| 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, 234107 (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.cpp | 
| 45 | * @author tlin | 
| 46 | * @date 11/11/2004 | 
| 47 | * @version 1.0 | 
| 48 | */ | 
| 49 |  | 
| 50 | #include "brains/Snapshot.hpp" | 
| 51 | #include "utils/NumericConstant.hpp" | 
| 52 | #include "utils/simError.h" | 
| 53 | #include "utils/Utility.hpp" | 
| 54 | #include <cstdio> | 
| 55 |  | 
| 56 | namespace OpenMD { | 
| 57 |  | 
| 58 | Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) : | 
| 59 | atomData(nAtoms), rigidbodyData(nRigidbodies), | 
| 60 | cgData(nCutoffGroups, DataStorage::dslPosition), | 
| 61 | orthoTolerance_(1e-6) { | 
| 62 |  | 
| 63 | frameData.id = -1; | 
| 64 | frameData.currentTime = 0; | 
| 65 | frameData.hmat = Mat3x3d(0.0); | 
| 66 | frameData.invHmat = Mat3x3d(0.0); | 
| 67 | frameData.orthoRhombic = false; | 
| 68 | frameData.bondPotential = 0.0; | 
| 69 | frameData.bendPotential = 0.0; | 
| 70 | frameData.torsionPotential = 0.0; | 
| 71 | frameData.inversionPotential = 0.0; | 
| 72 | frameData.lrPotentials = potVec(0.0); | 
| 73 | frameData.reciprocalPotential = 0.0; | 
| 74 | frameData.excludedPotentials = potVec(0.0); | 
| 75 | frameData.restraintPotential = 0.0; | 
| 76 | frameData.rawPotential = 0.0; | 
| 77 | frameData.xyArea = 0.0; | 
| 78 | frameData.volume = 0.0; | 
| 79 | frameData.thermostat = make_pair(0.0, 0.0); | 
| 80 | frameData.electronicThermostat = make_pair(0.0, 0.0); | 
| 81 | frameData.barostat = Mat3x3d(0.0); | 
| 82 | frameData.stressTensor = Mat3x3d(0.0); | 
| 83 | frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0); | 
| 84 |  | 
| 85 | clearDerivedProperties(); | 
| 86 | } | 
| 87 |  | 
| 88 | Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, | 
| 89 | int storageLayout) : | 
| 90 | atomData(nAtoms, storageLayout), | 
| 91 | rigidbodyData(nRigidbodies, storageLayout), | 
| 92 | cgData(nCutoffGroups, DataStorage::dslPosition), | 
| 93 | orthoTolerance_(1e-6) { | 
| 94 |  | 
| 95 | frameData.id = -1; | 
| 96 | frameData.currentTime = 0; | 
| 97 | frameData.hmat = Mat3x3d(0.0); | 
| 98 | frameData.invHmat = Mat3x3d(0.0); | 
| 99 | frameData.bBox = Mat3x3d(0.0); | 
| 100 | frameData.invBbox = Mat3x3d(0.0); | 
| 101 | frameData.orthoRhombic = false; | 
| 102 | frameData.bondPotential = 0.0; | 
| 103 | frameData.bendPotential = 0.0; | 
| 104 | frameData.torsionPotential = 0.0; | 
| 105 | frameData.inversionPotential = 0.0; | 
| 106 | frameData.lrPotentials = potVec(0.0); | 
| 107 | frameData.reciprocalPotential = 0.0; | 
| 108 | frameData.excludedPotentials = potVec(0.0); | 
| 109 | frameData.restraintPotential = 0.0; | 
| 110 | frameData.rawPotential = 0.0; | 
| 111 | frameData.xyArea = 0.0; | 
| 112 | frameData.volume = 0.0; | 
| 113 | frameData.thermostat = make_pair(0.0, 0.0); | 
| 114 | frameData.electronicThermostat = make_pair(0.0, 0.0); | 
| 115 | frameData.barostat = Mat3x3d(0.0); | 
| 116 | frameData.stressTensor = Mat3x3d(0.0); | 
| 117 | frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0); | 
| 118 |  | 
| 119 | clearDerivedProperties(); | 
| 120 | } | 
| 121 |  | 
