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Comparing trunk/src/brains/BlockSnapshotManager.hpp (file contents):
Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
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).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41   #ifndef BRAINS_BLOCKSNAPSHOTMANAGER_HPP
42   #define BRAINS_BLOCKSNAPSHOTMANAGER_HPP
43   #include <vector>
44  
45   #include "brains/SnapshotManager.hpp"
46 < namespace oopse {
46 > namespace OpenMD {
47  
48 < class SimInfo;
49 < class DumpReader;
48 >  class SimInfo;
49 >  class DumpReader;
50  
51 < typedef std::pair<int, int> SnapshotBlock;
51 >  typedef std::pair<int, int> SnapshotBlock;
52  
53 < /**
54 < * @class BlockSnapshotManager
55 < * @todo document
56 < */
57 < class BlockSnapshotManager : public SnapshotManager{
53 >  /**
54 >   * @class BlockSnapshotManager
55 >   * @todo document
56 >   */
57 >  class BlockSnapshotManager : public SnapshotManager{
58  
59 <    public:
60 <        BlockSnapshotManager(SimInfo* info, const std::string& filename, int storageLayout, int blockCapacity = 2);
61 <        ~BlockSnapshotManager();
59 >  public:
60 >    BlockSnapshotManager(SimInfo* info, const std::string& filename, int storageLayout, int blockCapacity = 2);
61 >    ~BlockSnapshotManager();
62          
63 <        virtual Snapshot* getSnapshot(int id) { return snapshots_[id]; }
63 >    virtual Snapshot* getSnapshot(int id);
64  
65 –        /** Returns number of snapshot blocks in this BlockSnapshotManager*/
66 –        int getNBlocks() {
67 –            return blocks_.size();
68 –        }
65  
66 <        SnapshotBlock getSnapshotBlock(int block) {
67 <            return blocks_.at(block);
68 <        }
66 >    /** Returns number of snapshot blocks in this BlockSnapshotManager*/
67 >    int getNBlocks() {
68 >      return blocks_.size();
69 >    }
70 >
71 >    SnapshotBlock getSnapshotBlock(int block) {
72 >      return blocks_.at(block);
73 >    }
74          
75 <        int getNActiveBlocks();
75 >    int getNActiveBlocks();
76 >
77 >    void needCOMprops(bool ncp);
78 >
79 >
80 >    bool isBlockActive(int block) {
81 >      return  findActiveBlock(block) != activeBlocks_.end() ? true : false;
82 >    }        
83 >
84 >    bool loadBlock(int block);
85          
86 <        bool isBlockActive(int block);
77 <        
78 <        bool loadBlock(int block);
79 <        
80 <        bool unloadBlock(int block);
86 >    bool unloadBlock(int block);
87  
88 <        std::vector<int> getActiveBlocks();
88 >    std::vector<int> getActiveBlocks();
89  
90 <        int getBlockCapacity() {
91 <            return blockCapacity_;                
92 <        }
90 >    int getBlockCapacity() {
91 >      return blockCapacity_;                
92 >    }
93  
94 <        int getNFrames();
94 >    int getNFrames();
95          
96 <    private:
96 >  private:
97  
98 <        Snapshot* loadFrame(int frame);
98 >    std::vector<int>::iterator findActiveBlock(int block) {
99 >      return std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
100 >    }
101 >
102 >    bool hasZeroRefBlock();
103 >
104 >    int getFirstZeroRefBlock();
105 >
106 >    void internalLoad(int block);
107 >    void internalUnload(int block);
108 >    Snapshot* loadFrame(int frame);
109          
110 <        SimInfo* info_;
111 <        int blockCapacity_;
110 >    SimInfo* info_;
111 >    int blockCapacity_;
112  
113 <        std::vector<Snapshot*> snapshots_;
114 <        std::vector<SnapshotBlock> blocks_;        
115 <        std::vector<int> activeBlocks_;
113 >    std::vector<Snapshot*> snapshots_;
114 >    std::vector<SnapshotBlock> blocks_;        
115 >    std::vector<int> activeBlocks_;
116 >    std::vector<int> activeRefCount_;
117          
118 <        int nAtoms_;
119 <        int nRigidBodies_;
118 >    int nAtoms_;
119 >    int nRigidBodies_;
120      
121 <        DumpReader* reader_;
122 <        int nframes_;
123 <        int nSnapshotPerBlock_;
121 >    DumpReader* reader_;
122 >    int nframes_;
123 >    int nSnapshotPerBlock_;
124  
125 < };
125 >  };
126  
127   }
128  

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