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Revision 1722 by tim, Tue Nov 9 23:11:39 2004 UTC vs.
Revision 1738 by tim, Sat Nov 13 05:08:12 2004 UTC

# Line 47 | Line 47 | namespace oopse{
47  
48   /**
49   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
50 < * @brief
50 > * @brief As one of the heavy weight class of OOPSE, SimInfo
51 > * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
52 > * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
53 > * cutoff groups, constrains).
54 > * Another major change is the index. No matter single version or parallel version,  atoms and
55 > * rigid bodies have both global index and local index. Local index is not important to molecule as well as
56 > * cutoff group.
57   */
58   class SimInfo {
59      public:
60 <        SimInfo();
60 >        typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
61 >
62 >        /**
63 >         * Constructor of SimInfo
64 >         * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
65 >         * second element is the total number of molecules with the same molecule stamp in the system
66 >         * @param ff pointer of a concrete ForceField instance
67 >         * @param globals
68 >         * @note
69 >         */
70 >        SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals);
71          virtual ~SimInfo();
72  
73          /**
# Line 67 | Line 83 | class SimInfo {
83           */
84          bool removeMolecule(Molecule* mol);
85  
86 +        /** Returns the total number of molecules in the system. */
87 +        int getNGlobalMolecules() {
88 +            return nGlobalMols_;
89 +        }
90 +
91 +        /** Returns the total number of atoms in the system. */
92 +        int getNGlobalAtoms() {
93 +            return nGlobalAtoms_;
94 +        }
95 +
96 +        /** Returns the total number of cutoff groups in the system. */
97 +        int getNGlobalCutoffGroups() {
98 +            return nGlobalCutoffGroups_;
99 +        }
100 +        
101          /**
102 <         * Returns the number of molecules.
103 <         * @return the number of molecules in this SimInfo
102 >         * Returns the number of local molecules.
103 >         * @return the number of local molecules
104           */
105          int getNMolecules() {
106              return molecules_.size();
107          }
108  
109 <        /** Returns the total number of atoms in this SimInfo */
109 >        /** Returns the number of local atoms */
110          unsigned int getNAtoms() {
111              return nAtoms_;
112          }
113  
114 <        /** Returns the total number of bonds in this SimInfo */        
114 >        /** Returns the number of local bonds */        
115          unsigned int getNBonds(){
116              return nBonds_;
117          }
118  
119 <        /** Returns the total number of bends in this SimInfo */        
119 >        /** Returns the number of local bends */        
120          unsigned int getNBends() {
121              return nBends_;
122          }
123  
124 <        /** Returns the total number of torsions in this SimInfo */        
124 >        /** Returns the number of local torsions */        
125          unsigned int getNTorsions() {
126              return nTorsions_;
127          }
128  
129 <        /** Returns the total number of rigid bodies in this SimInfo */        
129 >        /** Returns the number of local rigid bodies */        
130          unsigned int getNRigidBodies() {
131              return nRigidBodies_;
132          }
133  
134 <        /** Returns the total number of integrable objects in this SimInfo */
134 >        /** Returns the number of local integrable objects */
135          unsigned int getNIntegrableObjects() {
136              return nIntegrableObjects_;
137          }
138  
139 <        /** Returns the total number of cutoff groups in this SimInfo */
139 >        /** Returns the number of local cutoff groups */
140          unsigned int getNCutoffGroups() {
141              return nCutoffGroups_;
142          }
# Line 120 | Line 151 | class SimInfo {
151           * @return the first molecule, return NULL if there is not molecule in this SimInfo
152           * @param i the iterator of molecule array (user shouldn't change it)
153           */
154 <        Molecule* beginMolecule(std::vector<Molecule*>::iterator& i);
154 >        Molecule* beginMolecule(MoleculeIterator& i);
155  
156          /**
157            * Returns the next avaliable Molecule based on the iterator.
158            * @return the next avaliable molecule, return NULL if reaching the end of the array
159            * @param i the iterator of molecule array
160            */
161 <        Molecule* nextMolecule(std::vector<Molecule*>::iterator& i);
161 >        Molecule* nextMolecule(MoleculeIterator& i);
162  
163          /** Returns the number of degrees of freedom */
164          int getNdf() {
# Line 144 | Line 175 | class SimInfo {
175              return ndfTrans_;
176          }
177  
178 +        //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
179 +        
180 +        /** Returns the total number of z-constraint molecules in the system */
181 +        int getNZconstraint() {
182 +            return nZconstraint_;
183 +        }
184 +
185 +        /**
186 +         * Sets the number of z-constraint molecules in the system.
