| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <cmath> |
| 43 |
#include "rnemd/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" |
| 49 |
#include "primitives/StuntDouble.hpp" |
| 50 |
#include "utils/PhysicalConstants.hpp" |
| 51 |
#include "utils/Tuple.hpp" |
| 52 |
#ifdef IS_MPI |
| 53 |
#include <mpi.h> |
| 54 |
#endif |
| 55 |
|
| 56 |
#ifdef _MSC_VER |
| 57 |
#define isnan(x) _isnan((x)) |
| 58 |
#define isinf(x) (!_finite(x) && !_isnan(x)) |
| 59 |
#endif |
| 60 |
|
| 61 |
#define HONKING_LARGE_VALUE 1.0e10 |
| 62 |
|
| 63 |
using namespace std; |
| 64 |
namespace OpenMD { |
| 65 |
|
| 66 |
RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), |
| 67 |
usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { |
| 68 |
|
| 69 |
trialCount_ = 0; |
| 70 |
failTrialCount_ = 0; |
| 71 |
failRootCount_ = 0; |
| 72 |
|
| 73 |
Globals * simParams = info->getSimParams(); |
| 74 |
RNEMDParameters* rnemdParams = simParams->getRNEMDParameters(); |
| 75 |
|
| 76 |
doRNEMD_ = rnemdParams->getUseRNEMD(); |
| 77 |
if (!doRNEMD_) return; |
| 78 |
|
| 79 |
stringToMethod_["Swap"] = rnemdSwap; |
| 80 |
stringToMethod_["NIVS"] = rnemdNIVS; |
| 81 |
stringToMethod_["VSS"] = rnemdVSS; |
| 82 |
|
| 83 |
stringToFluxType_["KE"] = rnemdKE; |
| 84 |
stringToFluxType_["Px"] = rnemdPx; |
| 85 |
stringToFluxType_["Py"] = rnemdPy; |
| 86 |
stringToFluxType_["Pz"] = rnemdPz; |
| 87 |
stringToFluxType_["Pvector"] = rnemdPvector; |
| 88 |
stringToFluxType_["KE+Px"] = rnemdKePx; |
| 89 |
stringToFluxType_["KE+Py"] = rnemdKePy; |
| 90 |
stringToFluxType_["KE+Pvector"] = rnemdKePvector; |
| 91 |
|
| 92 |
runTime_ = simParams->getRunTime(); |
| 93 |
statusTime_ = simParams->getStatusTime(); |
| 94 |
|
| 95 |
rnemdObjectSelection_ = rnemdParams->getObjectSelection(); |
| 96 |
evaluator_.loadScriptString(rnemdObjectSelection_); |
| 97 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 98 |
|
| 99 |
const string methStr = rnemdParams->getMethod(); |
| 100 |
bool hasFluxType = rnemdParams->haveFluxType(); |
| 101 |
|
| 102 |
string fluxStr; |
| 103 |
if (hasFluxType) { |
| 104 |
fluxStr = rnemdParams->getFluxType(); |
| 105 |
} else { |
| 106 |
sprintf(painCave.errMsg, |
| 107 |
"RNEMD: No fluxType was set in the md file. This parameter,\n" |
| 108 |
"\twhich must be one of the following values:\n" |
| 109 |
"\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n" |
| 110 |
"\tmust be set to use RNEMD\n"); |
| 111 |
painCave.isFatal = 1; |
| 112 |
painCave.severity = OPENMD_ERROR; |
| 113 |
simError(); |
| 114 |
} |
| 115 |
|
| 116 |
bool hasKineticFlux = rnemdParams->haveKineticFlux(); |
| 117 |
bool hasMomentumFlux = rnemdParams->haveMomentumFlux(); |
| 118 |
bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector(); |
| 119 |
bool hasSlabWidth = rnemdParams->haveSlabWidth(); |
| 120 |
bool hasSlabACenter = rnemdParams->haveSlabACenter(); |
| 121 |
bool hasSlabBCenter = rnemdParams->haveSlabBCenter(); |
| 122 |
bool hasOutputFileName = rnemdParams->haveOutputFileName(); |
| 123 |
bool hasOutputFields = rnemdParams->haveOutputFields(); |
| 124 |
|
| 125 |
map<string, RNEMDMethod>::iterator i; |
| 126 |
i = stringToMethod_.find(methStr); |
| 127 |
if (i != stringToMethod_.end()) |
| 128 |
rnemdMethod_ = i->second; |
| 129 |
else { |
| 130 |
sprintf(painCave.errMsg, |
| 131 |
"RNEMD: The current method,\n" |
| 132 |
"\t\t%s is not one of the recognized\n" |
| 133 |
"\texchange methods: Swap, NIVS, or VSS\n", |
| 134 |
methStr.c_str()); |
| 135 |
painCave.isFatal = 1; |
| 136 |
painCave.severity = OPENMD_ERROR; |
| 137 |
simError(); |
| 138 |
} |
| 139 |
|
| 140 |
map<string, RNEMDFluxType>::iterator j; |
| 141 |
j = stringToFluxType_.find(fluxStr); |
| 142 |
if (j != stringToFluxType_.end()) |
| 143 |
rnemdFluxType_ = j->second; |
| 144 |
else { |
| 145 |
sprintf(painCave.errMsg, |
| 146 |
"RNEMD: The current fluxType,\n" |
| 147 |
"\t\t%s\n" |
| 148 |
"\tis not one of the recognized flux types.\n", |
| 149 |
fluxStr.c_str()); |
| 150 |
painCave.isFatal = 1; |
| 151 |
painCave.severity = OPENMD_ERROR; |
| 152 |
simError(); |
| 153 |
} |
| 154 |
|
| 155 |
bool methodFluxMismatch = false; |
| 156 |
bool hasCorrectFlux = false; |
| 157 |
switch(rnemdMethod_) { |
| 158 |
case rnemdSwap: |
| 159 |
switch (rnemdFluxType_) { |
| 160 |
case rnemdKE: |
| 161 |
hasCorrectFlux = hasKineticFlux; |
| 162 |
break; |
| 163 |
case rnemdPx: |
| 164 |
case rnemdPy: |
| 165 |
case rnemdPz: |
| 166 |
hasCorrectFlux = hasMomentumFlux; |
| 167 |
break; |
| 168 |
default : |
| 169 |
methodFluxMismatch = true; |
| 170 |
break; |
| 171 |
} |
| 172 |
break; |
| 173 |
case rnemdNIVS: |
| 174 |
switch (rnemdFluxType_) { |
| 175 |
case rnemdKE: |
| 176 |
case rnemdRotKE: |
| 177 |
case rnemdFullKE: |
| 178 |
hasCorrectFlux = hasKineticFlux; |
| 179 |
break; |
| 180 |
case rnemdPx: |
| 181 |
case rnemdPy: |
| 182 |
case rnemdPz: |
| 183 |
hasCorrectFlux = hasMomentumFlux; |
| 184 |
break; |
| 185 |
case rnemdKePx: |
| 186 |
case rnemdKePy: |
| 187 |
hasCorrectFlux = hasMomentumFlux && hasKineticFlux; |
| 188 |
break; |
| 189 |
default: |
| 190 |
methodFluxMismatch = true; |
| 191 |
break; |
| 192 |
} |
| 193 |
break; |
| 194 |
case rnemdVSS: |
| 195 |
switch (rnemdFluxType_) { |
| 196 |
case rnemdKE: |
| 197 |
case rnemdRotKE: |
| 198 |
case rnemdFullKE: |
| 199 |
hasCorrectFlux = hasKineticFlux; |
| 200 |
break; |
| 201 |
case rnemdPx: |
| 202 |
case rnemdPy: |
| 203 |
case rnemdPz: |
| 204 |
hasCorrectFlux = hasMomentumFlux; |
| 205 |
break; |
| 206 |
case rnemdPvector: |
| 207 |
hasCorrectFlux = hasMomentumFluxVector; |
| 208 |
break; |
| 209 |
case rnemdKePx: |
| 210 |
case rnemdKePy: |
| 211 |
hasCorrectFlux = hasMomentumFlux && hasKineticFlux; |
| 212 |
break; |
| 213 |
case rnemdKePvector: |
| 214 |
hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux; |
| 215 |
break; |
| 216 |
default: |
| 217 |
methodFluxMismatch = true; |
| 218 |
break; |
| 219 |
} |
| 220 |
default: |
| 221 |
break; |
| 222 |
} |
| 223 |
|
| 224 |
if (methodFluxMismatch) { |
| 225 |
sprintf(painCave.errMsg, |
| 226 |
"RNEMD: The current method,\n" |
| 227 |
"\t\t%s\n" |
| 228 |
"\tcannot be used with the current flux type, %s\n", |
| 229 |
methStr.c_str(), fluxStr.c_str()); |
| 230 |
painCave.isFatal = 1; |
| 231 |
painCave.severity = OPENMD_ERROR; |
| 232 |
simError(); |
| 233 |
} |
| 234 |
if (!hasCorrectFlux) { |
| 235 |
sprintf(painCave.errMsg, |
| 236 |
"RNEMD: The current method, %s, and flux type, %s,\n" |
| 237 |
"\tdid not have the correct flux value specified. Options\n" |
| 238 |
"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n", |
| 239 |
methStr.c_str(), fluxStr.c_str()); |
| 240 |
painCave.isFatal = 1; |
| 241 |
painCave.severity = OPENMD_ERROR; |
| 242 |
simError(); |
| 243 |
} |
| 244 |
|
| 245 |
if (hasKineticFlux) { |
| 246 |
// convert the kcal / mol / Angstroms^2 / fs values in the md file |
| 247 |
// into amu / fs^3: |
| 248 |
kineticFlux_ = rnemdParams->getKineticFlux() |
| 249 |
* PhysicalConstants::energyConvert; |
| 250 |
} else { |
| 251 |
kineticFlux_ = 0.0; |
| 252 |
} |
| 253 |
if (hasMomentumFluxVector) { |
| 254 |
momentumFluxVector_ = rnemdParams->getMomentumFluxVector(); |
| 255 |
} else { |
| 256 |
momentumFluxVector_ = V3Zero; |
| 257 |
if (hasMomentumFlux) { |
| 258 |
RealType momentumFlux = rnemdParams->getMomentumFlux(); |
| 259 |
switch (rnemdFluxType_) { |
| 260 |
case rnemdPx: |
| 261 |
momentumFluxVector_.x() = momentumFlux; |
| 262 |
break; |
| 263 |
case rnemdPy: |
| 264 |
momentumFluxVector_.y() = momentumFlux; |
| 265 |
break; |
| 266 |
case rnemdPz: |
| 267 |
momentumFluxVector_.z() = momentumFlux; |
| 268 |
break; |
| 269 |
case rnemdKePx: |
| 270 |
