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root/OpenMD/trunk/src/brains/SimInfo.hpp
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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 384 by tim, Tue Mar 1 19:11:47 2005 UTC vs.
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 68 | Line 68 | namespace oopse{
68  
69   namespace oopse{
70  
71 < //forward decalration
72 < class SnapshotManager;
73 < class Molecule;
74 < class SelectionManager;
75 < /**
76 < * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77 < * @brief As one of the heavy weight class of OOPSE, SimInfo
78 < * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79 < * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80 < * cutoff groups, constrains).
81 < * Another major change is the index. No matter single version or parallel version,  atoms and
82 < * rigid bodies have both global index and local index. Local index is not important to molecule as well as
83 < * cutoff group.
84 < */
85 < class SimInfo {
86 <    public:
87 <        typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
71 >  //forward decalration
72 >  class SnapshotManager;
73 >  class Molecule;
74 >  class SelectionManager;
75 >  /**
76 >   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77 >   * @brief As one of the heavy weight class of OOPSE, SimInfo
78 >   * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79 >   * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80 >   * cutoff groups, constrains).
81 >   * Another major change is the index. No matter single version or parallel version,  atoms and
82 >   * rigid bodies have both global index and local index. Local index is not important to molecule as well as
83 >   * cutoff group.
84 >   */
85 >  class SimInfo {
86 >  public:
87 >    typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
88  
89 <        /**
90 <         * Constructor of SimInfo
91 <         * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
92 <         * second element is the total number of molecules with the same molecule stamp in the system
93 <         * @param ff pointer of a concrete ForceField instance
94 <         * @param simParams
95 <         * @note
96 <         */
97 <        SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98 <        virtual ~SimInfo();
89 >    /**
90 >     * Constructor of SimInfo
91 >     * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
92 >     * second element is the total number of molecules with the same molecule stamp in the system
93 >     * @param ff pointer of a concrete ForceField instance
94 >     * @param simParams
95 >     * @note
96 >     */
97 >    SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98 >    virtual ~SimInfo();
99  
100 <        /**
101 <         * Adds a molecule
102 <         * @return return true if adding successfully, return false if the molecule is already in SimInfo
103 <         * @param mol molecule to be added
104 <         */
105 <        bool addMolecule(Molecule* mol);
100 >    /**
101 >     * Adds a molecule
102 >     * @return return true if adding successfully, return false if the molecule is already in SimInfo
103 >     * @param mol molecule to be added
104 >     */
105 >    bool addMolecule(Molecule* mol);
106  
107 <        /**
108 <         * Removes a molecule from SimInfo
109 <         * @return true if removing successfully, return false if molecule is not in this SimInfo
110 <         */
111 <        bool removeMolecule(Molecule* mol);
107 >    /**
108 >     * Removes a molecule from SimInfo
109 >     * @return true if removing successfully, return false if molecule is not in this SimInfo
110 >     */
111 >    bool removeMolecule(Molecule* mol);
112  
113 <        /** Returns the total number of molecules in the system. */
114 <        int getNGlobalMolecules() {
115 <            return nGlobalMols_;
116 <        }
113 >    /** Returns the total number of molecules in the system. */
114 >    int getNGlobalMolecules() {
115 >      return nGlobalMols_;
116 >    }
117  
118 <        /** Returns the total number of atoms in the system. */
119 <        int getNGlobalAtoms() {
120 <            return nGlobalAtoms_;
121 <        }
118 >    /** Returns the total number of atoms in the system. */
119 >    int getNGlobalAtoms() {
120 >      return nGlobalAtoms_;
121 >    }
122  
123 <        /** Returns the total number of cutoff groups in the system. */
124 <        int getNGlobalCutoffGroups() {
125 <            return nGlobalCutoffGroups_;
126 <        }
123 >    /** Returns the total number of cutoff groups in the system. */
124 >    int getNGlobalCutoffGroups() {
125 >      return nGlobalCutoffGroups_;
126 >    }
127  
128 <        /**
129 <         * Returns the total number of integrable objects (total number of rigid bodies plus the total number
130 <         * of atoms which do not belong to the rigid bodies) in the system
131 <         */
132 <        int getNGlobalIntegrableObjects() {
133 <            return nGlobalIntegrableObjects_;
134 <        }
128 >    /**
129 >     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
130 >     * of atoms which do not belong to the rigid bodies) in the system
131 >     */
132 >    int getNGlobalIntegrableObjects() {
133 >      return nGlobalIntegrableObjects_;
134 >    }
135  
136 <        /**
137 <         * Returns the total number of integrable objects (total number of rigid bodies plus the total number
138 <         * of atoms which do not belong to the rigid bodies) in the system
139 <         */
140 <        int getNGlobalRigidBodies() {
141 <            return nGlobalRigidBodies_;
142 <        }
136 >    /**
137 >     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
138 >     * of atoms which do not belong to the rigid bodies) in the system
139 >     */
140 >    int getNGlobalRigidBodies() {
141 >      return nGlobalRigidBodies_;
142 >    }
143  
144 <        int getNGlobalConstraints();
145 <        /**
146 <         * Returns the number of local molecules.
