| 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 |
+ |
|