| 122 | void Snapshot::clearDerivedProperties() { | 
| 123 | frameData.totalEnergy = 0.0; | 
| 124 | frameData.translationalKinetic = 0.0; | 
| 125 | frameData.rotationalKinetic = 0.0; | 
| 126 | frameData.kineticEnergy = 0.0; | 
| 127 | frameData.potentialEnergy = 0.0; | 
| 128 | frameData.shortRangePotential = 0.0; | 
| 129 | frameData.longRangePotential = 0.0; | 
| 130 | frameData.pressure = 0.0; | 
| 131 | frameData.temperature = 0.0; | 
| 132 | frameData.pressureTensor = Mat3x3d(0.0); | 
| 133 | frameData.systemDipole = Vector3d(0.0); | 
| 134 | frameData.systemQuadrupole = Mat3x3d(0.0); | 
| 135 | frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0); | 
| 136 | frameData.electronicTemperature = 0.0; | 
| 137 | frameData.COM = V3Zero; | 
| 138 | frameData.COMvel = V3Zero; | 
| 139 | frameData.COMw = V3Zero; | 
| 140 |  | 
| 141 | hasTotalEnergy = false; | 
| 142 | hasTranslationalKineticEnergy = false; | 
| 143 | hasRotationalKineticEnergy = false; | 
| 144 | hasKineticEnergy = false; | 
| 145 | hasShortRangePotential = false; | 
| 146 | hasLongRangePotential = false; | 
| 147 | hasPotentialEnergy = false; | 
| 148 | hasXYarea = false; | 
| 149 | hasVolume = false; | 
| 150 | hasPressure = false; | 
| 151 | hasTemperature = false; | 
| 152 | hasElectronicTemperature = false; | 
| 153 | hasCOM = false; | 
| 154 | hasCOMvel = false; | 
| 155 | hasCOMw = false; | 
| 156 | hasPressureTensor = false; | 
| 157 | hasSystemDipole = false; | 
| 158 | hasSystemQuadrupole = false; | 
| 159 | hasConvectiveHeatFlux = false; | 
| 160 | hasInertiaTensor = false; | 
| 161 | hasGyrationalVolume = false; | 
| 162 | hasHullVolume = false; | 
| 163 | hasConservedQuantity = false; | 
| 164 | hasBoundingBox = false; | 
| 165 | } | 
| 166 |  | 
| 167 | /** Returns the id of this Snapshot */ | 
| 168 | int Snapshot::getID() { | 
| 169 | return frameData.id; | 
| 170 | } | 
| 171 |  | 
| 172 | /** Sets the id of this Snapshot */ | 
| 173 | void Snapshot::setID(int id) { | 
| 174 | frameData.id = id; | 
| 175 | } | 
| 176 |  | 
| 177 | int Snapshot::getSize() { | 
| 178 | return atomData.getSize() + rigidbodyData.getSize(); | 
| 179 | } | 
| 180 |  | 
| 181 | /** Returns the number of atoms */ | 
| 182 | int Snapshot::getNumberOfAtoms() { | 
| 183 | return atomData.getSize(); | 
| 184 | } | 
| 185 |  | 
| 186 | /** Returns the number of rigid bodies */ | 
| 187 | int Snapshot::getNumberOfRigidBodies() { | 
| 188 | return rigidbodyData.getSize(); | 
| 189 | } | 
| 190 |  | 
| 191 | /** Returns the number of rigid bodies */ | 
| 192 | int Snapshot::getNumberOfCutoffGroups() { | 
| 193 | return cgData.getSize(); | 
| 194 | } | 
| 195 |  | 
| 196 | /** Returns the number of bytes in a FrameData structure */ | 
| 197 | int Snapshot::getFrameDataSize() { | 
| 198 | return sizeof(FrameData); | 
| 199 | } | 
| 200 |  | 
| 201 | /** Returns the H-Matrix */ | 
| 202 | Mat3x3d Snapshot::getHmat() { | 
| 203 | return frameData.hmat; | 
| 204 | } | 
| 205 |  | 
| 206 | /** Sets the H-Matrix */ | 
| 207 | void Snapshot::setHmat(const Mat3x3d& m) { | 
| 208 | hasVolume = false; | 
| 209 | frameData.hmat = m; | 
| 210 | frameData.invHmat = frameData.hmat.inverse(); | 
