| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
*/ |
| 41 |
|
| 42 |
/** |
| 43 |
* @file Snapshot.hpp |
| 44 |
* @author tlin |
| 45 |
* @date 10/20/2004 |
| 46 |
* @time 23:56am |
| 47 |
* @version 1.0 |
| 48 |
*/ |
| 49 |
|
| 50 |
#ifndef BRAINS_SNAPSHOT_HPP |
| 51 |
#define BRAINS_SNAPSHOT_HPP |
| 52 |
|
| 53 |
#include <vector> |
| 54 |
|
| 55 |
#include "brains/DataStorage.hpp" |
| 56 |
#include "brains/Stats.hpp" |
| 57 |
#include "UseTheForce/DarkSide/simulation_interface.h" |
| 58 |
|
| 59 |
|
| 60 |
namespace OpenMD{ |
| 61 |
|
| 62 |
/** |
| 63 |
* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" |
| 64 |
* @brief Snapshot class is a repository class for storing dynamic data during |
| 65 |
* Simulation |
| 66 |
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
| 67 |
* for rigid bodies. |
| 68 |
*/ |
| 69 |
class Snapshot { |
| 70 |
public: |
| 71 |
|
| 72 |
Snapshot(int nAtoms, int nRigidbodies, |
| 73 |
int nCutoffGroups) : atomData(nAtoms), |
| 74 |
rigidbodyData(nRigidbodies), |
| 75 |
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) { |
| 83 |
|
| 84 |
} |
| 85 |
|
| 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() { |
| 99 |
return id_; |
| 100 |
} |
| 101 |
|
| 102 |
/** Sets the id of this Snapshot */ |
| 103 |
void setID(int id) { |
| 104 |
id_ = id; |
| 105 |
} |
| 106 |
|
| 107 |
int getSize() { |
| 108 |
return atomData.getSize() + rigidbodyData.getSize(); |
| 109 |
} |
| 110 |
|
| 111 |
/** Returns the number of atoms */ |
| 112 |
int getNumberOfAtoms() { |
| 113 |
return atomData.getSize(); |
| 114 |
} |
| 115 |
|
| 116 |
/** Returns the number of rigid bodies */ |
| 117 |
int getNumberOfRigidBodies() { |
| 118 |
return rigidbodyData.getSize(); |
| 119 |
} |
| 120 |
|
| 121 |
/** Returns the number of rigid bodies */ |
| 122 |
int getNumberOfCutoffGroups() { |
| 123 |
return cgData.getSize(); |
| 124 |
} |
| 125 |
|
| 126 |
/** Returns the H-Matrix */ |
| 127 |
Mat3x3d getHmat() { |
| 128 |
return hmat_; |
| 129 |
} |
| 130 |
|
| 131 |
/** Sets the H-Matrix */ |
| 132 |
void setHmat(const Mat3x3d& m); |
| 133 |
|
| 134 |
RealType getVolume() { |
| 135 |
if (hasVolume_){ |
| 136 |
return volume_; |
| 137 |
}else{ |
| 138 |
return hmat_.determinant(); |
| 139 |
} |
| 140 |
} |
| 141 |
|
| 142 |
void setVolume(RealType volume){ |
| 143 |
hasVolume_=true; |
| 144 |
volume_ = volume; |
| 145 |
} |
| 146 |
|
| 147 |
/** Returns the inverse H-Matrix */ |
| 148 |
Mat3x3d getInvHmat() { |
| 149 |
return invHmat_; |
| 150 |
} |
| 151 |
|
| 152 |
/** Wrapping the vector according to periodic boundary condition*/ |
| 153 |
void wrapVector(Vector3d& v); |
| 154 |
Vector3d getCOM(); |
| 155 |
Vector3d getCOMvel(); |
| 156 |
Vector3d getCOMw(); |
| 157 |
|
| 158 |
RealType getTime() { |
| 159 |
return currentTime_; |
| 160 |
} |
| 161 |
|
| 162 |
void increaseTime(RealType dt) { |
| 163 |
setTime(getTime() + dt); |
| 164 |
} |
| 165 |
|
| 166 |
