| 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). | 
| 39 | > | * [4]  Vardeman & Gezelter, in progress (2009). | 
| 40 |  | */ | 
| 41 |  |  | 
| 42 |  | #include <cmath> | 
| 43 |  | #include "integrators/RNEMD.hpp" | 
| 44 |  | #include "math/Vector3.hpp" | 
| 45 | + | #include "math/Vector.hpp" | 
| 46 |  | #include "math/SquareMatrix3.hpp" | 
| 47 |  | #include "math/Polynomial.hpp" | 
| 48 |  | #include "primitives/Molecule.hpp" | 
| 53 |  | #ifndef IS_MPI | 
| 54 |  | #include "math/SeqRandNumGen.hpp" | 
| 55 |  | #else | 
| 56 | – | #include <mpi.h> | 
| 56 |  | #include "math/ParallelRandNumGen.hpp" | 
| 57 |  | #endif | 
| 58 |  |  | 
| 72 |  |  | 
| 73 |  | stringToEnumMap_["KineticSwap"] = rnemdKineticSwap; | 
| 74 |  | stringToEnumMap_["KineticScale"] = rnemdKineticScale; | 
| 75 | + | stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM; | 
| 76 | + | stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM; | 
| 77 |  | stringToEnumMap_["PxScale"] = rnemdPxScale; | 
| 78 |  | stringToEnumMap_["PyScale"] = rnemdPyScale; | 
| 79 |  | stringToEnumMap_["PzScale"] = rnemdPzScale; | 
| 80 |  | stringToEnumMap_["Px"] = rnemdPx; | 
| 81 |  | stringToEnumMap_["Py"] = rnemdPy; | 
| 82 |  | stringToEnumMap_["Pz"] = rnemdPz; | 
| 83 | + | stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV; | 
| 84 | + | stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM; | 
| 85 |  | stringToEnumMap_["Unknown"] = rnemdUnknown; | 
| 86 |  |  | 
| 87 |  | rnemdObjectSelection_ = simParams->getRNEMD_objectSelection(); | 
| 125 |  | simError(); | 
| 126 |  | } | 
| 127 |  |  | 
| 128 | + | outputTemp_ = false; | 
| 129 | + | if (simParams->haveRNEMD_outputTemperature()) { | 
| 130 | + | outputTemp_ = simParams->getRNEMD_outputTemperature(); | 
| 131 | + | } else if ((rnemdType_ == rnemdKineticSwap) || | 
| 132 | + | (rnemdType_ == rnemdKineticScale) || | 
| 133 | + | (rnemdType_ == rnemdKineticScaleVAM) || | 
| 134 | + | (rnemdType_ == rnemdKineticScaleAM)) { | 
| 135 | + | outputTemp_ = true; | 
| 136 | + | } | 
| 137 | + | outputVx_ = false; | 
| 138 | + | if (simParams->haveRNEMD_outputVx()) { | 
| 139 | + | outputVx_ = simParams->getRNEMD_outputVx(); | 
| 140 | + | } else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) { | 
| 141 | + | outputVx_ = true; | 
| 142 | + | } | 
| 143 | + | outputVy_ = false; | 
| 144 | + | if (simParams->haveRNEMD_outputVy()) { | 
| 145 | + | outputVy_ = simParams->getRNEMD_outputVy(); | 
| 146 | + | } else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) { | 
| 147 | + | outputVy_ = true; | 
| 148 | + | } | 
| 149 |  | output3DTemp_ = false; | 
| 150 | < | if (simParams->haveRNEMD_outputDimensionalTemperature()) { | 
| 151 | < | output3DTemp_ = simParams->getRNEMD_outputDimensionalTemperature(); | 
| 150 | > | if (simParams->haveRNEMD_outputXyzTemperature()) { | 
| 151 | > | output3DTemp_ = simParams->getRNEMD_outputXyzTemperature(); | 
| 152 |  | } | 
| 153 | + | outputRotTemp_ = false; | 
| 154 | + | if (simParams->haveRNEMD_outputRotTemperature()) { | 
| 155 | + | outputRotTemp_ = simParams->getRNEMD_outputRotTemperature(); | 
| 156 | + | } | 
| 157 |  |  | 
| 158 |  | #ifdef IS_MPI | 
| 159 |  | if (worldRank == 0) { | 
| 160 |  | #endif | 
| 161 |  |  | 
| 162 | + | //may have rnemdWriter separately | 
| 163 |  | string rnemdFileName; | 
| 164 | < | switch(rnemdType_) { | 
| 165 | < | case rnemdKineticSwap : | 
| 137 | < | case rnemdKineticScale : | 
| 164 | > |  | 
| 165 | > | if (outputTemp_) { | 
| 166 |  | rnemdFileName = "temperature.log"; | 
| 167 | < | break; | 
| 140 | < | case rnemdPx : | 
| 141 | < | case rnemdPxScale : | 
| 142 | < | case rnemdPy : | 
| 143 | < | case rnemdPyScale : | 
| 144 | < | rnemdFileName = "momemtum.log"; | 
| 145 | < | break; | 
| 146 | < | case rnemdPz : | 
| 147 | < | case rnemdPzScale : | 
| 148 | < | case rnemdUnknown : | 
| 149 | < | default : | 
| 150 | < | rnemdFileName = "rnemd.log"; | 
| 151 | < | break; | 
| 167 | > | tempLog_.open(rnemdFileName.c_str()); | 
| 168 |  | } | 
| 169 | < | rnemdLog_.open(rnemdFileName.c_str()); | 
| 169 | > | if (outputVx_) { | 
| 170 | > | rnemdFileName = "velocityX.log"; | 
| 171 | > | vxzLog_.open(rnemdFileName.c_str()); | 
| 172 | > | } | 
| 173 | > | if (outputVy_) { | 
| 174 | > | rnemdFileName = "velocityY.log"; | 
| 175 | > | vyzLog_.open(rnemdFileName.c_str()); | 
| 176 | > | } | 
| 177 |  |  | 
| 155 | – | string xTempFileName; | 
| 156 | – | string yTempFileName; | 
| 157 | – | string zTempFileName; | 
| 178 |  | if (output3DTemp_) { | 
| 179 | < | xTempFileName = "temperatureX.log"; | 
| 180 | < | yTempFileName = "temperatureY.log"; | 
| 181 | < | zTempFileName = "temperatureZ.log"; | 
| 182 | < | xTempLog_.open(xTempFileName.c_str()); | 
| 183 | < | yTempLog_.open(yTempFileName.c_str()); | 
| 184 | < | zTempLog_.open(zTempFileName.c_str()); | 
| 179 | > | rnemdFileName = "temperatureX.log"; | 
| 180 | > | xTempLog_.open(rnemdFileName.c_str()); | 
| 181 | > | rnemdFileName = "temperatureY.log"; | 
| 182 | > | yTempLog_.open(rnemdFileName.c_str()); | 
| 183 | > | rnemdFileName = "temperatureZ.log"; | 
| 184 | > | zTempLog_.open(rnemdFileName.c_str()); | 
| 185 |  | } | 
| 186 | + | if (outputRotTemp_) { | 
| 187 | + | rnemdFileName = "temperatureR.log"; | 
| 188 | + | rotTempLog_.open(rnemdFileName.c_str()); | 
| 189 | + | } | 
| 190 |  |  | 
| 191 |  | #ifdef IS_MPI | 
| 192 |  | } | 
| 204 |  | } else { | 
| 205 |  | zShift_ = 0.0; | 
| 206 |  | } | 
| 207 | < | //cerr << "we have zShift_ = " << zShift_ << "\n"; | 
| 208 | < | //shift slabs by half slab width, might be useful in heterogeneous systems | 
| 209 | < | //set to 0.0 if not using it; can NOT be used in status output yet | 
| 207 | > | //cerr << "I shift slabs by " << zShift_ << " Lz\n"; | 
| 208 | > | //shift slabs by half slab width, maybe useful in heterogeneous systems | 
| 209 | > | //set to 0.0 if not using it; N/A in status output yet | 
| 210 |  | if (simParams->haveRNEMD_logWidth()) { | 
| 211 |  | set_RNEMD_logWidth(simParams->getRNEMD_logWidth()); | 
| 212 | < | /*arbitary rnemdLogWidth_ no checking | 
| 213 | < | if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) { | 
| 212 | > | /*arbitary rnemdLogWidth_, no checking; | 
| 213 | > | if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) { | 
| 214 |  | cerr << "WARNING! RNEMD_logWidth has abnormal value!\n"; | 
| 215 |  | cerr << "Automaically set back to default.\n"; | 
| 216 |  | rnemdLogWidth_ = nBins_; | 
| 217 | < | }*/ | 
| 217 | > | }*/ | 
| 218 |  | } else { | 
| 219 |  | set_RNEMD_logWidth(nBins_); | 
| 220 |  | } | 
| 221 | < | valueHist_.resize(rnemdLogWidth_, 0.0); | 
| 222 | < | valueCount_.resize(rnemdLogWidth_, 0); | 
| 221 | > | tempHist_.resize(rnemdLogWidth_, 0.0); | 
| 222 | > | tempCount_.resize(rnemdLogWidth_, 0); | 
| 223 | > | pxzHist_.resize(rnemdLogWidth_, 0.0); | 
| 224 | > | //vxzCount_.resize(rnemdLogWidth_, 0); | 
| 225 | > | pyzHist_.resize(rnemdLogWidth_, 0.0); | 
| 226 | > | //vyzCount_.resize(rnemdLogWidth_, 0); | 
| 227 | > |  | 
| 228 | > | mHist_.resize(rnemdLogWidth_, 0.0); | 
| 229 |  | xTempHist_.resize(rnemdLogWidth_, 0.0); | 
| 230 |  | yTempHist_.resize(rnemdLogWidth_, 0.0); | 
| 231 |  | zTempHist_.resize(rnemdLogWidth_, 0.0); | 
| 232 |  | xyzTempCount_.resize(rnemdLogWidth_, 0); | 
| 233 | + | rotTempHist_.resize(rnemdLogWidth_, 0.0); | 
| 234 | + | rotTempCount_.resize(rnemdLogWidth_, 0); | 
| 235 |  |  | 
| 236 |  | set_RNEMD_exchange_total(0.0); | 
| 237 |  | if (simParams->haveRNEMD_targetFlux()) { | 
| 239 |  | } else { | 
| 240 |  | set_RNEMD_target_flux(0.0); | 
| 241 |  | } | 
| 242 | + | if (simParams->haveRNEMD_targetJzKE()) { | 
| 243 | + | set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE()); | 