momentumFluxVector_.x() = momentumFlux; |
| 271 |
break; |
| 272 |
case rnemdKePy: |
| 273 |
momentumFluxVector_.y() = momentumFlux; |
| 274 |
break; |
| 275 |
default: |
| 276 |
break; |
| 277 |
} |
| 278 |
} |
| 279 |
} |
| 280 |
|
| 281 |
// do some sanity checking |
| 282 |
|
| 283 |
int selectionCount = seleMan_.getSelectionCount(); |
| 284 |
int nIntegrable = info->getNGlobalIntegrableObjects(); |
| 285 |
|
| 286 |
if (selectionCount > nIntegrable) { |
| 287 |
sprintf(painCave.errMsg, |
| 288 |
"RNEMD: The current objectSelection,\n" |
| 289 |
"\t\t%s\n" |
| 290 |
"\thas resulted in %d selected objects. However,\n" |
| 291 |
"\tthe total number of integrable objects in the system\n" |
| 292 |
"\tis only %d. This is almost certainly not what you want\n" |
| 293 |
"\tto do. A likely cause of this is forgetting the _RB_0\n" |
| 294 |
"\tselector in the selection script!\n", |
| 295 |
rnemdObjectSelection_.c_str(), |
| 296 |
selectionCount, nIntegrable); |
| 297 |
painCave.isFatal = 0; |
| 298 |
painCave.severity = OPENMD_WARNING; |
| 299 |
simError(); |
| 300 |
} |
| 301 |
|
| 302 |
areaAccumulator_ = new Accumulator(); |
| 303 |
|
| 304 |
nBins_ = rnemdParams->getOutputBins(); |
| 305 |
|
| 306 |
data_.resize(RNEMD::ENDINDEX); |
| 307 |
OutputData z; |
| 308 |
z.units = "Angstroms"; |
| 309 |
z.title = "Z"; |
| 310 |
z.dataType = "RealType"; |
| 311 |
z.accumulator.reserve(nBins_); |
| 312 |
for (int i = 0; i < nBins_; i++) |
| 313 |
z.accumulator.push_back( new Accumulator() ); |
| 314 |
data_[Z] = z; |
| 315 |
outputMap_["Z"] = Z; |
| 316 |
|
| 317 |
OutputData temperature; |
| 318 |
temperature.units = "K"; |
| 319 |
temperature.title = "Temperature"; |
| 320 |
temperature.dataType = "RealType"; |
| 321 |
temperature.accumulator.reserve(nBins_); |
| 322 |
for (int i = 0; i < nBins_; i++) |
| 323 |
temperature.accumulator.push_back( new Accumulator() ); |
| 324 |
data_[TEMPERATURE] = temperature; |
| 325 |
outputMap_["TEMPERATURE"] = TEMPERATURE; |
| 326 |
|
| 327 |
OutputData velocity; |
| 328 |
velocity.units = "angstroms/fs"; |
| 329 |
velocity.title = "Velocity"; |
| 330 |
velocity.dataType = "Vector3d"; |
| 331 |
velocity.accumulator.reserve(nBins_); |
| 332 |
for (int i = 0; i < nBins_; i++) |
| 333 |
velocity.accumulator.push_back( new VectorAccumulator() ); |
| 334 |
data_[VELOCITY] = velocity; |
| 335 |
outputMap_["VELOCITY"] = VELOCITY; |
| 336 |
|
| 337 |
OutputData density; |
| 338 |
density.units = "g cm^-3"; |
| 339 |
density.title = "Density"; |
| 340 |
density.dataType = "RealType"; |
| 341 |
density.accumulator.reserve(nBins_); |
| 342 |
for (int i = 0; i < nBins_; i++) |
| 343 |
density.accumulator.push_back( new Accumulator() ); |
| 344 |
data_[DENSITY] = density; |
| 345 |
outputMap_["DENSITY"] = DENSITY; |
| 346 |
|
| 347 |
if (hasOutputFields) { |
| 348 |
parseOutputFileFormat(rnemdParams->getOutputFields()); |
| 349 |
} else { |
| 350 |
outputMask_.set(Z); |
| 351 |
switch (rnemdFluxType_) { |
| 352 |
case rnemdKE: |
| 353 |
case rnemdRotKE: |
| 354 |
case rnemdFullKE: |
| 355 |
outputMask_.set(TEMPERATURE); |
| 356 |
break; |
| 357 |
case rnemdPx: |
| 358 |
case rnemdPy: |
| 359 |
outputMask_.set(VELOCITY); |
| 360 |
break; |
| 361 |
case rnemdPz: |
| 362 |
case rnemdPvector: |
| 363 |
outputMask_.set(VELOCITY); |
| 364 |
outputMask_.set(DENSITY); |
| 365 |
break; |
| 366 |
case rnemdKePx: |
| 367 |
case rnemdKePy: |
| 368 |
outputMask_.set(TEMPERATURE); |
| 369 |
outputMask_.set(VELOCITY); |
| 370 |
break; |
| 371 |
case rnemdKePvector: |
| 372 |
outputMask_.set(TEMPERATURE); |
| 373 |
outputMask_.set(VELOCITY); |
| 374 |
outputMask_.set(DENSITY); |
| 375 |
break; |
| 376 |
default: |
| 377 |
break; |
| 378 |
} |
| 379 |
} |
| 380 |
|
| 381 |
if (hasOutputFileName) { |
| 382 |
rnemdFileName_ = rnemdParams->getOutputFileName(); |
| 383 |
} else { |
| 384 |
rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd"; |
| 385 |
} |
| 386 |
|
| 387 |
exchangeTime_ = rnemdParams->getExchangeTime(); |
| 388 |
|
| 389 |
Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot(); |
| 390 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 391 |
|
| 392 |
// Target exchange quantities (in each exchange) = 2 Lx Ly dt flux |
| 393 |
// Lx, Ly = box dimensions in x & y |
| 394 |
// dt = exchange time interval |
| 395 |
// flux = target flux |
| 396 |
|
| 397 |
RealType area = currentSnap_->getXYarea(); |
| 398 |
kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area; |
| 399 |
momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area; |
| 400 |
|
| 401 |
// total exchange sums are zeroed out at the beginning: |
| 402 |
|
| 403 |
kineticExchange_ = 0.0; |
| 404 |
momentumExchange_ = V3Zero; |
| 405 |
|
| 406 |
if (hasSlabWidth) |
| 407 |
slabWidth_ = rnemdParams->getSlabWidth(); |
| 408 |
else |
| 409 |
slabWidth_ = hmat(2,2) / 10.0; |
| 410 |
|
| 411 |
if (hasSlabACenter) |
| 412 |
slabACenter_ = rnemdParams->getSlabACenter(); |
| 413 |
else |
| 414 |
slabACenter_ = 0.0; |
| 415 |
|
| 416 |
if (hasSlabBCenter) |
| 417 |
slabBCenter_ = rnemdParams->getSlabBCenter(); |
| 418 |
else |
| 419 |
slabBCenter_ = hmat(2,2) / 2.0; |
| 420 |
|
| 421 |
} |
| 422 |
|
| 423 |
RNEMD::~RNEMD() { |
| 424 |
if (!doRNEMD_) return; |
| 425 |
#ifdef IS_MPI |
| 426 |
if (worldRank == 0) { |
| 427 |
#endif |
| 428 |
|
| 429 |
writeOutputFile(); |
| 430 |
|
| 431 |
rnemdFile_.close(); |
| 432 |
|
| 433 |
#ifdef IS_MPI |
| 434 |
} |
| 435 |
#endif |
| 436 |
} |
| 437 |
|
| 438 |
bool RNEMD::inSlabA(Vector3d pos) { |
| 439 |
return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_); |
| 440 |
} |
| 441 |
bool RNEMD::inSlabB(Vector3d pos) { |
| 442 |
return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_); |
| 443 |
} |
| 444 |
|
| 445 |
void RNEMD::doSwap() { |
| 446 |
if (!doRNEMD_) return; |
| 447 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 448 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 449 |
|
| 450 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 451 |
|
| 452 |
int selei; |
| 453 |
StuntDouble* sd; |
| 454 |
int idx; |
| 455 |
|
| 456 |
RealType min_val; |
| 457 |
bool min_found = false; |
| 458 |
StuntDouble* min_sd; |
| 459 |
|
| 460 |
RealType max_val; |
| 461 |
bool max_found = false; |
| 462 |
StuntDouble* max_sd; |
| 463 |
|
| 464 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 465 |
sd = seleMan_.nextSelected(selei)) { |
| 466 |
|
| 467 |
idx = sd->getLocalIndex(); |
| 468 |
|
| 469 |
Vector3d pos = sd->getPos(); |
| 470 |
|
| 471 |
// wrap the stuntdouble's position back into the box: |
| 472 |
|
| 473 |
if (usePeriodicBoundaryConditions_) |
| 474 |
currentSnap_->wrapVector(pos); |
| 475 |
bool inA = inSlabA(pos); |
| 476 |
bool inB = inSlabB(pos); |
| 477 |
|
| 478 |
if (inA || inB) { |
| 479 |
|
| 480 |
RealType mass = sd->getMass(); |
| 481 |
Vector3d vel = sd->getVel(); |
| 482 |
RealType value; |
| 483 |
|
| 484 |
switch(rnemdFluxType_) { |
| 485 |
case rnemdKE : |
| 486 |
|
| 487 |
value = mass * vel.lengthSquare(); |
| 488 |
|
| 489 |
if (sd->isDirectional()) { |
| 490 |
Vector3d angMom = sd->getJ(); |
| 491 |
Mat3x3d I = sd->getI(); |
| 492 |
|
| 493 |
if (sd->isLinear()) { |
| 494 |
int i = sd->linearAxis(); |
| 495 |
int j = (i + 1) % 3; |
| 496 |
int k = (i + 2) % 3; |
| 497 |
value += angMom[j] * angMom[j] / I(j, j) + |
| 498 |
angMom[k] * angMom[k] / I(k, k); |
| 499 |
} else { |
| 500 |
value += angMom[0]*angMom[0]/I(0, 0) |
| 501 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 502 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 503 |
} |
| 504 |
} //angular momenta exchange enabled |
| 505 |
value *= 0.5; |
| 506 |
break; |
| 507 |
case rnemdPx : |
| 508 |
value = mass * vel[0]; |
| 509 |
break; |
