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root/OpenMD/branches/development/src/brains/SimInfo.hpp
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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC vs.
Revision 1838 by gezelter, Tue Jan 22 16:20:11 2013 UTC

# 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_));
# Line 394 | Line 397 | namespace OpenMD{
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_));
# Line 610 | Line 612 | namespace OpenMD{
612  
613      PropertyMap properties_;       /**< Generic Properties can be added */
614      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
615 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
616  
617      /**
618       * The reason to have a local index manager is that when molecule
# Line 629 | Line 632 | namespace OpenMD{
632      string dumpFileName_;
633      string statFileName_;
634      string restFileName_;
632 –        
635  
636      bool topologyDone_;  /** flag to indicate whether the topology has
637                               been scanned and all the relevant
# Line 667 | Line 669 | namespace OpenMD{
669      
670      /**
671       * Set MolToProcMap array
670 –     * @see #SimCreator::divideMolecules
672       */
673      void setMolToProcMap(const vector<int>& molToProcMap) {
674        molToProcMap_ = molToProcMap;

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