| 211 |  | 
| 212 | //determine whether the box is orthoTolerance or not | 
| 213 | bool oldOrthoRhombic = frameData.orthoRhombic; | 
| 214 |  | 
| 215 | RealType smallDiag = fabs(frameData.hmat(0, 0)); | 
| 216 | if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1)); | 
| 217 | if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2)); | 
| 218 | RealType tol = smallDiag * orthoTolerance_; | 
| 219 |  | 
| 220 | frameData.orthoRhombic = true; | 
| 221 |  | 
| 222 | for (int i = 0; i < 3; i++ ) { | 
| 223 | for (int j = 0 ; j < 3; j++) { | 
| 224 | if (i != j) { | 
| 225 | if (frameData.orthoRhombic) { | 
| 226 | if ( fabs(frameData.hmat(i, j)) >= tol) | 
| 227 | frameData.orthoRhombic = false; | 
| 228 | } | 
| 229 | } | 
| 230 | } | 
| 231 | } | 
| 232 |  | 
| 233 | if( oldOrthoRhombic != frameData.orthoRhombic){ | 
| 234 |  | 
| 235 | // It is finally time to suppress these warnings once and for | 
| 236 | // all.  They were annoying and not very informative. | 
| 237 |  | 
| 238 | // if( frameData.orthoRhombic ) { | 
| 239 | //   sprintf( painCave.errMsg, | 
| 240 | //         "OpenMD is switching from the default Non-Orthorhombic\n" | 
| 241 | //         "\tto the faster Orthorhombic periodic boundary computations.\n" | 
| 242 | //         "\tThis is usually a good thing, but if you want the\n" | 
| 243 | //         "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" | 
| 244 | //         "\tvariable ( currently set to %G ) smaller.\n", | 
| 245 | //         orthoTolerance_); | 
| 246 | //   painCave.severity = OPENMD_INFO; | 
| 247 | //   simError(); | 
| 248 | // } | 
| 249 | // else { | 
| 250 | //   sprintf( painCave.errMsg, | 
| 251 | //         "OpenMD is switching from the faster Orthorhombic to the more\n" | 
| 252 | //         "\tflexible Non-Orthorhombic periodic boundary computations.\n" | 
| 253 | //         "\tThis is usually because the box has deformed under\n" | 
| 254 | //         "\tNPTf integration. If you want to live on the edge with\n" | 
| 255 | //         "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" | 
| 256 | //         "\tvariable ( currently set to %G ) larger.\n", | 
| 257 | //         orthoTolerance_); | 
| 258 | //   painCave.severity = OPENMD_WARNING; | 
| 259 | //   simError(); | 
| 260 | // } | 
| 261 | } | 
| 262 | } | 
| 263 |  | 
| 264 | /** Returns the inverse H-Matrix */ | 
| 265 | Mat3x3d Snapshot::getInvHmat() { | 
| 266 | return frameData.invHmat; | 
| 267 | } | 
| 268 |  | 
| 269 | /** Returns the Bounding Box */ | 
| 270 | Mat3x3d Snapshot::getBoundingBox() { | 
| 271 | return frameData.bBox; | 
| 272 | } | 
| 273 |  | 
| 274 | /** Sets the Bounding Box */ | 
| 275 | void Snapshot::setBoundingBox(const Mat3x3d& m) { | 
| 276 | frameData.bBox = m; | 
| 277 | frameData.invBbox = frameData.bBox.inverse(); | 
| 278 | hasBoundingBox = true; | 
| 279 | } | 
| 280 |  | 
| 281 | /** Returns the inverse Bounding Box */ | 
| 282 | Mat3x3d Snapshot::getInvBoundingBox() { | 
| 283 | return frameData.invBbox; | 
| 284 | } | 
| 285 |  | 
| 286 | RealType Snapshot::getXYarea() { | 
| 287 | if (!hasXYarea) { | 
| 288 | Vector3d x = frameData.hmat.getColumn(0); | 