| 510 |
case rnemdPy : |
| 511 |
value = mass * vel[1]; |
| 512 |
break; |
| 513 |
case rnemdPz : |
| 514 |
value = mass * vel[2]; |
| 515 |
break; |
| 516 |
default : |
| 517 |
break; |
| 518 |
} |
| 519 |
|
| 520 |
if (inA == 0) { |
| 521 |
if (!min_found) { |
| 522 |
min_val = value; |
| 523 |
min_sd = sd; |
| 524 |
min_found = true; |
| 525 |
} else { |
| 526 |
if (min_val > value) { |
| 527 |
min_val = value; |
| 528 |
min_sd = sd; |
| 529 |
} |
| 530 |
} |
| 531 |
} else { |
| 532 |
if (!max_found) { |
| 533 |
max_val = value; |
| 534 |
max_sd = sd; |
| 535 |
max_found = true; |
| 536 |
} else { |
| 537 |
if (max_val < value) { |
| 538 |
max_val = value; |
| 539 |
max_sd = sd; |
| 540 |
} |
| 541 |
} |
| 542 |
} |
| 543 |
} |
| 544 |
} |
| 545 |
|
| 546 |
#ifdef IS_MPI |
| 547 |
int nProc, worldRank; |
| 548 |
|
| 549 |
nProc = MPI::COMM_WORLD.Get_size(); |
| 550 |
worldRank = MPI::COMM_WORLD.Get_rank(); |
| 551 |
|
| 552 |
bool my_min_found = min_found; |
| 553 |
bool my_max_found = max_found; |
| 554 |
|
| 555 |
// Even if we didn't find a minimum, did someone else? |
| 556 |
MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR); |
| 557 |
// Even if we didn't find a maximum, did someone else? |
| 558 |
MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR); |
| 559 |
#endif |
| 560 |
|
| 561 |
if (max_found && min_found) { |
| 562 |
|
| 563 |
#ifdef IS_MPI |
| 564 |
struct { |
| 565 |
RealType val; |
| 566 |
int rank; |
| 567 |
} max_vals, min_vals; |
| 568 |
|
| 569 |
if (my_min_found) { |
| 570 |
min_vals.val = min_val; |
| 571 |
} else { |
| 572 |
min_vals.val = HONKING_LARGE_VALUE; |
| 573 |
} |
| 574 |
min_vals.rank = worldRank; |
| 575 |
|
| 576 |
// Who had the minimum? |
| 577 |
MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals, |
| 578 |
1, MPI::REALTYPE_INT, MPI::MINLOC); |
| 579 |
min_val = min_vals.val; |
| 580 |
|
| 581 |
if (my_max_found) { |
| 582 |
max_vals.val = max_val; |
| 583 |
} else { |
| 584 |
max_vals.val = -HONKING_LARGE_VALUE; |
| 585 |
} |
| 586 |
max_vals.rank = worldRank; |
| 587 |
|
| 588 |
// Who had the maximum? |
| 589 |
MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals, |
| 590 |
1, MPI::REALTYPE_INT, MPI::MAXLOC); |
| 591 |
max_val = max_vals.val; |
| 592 |
#endif |
| 593 |
|
| 594 |
if (min_val < max_val) { |
| 595 |
|
| 596 |
#ifdef IS_MPI |
| 597 |
if (max_vals.rank == worldRank && min_vals.rank == worldRank) { |
| 598 |
// I have both maximum and minimum, so proceed like a single |
| 599 |
// processor version: |
| 600 |
#endif |
| 601 |
|
| 602 |
Vector3d min_vel = min_sd->getVel(); |
| 603 |
Vector3d max_vel = max_sd->getVel(); |
| 604 |
RealType temp_vel; |
| 605 |
|
| 606 |
switch(rnemdFluxType_) { |
| 607 |
case rnemdKE : |
| 608 |
min_sd->setVel(max_vel); |
| 609 |
max_sd->setVel(min_vel); |
| 610 |
if (min_sd->isDirectional() && max_sd->isDirectional()) { |
| 611 |
Vector3d min_angMom = min_sd->getJ(); |
| 612 |
Vector3d max_angMom = max_sd->getJ(); |
| 613 |
min_sd->setJ(max_angMom); |
| 614 |
max_sd->setJ(min_angMom); |
| 615 |
}//angular momenta exchange enabled |
| 616 |
//assumes same rigid body identity |
| 617 |
break; |
| 618 |
case rnemdPx : |
| 619 |
temp_vel = min_vel.x(); |
| 620 |
min_vel.x() = max_vel.x(); |
| 621 |
max_vel.x() = temp_vel; |
| 622 |
min_sd->setVel(min_vel); |
| 623 |
max_sd->setVel(max_vel); |
| 624 |
break; |
| 625 |
case rnemdPy : |
| 626 |
temp_vel = min_vel.y(); |
| 627 |
min_vel.y() = max_vel.y(); |
| 628 |
max_vel.y() = temp_vel; |
| 629 |
min_sd->setVel(min_vel); |
| 630 |
max_sd->setVel(max_vel); |
| 631 |
break; |
| 632 |
case rnemdPz : |
| 633 |
temp_vel = min_vel.z(); |
| 634 |
min_vel.z() = max_vel.z(); |
| 635 |
max_vel.z() = temp_vel; |
| 636 |
min_sd->setVel(min_vel); |
| 637 |
max_sd->setVel(max_vel); |
| 638 |
break; |
| 639 |
default : |
| 640 |
break; |
| 641 |
} |
| 642 |
|
| 643 |
#ifdef IS_MPI |
| 644 |
// the rest of the cases only apply in parallel simulations: |
| 645 |
} else if (max_vals.rank == worldRank) { |
| 646 |
// I had the max, but not the minimum |
| 647 |
|
| 648 |
Vector3d min_vel; |
| 649 |
Vector3d max_vel = max_sd->getVel(); |
| 650 |
MPI::Status status; |
| 651 |
|
| 652 |
// point-to-point swap of the velocity vector |
| 653 |
MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 654 |
min_vals.rank, 0, |
| 655 |
min_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 656 |
min_vals.rank, 0, status); |
| 657 |
|
| 658 |
switch(rnemdFluxType_) { |
| 659 |
case rnemdKE : |
| 660 |
max_sd->setVel(min_vel); |
| 661 |
//angular momenta exchange enabled |
| 662 |
if (max_sd->isDirectional()) { |
| 663 |
Vector3d min_angMom; |
| 664 |
Vector3d max_angMom = max_sd->getJ(); |
| 665 |
|
| 666 |
// point-to-point swap of the angular momentum vector |
| 667 |
MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3, |
| 668 |
MPI::REALTYPE, min_vals.rank, 1, |
| 669 |
min_angMom.getArrayPointer(), 3, |
| 670 |
MPI::REALTYPE, min_vals.rank, 1, |
| 671 |
status); |
| 672 |
|
| 673 |
max_sd->setJ(min_angMom); |
| 674 |
} |
| 675 |
break; |
| 676 |
case rnemdPx : |
| 677 |
max_vel.x() = min_vel.x(); |
| 678 |
max_sd->setVel(max_vel); |
| 679 |
break; |
| 680 |
case rnemdPy : |
| 681 |
max_vel.y() = min_vel.y(); |
| 682 |
max_sd->setVel(max_vel); |
| 683 |
break; |
| 684 |
case rnemdPz : |
| 685 |
max_vel.z() = min_vel.z(); |
| 686 |
max_sd->setVel(max_vel); |
| 687 |
break; |
| 688 |
default : |
| 689 |
break; |
| 690 |
} |
| 691 |
} else if (min_vals.rank == worldRank) { |
| 692 |
// I had the minimum but not the maximum: |
| 693 |
|
| 694 |
Vector3d max_vel; |
| 695 |
Vector3d min_vel = min_sd->getVel(); |
| 696 |
MPI::Status status; |
| 697 |
|
| 698 |
// point-to-point swap of the velocity vector |
| 699 |
MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 700 |
max_vals.rank, 0, |
| 701 |
max_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 702 |
max_vals.rank, 0, status); |
| 703 |
|
| 704 |
switch(rnemdFluxType_) { |
| 705 |
case rnemdKE : |
| 706 |
min_sd->setVel(max_vel); |
| 707 |
//angular momenta exchange enabled |
| 708 |
if (min_sd->isDirectional()) { |
| 709 |
Vector3d min_angMom = min_sd->getJ(); |
| 710 |
Vector3d max_angMom; |
| 711 |
|
| 712 |
// point-to-point swap of the angular momentum vector |
| 713 |
MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3, |
| 714 |
MPI::REALTYPE, max_vals.rank, 1, |
| 715 |
max_angMom.getArrayPointer(), 3, |
| 716 |
MPI::REALTYPE, max_vals.rank, 1, |
| 717 |
status); |
| 718 |
|
| 719 |
min_sd->setJ(max_angMom); |
| 720 |
} |
| 721 |
break; |
| 722 |
case rnemdPx : |
| 723 |
min_vel.x() = max_vel.x(); |
| 724 |
min_sd->setVel(min_vel); |
| 725 |
break; |
| 726 |
case rnemdPy : |
| 727 |
min_vel.y() = max_vel.y(); |
| 728 |
min_sd->setVel(min_vel); |
| 729 |
break; |
| 730 |
case rnemdPz : |
| 731 |
min_vel.z() = max_vel.z(); |
| 732 |
min_sd->setVel(min_vel); |
| 733 |
break; |
| 734 |
default : |
| 735 |
break; |
| 736 |
} |
| 737 |
} |
| 738 |
#endif |
| 739 |
|
| 740 |
switch(rnemdFluxType_) { |
| 741 |
case rnemdKE: |
| 742 |
kineticExchange_ += max_val - min_val; |
| 743 |
break; |
| 744 |
case rnemdPx: |
| 745 |
momentumExchange_.x() += max_val - min_val; |
| 746 |
break; |
| 747 |
case rnemdPy: |
| 748 |
momentumExchange_.y() += max_val - min_val; |
| 749 |
break; |
| 750 |
case rnemdPz: |
| 751 |
momentumExchange_.z() += max_val - min_val; |
| 752 |
break; |
| 753 |
default: |
| 754 |
break; |
| 755 |
} |
| 756 |
} else { |
| 757 |
sprintf(painCave.errMsg, |
| 758 |
"RNEMD::doSwap exchange NOT performed because min_val > max_val\n"); |
| 759 |
painCave.isFatal = 0; |
| 760 |
painCave.severity = OPENMD_INFO; |
| 761 |
simError(); |
| 762 |
failTrialCount_++; |
