| 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. |
| 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, 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 |
|
*/ |
| 42 |
|
#ifndef BRAINS_BLOCKSNAPSHOTMANAGER_HPP |
| 43 |
|
#define BRAINS_BLOCKSNAPSHOTMANAGER_HPP |
| 44 |
|
#include <vector> |
| 45 |
|
|
| 46 |
|
#include "brains/SnapshotManager.hpp" |
| 47 |
< |
namespace oopse { |
| 47 |
> |
namespace OpenMD { |
| 48 |
|
|
| 49 |
< |
class SimInfo; |
| 50 |
< |
class DumpReader; |
| 49 |
> |
class SimInfo; |
| 50 |
> |
class DumpReader; |
| 51 |
|
|
| 52 |
< |
typedef std::pair<int, int> SnapshotBlock; |
| 52 |
> |
typedef std::pair<int, int> SnapshotBlock; |
| 53 |
|
|
| 54 |
< |
/** |
| 55 |
< |
* @class BlockSnapshotManager |
| 56 |
< |
* @todo document |
| 57 |
< |
*/ |
| 58 |
< |
class BlockSnapshotManager : public SnapshotManager{ |
| 54 |
> |
/** |
| 55 |
> |
* @class BlockSnapshotManager |
| 56 |
> |
* @todo document |
| 57 |
> |
*/ |
| 58 |
> |
class BlockSnapshotManager : public SnapshotManager{ |
| 59 |
|
|
| 60 |
< |
public: |
| 61 |
< |
BlockSnapshotManager(SimInfo* info, const std::string& filename, int storageLayout, int blockCapacity = 2); |
| 62 |
< |
~BlockSnapshotManager(); |
| 60 |
> |
public: |
| 61 |
> |
BlockSnapshotManager(SimInfo* info, const std::string& filename, int storageLayout, long long int memSize, int blockCapacity = 2); |
| 62 |
> |
~BlockSnapshotManager(); |
| 63 |
|
|
| 64 |
< |
virtual Snapshot* getSnapshot(int id) { return snapshots_[id]; } |
| 64 |
> |
virtual Snapshot* getSnapshot(int id); |
| 65 |
|
|
| 65 |
– |
/** Returns number of snapshot blocks in this BlockSnapshotManager*/ |
| 66 |
– |
int getNBlocks() { |
| 67 |
– |
return blocks_.size(); |
| 68 |
– |
} |
| 66 |
|
|
| 67 |
< |
SnapshotBlock getSnapshotBlock(int block) { |
| 68 |
< |
return blocks_.at(block); |
| 69 |
< |
} |
| 67 |
> |
/** Returns number of snapshot blocks in this BlockSnapshotManager*/ |
| 68 |
> |
int getNBlocks() { |
| 69 |
> |
return blocks_.size(); |
| 70 |
> |
} |
| 71 |
> |
|
| 72 |
> |
SnapshotBlock getSnapshotBlock(int block) { |
| 73 |
> |
return blocks_.at(block); |
| 74 |
> |
} |
| 75 |
|
|
| 76 |
< |
int getNActiveBlocks(); |
| 75 |
< |
|
| 76 |
> |
int getNActiveBlocks(); |
| 77 |
|
|
| 78 |
< |
bool isBlockActive(int block) { |
| 78 |
< |
return findActiveBlock(block) != activeBlocks_.end() ? true : false; |
| 79 |
< |
} |
| 78 |
> |
void needCOMprops(bool ncp); |
| 79 |
|
|
| 80 |
< |
bool loadBlock(int block); |
| 80 |
> |
|
| 81 |
> |
bool isBlockActive(int block) { |
| 82 |
> |
return findActiveBlock(block) != activeBlocks_.end() ? true : false; |
| 83 |
> |
} |
| 84 |
> |
|
| 85 |
> |
bool loadBlock(int block); |
| 86 |
|
|
| 87 |
< |
bool unloadBlock(int block); |
| 87 |
> |
bool unloadBlock(int block); |
| 88 |
|
|
| 89 |
< |
std::vector<int> getActiveBlocks(); |
| 89 |
> |
std::vector<int> getActiveBlocks(); |
| 90 |
|
|
| 91 |
< |
int getBlockCapacity() { |
| 92 |
< |
return blockCapacity_; |
| 93 |
< |
} |
| 91 |
> |
int getBlockCapacity() { |
| 92 |
> |
return blockCapacity_; |
| 93 |
> |
} |
| 94 |
|
|
| 95 |
< |
int getNFrames(); |
| 95 |
> |
int getNFrames(); |
| 96 |
|
|
| 97 |
< |
private: |
| 97 |
> |
private: |
| 98 |
|
|
| 99 |
< |
std::vector<int>::iterator findActiveBlock(int block) { |
| 100 |
< |
return std::find(activeBlocks_.begin(), activeBlocks_.end(), block); |
| 101 |
< |
} |
| 99 |
> |
std::vector<int>::iterator findActiveBlock(int block) { |
| 100 |
> |
return std::find(activeBlocks_.begin(), activeBlocks_.end(), block); |
| 101 |
> |
} |
| 102 |
|
|
| 103 |
< |
bool hasZeroRefBlock(); |
| 103 |
> |
bool hasZeroRefBlock(); |
| 104 |
|
|
| 105 |
< |
int getFirstZeroRefBlock(); |
| 105 |
> |
int getFirstZeroRefBlock(); |
| 106 |
|
|
| 107 |
< |
void internalLoad(int block); |
| 108 |
< |
void internalUnload(int block); |
| 109 |
< |
Snapshot* loadFrame(int frame); |
| 107 |
> |
void internalLoad(int block); |
| 108 |
> |
void internalUnload(int block); |
| 109 |
> |
Snapshot* loadFrame(int frame); |
| 110 |
|
|
| 111 |
< |
SimInfo* info_; |
| 112 |
< |
int blockCapacity_; |
| 111 |
> |
SimInfo* info_; |
| 112 |
> |
int blockCapacity_; |
| 113 |
> |
long long int memSize_; |
| 114 |
|
|
| 115 |
< |
std::vector<Snapshot*> snapshots_; |
| 116 |
< |
std::vector<SnapshotBlock> blocks_; |
| 117 |
< |
std::vector<int> activeBlocks_; |
| 118 |
< |
std::vector<int> activeRefCount_; |
| 115 |
> |
std::vector<Snapshot*> snapshots_; |
| 116 |
> |
std::vector<SnapshotBlock> blocks_; |
| 117 |
> |
std::vector<int> activeBlocks_; |
| 118 |
> |
std::vector<int> activeRefCount_; |
| 119 |
|
|
| 120 |
< |
int nAtoms_; |
| 121 |
< |
int nRigidBodies_; |
| 120 |
> |
int nAtoms_; |
| 121 |
> |
int nRigidBodies_; |
| 122 |
> |
int nCutoffGroups_; |
| 123 |
|
|
| 124 |
< |
DumpReader* reader_; |
| 125 |
< |
int nframes_; |
| 126 |
< |
int nSnapshotPerBlock_; |
| 124 |
> |
DumpReader* reader_; |
| 125 |
> |
int nframes_; |
| 126 |
> |
int nSnapshotPerBlock_; |
| 127 |
|
|
| 128 |
< |
}; |
| 128 |
> |
}; |
| 129 |
|
|
| 130 |
|
} |
| 131 |
|
|
