MoleculeIterator& i);
164  
165          /**
166            * Returns the next avaliable Molecule based on the iterator.
167            * @return the next avaliable molecule, return NULL if reaching the end of the array
168            * @param i the iterator of molecule array
169            */
170 <        Molecule* nextMolecule(std::vector<Molecule*>::iterator& i);
170 >        Molecule* nextMolecule(MoleculeIterator& i);
171  
172          /** Returns the number of degrees of freedom */
173          int getNdf() {
# Line 144 | Line 184 | class SimInfo {
184              return ndfTrans_;
185          }
186  
187 +        //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
188 +        
189 +        /** Returns the total number of z-constraint molecules in the system */
190 +        int getNZconstraint() {
191 +            return nZconstraint_;
192 +        }
193 +
194 +        /**
195 +         * Sets the number of z-constraint molecules in the system.
196 +         */
197 +        int setNZconstraint(int nZconstraint) {
198 +            nZconstraint_ = nZconstraint;
199 +        }
200 +        
201          /** Returns the snapshot manager. */
202          SnapshotManager* getSnapshotManager() {
203              return sman_;
# Line 159 | Line 213 | class SimInfo {
213              return forceField_;
214          }
215  
162 –        /** Sets the force field */
163 –        void setForceField(ForceField* ff) {
164 –            forceField_ = ff;
165 –        }
166 –
216          Globals* getGlobals() {
217              return globals_;
218          }
170 –        
171 –        void setGlobals(Globals* globals) {
172 –            globals_ = globals;
173 –        }
219  
220 <        int* getExcludeList() {
176 <            return exclude_.getExcludeList();
177 <        }
178 <
220 >        /** Returns the velocity of center of mass of the whole system.*/
221          Vector3d getComVel();
222 <        
222 >
223 >        /** Returns the center of the mass of the whole system.*/
224          Vector3d getCom();
225  
226 +        /** Returns the seed (used for random number generator) */
227          int getSeed() {
228              return seed_;
229          }
230  
231 +        /** Sets the seed*/
232          void setSeed(int seed) {
233              seed_ = seed;
234          }
235 +
236 +        /** main driver function to interact with fortran during the initialization and molecule migration */
237 +        void update();
238 +
239 +        /** Returns the local index manager */
240 +        LocalIndexManager* getLocalIndexManager() {
241 +            return &localIndexMan_;
242 +        }
243 +
244 +        int getMoleculeStampId(int globalIndex) {
245 +            //assert(globalIndex < molStampIds_.size())
246 +            return molStampIds_[globalIndex];
247 +        }
248 +
249 +        /** Returns the molecule stamp */
250 +        MoleculeStamp* getMoleculeStamp(int id) {
251 +            return moleculeStamps_[id];
252 +        }
253          
254 +        /**
255 +         * Finds a molecule with a specified global index
256 +         * @return a pointer point to found molecule
257 +         * @param index
258 +         */
259 +        Molecule* getMoleculeByGlobalIndex(int index) {
260 +            std::map<int, Molecule*> i;
261 +            i = molecules_.find(index);
262 +
263 +            return i != molecules_.end() ? i->second : NULL;
264 +        }
265 +
266 +        /** Calculate the maximum cutoff radius based on the atom types */
267 +        double calcMaxCutoffRadius();
268 +
269 +        double getRcut() {
270 +            return rcut_;
271 +        }
272 +
273 +        double getRsw() {
274 +            return rsw_;
275 +        }
276 +        
277 +        std::string getFinalConfigFileName() {
278 +            return finalConfigFileName_;
279 +        }
280 +        
281 +        void setFinalConfigFileName(const std::string& fileName) {
282 +            finalConfigFileName_ = fileName;
283 +        }
284 +
285 +        std::string getDumpFileName() {
286 +            return dumpFileName_;
287 +        }
288 +        
289 +        void setDumpFileName(const std::string& fileName) {
290 +            dumpFileName_ = fileName;
291 +        }
292 +
293 +        std::string getStatFileName() {
294 +            return statFileName_;
295 +        }
296 +        
297 +        void setStatFileName(const std::string& fileName) {
298 +            statFileName_ = fileName;
299 +        }
300 +
301 +        /**
302 +         * Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
303 +         * @see #SimCreator::setGlobalIndex
304 +         */  
305 +        int* getGlobalGroupMembershipPointer() {
306 +            return globalGroupMembership_[0];
307 +        }
308 +
309 +        /**
310 +         * Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
311 +         * @see #SimCreator::setGlobalIndex
312 +         */        
313 +        int* getGlobalMolMembershipPointer() {
314 +            return globalMolMembership_[0];
315 +        }
316 +
317 +
318 +        bool isFortranInitialized() {
319 +            return fortranInitialized_;
320 +        }
321 +        
322 +        //below functions are just forward functions
323 +        //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
324 +        //the other hand, has-a relation need composing.