| 763 |
} |
| 764 |
} else { |
| 765 |
sprintf(painCave.errMsg, |
| 766 |
"RNEMD::doSwap exchange NOT performed because selected object\n" |
| 767 |
"\twas not present in at least one of the two slabs.\n"); |
| 768 |
painCave.isFatal = 0; |
| 769 |
painCave.severity = OPENMD_INFO; |
| 770 |
simError(); |
| 771 |
failTrialCount_++; |
| 772 |
} |
| 773 |
} |
| 774 |
|
| 775 |
void RNEMD::doNIVS() { |
| 776 |
if (!doRNEMD_) return; |
| 777 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 778 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 779 |
|
| 780 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 781 |
|
| 782 |
int selei; |
| 783 |
StuntDouble* sd; |
| 784 |
int idx; |
| 785 |
|
| 786 |
vector<StuntDouble*> hotBin, coldBin; |
| 787 |
|
| 788 |
RealType Phx = 0.0; |
| 789 |
RealType Phy = 0.0; |
| 790 |
RealType Phz = 0.0; |
| 791 |
RealType Khx = 0.0; |
| 792 |
RealType Khy = 0.0; |
| 793 |
RealType Khz = 0.0; |
| 794 |
RealType Khw = 0.0; |
| 795 |
RealType Pcx = 0.0; |
| 796 |
RealType Pcy = 0.0; |
| 797 |
RealType Pcz = 0.0; |
| 798 |
RealType Kcx = 0.0; |
| 799 |
RealType Kcy = 0.0; |
| 800 |
RealType Kcz = 0.0; |
| 801 |
RealType Kcw = 0.0; |
| 802 |
|
| 803 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 804 |
sd = seleMan_.nextSelected(selei)) { |
| 805 |
|
| 806 |
idx = sd->getLocalIndex(); |
| 807 |
|
| 808 |
Vector3d pos = sd->getPos(); |
| 809 |
|
| 810 |
// wrap the stuntdouble's position back into the box: |
| 811 |
|
| 812 |
if (usePeriodicBoundaryConditions_) |
| 813 |
currentSnap_->wrapVector(pos); |
| 814 |
|
| 815 |
// which bin is this stuntdouble in? |
| 816 |
bool inA = inSlabA(pos); |
| 817 |
bool inB = inSlabB(pos); |
| 818 |
|
| 819 |
if (inA || inB) { |
| 820 |
|
| 821 |
RealType mass = sd->getMass(); |
| 822 |
Vector3d vel = sd->getVel(); |
| 823 |
|
| 824 |
if (inA) { |
| 825 |
hotBin.push_back(sd); |
| 826 |
Phx += mass * vel.x(); |
| 827 |
Phy += mass * vel.y(); |
| 828 |
Phz += mass * vel.z(); |
| 829 |
Khx += mass * vel.x() * vel.x(); |
| 830 |
Khy += mass * vel.y() * vel.y(); |
| 831 |
Khz += mass * vel.z() * vel.z(); |
| 832 |
if (sd->isDirectional()) { |
| 833 |
Vector3d angMom = sd->getJ(); |
| 834 |
Mat3x3d I = sd->getI(); |
| 835 |
if (sd->isLinear()) { |
| 836 |
int i = sd->linearAxis(); |
| 837 |
int j = (i + 1) % 3; |
| 838 |
int k = (i + 2) % 3; |
| 839 |
Khw += angMom[j] * angMom[j] / I(j, j) + |
| 840 |
angMom[k] * angMom[k] / I(k, k); |
| 841 |
} else { |
| 842 |
Khw += angMom[0]*angMom[0]/I(0, 0) |
| 843 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 844 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 845 |
} |
| 846 |
} |
| 847 |
} else { |
| 848 |
coldBin.push_back(sd); |
| 849 |
Pcx += mass * vel.x(); |
| 850 |
Pcy += mass * vel.y(); |
| 851 |
Pcz += mass * vel.z(); |
| 852 |
Kcx += mass * vel.x() * vel.x(); |
| 853 |
Kcy += mass * vel.y() * vel.y(); |
| 854 |
Kcz += mass * vel.z() * vel.z(); |
| 855 |
if (sd->isDirectional()) { |
| 856 |
Vector3d angMom = sd->getJ(); |
| 857 |
Mat3x3d I = sd->getI(); |
| 858 |
if (sd->isLinear()) { |
| 859 |
int i = sd->linearAxis(); |
| 860 |
int j = (i + 1) % 3; |
| 861 |
int k = (i + 2) % 3; |
| 862 |
Kcw += angMom[j] * angMom[j] / I(j, j) + |
| 863 |
angMom[k] * angMom[k] / I(k, k); |
| 864 |
} else { |
| 865 |
Kcw += angMom[0]*angMom[0]/I(0, 0) |
| 866 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 867 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 868 |
} |
| 869 |
} |
| 870 |
} |
| 871 |
} |
| 872 |
} |
| 873 |
|
| 874 |
Khx *= 0.5; |
| 875 |
Khy *= 0.5; |
| 876 |
Khz *= 0.5; |
| 877 |
Khw *= 0.5; |
| 878 |
Kcx *= 0.5; |
| 879 |
Kcy *= 0.5; |
| 880 |
Kcz *= 0.5; |
| 881 |
Kcw *= 0.5; |
| 882 |
|
| 883 |
#ifdef IS_MPI |
| 884 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM); |
| 885 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM); |
| 886 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM); |
| 887 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM); |
| 888 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM); |
| 889 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM); |
| 890 |
|
| 891 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM); |
| 892 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM); |
| 893 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM); |
| 894 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM); |
| 895 |
|
| 896 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM); |
| 897 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM); |
| 898 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM); |
| 899 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM); |
| 900 |
#endif |
| 901 |
|
| 902 |
//solve coldBin coeff's first |
| 903 |
RealType px = Pcx / Phx; |
| 904 |
RealType py = Pcy / Phy; |
| 905 |
RealType pz = Pcz / Phz; |
| 906 |
RealType c, x, y, z; |
| 907 |
bool successfulScale = false; |
| 908 |
if ((rnemdFluxType_ == rnemdFullKE) || |
| 909 |
(rnemdFluxType_ == rnemdRotKE)) { |
| 910 |
//may need sanity check Khw & Kcw > 0 |
| 911 |
|
| 912 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 913 |
c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw); |
| 914 |
} else { |
| 915 |
c = 1.0 - kineticTarget_ / Kcw; |
| 916 |
} |
| 917 |
|
| 918 |
if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients |
| 919 |
c = sqrt(c); |
| 920 |
//std::cerr << "cold slab scaling coefficient: " << c << endl; |
| 921 |
//now convert to hotBin coefficient |
| 922 |
RealType w = 0.0; |
| 923 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 924 |
x = 1.0 + px * (1.0 - c); |
| 925 |
y = 1.0 + py * (1.0 - c); |
| 926 |
z = 1.0 + pz * (1.0 - c); |
| 927 |
/* more complicated way |
| 928 |
w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz |
| 929 |
+ Khx * px * px + Khy * py * py + Khz * pz * pz) |
| 930 |
- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py) |
| 931 |
+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px) |
| 932 |
+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) |
| 933 |
- Kcx - Kcy - Kcz)) / Khw; the following is simpler |
| 934 |
*/ |
| 935 |
if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) && |
| 936 |
(fabs(z - 1.0) < 0.1)) { |
| 937 |
w = 1.0 + (kineticTarget_ |
| 938 |
+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y) |
| 939 |
+ Khz * (1.0 - z * z)) / Khw; |
| 940 |
}//no need to calculate w if x, y or z is out of range |
| 941 |
} else { |
| 942 |
w = 1.0 + kineticTarget_ / Khw; |
| 943 |
} |
| 944 |
if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients |
| 945 |
//if w is in the right range, so should be x, y, z. |
| 946 |
vector<StuntDouble*>::iterator sdi; |
| 947 |
Vector3d vel; |
| 948 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 949 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 950 |
vel = (*sdi)->getVel() * c; |
| 951 |
(*sdi)->setVel(vel); |
| 952 |
} |
| 953 |
if ((*sdi)->isDirectional()) { |
| 954 |
Vector3d angMom = (*sdi)->getJ() * c; |
| 955 |
(*sdi)->setJ(angMom); |
| 956 |
} |
| 957 |
} |
| 958 |
w = sqrt(w); |
| 959 |
// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z |
| 960 |
// << "\twh= " << w << endl; |
| 961 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 962 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 963 |
vel = (*sdi)->getVel(); |
| 964 |
vel.x() *= x; |
| 965 |
vel.y() *= y; |
| 966 |
vel.z() *= z; |
| 967 |
(*sdi)->setVel(vel); |
| 968 |
} |
| 969 |
if ((*sdi)->isDirectional()) { |
| 970 |
Vector3d angMom = (*sdi)->getJ() * w; |
| 971 |
(*sdi)->setJ(angMom); |
| 972 |
} |
| 973 |
} |
| 974 |
successfulScale = true; |
| 975 |
kineticExchange_ += kineticTarget_; |
| 976 |
} |
| 977 |
} |
| 978 |
} else { |
| 979 |
