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root/OpenMD/trunk/src/brains/SimInfo.hpp
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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC

# 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 298 | Line 298 | namespace oopse{
298  
299        return i != molecules_.end() ? i->second : NULL;
300      }
301 –
302 –    /** Calculate the maximum cutoff radius based on the atom types */
303 –    double calcMaxCutoffRadius();
301  
302      double getRcut() {
303        return rcut_;
# Line 309 | Line 306 | namespace oopse{
306      double getRsw() {
307        return rsw_;
308      }
309 +
310 +    double getList() {
311 +      return rlist_;
312 +    }
313          
314      std::string getFinalConfigFileName() {
315        return finalConfigFileName_;
# Line 449 | Line 450 | namespace oopse{
450      void calcNdfRaw();
451      void calcNdfTrans();
452  
453 +    ForceField* forceField_;      
454 +    Globals* simParams_;
455 +
456 +    std::map<int, Molecule*>  molecules_; /**< Molecule array */
457 +
458      /**
459       * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
460       * system.
461       */
462      void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
457 –
458 –    MakeStamps* stamps_;
459 –    ForceField* forceField_;      
460 –    Globals* simParams_;
461 –
462 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
463          
464      //degress of freedom
465      int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
# Line 522 | Line 522 | namespace oopse{
522          
523      double rcut_;       /**< cutoff radius*/
524      double rsw_;        /**< radius of switching function*/
525 +    double rlist_;      /**< neighbor list radius */
526  
527      bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
528  

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