| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#include <cmath> |
| 44 |
|
| 45 |
|
| 46 |
#include "io/StatWriter.hpp" |
| 47 |
#include "minimizers/Minimizer.hpp" |
| 48 |
#include "primitives/Molecule.hpp" |
| 49 |
#ifdef IS_MPI |
| 50 |
#include <mpi.h> |
| 51 |
#endif |
| 52 |
namespace OpenMD { |
| 53 |
|
| 54 |
Minimizer::Minimizer(SimInfo* rhs) : |
| 55 |
info(rhs), usingShake(false) { |
| 56 |
|
| 57 |
forceMan = new ForceManager(info); |
| 58 |
paramSet= new MinimizerParameterSet(info), calcDim(); |
| 59 |
curX = getCoor(); |
| 60 |
curG.resize(ndim); |
| 61 |
} |
| 62 |
|
| 63 |
Minimizer::~Minimizer() { |
| 64 |
delete forceMan; |
| 65 |
delete paramSet; |
| 66 |
} |
| 67 |
|
| 68 |
// void Minimizer::calcEnergyGradient(std::vector<RealType> &x, |
| 69 |
// std::vector<RealType> &grad, |
| 70 |
// RealType&energy, int&status) { |
| 71 |
|
| 72 |
// SimInfo::MoleculeIterator i; |
| 73 |
// Molecule::IntegrableObjectIterator j; |
| 74 |
// Molecule* mol; |
| 75 |
// StuntDouble* integrableObject; |
| 76 |
// std::vector<RealType> myGrad; |
| 77 |
// int shakeStatus; |
| 78 |
|
| 79 |
// status = 1; |
| 80 |
|
| 81 |
// setCoor(x); |
| 82 |
|
| 83 |
// if (usingShake) { |
| 84 |
// shakeStatus = shakeR(); |
| 85 |
// } |
| 86 |
|
| 87 |
// energy = calcPotential(); |
| 88 |
|
| 89 |
// if (usingShake) { |
| 90 |
// shakeStatus = shakeF(); |
| 91 |
// } |
| 92 |
|
| 93 |
// x = getCoordinates(); |
| 94 |
|
| 95 |
// int index = 0; |
| 96 |
|
| 97 |
// for (mol = info->beginMolecule(i); mol != NULL; |
| 98 |
// mol = info->nextMolecule(i)) { |
| 99 |
// for (integrableObject = mol->beginIntegrableObject(j); |
| 100 |
// integrableObject != NULL; |
| 101 |
// integrableObject = mol->nextIntegrableObject(j)) { |
| 102 |
// myGrad = integrableObject->getGrad(); |
| 103 |
// for (unsigned int k = 0; k < myGrad.size(); ++k) { |
| 104 |
// grad[index++] = myGrad[k]; |
| 105 |
// } |
| 106 |
// } |
| 107 |
// } |
| 108 |
// } |
| 109 |
|
| 110 |
void Minimizer::setCoor(std::vector<RealType> &x) { |
| 111 |
Vector3d position; |
| 112 |
Vector3d eulerAngle; |
| 113 |
SimInfo::MoleculeIterator i; |
| 114 |
Molecule::IntegrableObjectIterator j; |
| 115 |
Molecule* mol; |
| 116 |
StuntDouble* integrableObject; |
| 117 |
int index = 0; |
| 118 |
|
| 119 |
for (mol = info->beginMolecule(i); mol != NULL; |
| 120 |
mol = info->nextMolecule(i)) { |
| 121 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 122 |
integrableObject != NULL; |
| 123 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 124 |
|
| 125 |
position[0] = x[index++]; |
| 126 |
position[1] = x[index++]; |
| 127 |
position[2] = x[index++]; |
| 128 |
|
| 129 |
integrableObject->setPos(position); |
| 130 |
|
| 131 |
if (integrableObject->isDirectional()) { |
| 132 |
eulerAngle[0] = x[index++]; |
| 133 |