void setTime(RealType time) { |
| 167 |
currentTime_ =time; |
| 168 |
//time at statData is redundant |
| 169 |
statData[Stats::TIME] = currentTime_; |
| 170 |
} |
| 171 |
|
| 172 |
RealType getChi() { |
| 173 |
return chi_; |
| 174 |
} |
| 175 |
|
| 176 |
void setChi(RealType chi) { |
| 177 |
chi_ = chi; |
| 178 |
} |
| 179 |
|
| 180 |
RealType getIntegralOfChiDt() { |
| 181 |
return integralOfChiDt_; |
| 182 |
} |
| 183 |
|
| 184 |
void setIntegralOfChiDt(RealType integralOfChiDt) { |
| 185 |
integralOfChiDt_ = integralOfChiDt; |
| 186 |
} |
| 187 |
|
| 188 |
|
| 189 |
void setOrthoTolerance(RealType orthoTolerance) { |
| 190 |
orthoTolerance_ = orthoTolerance; |
| 191 |
} |
| 192 |
|
| 193 |
Mat3x3d getEta() { |
| 194 |
return eta_; |
| 195 |
} |
| 196 |
|
| 197 |
void setEta(const Mat3x3d& eta) { |
| 198 |
eta_ = eta; |
| 199 |
} |
| 200 |
|
| 201 |
bool hasCOM() { |
| 202 |
return hasCOM_; |
| 203 |
} |
| 204 |
|
| 205 |
void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) { |
| 206 |
COM_ = COM; |
| 207 |
COMvel_ = COMvel; |
| 208 |
COMw_ = COMw; |
| 209 |
hasCOM_ = true; |
| 210 |
} |
| 211 |
|
| 212 |
Vector3d getAtomPosByIindex(int iIndex) { |
| 213 |
#ifdef IS_MPI |
| 214 |
return atomIData.position[iIndex]; |
| 215 |
#else |
| 216 |
return atomData.position[iIndex]; |
| 217 |
#endif |
| 218 |
} |
| 219 |
Vector3d getAtomPosByJindex(int jIndex) { |
| 220 |
#ifdef IS_MPI |
| 221 |
return atomJData.position[jIndex]; |
| 222 |
#else |
| 223 |
return atomData.position[jIndex]; |
| 224 |
#endif |
| 225 |
} |
| 226 |
|
| 227 |
Vector3d getCutoffGroupPosByIindex(int iIndex) { |
| 228 |
#ifdef IS_MPI |
| 229 |
return cgIData.position[iIndex]; |
| 230 |
#else |
| 231 |
return cgData.position[iIndex]; |
| 232 |
#endif |
| 233 |
} |
| 234 |
Vector3d getCutoffGroupPosByJindex(int jIndex) { |
| 235 |
#ifdef IS_MPI |
| 236 |
return cgJData.position[jIndex]; |
| 237 |
#else |
| 238 |
return cgData.position[jIndex]; |
| 239 |
#endif |
| 240 |
} |
| 241 |
|
| 242 |
DataStorage atomData; |
| 243 |
DataStorage rigidbodyData; |
| 244 |
DataStorage cgData; |
| 245 |
Stats statData; |
| 246 |
|
| 247 |
#ifdef IS_MPI |
| 248 |
DataStorage atomIData; |
| 249 |
DataStorage atomJData; |
| 250 |
DataStorage cgIData; |
| 251 |
DataStorage cgJData; |
| 252 |
#endif |
| 253 |
|
| 254 |
|
| 255 |
private: |
| 256 |
RealType currentTime_; |
| 257 |
|
| 258 |
Mat3x3d hmat_; |
| 259 |
Mat3x3d invHmat_; |
| 260 |
RealType orthoTolerance_; |
| 261 |
int orthoRhombic_; |
| 262 |
RealType volume_; |
| 263 |
|
| 264 |
RealType chi_; |
| 265 |
RealType integralOfChiDt_; |
| 266 |
Mat3x3d eta_; |
| 267 |
Vector3d COM_; |
| 268 |
Vector3d COMvel_; |
| 269 |
Vector3d COMw_; |
| 270 |
int id_; /**< identification number of the snapshot */ |
| 271 |
bool hasCOM_; |
| 272 |
bool hasVolume_; |
| 273 |
|
| 274 |
}; |
| 275 |
|
| 276 |
typedef DataStorage (Snapshot::*DataStoragePointer); |
| 277 |
} |
| 278 |
#endif //BRAINS_SNAPSHOT_HPP |