| 244 | + | } else { | 
| 245 | + | set_RNEMD_target_JzKE(0.0); | 
| 246 | + | } | 
| 247 | + | if (simParams->haveRNEMD_targetJzpx()) { | 
| 248 | + | set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx()); | 
| 249 | + | } else { | 
| 250 | + | set_RNEMD_target_jzpx(0.0); | 
| 251 | + | } | 
| 252 | + | jzp_.x() = targetJzpx_; | 
| 253 | + | njzp_.x() = -targetJzpx_; | 
| 254 | + | if (simParams->haveRNEMD_targetJzpy()) { | 
| 255 | + | set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy()); | 
| 256 | + | } else { | 
| 257 | + | set_RNEMD_target_jzpy(0.0); | 
| 258 | + | } | 
| 259 | + | jzp_.y() = targetJzpy_; | 
| 260 | + | njzp_.y() = -targetJzpy_; | 
| 261 | + | if (simParams->haveRNEMD_targetJzpz()) { | 
| 262 | + | set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz()); | 
| 263 | + | } else { | 
| 264 | + | set_RNEMD_target_jzpz(0.0); | 
| 265 | + | } | 
| 266 | + | jzp_.z() = targetJzpz_; | 
| 267 | + | njzp_.z() = -targetJzpz_; | 
| 268 |  |  | 
| 269 |  | #ifndef IS_MPI | 
| 270 |  | if (simParams->haveSeed()) { | 
| 297 |  | painCave.severity = OPENMD_INFO; | 
| 298 |  | simError(); | 
| 299 |  |  | 
| 300 | < | rnemdLog_.close(); | 
| 301 | < | if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || rnemdType_ == rnemdPyScale) { | 
| 300 | > | if (outputTemp_) tempLog_.close(); | 
| 301 | > | if (outputVx_)   vxzLog_.close(); | 
| 302 | > | if (outputVy_)   vyzLog_.close(); | 
| 303 | > |  | 
| 304 | > | if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || | 
| 305 | > | rnemdType_ == rnemdPyScale) { | 
| 306 |  | sprintf(painCave.errMsg, | 
| 307 |  | "RNEMD: total root-checking warnings: %d\n", | 
| 308 |  | failRootCount_); | 
| 315 |  | yTempLog_.close(); | 
| 316 |  | zTempLog_.close(); | 
| 317 |  | } | 
| 318 | + | if (outputRotTemp_) rotTempLog_.close(); | 
| 319 | + |  | 
| 320 |  | #ifdef IS_MPI | 
| 321 |  | } | 
| 322 |  | #endif | 
| 369 |  | switch(rnemdType_) { | 
| 370 |  | case rnemdKineticSwap : | 
| 371 |  |  | 
| 372 | < | value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + | 
| 373 | < | vel[2]*vel[2]); | 
| 374 | < | /* | 
| 311 | < | if (sd->isDirectional()) { | 
| 372 | > | value = mass * vel.lengthSquare(); | 
| 373 | > |  | 
| 374 | > | if (sd->isDirectional()) { | 
| 375 |  | Vector3d angMom = sd->getJ(); | 
| 376 |  | Mat3x3d I = sd->getI(); | 
| 377 |  |  | 
| 378 |  | if (sd->isLinear()) { | 
| 379 | < | int i = sd->linearAxis(); | 
| 380 | < | int j = (i + 1) % 3; | 
| 381 | < | int k = (i + 2) % 3; | 
| 382 | < | value += angMom[j] * angMom[j] / I(j, j) + | 
| 383 | < | angMom[k] * angMom[k] / I(k, k); | 
| 384 | < | } else { | 
| 385 | < | value += angMom[0]*angMom[0]/I(0, 0) | 
| 386 | < | + angMom[1]*angMom[1]/I(1, 1) | 
| 387 | < | + angMom[2]*angMom[2]/I(2, 2); | 
| 379 | > | int i = sd->linearAxis(); | 
| 380 | > | int j = (i + 1) % 3; | 
| 381 | > | int k = (i + 2) % 3; | 
| 382 | > | value += angMom[j] * angMom[j] / I(j, j) + | 
| 383 | > | angMom[k] * angMom[k] / I(k, k); | 
| 384 | > | } else { | 
| 385 | > | value += angMom[0]*angMom[0]/I(0, 0) | 
| 386 | > | + angMom[1]*angMom[1]/I(1, 1) | 
| 387 | > | + angMom[2]*angMom[2]/I(2, 2); | 
| 388 |  | } | 
| 389 | < | } no exchange of angular momenta | 
| 390 | < | */ | 
| 389 | > | } //angular momenta exchange enabled | 
| 390 | > | //energyConvert temporarily disabled | 
| 391 |  | //make exchangeSum_ comparable between swap & scale | 
| 329 | – | //temporarily without using energyConvert | 
| 392 |  | //value = value * 0.5 / PhysicalConstants::energyConvert; | 
| 393 |  | value *= 0.5; | 
| 394 |  | break; | 
| 444 |  | MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR); | 
| 445 |  | // Even if we didn't find a maximum, did someone else? | 
| 446 |  | MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR); | 
| 447 | < | struct { | 
| 448 | < | RealType val; | 
| 449 | < | int rank; | 
| 450 | < | } max_vals, min_vals; | 
| 447 | > | #endif | 
| 448 | > |  | 
| 449 | > | if (max_found && min_found) { | 
| 450 | > |  | 
| 451 | > | #ifdef IS_MPI | 
| 452 | > | struct { | 
| 453 | > | RealType val; | 
| 454 | > | int rank; | 
| 455 | > | } max_vals, min_vals; | 
| 456 |  |  | 
| 457 | < | if (min_found) { | 
| 391 | < | if (my_min_found) | 
| 457 | > | if (my_min_found) { | 
| 458 |  | min_vals.val = min_val; | 
| 459 | < | else | 
| 459 | > | } else { | 
| 460 |  | min_vals.val = HONKING_LARGE_VALUE; | 
| 461 | < |  | 
| 461 | > | } | 
| 462 |  | min_vals.rank = worldRank; | 
| 463 |  |  | 
| 464 |  | // Who had the minimum? | 
| 465 |  | MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals, | 
| 466 |  | 1, MPI::REALTYPE_INT, MPI::MINLOC); | 
| 467 |  | min_val = min_vals.val; | 
| 402 | – | } | 
| 468 |  |  | 
| 469 | < | if (max_found) { | 
| 405 | < | if (my_max_found) | 
| 469 | > | if (my_max_found) { | 
| 470 |  | max_vals.val = max_val; | 
| 471 | < | else | 
| 471 | > | } else { | 
| 472 |  | max_vals.val = -HONKING_LARGE_VALUE; | 
| 473 | < |  | 
| 473 | > | } | 
| 474 |  | max_vals.rank = worldRank; | 
| 475 |  |  | 
| 476 |  | // Who had the maximum? | 
| 477 |  | MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals, | 
| 478 |  | 1, MPI::REALTYPE_INT, MPI::MAXLOC); | 
| 479 |  | max_val = max_vals.val; | 
| 416 | – | } | 
| 480 |  | #endif | 
| 481 | < |  | 
| 419 | < | if (max_found && min_found) { | 
| 481 | > |  | 
| 482 |  | if (min_val < max_val) { | 
| 483 | < |  | 
| 483 | > |  | 
| 484 |  | #ifdef IS_MPI | 
| 485 |  | if (max_vals.rank == worldRank && min_vals.rank == worldRank) { | 
| 486 |  | // I have both maximum and minimum, so proceed like a single | 
| 487 |  | // processor version: | 
| 488 |  | #endif | 
| 489 | < | // objects to be swapped: velocity ONLY | 
| 489 | > |  | 
| 490 |  | Vector3d min_vel = min_sd->getVel(); | 
| 491 |  | Vector3d max_vel = max_sd->getVel(); | 
| 492 |  | RealType temp_vel; | 
| 495 |  | case rnemdKineticSwap : | 
| 496 |  | min_sd->setVel(max_vel); | 
| 497 |  | max_sd->setVel(min_vel); | 
| 498 | < | /* | 
| 437 | < | if (min_sd->isDirectional() && max_sd->isDirectional()) { | 
| 498 | > | if (min_sd->isDirectional() && max_sd->isDirectional()) { | 
| 499 |  | Vector3d min_angMom = min_sd->getJ(); | 
| 500 |  | Vector3d max_angMom = max_sd->getJ(); | 
| 501 |  | min_sd->setJ(max_angMom); | 
| 502 |  | max_sd->setJ(min_angMom); | 
| 503 | < | } no angular momentum exchange | 
| 504 | < | */ | 
| 503 | > | }//angular momenta exchange enabled | 
| 504 | > | //assumes same rigid body identity | 
| 505 |  | break; | 
| 506 |  | case rnemdPx : | 
| 507 |  | temp_vel = min_vel.x(); | 
| 527 |  | default : | 
| 528 |  | break; | 
| 529 |  | } | 
| 530 | + |  | 
| 531 |  | #ifdef IS_MPI | 
| 532 |  | // the rest of the cases only apply in parallel simulations: | 
| 533 |  | } else if (max_vals.rank == worldRank) { | 
| 546 |  | switch(rnemdType_) { | 
| 547 |  | case rnemdKineticSwap : | 
| 548 |  | max_sd->setVel(min_vel); | 
| 549 | < | //no angular momentum exchange for now | 
| 488 | < | /* | 
| 549 | > | //angular momenta exchange enabled | 
| 550 |  | if (max_sd->isDirectional()) { | 
| 551 |  | Vector3d min_angMom; | 
| 552 |  | Vector3d max_angMom = max_sd->getJ(); | 
| 559 |  | status); | 
| 560 |  |  | 
| 561 |  | max_sd->setJ(min_angMom); | 
| 562 | < | } | 
| 502 | < | */ | 
| 562 | > | } | 
| 563 |  | break; | 
| 564 |  | case rnemdPx : | 
| 565 |  | max_vel.x() = min_vel.x(); | 
| 592 |  | switch(rnemdType_) { | 
| 593 |  | case rnemdKineticSwap : | 
| 594 |  | min_sd->setVel(max_vel); | 
| 595 | < | // no angular momentum exchange for now | 
| 536 | < | /* | 
| 595 | > | //angular momenta exchange enabled | 
| 596 |  | if (min_sd->isDirectional()) { | 
| 597 |  | Vector3d min_angMom = min_sd->getJ(); | 