147 <         * @return the number of local molecules
148 <         */
149 <        int getNMolecules() {
150 <            return molecules_.size();
151 <        }
144 >    int getNGlobalConstraints();
145 >    /**
146 >     * Returns the number of local molecules.
147 >     * @return the number of local molecules
148 >     */
149 >    int getNMolecules() {
150 >      return molecules_.size();
151 >    }
152  
153 <        /** Returns the number of local atoms */
154 <        unsigned int getNAtoms() {
155 <            return nAtoms_;
156 <        }
153 >    /** Returns the number of local atoms */
154 >    unsigned int getNAtoms() {
155 >      return nAtoms_;
156 >    }
157  
158 <        /** Returns the number of local bonds */        
159 <        unsigned int getNBonds(){
160 <            return nBonds_;
161 <        }
158 >    /** Returns the number of local bonds */        
159 >    unsigned int getNBonds(){
160 >      return nBonds_;
161 >    }
162  
163 <        /** Returns the number of local bends */        
164 <        unsigned int getNBends() {
165 <            return nBends_;
166 <        }
163 >    /** Returns the number of local bends */        
164 >    unsigned int getNBends() {
165 >      return nBends_;
166 >    }
167  
168 <        /** Returns the number of local torsions */        
169 <        unsigned int getNTorsions() {
170 <            return nTorsions_;
171 <        }
168 >    /** Returns the number of local torsions */        
169 >    unsigned int getNTorsions() {
170 >      return nTorsions_;
171 >    }
172  
173 <        /** Returns the number of local rigid bodies */        
174 <        unsigned int getNRigidBodies() {
175 <            return nRigidBodies_;
176 <        }
173 >    /** Returns the number of local rigid bodies */        
174 >    unsigned int getNRigidBodies() {
175 >      return nRigidBodies_;
176 >    }
177  
178 <        /** Returns the number of local integrable objects */
179 <        unsigned int getNIntegrableObjects() {
180 <            return nIntegrableObjects_;
181 <        }
178 >    /** Returns the number of local integrable objects */
179 >    unsigned int getNIntegrableObjects() {
180 >      return nIntegrableObjects_;
181 >    }
182  
183 <        /** Returns the number of local cutoff groups */
184 <        unsigned int getNCutoffGroups() {
185 <            return nCutoffGroups_;
186 <        }
183 >    /** Returns the number of local cutoff groups */
184 >    unsigned int getNCutoffGroups() {
185 >      return nCutoffGroups_;
186 >    }
187  
188 <        /** Returns the total number of constraints in this SimInfo */
189 <        unsigned int getNConstraints() {
190 <            return nConstraints_;
191 <        }
188 >    /** Returns the total number of constraints in this SimInfo */
189 >    unsigned int getNConstraints() {
190 >      return nConstraints_;
191 >    }
192          
193 <        /**
194 <         * Returns the first molecule in this SimInfo and intialize the iterator.
195 <         * @return the first molecule, return NULL if there is not molecule in this SimInfo
196 <         * @param i the iterator of molecule array (user shouldn't change it)
197 <         */
198 <        Molecule* beginMolecule(MoleculeIterator& i);
193 >    /**
194 >     * Returns the first molecule in this SimInfo and intialize the iterator.