eulerAngle[1] = x[index++]; |
| 134 |
eulerAngle[2] = x[index++]; |
| 135 |
|
| 136 |
integrableObject->setEuler(eulerAngle); |
| 137 |
} |
| 138 |
} |
| 139 |
} |
| 140 |
} |
| 141 |
|
| 142 |
std::vector<RealType> Minimizer::getCoor() { |
| 143 |
Vector3d position; |
| 144 |
Vector3d eulerAngle; |
| 145 |
SimInfo::MoleculeIterator i; |
| 146 |
Molecule::IntegrableObjectIterator j; |
| 147 |
Molecule* mol; |
| 148 |
StuntDouble* integrableObject; |
| 149 |
int index = 0; |
| 150 |
std::vector<RealType> x(getDim()); |
| 151 |
|
| 152 |
for (mol = info->beginMolecule(i); mol != NULL; |
| 153 |
mol = info->nextMolecule(i)) { |
| 154 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 155 |
integrableObject != NULL; |
| 156 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 157 |
|
| 158 |
position = integrableObject->getPos(); |
| 159 |
x[index++] = position[0]; |
| 160 |
x[index++] = position[1]; |
| 161 |
x[index++] = position[2]; |
| 162 |
|
| 163 |
if (integrableObject->isDirectional()) { |
| 164 |
eulerAngle = integrableObject->getEuler(); |
| 165 |
x[index++] = eulerAngle[0]; |
| 166 |
x[index++] = eulerAngle[1]; |
| 167 |
x[index++] = eulerAngle[2]; |
| 168 |
} |
| 169 |
} |
| 170 |
} |
| 171 |
return x; |
| 172 |
} |
| 173 |
|
| 174 |
|
| 175 |
/* |
| 176 |
int Minimizer::shakeR() { |
| 177 |
int i, j; |
| 178 |
|
| 179 |
int done; |
| 180 |
|
| 181 |
RealType posA[3], posB[3]; |
| 182 |
|
| 183 |
RealType velA[3], velB[3]; |
| 184 |
|
| 185 |
RealType pab[3]; |
| 186 |
|
| 187 |
RealType rab[3]; |
| 188 |
|
| 189 |
int a, b, |
| 190 |
ax, ay, |
| 191 |
az, bx, |
| 192 |
by, bz; |
| 193 |
|
| 194 |
RealType rma, rmb; |
| 195 |
|
| 196 |
RealType dx, dy, |
| 197 |
dz; |
| 198 |
|
| 199 |
RealType rpab; |
| 200 |
|
| 201 |
RealType rabsq, pabsq, |
| 202 |
rpabsq; |
| 203 |
|
| 204 |
RealType diffsq; |
| 205 |
|
| 206 |
RealType gab; |
| 207 |
|
| 208 |
int iteration; |
| 209 |
|
| 210 |
for(i = 0; i < nAtoms; i++) { |
| 211 |
moving[i] = 0; |
| 212 |
|
| 213 |
moved[i] = 1; |
| 214 |
} |
| 215 |
|
| 216 |
iteration = 0; |
| 217 |
|
| 218 |
done = 0; |
| 219 |
|
| 220 |
while (!done && (iteration < maxIteration)) { |
| 221 |
done = 1; |
| 222 |
|
| 223 |
for(i = 0; i < nConstrained; i++) { |
| 224 |
a = constrainedA[i]; |
| 225 |
|
| 226 |
b = constrainedB[i]; |
| 227 |
|
| 228 |
ax = (a * 3) + 0; |
| 229 |
|
| 230 |
ay = (a * 3) + 1; |
| 231 |
|
| 232 |
az = (a * 3) + 2; |
| 233 |
|
| 234 |
bx = (b * 3) + 0; |
| 235 |
|
| 236 |
by = (b * 3) + 1; |
| 237 |
|
| 238 |
bz = (b * 3) + 2; |
| 239 |
|
| 240 |
if (moved[a] || moved[b]) { |
| 241 |
posA = atoms[a]->getPos(); |
| 242 |
|
| 243 |
posB = atoms[b]->getPos(); |
| 244 |
|
| 245 |
for(j = 0; j < 3; j++) |
| 246 |
pab[j] = posA[j] - posB[j]; |
| 247 |
|
| 248 |
//periodic boundary condition |
| 249 |
|
| 250 |