| 598 |  | Vector3d max_angMom; | 
| 606 |  |  | 
| 607 |  | min_sd->setJ(max_angMom); | 
| 608 |  | } | 
| 550 | – | */ | 
| 609 |  | break; | 
| 610 |  | case rnemdPx : | 
| 611 |  | min_vel.x() = max_vel.x(); | 
| 635 |  | } | 
| 636 |  | } else { | 
| 637 |  | sprintf(painCave.errMsg, | 
| 638 | < | "RNEMD: exchange NOT performed because at least one\n" | 
| 639 | < | "\tof the two slabs is empty\n"); | 
| 638 | > | "RNEMD: exchange NOT performed because selected object\n" | 
| 639 | > | "\tnot present in at least one of the two slabs.\n"); | 
| 640 |  | painCave.isFatal = 0; | 
| 641 |  | painCave.severity = OPENMD_INFO; | 
| 642 |  | simError(); | 
| 664 |  | RealType Khx = 0.0; | 
| 665 |  | RealType Khy = 0.0; | 
| 666 |  | RealType Khz = 0.0; | 
| 667 | + | RealType Khw = 0.0; | 
| 668 |  | RealType Pcx = 0.0; | 
| 669 |  | RealType Pcy = 0.0; | 
| 670 |  | RealType Pcz = 0.0; | 
| 671 |  | RealType Kcx = 0.0; | 
| 672 |  | RealType Kcy = 0.0; | 
| 673 |  | RealType Kcz = 0.0; | 
| 674 | + | RealType Kcw = 0.0; | 
| 675 |  |  | 
| 676 |  | for (sd = seleMan_.beginSelected(selei); sd != NULL; | 
| 677 |  | sd = seleMan_.nextSelected(selei)) { | 
| 704 |  | Khx += mass * vel.x() * vel.x(); | 
| 705 |  | Khy += mass * vel.y() * vel.y(); | 
| 706 |  | Khz += mass * vel.z() * vel.z(); | 
| 707 | + | //if (rnemdType_ == rnemdKineticScaleVAM) { | 
| 708 | + | if (sd->isDirectional()) { | 
| 709 | + | Vector3d angMom = sd->getJ(); | 
| 710 | + | Mat3x3d I = sd->getI(); | 
| 711 | + | if (sd->isLinear()) { | 
| 712 | + | int i = sd->linearAxis(); | 
| 713 | + | int j = (i + 1) % 3; | 
| 714 | + | int k = (i + 2) % 3; | 
| 715 | + | Khw += angMom[j] * angMom[j] / I(j, j) + | 
| 716 | + | angMom[k] * angMom[k] / I(k, k); | 
| 717 | + | } else { | 
| 718 | + | Khw += angMom[0]*angMom[0]/I(0, 0) | 
| 719 | + | + angMom[1]*angMom[1]/I(1, 1) | 
| 720 | + | + angMom[2]*angMom[2]/I(2, 2); | 
| 721 | + | } | 
| 722 | + | } | 
| 723 | + | //} | 
| 724 |  | } else { //midBin_ | 
| 725 |  | coldBin.push_back(sd); | 
| 726 |  | Pcx += mass * vel.x(); | 
| 729 |  | Kcx += mass * vel.x() * vel.x(); | 
| 730 |  | Kcy += mass * vel.y() * vel.y(); | 
| 731 |  | Kcz += mass * vel.z() * vel.z(); | 
| 732 | + | //if (rnemdType_ == rnemdKineticScaleVAM) { | 
| 733 | + | if (sd->isDirectional()) { | 
| 734 | + | Vector3d angMom = sd->getJ(); | 
| 735 | + | Mat3x3d I = sd->getI(); | 
| 736 | + | if (sd->isLinear()) { | 
| 737 | + | int i = sd->linearAxis(); | 
| 738 | + | int j = (i + 1) % 3; | 
| 739 | + | int k = (i + 2) % 3; | 
| 740 | + | Kcw += angMom[j] * angMom[j] / I(j, j) + | 
| 741 | + | angMom[k] * angMom[k] / I(k, k); | 
| 742 | + | } else { | 
| 743 | + | Kcw += angMom[0]*angMom[0]/I(0, 0) | 
| 744 | + | + angMom[1]*angMom[1]/I(1, 1) | 
| 745 | + | + angMom[2]*angMom[2]/I(2, 2); | 
| 746 | + | } | 
| 747 | + | } | 
| 748 | + | //} | 
| 749 |  | } | 
| 750 |  | } | 
| 751 |  | } | 
| 752 | < |  | 
| 752 | > |  | 
| 753 |  | Khx *= 0.5; | 
| 754 |  | Khy *= 0.5; | 
| 755 |  | Khz *= 0.5; | 
| 756 | + | Khw *= 0.5; | 
| 757 |  | Kcx *= 0.5; | 
| 758 |  | Kcy *= 0.5; | 
| 759 |  | Kcz *= 0.5; | 
| 760 | + | Kcw *= 0.5; | 
| 761 |  |  | 
| 762 | + | std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz | 
| 763 | + | << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy | 
| 764 | + | << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n"; | 
| 765 | + | std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz | 
| 766 | + | << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n"; | 
| 767 | + |  | 
| 768 |  | #ifdef IS_MPI | 
| 769 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM); | 
| 770 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM); | 
| 776 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM); | 
| 777 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM); | 
| 778 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM); | 
| 779 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM); | 
| 780 | + |  | 
| 781 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM); | 
| 782 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM); | 
| 783 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM); | 
| 784 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM); | 
| 785 |  | #endif | 
| 786 |  |  | 
| 787 | < | //use coldBin coeff's | 
| 787 | > | //solve coldBin coeff's first | 
| 788 |  | RealType px = Pcx / Phx; | 
| 789 |  | RealType py = Pcy / Phy; | 
| 790 |  | RealType pz = Pcz / Phz; | 
| 791 | + | RealType c, x, y, z; | 
| 792 | + | bool successfulScale = false; | 
| 793 | + | if ((rnemdType_ == rnemdKineticScaleVAM) || | 
| 794 | + | (rnemdType_ == rnemdKineticScaleAM)) { | 
| 795 | + | //may need sanity check Khw & Kcw > 0 | 
| 796 |  |  | 
| 797 | < | RealType a000, a110, c0, a001, a111, b01, b11, c1, c; | 
| 798 | < | switch(rnemdType_) { | 
| 799 | < | case rnemdKineticScale : | 
| 800 | < | // used hotBin coeff's & only scale x & y dimensions | 
| 801 | < | /* | 
| 692 | < | RealType px = Phx / Pcx; | 
| 693 | < | RealType py = Phy / Pcy; | 
| 694 | < | a110 = Khy; | 
| 695 | < | c0 = - Khx - Khy - targetFlux_; | 
| 696 | < | a000 = Khx; | 
| 697 | < | a111 = Kcy * py * py; | 
| 698 | < | b11 = -2.0 * Kcy * py * (1.0 + py); | 
| 699 | < | c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_; | 
| 700 | < | b01 = -2.0 * Kcx * px * (1.0 + px); | 
| 701 | < | a001 = Kcx * px * px; | 
| 702 | < | */ | 
| 703 | < | //scale all three dimensions, let c_x = c_y | 
| 704 | < | a000 = Kcx + Kcy; | 
| 705 | < | a110 = Kcz; | 
| 706 | < | c0 = targetFlux_ - Kcx - Kcy - Kcz; | 
| 707 | < | a001 = Khx * px * px + Khy * py * py; | 
| 708 | < | a111 = Khz * pz * pz; | 
| 709 | < | b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)); | 
| 710 | < | b11 = -2.0 * Khz * pz * (1.0 + pz); | 
| 711 | < | c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) | 
| 712 | < | + Khz * pz * (2.0 + pz) - targetFlux_; | 
| 713 | < | break; | 
| 714 | < | case rnemdPxScale : | 
| 715 | < | c = 1 - targetFlux_ / Pcx; | 
| 716 | < | a000 = Kcy; | 
| 717 | < | a110 = Kcz; | 
| 718 | < | c0 = Kcx * c * c - Kcx - Kcy - Kcz; | 
| 719 | < | a001 = py * py * Khy; | 
| 720 | < | a111 = pz * pz * Khz; | 
| 721 | < | b01 = -2.0 * Khy * py * (1.0 + py); | 
| 722 | < | b11 = -2.0 * Khz * pz * (1.0 + pz); | 
| 723 | < | c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) | 
| 724 | < | + Khx * (fastpow(c * px - px - 1.0, 2) - 1.0); | 
| 725 | < | break; | 
| 726 | < | case rnemdPyScale : | 
| 727 | < | c = 1 - targetFlux_ / Pcy; | 
| 728 | < | a000 = Kcx; | 
| 729 | < | a110 = Kcz; | 
| 730 | < | c0 = Kcy * c * c - Kcx - Kcy - Kcz; | 
| 731 | < | a001 = px * px * Khx; | 
| 732 | < | a111 = pz * pz * Khz; | 
| 733 | < | b01 = -2.0 * Khx * px * (1.0 + px); | 
| 734 | < | b11 = -2.0 * Khz * pz * (1.0 + pz); | 
| 735 | < | c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz) | 
| 736 | < | + Khy * (fastpow(c * py - py - 1.0, 2) - 1.0); | 
| 737 | < | break; | 
| 738 | < | case rnemdPzScale ://we don't really do this, do we? | 
| 739 | < | c = 1 - targetFlux_ / Pcz; | 
| 740 | < | a000 = Kcx; | 
| 741 | < | a110 = Kcy; | 
| 742 | < | c0 = Kcz * c * c - Kcx - Kcy - Kcz; | 
| 743 | < | a001 = px * px * Khx; | 
| 744 | < | a111 = py * py * Khy; | 
| 745 | < | b01 = -2.0 * Khx * px * (1.0 + px); | 
| 746 | < | b11 = -2.0 * Khy * py * (1.0 + py); | 
| 747 | < | c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) | 
| 748 | < | + Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0); | 
| 749 | < | break; | 
| 750 | < | default : | 
| 751 | < | break; | 
| 752 | < | } | 
| 797 | > | if (rnemdType_ == rnemdKineticScaleVAM) { | 
| 798 | > | c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw); | 
| 799 | > | } else { | 
