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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.hpp (file contents):
Revision 2000 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
Revision 2252 by chuckv, Mon May 30 14:01:52 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 57 | Line 57
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"
# Line 68 | Line 69 | namespace oopse{
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;
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(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
99 <        virtual ~SimInfo();
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);
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);
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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 <        }
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);
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);
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 <        }
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 <        }
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 <        }
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
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 <        }
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 <        }
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 <        }
237 >    /** Returns the snapshot manager. */
238 >    SnapshotManager* getSnapshotManager() {
239 >      return sman_;
240 >    }
241  
242 <        /** Sets the snapshot manager. */
243 <        void setSnapshotManager(SnapshotManager* sman);
242 >    /** Sets the snapshot manager. */
243 >    void setSnapshotManager(SnapshotManager* sman);
244          
245 <        /** Returns the force field */
246 <        ForceField* getForceField() {
247 <            return forceField_;
248 <        }
245 >    /** Returns the force field */
246 >    ForceField* getForceField() {
247 >      return forceField_;
248 >    }
249  
250 <        Globals* getSimParams() {
251 <            return simParams_;
252 <        }
250 >    Globals* getSimParams() {
251 >      return simParams_;
252 >    }
253  
254 <        /** Returns the velocity of center of mass of the whole system.*/
255 <        Vector3d getComVel();
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();
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 the seed (used for random number generator) */
263 <        int getSeed() {
264 <            return seed_;
265 <        }
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 <        /** Sets the seed*/
269 <        void setSeed(int seed) {
266 <            seed_ = seed;
267 <        }
268 >    /** main driver function to interact with fortran during the initialization and molecule migration */
269 >    void update();
270  
271 <        /** main driver function to interact with fortran during the initialization and molecule migration */
272 <        void update();
271 >    /** Returns the local index manager */
272 >    LocalIndexManager* getLocalIndexManager() {
273 >      return &localIndexMan_;
274 >    }
275  
276 <        /** Returns the local index manager */
277 <        LocalIndexManager* getLocalIndexManager() {
278 <            return &localIndexMan_;
279 <        }
276 >    int getMoleculeStampId(int globalIndex) {
277 >      //assert(globalIndex < molStampIds_.size())
278 >      return molStampIds_[globalIndex];
279 >    }
280  
281 <        int getMoleculeStampId(int globalIndex) {
282 <            //assert(globalIndex < molStampIds_.size())
283 <            return molStampIds_[globalIndex];
284 <        }
281 >    /** Returns the molecule stamp */
282 >    MoleculeStamp* getMoleculeStamp(int id) {
283 >      return moleculeStamps_[id];
284 >    }
285  
286 <        /** Returns the molecule stamp */
287 <        MoleculeStamp* getMoleculeStamp(int id) {
288 <            return moleculeStamps_[id];
289 <        }
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 the total number of the molecule stamps */
300 <        int getNMoleculeStamp() {
289 <            return moleculeStamps_.size();
290 <        }
291 <        /**
292 <         * Finds a molecule with a specified global index
293 <         * @return a pointer point to found molecule
294 <         * @param index
295 <         */
296 <        Molecule* getMoleculeByGlobalIndex(int index) {
297 <            MoleculeIterator i;
298 <            i = molecules_.find(index);
299 >      return i != molecules_.end() ? i->second : NULL;
300 >    }
301  
302 <            return i != molecules_.end() ? i->second : NULL;
303 <        }
302 >    /** Calculate the maximum cutoff radius based on the atom types */
303 >    double calcMaxCutoffRadius();
304  
305 <        /** Calculate the maximum cutoff radius based on the atom types */
306 <        double calcMaxCutoffRadius();
305 >    double getRcut() {
306 >      return rcut_;
307 >    }
308  
309 <        double getRcut() {
310 <            return rcut_;
311 <        }
309 <
310 <        double getRsw() {
311 <            return rsw_;
312 <        }
309 >    double getRsw() {
310 >      return rsw_;
311 >    }
312          
313 <        std::string getFinalConfigFileName() {
314 <            return finalConfigFileName_;
315 <        }
313 >    std::string getFinalConfigFileName() {
314 >      return finalConfigFileName_;
315 >    }
316          
317 <        void setFinalConfigFileName(const std::string& fileName) {
318 <            finalConfigFileName_ = fileName;
319 <        }
317 >    void setFinalConfigFileName(const std::string& fileName) {
318 >      finalConfigFileName_ = fileName;
319 >    }
320  
321 <        std::string getDumpFileName() {
322 <            return dumpFileName_;
323 <        }
321 >    std::string getDumpFileName() {
322 >      return dumpFileName_;
323 >    }
324          
325 <        void setDumpFileName(const std::string& fileName) {
326 <            dumpFileName_ = fileName;
327 <        }
