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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
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* the article in which the program was described (Matthew |
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< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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+ |
* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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/** |
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#include "brains/Stats.hpp" |
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#include "UseTheForce/DarkSide/simulation_interface.h" |
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|
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– |
namespace oopse{ |
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|
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namespace OpenMD{ |
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+ |
|
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/** |
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* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" |
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* @brief Snapshot class is a repository class for storing dynamic data during |
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class Snapshot { |
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public: |
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|
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< |
Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), |
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< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
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> |
Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), |
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> |
rigidbodyData(nRigidbodies), |
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> |
currentTime_(0), |
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> |
orthoTolerance_(1e-6), |
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> |
orthoRhombic_(0), |
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> |
chi_(0.0), |
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> |
integralOfChiDt_(0.0), |
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> |
eta_(0.0), id_(-1), |
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> |
hasCOM_(false), hasVolume_(false), volume_(0.0) { |
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|
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} |
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|
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Snapshot(int nAtoms, int nRigidbodies, int storageLayout) |
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: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout), |
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< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 85 |
> |
: atomData(nAtoms, storageLayout), |
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> |
rigidbodyData(nRigidbodies, storageLayout), |
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> |
currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), |
| 88 |
> |
integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0) { |
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|
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} |
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|
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|
void setHmat(const Mat3x3d& m); |
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|
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RealType getVolume() { |
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< |
return hmat_.determinant(); |
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> |
if (hasVolume_){ |
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> |
return volume_; |
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> |
}else{ |
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> |
return hmat_.determinant(); |
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> |
} |
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|
} |
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|
|
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+ |
void setVolume(RealType volume){ |
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+ |
hasVolume_=true; |
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+ |
volume_ = volume; |
| 135 |
+ |
} |
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+ |
|
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/** Returns the inverse H-Matrix */ |
| 138 |
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Mat3x3d getInvHmat() { |
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return invHmat_; |
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|
| 142 |
|
/** Wrapping the vector according to periodic boundary condition*/ |
| 143 |
|
void wrapVector(Vector3d& v); |
| 144 |
< |
|
| 144 |
> |
Vector3d getCOM(); |
| 145 |
> |
Vector3d getCOMvel(); |
| 146 |
> |
Vector3d getCOMw(); |
| 147 |
|
|
| 148 |
|
RealType getTime() { |
| 149 |
|
return currentTime_; |
| 175 |
|
integralOfChiDt_ = integralOfChiDt; |
| 176 |
|
} |
| 177 |
|
|
| 178 |
+ |
|
| 179 |
+ |
void setOrthoTolerance(RealType orthoTolerance) { |
| 180 |
+ |
orthoTolerance_ = orthoTolerance; |
| 181 |
+ |
} |
| 182 |
+ |
|
| 183 |
|
Mat3x3d getEta() { |
| 184 |
|
return eta_; |
| 185 |
|
} |
| 187 |
|
void setEta(const Mat3x3d& eta) { |
| 188 |
|
eta_ = eta; |
| 189 |
|
} |
| 190 |
< |
|
| 190 |
> |
|
| 191 |
> |
bool hasCOM() { |
| 192 |
> |
return hasCOM_; |
| 193 |
> |
} |
| 194 |
> |
|
| 195 |
> |
void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) { |
| 196 |
> |
COM_ = COM; |
| 197 |
> |
COMvel_ = COMvel; |
| 198 |
> |
COMw_ = COMw; |
| 199 |
> |
hasCOM_ = true; |
| 200 |
> |
} |
| 201 |
> |
|
| 202 |
|
DataStorage atomData; |
| 203 |
|
DataStorage rigidbodyData; |
| 204 |
|
Stats statData; |
| 208 |
|
|
| 209 |
|
Mat3x3d hmat_; |
| 210 |
|
Mat3x3d invHmat_; |
| 211 |
+ |
RealType orthoTolerance_; |
| 212 |
|
int orthoRhombic_; |
| 213 |
+ |
RealType volume_; |
| 214 |
|
|
| 215 |
|
RealType chi_; |
| 216 |
|
RealType integralOfChiDt_; |
| 217 |
|
Mat3x3d eta_; |
| 218 |
< |
|
| 218 |
> |
Vector3d COM_; |
| 219 |
> |
Vector3d COMvel_; |
| 220 |
> |
Vector3d COMw_; |
| 221 |
|
int id_; /**< identification number of the snapshot */ |
| 222 |
+ |
bool hasCOM_; |
| 223 |
+ |
bool hasVolume_; |
| 224 |
+ |
|
| 225 |
|
}; |
| 226 |
|
|
| 227 |
|
typedef DataStorage (Snapshot::*DataStoragePointer); |