info->wrapVector(pab); |
| 251 |
|
| 252 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 253 |
|
| 254 |
rabsq = constrainedDsqr[i]; |
| 255 |
|
| 256 |
diffsq = rabsq - pabsq; |
| 257 |
|
| 258 |
// the original rattle code from alan tidesley |
| 259 |
|
| 260 |
if (fabs(diffsq) > (tol * rabsq * 2)) { |
| 261 |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 262 |
|
| 263 |
rab[1] = oldPos[ay] - oldPos[by]; |
| 264 |
|
| 265 |
rab[2] = oldPos[az] - oldPos[bz]; |
| 266 |
|
| 267 |
info->wrapVector(rab); |
| 268 |
|
| 269 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 270 |
|
| 271 |
rpabsq = rpab * rpab; |
| 272 |
|
| 273 |
if (rpabsq < (rabsq * -diffsq)) { |
| 274 |
|
| 275 |
#ifdef IS_MPI |
| 276 |
|
| 277 |
a = atoms[a]->getGlobalIndex(); |
| 278 |
|
| 279 |
b = atoms[b]->getGlobalIndex(); |
| 280 |
|
| 281 |
#endif //is_mpi |
| 282 |
|
| 283 |
//std::cerr << "Waring: constraint failure" << std::endl; |
| 284 |
|
| 285 |
gab = sqrt(rabsq / pabsq); |
| 286 |
|
| 287 |
rab[0] = (posA[0] - posB[0]) |
| 288 |
* gab; |
| 289 |
|
| 290 |
rab[1] = (posA[1] - posB[1]) |
| 291 |
* gab; |
| 292 |
|
| 293 |
rab[2] = (posA[2] - posB[2]) |
| 294 |
* gab; |
| 295 |
|
| 296 |
info->wrapVector(rab); |
| 297 |
|
| 298 |
rpab = |
| 299 |
rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 300 |
} |
| 301 |
|
| 302 |
//rma = 1.0 / atoms[a]->getMass(); |
| 303 |
|
| 304 |
//rmb = 1.0 / atoms[b]->getMass(); |
| 305 |
|
| 306 |
rma = 1.0; |
| 307 |
|
| 308 |
rmb = 1.0; |
| 309 |
|
| 310 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 311 |
|
| 312 |
dx = rab[0]* |
| 313 |
gab; |
| 314 |
|
| 315 |
dy = rab[1]* |
| 316 |
gab; |
| 317 |
|
| 318 |
dz = rab[2]* |
| 319 |
gab; |
| 320 |
|
| 321 |
posA[0] += rma *dx; |
| 322 |
|
| 323 |
posA[1] += rma *dy; |
| 324 |
|
| 325 |
posA[2] += rma *dz; |
| 326 |
|
| 327 |
atoms[a]->setPos(posA); |
| 328 |
|
| 329 |
posB[0] -= rmb *dx; |
| 330 |
|
| 331 |
posB[1] -= rmb *dy; |
| 332 |
|
| 333 |
posB[2] -= rmb *dz; |
| 334 |
|
| 335 |
atoms[b]->setPos(posB); |
| 336 |
|
| 337 |
moving[a] = 1; |
| 338 |
|
| 339 |
moving[b] = 1; |
| 340 |
|
| 341 |
done = 0; |
| 342 |
} |
| 343 |
} |
| 344 |
} |
| 345 |
|
| 346 |
for(i = 0; i < nAtoms; i++) { |
| 347 |
moved[i] = moving[i]; |
| 348 |
|
| 349 |
moving[i] = 0; |
| 350 |
} |
| 351 |
|
| 352 |
iteration++; |
| 353 |
} |
| 354 |
|
| 355 |
if (!done) { |
| 356 |
std::cerr << "Waring: can not constraint within maxIteration" |
| 357 |
<< std::endl; |
| 358 |
|
| 359 |
return -1; |
| 360 |
} else |
| 361 |
return 1; |
| 362 |
} |
| 363 |
|
| 364 |
//remove constraint force along the bond direction |
| 365 |
|
| 366 |
|
| 367 |
int Minimizer::shakeF() { |
| 368 |
int i, j; |
| 369 |
|
| 370 |
int done; |
| 371 |
|
| 372 |
RealType posA[3], posB[3]; |
| 373 |
|
| 374 |
RealType frcA[3], frcB[3]; |