195 >     * @return the first molecule, return NULL if there is not molecule in this SimInfo
196 >     * @param i the iterator of molecule array (user shouldn't change it)
197 >     */
198 >    Molecule* beginMolecule(MoleculeIterator& i);
199  
200 <        /**
201 <          * Returns the next avaliable Molecule based on the iterator.
202 <          * @return the next avaliable molecule, return NULL if reaching the end of the array
203 <          * @param i the iterator of molecule array
204 <          */
205 <        Molecule* nextMolecule(MoleculeIterator& i);
200 >    /**
201 >     * Returns the next avaliable Molecule based on the iterator.
202 >     * @return the next avaliable molecule, return NULL if reaching the end of the array
203 >     * @param i the iterator of molecule array
204 >     */
205 >    Molecule* nextMolecule(MoleculeIterator& i);
206  
207 <        /** Returns the number of degrees of freedom */
208 <        int getNdf() {
209 <            return ndf_;
210 <        }
207 >    /** Returns the number of degrees of freedom */
208 >    int getNdf() {
209 >      return ndf_;
210 >    }
211  
212 <        /** Returns the number of raw degrees of freedom */
213 <        int getNdfRaw() {
214 <            return ndfRaw_;
215 <        }
212 >    /** Returns the number of raw degrees of freedom */
213 >    int getNdfRaw() {
214 >      return ndfRaw_;
215 >    }
216  
217 <        /** Returns the number of translational degrees of freedom */
218 <        int getNdfTrans() {
219 <            return ndfTrans_;
220 <        }
217 >    /** Returns the number of translational degrees of freedom */
218 >    int getNdfTrans() {
219 >      return ndfTrans_;
220 >    }
221  
222 <        //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
222 >    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
223          
224 <        /** Returns the total number of z-constraint molecules in the system */
225 <        int getNZconstraint() {
226 <            return nZconstraint_;
227 <        }
224 >    /** Returns the total number of z-constraint molecules in the system */
225 >    int getNZconstraint() {
226 >      return nZconstraint_;
227 >    }
228  
229 <        /**
230 <         * Sets the number of z-constraint molecules in the system.
231 <         */
232 <        void setNZconstraint(int nZconstraint) {
233 <            nZconstraint_ = nZconstraint;
234 <        }
229 >    /**
230 >     * Sets the number of z-constraint molecules in the system.
231 >     */
232 >    void setNZconstraint(int nZconstraint) {
233 >      nZconstraint_ = nZconstraint;
234 >    }
235          
236 <        /** Returns the snapshot manager. */
237 <        SnapshotManager* getSnapshotManager() {
238 <            return sman_;
239 <        }
236 >    /** Returns the snapshot manager. */
237 >    SnapshotManager* getSnapshotManager() {
238 >      return sman_;
239 >    }
240  
241 <        /** Sets the snapshot manager. */
242 <        void setSnapshotManager(SnapshotManager* sman);
241 >    /** Sets the snapshot manager. */
242 >    void setSnapshotManager(SnapshotManager* sman);
243          
244 <        /** Returns the force field */
245 <        ForceField* getForceField() {
246 <            return forceField_;
247 <        }
244 >    /** Returns the force field */
245 >    ForceField* getForceField() {
246 >      return forceField_;
247 >    }
248  
249 <        Globals* getSimParams() {
250 <            return simParams_;
251 <        }
249 >    Globals* getSimParams() {
250 >      return simParams_;
251 >    }
252  
253 <        /** Returns the velocity of center of mass of the whole system.*/
254 <        Vector3d getComVel();
253 >    /** Returns the velocity of center of mass of the whole system.*/
254 >    Vector3d getComVel();
255  
256 <        /** Returns the center of the mass of the whole system.*/
257 <        Vector3d getCom();
256 >    /** Returns the center of the mass of the whole system.*/
257 >    Vector3d getCom();
258  
259 <        /** main driver function to interact with fortran during the initialization and molecule migration */
260 <        void update();
259 >    /** main driver function to interact with fortran during the initialization and molecule migration */
260 >    void update();
261  
262 <        /** Returns the local index manager */
263 <        LocalIndexManager* getLocalIndexManager() {
264 <            return &localIndexMan_;
265 <        }
262 >    /** Returns the local index manager */
263 >    LocalIndexManager* getLocalIndexManager() {
264 >      return &localIndexMan_;
265 >    }
266  
267 <        int getMoleculeStampId(int globalIndex) {
268 <            //assert(globalIndex < molStampIds_.size())
269 <            return molStampIds_[globalIndex];
270 <        }
267 >    int getMoleculeStampId(int globalIndex) {
268 >      //assert(globalIndex < molStampIds_.size())
269 >      return molStampIds_[globalIndex];
270 >    }
271  
272 <        /** Returns the molecule stamp */
273 <        MoleculeStamp* getMoleculeStamp(int id) {
274 <            return moleculeStamps_[id];
275 <        }