187 +         */
188 +        int setNZconstraint(int nZconstraint) {
189 +            nZconstraint_ = nZconstraint;
190 +        }
191 +        
192          /** Returns the snapshot manager. */
193          SnapshotManager* getSnapshotManager() {
194              return sman_;
# Line 159 | Line 204 | class SimInfo {
204              return forceField_;
205          }
206  
162 –        /** Sets the force field */
163 –        void setForceField(ForceField* ff) {
164 –            forceField_ = ff;
165 –        }
166 –
207          Globals* getGlobals() {
208              return globals_;
209          }
170 –        
171 –        void setGlobals(Globals* globals) {
172 –            globals_ = globals;
173 –        }
210  
211 <        int* getExcludeList() {
176 <            return exclude_.getExcludeList();
177 <        }
178 <
211 >        /** Returns the velocity of center of mass of the whole system.*/
212          Vector3d getComVel();
213 <        
213 >
214 >        /** Returns the center of the mass of the whole system.*/
215          Vector3d getCom();
216  
217 +        /** Returns the seed (used for random number generator) */
218          int getSeed() {
219              return seed_;
220          }
221  
222 +        /** Sets the seed*/
223          void setSeed(int seed) {
224              seed_ = seed;
225          }
226 +
227 +        /** main driver function to interact with fortran during the initialization and molecule migration */
228 +        void update();
229 +
230 +        /** Returns the local index manager */
231 +        LocalIndexManager* getLocalIndexManager() {
232 +            return &localIndexMan_;
233 +        }
234 +
235 +        int getMoleculeStampId(int globalIndex) {
236 +            //assert(globalIndex < molStampIds_.size())
237 +            return molStampIds_[globalIndex];
238 +        }
239 +
240 +        /** Returns the molecule stamp */
241 +        MoleculeStamp* getMoleculeStamp(int id) {
242 +            return moleculeStamps_[id];
243 +        }
244          
245 +        /**
246 +         * Finds a molecule with a specified global index
247 +         * @return a pointer point to found molecule
248 +         * @param index
249 +         */
250 +        Molecule* getMoleculeByGlobalIndex(int index) {
251 +            std::map<int, Molecule*> i;
252 +            i = molecules_.find(index);
253 +
254 +            return i != molecules_.end() ? i->second : NULL;
255 +        }
256 +
257 +        /** Calculate the maximum cutoff radius based on the atom types */
258 +        double calcMaxCutoffRadius();
259 +
260 +        double getRcut() {
261 +            return rcut_;
262 +        }
263 +
264 +        double getRsw() {
265 +            return rsw_;
266 +        }
267 +        
268 +        std::string getFinalConfigFileName() {
269 +            return finalConfigFileName_;
270 +        }
271 +        
272 +        void setFinalConfigFileName(const std::string& fileName) {
273 +            finalConfigFileName_ = fileName;
274 +        }
275 +
276 +        std::string getDumpFileName() {
277 +            return dumpFileName_;
278 +        }
279 +        
280 +        void setDumpFileName(const std::string& fileName) {
281 +            dumpFileName_ = fileName;
282 +        }
283 +
284 +        std::string getStatFileName() {
285 +            return statFileName_;
286 +        }
287 +        
288 +        void setStatFileName(const std::string& fileName) {
289 +            statFileName_ = fileName;
290 +        }
291 +
292 +        /**
293 +         * Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
294 +         * @see #SimCreator::setGlobalIndex
295 +         */  
296 +        int* getGlobalGroupMembershipPointer() {
297 +            return globalGroupMembership_[0];
298 +        }
299 +
300 +        /**
301 +         * Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
302 +         * @see #SimCreator::setGlobalIndex
303 +         */        
304 +        int* getGlobalMolMembershipPointer() {
305 +            return globalMolMembership_[0];
306 +        }
307 +
308 +
309 +        bool isFortranInitialized() {
310 +            return fortranInitialized_;
311 +        }
312 +        
313 +        //below functions are just forward functions
314 +        //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
315 +        //the other hand, has-a relation need composing.
316 +        /**
317 +         * Adds property into property map
318 +         * @param genData GenericData to be added into PropertyMap
319 +         */
320 +        void addProperty(GenericData* genData);
321 +
322 +        /**
323 +         * Removes property from PropertyMap by name
324 +         * @param propName the name of property to be removed
325 +         */
326 +        void removeProperty(const std::string& propName);
327 +
328 +        /**
329 +         * clear all of the properties
330 +         */
331 +        void clearProperties();
332 +
333 +        /**
334 +         * Returns all names of properties
335 +         * @return all names of properties
336 +         */
337 +        std::vector<std::string> getPropertyNames();
338 +
339 +        /**
340 +         * Returns all of the properties in PropertyMap
341 +         * @return all of the properties in PropertyMap
342 +         */      
343 +        std::vector<GenericData*> getProperties();
344 +
345 +        /**
346 +         * Returns property
347 +         * @param propName name of property
348 +         * @return a pointer point to property with propName. If no property named propName
349 +         * exists, return NULL
350 +         */      
351 +        GenericData* getPropertyByName(const std::string& propName);
352 +                
353 +        friend std::ostream& operator <<(ostream& o, SimInfo& info);
354 +        
355      private:
356  
357 +        
358 +        /** Returns the unique atom types of local processor in an array */
359 +        std::set<AtomType*> SimInfo::getUniqueAtomTypes();
360 +
361 +        /** fill up the simtype struct*/
362 +        void setupSimType();
363 +
364 +        /**
365 +         * Setup Fortran Simulation
366 +         * @see #setupFortranParallel
367 +         */
368 +        void setupFortranSim();
369 +
370 +        /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
371 +        void setupCutoff();
372 +
373 +        /** Calculates the number of degress of freedom in the whole system */
374          void calcNdf();
375          void calcNdfRaw();
376          void calcNdfTrans();
# Line 197 | Line 378 | class SimInfo {
378          void addExcludePairs(Molecule* mol);
379          void removeExcludePairs(Molecule* mol);
380  
381 <        int ndf_;
382 <        int ndfRaw_;
383 <        int ndfTrans_;
381 >        /**
382 >         * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
383 >         * system.