325 +        /**
326 +         * Adds property into property map
327 +         * @param genData GenericData to be added into PropertyMap
328 +         */
329 +        void addProperty(GenericData* genData);
330 +
331 +        /**
332 +         * Removes property from PropertyMap by name
333 +         * @param propName the name of property to be removed
334 +         */
335 +        void removeProperty(const std::string& propName);
336 +
337 +        /**
338 +         * clear all of the properties
339 +         */
340 +        void clearProperties();
341 +
342 +        /**
343 +         * Returns all names of properties
344 +         * @return all names of properties
345 +         */
346 +        std::vector<std::string> getPropertyNames();
347 +
348 +        /**
349 +         * Returns all of the properties in PropertyMap
350 +         * @return all of the properties in PropertyMap
351 +         */      
352 +        std::vector<GenericData*> getProperties();
353 +
354 +        /**
355 +         * Returns property
356 +         * @param propName name of property
357 +         * @return a pointer point to property with propName. If no property named propName
358 +         * exists, return NULL
359 +         */      
360 +        GenericData* getPropertyByName(const std::string& propName);
361 +                
362 +        friend std::ostream& operator <<(ostream& o, SimInfo& info);
363 +        
364      private:
365  
366 +        
367 +        /** Returns the unique atom types of local processor in an array */
368 +        std::set<AtomType*> SimInfo::getUniqueAtomTypes();
369 +
370 +        /** fill up the simtype struct*/
371 +        void setupSimType();
372 +
373 +        /**
374 +         * Setup Fortran Simulation
375 +         * @see #setupFortranParallel
376 +         */
377 +        void setupFortranSim();
378 +
379 +        /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
380 +        void setupCutoff();
381 +
382 +        /** Calculates the number of degress of freedom in the whole system */
383          void calcNdf();
384          void calcNdfRaw();
385          void calcNdfTrans();
# Line 197 | Line 387 | class SimInfo {
387          void addExcludePairs(Molecule* mol);
388          void removeExcludePairs(Molecule* mol);
389  
390 <        int ndf_;
391 <        int ndfRaw_;
392 <        int ndfTrans_;
390 >        /**
391 >         * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
392 >         * system.
393 >         */
394 >        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
395 >
396 >        std::map<int, Molecule*>  molecules_; /**< Molecule array */
397          
398 <        int nAtoms_;
399 <        int nBonds_;
400 <        int nBends_;
401 <        int nTorsions_;
402 <        int nRigidBodies_;
403 <        int nIntegrableObjects_;
404 <        int nCutoffGroups_;
405 <        int nConstraints_;
398 >        //degress of freedom
399 >        int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
400 >        int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
401 >        int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
402 >        int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
403 >        
404 >        //number of global objects
405 >        int nGlobalMols_;       /**< number of molecules in the system */
406 >        int nGlobalAtoms_;   /**< number of atoms in the system */
407 >        int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
408 >        int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
409  
410 <        simtype fInfo_;
411 <        Exclude exclude_;
412 <        ForceField* forceField_;
410 >        /**
411 >         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
412 >         * corresponding content is the global index of cutoff group this atom belong to.
413 >         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
414 >         */
415 >        std::vector<int> globalGroupMembership_;
416 >
417 >        /**
418 >         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
419 >         * corresponding content is the global index of molecule this atom belong to.
420 >         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
421 >         */
422 >        std::vector<int> globalMolMembership_;        
423 >
424          
425 <        std::vector<Molecule*> molecules_; /**< Molecule array */
426 <        PropertyMap properties_;                  /** Generic Property */
427 <        SnapshotManager* sman_;               /** SnapshotManager */
425 >        std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
426 >        std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
427 >        
428 >        //number of local objects
429 >        int nAtoms_;                        /**< number of atoms in local processor */
430 >        int nBonds_;                        /**< number of bonds in local processor */
431 >        int nBends_;                        /**< number of bends in local processor */
432 >        int nTorsions_;                    /**< number of torsions in local processor */
433 >        int nRigidBodies_;              /**< number of rigid bodies in local processor */
434 >        int nIntegrableObjects_;    /**< number of integrable objects in local processor */
435 >        int nCutoffGroups_;             /**< number of cutoff groups in local processor */
436 >        int nConstraints_;              /**< number of constraints in local processors */
437  
438 <        std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_;
438 >        simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
439 >        Exclude exclude_;
440 >        ForceField* forceField_;            
441 >        PropertyMap properties_;                  /**< Generic Property */
442 >        SnapshotManager* sman_;               /**< SnapshotManager */
443          Globals* globals_;
444 +        int seed_; /**< seed for random number generator */
445  
446 <        int seed_;
446 >        /**
447 >         * The reason to have a local index manager is that when molecule is migrating to other processors,
448 >         * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
449 >         * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
450 >         * to make a efficient data moving plan.
451 >         */        
452 >        LocalIndexManager localIndexMan_;
453 >
454 >        //file names
455 >        std::string finalConfigFileName_;
456 >        std::string dumpFileName_;
457 >        std::string statFileName_;
458 >
459 >        double rcut_;       /**< cutoff radius*/
460 >        double rsw_;        /**< radius of switching function*/
461 >
462 >        bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
463 >        
464 > #ifdef IS_MPI
465 >    //in Parallel version, we need MolToProc
466 >    public:
467 >                
468 >        /**
469 >         * Finds the processor where a molecule resides
470 >         * @return the id of the processor which contains the molecule
471 >         * @param globalIndex global Index of the molecule
472 >         */
473 >        int getMolToProc(int globalIndex) {
474 >            //assert(globalIndex < molToProcMap_.size());
475 >            return molToProcMap_[globalIndex];
476 >        }
477 >
478 >        /**
479 >         * Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
480 >         * @see #SimCreator::divideMolecules
481 >         */
482 >        int* getMolToProcMapPointer() {
483 >            return &molToProcMap_[0];
484 >        }
485 >        
486 >    private:
487 >
488 >        void setupFortranParallel();
489 >        
490 >        /**
491 >         * The size of molToProcMap_ is equal to total number of molecules in the system.
492 >         *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
493 >         * once.
494 >         */        
495 >        std::vector<int> molToProcMap_;
496 > #endif
497 >
498   };
499  
500   } //namespace oopse

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