272 >    /** Returns the molecule stamp */
273 >    MoleculeStamp* getMoleculeStamp(int id) {
274 >      return moleculeStamps_[id];
275 >    }
276  
277 <        /** Return the total number of the molecule stamps */
278 <        int getNMoleculeStamp() {
279 <            return moleculeStamps_.size();
280 <        }
281 <        /**
282 <         * Finds a molecule with a specified global index
283 <         * @return a pointer point to found molecule
284 <         * @param index
285 <         */
286 <        Molecule* getMoleculeByGlobalIndex(int index) {
287 <            MoleculeIterator i;
288 <            i = molecules_.find(index);
277 >    /** Return the total number of the molecule stamps */
278 >    int getNMoleculeStamp() {
279 >      return moleculeStamps_.size();
280 >    }
281 >    /**
282 >     * Finds a molecule with a specified global index
283 >     * @return a pointer point to found molecule
284 >     * @param index
285 >     */
286 >    Molecule* getMoleculeByGlobalIndex(int index) {
287 >      MoleculeIterator i;
288 >      i = molecules_.find(index);
289  
290 <            return i != molecules_.end() ? i->second : NULL;
291 <        }
290 >      return i != molecules_.end() ? i->second : NULL;
291 >    }
292  
293 <        /** Calculate the maximum cutoff radius based on the atom types */
294 <        double calcMaxCutoffRadius();
293 >    /** Calculate the maximum cutoff radius based on the atom types */
294 >    double calcMaxCutoffRadius();
295  
296 <        double getRcut() {
297 <            return rcut_;
298 <        }
296 >    double getRcut() {
297 >      return rcut_;
298 >    }
299  
300 <        double getRsw() {
301 <            return rsw_;
302 <        }
300 >    double getRsw() {
301 >      return rsw_;
302 >    }
303          
304 <        std::string getFinalConfigFileName() {
305 <            return finalConfigFileName_;
306 <        }
304 >    std::string getFinalConfigFileName() {
305 >      return finalConfigFileName_;
306 >    }
307          
308 <        void setFinalConfigFileName(const std::string& fileName) {
309 <            finalConfigFileName_ = fileName;
310 <        }
308 >    void setFinalConfigFileName(const std::string& fileName) {
309 >      finalConfigFileName_ = fileName;
310 >    }
311  
312 <        std::string getDumpFileName() {
313 <            return dumpFileName_;
314 <        }
312 >    std::string getDumpFileName() {
313 >      return dumpFileName_;
314 >    }
315          
316 <        void setDumpFileName(const std::string& fileName) {
317 <            dumpFileName_ = fileName;
318 <        }
316 >    void setDumpFileName(const std::string& fileName) {
317 >      dumpFileName_ = fileName;
318 >    }
319  
320 <        std::string getStatFileName() {
321 <            return statFileName_;
322 <        }
320 >    std::string getStatFileName() {
321 >      return statFileName_;
322 >    }
323          
324 <        void setStatFileName(const std::string& fileName) {
325 <            statFileName_ = fileName;
326 <        }
324 >    void setStatFileName(const std::string& fileName) {
325 >      statFileName_ = fileName;
326 >    }
327 >        
328 >    std::string getRestFileName() {
329 >      return restFileName_;
330 >    }
331 >        
332 >    void setRestFileName(const std::string& fileName) {
333 >      restFileName_ = fileName;
334 >    }
335  
336 <        /**
337 <         * Sets GlobalGroupMembership
338 <         * @see #SimCreator::setGlobalIndex
339 <         */  
340 <        void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
341 <            assert(globalGroupMembership.size() == nGlobalAtoms_);
342 <            globalGroupMembership_ = globalGroupMembership;
343 <        }
336 >    /**
337 >     * Sets GlobalGroupMembership
338 >     * @see #SimCreator::setGlobalIndex
339 >     */  
340 >    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
341 >      assert(globalGroupMembership.size() == nGlobalAtoms_);
342 >      globalGroupMembership_ = globalGroupMembership;
343 >    }
344  
345 <        /**
346 <         * Sets GlobalMolMembership
347 <         * @see #SimCreator::setGlobalIndex
348 <         */        
349 <        void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
350 <            assert(globalMolMembership.size() == nGlobalAtoms_);
351 <            globalMolMembership_ = globalMolMembership;
352 <        }
345 >    /**
346 >     * Sets GlobalMolMembership
347 >     * @see #SimCreator::setGlobalIndex
348 >     */        
349 >    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
350 >      assert(globalMolMembership.size() == nGlobalAtoms_);
351 >      globalMolMembership_ = globalMolMembership;
352 >    }
353  
354  
355 <        bool isFortranInitialized() {
356 <            return fortranInitialized_;
357 <        }
355 >    bool isFortranInitialized() {
356 >      return fortranInitialized_;
357 >    }
358          
359 <        //below functions are just forward functions
360 <        //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
361 <        //the other hand, has-a relation need composing.
