| 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 oopse{ |
| 59 |
> |
namespace OpenMD{ |
| 60 |
|
|
| 61 |
+ |
struct FrameData { |
| 62 |
+ |
int id; /**< identification number of the snapshot */ |
| 63 |
+ |
RealType currentTime; /**< current time */ |
| 64 |
+ |
Mat3x3d hmat; /**< axes of the periodic box in matrix form */ |
| 65 |
+ |
Mat3x3d invHmat; /**< the inverse of the Hmat matrix */ |
| 66 |
+ |
bool orthoRhombic; /**< is this an orthorhombic periodic box? */ |
| 67 |
+ |
RealType volume; /**< total volume of this frame */ |
| 68 |
+ |
RealType pressure; /**< pressure of this frame */ |
| 69 |
+ |
RealType totalEnergy; /**< total energy of this frame */ |
| 70 |
+ |
RealType kineticEnergy; /**< kinetic energy of this frame */ |
| 71 |
+ |
RealType potentialEnergy; /**< potential energy of this frame */ |
| 72 |
+ |
RealType temperature; /**< temperature of this frame */ |
| 73 |
+ |
RealType chi; /**< thermostat velocity */ |
| 74 |
+ |
RealType integralOfChiDt; /**< the actual thermostat */ |
| 75 |
+ |
RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */ |
| 76 |
+ |
RealType chiQ; /**< fluctuating charge thermostat velocity */ |
| 77 |
+ |
RealType integralOfChiQDt; /**< the actual fluctuating charge thermostat */ |
| 78 |
+ |
Mat3x3d eta; /**< barostat matrix */ |
| 79 |
+ |
Vector3d COM; /**< location of center of mass */ |
| 80 |
+ |
Vector3d COMvel; /**< system center of mass velocity */ |
| 81 |
+ |
Vector3d COMw; /**< system center of mass angular velocity */ |
| 82 |
+ |
Mat3x3d stressTensor; /**< stress tensor */ |
| 83 |
+ |
Mat3x3d pressureTensor; /**< pressure tensor */ |
| 84 |
+ |
Vector3d systemDipole; /**< total system dipole moment */ |
| 85 |
+ |
Vector3d conductiveHeatFlux; /**< heat flux vector (conductive only) */ |
| 86 |
+ |
}; |
| 87 |
+ |
|
| 88 |
+ |
|
| 89 |
|
/** |
| 90 |
|
* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" |
| 91 |
|
* @brief Snapshot class is a repository class for storing dynamic data during |
| 92 |
|
* Simulation |
| 93 |
< |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
| 93 |
> |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
| 94 |
|
* for rigid bodies. |
| 95 |
|
*/ |
| 96 |
|
class Snapshot { |
| 97 |
|
public: |
| 98 |
|
|
| 99 |
< |
Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), |
| 100 |
< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 101 |
< |
|
| 99 |
> |
Snapshot(int nAtoms, int nRigidbodies, |
| 100 |
> |
int nCutoffGroups) : atomData(nAtoms), |
| 101 |
> |
rigidbodyData(nRigidbodies), |
| 102 |
> |
cgData(nCutoffGroups, DataStorage::dslPosition), |
| 103 |
> |
orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){ |
| 104 |
> |
|
| 105 |
> |
frameData.id = -1; |
| 106 |
> |
frameData.currentTime = 0; |