| 375 |
|
| 376 |
RealType rab[3], fpab[3]; |
| 377 |
|
| 378 |
int a, b, |
| 379 |
ax, ay, |
| 380 |
az, bx, |
| 381 |
by, bz; |
| 382 |
|
| 383 |
RealType rma, rmb; |
| 384 |
|
| 385 |
RealType rvab; |
| 386 |
|
| 387 |
RealType gab; |
| 388 |
|
| 389 |
RealType rabsq; |
| 390 |
|
| 391 |
RealType rfab; |
| 392 |
|
| 393 |
int iteration; |
| 394 |
|
| 395 |
for(i = 0; i < nAtoms; i++) { |
| 396 |
moving[i] = 0; |
| 397 |
|
| 398 |
moved[i] = 1; |
| 399 |
} |
| 400 |
|
| 401 |
done = 0; |
| 402 |
|
| 403 |
iteration = 0; |
| 404 |
|
| 405 |
while (!done && (iteration < maxIteration)) { |
| 406 |
done = 1; |
| 407 |
|
| 408 |
for(i = 0; i < nConstrained; i++) { |
| 409 |
a = constrainedA[i]; |
| 410 |
|
| 411 |
b = constrainedB[i]; |
| 412 |
|
| 413 |
ax = (a * 3) + 0; |
| 414 |
|
| 415 |
ay = (a * 3) + 1; |
| 416 |
|
| 417 |
az = (a * 3) + 2; |
| 418 |
|
| 419 |
bx = (b * 3) + 0; |
| 420 |
|
| 421 |
by = (b * 3) + 1; |
| 422 |
|
| 423 |
bz = (b * 3) + 2; |
| 424 |
|
| 425 |
if (moved[a] || moved[b]) { |
| 426 |
posA = atoms[a]->getPos(); |
| 427 |
|
| 428 |
posB = atoms[b]->getPos(); |
| 429 |
|
| 430 |
for(j = 0; j < 3; j++) |
| 431 |
rab[j] = posA[j] - posB[j]; |
| 432 |
|
| 433 |
info->wrapVector(rab); |
| 434 |
|
| 435 |
atoms[a]->getFrc(frcA); |
| 436 |
|
| 437 |
atoms[b]->getFrc(frcB); |
| 438 |
|
| 439 |
//rma = 1.0 / atoms[a]->getMass(); |
| 440 |
|
| 441 |
//rmb = 1.0 / atoms[b]->getMass(); |
| 442 |
|
| 443 |
rma = 1.0; |
| 444 |
|
| 445 |
rmb = 1.0; |
| 446 |
|
| 447 |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 448 |
|
| 449 |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 450 |
|
| 451 |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 452 |
|
| 453 |
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 454 |
|
| 455 |
if (gab < 1.0) |
| 456 |
gab = 1.0; |
| 457 |
|
| 458 |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 459 |
|
| 460 |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 461 |
|
| 462 |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
| 463 |
gab = -rfab / (rabsq * (rma + rmb)); |
| 464 |
|
| 465 |
frcA[0] = rab[0]* |
| 466 |
gab; |
| 467 |
|
| 468 |
frcA[1] = rab[1]* |
| 469 |
gab; |
| 470 |
|
| 471 |
frcA[2] = rab[2]* |
| 472 |
gab; |
| 473 |
|
| 474 |
atoms[a]->addFrc(frcA); |
| 475 |
|
| 476 |
frcB[0] = -rab[0]*gab; |
| 477 |
|
| 478 |
frcB[1] = -rab[1]*gab; |
| 479 |
|
| 480 |
frcB[2] = -rab[2]*gab; |
| 481 |
|
| 482 |
atoms[b]->addFrc(frcB); |
| 483 |
|
| 484 |
moving[a] = 1; |
| 485 |
|
| 486 |
moving[b] = 1; |
| 487 |
|
| 488 |
done = 0; |
| 489 |
} |
| 490 |
} |
| 491 |
} |
| 492 |
|
| 493 |
for(i = 0; i < nAtoms; i++) { |
| 494 |
moved[i] = moving[i]; |
| 495 |
|
| 496 |
moving[i] = 0; |
| 497 |
} |
| 498 |
|
| 499 |
iteration++; |
| 500 |
} |
| 501 |
|
| 502 |
if (!done) { |
| 503 |