362 <        /**
363 <         * Adds property into property map
364 <         * @param genData GenericData to be added into PropertyMap
365 <         */
366 <        void addProperty(GenericData* genData);
359 >    //below functions are just forward functions
360 >    //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
361 >    //the other hand, has-a relation need composing.
362 >    /**
363 >     * Adds property into property map
364 >     * @param genData GenericData to be added into PropertyMap
365 >     */
366 >    void addProperty(GenericData* genData);
367  
368 <        /**
369 <         * Removes property from PropertyMap by name
370 <         * @param propName the name of property to be removed
371 <         */
372 <        void removeProperty(const std::string& propName);
368 >    /**
369 >     * Removes property from PropertyMap by name
370 >     * @param propName the name of property to be removed
371 >     */
372 >    void removeProperty(const std::string& propName);
373  
374 <        /**
375 <         * clear all of the properties
376 <         */
377 <        void clearProperties();
374 >    /**
375 >     * clear all of the properties
376 >     */
377 >    void clearProperties();
378  
379 <        /**
380 <         * Returns all names of properties
381 <         * @return all names of properties
382 <         */
383 <        std::vector<std::string> getPropertyNames();
379 >    /**
380 >     * Returns all names of properties
381 >     * @return all names of properties
382 >     */
383 >    std::vector<std::string> getPropertyNames();
384  
385 <        /**
386 <         * Returns all of the properties in PropertyMap
387 <         * @return all of the properties in PropertyMap
388 <         */      
389 <        std::vector<GenericData*> getProperties();
385 >    /**
386 >     * Returns all of the properties in PropertyMap
387 >     * @return all of the properties in PropertyMap
388 >     */      
389 >    std::vector<GenericData*> getProperties();
390  
391 <        /**
392 <         * Returns property
393 <         * @param propName name of property
394 <         * @return a pointer point to property with propName. If no property named propName
395 <         * exists, return NULL
396 <         */      
397 <        GenericData* getPropertyByName(const std::string& propName);
391 >    /**
392 >     * Returns property
393 >     * @param propName name of property
394 >     * @return a pointer point to property with propName. If no property named propName
395 >     * exists, return NULL
396 >     */      
397 >    GenericData* getPropertyByName(const std::string& propName);
398  
399 <        /**
400 <         * add all exclude pairs of a molecule into exclude list.
401 <         */
402 <        void addExcludePairs(Molecule* mol);
399 >    /**
400 >     * add all exclude pairs of a molecule into exclude list.
