| 6 |
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* 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 |
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* 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 |
+ |
* |
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+ |
* 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 |
|
*/ |
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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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* Simulation |
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< |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
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> |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
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* for rigid bodies. |
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|
*/ |
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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) { |
| 72 |
> |
Snapshot(int nAtoms, int nRigidbodies, |
| 73 |
> |
int nCutoffGroups) : atomData(nAtoms), |
| 74 |
> |
rigidbodyData(nRigidbodies), |
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> |
cgData(nCutoffGroups, DataStorage::dslPosition), |
| 76 |
> |
currentTime_(0), |
| 77 |
> |
orthoTolerance_(1e-6), |
| 78 |
> |
orthoRhombic_(0), |
| 79 |
> |
chi_(0.0), |
| 80 |
> |
integralOfChiDt_(0.0), |
| 81 |
> |
eta_(0.0), id_(-1), hasCOM_(false), |
| 82 |
> |
hasVolume_(false), volume_(0.0) { |
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|
|
| 84 |
|
} |
| 85 |
|
|
| 86 |
< |
Snapshot(int nAtoms, int nRigidbodies, int storageLayout) |
| 87 |
< |
: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout), |
| 88 |
< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 89 |
< |
|
| 90 |
< |
} |
| 91 |
< |
|
| 86 |
> |
Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, |
| 87 |
> |
int storageLayout) : atomData(nAtoms, storageLayout), |
| 88 |
> |
rigidbodyData(nRigidbodies, storageLayout), |
| 89 |
> |
cgData(nCutoffGroups, DataStorage::dslPosition), |
| 90 |
> |
currentTime_(0), orthoTolerance_(1e-6), |
| 91 |
> |
orthoRhombic_(0), chi_(0.0), |
| 92 |
> |
integralOfChiDt_(0.0), eta_(0.0), id_(-1), |
| 93 |
> |
hasCOM_(false), hasVolume_(false), |
| 94 |
> |
volume_(0.0) { |
| 95 |
> |
} |
| 96 |
> |
|
| 97 |
|
/** Returns the id of this Snapshot */ |
| 98 |
|
int getID() { |
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|
return id_; |
| 127 |
|
void setHmat(const Mat3x3d& m); |
| 128 |
|
|
| 129 |
|
RealType getVolume() { |
| 130 |
< |
return hmat_.determinant(); |
| 130 |
> |
if (hasVolume_){ |
| 131 |
> |
return volume_; |
| 132 |
> |
}else{ |
| 133 |
> |
return hmat_.determinant(); |
| 134 |
> |
} |
| 135 |
|
} |
| 136 |
|
|
| 137 |
+ |
void setVolume(RealType volume){ |
| 138 |
+ |
hasVolume_=true; |
| 139 |
+ |
volume_ = volume; |
| 140 |
+ |
} |
| 141 |
+ |
|
| 142 |
|
/** Returns the inverse H-Matrix */ |
| 143 |
|
Mat3x3d getInvHmat() { |
| 144 |
|
return invHmat_; |
| 146 |
|
|
| 147 |