| 289 | Vector3d y = frameData.hmat.getColumn(1); | 
| 290 | frameData.xyArea = cross(x,y).length(); | 
| 291 | hasXYarea = true; | 
| 292 | } | 
| 293 | return frameData.xyArea; | 
| 294 | } | 
| 295 |  | 
| 296 | RealType Snapshot::getVolume() { | 
| 297 | if (!hasVolume) { | 
| 298 | frameData.volume = frameData.hmat.determinant(); | 
| 299 | hasVolume = true; | 
| 300 | } | 
| 301 | return frameData.volume; | 
| 302 | } | 
| 303 |  | 
| 304 | void Snapshot::setVolume(RealType vol) { | 
| 305 | hasVolume = true; | 
| 306 | frameData.volume = vol; | 
| 307 | } | 
| 308 |  | 
| 309 |  | 
| 310 | /** Wrap a vector according to periodic boundary conditions */ | 
| 311 | void Snapshot::wrapVector(Vector3d& pos) { | 
| 312 |  | 
| 313 | if( !frameData.orthoRhombic ) { | 
| 314 | Vector3d scaled = frameData.invHmat * pos; | 
| 315 | for (int i = 0; i < 3; i++) { | 
| 316 | scaled[i] -= roundMe( scaled[i] ); | 
| 317 | } | 
| 318 | // calc the wrapped real coordinates from the wrapped scaled coordinates | 
| 319 | pos = frameData.hmat * scaled; | 
| 320 | } else { | 
| 321 | RealType scaled; | 
| 322 | for (int i=0; i<3; i++) { | 
| 323 | scaled = pos[i] * frameData.invHmat(i,i); | 
| 324 | scaled -= roundMe( scaled ); | 
| 325 | pos[i] = scaled * frameData.hmat(i,i); | 
| 326 | } | 
| 327 | } | 
| 328 | } | 
| 329 |  | 
| 330 | /** Scaling a vector to multiples of the periodic box */ | 
| 331 | inline Vector3d Snapshot::scaleVector(Vector3d& pos) { | 
| 332 |  | 
| 333 | Vector3d scaled; | 
| 334 |  | 
| 335 | if( !frameData.orthoRhombic ) | 
| 336 | scaled = frameData.invHmat * pos; | 
| 337 | else { | 
| 338 | // calc the scaled coordinates. | 
| 339 | for (int i=0; i<3; i++) | 
| 340 | scaled[i] = pos[i] * frameData.invHmat(i, i); | 
| 341 | } | 
| 342 |  | 
| 343 | return scaled; | 
| 344 | } | 
| 345 |  | 
| 346 | void Snapshot::setCOM(const Vector3d& com) { | 
| 347 | frameData.COM = com; | 
| 348 | hasCOM = true; | 
| 349 | } | 
| 350 |  | 
| 351 | void Snapshot::setCOMvel(const Vector3d& comVel) { | 
| 352 | frameData.COMvel = comVel; | 
| 353 | hasCOMvel = true; | 
| 354 | } | 
| 355 |  | 
| 356 | void Snapshot::setCOMw(const Vector3d& comw) { | 
| 357 | frameData.COMw = comw; | 
| 358 | hasCOMw = true; | 
| 359 | } | 
| 360 |  | 
| 361 | Vector3d Snapshot::getCOM() { | 
| 362 | return frameData.COM; | 
| 363 | } | 
| 364 |  | 
| 365 | Vector3d Snapshot::getCOMvel() { | 
| 366 | return frameData.COMvel; | 
| 367 | } | 
| 368 |  | 
| 369 | Vector3d Snapshot::getCOMw() { | 
| 370 | return frameData.COMw; | 
| 371 | } | 
| 372 |  | 
| 373 | RealType Snapshot::getTime() { | 
| 374 | return frameData.currentTime; | 
| 375 | } | 
| 376 |  | 
| 377 | void Snapshot::increaseTime(RealType dt) { | 
| 378 | setTime(getTime() + dt); | 
| 379 | } | 
| 380 |  | 
| 381 | void Snapshot::setTime(RealType time) { | 
| 382 | frameData.currentTime = time; | 
| 383 | } | 
| 384 |  | 
| 385 | void Snapshot::setBondPotential(RealType bp) { | 
| 386 | frameData.bondPotential = bp; | 
| 387 | } | 
| 388 |  | 
| 389 | void Snapshot::setBendPotential(RealType bp) { | 
| 390 | frameData.bendPotential = bp; | 