401 >     */
402 >    void addExcludePairs(Molecule* mol);
403  
404 <        /**
405 <         * remove all exclude pairs which belong to a molecule from exclude list
406 <         */
404 >    /**
405 >     * remove all exclude pairs which belong to a molecule from exclude list
406 >     */
407  
408 <        void removeExcludePairs(Molecule* mol);
408 >    void removeExcludePairs(Molecule* mol);
409  
410  
411 <        SelectionManager* getSelectionManager() {
412 <            return selectMan_;
405 <        }
406 <
407 <        /** Returns the unique atom types of local processor in an array */
408 <        std::set<AtomType*> getUniqueAtomTypes();
411 >    /** Returns the unique atom types of local processor in an array */
412 >    std::set<AtomType*> getUniqueAtomTypes();
413          
414 <        friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
414 >    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
415  
416 <        void getCutoff(double& rcut, double& rsw);
416 >    void getCutoff(double& rcut, double& rsw);
417          
418 <    private:
418 >  private:
419  
420 <        /** fill up the simtype struct*/
421 <        void setupSimType();
420 >    /** fill up the simtype struct*/
421 >    void setupSimType();
422  
423 <        /**
424 <         * Setup Fortran Simulation
425 <         * @see #setupFortranParallel
426 <         */
427 <        void setupFortranSim();
423 >    /**
424 >     * Setup Fortran Simulation
425 >     * @see #setupFortranParallel
426 >     */
427 >    void setupFortranSim();
428  
429 <        /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
430 <        void setupCutoff();
429 >    /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
430 >    void setupCutoff();
431  
432 <        /** Calculates the number of degress of freedom in the whole system */
433 <        void calcNdf();
434 <        void calcNdfRaw();
435 <        void calcNdfTrans();
432 >    /** Calculates the number of degress of freedom in the whole system */
433 >    void calcNdf();
434 >    void calcNdfRaw();
435 >    void calcNdfTrans();
436  
437 <        /**
438 <         * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
439 <         * system.
440 <         */
441 <        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
437 >    /**
438 >     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
439 >     * system.
440 >     */
441 >    void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
442  
443 <        ForceField* forceField_;      
444 <        Globals* simParams_;
443 >    MakeStamps* stamps_;
444 >    ForceField* forceField_;      
445 >    Globals* simParams_;
446  
447 <        std::map<int, Molecule*>  molecules_; /**< Molecule array */
447 >    std::map<int, Molecule*>  molecules_; /**< Molecule array */
448          
449 <        //degress of freedom
450 <        int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
451 <        int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
452 <        int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
453 <        int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
449 >    //degress of freedom
450 >    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
451 >    int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
452 >    int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
453 >    int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
454          
455 <        //number of global objects
456 <        int nGlobalMols_;       /**< number of molecules in the system */
457 <        int nGlobalAtoms_;   /**< number of atoms in the system */
458 <        int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
459 <        int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
460 <        int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
461 <        /**
462 <         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
463 <         * corresponding content is the global index of cutoff group this atom belong to.
464 <         * It is filled by SimCreator once and only once, since it never changed during the simulation.
465 <         */
466 <        std::vector<int> globalGroupMembership_;
455 >    //number of global objects
456 >    int nGlobalMols_;       /**< number of molecules in the system */
457 >    int nGlobalAtoms_;   /**< number of atoms in the system */
458 >    int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
459 >    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
460 >    int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
461 >    /**
462 >     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
463 >     * corresponding content is the global index of cutoff group this atom belong to.
464 >     * It is filled by SimCreator once and only once, since it never changed during the simulation.
465 >     */
466 >    std::vector<int> globalGroupMembership_;
467  
468 <        /**
469 <         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
470 <         * corresponding content is the global index of molecule this atom belong to.
471 <         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
472 <         */
473 <        std::vector<int> globalMolMembership_;        
468 >    /**
469 >     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
470 >     * corresponding content is the global index of molecule this atom belong to.
471 >     * It is filled by SimCreator once and only once, since it is never changed during the simulation.