| 800 | > | c = 1.0 - targetFlux_ / Kcw; | 
| 801 | > | } | 
| 802 |  |  | 
| 803 | < | RealType v1 = a000 * a111 - a001 * a110; | 
| 804 | < | RealType v2 = a000 * b01; | 
| 805 | < | RealType v3 = a000 * b11; | 
| 806 | < | RealType v4 = a000 * c1 - a001 * c0; | 
| 807 | < | RealType v8 = a110 * b01; | 
| 808 | < | RealType v10 = - b01 * c0; | 
| 809 | < |  | 
| 810 | < | RealType u0 = v2 * v10 - v4 * v4; | 
| 811 | < | RealType u1 = -2.0 * v3 * v4; | 
| 812 | < | RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4; | 
| 813 | < | RealType u3 = -2.0 * v1 * v3; | 
| 814 | < | RealType u4 = - v1 * v1; | 
| 815 | < | //rescale coefficients | 
| 816 | < | RealType maxAbs = fabs(u0); | 
| 817 | < | if (maxAbs < fabs(u1)) maxAbs = fabs(u1); | 
| 818 | < | if (maxAbs < fabs(u2)) maxAbs = fabs(u2); | 
| 819 | < | if (maxAbs < fabs(u3)) maxAbs = fabs(u3); | 
| 820 | < | if (maxAbs < fabs(u4)) maxAbs = fabs(u4); | 
| 821 | < | u0 /= maxAbs; | 
| 822 | < | u1 /= maxAbs; | 
| 823 | < | u2 /= maxAbs; | 
| 824 | < | u3 /= maxAbs; | 
| 825 | < | u4 /= maxAbs; | 
| 826 | < | //max_element(start, end) is also available. | 
| 827 | < | Polynomial<RealType> poly; //same as DoublePolynomial poly; | 
| 828 | < | poly.setCoefficient(4, u4); | 
| 829 | < | poly.setCoefficient(3, u3); | 
| 830 | < | poly.setCoefficient(2, u2); | 
| 831 | < | poly.setCoefficient(1, u1); | 
| 832 | < | poly.setCoefficient(0, u0); | 
| 833 | < | vector<RealType> realRoots = poly.FindRealRoots(); | 
| 834 | < |  | 
| 835 | < | vector<RealType>::iterator ri; | 
| 836 | < | RealType r1, r2, alpha0; | 
| 837 | < | vector<pair<RealType,RealType> > rps; | 
| 838 | < | for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) { | 
| 839 | < | r2 = *ri; | 
| 840 | < | //check if FindRealRoots() give the right answer | 
| 841 | < | if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { | 
| 842 | < | sprintf(painCave.errMsg, | 
| 843 | < | "RNEMD Warning: polynomial solve seems to have an error!"); | 
| 844 | < | painCave.isFatal = 0; | 
| 845 | < | simError(); | 
| 846 | < | failRootCount_++; | 
| 803 | > | if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients | 
| 804 | > | c = sqrt(c); | 
| 805 | > | std::cerr << "cold slab scaling coefficient: " << c << endl; | 
| 806 | > | //now convert to hotBin coefficient | 
| 807 | > | RealType w = 0.0; | 
| 808 | > | if (rnemdType_ ==  rnemdKineticScaleVAM) { | 
| 809 | > | x = 1.0 + px * (1.0 - c); | 
| 810 | > | y = 1.0 + py * (1.0 - c); | 
| 811 | > | z = 1.0 + pz * (1.0 - c); | 
| 812 | > | /* more complicated way | 
| 813 | > | w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz | 
| 814 | > | + Khx * px * px + Khy * py * py + Khz * pz * pz) | 
| 815 | > | - 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py) | 
| 816 | > | + Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px) | 
| 817 | > | + Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) | 
| 818 | > | - Kcx - Kcy - Kcz)) / Khw; the following is simpler | 
| 819 | > | */ | 
| 820 | > | if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) && | 
| 821 | > | (fabs(z - 1.0) < 0.1)) { | 
| 822 | > | w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y) | 
| 823 | > | + Khz * (1.0 - z * z)) / Khw; | 
| 824 | > | }//no need to calculate w if x, y or z is out of range | 
| 825 | > | } else { | 
| 826 | > | w = 1.0 + targetFlux_ / Khw; | 
| 827 | > | } | 
| 828 | > | if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients | 
| 829 | > | //if w is in the right range, so should be x, y, z. | 
| 830 | > | vector<StuntDouble*>::iterator sdi; | 
| 831 | > | Vector3d vel; | 
| 832 | > | for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { | 
| 833 | > | if (rnemdType_ == rnemdKineticScaleVAM) { | 
| 834 | > | vel = (*sdi)->getVel() * c; | 
| 835 | > | //vel.x() *= c; | 
| 836 | > | //vel.y() *= c; | 
| 837 | > | //vel.z() *= c; | 
| 838 | > | (*sdi)->setVel(vel); | 
| 839 | > | } | 
| 840 | > | if ((*sdi)->isDirectional()) { | 
| 841 | > | Vector3d angMom = (*sdi)->getJ() * c; | 
| 842 | > | //angMom[0] *= c; | 
| 843 | > | //angMom[1] *= c; | 
| 844 | > | //angMom[2] *= c; | 
| 845 | > | (*sdi)->setJ(angMom); | 
| 846 | > | } | 
| 847 | > | } | 
| 848 | > | w = sqrt(w); | 
| 849 | > | std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z | 
| 850 | > | << "\twh= " << w << endl; | 
| 851 | > | for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { | 
| 852 | > | if (rnemdType_ == rnemdKineticScaleVAM) { | 
| 853 | > | vel = (*sdi)->getVel(); | 
| 854 | > | vel.x() *= x; | 
| 855 | > | vel.y() *= y; | 
| 856 | > | vel.z() *= z; | 
| 857 | > | (*sdi)->setVel(vel); | 
| 858 | > | } | 
| 859 | > | if ((*sdi)->isDirectional()) { | 
| 860 | > | Vector3d angMom = (*sdi)->getJ() * w; | 
| 861 | > | //angMom[0] *= w; | 
| 862 | > | //angMom[1] *= w; | 
| 863 | > | //angMom[2] *= w; | 
| 864 | > | (*sdi)->setJ(angMom); | 
| 865 | > | } | 
| 866 | > | } | 
| 867 | > | successfulScale = true; | 
| 868 | > | exchangeSum_ += targetFlux_; | 
| 869 | > | } | 
| 870 |  | } | 
| 871 | < | //might not be useful w/o rescaling coefficients | 
| 872 | < | alpha0 = -c0 - a110 * r2 * r2; | 
| 801 | < | if (alpha0 >= 0.0) { | 
| 802 | < | r1 = sqrt(alpha0 / a000); | 
| 803 | < | if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) < 1e-6) | 
| 804 | < | { rps.push_back(make_pair(r1, r2)); } | 
| 805 | < | if (r1 > 1e-6) { //r1 non-negative | 
| 806 | < | r1 = -r1; | 
| 807 | < | if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) <1e-6) | 
| 808 | < | { rps.push_back(make_pair(r1, r2)); } | 
| 809 | < | } | 
| 810 | < | } | 
| 811 | < | } | 
| 812 | < | // Consider combining together the solving pair part w/ the searching | 
| 813 | < | // best solution part so that we don't need the pairs vector | 
| 814 | < | if (!rps.empty()) { | 
| 815 | < | RealType smallestDiff = HONKING_LARGE_VALUE; | 
| 816 | < | RealType diff; | 
| 817 | < | pair<RealType,RealType> bestPair = make_pair(1.0, 1.0); | 
| 818 | < | vector<pair<RealType,RealType> >::iterator rpi; | 
| 819 | < | for (rpi = rps.begin(); rpi != rps.end(); rpi++) { | 
| 820 | < | r1 = (*rpi).first; | 
| 821 | < | r2 = (*rpi).second; | 
| 822 | < | switch(rnemdType_) { | 
| 823 | < | case rnemdKineticScale : | 
| 824 | < | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 825 | < | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2) | 
| 826 | < | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); | 
| 827 | < | break; | 
| 828 | < | case rnemdPxScale : | 
| 829 | < | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 830 | < | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); | 
| 831 | < | break; | 
| 832 | < | case rnemdPyScale : | 
| 833 | < | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 834 | < | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); | 
| 835 | < | break; | 
| 836 | < | case rnemdPzScale : | 
| 837 | < | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 838 | < | + fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); | 
| 839 | < | default : | 
| 840 | < | break; | 
| 841 | < | } | 
| 842 | < | if (diff < smallestDiff) { | 
| 843 | < | smallestDiff = diff; | 
| 844 | < | bestPair = *rpi; | 
| 845 | < | } | 
| 846 | < | } | 
| 847 | < | #ifdef IS_MPI | 
| 848 | < | if (worldRank == 0) { | 
| 849 | < | #endif | 
| 850 | < | sprintf(painCave.errMsg, | 
| 851 | < | "RNEMD: roots r1= %lf\tr2 = %lf\n", | 
| 852 | < | bestPair.first, bestPair.second); | 
| 853 | < | painCave.isFatal = 0; | 
| 854 | < | painCave.severity = OPENMD_INFO; | 
| 855 | < | simError(); | 
| 856 | < | #ifdef IS_MPI | 
| 857 | < | } | 
| 858 | < | #endif | 
| 859 | < |  | 
| 860 | < | RealType x, y, z; | 
| 871 | > | } else { | 
| 872 | > | RealType a000, a110, c0, a001, a111, b01, b11, c1; | 