| 391 | } | 
| 392 |  | 
| 393 | void Snapshot::setTorsionPotential(RealType tp) { | 
| 394 | frameData.torsionPotential = tp; | 
| 395 | } | 
| 396 |  | 
| 397 | void Snapshot::setInversionPotential(RealType ip) { | 
| 398 | frameData.inversionPotential = ip; | 
| 399 | } | 
| 400 |  | 
| 401 |  | 
| 402 | RealType Snapshot::getBondPotential() { | 
| 403 | return frameData.bondPotential; | 
| 404 | } | 
| 405 | RealType Snapshot::getBendPotential() { | 
| 406 | return frameData.bendPotential; | 
| 407 | } | 
| 408 | RealType Snapshot::getTorsionPotential() { | 
| 409 | return frameData.torsionPotential; | 
| 410 | } | 
| 411 | RealType Snapshot::getInversionPotential() { | 
| 412 | return frameData.inversionPotential; | 
| 413 | } | 
| 414 |  | 
| 415 | RealType Snapshot::getShortRangePotential() { | 
| 416 | if (!hasShortRangePotential) { | 
| 417 | frameData.shortRangePotential = frameData.bondPotential; | 
| 418 | frameData.shortRangePotential += frameData.bendPotential; | 
| 419 | frameData.shortRangePotential += frameData.torsionPotential; | 
| 420 | frameData.shortRangePotential += frameData.inversionPotential; | 
| 421 | hasShortRangePotential = true; | 
| 422 | } | 
| 423 | return frameData.shortRangePotential; | 
| 424 | } | 
| 425 |  | 
| 426 | void Snapshot::setReciprocalPotential(RealType rp){ | 
| 427 | frameData.reciprocalPotential = rp; | 
| 428 | } | 
| 429 |  | 
| 430 | RealType Snapshot::getReciprocalPotential() { | 
| 431 | return frameData.reciprocalPotential; | 
| 432 | } | 
| 433 |  | 
| 434 | void Snapshot::setLongRangePotential(potVec lrPot) { | 
| 435 | frameData.lrPotentials = lrPot; | 
| 436 | } | 
| 437 |  | 
| 438 | RealType Snapshot::getLongRangePotential() { | 
| 439 | if (!hasLongRangePotential) { | 
| 440 | for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { | 
| 441 | frameData.longRangePotential += frameData.lrPotentials[i]; | 
| 442 | } | 
| 443 | frameData.longRangePotential += frameData.reciprocalPotential; | 
| 444 | hasLongRangePotential = true; | 
| 445 | } | 
| 446 | return frameData.longRangePotential; | 
| 447 | } | 
| 448 |  | 
| 449 | potVec Snapshot::getLongRangePotentials() { | 
| 450 | return frameData.lrPotentials; | 
| 451 | } | 
| 452 |  | 
| 453 | RealType Snapshot::getPotentialEnergy() { | 
| 454 | if (!hasPotentialEnergy) { | 
| 455 | frameData.potentialEnergy = this->getLongRangePotential(); | 
| 456 | frameData.potentialEnergy += this->getShortRangePotential(); | 
| 457 | hasPotentialEnergy = true; | 
| 458 | } | 
| 459 | return frameData.potentialEnergy; | 
| 460 | } | 
| 461 |  | 
| 462 | void Snapshot::setExcludedPotentials(potVec exPot) { | 
| 463 | frameData.excludedPotentials = exPot; | 
| 464 | } | 
| 465 |  | 
| 466 | potVec Snapshot::getExcludedPotentials() { | 
| 467 | return frameData.excludedPotentials; | 
| 468 | } | 
| 469 |  | 
| 470 | void Snapshot::setRestraintPotential(RealType rp) { | 
| 471 | frameData.restraintPotential = rp; | 
| 472 | } | 
| 473 |  | 
| 474 | RealType Snapshot::getRestraintPotential() { | 
| 475 | return frameData.restraintPotential; | 
| 476 | } | 
| 477 |  | 
| 478 | void Snapshot::setRawPotential(RealType rp) { | 
