| 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, 24107 (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 |
|
|
| 43 |
|
/** |
| 55 |
|
|
| 56 |
|
#include "brains/DataStorage.hpp" |
| 57 |
|
#include "brains/Stats.hpp" |
| 57 |
– |
#include "UseTheForce/DarkSide/simulation_interface.h" |
| 58 |
|
|
| 59 |
+ |
namespace OpenMD{ |
| 60 |
|
|
| 60 |
– |
namespace oopse{ |
| 61 |
– |
|
| 61 |
|
/** |
| 62 |
|
* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" |
| 63 |
|
* @brief Snapshot class is a repository class for storing dynamic data during |
| 64 |
|
* Simulation |
| 65 |
< |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
| 65 |
> |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
| 66 |
|
* for rigid bodies. |
| 67 |
|
*/ |
| 68 |
|
class Snapshot { |
| 69 |
|
public: |
| 70 |
|
|
| 71 |
< |
Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), |
| 72 |
< |
rigidbodyData(nRigidbodies), |
| 73 |
< |
currentTime_(0), |
| 74 |
< |
orthoTolerance_(1e-6), |
| 75 |
< |
orthoRhombic_(0), |
| 76 |
< |
chi_(0.0), |
| 77 |
< |
integralOfChiDt_(0.0), |
| 78 |
< |
eta_(0.0), id_(-1), |
| 79 |
< |
hasCOM_(false), hasVolume_(false), volume_(0.0) { |
| 71 |
> |
Snapshot(int nAtoms, int nRigidbodies, |
| 72 |
> |
int nCutoffGroups) : atomData(nAtoms), |
| 73 |
> |
rigidbodyData(nRigidbodies), |
| 74 |
> |
cgData(nCutoffGroups, DataStorage::dslPosition), |
| 75 |
> |
currentTime_(0), |
| 76 |
> |
orthoTolerance_(1e-6), |
| 77 |
> |
orthoRhombic_(0), |
| 78 |
> |
chi_(0.0), |
| 79 |
> |
integralOfChiDt_(0.0), |
| 80 |
> |
eta_(0.0), id_(-1), hasCOM_(false), |
| 81 |
> |
volume_(0.0), hasVolume_(false) { |
| 82 |
|
|
| 83 |
|
} |
| 84 |
|
|
| 85 |
< |
Snapshot(int nAtoms, int nRigidbodies, int storageLayout) |
| 86 |
< |
: atomData(nAtoms, storageLayout), |
| 87 |
< |
rigidbodyData(nRigidbodies, storageLayout), |
| 88 |
< |
currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), |
| 89 |
< |
integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0) { |
| 90 |
< |
|
| 91 |
< |
} |
| 92 |
< |
|
| 85 |
> |
Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, |
| 86 |
> |
int storageLayout) : atomData(nAtoms, storageLayout), |
| 87 |
> |
rigidbodyData(nRigidbodies, storageLayout), |
| 88 |
> |
cgData(nCutoffGroups, DataStorage::dslPosition), |
| 89 |
> |
currentTime_(0), orthoTolerance_(1e-6), |
| 90 |
> |
orthoRhombic_(0), chi_(0.0), |
| 91 |
> |
integralOfChiDt_(0.0), eta_(0.0), id_(-1), |
| 92 |
> |
hasCOM_(false), volume_(0.0), |
| 93 |
> |
hasVolume_(false) { |
| 94 |
> |
} |
| 95 |
> |
|
| 96 |
|
/** Returns the id of this Snapshot */ |
| 97 |
|
int getID() { |
| 98 |
|
return id_; |
| 117 |
|
return rigidbodyData.getSize(); |
| 118 |
|
} |
| 119 |
|
|
| 120 |
+ |
/** Returns the number of rigid bodies */ |
| 121 |
+ |
int getNumberOfCutoffGroups() { |
| 122 |
+ |
return cgData.getSize(); |
| 123 |
+ |
} |
| 124 |
+ |
|
| 125 |
|
/** Returns the H-Matrix */ |
| 126 |
|
Mat3x3d getHmat() { |
| 127 |
|
return hmat_; |
| 150 |
|
|
| 151 |
|
/** Wrapping the vector according to periodic boundary condition*/ |
| 152 |
|
void wrapVector(Vector3d& v); |
| 153 |
+ |
/** Scaling a vector to multiples of the periodic box */ |
| 154 |
+ |
Vector3d scaleVector(Vector3d &v); |
| 155 |
+ |
|
| 156 |
+ |
|
| 157 |
|
Vector3d getCOM(); |
| 158 |
|
Vector3d getCOMvel(); |
| 159 |
|
Vector3d getCOMw(); |
| 211 |
|
COMw_ = COMw; |
| 212 |
|
hasCOM_ = true; |
| 213 |
|
} |
| 214 |
< |
|
| 214 |
> |
|
| 215 |
|
DataStorage atomData; |
| 216 |
|
DataStorage rigidbodyData; |
| 217 |
+ |
DataStorage cgData; |
| 218 |
|
Stats statData; |
| 219 |
< |
|
| 219 |
> |
|
| 220 |
|
private: |
| 221 |
|
RealType currentTime_; |
| 222 |
|
|