| 873 |  | switch(rnemdType_) { | 
| 874 |  | case rnemdKineticScale : | 
| 875 | < | x = bestPair.first; | 
| 876 | < | y = bestPair.first; | 
| 877 | < | z = bestPair.second; | 
| 878 | < | break; | 
| 875 | > | /* used hotBin coeff's & only scale x & y dimensions | 
| 876 | > | RealType px = Phx / Pcx; | 
| 877 | > | RealType py = Phy / Pcy; | 
| 878 | > | a110 = Khy; | 
| 879 | > | c0 = - Khx - Khy - targetFlux_; | 
| 880 | > | a000 = Khx; | 
| 881 | > | a111 = Kcy * py * py; | 
| 882 | > | b11 = -2.0 * Kcy * py * (1.0 + py); | 
| 883 | > | c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_; | 
| 884 | > | b01 = -2.0 * Kcx * px * (1.0 + px); | 
| 885 | > | a001 = Kcx * px * px; | 
| 886 | > | */ | 
| 887 | > | //scale all three dimensions, let c_x = c_y | 
| 888 | > | a000 = Kcx + Kcy; | 
| 889 | > | a110 = Kcz; | 
| 890 | > | c0 = targetFlux_ - Kcx - Kcy - Kcz; | 
| 891 | > | a001 = Khx * px * px + Khy * py * py; | 
| 892 | > | a111 = Khz * pz * pz; | 
| 893 | > | b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)); | 
| 894 | > | b11 = -2.0 * Khz * pz * (1.0 + pz); | 
| 895 | > | c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) | 
| 896 | > | + Khz * pz * (2.0 + pz) - targetFlux_; | 
| 897 | > | break; | 
| 898 |  | case rnemdPxScale : | 
| 899 | < | x = c; | 
| 900 | < | y = bestPair.first; | 
| 901 | < | z = bestPair.second; | 
| 902 | < | break; | 
| 899 | > | c = 1 - targetFlux_ / Pcx; | 
| 900 | > | a000 = Kcy; | 
| 901 | > | a110 = Kcz; | 
| 902 | > | c0 = Kcx * c * c - Kcx - Kcy - Kcz; | 
| 903 | > | a001 = py * py * Khy; | 
| 904 | > | a111 = pz * pz * Khz; | 
| 905 | > | b01 = -2.0 * Khy * py * (1.0 + py); | 
| 906 | > | b11 = -2.0 * Khz * pz * (1.0 + pz); | 
| 907 | > | c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) | 
| 908 | > | + Khx * (fastpow(c * px - px - 1.0, 2) - 1.0); | 
| 909 | > | break; | 
| 910 |  | case rnemdPyScale : | 
| 911 | < | x = bestPair.first; | 
| 912 | < | y = c; | 
| 913 | < | z = bestPair.second; | 
| 914 | < | break; | 
| 915 | < | case rnemdPzScale : | 
| 916 | < | x = bestPair.first; | 
| 917 | < | y = bestPair.second; | 
| 918 | < | z = c; | 
| 919 | < | break; | 
| 920 | < | default : | 
| 921 | < | break; | 
| 922 | < | } | 
| 923 | < | vector<StuntDouble*>::iterator sdi; | 
| 924 | < | Vector3d vel; | 
| 925 | < | for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { | 
| 926 | < | vel = (*sdi)->getVel(); | 
| 927 | < | vel.x() *= x; | 
| 928 | < | vel.y() *= y; | 
| 929 | < | vel.z() *= z; | 
| 930 | < | (*sdi)->setVel(vel); | 
| 931 | < | } | 
| 932 | < | //convert to hotBin coefficient | 
| 933 | < | x = 1.0 + px * (1.0 - x); | 
| 934 | < | y = 1.0 + py * (1.0 - y); | 
| 935 | < | z = 1.0 + pz * (1.0 - z); | 
| 898 | < | for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { | 
| 899 | < | vel = (*sdi)->getVel(); | 
| 900 | < | vel.x() *= x; | 
| 901 | < | vel.y() *= y; | 
| 902 | < | vel.z() *= z; | 
| 903 | < | (*sdi)->setVel(vel); | 
| 911 | > | c = 1 - targetFlux_ / Pcy; | 
| 912 | > | a000 = Kcx; | 
| 913 | > | a110 = Kcz; | 
| 914 | > | c0 = Kcy * c * c - Kcx - Kcy - Kcz; | 
| 915 | > | a001 = px * px * Khx; | 
| 916 | > | a111 = pz * pz * Khz; | 
| 917 | > | b01 = -2.0 * Khx * px * (1.0 + px); | 
| 918 | > | b11 = -2.0 * Khz * pz * (1.0 + pz); | 
| 919 | > | c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz) | 
| 920 | > | + Khy * (fastpow(c * py - py - 1.0, 2) - 1.0); | 
| 921 | > | break; | 
| 922 | > | case rnemdPzScale ://we don't really do this, do we? | 
| 923 | > | c = 1 - targetFlux_ / Pcz; | 
| 924 | > | a000 = Kcx; | 
| 925 | > | a110 = Kcy; | 
| 926 | > | c0 = Kcz * c * c - Kcx - Kcy - Kcz; | 
| 927 | > | a001 = px * px * Khx; | 
| 928 | > | a111 = py * py * Khy; | 
| 929 | > | b01 = -2.0 * Khx * px * (1.0 + px); | 
| 930 | > | b11 = -2.0 * Khy * py * (1.0 + py); | 
| 931 | > | c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) | 
| 932 | > | + Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0); | 
| 933 | > | break; | 
| 934 | > | default : | 
| 935 | > | break; | 
| 936 |  | } | 
| 937 | < | exchangeSum_ += targetFlux_; | 
| 938 | < | //we may want to check whether the exchange has been successful | 
| 939 | < | } else { | 
| 937 | > |  | 
| 938 | > | RealType v1 = a000 * a111 - a001 * a110; | 
| 939 | > | RealType v2 = a000 * b01; | 
| 940 | > | RealType v3 = a000 * b11; | 
| 941 | > | RealType v4 = a000 * c1 - a001 * c0; | 
| 942 | > | RealType v8 = a110 * b01; | 
| 943 | > | RealType v10 = - b01 * c0; | 
| 944 | > |  | 
| 945 | > | RealType u0 = v2 * v10 - v4 * v4; | 
| 946 | > | RealType u1 = -2.0 * v3 * v4; | 
| 947 | > | RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4; | 
| 948 | > | RealType u3 = -2.0 * v1 * v3; | 
| 949 | > | RealType u4 = - v1 * v1; | 
| 950 | > | //rescale coefficients | 
| 951 | > | RealType maxAbs = fabs(u0); | 
| 952 | > | if (maxAbs < fabs(u1)) maxAbs = fabs(u1); | 
| 953 | > | if (maxAbs < fabs(u2)) maxAbs = fabs(u2); | 
| 954 | > | if (maxAbs < fabs(u3)) maxAbs = fabs(u3); | 
| 955 | > | if (maxAbs < fabs(u4)) maxAbs = fabs(u4); | 
| 956 | > | u0 /= maxAbs; | 
| 957 | > | u1 /= maxAbs; | 
| 958 | > | u2 /= maxAbs; | 
| 959 | > | u3 /= maxAbs; | 
| 960 | > | u4 /= maxAbs; | 
| 961 | > | //max_element(start, end) is also available. | 
| 962 | > | Polynomial<RealType> poly; //same as DoublePolynomial poly; | 
| 963 | > | poly.setCoefficient(4, u4); | 
| 964 | > | poly.setCoefficient(3, u3); | 
| 965 | > | poly.setCoefficient(2, u2); | 
| 966 | > | poly.setCoefficient(1, u1); | 
| 967 | > | poly.setCoefficient(0, u0); | 
| 968 | > | vector<RealType> realRoots = poly.FindRealRoots(); | 
| 969 | > |  | 
| 970 | > | vector<RealType>::iterator ri; | 
| 971 | > | RealType r1, r2, alpha0; | 
| 972 | > | vector<pair<RealType,RealType> > rps; | 
| 973 | > | for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) { | 
| 974 | > | r2 = *ri; | 
| 975 | > | //check if FindRealRoots() give the right answer | 
| 976 | > | if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { | 
| 977 | > | sprintf(painCave.errMsg, | 
| 978 | > | "RNEMD Warning: polynomial solve seems to have an error!"); | 
| 979 | > | painCave.isFatal = 0; | 
| 980 | > | simError(); | 
| 981 | > | failRootCount_++; | 
| 982 | > | } | 
| 983 | > | //might not be useful w/o rescaling coefficients | 
| 984 | > | alpha0 = -c0 - a110 * r2 * r2; | 
| 985 | > | if (alpha0 >= 0.0) { | 
| 986 | > | r1 = sqrt(alpha0 / a000); | 
| 987 | > | if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) | 
| 988 | > | < 1e-6) | 
| 989 | > | { rps.push_back(make_pair(r1, r2)); } | 
| 990 | > | if (r1 > 1e-6) { //r1 non-negative | 
| 991 | > | r1 = -r1; | 
| 992 | > | if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) | 
| 993 | > | < 1e-6) | 
| 994 | > | { rps.push_back(make_pair(r1, r2)); } | 
| 995 | > | } | 
| 996 | > | } | 
| 997 | > | } | 
| 998 | > | // Consider combining together the solving pair part w/ the searching | 
| 999 | > | // best solution part so that we don't need the pairs vector | 
| 1000 | > | if (!rps.empty()) { | 
| 1001 | > | RealType smallestDiff = HONKING_LARGE_VALUE; | 
| 1002 | > | RealType diff; | 
| 1003 | > | pair<RealType,RealType> bestPair = make_pair(1.0, 1.0); | 
| 1004 | > | vector<pair<RealType,RealType> >::iterator rpi; | 
| 1005 | > | for (rpi = rps.begin(); rpi != rps.end(); rpi++) { | 
| 1006 | > | r1 = (*rpi).first; | 
| 1007 | > | r2 = (*rpi).second; | 
| 1008 | > | switch(rnemdType_) { | 
| 1009 | > | case rnemdKineticScale : | 
| 1010 | > | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 1011 | > | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2) | 
| 1012 | > | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); | 
| 1013 | > | break; | 
| 1014 | > | case rnemdPxScale : | 