std::cerr << "Waring: can not constraint within maxIteration" |
| 504 |
<< std::endl; |
| 505 |
|
| 506 |
return -1; |
| 507 |
} else |
| 508 |
return 1; |
| 509 |
} |
| 510 |
|
| 511 |
*/ |
| 512 |
|
| 513 |
//calculate the value of object function |
| 514 |
|
| 515 |
void Minimizer::calcF() { |
| 516 |
egEvalStatus = calcEnergyGradient(curX, curG, curF); |
| 517 |
} |
| 518 |
|
| 519 |
void Minimizer::calcF(std::vector < RealType > &x, RealType&f, int&status) { |
| 520 |
std::vector < RealType > tempG; |
| 521 |
|
| 522 |
tempG.resize(x.size()); |
| 523 |
|
| 524 |
status = calcEnergyGradient(x, tempG, f); |
| 525 |
} |
| 526 |
|
| 527 |
//calculate the gradient |
| 528 |
|
| 529 |
void Minimizer::calcG() { |
| 530 |
egEvalStatus = calcEnergyGradient(curX, curG, curF); |
| 531 |
} |
| 532 |
|
| 533 |
void Minimizer::calcG(std::vector<RealType>& x, |
| 534 |
std::vector<RealType>& g, RealType&f, int&status) { |
| 535 |
status = calcEnergyGradient(x, g, f); |
| 536 |
} |
| 537 |
|
| 538 |
void Minimizer::calcDim() { |
| 539 |
|
| 540 |
SimInfo::MoleculeIterator i; |
| 541 |
Molecule::IntegrableObjectIterator j; |
| 542 |
Molecule* mol; |
| 543 |
StuntDouble* integrableObject; |
| 544 |
ndim = 0; |
| 545 |
|
| 546 |
for (mol = info->beginMolecule(i); mol != NULL; |
| 547 |
mol = info->nextMolecule(i)) { |
| 548 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 549 |
integrableObject != NULL; |
| 550 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 551 |
|
| 552 |
ndim += 3; |
| 553 |
|
| 554 |
if (integrableObject->isDirectional()) { |
| 555 |
ndim += 3; |
| 556 |
} |
| 557 |
} |
| 558 |
} |
| 559 |
} |
| 560 |
|
| 561 |
void Minimizer::setX(std::vector<RealType> &x) { |
| 562 |
if (x.size() != ndim) { |
| 563 |
sprintf(painCave.errMsg, |
| 564 |
"Minimizer setX: dimensions of x and curX do not match\n"); |
| 565 |
painCave.isFatal = 1; |
| 566 |
simError(); |
| 567 |
} |
| 568 |
|
| 569 |
curX = x; |
| 570 |
} |
| 571 |
|
| 572 |
void Minimizer::setG(std::vector <RealType> &g) { |
| 573 |
if (g.size() != ndim) { |
| 574 |
sprintf(painCave.errMsg, |
| 575 |
"Minimizer setG: dimensions of g and curG do not match\n"); |
| 576 |
painCave.isFatal = 1; |
| 577 |
simError(); |
| 578 |
} |
| 579 |
|
| 580 |
curG = g; |
| 581 |
} |
| 582 |
|
| 583 |
|
| 584 |
/** |
| 585 |
* In theory, we need to find the minimum along the search direction |
| 586 |
* However, function evaluation is usually too expensive. At the |
| 587 |
* very begining of the problem, we check the search direction and |
| 588 |
* make sure it is a descent direction we will compare the energy of |
| 589 |
* two end points, if the right end point has lower energy, we'll |
| 590 |
* just take it. |
| 591 |
*/ |
| 592 |
|
| 593 |
int Minimizer::doLineSearch(std::vector<RealType> &direction, |
| 594 |