RealType a000, a110, c0, a001, a111, b01, b11, c1; |
| 980 |
switch(rnemdFluxType_) { |
| 981 |
case rnemdKE : |
| 982 |
/* used hotBin coeff's & only scale x & y dimensions |
| 983 |
RealType px = Phx / Pcx; |
| 984 |
RealType py = Phy / Pcy; |
| 985 |
a110 = Khy; |
| 986 |
c0 = - Khx - Khy - kineticTarget_; |
| 987 |
a000 = Khx; |
| 988 |
a111 = Kcy * py * py; |
| 989 |
b11 = -2.0 * Kcy * py * (1.0 + py); |
| 990 |
c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_; |
| 991 |
b01 = -2.0 * Kcx * px * (1.0 + px); |
| 992 |
a001 = Kcx * px * px; |
| 993 |
*/ |
| 994 |
//scale all three dimensions, let c_x = c_y |
| 995 |
a000 = Kcx + Kcy; |
| 996 |
a110 = Kcz; |
| 997 |
c0 = kineticTarget_ - Kcx - Kcy - Kcz; |
| 998 |
a001 = Khx * px * px + Khy * py * py; |
| 999 |
a111 = Khz * pz * pz; |
| 1000 |
b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)); |
| 1001 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 1002 |
c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) |
| 1003 |
+ Khz * pz * (2.0 + pz) - kineticTarget_; |
| 1004 |
break; |
| 1005 |
case rnemdPx : |
| 1006 |
c = 1 - momentumTarget_.x() / Pcx; |
| 1007 |
a000 = Kcy; |
| 1008 |
a110 = Kcz; |
| 1009 |
c0 = Kcx * c * c - Kcx - Kcy - Kcz; |
| 1010 |
a001 = py * py * Khy; |
| 1011 |
a111 = pz * pz * Khz; |
| 1012 |
b01 = -2.0 * Khy * py * (1.0 + py); |
| 1013 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 1014 |
c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) |
| 1015 |
+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0); |
| 1016 |
break; |
| 1017 |
case rnemdPy : |
| 1018 |
c = 1 - momentumTarget_.y() / Pcy; |
| 1019 |
a000 = Kcx; |
| 1020 |
a110 = Kcz; |
| 1021 |
c0 = Kcy * c * c - Kcx - Kcy - Kcz; |
| 1022 |
a001 = px * px * Khx; |
| 1023 |
a111 = pz * pz * Khz; |
| 1024 |
b01 = -2.0 * Khx * px * (1.0 + px); |
| 1025 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 1026 |
c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz) |
| 1027 |
+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0); |
| 1028 |
break; |
| 1029 |
case rnemdPz ://we don't really do this, do we? |
| 1030 |
c = 1 - momentumTarget_.z() / Pcz; |
| 1031 |
a000 = Kcx; |
| 1032 |
a110 = Kcy; |
| 1033 |
c0 = Kcz * c * c - Kcx - Kcy - Kcz; |
| 1034 |
a001 = px * px * Khx; |
| 1035 |
a111 = py * py * Khy; |
| 1036 |
b01 = -2.0 * Khx * px * (1.0 + px); |
| 1037 |
b11 = -2.0 * Khy * py * (1.0 + py); |
| 1038 |
c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) |
| 1039 |
+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0); |
| 1040 |
break; |
| 1041 |
default : |
| 1042 |
break; |
| 1043 |
} |
| 1044 |
|
| 1045 |
RealType v1 = a000 * a111 - a001 * a110; |
| 1046 |
RealType v2 = a000 * b01; |
| 1047 |
RealType v3 = a000 * b11; |
| 1048 |
RealType v4 = a000 * c1 - a001 * c0; |
| 1049 |
RealType v8 = a110 * b01; |
| 1050 |
RealType v10 = - b01 * c0; |
| 1051 |
|
| 1052 |
RealType u0 = v2 * v10 - v4 * v4; |
| 1053 |
RealType u1 = -2.0 * v3 * v4; |
| 1054 |
RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4; |
| 1055 |
RealType u3 = -2.0 * v1 * v3; |
| 1056 |
RealType u4 = - v1 * v1; |
| 1057 |
//rescale coefficients |
| 1058 |
RealType maxAbs = fabs(u0); |
| 1059 |
if (maxAbs < fabs(u1)) maxAbs = fabs(u1); |
| 1060 |
if (maxAbs < fabs(u2)) maxAbs = fabs(u2); |
| 1061 |
if (maxAbs < fabs(u3)) maxAbs = fabs(u3); |
| 1062 |
if (maxAbs < fabs(u4)) maxAbs = fabs(u4); |
| 1063 |
u0 /= maxAbs; |
| 1064 |
u1 /= maxAbs; |
| 1065 |
u2 /= maxAbs; |
| 1066 |
u3 /= maxAbs; |
| 1067 |
u4 /= maxAbs; |
| 1068 |
//max_element(start, end) is also available. |
| 1069 |
Polynomial<RealType> poly; //same as DoublePolynomial poly; |
| 1070 |
poly.setCoefficient(4, u4); |
| 1071 |
poly.setCoefficient(3, u3); |
| 1072 |
poly.setCoefficient(2, u2); |
| 1073 |
poly.setCoefficient(1, u1); |
| 1074 |
poly.setCoefficient(0, u0); |
| 1075 |
vector<RealType> realRoots = poly.FindRealRoots(); |
| 1076 |
|
| 1077 |
vector<RealType>::iterator ri; |
| 1078 |
RealType r1, r2, alpha0; |
| 1079 |
vector<pair<RealType,RealType> > rps; |
| 1080 |
for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) { |
| 1081 |
r2 = *ri; |
| 1082 |
//check if FindRealRoots() give the right answer |
| 1083 |
if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { |
| 1084 |
sprintf(painCave.errMsg, |
| 1085 |
"RNEMD Warning: polynomial solve seems to have an error!"); |
| 1086 |
painCave.isFatal = 0; |
| 1087 |
simError(); |
| 1088 |
failRootCount_++; |
| 1089 |
} |
| 1090 |
//might not be useful w/o rescaling coefficients |
| 1091 |
alpha0 = -c0 - a110 * r2 * r2; |
| 1092 |
if (alpha0 >= 0.0) { |
| 1093 |
r1 = sqrt(alpha0 / a000); |
| 1094 |
if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) |
| 1095 |
< 1e-6) |
| 1096 |
{ rps.push_back(make_pair(r1, r2)); } |
| 1097 |
if (r1 > 1e-6) { //r1 non-negative |
| 1098 |
r1 = -r1; |
| 1099 |
if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) |
| 1100 |
< 1e-6) |
| 1101 |
{ rps.push_back(make_pair(r1, r2)); } |
| 1102 |
} |
| 1103 |
} |
| 1104 |
} |
| 1105 |
// Consider combining together the solving pair part w/ the searching |
| 1106 |
// best solution part so that we don't need the pairs vector |
| 1107 |
if (!rps.empty()) { |
| 1108 |
RealType smallestDiff = HONKING_LARGE_VALUE; |
| 1109 |
RealType diff; |
| 1110 |
pair<RealType,RealType> bestPair = make_pair(1.0, 1.0); |
| 1111 |
vector<pair<RealType,RealType> >::iterator rpi; |
| 1112 |
for (rpi = rps.begin(); rpi != rps.end(); rpi++) { |
| 1113 |
r1 = (*rpi).first; |
| 1114 |
r2 = (*rpi).second; |
| 1115 |
switch(rnemdFluxType_) { |
| 1116 |
case rnemdKE : |
| 1117 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1118 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2) |
| 1119 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); |
| 1120 |
break; |
| 1121 |
case rnemdPx : |
| 1122 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1123 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); |
| 1124 |
break; |
| 1125 |
case rnemdPy : |
| 1126 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1127 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); |
| 1128 |
break; |
| 1129 |
case rnemdPz : |
| 1130 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1131 |
+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); |
| 1132 |
default : |
| 1133 |
break; |
| 1134 |
} |
| 1135 |
if (diff < smallestDiff) { |
| 1136 |
smallestDiff = diff; |
| 1137 |
bestPair = *rpi; |
| 1138 |
} |
| 1139 |
} |
| 1140 |
#ifdef IS_MPI |
| 1141 |
if (worldRank == 0) { |
| 1142 |
#endif |
| 1143 |
// sprintf(painCave.errMsg, |
| 1144 |
// "RNEMD: roots r1= %lf\tr2 = %lf\n", |
| 1145 |
// bestPair.first, bestPair.second); |
| 1146 |
// painCave.isFatal = 0; |
| 1147 |
// painCave.severity = OPENMD_INFO; |
| 1148 |
// simError(); |
| 1149 |
#ifdef IS_MPI |
| 1150 |
} |
| 1151 |
#endif |
| 1152 |
|
| 1153 |
switch(rnemdFluxType_) { |
| 1154 |
case rnemdKE : |
| 1155 |
x = bestPair.first; |
| 1156 |
y = bestPair.first; |
| 1157 |
z = bestPair.second; |
| 1158 |
break; |
| 1159 |
case rnemdPx : |
| 1160 |
x = c; |
| 1161 |
y = bestPair.first; |
| 1162 |
z = bestPair.second; |
| 1163 |
break; |
| 1164 |
case rnemdPy : |
| 1165 |
x = bestPair.first; |
| 1166 |
y = c; |
| 1167 |
z = bestPair.second; |
| 1168 |
break; |
| 1169 |
case rnemdPz : |
| 1170 |
x = bestPair.first; |
| 1171 |
y = bestPair.second; |
| 1172 |
z = c; |
| 1173 |
break; |
| 1174 |
default : |
| 1175 |
break; |
| 1176 |
} |
| 1177 |
vector<StuntDouble*>::iterator sdi; |
| 1178 |
Vector3d vel; |
| 1179 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1180 |
vel = (*sdi)->getVel(); |
| 1181 |
vel.x() *= x; |
| 1182 |
vel.y() *= y; |
| 1183 |
vel.z() *= z; |
| 1184 |