| 1015 | > | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 1016 | > | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); | 
| 1017 | > | break; | 
| 1018 | > | case rnemdPyScale : | 
| 1019 | > | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 1020 | > | + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); | 
| 1021 | > | break; | 
| 1022 | > | case rnemdPzScale : | 
| 1023 | > | diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) | 
| 1024 | > | + fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); | 
| 1025 | > | default : | 
| 1026 | > | break; | 
| 1027 | > | } | 
| 1028 | > | if (diff < smallestDiff) { | 
| 1029 | > | smallestDiff = diff; | 
| 1030 | > | bestPair = *rpi; | 
| 1031 | > | } | 
| 1032 | > | } | 
| 1033 | > | #ifdef IS_MPI | 
| 1034 | > | if (worldRank == 0) { | 
| 1035 | > | #endif | 
| 1036 | > | sprintf(painCave.errMsg, | 
| 1037 | > | "RNEMD: roots r1= %lf\tr2 = %lf\n", | 
| 1038 | > | bestPair.first, bestPair.second); | 
| 1039 | > | painCave.isFatal = 0; | 
| 1040 | > | painCave.severity = OPENMD_INFO; | 
| 1041 | > | simError(); | 
| 1042 | > | #ifdef IS_MPI | 
| 1043 | > | } | 
| 1044 | > | #endif | 
| 1045 | > |  | 
| 1046 | > | switch(rnemdType_) { | 
| 1047 | > | case rnemdKineticScale : | 
| 1048 | > | x = bestPair.first; | 
| 1049 | > | y = bestPair.first; | 
| 1050 | > | z = bestPair.second; | 
| 1051 | > | break; | 
| 1052 | > | case rnemdPxScale : | 
| 1053 | > | x = c; | 
| 1054 | > | y = bestPair.first; | 
| 1055 | > | z = bestPair.second; | 
| 1056 | > | break; | 
| 1057 | > | case rnemdPyScale : | 
| 1058 | > | x = bestPair.first; | 
| 1059 | > | y = c; | 
| 1060 | > | z = bestPair.second; | 
| 1061 | > | break; | 
| 1062 | > | case rnemdPzScale : | 
| 1063 | > | x = bestPair.first; | 
| 1064 | > | y = bestPair.second; | 
| 1065 | > | z = c; | 
| 1066 | > | break; | 
| 1067 | > | default : | 
| 1068 | > | break; | 
| 1069 | > | } | 
| 1070 | > | vector<StuntDouble*>::iterator sdi; | 
| 1071 | > | Vector3d vel; | 
| 1072 | > | for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { | 
| 1073 | > | vel = (*sdi)->getVel(); | 
| 1074 | > | vel.x() *= x; | 
| 1075 | > | vel.y() *= y; | 
| 1076 | > | vel.z() *= z; | 
| 1077 | > | (*sdi)->setVel(vel); | 
| 1078 | > | } | 
| 1079 | > | //convert to hotBin coefficient | 
| 1080 | > | x = 1.0 + px * (1.0 - x); | 
| 1081 | > | y = 1.0 + py * (1.0 - y); | 
| 1082 | > | z = 1.0 + pz * (1.0 - z); | 
| 1083 | > | for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { | 
| 1084 | > | vel = (*sdi)->getVel(); | 
| 1085 | > | vel.x() *= x; | 
| 1086 | > | vel.y() *= y; | 
| 1087 | > | vel.z() *= z; | 
| 1088 | > | (*sdi)->setVel(vel); | 
| 1089 | > | } | 
| 1090 | > | successfulScale = true; | 
| 1091 | > | exchangeSum_ += targetFlux_; | 
| 1092 | > | } | 
| 1093 | > | } | 
| 1094 | > | if (successfulScale != true) { | 
| 1095 |  | sprintf(painCave.errMsg, | 
| 1096 | < | "RNEMD: exchange NOT performed!\n"); | 
| 1096 | > | "RNEMD: exchange NOT performed!\n"); | 
| 1097 |  | painCave.isFatal = 0; | 
| 1098 |  | painCave.severity = OPENMD_INFO; | 
| 1099 |  | simError(); | 
| 1100 |  | failTrialCount_++; | 
| 1101 |  | } | 
| 1102 | + | } | 
| 1103 |  |  | 
| 1104 | + | void RNEMD::doShiftScale() { | 
| 1105 | + |  | 
| 1106 | + | Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); | 
| 1107 | + | Mat3x3d hmat = currentSnap_->getHmat(); | 
| 1108 | + |  | 
| 1109 | + | seleMan_.setSelectionSet(evaluator_.evaluate()); | 
| 1110 | + |  | 
| 1111 | + | int selei; | 
| 1112 | + | StuntDouble* sd; | 
| 1113 | + | int idx; | 
| 1114 | + |  | 
| 1115 | + | vector<StuntDouble*> hotBin, coldBin; | 
| 1116 | + |  | 
| 1117 | + | Vector3d Ph(V3Zero); | 
| 1118 | + | RealType Mh = 0.0; | 
| 1119 | + | RealType Kh = 0.0; | 
| 1120 | + | Vector3d Pc(V3Zero); | 
| 1121 | + | RealType Mc = 0.0; | 
| 1122 | + | RealType Kc = 0.0; | 
| 1123 | + |  | 
| 1124 | + | for (sd = seleMan_.beginSelected(selei); sd != NULL; | 
| 1125 | + | sd = seleMan_.nextSelected(selei)) { | 
| 1126 | + |  | 
| 1127 | + | idx = sd->getLocalIndex(); | 
| 1128 | + |  | 
| 1129 | + | Vector3d pos = sd->getPos(); | 
| 1130 | + |  | 
| 1131 | + | // wrap the stuntdouble's position back into the box: | 
| 1132 | + |  | 
| 1133 | + | if (usePeriodicBoundaryConditions_) | 
| 1134 | + | currentSnap_->wrapVector(pos); | 
| 1135 | + |  | 
| 1136 | + | // which bin is this stuntdouble in? | 
| 1137 | + | // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] | 
| 1138 | + |  | 
| 1139 | + | int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; | 
| 1140 | + |  | 
| 1141 | + | // if we're in bin 0 or the middleBin | 
| 1142 | + | if (binNo == 0 || binNo == midBin_) { | 
| 1143 | + |  | 
| 1144 | + | RealType mass = sd->getMass(); | 
| 1145 | + | Vector3d vel = sd->getVel(); | 
| 1146 | + |  | 
| 1147 | + | if (binNo == 0) { | 
| 1148 | + | hotBin.push_back(sd); | 
| 1149 | + | //std::cerr << "before, velocity = " << vel << endl; | 
| 1150 | + | Ph += mass * vel; | 
| 1151 | + | //std::cerr << "after, velocity = " << vel << endl; | 
| 1152 | + | Mh += mass; | 
| 1153 | + | Kh += mass * vel.lengthSquare(); | 
| 1154 | + | if (rnemdType_ == rnemdShiftScaleVAM) { | 
| 1155 | + | if (sd->isDirectional()) { | 
| 1156 | + | Vector3d angMom = sd->getJ(); | 
| 1157 | + | Mat3x3d I = sd->getI(); | 
| 1158 | + | if (sd->isLinear()) { | 
| 1159 | + | int i = sd->linearAxis(); | 
| 1160 | + | int j = (i + 1) % 3; | 
| 1161 | + | int k = (i + 2) % 3; | 
| 1162 | + | Kh += angMom[j] * angMom[j] / I(j, j) + | 
| 1163 | + | angMom[k] * angMom[k] / I(k, k); | 
| 1164 | + | } else { | 
| 1165 | + | Kh += angMom[0] * angMom[0] / I(0, 0) + | 
| 1166 | + | angMom[1] * angMom[1] / I(1, 1) + | 
| 1167 | + | angMom[2] * angMom[2] / I(2, 2); | 
| 1168 | + | } | 
| 1169 | + | } | 
| 1170 | + | } | 
| 1171 | + | } else { //midBin_ | 
| 1172 | + | coldBin.push_back(sd); | 
| 1173 | + | Pc += mass * vel; | 
| 1174 | + | Mc += mass; | 
| 1175 | + | Kc += mass * vel.lengthSquare(); | 
| 1176 | + | if (rnemdType_ == rnemdShiftScaleVAM) { | 
| 1177 | + | if (sd->isDirectional()) { | 
| 1178 | + | Vector3d angMom = sd->getJ(); | 
| 1179 | + | Mat3x3d I = sd->getI(); | 
| 1180 | + | if (sd->isLinear()) { | 
| 1181 | + | int i = sd->linearAxis(); | 
| 1182 | + | int j = (i + 1) % 3; | 
| 1183 | + | int k = (i + 2) % 3; | 
| 1184 | + | Kc += angMom[j] * angMom[j] / I(j, j) + | 
| 1185 | + | angMom[k] * angMom[k] / I(k, k); | 
| 1186 | + | } else { | 
| 1187 | + | Kc += angMom[0] * angMom[0] / I(0, 0) + | 
| 1188 | + | angMom[1] * angMom[1] / I(1, 1) + | 
| 1189 | + | angMom[2] * angMom[2] / I(2, 2); | 
| 1190 | + | } | 
| 1191 | + | } | 
| 1192 | + | } | 
| 1193 | + | } | 
| 1194 | + | } | 
| 1195 | + | } | 
| 1196 | + |  | 
| 1197 | + | Kh *= 0.5; | 
| 1198 | + | Kc *= 0.5; | 
| 1199 | + |  | 
| 1200 | + | std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc | 
| 1201 | + | << "\tKc= " << Kc << endl; | 
| 1202 | + | std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl; | 
| 1203 | + |  | 
| 1204 | + | #ifdef IS_MPI | 
| 1205 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM); | 
| 1206 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM); | 
| 1207 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM); | 
| 1208 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM); | 
| 1209 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM); | 
| 1210 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM); | 
| 1211 | + | #endif | 
| 1212 | + |  | 
| 1213 | + | bool successfulExchange = false; | 
| 1214 | + | if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty | 
| 1215 | + | Vector3d vc = Pc / Mc; | 
| 1216 | + | Vector3d ac = njzp_ / Mc + vc; | 
| 1217 | + | RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare(); | 