384 >         */
385 >        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
386 >
387 >        std::map<int, Molecule*>  molecules_; /**< Molecule array */
388          
389 <        int nAtoms_;
390 <        int nBonds_;
391 <        int nBends_;
392 <        int nTorsions_;
393 <        int nRigidBodies_;
394 <        int nIntegrableObjects_;
395 <        int nCutoffGroups_;
396 <        int nConstraints_;
389 >        //degress of freedom
390 >        int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
391 >        int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
392 >        int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
393 >        int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
394 >        
395 >        //number of global objects
396 >        int nGlobalMols_;       /**< number of molecules in the system */
397 >        int nGlobalAtoms_;   /**< number of atoms in the system */
398 >        int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
399  
400 <        simtype fInfo_;
401 <        Exclude exclude_;
402 <        ForceField* forceField_;
400 >        /**
401 >         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
402 >         * corresponding content is the global index of cutoff group this atom belong to.
403 >         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
404 >         */
405 >        std::vector<int> globalGroupMembership_;
406 >
407 >        /**
408 >         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
409 >         * corresponding content is the global index of molecule this atom belong to.
410 >         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
411 >         */
412 >        std::vector<int> globalMolMembership_;        
413 >
414          
415 <        std::vector<Molecule*> molecules_; /**< Molecule array */
416 <        PropertyMap properties_;                  /** Generic Property */
417 <        SnapshotManager* sman_;               /** SnapshotManager */
415 >        std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
416 >        std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
417 >        
418 >        //number of local objects
419 >        int nAtoms_;                        /**< number of atoms in local processor */
420 >        int nBonds_;                        /**< number of bonds in local processor */
421 >        int nBends_;                        /**< number of bends in local processor */
422 >        int nTorsions_;                    /**< number of torsions in local processor */
423 >        int nRigidBodies_;              /**< number of rigid bodies in local processor */
424 >        int nIntegrableObjects_;    /**< number of integrable objects in local processor */
425 >        int nCutoffGroups_;             /**< number of cutoff groups in local processor */
426 >        int nConstraints_;              /**< number of constraints in local processors */
427  
428 <        std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_;
428 >        simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
429 >        Exclude exclude_;
430 >        ForceField* forceField_;            
431 >        PropertyMap properties_;                  /**< Generic Property */
432 >        SnapshotManager* sman_;               /**< SnapshotManager */
433          Globals* globals_;
434 +        int seed_; /**< seed for random number generator */
435  
436 <        int seed_;
436 >        /**
437 >         * The reason to have a local index manager is that when molecule is migrating to other processors,
438 >         * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
439 >         * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
440 >         * to make a efficient data moving plan.
441 >         */        
442 >        LocalIndexManager localIndexMan_;
443 >
444 >        //file names
445 >        std::string finalConfigFileName_;
446 >        std::string dumpFileName_;
447 >        std::string statFileName_;
448 >
449 >        double rcut_;       /**< cutoff radius*/
450 >        double rsw_;        /**< radius of switching function*/
451 >
452 >        bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
453 >        
454 > #ifdef IS_MPI
455 >    //in Parallel version, we need MolToProc
456 >    public:
457 >                
458 >        /**
459 >         * Finds the processor where a molecule resides
460 >         * @return the id of the processor which contains the molecule
461 >         * @param globalIndex global Index of the molecule
462 >         */
463 >        int getMolToProc(int globalIndex) {
464 >            //assert(globalIndex < molToProcMap_.size());
465 >            return molToProcMap_[globalIndex];
466 >        }
467 >
468 >        /**
469 >         * Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
470 >         * @see #SimCreator::divideMolecules
471 >         */
472 >        int* getMolToProcMapPointer() {
473 >            return &molToProcMap_[0];
474 >        }
475 >        
476 >    private:
477 >
478 >        void setupFortranParallel();
479 >        
480 >        /**
481 >         * The size of molToProcMap_ is equal to total number of molecules in the system.
482 >         *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
483 >         * once.
484 >         */        
485 >        std::vector<int> molToProcMap_;
486 > #endif
487 >
488   };
489  
490   } //namespace oopse

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