(*sdi)->setVel(vel); |
| 1185 |
} |
| 1186 |
//convert to hotBin coefficient |
| 1187 |
x = 1.0 + px * (1.0 - x); |
| 1188 |
y = 1.0 + py * (1.0 - y); |
| 1189 |
z = 1.0 + pz * (1.0 - z); |
| 1190 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1191 |
vel = (*sdi)->getVel(); |
| 1192 |
vel.x() *= x; |
| 1193 |
vel.y() *= y; |
| 1194 |
vel.z() *= z; |
| 1195 |
(*sdi)->setVel(vel); |
| 1196 |
} |
| 1197 |
successfulScale = true; |
| 1198 |
switch(rnemdFluxType_) { |
| 1199 |
case rnemdKE : |
| 1200 |
kineticExchange_ += kineticTarget_; |
| 1201 |
break; |
| 1202 |
case rnemdPx : |
| 1203 |
case rnemdPy : |
| 1204 |
case rnemdPz : |
| 1205 |
momentumExchange_ += momentumTarget_; |
| 1206 |
break; |
| 1207 |
default : |
| 1208 |
break; |
| 1209 |
} |
| 1210 |
} |
| 1211 |
} |
| 1212 |
if (successfulScale != true) { |
| 1213 |
sprintf(painCave.errMsg, |
| 1214 |
"RNEMD::doNIVS exchange NOT performed - roots that solve\n" |
| 1215 |
"\tthe constraint equations may not exist or there may be\n" |
| 1216 |
"\tno selected objects in one or both slabs.\n"); |
| 1217 |
painCave.isFatal = 0; |
| 1218 |
painCave.severity = OPENMD_INFO; |
| 1219 |
simError(); |
| 1220 |
failTrialCount_++; |
| 1221 |
} |
| 1222 |
} |
| 1223 |
|
| 1224 |
void RNEMD::doVSS() { |
| 1225 |
if (!doRNEMD_) return; |
| 1226 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1227 |
RealType time = currentSnap_->getTime(); |
| 1228 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1229 |
|
| 1230 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 1231 |
|
| 1232 |
int selei; |
| 1233 |
StuntDouble* sd; |
| 1234 |
int idx; |
| 1235 |
|
| 1236 |
vector<StuntDouble*> hotBin, coldBin; |
| 1237 |
|
| 1238 |
Vector3d Ph(V3Zero); |
| 1239 |
RealType Mh = 0.0; |
| 1240 |
RealType Kh = 0.0; |
| 1241 |
Vector3d Pc(V3Zero); |
| 1242 |
RealType Mc = 0.0; |
| 1243 |
RealType Kc = 0.0; |
| 1244 |
|
| 1245 |
|
| 1246 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 1247 |
sd = seleMan_.nextSelected(selei)) { |
| 1248 |
|
| 1249 |
idx = sd->getLocalIndex(); |
| 1250 |
|
| 1251 |
Vector3d pos = sd->getPos(); |
| 1252 |
|
| 1253 |
// wrap the stuntdouble's position back into the box: |
| 1254 |
|
| 1255 |
if (usePeriodicBoundaryConditions_) |
| 1256 |
currentSnap_->wrapVector(pos); |
| 1257 |
|
| 1258 |
// which bin is this stuntdouble in? |
| 1259 |
bool inA = inSlabA(pos); |
| 1260 |
bool inB = inSlabB(pos); |
| 1261 |
|
| 1262 |
if (inA || inB) { |
| 1263 |
|
| 1264 |
RealType mass = sd->getMass(); |
| 1265 |
Vector3d vel = sd->getVel(); |
| 1266 |
|
| 1267 |
if (inA) { |
| 1268 |
hotBin.push_back(sd); |
| 1269 |
//std::cerr << "before, velocity = " << vel << endl; |
| 1270 |
Ph += mass * vel; |
| 1271 |
//std::cerr << "after, velocity = " << vel << endl; |
| 1272 |
Mh += mass; |
| 1273 |
Kh += mass * vel.lengthSquare(); |
| 1274 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1275 |
if (sd->isDirectional()) { |
| 1276 |
Vector3d angMom = sd->getJ(); |
| 1277 |
Mat3x3d I = sd->getI(); |
| 1278 |
if (sd->isLinear()) { |
| 1279 |
int i = sd->linearAxis(); |
| 1280 |
int j = (i + 1) % 3; |
| 1281 |
int k = (i + 2) % 3; |
| 1282 |
Kh += angMom[j] * angMom[j] / I(j, j) + |
| 1283 |
angMom[k] * angMom[k] / I(k, k); |
| 1284 |
} else { |
| 1285 |
Kh += angMom[0] * angMom[0] / I(0, 0) + |
| 1286 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1287 |
angMom[2] * angMom[2] / I(2, 2); |
| 1288 |
} |
| 1289 |
} |
| 1290 |
} |
| 1291 |
} else { //midBin_ |
| 1292 |
coldBin.push_back(sd); |
| 1293 |
Pc += mass * vel; |
| 1294 |
Mc += mass; |
| 1295 |
Kc += mass * vel.lengthSquare(); |
| 1296 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1297 |
if (sd->isDirectional()) { |
| 1298 |
Vector3d angMom = sd->getJ(); |
| 1299 |
Mat3x3d I = sd->getI(); |
| 1300 |
if (sd->isLinear()) { |
| 1301 |
int i = sd->linearAxis(); |
| 1302 |
int j = (i + 1) % 3; |
| 1303 |
int k = (i + 2) % 3; |
| 1304 |
Kc += angMom[j] * angMom[j] / I(j, j) + |
| 1305 |
angMom[k] * angMom[k] / I(k, k); |
| 1306 |
} else { |
| 1307 |
Kc += angMom[0] * angMom[0] / I(0, 0) + |
| 1308 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1309 |
angMom[2] * angMom[2] / I(2, 2); |
| 1310 |
} |
| 1311 |
} |
| 1312 |
} |
| 1313 |
} |
| 1314 |
} |
| 1315 |
} |
| 1316 |
|
| 1317 |
Kh *= 0.5; |
| 1318 |
Kc *= 0.5; |
| 1319 |
|
| 1320 |
// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc |
| 1321 |
// << "\tKc= " << Kc << endl; |
| 1322 |
// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl; |
| 1323 |
|
| 1324 |
#ifdef IS_MPI |
| 1325 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1326 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1327 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM); |
| 1328 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM); |
| 1329 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM); |
| 1330 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM); |
| 1331 |
#endif |
| 1332 |
|
| 1333 |
bool successfulExchange = false; |
| 1334 |
if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty |
| 1335 |
Vector3d vc = Pc / Mc; |
| 1336 |
Vector3d ac = -momentumTarget_ / Mc + vc; |
| 1337 |
Vector3d acrec = -momentumTarget_ / Mc; |
| 1338 |
RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare(); |
| 1339 |
if (cNumerator > 0.0) { |
| 1340 |
RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare(); |
| 1341 |
if (cDenominator > 0.0) { |
| 1342 |
RealType c = sqrt(cNumerator / cDenominator); |
| 1343 |
if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients |
| 1344 |
Vector3d vh = Ph / Mh; |
| 1345 |
Vector3d ah = momentumTarget_ / Mh + vh; |
| 1346 |
Vector3d ahrec = momentumTarget_ / Mh; |
| 1347 |
RealType hNumerator = Kh + kineticTarget_ |
| 1348 |
- 0.5 * Mh * ah.lengthSquare(); |
| 1349 |
if (hNumerator > 0.0) { |
| 1350 |
RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare(); |
| 1351 |
if (hDenominator > 0.0) { |
| 1352 |
RealType h = sqrt(hNumerator / hDenominator); |
| 1353 |
if ((h > 0.9) && (h < 1.1)) { |
| 1354 |
// std::cerr << "cold slab scaling coefficient: " << c << "\n"; |
| 1355 |
// std::cerr << "hot slab scaling coefficient: " << h << "\n"; |
| 1356 |
vector<StuntDouble*>::iterator sdi; |
| 1357 |
Vector3d vel; |
| 1358 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1359 |
//vel = (*sdi)->getVel(); |
| 1360 |
vel = ((*sdi)->getVel() - vc) * c + ac; |
| 1361 |
(*sdi)->setVel(vel); |
| 1362 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1363 |
if ((*sdi)->isDirectional()) { |
| 1364 |
Vector3d angMom = (*sdi)->getJ() * c; |
| 1365 |
(*sdi)->setJ(angMom); |
| 1366 |
} |
| 1367 |
} |
| 1368 |
} |
| 1369 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1370 |
//vel = (*sdi)->getVel(); |
| 1371 |
vel = ((*sdi)->getVel() - vh) * h + ah; |
| 1372 |
(*sdi)->setVel(vel); |
| 1373 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1374 |
if ((*sdi)->isDirectional()) { |
| 1375 |
Vector3d angMom = (*sdi)->getJ() * h; |
| 1376 |
(*sdi)->setJ(angMom); |
| 1377 |
} |
| 1378 |
} |
| 1379 |
} |
| 1380 |
successfulExchange = true; |
| 1381 |
kineticExchange_ += kineticTarget_; |
| 1382 |
momentumExchange_ += momentumTarget_; |
| 1383 |
} |
| 1384 |
} |
| 1385 |
} |
| 1386 |
} |
| 1387 |
} |
| 1388 |
} |
| 1389 |
} |
| 1390 |
if (successfulExchange != true) { |
| 1391 |
sprintf(painCave.errMsg, |
| 1392 |
"RNEMD::doVSS exchange NOT performed - roots that solve\n" |
| 1393 |
"\tthe constraint equations may not exist or there may be\n" |
| 1394 |
"\tno selected objects in one or both slabs.\n"); |
| 1395 |
painCave.isFatal = 0; |
| 1396 |
painCave.severity = OPENMD_INFO; |
| 1397 |
simError(); |
| 1398 |
failTrialCount_++; |
| 1399 |
} |
| 1400 |
} |
| 1401 |