| 1218 | + | if (cNumerator > 0.0) { | 
| 1219 | + | RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare(); | 
| 1220 | + | if (cDenominator > 0.0) { | 
| 1221 | + | RealType c = sqrt(cNumerator / cDenominator); | 
| 1222 | + | if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients | 
| 1223 | + | Vector3d vh = Ph / Mh; | 
| 1224 | + | Vector3d ah = jzp_ / Mh + vh; | 
| 1225 | + | RealType hNumerator = Kh + targetJzKE_ | 
| 1226 | + | - 0.5 * Mh * ah.lengthSquare(); | 
| 1227 | + | if (hNumerator > 0.0) { | 
| 1228 | + | RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare(); | 
| 1229 | + | if (hDenominator > 0.0) { | 
| 1230 | + | RealType h = sqrt(hNumerator / hDenominator); | 
| 1231 | + | if ((h > 0.9) && (h < 1.1)) { | 
| 1232 | + | std::cerr << "cold slab scaling coefficient: " << c << "\n"; | 
| 1233 | + | std::cerr << "hot slab scaling coefficient: " << h << "\n"; | 
| 1234 | + | vector<StuntDouble*>::iterator sdi; | 
| 1235 | + | Vector3d vel; | 
| 1236 | + | for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { | 
| 1237 | + | //vel = (*sdi)->getVel(); | 
| 1238 | + | vel = ((*sdi)->getVel() - vc) * c + ac; | 
| 1239 | + | (*sdi)->setVel(vel); | 
| 1240 | + | if (rnemdType_ == rnemdShiftScaleVAM) { | 
| 1241 | + | if ((*sdi)->isDirectional()) { | 
| 1242 | + | Vector3d angMom = (*sdi)->getJ() * c; | 
| 1243 | + | (*sdi)->setJ(angMom); | 
| 1244 | + | } | 
| 1245 | + | } | 
| 1246 | + | } | 
| 1247 | + | for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { | 
| 1248 | + | //vel = (*sdi)->getVel(); | 
| 1249 | + | vel = ((*sdi)->getVel() - vh) * h + ah; | 
| 1250 | + | (*sdi)->setVel(vel); | 
| 1251 | + | if (rnemdType_ == rnemdShiftScaleVAM) { | 
| 1252 | + | if ((*sdi)->isDirectional()) { | 
| 1253 | + | Vector3d angMom = (*sdi)->getJ() * h; | 
| 1254 | + | (*sdi)->setJ(angMom); | 
| 1255 | + | } | 
| 1256 | + | } | 
| 1257 | + | } | 
| 1258 | + | successfulExchange = true; | 
| 1259 | + | exchangeSum_ += targetFlux_; | 
| 1260 | + | // this is a redundant variable for doShiftScale() so that | 
| 1261 | + | // RNEMD can output one exchange quantity needed in a job. | 
| 1262 | + | // need a better way to do this. | 
| 1263 | + | } | 
| 1264 | + | } | 
| 1265 | + | } | 
| 1266 | + | } | 
| 1267 | + | } | 
| 1268 | + | } | 
| 1269 | + | } | 
| 1270 | + | if (successfulExchange != true) { | 
| 1271 | + | sprintf(painCave.errMsg, | 
| 1272 | + | "RNEMD: exchange NOT performed!\n"); | 
| 1273 | + | painCave.isFatal = 0; | 
| 1274 | + | painCave.severity = OPENMD_INFO; | 
| 1275 | + | simError(); | 
| 1276 | + | failTrialCount_++; | 
| 1277 | + | } | 
| 1278 |  | } | 
| 1279 |  |  | 
| 1280 |  | void RNEMD::doRNEMD() { | 
| 1281 |  |  | 
| 1282 |  | switch(rnemdType_) { | 
| 1283 |  | case rnemdKineticScale : | 
| 1284 | + | case rnemdKineticScaleVAM : | 
| 1285 | + | case rnemdKineticScaleAM : | 
| 1286 |  | case rnemdPxScale : | 
| 1287 |  | case rnemdPyScale : | 
| 1288 |  | case rnemdPzScale : | 
| 1294 |  | case rnemdPz : | 
| 1295 |  | doSwap(); | 
| 1296 |  | break; | 
| 1297 | + | case rnemdShiftScaleV : | 
| 1298 | + | case rnemdShiftScaleVAM : | 
| 1299 | + | doShiftScale(); | 
| 1300 | + | break; | 
| 1301 |  | case rnemdUnknown : | 
| 1302 |  | default : | 
| 1303 |  | break; | 
| 1346 |  |  | 
| 1347 |  | int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) % | 
| 1348 |  | rnemdLogWidth_; | 
| 1349 | < | // no symmetrization allowed due to arbitary rnemdLogWidth_ value | 
| 1349 | > | // no symmetrization allowed due to arbitary rnemdLogWidth_ | 
| 1350 |  | /* | 
| 1351 |  | if (rnemdLogWidth_ == midBin_ + 1) | 
| 1352 |  | if (binNo > midBin_) | 
| 1353 |  | binNo = nBins_ - binNo; | 
| 1354 |  | */ | 
| 1355 |  | RealType mass = sd->getMass(); | 
| 1356 | + | mHist_[binNo] += mass; | 
| 1357 |  | Vector3d vel = sd->getVel(); | 
| 1358 |  | RealType value; | 
| 1359 | < | RealType xVal, yVal, zVal; | 
| 1359 | > | //RealType xVal, yVal, zVal; | 
| 1360 |  |  | 
| 1361 | < | switch(rnemdType_) { | 
| 1362 | < | case rnemdKineticSwap : | 
| 1363 | < | case rnemdKineticScale : | 
| 995 | < |  | 
| 996 | < | value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); | 
| 997 | < |  | 
| 998 | < | valueCount_[binNo] += 3; | 
| 1361 | > | if (outputTemp_) { | 
| 1362 | > | value = mass * vel.lengthSquare(); | 
| 1363 | > | tempCount_[binNo] += 3; | 
| 1364 |  | if (sd->isDirectional()) { | 
| 1365 |  | Vector3d angMom = sd->getJ(); | 
| 1366 |  | Mat3x3d I = sd->getI(); | 
| 1002 | – |  | 
| 1367 |  | if (sd->isLinear()) { | 
| 1368 |  | int i = sd->linearAxis(); | 
| 1369 |  | int j = (i + 1) % 3; | 
| 1370 |  | int k = (i + 2) % 3; | 
| 1371 |  | value += angMom[j] * angMom[j] / I(j, j) + | 
| 1372 |  | angMom[k] * angMom[k] / I(k, k); | 
| 1373 | < |  | 
| 1010 | < | valueCount_[binNo] +=2; | 
| 1011 | < |  | 
| 1373 | > | tempCount_[binNo] +=2; | 
| 1374 |  | } else { | 
| 1375 | < | value += angMom[0]*angMom[0]/I(0, 0) | 
| 1376 | < | + angMom[1]*angMom[1]/I(1, 1) | 
| 1377 | < | + angMom[2]*angMom[2]/I(2, 2); | 
| 1378 | < | valueCount_[binNo] +=3; | 
| 1375 | > | value += angMom[0] * angMom[0] / I(0, 0) + | 
| 1376 | > | angMom[1]*angMom[1]/I(1, 1) + | 
| 1377 | > | angMom[2]*angMom[2]/I(2, 2); | 
| 1378 | > | tempCount_[binNo] +=3; | 
| 1379 |  | } | 
| 1380 |  | } | 
| 1381 | < | value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb; | 
| 1382 | < |  | 
| 1383 | < | break; | 
| 1384 | < | case rnemdPx : | 
| 1385 | < | case rnemdPxScale : | 
| 1381 | > | value = value / PhysicalConstants::energyConvert | 
| 1382 | > | / PhysicalConstants::kb;//may move to getStatus() | 
| 1383 | > | tempHist_[binNo] += value; | 
| 1384 | > | } | 
| 1385 | > | if (outputVx_) { | 
| 1386 |  | value = mass * vel[0]; | 
| 1387 | < | valueCount_[binNo]++; | 
| 1388 | < | break; | 
| 1389 | < | case rnemdPy : | 
| 1390 | < | case rnemdPyScale : | 
| 1387 | > | //vxzCount_[binNo]++; | 
| 1388 | > | pxzHist_[binNo] += value; | 
| 1389 | > | } | 
| 1390 | > | if (outputVy_) { | 
| 1391 |  | value = mass * vel[1]; | 
| 1392 | < | valueCount_[binNo]++; | 
| 1393 | < | break; | 
| 1032 | < | case rnemdPz : | 
| 1033 | < | case rnemdPzScale : | 
| 1034 | < | value = pos.z(); //temporarily for homogeneous systems ONLY | 
| 1035 | < | valueCount_[binNo]++; | 
| 1036 | < | break; | 
| 1037 | < | case rnemdUnknown : | 
| 1038 | < | default : | 
| 1039 | < | value = 1.0; | 
| 1040 | < | valueCount_[binNo]++; | 
| 1041 | < | break; | 
| 1392 | > | //vyzCount_[binNo]++; | 
| 1393 | > | pyzHist_[binNo] += value; | 
| 1394 |  | } | 
| 1043 | – | valueHist_[binNo] += value; | 
| 1395 |  |  | 
| 1396 |  | if (output3DTemp_) { | 
| 1397 | < | xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert | 
| 1397 | > | value = mass * vel.x() * vel.x(); | 
| 1398 | > | xTempHist_[binNo] += value; | 
| 1399 | > | value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert | 
| 1400 |  | / PhysicalConstants::kb; | 
| 1401 | < | yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert | 
| 1401 | > | yTempHist_[binNo] += value; | 
| 1402 | > | value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert | 
| 1403 |  | / PhysicalConstants::kb; | 
| 1404 | < | zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert | 
| 1051 | < | / PhysicalConstants::kb; | 
| 1052 | < | xTempHist_[binNo] += xVal; | 
| 1053 | < | yTempHist_[binNo] += yVal; | 
| 1054 | < | zTempHist_[binNo] += zVal; | 
| 1404 | > | zTempHist_[binNo] += value; | 
| 1405 |  | xyzTempCount_[binNo]++; | 
| 1406 |  | } | 
| 1407 | + | if (outputRotTemp_) { | 
| 1408 | + | if (sd->isDirectional()) { | 
| 1409 | + | Vector3d angMom = sd->getJ(); | 
| 1410 | + | Mat3x3d I = sd->getI(); | 
| 1411 | + | if (sd->isLinear()) { | 