472 >     */
473 >    std::vector<int> globalMolMembership_;        
474  
475          
476 <        std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
477 <        std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
476 >    std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
477 >    std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
478          
479 <        //number of local objects
480 <        int nAtoms_;                        /**< number of atoms in local processor */
481 <        int nBonds_;                        /**< number of bonds in local processor */
482 <        int nBends_;                        /**< number of bends in local processor */
483 <        int nTorsions_;                    /**< number of torsions in local processor */
484 <        int nRigidBodies_;              /**< number of rigid bodies in local processor */
485 <        int nIntegrableObjects_;    /**< number of integrable objects in local processor */
486 <        int nCutoffGroups_;             /**< number of cutoff groups in local processor */
487 <        int nConstraints_;              /**< number of constraints in local processors */
479 >    //number of local objects
480 >    int nAtoms_;                        /**< number of atoms in local processor */
481 >    int nBonds_;                        /**< number of bonds in local processor */
482 >    int nBends_;                        /**< number of bends in local processor */
483 >    int nTorsions_;                    /**< number of torsions in local processor */
484 >    int nRigidBodies_;              /**< number of rigid bodies in local processor */
485 >    int nIntegrableObjects_;    /**< number of integrable objects in local processor */
486 >    int nCutoffGroups_;             /**< number of cutoff groups in local processor */
487 >    int nConstraints_;              /**< number of constraints in local processors */
488  
489 <        simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
490 <        Exclude exclude_;      
491 <        PropertyMap properties_;                  /**< Generic Property */
492 <        SnapshotManager* sman_;               /**< SnapshotManager */
489 >    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
490 >    Exclude exclude_;      
491 >    PropertyMap properties_;                  /**< Generic Property */
492 >    SnapshotManager* sman_;               /**< SnapshotManager */
493  
494 <        /**
495 <         * The reason to have a local index manager is that when molecule is migrating to other processors,
496 <         * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
497 <         * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
498 <         * to make a efficient data moving plan.
499 <         */        
500 <        LocalIndexManager localIndexMan_;
494 >    /**
495 >     * The reason to have a local index manager is that when molecule is migrating to other processors,
496 >     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
497 >     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
498 >     * to make a efficient data moving plan.
499 >     */        
500 >    LocalIndexManager localIndexMan_;
501  
502 <        //file names
503 <        std::string finalConfigFileName_;
504 <        std::string dumpFileName_;
505 <        std::string statFileName_;
502 >    //file names
503 >    std::string finalConfigFileName_;
504 >    std::string dumpFileName_;
505 >    std::string statFileName_;
506 >    std::string restFileName_;
507 >        
508 >    double rcut_;       /**< cutoff radius*/
509 >    double rsw_;        /**< radius of switching function*/
510  
511 <        double rcut_;       /**< cutoff radius*/
503 <        double rsw_;        /**< radius of switching function*/
511 >    bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
512  
505 –        bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
506 –
507 –        SelectionManager* selectMan_;
513   #ifdef IS_MPI
514      //in Parallel version, we need MolToProc
515 <    public:
515 >  public:
516                  
517 <        /**
518 <         * Finds the processor where a molecule resides
519 <         * @return the id of the processor which contains the molecule
520 <         * @param globalIndex global Index of the molecule
521 <         */
522 <        int getMolToProc(int globalIndex) {
523 <            //assert(globalIndex < molToProcMap_.size());
524 <            return molToProcMap_[globalIndex];
525 <        }
517 >    /**
518 >     * Finds the processor where a molecule resides
519 >     * @return the id of the processor which contains the molecule
520 >     * @param globalIndex global Index of the molecule
521 >     */
522 >    int getMolToProc(int globalIndex) {
523 >      //assert(globalIndex < molToProcMap_.size());
524 >      return molToProcMap_[globalIndex];
525 >    }
526  
527 <        /**
528 <         * Set MolToProcMap array
529 <         * @see #SimCreator::divideMolecules
530 <         */
531 <        void setMolToProcMap(const std::vector<int>& molToProcMap) {
532 <            molToProcMap_ = molToProcMap;
533 <        }
527 >    /**
528 >     * Set MolToProcMap array
529 >     * @see #SimCreator::divideMolecules
530 >     */
531 >    void setMolToProcMap(const std::vector<int>& molToProcMap) {
532 >      molToProcMap_ = molToProcMap;
533 >    }
534          
535 <    private:
535 >  private:
536  
537 <        void setupFortranParallel();
537 >    void setupFortranParallel();
538          
539 <        /**
540 <         * The size of molToProcMap_ is equal to total number of molecules in the system.
541 <         *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
542 <         * once.
543 <         */        
544 <        std::vector<int> molToProcMap_;
539 >    /**
540 >     * The size of molToProcMap_ is equal to total number of molecules in the system.
541 >     *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
542 >     * once.
543 >     */        
544 >    std::vector<int> molToProcMap_;
545  
546   #endif
547  
548 < };
548 >  };
549  
550   } //namespace oopse
551   #endif //BRAINS_SIMMODEL_HPP

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