|
| 1402 |
void RNEMD::doRNEMD() { |
| 1403 |
if (!doRNEMD_) return; |
| 1404 |
trialCount_++; |
| 1405 |
switch(rnemdMethod_) { |
| 1406 |
case rnemdSwap: |
| 1407 |
doSwap(); |
| 1408 |
break; |
| 1409 |
case rnemdNIVS: |
| 1410 |
doNIVS(); |
| 1411 |
break; |
| 1412 |
case rnemdVSS: |
| 1413 |
doVSS(); |
| 1414 |
break; |
| 1415 |
case rnemdUnkownMethod: |
| 1416 |
default : |
| 1417 |
break; |
| 1418 |
} |
| 1419 |
} |
| 1420 |
|
| 1421 |
void RNEMD::collectData() { |
| 1422 |
if (!doRNEMD_) return; |
| 1423 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1424 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1425 |
|
| 1426 |
areaAccumulator_->add(currentSnap_->getXYarea()); |
| 1427 |
|
| 1428 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 1429 |
|
| 1430 |
int selei; |
| 1431 |
StuntDouble* sd; |
| 1432 |
int idx; |
| 1433 |
|
| 1434 |
vector<RealType> binMass(nBins_, 0.0); |
| 1435 |
vector<RealType> binPx(nBins_, 0.0); |
| 1436 |
vector<RealType> binPy(nBins_, 0.0); |
| 1437 |
vector<RealType> binPz(nBins_, 0.0); |
| 1438 |
vector<RealType> binKE(nBins_, 0.0); |
| 1439 |
vector<int> binDOF(nBins_, 0); |
| 1440 |
vector<int> binCount(nBins_, 0); |
| 1441 |
|
| 1442 |
// alternative approach, track all molecules instead of only those |
| 1443 |
// selected for scaling/swapping: |
| 1444 |
/* |
| 1445 |
SimInfo::MoleculeIterator miter; |
| 1446 |
vector<StuntDouble*>::iterator iiter; |
| 1447 |
Molecule* mol; |
| 1448 |
StuntDouble* sd; |
| 1449 |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 1450 |
mol = info_->nextMolecule(miter)) |
| 1451 |
sd is essentially sd |
| 1452 |
for (sd = mol->beginIntegrableObject(iiter); |
| 1453 |
sd != NULL; |
| 1454 |
sd = mol->nextIntegrableObject(iiter)) |
| 1455 |
*/ |
| 1456 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 1457 |
sd = seleMan_.nextSelected(selei)) { |
| 1458 |
|
| 1459 |
idx = sd->getLocalIndex(); |
| 1460 |
|
| 1461 |
Vector3d pos = sd->getPos(); |
| 1462 |
|
| 1463 |
// wrap the stuntdouble's position back into the box: |
| 1464 |
|
| 1465 |
if (usePeriodicBoundaryConditions_) |
| 1466 |
currentSnap_->wrapVector(pos); |
| 1467 |
|
| 1468 |
|
| 1469 |
// which bin is this stuntdouble in? |
| 1470 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 1471 |
// Shift molecules by half a box to have bins start at 0 |
| 1472 |
// The modulo operator is used to wrap the case when we are |
| 1473 |
// beyond the end of the bins back to the beginning. |
| 1474 |
int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_; |
| 1475 |
|
| 1476 |
RealType mass = sd->getMass(); |
| 1477 |
Vector3d vel = sd->getVel(); |
| 1478 |
|
| 1479 |
binCount[binNo]++; |
| 1480 |
binMass[binNo] += mass; |
| 1481 |
binPx[binNo] += mass*vel.x(); |
| 1482 |
binPy[binNo] += mass*vel.y(); |
| 1483 |
binPz[binNo] += mass*vel.z(); |
| 1484 |
binKE[binNo] += 0.5 * (mass * vel.lengthSquare()); |
| 1485 |
binDOF[binNo] += 3; |
| 1486 |
|
| 1487 |
if (sd->isDirectional()) { |
| 1488 |
Vector3d angMom = sd->getJ(); |
| 1489 |
Mat3x3d I = sd->getI(); |
| 1490 |
if (sd->isLinear()) { |
| 1491 |
int i = sd->linearAxis(); |
| 1492 |
int j = (i + 1) % 3; |
| 1493 |
int k = (i + 2) % 3; |
| 1494 |
binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) + |
| 1495 |
angMom[k] * angMom[k] / I(k, k)); |
| 1496 |
binDOF[binNo] += 2; |
| 1497 |
} else { |
| 1498 |
binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) + |
| 1499 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1500 |
angMom[2] * angMom[2] / I(2, 2)); |
| 1501 |
binDOF[binNo] += 3; |
| 1502 |
} |
| 1503 |
} |
| 1504 |
} |
| 1505 |
|
| 1506 |
|
| 1507 |
#ifdef IS_MPI |
| 1508 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0], |
| 1509 |
nBins_, MPI::INT, MPI::SUM); |
| 1510 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0], |
| 1511 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1512 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0], |
| 1513 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1514 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0], |
| 1515 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1516 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0], |
| 1517 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1518 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0], |
| 1519 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1520 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0], |
| 1521 |
nBins_, MPI::INT, MPI::SUM); |
| 1522 |
#endif |
| 1523 |
|
| 1524 |
Vector3d vel; |
| 1525 |
RealType den; |
| 1526 |
RealType temp; |
| 1527 |
RealType z; |
| 1528 |
for (int i = 0; i < nBins_; i++) { |
| 1529 |
z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2); |
| 1530 |
vel.x() = binPx[i] / binMass[i]; |
| 1531 |
vel.y() = binPy[i] / binMass[i]; |
| 1532 |
vel.z() = binPz[i] / binMass[i]; |
| 1533 |
|
| 1534 |
den = binMass[i] * nBins_ * PhysicalConstants::densityConvert |
| 1535 |
/ currentSnap_->getVolume() ; |
| 1536 |
|
| 1537 |
temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb * |
| 1538 |
PhysicalConstants::energyConvert); |
| 1539 |
|
| 1540 |
for (unsigned int j = 0; j < outputMask_.size(); ++j) { |
| 1541 |
if(outputMask_[j]) { |
| 1542 |
switch(j) { |
| 1543 |
case Z: |
| 1544 |
(data_[j].accumulator[i])->add(z); |
| 1545 |
break; |
| 1546 |
case TEMPERATURE: |
| 1547 |
data_[j].accumulator[i]->add(temp); |
| 1548 |
break; |
| 1549 |
case VELOCITY: |
| 1550 |
dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel); |
| 1551 |
break; |
| 1552 |
case DENSITY: |
| 1553 |
data_[j].accumulator[i]->add(den); |
| 1554 |
break; |
| 1555 |
} |
| 1556 |
} |
| 1557 |
} |
| 1558 |
} |
| 1559 |
} |
| 1560 |
|
| 1561 |
void RNEMD::getStarted() { |
| 1562 |
if (!doRNEMD_) return; |
| 1563 |
collectData(); |
| 1564 |
writeOutputFile(); |
| 1565 |
} |
| 1566 |
|
| 1567 |
void RNEMD::parseOutputFileFormat(const std::string& format) { |
| 1568 |
if (!doRNEMD_) return; |
| 1569 |
StringTokenizer tokenizer(format, " ,;|\t\n\r"); |
| 1570 |
|
| 1571 |
while(tokenizer.hasMoreTokens()) { |
| 1572 |
std::string token(tokenizer.nextToken()); |
| 1573 |
toUpper(token); |
| 1574 |
OutputMapType::iterator i = outputMap_.find(token); |
| 1575 |
if (i != outputMap_.end()) { |
| 1576 |
outputMask_.set(i->second); |
| 1577 |
} else { |
| 1578 |
sprintf( painCave.errMsg, |
| 1579 |
"RNEMD::parseOutputFileFormat: %s is not a recognized\n" |
| 1580 |
"\toutputFileFormat keyword.\n", token.c_str() ); |
| 1581 |
painCave.isFatal = 0; |
| 1582 |
painCave.severity = OPENMD_ERROR; |
| 1583 |
simError(); |
| 1584 |
} |
| 1585 |
} |
| 1586 |
} |
| 1587 |
|
| 1588 |
void RNEMD::writeOutputFile() { |
| 1589 |
if (!doRNEMD_) return; |
| 1590 |
|
| 1591 |
#ifdef IS_MPI |
| 1592 |
// If we're the root node, should we print out the results |
| 1593 |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 1594 |
if (worldRank == 0) { |
| 1595 |
#endif |
| 1596 |
rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc ); |
| 1597 |
|
| 1598 |
if( !rnemdFile_ ){ |
| 1599 |
sprintf( painCave.errMsg, |
| 1600 |
"Could not open \"%s\" for RNEMD output.\n", |
| 1601 |
rnemdFileName_.c_str()); |
| 1602 |
painCave.isFatal = 1; |
| 1603 |
simError(); |
| 1604 |
} |
| 1605 |
|
| 1606 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1607 |
|
| 1608 |
RealType time = currentSnap_->getTime(); |
| 1609 |
RealType avgArea; |
| 1610 |
areaAccumulator_->getAverage(avgArea); |
| 1611 |
RealType Jz = kineticExchange_ / (2.0 * time * avgArea) |
| 1612 |
/ PhysicalConstants::energyConvert; |
| 1613 |
Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea); |
| 1614 |
|
| 1615 |
rnemdFile_ << "#######################################################\n"; |