| 1412 | + | int i = sd->linearAxis(); | 
| 1413 | + | int j = (i + 1) % 3; | 
| 1414 | + | int k = (i + 2) % 3; | 
| 1415 | + | value = angMom[j] * angMom[j] / I(j, j) + | 
| 1416 | + | angMom[k] * angMom[k] / I(k, k); | 
| 1417 | + | rotTempCount_[binNo] +=2; | 
| 1418 | + | } else { | 
| 1419 | + | value = angMom[0] * angMom[0] / I(0, 0) + | 
| 1420 | + | angMom[1] * angMom[1] / I(1, 1) + | 
| 1421 | + | angMom[2] * angMom[2] / I(2, 2); | 
| 1422 | + | rotTempCount_[binNo] +=3; | 
| 1423 | + | } | 
| 1424 | + | } | 
| 1425 | + | value = value / PhysicalConstants::energyConvert | 
| 1426 | + | / PhysicalConstants::kb;//may move to getStatus() | 
| 1427 | + | rotTempHist_[binNo] += value; | 
| 1428 | + | } | 
| 1429 | + |  | 
| 1430 |  | } | 
| 1431 |  | } | 
| 1432 |  |  | 
| 1433 |  | void RNEMD::getStarted() { | 
| 1434 |  | collectData(); | 
| 1435 | < | /* now should be able to output profile in step 0, but might not be useful | 
| 1436 | < | Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); | 
| 1437 | < | Stats& stat = currentSnap_->statData; | 
| 1438 | < | stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_; | 
| 1435 | > | /*now can output profile in step 0, but might not be useful; | 
| 1436 | > | Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); | 
| 1437 | > | Stats& stat = currentSnap_->statData; | 
| 1438 | > | stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_; | 
| 1439 |  | */ | 
| 1440 | + | //may output a header for the log file here | 
| 1441 |  | getStatus(); | 
| 1442 |  | } | 
| 1443 |  |  | 
| 1456 |  | // all processors have the same number of bins, and STL vectors pack their | 
| 1457 |  | // arrays, so in theory, this should be safe: | 
| 1458 |  |  | 
| 1459 | < | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist_[0], | 
| 1460 | < | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1461 | < | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount_[0], | 
| 1462 | < | rnemdLogWidth_, MPI::INT, MPI::SUM); | 
| 1459 | > | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0], | 
| 1460 | > | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1461 | > | if (outputTemp_) { | 
| 1462 | > | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0], | 
| 1463 | > | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1464 | > | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0], | 
| 1465 | > | rnemdLogWidth_, MPI::INT, MPI::SUM); | 
| 1466 | > | } | 
| 1467 | > | if (outputVx_) { | 
| 1468 | > | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0], | 
| 1469 | > | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1470 | > | //MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0], | 
| 1471 | > | //                        rnemdLogWidth_, MPI::INT, MPI::SUM); | 
| 1472 | > | } | 
| 1473 | > | if (outputVy_) { | 
| 1474 | > | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0], | 
| 1475 | > | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1476 | > | //MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0], | 
| 1477 | > | //                        rnemdLogWidth_, MPI::INT, MPI::SUM); | 
| 1478 | > | } | 
| 1479 |  | if (output3DTemp_) { | 
| 1480 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0], | 
| 1481 |  | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1486 |  | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0], | 
| 1487 |  | rnemdLogWidth_, MPI::INT, MPI::SUM); | 
| 1488 |  | } | 
| 1489 | + | if (outputRotTemp_) { | 
| 1490 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0], | 
| 1491 | + | rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); | 
| 1492 | + | MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0], | 
| 1493 | + | rnemdLogWidth_, MPI::INT, MPI::SUM); | 
| 1494 | + | } | 
| 1495 | + |  | 
| 1496 |  | // If we're the root node, should we print out the results | 
| 1497 |  | int worldRank = MPI::COMM_WORLD.Get_rank(); | 
| 1498 |  | if (worldRank == 0) { | 
| 1499 |  | #endif | 
| 1500 | < | rnemdLog_ << time; | 
| 1501 | < | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1502 | < | rnemdLog_ << "\t" << valueHist_[j] / (RealType)valueCount_[j]; | 
| 1500 | > |  | 
| 1501 | > | if (outputTemp_) { | 
| 1502 | > | tempLog_ << time; | 
| 1503 | > | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1504 | > | tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j]; | 
| 1505 | > | } | 
| 1506 | > | tempLog_ << endl; | 
| 1507 |  | } | 
| 1508 | < | rnemdLog_ << "\n"; | 
| 1508 | > | if (outputVx_) { | 
| 1509 | > | vxzLog_ << time; | 
| 1510 | > | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1511 | > | vxzLog_ << "\t" << pxzHist_[j] / mHist_[j]; | 
| 1512 | > | } | 
| 1513 | > | vxzLog_ << endl; | 
| 1514 | > | } | 
| 1515 | > | if (outputVy_) { | 
| 1516 | > | vyzLog_ << time; | 
| 1517 | > | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1518 | > | vyzLog_ << "\t" << pyzHist_[j] / mHist_[j]; | 
| 1519 | > | } | 
| 1520 | > | vyzLog_ << endl; | 
| 1521 | > | } | 
| 1522 | > |  | 
| 1523 |  | if (output3DTemp_) { | 
| 1524 | < | xTempLog_ << time; | 
| 1524 | > | RealType temp; | 
| 1525 | > | xTempLog_ << time; | 
| 1526 |  | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1527 | < | xTempLog_ << "\t" << xTempHist_[j] / (RealType)xyzTempCount_[j]; | 
| 1527 | > | if (outputVx_) | 
| 1528 | > | xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j]; | 
| 1529 | > | temp = xTempHist_[j] / (RealType)xyzTempCount_[j] | 
| 1530 | > | / PhysicalConstants::energyConvert / PhysicalConstants::kb; | 
| 1531 | > | xTempLog_ << "\t" << temp; | 
| 1532 |  | } | 
| 1533 | < | xTempLog_ << "\n"; | 
| 1533 | > | xTempLog_ << endl; | 
| 1534 |  | yTempLog_ << time; | 
| 1535 |  | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1536 |  | yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j]; | 
| 1537 |  | } | 
| 1538 | < | yTempLog_ << "\n"; | 
| 1538 | > | yTempLog_ << endl; | 
| 1539 |  | zTempLog_ << time; | 
| 1540 |  | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1541 |  | zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j]; | 
| 1542 |  | } | 
| 1543 | < | zTempLog_ << "\n"; | 
| 1543 | > | zTempLog_ << endl; | 
| 1544 |  | } | 
| 1545 | + | if (outputRotTemp_) { | 
| 1546 | + | rotTempLog_ << time; | 
| 1547 | + | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1548 | + | rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j]; | 
| 1549 | + | } | 
| 1550 | + | rotTempLog_ << endl; | 
| 1551 | + | } | 
| 1552 | + |  | 
| 1553 |  | #ifdef IS_MPI | 
| 1554 |  | } | 
| 1555 |  | #endif | 
| 1556 | + |  | 
| 1557 |  | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1558 | < | valueCount_[j] = 0; | 
| 1130 | < | valueHist_[j] = 0.0; | 
| 1558 | > | mHist_[j] = 0.0; | 
| 1559 |  | } | 
| 1560 | + | if (outputTemp_) | 
| 1561 | + | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1562 | + | tempCount_[j] = 0; | 
| 1563 | + | tempHist_[j] = 0.0; | 
| 1564 | + | } | 
| 1565 | + | if (outputVx_) | 
| 1566 | + | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1567 | + | //pxzCount_[j] = 0; | 
| 1568 | + | pxzHist_[j] = 0.0; | 
| 1569 | + | } | 
| 1570 | + | if (outputVy_) | 
| 1571 | + | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1572 | + | //pyzCount_[j] = 0; | 
| 1573 | + | pyzHist_[j] = 0.0; | 
| 1574 | + | } | 
| 1575 | + |  | 
| 1576 |  | if (output3DTemp_) | 
| 1577 |  | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1578 |  | xTempHist_[j] = 0.0; | 
| 1580 |  | zTempHist_[j] = 0.0; | 
| 1581 |  | xyzTempCount_[j] = 0; | 
| 1582 |  | } | 
| 1583 | + | if (outputRotTemp_) | 
| 1584 | + | for (j = 0; j < rnemdLogWidth_; j++) { | 
| 1585 | + | rotTempCount_[j] = 0; | 
| 1586 | + | rotTempHist_[j] = 0.0; | 
| 1587 | + | } | 
| 1588 |  | } | 
| 1589 |  | } | 
| 1590 | + |  |