325 >    void setDumpFileName(const std::string& fileName) {
326 >      dumpFileName_ = fileName;
327 >    }
328  
329 <        std::string getStatFileName() {
330 <            return statFileName_;
331 <        }
329 >    std::string getStatFileName() {
330 >      return statFileName_;
331 >    }
332          
333 <        void setStatFileName(const std::string& fileName) {
334 <            statFileName_ = fileName;
335 <        }
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 <        }
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 <        }
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 <        }
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);
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);
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();
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();
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();
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);
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);
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 <         */
413 >    /**
414 >     * remove all exclude pairs which belong to a molecule from exclude list
415 >     */
416  
417 <        void removeExcludePairs(Molecule* mol);
417 >    void removeExcludePairs(Molecule* mol);
418  
419  
420 <        SelectionManager* getSelectionManager() {
421 <            return selectMan_;
415 <        }
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);
418 <        
419 <    private:
423 >    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
424  
425 +    void getCutoff(double& rcut, double& rsw);
426          
427 <        /** Returns the unique atom types of local processor in an array */
423 <        std::set<AtomType*> getUniqueAtomTypes();
427 >  private:
428  
429 <        /** fill up the simtype struct*/
430 <        void setupSimType();
429 >    /** fill up the simtype struct*/
430 >    void setupSimType();
431  
432 <        /**
433 <         * Setup Fortran Simulation
434 <         * @see #setupFortranParallel
435 <         */
436 <        void setupFortranSim();
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();
438 >    /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
439 >    void setupCutoff();
440  
441 <        /** Calculates the number of degress of freedom in the whole system */
442 <        void calcNdf();
443 <        void calcNdfRaw();
444 <        void calcNdfTrans();
441 >    /** Calculates the number of degress of freedom in the whole system */
442 >    void calcNdf();
443 >    void calcNdfRaw();
444 >    void calcNdfTrans();
445  
446 <        /**
447 <         * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
448 <         * system.
449 <         */
450 <        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
446 >    /**
447 >     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
448 >     * system.
449 >     */
450 >    void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
451  
452 <        ForceField* forceField_;      
453 <        Globals* simParams_;
452 >    MakeStamps* stamps_;
453 >    ForceField* forceField_;      
454 >    Globals* simParams_;
455  
456 <        std::map<int, Molecule*>  molecules_; /**< Molecule array */
456 >    std::map<int, Molecule*>  molecules_; /**< Molecule array */
457          
458 <        //degress of freedom
459 <        int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
460 <        int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
461 <        int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
462 <        int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
458 >    //degress of freedom
459 >    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
460 >    int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
461 >    int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
462 >    int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
463          
464 <        //number of global objects
465 <        int nGlobalMols_;       /**< number of molecules in the system */
466 <        int nGlobalAtoms_;   /**< number of atoms in the system */
467 <        int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
468 <        int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
469 <        int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
470 <        /**
471 <         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
472 <         * corresponding content is the global index of cutoff group this atom belong to.
473 <         * It is filled by SimCreator once and only once, since it never changed during the simulation.
474 <         */
475 <        std::vector<int> globalGroupMembership_;
464 >    //number of global objects
465 >    int nGlobalMols_;       /**< number of molecules in the system */
466 >    int nGlobalAtoms_;   /**< number of atoms in the system */
467 >    int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
468 >    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
469 >    int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
470 >    /**
471 >     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
472 >     * corresponding content is the global index of cutoff group this atom belong to.
473 >     * It is filled by SimCreator once and only once, since it never changed during the simulation.
474 >     */
475 >    std::vector<int> globalGroupMembership_;
476  
477 <        /**
478 <         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
479 <         * corresponding content is the global index of molecule this atom belong to.
480 <         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
481 <         */
482 <        std::vector<int> globalMolMembership_;        
477 >    /**
478 >     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
479 >     * corresponding content is the global index of molecule this atom belong to.
480 >     * It is filled by SimCreator once and only once, since it is never changed during the simulation.