| 1616 |
rnemdFile_ << "# RNEMD {\n"; |
| 1617 |
|
| 1618 |
map<string, RNEMDMethod>::iterator mi; |
| 1619 |
for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) { |
| 1620 |
if ( (*mi).second == rnemdMethod_) |
| 1621 |
rnemdFile_ << "# exchangeMethod = \"" << (*mi).first << "\";\n"; |
| 1622 |
} |
| 1623 |
map<string, RNEMDFluxType>::iterator fi; |
| 1624 |
for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) { |
| 1625 |
if ( (*fi).second == rnemdFluxType_) |
| 1626 |
rnemdFile_ << "# fluxType = \"" << (*fi).first << "\";\n"; |
| 1627 |
} |
| 1628 |
|
| 1629 |
rnemdFile_ << "# exchangeTime = " << exchangeTime_ << ";\n"; |
| 1630 |
|
| 1631 |
rnemdFile_ << "# objectSelection = \"" |
| 1632 |
<< rnemdObjectSelection_ << "\";\n"; |
| 1633 |
rnemdFile_ << "# slabWidth = " << slabWidth_ << ";\n"; |
| 1634 |
rnemdFile_ << "# slabAcenter = " << slabACenter_ << ";\n"; |
| 1635 |
rnemdFile_ << "# slabBcenter = " << slabBCenter_ << ";\n"; |
| 1636 |
rnemdFile_ << "# }\n"; |
| 1637 |
rnemdFile_ << "#######################################################\n"; |
| 1638 |
rnemdFile_ << "# RNEMD report:\n"; |
| 1639 |
rnemdFile_ << "# running time = " << time << " fs\n"; |
| 1640 |
rnemdFile_ << "# target flux:\n"; |
| 1641 |
rnemdFile_ << "# kinetic = " |
| 1642 |
<< kineticFlux_ / PhysicalConstants::energyConvert |
| 1643 |
<< " (kcal/mol/A^2/fs)\n"; |
| 1644 |
rnemdFile_ << "# momentum = " << momentumFluxVector_ |
| 1645 |
<< " (amu/A/fs^2)\n"; |
| 1646 |
rnemdFile_ << "# target one-time exchanges:\n"; |
| 1647 |
rnemdFile_ << "# kinetic = " |
| 1648 |
<< kineticTarget_ / PhysicalConstants::energyConvert |
| 1649 |
<< " (kcal/mol)\n"; |
| 1650 |
rnemdFile_ << "# momentum = " << momentumTarget_ |
| 1651 |
<< " (amu*A/fs)\n"; |
| 1652 |
rnemdFile_ << "# actual exchange totals:\n"; |
| 1653 |
rnemdFile_ << "# kinetic = " |
| 1654 |
<< kineticExchange_ / PhysicalConstants::energyConvert |
| 1655 |
<< " (kcal/mol)\n"; |
| 1656 |
rnemdFile_ << "# momentum = " << momentumExchange_ |
| 1657 |
<< " (amu*A/fs)\n"; |
| 1658 |
rnemdFile_ << "# actual flux:\n"; |
| 1659 |
rnemdFile_ << "# kinetic = " << Jz |
| 1660 |
<< " (kcal/mol/A^2/fs)\n"; |
| 1661 |
rnemdFile_ << "# momentum = " << JzP |
| 1662 |
<< " (amu/A/fs^2)\n"; |
| 1663 |
rnemdFile_ << "# exchange statistics:\n"; |
| 1664 |
rnemdFile_ << "# attempted = " << trialCount_ << "\n"; |
| 1665 |
rnemdFile_ << "# failed = " << failTrialCount_ << "\n"; |
| 1666 |
if (rnemdMethod_ == rnemdNIVS) { |
| 1667 |
rnemdFile_ << "# NIVS root-check errors = " |
| 1668 |
<< failRootCount_ << "\n"; |
| 1669 |
} |
| 1670 |
rnemdFile_ << "#######################################################\n"; |
| 1671 |
|
| 1672 |
|
| 1673 |
|
| 1674 |
//write title |
| 1675 |
rnemdFile_ << "#"; |
| 1676 |
for (unsigned int i = 0; i < outputMask_.size(); ++i) { |
| 1677 |
if (outputMask_[i]) { |
| 1678 |
rnemdFile_ << "\t" << data_[i].title << |
| 1679 |
"(" << data_[i].units << ")"; |
| 1680 |
// add some extra tabs for column alignment |
| 1681 |
if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t"; |
| 1682 |
} |
| 1683 |
} |
| 1684 |
rnemdFile_ << std::endl; |
| 1685 |
|
| 1686 |
rnemdFile_.precision(8); |
| 1687 |
|
| 1688 |
for (int j = 0; j < nBins_; j++) { |
| 1689 |
|
| 1690 |
for (unsigned int i = 0; i < outputMask_.size(); ++i) { |
| 1691 |
if (outputMask_[i]) { |
| 1692 |
if (data_[i].dataType == "RealType") |
| 1693 |
writeReal(i,j); |
| 1694 |
else if (data_[i].dataType == "Vector3d") |
| 1695 |
writeVector(i,j); |
| 1696 |
else { |
| 1697 |
sprintf( painCave.errMsg, |
| 1698 |
"RNEMD found an unknown data type for: %s ", |
| 1699 |
data_[i].title.c_str()); |
| 1700 |
painCave.isFatal = 1; |
| 1701 |
simError(); |
| 1702 |
} |
| 1703 |
} |
| 1704 |
} |
| 1705 |
rnemdFile_ << std::endl; |
| 1706 |
|
| 1707 |
} |
| 1708 |
|
| 1709 |
rnemdFile_ << "#######################################################\n"; |
| 1710 |
rnemdFile_ << "# Standard Deviations in those quantities follow:\n"; |
| 1711 |
rnemdFile_ << "#######################################################\n"; |
| 1712 |
|
| 1713 |
|
| 1714 |
for (int j = 0; j < nBins_; j++) { |
| 1715 |
rnemdFile_ << "#"; |
| 1716 |
for (unsigned int i = 0; i < outputMask_.size(); ++i) { |
| 1717 |
if (outputMask_[i]) { |
| 1718 |
if (data_[i].dataType == "RealType") |
| 1719 |
writeRealStdDev(i,j); |
| 1720 |
else if (data_[i].dataType == "Vector3d") |
| 1721 |
writeVectorStdDev(i,j); |
| 1722 |
else { |
| 1723 |
sprintf( painCave.errMsg, |
| 1724 |
"RNEMD found an unknown data type for: %s ", |
| 1725 |
data_[i].title.c_str()); |
| 1726 |
painCave.isFatal = 1; |
| 1727 |
simError(); |
| 1728 |
} |
| 1729 |
} |
| 1730 |
} |
| 1731 |
rnemdFile_ << std::endl; |
| 1732 |
|
| 1733 |
} |
| 1734 |
|
| 1735 |
rnemdFile_.flush(); |
| 1736 |
rnemdFile_.close(); |
| 1737 |
|
| 1738 |
#ifdef IS_MPI |
| 1739 |
} |
| 1740 |
#endif |
| 1741 |
|
| 1742 |
} |
| 1743 |
|
| 1744 |
void RNEMD::writeReal(int index, unsigned int bin) { |
| 1745 |
if (!doRNEMD_) return; |
| 1746 |
assert(index >=0 && index < ENDINDEX); |
| 1747 |
assert(bin < nBins_); |
| 1748 |
RealType s; |
| 1749 |
|
| 1750 |
data_[index].accumulator[bin]->getAverage(s); |
| 1751 |
|
| 1752 |
if (! isinf(s) && ! isnan(s)) { |
| 1753 |
rnemdFile_ << "\t" << s; |
| 1754 |
} else{ |
| 1755 |
sprintf( painCave.errMsg, |
| 1756 |
"RNEMD detected a numerical error writing: %s for bin %d", |
| 1757 |
data_[index].title.c_str(), bin); |
| 1758 |
painCave.isFatal = 1; |
| 1759 |
simError(); |
| 1760 |
} |
| 1761 |
} |
| 1762 |
|
| 1763 |
void RNEMD::writeVector(int index, unsigned int bin) { |
| 1764 |
if (!doRNEMD_) return; |
| 1765 |
assert(index >=0 && index < ENDINDEX); |
| 1766 |
assert(bin < nBins_); |
| 1767 |
Vector3d s; |
| 1768 |
dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s); |
| 1769 |
if (isinf(s[0]) || isnan(s[0]) || |
| 1770 |
isinf(s[1]) || isnan(s[1]) || |
| 1771 |
isinf(s[2]) || isnan(s[2]) ) { |
| 1772 |
sprintf( painCave.errMsg, |
| 1773 |
"RNEMD detected a numerical error writing: %s for bin %d", |
| 1774 |
data_[index].title.c_str(), bin); |
| 1775 |
painCave.isFatal = 1; |
| 1776 |
simError(); |
| 1777 |
} else { |
| 1778 |
rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; |
| 1779 |
} |
| 1780 |
} |
| 1781 |
|
| 1782 |
void RNEMD::writeRealStdDev(int index, unsigned int bin) { |
| 1783 |
if (!doRNEMD_) return; |
| 1784 |
assert(index >=0 && index < ENDINDEX); |
| 1785 |
assert(bin < nBins_); |
| 1786 |
RealType s; |
| 1787 |
|
| 1788 |
data_[index].accumulator[bin]->getStdDev(s); |
| 1789 |
|
| 1790 |
if (! isinf(s) && ! isnan(s)) { |
| 1791 |
rnemdFile_ << "\t" << s; |
| 1792 |
} else{ |
| 1793 |
sprintf( painCave.errMsg, |
| 1794 |
"RNEMD detected a numerical error writing: %s std. dev. for bin %d", |
| 1795 |
data_[index].title.c_str(), bin); |
| 1796 |
painCave.isFatal = 1; |
| 1797 |
simError(); |
| 1798 |
} |
| 1799 |
} |
| 1800 |
|
| 1801 |
void RNEMD::writeVectorStdDev(int index, unsigned int bin) { |
| 1802 |
if (!doRNEMD_) return; |
| 1803 |
assert(index >=0 && index < ENDINDEX); |
| 1804 |
assert(bin < nBins_); |
| 1805 |
Vector3d s; |
| 1806 |
dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s); |
| 1807 |
if (isinf(s[0]) || isnan(s[0]) || |
| 1808 |
isinf(s[1]) || isnan(s[1]) || |
| 1809 |
isinf(s[2]) || isnan(s[2]) ) { |
| 1810 |
sprintf( painCave.errMsg, |
| 1811 |
"RNEMD detected a numerical error writing: %s std. dev. for bin %d", |
| 1812 |
data_[index].title.c_str(), bin); |
| 1813 |
painCave.isFatal = 1; |
| 1814 |
simError(); |
| 1815 |
} else { |
| 1816 |
rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; |
| 1817 |
} |
| 1818 |
} |
| 1819 |
} |
| 1820 |
|
