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root/OpenMD/trunk/src/brains/SimInfo.hpp
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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 91 | Line 91 | namespace OpenMD{
91      /**
92       * Constructor of SimInfo
93       *
94 <     * @param molStampPairs MoleculeStamp Array. The first element of
95 <     * the pair is molecule stamp, the second element is the total
96 <     * number of molecules with the same molecule stamp in the system
97 <     *
98 <     * @param ff pointer of a concrete ForceField instance
94 >     * @param ff pointer to a concrete ForceField instance
95       *
96 <     * @param simParams
96 >     * @param simParams pointer to the simulation parameters in a Globals object
97       */
98      SimInfo(ForceField* ff, Globals* simParams);
99      virtual ~SimInfo();
# Line 108 | Line 104 | namespace OpenMD{
104       * @return return true if adding successfully, return false if the
105       * molecule is already in SimInfo
106       *
107 <     * @param mol molecule to be added
107 >     * @param mol Molecule to be added
108       */
109      bool addMolecule(Molecule* mol);
110  
# Line 274 | Line 270 | namespace OpenMD{
270      SnapshotManager* getSnapshotManager() {
271        return sman_;
272      }
273 <
273 >    /** Returns the storage layout (computed by SimCreator) */
274 >    int getStorageLayout() {
275 >      return storageLayout_;
276 >    }
277 >    /** Sets the storage layout (computed by SimCreator) */
278 >    void setStorageLayout(int sl) {
279 >      storageLayout_ = sl;
280 >    }
281 >    
282      /** Sets the snapshot manager. */
283      void setSnapshotManager(SnapshotManager* sman);
284          
# Line 385 | Line 389 | namespace OpenMD{
389  
390      /**
391       * Sets GlobalGroupMembership
388 –     * @see #SimCreator::setGlobalIndex
392       */  
393 <    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
394 <      assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
395 <      globalGroupMembership_ = globalGroupMembership;
393 >    void setGlobalGroupMembership(const vector<int>& ggm) {
394 >      assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
395 >      globalGroupMembership_ = ggm;
396      }
397  
398      /**
399       * Sets GlobalMolMembership
397 –     * @see #SimCreator::setGlobalIndex
400       */        
401 <    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
402 <      assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
403 <      globalMolMembership_ = globalMolMembership;
401 >    void setGlobalMolMembership(const vector<int>& gmm) {
402 >      assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
403 >                                                nGlobalRigidBodies_)));
404 >      globalMolMembership_ = gmm;
405      }
406  
407  
# Line 465 | Line 468 | namespace OpenMD{
468  
469      /** Returns the set of atom types present in this simulation */
470      set<AtomType*> getSimulatedAtomTypes();
471 +
472 +    /** Returns the global count of atoms of a particular type */
473 +    int getGlobalCountOfType(AtomType* atype);
474          
475      friend ostream& operator <<(ostream& o, SimInfo& info);
476  
# Line 582 | Line 588 | namespace OpenMD{
588      vector<int> identArray_;
589    public:
590      vector<int> getIdentArray() { return identArray_; }
591 +
592 +    /**
593 +     * A vector that contains information about the local region of an
594 +     * atom (used for fluctuating charges, etc.)
595 +     */
596    private:
597 <    
597 >    vector<int> regions_;
598 >  public:
599 >    vector<int> getRegions() { return regions_; }
600 >  private:
601      /**
602       * A vector which contains the fractional contribution of an
603       * atom's mass to the total mass of the cutoffGroup that atom
# Line 610 | Line 624 | namespace OpenMD{
624  
625      PropertyMap properties_;       /**< Generic Properties can be added */
626      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
627 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
628  
629      /**
630       * The reason to have a local index manager is that when molecule
# Line 629 | Line 644 | namespace OpenMD{
644      string dumpFileName_;
645      string statFileName_;
646      string restFileName_;
632 –        
647  
648      bool topologyDone_;  /** flag to indicate whether the topology has
649                               been scanned and all the relevant
# Line 667 | Line 681 | namespace OpenMD{
681      
682      /**
683       * Set MolToProcMap array
670 –     * @see #SimCreator::divideMolecules
684       */
685      void setMolToProcMap(const vector<int>& molToProcMap) {
686        molToProcMap_ = molToProcMap;

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