481 >     */
482 >    std::vector<int> globalMolMembership_;        
483  
484          
485 <        std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
486 <        std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
485 >    std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
486 >    std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
487          
488 <        //number of local objects
489 <        int nAtoms_;                        /**< number of atoms in local processor */
490 <        int nBonds_;                        /**< number of bonds in local processor */
491 <        int nBends_;                        /**< number of bends in local processor */
492 <        int nTorsions_;                    /**< number of torsions in local processor */
493 <        int nRigidBodies_;              /**< number of rigid bodies in local processor */
494 <        int nIntegrableObjects_;    /**< number of integrable objects in local processor */
495 <        int nCutoffGroups_;             /**< number of cutoff groups in local processor */
496 <        int nConstraints_;              /**< number of constraints in local processors */
488 >    //number of local objects
489 >    int nAtoms_;                        /**< number of atoms in local processor */
490 >    int nBonds_;                        /**< number of bonds in local processor */
491 >    int nBends_;                        /**< number of bends in local processor */
492 >    int nTorsions_;                    /**< number of torsions in local processor */
493 >    int nRigidBodies_;              /**< number of rigid bodies in local processor */
494 >    int nIntegrableObjects_;    /**< number of integrable objects in local processor */
495 >    int nCutoffGroups_;             /**< number of cutoff groups in local processor */
496 >    int nConstraints_;              /**< number of constraints in local processors */
497  
498 <        simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
499 <        Exclude exclude_;      
500 <        PropertyMap properties_;                  /**< Generic Property */
501 <        SnapshotManager* sman_;               /**< SnapshotManager */
498 >    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
499 >    Exclude exclude_;      
500 >    PropertyMap properties_;                  /**< Generic Property */
501 >    SnapshotManager* sman_;               /**< SnapshotManager */
502  
503 <        int seed_; /**< seed for random number generator */
503 >    /**
504 >     * The reason to have a local index manager is that when molecule is migrating to other processors,
505 >     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
506 >     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
507 >     * to make a efficient data moving plan.
508 >     */        
509 >    LocalIndexManager localIndexMan_;
510  
511 <        /**
512 <         * The reason to have a local index manager is that when molecule is migrating to other processors,
513 <         * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
514 <         * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
515 <         * to make a efficient data moving plan.
516 <         */        
517 <        LocalIndexManager localIndexMan_;
511 >    //file names
512 >    std::string finalConfigFileName_;
513 >    std::string dumpFileName_;
514 >    std::string statFileName_;
515 >    std::string restFileName_;
516 >        
517 >    double rcut_;       /**< cutoff radius*/
518 >    double rsw_;        /**< radius of switching function*/
519  
520 <        //file names
509 <        std::string finalConfigFileName_;
510 <        std::string dumpFileName_;
511 <        std::string statFileName_;
520 >    bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
521  
513 –        double rcut_;       /**< cutoff radius*/
514 –        double rsw_;        /**< radius of switching function*/
515 –
516 –        bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
517 –
518 –        SelectionManager* selectMan_;
522   #ifdef IS_MPI
523      //in Parallel version, we need MolToProc
524 <    public:
524 >  public:
525                  
526 <        /**
527 <         * Finds the processor where a molecule resides
528 <         * @return the id of the processor which contains the molecule
529 <         * @param globalIndex global Index of the molecule
530 <         */
531 <        int getMolToProc(int globalIndex) {
532 <            //assert(globalIndex < molToProcMap_.size());
533 <            return molToProcMap_[globalIndex];
534 <        }
526 >    /**
527 >     * Finds the processor where a molecule resides
528 >     * @return the id of the processor which contains the molecule
529 >     * @param globalIndex global Index of the molecule
530 >     */
531 >    int getMolToProc(int globalIndex) {
532 >      //assert(globalIndex < molToProcMap_.size());
533 >      return molToProcMap_[globalIndex];
534 >    }
535  
536 <        /**
537 <         * Set MolToProcMap array
538 <         * @see #SimCreator::divideMolecules
539 <         */
540 <        void setMolToProcMap(const std::vector<int>& molToProcMap) {
541 <            molToProcMap_ = molToProcMap;
542 <        }
536 >    /**
537 >     * Set MolToProcMap array
538 >     * @see #SimCreator::divideMolecules
539 >     */
540 >    void setMolToProcMap(const std::vector<int>& molToProcMap) {
541 >      molToProcMap_ = molToProcMap;
542 >    }
543          
544 <    private:
544 >  private:
545  
546 <        void setupFortranParallel();
546 >    void setupFortranParallel();
547          
548 <        /**
549 <         * The size of molToProcMap_ is equal to total number of molecules in the system.
550 <         *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
551 <         * once.
552 <         */        
553 <        std::vector<int> molToProcMap_;
548 >    /**
549 >     * The size of molToProcMap_ is equal to total number of molecules in the system.
550 >     *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
551 >     * once.
552 >     */        
553 >    std::vector<int> molToProcMap_;
554  
555   #endif
556  
557 < };
557 >  };
558  
559   } //namespace oopse
560   #endif //BRAINS_SIMMODEL_HPP

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