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root/OpenMD/trunk/src/brains/SimInfo.hpp
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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC

# Line 73 | Line 73 | namespace oopse{
73    class SnapshotManager;
74    class Molecule;
75    class SelectionManager;
76 +  class StuntDouble;
77    /**
78     * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
79 <   * @brief As one of the heavy weight class of OOPSE, SimInfo
80 <   * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
81 <   * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
82 <   * cutoff groups, constrains).
83 <   * Another major change is the index. No matter single version or parallel version,  atoms and
84 <   * rigid bodies have both global index and local index. Local index is not important to molecule as well as
84 <   * cutoff group.
79 >   * @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
80 >   * The Molecule class maintains all of the concrete objects
81 >   * (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains).
82 >   * In both the  single and parallel versions,  atoms and
83 >   * rigid bodies have both global and local indices.  The local index is
84 >   * not relevant to molecules or cutoff groups.
85     */
86    class SimInfo {
87    public:
# Line 95 | Line 95 | namespace oopse{
95       * @param simParams
96       * @note
97       */
98 <    SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98 >    SimInfo(ForceField* ff, Globals* simParams);
99      virtual ~SimInfo();
100  
101      /**
# Line 207 | Line 207 | namespace oopse{
207  
208      /** Returns the number of degrees of freedom */
209      int getNdf() {
210 <      return ndf_;
210 >      return ndf_ - getFdf();
211      }
212  
213      /** Returns the number of raw degrees of freedom */
# Line 220 | Line 220 | namespace oopse{
220        return ndfTrans_;
221      }
222  
223 +    /** sets the current number of frozen degrees of freedom */
224 +    void setFdf(int fdf) {
225 +      fdf_local = fdf;
226 +    }
227 +
228 +    int getFdf();
229 +    
230      //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
231          
232      /** Returns the total number of z-constraint molecules in the system */
# Line 299 | Line 306 | namespace oopse{
306        return i != molecules_.end() ? i->second : NULL;
307      }
308  
309 <    /** Calculate the maximum cutoff radius based on the atom types */
303 <    double calcMaxCutoffRadius();
304 <
305 <    double getRcut() {
309 >    RealType getRcut() {
310        return rcut_;
311      }
312  
313 <    double getRsw() {
313 >    RealType getRsw() {
314        return rsw_;
315      }
316 +
317 +    RealType getList() {
318 +      return rlist_;
319 +    }
320          
321      std::string getFinalConfigFileName() {
322        return finalConfigFileName_;
323      }
324 <        
324 >
325      void setFinalConfigFileName(const std::string& fileName) {
326        finalConfigFileName_ = fileName;
327      }
328  
329 +    std::string getRawMetaData() {
330 +      return rawMetaData_;
331 +    }
332 +    void setRawMetaData(const std::string& rawMetaData) {
333 +      rawMetaData_ = rawMetaData;
334 +    }
335 +        
336      std::string getDumpFileName() {
337        return dumpFileName_;
338      }
# Line 365 | Line 380 | namespace oopse{
380        return fortranInitialized_;
381      }
382          
383 +    bool getCalcBoxDipole() {
384 +      return calcBoxDipole_;
385 +    }
386 +
387      //below functions are just forward functions
388      //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
389      //the other hand, has-a relation need composing.
# Line 422 | Line 441 | namespace oopse{
441          
442      friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
443  
444 <    void getCutoff(double& rcut, double& rsw);
444 >    void getCutoff(RealType& rcut, RealType& rsw);
445          
446    private:
447  
# Line 439 | Line 458 | namespace oopse{
458      void setupCutoff();
459  
460      /** Figure out which coulombic correction method to use and pass to fortran */
461 <    void setupCoulombicCorrection( int isError );
461 >    void setupElectrostaticSummationMethod( int isError );
462  
463 +    /** Figure out which polynomial type to use for the switching function */
464 +    void setupSwitchingFunction();
465 +
466 +    /** Determine if we need to accumulate the simulation box dipole */
467 +    void setupAccumulateBoxDipole();
468 +
469      /** Calculates the number of degress of freedom in the whole system */
470      void calcNdf();
471      void calcNdfRaw();
472      void calcNdfTrans();
473  
474 +    ForceField* forceField_;      
475 +    Globals* simParams_;
476 +
477 +    std::map<int, Molecule*>  molecules_; /**< Molecule array */
478 +
479      /**
480       * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
481       * system.
482       */
483      void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
454 –
455 –    MakeStamps* stamps_;
456 –    ForceField* forceField_;      
457 –    Globals* simParams_;
458 –
459 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
484          
485      //degress of freedom
486      int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
487 +    int fdf_local;       /**< number of frozen degrees of freedom */
488 +    int fdf_;            /**< number of frozen degrees of freedom */
489      int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
490      int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
491      int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
# Line 511 | Line 537 | namespace oopse{
537       */        
538      LocalIndexManager localIndexMan_;
539  
540 +    // unparsed MetaData block for storing in Dump and EOR files:
541 +    std::string rawMetaData_;
542 +
543      //file names
544      std::string finalConfigFileName_;
545      std::string dumpFileName_;
546      std::string statFileName_;
547      std::string restFileName_;
548          
549 <    double rcut_;       /**< cutoff radius*/
550 <    double rsw_;        /**< radius of switching function*/
549 >    RealType rcut_;       /**< cutoff radius*/
550 >    RealType rsw_;        /**< radius of switching function*/
551 >    RealType rlist_;      /**< neighbor list radius */
552  
553      bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
554  
555 +    bool calcBoxDipole_; /**< flag to indicate whether or not we calculate the simulation box dipole moment */
556 +
557 +    public:
558 +     /**
559 +      * return an integral objects by its global index. In MPI version, if the StuntDouble with specified
560 +      * global index does not belong to local processor, a NULL will be return.
561 +      */
562 +      StuntDouble* getIOIndexToIntegrableObject(int index);
563 +      void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
564 +    private:
565 +      std::vector<StuntDouble*> IOIndexToIntegrableObject;
566 +  //public:
567 +    //void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
568 +    /**
569 +     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
570 +     * global index does not belong to local processor, a NULL will be return.
571 +     */
572 +    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
573 +  //private:
574 +    //std::vector<StuntDouble*> sdByGlobalIndex_;
575 +    
576   #ifdef IS_MPI
577      //in Parallel version, we need MolToProc
578    public:
# Line 543 | Line 594 | namespace oopse{
594      void setMolToProcMap(const std::vector<int>& molToProcMap) {
595        molToProcMap_ = molToProcMap;
596      }
597 +
598 +    
599          
600    private:
601  

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