OpenMD 3.0
Molecular Dynamics in the Open
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BlockSnapshotManager.hpp
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32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#ifndef BRAINS_BLOCKSNAPSHOTMANAGER_HPP
46#define BRAINS_BLOCKSNAPSHOTMANAGER_HPP
47
48#include <vector>
49
51
52namespace OpenMD {
53
54 class SimInfo;
55 class DumpReader;
56
57 using SnapshotBlock = std::pair<int, int>;
58
59 /**
60 * @class BlockSnapshotManager
61 * @todo document
62 */
64 public:
65 BlockSnapshotManager(SimInfo* info, const std::string& filename,
66 int atomStorageLayout, int rigidBodyStorageLayout,
67 int cutoffGroupStorageLayout, long long int memSize,
68 int blockCapacity = 2);
70
71 virtual Snapshot* getSnapshot(int id);
72
73 /** Returns number of snapshot blocks in this BlockSnapshotManager*/
74 size_t getNBlocks() { return blocks_.size(); }
75
76 SnapshotBlock getSnapshotBlock(int block) { return blocks_.at(block); }
77
78 int getNActiveBlocks();
79
80 void needCOMprops(bool ncp);
81
82 bool isBlockActive(int block) {
83 return findActiveBlock(block) != activeBlocks_.end() ? true : false;
84 }
85
86 bool loadBlock(int block);
87
88 bool unloadBlock(int block);
89
90 std::vector<int> getActiveBlocks();
91
92 int getBlockCapacity() { return blockCapacity_; }
93
94 int getNFrames();
95
96 private:
97 std::vector<int>::iterator findActiveBlock(int block) {
98 return std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
99 }
100
101 bool hasZeroRefBlock();
102
103 int getFirstZeroRefBlock();
104
105 void internalLoad(int block);
106 void internalUnload(int block);
107 Snapshot* loadFrame(int frame);
108
109 int blockCapacity_;
110 long long int memSize_;
111
112 std::vector<Snapshot*> snapshots_;
113 std::vector<SnapshotBlock> blocks_;
114 std::vector<int> activeBlocks_;
115 std::vector<int> activeRefCount_;
116
117 int nAtoms_;
118 int nRigidBodies_;
119 int nCutoffGroups_;
120 bool usePBC_;
121
122 DumpReader* reader_;
123 int nframes_;
124 int nSnapshotPerBlock_;
125 };
126} // namespace OpenMD
127
128#endif
size_t getNBlocks()
Returns number of snapshot blocks in this BlockSnapshotManager.
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
The Snapshot class is a repository storing dynamic data during a Simulation.
Definition Snapshot.hpp:147
SnapshotManager class is an abstract class which maintains a series of snapshots.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.