| 479 | frameData.rawPotential = rp; | 
| 480 | } | 
| 481 |  | 
| 482 | RealType Snapshot::getRawPotential() { | 
| 483 | return frameData.rawPotential; | 
| 484 | } | 
| 485 |  | 
| 486 | RealType Snapshot::getTranslationalKineticEnergy() { | 
| 487 | return frameData.translationalKinetic; | 
| 488 | } | 
| 489 |  | 
| 490 | RealType Snapshot::getRotationalKineticEnergy() { | 
| 491 | return frameData.rotationalKinetic; | 
| 492 | } | 
| 493 |  | 
| 494 | RealType Snapshot::getKineticEnergy() { | 
| 495 | return frameData.kineticEnergy; | 
| 496 | } | 
| 497 |  | 
| 498 | void Snapshot::setTranslationalKineticEnergy(RealType tke) { | 
| 499 | hasTranslationalKineticEnergy = true; | 
| 500 | frameData.translationalKinetic = tke; | 
| 501 | } | 
| 502 |  | 
| 503 | void Snapshot::setRotationalKineticEnergy(RealType rke) { | 
| 504 | hasRotationalKineticEnergy = true; | 
| 505 | frameData.rotationalKinetic = rke; | 
| 506 | } | 
| 507 |  | 
| 508 | void Snapshot::setKineticEnergy(RealType ke) { | 
| 509 | hasKineticEnergy = true; | 
| 510 | frameData.kineticEnergy = ke; | 
| 511 | } | 
| 512 |  | 
| 513 | RealType Snapshot::getTotalEnergy() { | 
| 514 | return frameData.totalEnergy; | 
| 515 | } | 
| 516 |  | 
| 517 | void Snapshot::setTotalEnergy(RealType te) { | 
| 518 | hasTotalEnergy = true; | 
| 519 | frameData.totalEnergy = te; | 
| 520 | } | 
| 521 |  | 
| 522 | RealType Snapshot::getConservedQuantity() { | 
| 523 | return frameData.conservedQuantity; | 
| 524 | } | 
| 525 |  | 
| 526 | void Snapshot::setConservedQuantity(RealType cq) { | 
| 527 | hasConservedQuantity = true; | 
| 528 | frameData.conservedQuantity = cq; | 
| 529 | } | 
| 530 |  | 
| 531 | RealType Snapshot::getTemperature() { | 
| 532 | return frameData.temperature; | 
| 533 | } | 
| 534 |  | 
| 535 | void Snapshot::setTemperature(RealType temp) { | 
| 536 | hasTemperature = true; | 
| 537 | frameData.temperature = temp; | 
| 538 | } | 
| 539 |  | 
| 540 | RealType Snapshot::getElectronicTemperature() { | 
| 541 | return frameData.electronicTemperature; | 
| 542 | } | 
| 543 |  | 
| 544 | void Snapshot::setElectronicTemperature(RealType eTemp) { | 
| 545 | hasElectronicTemperature = true; | 
| 546 | frameData.electronicTemperature = eTemp; | 
| 547 | } | 
| 548 |  | 
| 549 | RealType Snapshot::getPressure() { | 
| 550 | return frameData.pressure; | 
| 551 | } | 
| 552 |  | 
| 553 | void Snapshot::setPressure(RealType pressure) { | 
| 554 | hasPressure = true; | 
| 555 | frameData.pressure = pressure; | 
| 556 | } | 
| 557 |  | 
| 558 | Mat3x3d Snapshot::getPressureTensor() { | 
| 559 | return frameData.pressureTensor; | 
| 560 | } | 
| 561 |  | 
| 562 |  | 
| 563 | void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) { | 
| 564 | hasPressureTensor = true; | 
| 565 | frameData.pressureTensor = pressureTensor; | 
| 566 | } | 
| 567 |  | 
| 568 | void Snapshot::setStressTensor(const Mat3x3d& stressTensor) { | 
| 569 | frameData.stressTensor = stressTensor; | 
| 570 | } | 
| 571 |  | 
| 572 | Mat3x3d  Snapshot::getStressTensor() { | 
| 573 | return frameData.stressTensor; | 
| 574 | } | 
| 575 |  | 