| 107 |
> |
frameData.hmat = Mat3x3d(0.0); |
| 108 |
> |
frameData.invHmat = Mat3x3d(0.0); |
| 109 |
> |
frameData.orthoRhombic = false; |
| 110 |
> |
frameData.volume = 0.0; |
| 111 |
> |
frameData.pressure = 0.0; |
| 112 |
> |
frameData.totalEnergy = 0.0; |
| 113 |
> |
frameData.kineticEnergy = 0.0; |
| 114 |
> |
frameData.potentialEnergy = 0.0; |
| 115 |
> |
frameData.temperature = 0.0; |
| 116 |
> |
frameData.chi = 0.0; |
| 117 |
> |
frameData.integralOfChiDt = 0.0; |
| 118 |
> |
frameData.electronicTemperature = 0.0; |
| 119 |
> |
frameData.chiQ = 0.0; |
| 120 |
> |
frameData.integralOfChiQDt = 0.0; |
| 121 |
> |
frameData.eta = Mat3x3d(0.0); |
| 122 |
> |
frameData.COM = V3Zero; |
| 123 |
> |
frameData.COMvel = V3Zero; |
| 124 |
> |
frameData.COMw = V3Zero; |
| 125 |
> |
frameData.stressTensor = Mat3x3d(0.0); |
| 126 |
> |
frameData.pressureTensor = Mat3x3d(0.0); |
| 127 |
> |
frameData.systemDipole = V3Zero; |
| 128 |
> |
frameData.conductiveHeatFlux = V3Zero; |
| 129 |
|
} |
| 130 |
|
|
| 131 |
< |
Snapshot(int nAtoms, int nRigidbodies, int storageLayout) |
| 132 |
< |
: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout), |
| 133 |
< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 134 |
< |
|
| 135 |
< |
} |
| 136 |
< |
|
| 131 |
> |
Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, |
| 132 |
> |
int storageLayout) : atomData(nAtoms, storageLayout), |
| 133 |
> |
rigidbodyData(nRigidbodies, storageLayout), |
| 134 |
> |
cgData(nCutoffGroups, DataStorage::dslPosition), |
| 135 |
> |
orthoTolerance_(1e-6), |
| 136 |
> |
hasCOM_(false), |
| 137 |
> |
hasVolume_(false) { |
| 138 |
> |
frameData.id = -1; |
| 139 |
> |
frameData.currentTime = 0; |
| 140 |
> |
frameData.hmat = Mat3x3d(0.0); |
| 141 |
> |
frameData.invHmat = Mat3x3d(0.0); |
| 142 |
> |
frameData.orthoRhombic = false; |
| 143 |
> |
frameData.volume = 0.0; |
| 144 |
> |
frameData.pressure = 0.0; |
| 145 |
> |
frameData.totalEnergy = 0.0; |
| 146 |
> |
frameData.kineticEnergy = 0.0; |
| 147 |
> |
frameData.potentialEnergy = 0.0; |
| 148 |
> |
frameData.temperature = 0.0; |
| 149 |
> |
frameData.chi = 0.0; |
| 150 |
> |
frameData.integralOfChiDt = 0.0; |
| 151 |
> |
frameData.electronicTemperature = 0.0; |
| 152 |
> |
frameData.chiQ = 0.0; |
| 153 |
> |
frameData.integralOfChiQDt = 0.0; |
| 154 |
> |
frameData.eta = Mat3x3d(0.0); |
| 155 |
> |
frameData.COM = V3Zero; |
| 156 |
> |
frameData.COMvel = V3Zero; |
| 157 |
> |
frameData.COMw = V3Zero; |
| 158 |
> |
frameData.stressTensor = Mat3x3d(0.0); |
| 159 |
> |
frameData.pressureTensor = Mat3x3d(0.0); |
| 160 |
> |
frameData.systemDipole = V3Zero; |
| 161 |
> |
frameData.conductiveHeatFlux = V3Zero; |
| 162 |
> |
} |
| 163 |
> |
|
| 164 |
|
/** Returns the id of this Snapshot */ |
