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root/OpenMD/branches/development/src/brains/SimInfo.hpp
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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 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 One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
# Line 271 | Line 272 | namespace oopse{
272      /** Returns system angular momentum */
273      Vector3d getAngularMomentum();
274  
275 +    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
276 +    void getGyrationalVolume(RealType &vol);
277 +    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
278 +    void getGyrationalVolume(RealType &vol, RealType &detI);
279      /** main driver function to interact with fortran during the initialization and molecule migration */
280      void update();
281  
# Line 305 | Line 310 | namespace oopse{
310        return i != molecules_.end() ? i->second : NULL;
311      }
312  
313 <    double getRcut() {
313 >    RealType getRcut() {
314        return rcut_;
315      }
316  
317 <    double getRsw() {
317 >    RealType getRsw() {
318        return rsw_;
319      }
320  
321 <    double getList() {
321 >    RealType getList() {
322        return rlist_;
323      }
324          
325      std::string getFinalConfigFileName() {
326        return finalConfigFileName_;
327      }
328 <        
328 >
329      void setFinalConfigFileName(const std::string& fileName) {
330        finalConfigFileName_ = fileName;
331      }
332  
333 +    std::string getRawMetaData() {
334 +      return rawMetaData_;
335 +    }
336 +    void setRawMetaData(const std::string& rawMetaData) {
337 +      rawMetaData_ = rawMetaData;
338 +    }
339 +        
340      std::string getDumpFileName() {
341        return dumpFileName_;
342      }
# Line 372 | Line 384 | namespace oopse{
384        return fortranInitialized_;
385      }
386          
387 +    bool getCalcBoxDipole() {
388 +      return calcBoxDipole_;
389 +    }
390 +
391 +    bool getUseAtomicVirial() {
392 +      return useAtomicVirial_;
393 +    }
394 +
395      //below functions are just forward functions
396      //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
397      //the other hand, has-a relation need composing.
# Line 429 | Line 449 | namespace oopse{
449          
450      friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
451  
452 <    void getCutoff(double& rcut, double& rsw);
452 >    void getCutoff(RealType& rcut, RealType& rsw);
453          
454    private:
455  
# Line 451 | Line 471 | namespace oopse{
471      /** Figure out which polynomial type to use for the switching function */
472      void setupSwitchingFunction();
473  
474 +    /** Determine if we need to accumulate the simulation box dipole */
475 +    void setupAccumulateBoxDipole();
476 +
477      /** Calculates the number of degress of freedom in the whole system */
478      void calcNdf();
479      void calcNdfRaw();
# Line 522 | Line 545 | namespace oopse{
545       */        
546      LocalIndexManager localIndexMan_;
547  
548 +    // unparsed MetaData block for storing in Dump and EOR files:
549 +    std::string rawMetaData_;
550 +
551      //file names
552      std::string finalConfigFileName_;
553      std::string dumpFileName_;
554      std::string statFileName_;
555      std::string restFileName_;
556          
557 <    double rcut_;       /**< cutoff radius*/
558 <    double rsw_;        /**< radius of switching function*/
559 <    double rlist_;      /**< neighbor list radius */
557 >    RealType rcut_;       /**< cutoff radius*/
558 >    RealType rsw_;        /**< radius of switching function*/
559 >    RealType rlist_;      /**< neighbor list radius */
560  
561 <    bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
561 >    bool ljsp_; /**< use shifted potential for LJ*/
562 >    bool ljsf_; /**< use shifted force for LJ*/
563  
564 +    bool fortranInitialized_; /**< flag indicate whether fortran side
565 +                                 is initialized */
566 +    
567 +    bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
568 +                            the simulation box dipole moment */
569 +    
570 +    bool useAtomicVirial_; /**< flag to indicate whether or not we use
571 +                              Atomic Virials to calculate the pressure */
572 +
573 +    public:
574 +     /**
575 +      * return an integral objects by its global index. In MPI version, if the StuntDouble with specified
576 +      * global index does not belong to local processor, a NULL will be return.
577 +      */
578 +      StuntDouble* getIOIndexToIntegrableObject(int index);
579 +      void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
580 +    private:
581 +      std::vector<StuntDouble*> IOIndexToIntegrableObject;
582 +  //public:
583 +    //void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
584 +    /**
585 +     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
586 +     * global index does not belong to local processor, a NULL will be return.
587 +     */
588 +    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
589 +  //private:
590 +    //std::vector<StuntDouble*> sdByGlobalIndex_;
591 +    
592   #ifdef IS_MPI
593      //in Parallel version, we need MolToProc
594    public:
# Line 555 | Line 610 | namespace oopse{
610      void setMolToProcMap(const std::vector<int>& molToProcMap) {
611        molToProcMap_ = molToProcMap;
612      }
613 +
614 +    
615          
616    private:
617  

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