| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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 |
/** |
| 44 |
* @file Snapshot.hpp |
| 45 |
* @author tlin |
| 46 |
* @date 10/20/2004 |
| 47 |
* @time 23:56am |
| 48 |
* @version 1.0 |
| 49 |
*/ |
| 50 |
|
| 51 |
#ifndef BRAINS_SNAPSHOT_HPP |
| 52 |
#define BRAINS_SNAPSHOT_HPP |
| 53 |
|
| 54 |
#include <vector> |
| 55 |
|
| 56 |
#include "brains/DataStorage.hpp" |
| 57 |
#include "brains/Stats.hpp" |
| 58 |
|
| 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 |
| 94 |
* for rigid bodies. |
| 95 |
*/ |
| 96 |
class Snapshot { |
| 97 |
public: |
| 98 |
|
| 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 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 frameData.id; |
| 167 |
} |
| 168 |
|
| 169 |
/** Sets the id of this Snapshot */ |
| 170 |
void setID(int id) { |
| 171 |
frameData.id = id; |
| 172 |
} |
| 173 |
|
| 174 |
int getSize() { |
| 175 |
return atomData.getSize() + rigidbodyData.getSize(); |
| 176 |
} |
| 177 |
|
| 178 |
/** Returns the number of atoms */ |
| 179 |
int getNumberOfAtoms() { |
| 180 |
return atomData.getSize(); |
| 181 |
} |
| 182 |
|
| 183 |
/** Returns the number of rigid bodies */ |
| 184 |
int getNumberOfRigidBodies() { |
| 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 frameData.hmat; |
| 196 |
} |
| 197 |
|
| 198 |
/** Sets the H-Matrix */ |
| 199 |
void setHmat(const Mat3x3d& m); |
| 200 |
|
| 201 |
RealType getVolume() { |
| 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 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 frameData.currentTime; |
| 231 |
} |
| 232 |
|
| 233 |
void increaseTime(RealType dt) { |
| 234 |
setTime(getTime() + dt); |
| 235 |
} |
| 236 |
|
| 237 |
void setTime(RealType time) { |
| 238 |
frameData.currentTime =time; |
| 239 |
//time at statData is redundant |
| 240 |
statData[Stats::TIME] = frameData.currentTime; |
| 241 |
} |
| 242 |
|
| 243 |
RealType getChi() { |
| 244 |
return frameData.chi; |
| 245 |
} |
| 246 |
|
| 247 |
void setChi(RealType chi) { |
| 248 |
frameData.chi = chi; |
| 249 |
} |
| 250 |
|
| 251 |
RealType getIntegralOfChiDt() { |
| 252 |
return frameData.integralOfChiDt; |
| 253 |
} |
| 254 |
|
| 255 |
void setIntegralOfChiDt(RealType 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 frameData.eta; |
| 282 |
} |
| 283 |
|
| 284 |
void setEta(const Mat3x3d& eta) { |
| 285 |
frameData.eta = eta; |
| 286 |
} |
| 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; |
| 320 |
|
| 321 |
private: |
| 322 |
RealType orthoTolerance_; |
| 323 |
bool hasCOM_; |
| 324 |
bool hasVolume_; |
| 325 |
}; |
| 326 |
|
| 327 |
typedef DataStorage (Snapshot::*DataStoragePointer); |
| 328 |
} |
| 329 |
#endif //BRAINS_SNAPSHOT_HPP |