| 165 |
|
int getID() { |
| 166 |
< |
return id_; |
| 166 |
> |
return frameData.id; |
| 167 |
|
} |
| 168 |
|
|
| 169 |
|
/** Sets the id of this Snapshot */ |
| 170 |
|
void setID(int id) { |
| 171 |
< |
id_ = id; |
| 171 |
> |
frameData.id = id; |
| 172 |
|
} |
| 173 |
|
|
| 174 |
|
int getSize() { |
| 185 |
|
return rigidbodyData.getSize(); |
| 186 |
|
} |
| 187 |
|
|
| 188 |
+ |
/** Returns the number of rigid bodies */ |
| 189 |
+ |
int getNumberOfCutoffGroups() { |
| 190 |
+ |
return cgData.getSize(); |
| 191 |
+ |
} |
| 192 |
+ |
|
| 193 |
|
/** Returns the H-Matrix */ |
| 194 |
|
Mat3x3d getHmat() { |
| 195 |
< |
return hmat_; |
| 195 |
> |
return frameData.hmat; |
| 196 |
|
} |
| 197 |
|
|
| 198 |
|
/** Sets the H-Matrix */ |
| 199 |
|
void setHmat(const Mat3x3d& m); |
| 200 |
|
|
| 201 |
|
RealType getVolume() { |
| 202 |
< |
return hmat_.determinant(); |
| 202 |
> |
if (hasVolume_){ |
| 203 |
> |
return frameData.volume; |
| 204 |
> |
}else{ |
| 205 |
> |
return frameData.hmat.determinant(); |
| 206 |
> |
} |
| 207 |
|
} |
| 208 |
|
|
| 209 |
+ |
void setVolume(RealType volume){ |
| 210 |
+ |
hasVolume_=true; |
| 211 |
+ |
frameData.volume = volume; |
| 212 |
+ |
} |
| 213 |
+ |
|
| 214 |
|
/** Returns the inverse H-Matrix */ |
| 215 |
|
Mat3x3d getInvHmat() { |
| 216 |
< |
return invHmat_; |
| 216 |
> |
return frameData.invHmat; |
| 217 |
|
} |
| 218 |
|
|
| 219 |
|
/** Wrapping the vector according to periodic boundary condition*/ |
| 220 |
|
void wrapVector(Vector3d& v); |
| 221 |
+ |
/** Scaling a vector to multiples of the periodic box */ |
| 222 |
+ |
Vector3d scaleVector(Vector3d &v); |
| 223 |
|
|
| 224 |
+ |
|
| 225 |
+ |
Vector3d getCOM(); |
| 226 |
+ |
Vector3d getCOMvel(); |
| 227 |
+ |
Vector3d getCOMw(); |
| 228 |
|
|
| 229 |
|
RealType getTime() { |
| 230 |
< |
return currentTime_; |
| 230 |
> |
return frameData.currentTime; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
|
void increaseTime(RealType dt) { |
| 235 |
|
} |
| 236 |
|
|
| 237 |
|
void setTime(RealType time) { |
| 238 |
< |
currentTime_ =time; |
| 238 |
> |
frameData.currentTime =time; |
| 239 |
|
//time at statData is redundant |
| 240 |
< |
statData[Stats::TIME] = currentTime_; |
| 240 |
> |
statData[Stats::TIME] = frameData.currentTime; |
| 241 |
|
} |
| 242 |
|
|
| 243 |
|
RealType getChi() { |
| 244 |
< |
return chi_; |
| 244 |
> |
return frameData.chi; |
| 245 |
|
} |
| 246 |
|
|
| 247 |
|
void setChi(RealType chi) { |
| 248 |
< |
chi_ = chi; |
| 248 |
> |
frameData.chi = chi; |
| 249 |
|
} |
| 250 |
|
|
| 251 |
|
RealType getIntegralOfChiDt() { |
| 252 |
< |
return integralOfChiDt_; |
| 252 |
> |
return frameData.integralOfChiDt; |
| 253 |
|
} |
| 254 |
|
|
| 255 |
|
void setIntegralOfChiDt(RealType integralOfChiDt) { |