|
/** Wrapping the vector according to periodic boundary condition*/ |
| 148 |
|
void wrapVector(Vector3d& v); |
| 149 |
< |
|
| 149 |
> |
Vector3d getCOM(); |
| 150 |
> |
Vector3d getCOMvel(); |
| 151 |
> |
Vector3d getCOMw(); |
| 152 |
|
|
| 153 |
|
RealType getTime() { |
| 154 |
|
return currentTime_; |
| 180 |
|
integralOfChiDt_ = integralOfChiDt; |
| 181 |
|
} |
| 182 |
|
|
| 183 |
+ |
|
| 184 |
+ |
void setOrthoTolerance(RealType orthoTolerance) { |
| 185 |
+ |
orthoTolerance_ = orthoTolerance; |
| 186 |
+ |
} |
| 187 |
+ |
|
| 188 |
|
Mat3x3d getEta() { |
| 189 |
|
return eta_; |
| 190 |
|
} |
| 192 |
|
void setEta(const Mat3x3d& eta) { |
| 193 |
|
eta_ = eta; |
| 194 |
|
} |
| 195 |
< |
|
| 195 |
> |
|
| 196 |
> |
bool hasCOM() { |
| 197 |
> |
return hasCOM_; |
| 198 |
> |
} |
| 199 |
> |
|
| 200 |
> |
void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) { |
| 201 |
> |
COM_ = COM; |
| 202 |
> |
COMvel_ = COMvel; |
| 203 |
> |
COMw_ = COMw; |
| 204 |
> |
hasCOM_ = true; |
| 205 |
> |
} |
| 206 |
> |
|
| 207 |
> |
Vector3d getAtomPosByIindex(int iIndex) { |
| 208 |
> |
#ifdef IS_MPI |
| 209 |
> |
return atomIData.position[iIndex]; |
| 210 |
> |
#else |
| 211 |
> |
return atomData.position[iIndex]; |
| 212 |
> |
#endif |
| 213 |
> |
} |
| 214 |
> |
Vector3d getAtomPosByJindex(int jIndex) { |
| 215 |
> |
#ifdef IS_MPI |
| 216 |
> |
return atomJData.position[jIndex]; |
| 217 |
> |
#else |
| 218 |
> |
return atomData.position[jIndex]; |
| 219 |
> |
#endif |
| 220 |
> |
} |
| 221 |
> |
|
| 222 |
> |
Vector3d getCutoffGroupPosByIindex(int iIndex) { |
| 223 |
> |
#ifdef IS_MPI |
| 224 |
> |
return cgIData.position[iIndex]; |
| 225 |
> |
#else |
| 226 |
> |
return cgData.position[iIndex]; |
| 227 |
> |
#endif |
| 228 |
> |
} |
| 229 |
> |
Vector3d getCutoffGroupPosByJindex(int jIndex) { |
| 230 |
> |
#ifdef IS_MPI |
| 231 |
> |
return cgJData.position[jIndex]; |
| 232 |
> |
#else |
| 233 |
> |
return cgData.position[jIndex]; |
| 234 |
> |
#endif |
| 235 |
> |
} |
| 236 |
> |
|
| 237 |
|
DataStorage atomData; |
| 238 |
|
DataStorage rigidbodyData; |
| 239 |
+ |
DataStorage cgData; |
| 240 |
|
Stats statData; |
| 241 |
+ |
|
| 242 |
+ |
#ifdef IS_MPI |
| 243 |
+ |
DataStorage atomIData; |
| 244 |
+ |
DataStorage atomJData; |
| 245 |
+ |
DataStorage cgIData; |
| 246 |
+ |
DataStorage cgJData; |
| 247 |
+ |
#endif |
| 248 |
+ |
|
| 249 |
|
|
| 250 |
|
private: |
| 251 |
|
RealType currentTime_; |
| 252 |
|
|
| 253 |
|
Mat3x3d hmat_; |
| 254 |
|
Mat3x3d invHmat_; |
| 255 |
+ |
RealType orthoTolerance_; |
| 256 |
|
int orthoRhombic_; |
| 257 |
+ |
RealType volume_; |
| 258 |
|
|
| 259 |
|
RealType chi_; |
| 260 |
|
RealType integralOfChiDt_; |
| 261 |
|
Mat3x3d eta_; |
| 262 |
< |
|
| 262 |
> |
Vector3d COM_; |
| 263 |
> |
Vector3d COMvel_; |
| 264 |
> |
Vector3d COMw_; |
| 265 |
|
int id_; /**< identification number of the snapshot */ |
| 266 |
+ |
bool hasCOM_; |
| 267 |
+ |
bool hasVolume_; |
| 268 |
+ |
|
| 269 |
|
}; |
| 270 |
|
|
| 271 |
|
typedef DataStorage (Snapshot::*DataStoragePointer); |