| 576 | void Snapshot::setConductiveHeatFlux(const Vector3d& chf) { | 
| 577 | frameData.conductiveHeatFlux = chf; | 
| 578 | } | 
| 579 |  | 
| 580 | Vector3d Snapshot::getConductiveHeatFlux() { | 
| 581 | return frameData.conductiveHeatFlux; | 
| 582 | } | 
| 583 |  | 
| 584 | Vector3d Snapshot::getConvectiveHeatFlux() { | 
| 585 | return frameData.convectiveHeatFlux; | 
| 586 | } | 
| 587 |  | 
| 588 | void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) { | 
| 589 | hasConvectiveHeatFlux = true; | 
| 590 | frameData.convectiveHeatFlux = chf; | 
| 591 | } | 
| 592 |  | 
| 593 | Vector3d Snapshot::getHeatFlux() { | 
| 594 | // BE CAREFUL WITH UNITS | 
| 595 | return getConductiveHeatFlux() + getConvectiveHeatFlux(); | 
| 596 | } | 
| 597 |  | 
| 598 | Vector3d Snapshot::getSystemDipole() { | 
| 599 | return frameData.systemDipole; | 
| 600 | } | 
| 601 |  | 
| 602 | void Snapshot::setSystemDipole(const Vector3d& bd) { | 
| 603 | hasSystemDipole = true; | 
| 604 | frameData.systemDipole = bd; | 
| 605 | } | 
| 606 |  | 
| 607 | Mat3x3d Snapshot::getSystemQuadrupole() { | 
| 608 | return frameData.systemQuadrupole; | 
| 609 | } | 
| 610 |  | 
| 611 | void Snapshot::setSystemQuadrupole(const Mat3x3d& bq) { | 
| 612 | hasSystemQuadrupole = true; | 
| 613 | frameData.systemQuadrupole = bq; | 
| 614 | } | 
| 615 |  | 
| 616 | void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) { | 
| 617 | frameData.thermostat = thermostat; | 
| 618 | } | 
| 619 |  | 
| 620 | pair<RealType, RealType> Snapshot::getThermostat() { | 
| 621 | return frameData.thermostat; | 
| 622 | } | 
| 623 |  | 
| 624 | void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) { | 
| 625 | frameData.electronicThermostat = eTherm; | 
| 626 | } | 
| 627 |  | 
| 628 | pair<RealType, RealType> Snapshot::getElectronicThermostat() { | 
| 629 | return frameData.electronicThermostat; | 
| 630 | } | 
| 631 |  | 
| 632 | void Snapshot::setBarostat(const Mat3x3d& barostat) { | 
| 633 | frameData.barostat = barostat; | 
| 634 | } | 
| 635 |  | 
| 636 | Mat3x3d Snapshot::getBarostat() { | 
| 637 | return frameData.barostat; | 
| 638 | } | 
| 639 |  | 
| 640 | void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) { | 
| 641 | frameData.inertiaTensor = inertiaTensor; | 
| 642 | hasInertiaTensor = true; | 
| 643 | } | 
| 644 |  | 
| 645 | Mat3x3d Snapshot::getInertiaTensor() { | 
| 646 | return frameData.inertiaTensor; | 
| 647 | } | 
| 648 |  | 
| 649 | void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) { | 
| 650 | frameData.gyrationalVolume = gyrationalVolume; | 
| 651 | hasGyrationalVolume = true; | 
| 652 | } | 
| 653 |  | 
| 654 | RealType Snapshot::getGyrationalVolume() { | 
| 655 | return frameData.gyrationalVolume; | 
| 656 | } | 
| 657 |  | 
| 658 | void Snapshot::setHullVolume(const RealType hullVolume) { | 
| 659 | frameData.hullVolume = hullVolume; | 
| 660 | hasHullVolume = true; | 
| 661 | } | 
| 662 |  | 
| 663 | RealType Snapshot::getHullVolume() { | 
| 664 | return frameData.hullVolume; | 
| 665 | } | 
| 666 |  | 
| 667 | void Snapshot::setOrthoTolerance(RealType ot) { | 
| 668 | orthoTolerance_ = ot; | 
| 669 | } | 
| 670 | } |