| 256 |
< |
integralOfChiDt_ = integralOfChiDt; |
| 256 |
> |
frameData.integralOfChiDt = integralOfChiDt; |
| 257 |
|
} |
| 258 |
|
|
| 259 |
+ |
RealType getChiElectronic() { |
| 260 |
+ |
return frameData.chiQ; |
| 261 |
+ |
} |
| 262 |
+ |
|
| 263 |
+ |
void setChiElectronic(RealType chiQ) { |
| 264 |
+ |
frameData.chiQ = chiQ; |
| 265 |
+ |
} |
| 266 |
+ |
|
| 267 |
+ |
RealType getIntegralOfChiElectronicDt() { |
| 268 |
+ |
return frameData.integralOfChiQDt; |
| 269 |
+ |
} |
| 270 |
+ |
|
| 271 |
+ |
void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) { |
| 272 |
+ |
frameData.integralOfChiQDt = integralOfChiQDt; |
| 273 |
+ |
} |
| 274 |
+ |
|
| 275 |
+ |
|
| 276 |
+ |
void setOrthoTolerance(RealType orthoTolerance) { |
| 277 |
+ |
orthoTolerance_ = orthoTolerance; |
| 278 |
+ |
} |
| 279 |
+ |
|
| 280 |
|
Mat3x3d getEta() { |
| 281 |
< |
return eta_; |
| 281 |
> |
return frameData.eta; |
| 282 |
|
} |
| 283 |
|
|
| 284 |
|
void setEta(const Mat3x3d& eta) { |
| 285 |
< |
eta_ = eta; |
| 285 |
> |
frameData.eta = eta; |
| 286 |
|
} |
| 287 |
< |
|
| 287 |
> |
|
| 288 |
> |
Mat3x3d getStressTensor() { |
| 289 |
> |
return frameData.stressTensor; |
| 290 |
> |
} |
| 291 |
> |
|
| 292 |
> |
void setStressTensor(const Mat3x3d& stressTensor) { |
| 293 |
> |
frameData.stressTensor = stressTensor; |
| 294 |
> |
} |
| 295 |
> |
|
| 296 |
> |
Vector3d getConductiveHeatFlux() { |
| 297 |
> |
return frameData.conductiveHeatFlux; |
| 298 |
> |
} |
| 299 |
> |
|
| 300 |
> |
void setConductiveHeatFlux(const Vector3d& heatFlux) { |
| 301 |
> |
frameData.conductiveHeatFlux = heatFlux; |
| 302 |
> |
} |
| 303 |
> |
|
| 304 |
> |
bool hasCOM() { |
| 305 |
> |
return hasCOM_; |
| 306 |
> |
} |
| 307 |
> |
|
| 308 |
> |
void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) { |
| 309 |
> |
frameData.COM = COM; |
| 310 |
> |
frameData.COMvel = COMvel; |
| 311 |
> |
frameData.COMw = COMw; |
| 312 |
> |
hasCOM_ = true; |
| 313 |
> |
} |
| 314 |
> |
|
| 315 |
|
DataStorage atomData; |
| 316 |
|
DataStorage rigidbodyData; |
| 317 |
+ |
DataStorage cgData; |
| 318 |
+ |
FrameData frameData; |
| 319 |
|
Stats statData; |
| 168 |
– |
|
| 169 |
– |
private: |
| 170 |
– |
RealType currentTime_; |
| 320 |
|
|
| 321 |
< |
Mat3x3d hmat_; |
| 322 |
< |
Mat3x3d invHmat_; |
| 323 |
< |
int orthoRhombic_; |
| 324 |
< |
|
| 176 |
< |
RealType chi_; |
| 177 |
< |
RealType integralOfChiDt_; |
| 178 |
< |
Mat3x3d eta_; |
| 179 |
< |
|
| 180 |
< |
int id_; /**< identification number of the snapshot */ |
| 321 |
> |
private: |
| 322 |
> |
RealType orthoTolerance_; |
| 323 |
> |
bool hasCOM_; |
| 324 |
> |
bool hasVolume_; |
| 325 |
|
}; |
| 326 |
|
|
| 327 |
|
typedef DataStorage (Snapshot::*DataStoragePointer); |