RealType stepSize) { |
| 595 |
|
| 596 |
std::vector<RealType> xa; |
| 597 |
std::vector<RealType> xb; |
| 598 |
std::vector<RealType> xc; |
| 599 |
std::vector<RealType> ga; |
| 600 |
std::vector<RealType> gb; |
| 601 |
std::vector<RealType> gc; |
| 602 |
RealType fa; |
| 603 |
RealType fb; |
| 604 |
RealType fc; |
| 605 |
RealType a; |
| 606 |
RealType b; |
| 607 |
RealType c; |
| 608 |
int status; |
| 609 |
RealType initSlope; |
| 610 |
RealType slopeA; |
| 611 |
RealType slopeB; |
| 612 |
RealType slopeC; |
| 613 |
bool foundLower; |
| 614 |
int iter; |
| 615 |
int maxLSIter; |
| 616 |
RealType mu; |
| 617 |
RealType eta; |
| 618 |
RealType ftol; |
| 619 |
RealType lsTol; |
| 620 |
|
| 621 |
xa.resize(ndim); |
| 622 |
xb.resize(ndim); |
| 623 |
xc.resize(ndim); |
| 624 |
ga.resize(ndim); |
| 625 |
gb.resize(ndim); |
| 626 |
gc.resize(ndim); |
| 627 |
|
| 628 |
a = 0.0; |
| 629 |
fa = curF; |
| 630 |
xa = curX; |
| 631 |
ga = curG; |
| 632 |
|
| 633 |
c = a + stepSize; |
| 634 |
|
| 635 |
ftol = paramSet->getFTol(); |
| 636 |
lsTol = paramSet->getLineSearchTol(); |
| 637 |
|
| 638 |
//calculate the derivative at a = 0 |
| 639 |
|
| 640 |
slopeA = 0; |
| 641 |
|
| 642 |
for(size_t i = 0; i < ndim; i++) { |
| 643 |
slopeA += curG[i] * direction[i]; |
| 644 |
} |
| 645 |
|
| 646 |
#ifdef IS_MPI |
| 647 |
// in parallel, we need to add up the contributions from all |
| 648 |
// processors: |
| 649 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &slopeA, 1, MPI::REALTYPE, |
| 650 |
MPI::SUM); |
| 651 |
#endif |
| 652 |
|
| 653 |
initSlope = slopeA; |
| 654 |
|
| 655 |
// if going uphill, use negative gradient as searching direction |
| 656 |
|
| 657 |
if (slopeA > 0) { |
| 658 |
|
| 659 |
for(size_t i = 0; i < ndim; i++) { |
| 660 |
direction[i] = -curG[i]; |
| 661 |
} |
| 662 |
|
| 663 |
for(size_t i = 0; i < ndim; i++) { |
| 664 |
slopeA += curG[i] * direction[i]; |
| 665 |
} |
| 666 |
|
| 667 |
#ifdef IS_MPI |
| 668 |
// in parallel, we need to add up the contributions from all |
| 669 |
// processors: |
| 670 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &slopeA, 1, MPI::REALTYPE, |
| 671 |
MPI::SUM); |
| 672 |
#endif |
| 673 |
initSlope = slopeA; |
| 674 |
} |
| 675 |
|
| 676 |
// Take a trial step |
| 677 |
|
| 678 |
for(size_t i = 0; i < ndim; i++) { |
| 679 |
xc[i] = curX[i] + direction[i]* c; |
| 680 |
} |
| 681 |
|
| 682 |
calcG(xc, gc, fc, status); |
| 683 |
|
| 684 |
if (status < 0) { |
| 685 |
if (bVerbose) |
| 686 |
std::cerr << "Function Evaluation Error" << std::endl; |
| 687 |
} |
| 688 |
|
| 689 |
//calculate the derivative at c |
| 690 |
|
| 691 |
slopeC = 0; |
| 692 |
|
| 693 |
for(size_t i = 0; i < ndim; i++) { |
| 694 |
slopeC += gc[i] * direction[i]; |
| 695 |
} |
| 696 |
// found a lower point |
| 697 |
|
| 698 |
if (fc < fa) { |
| 699 |
curX = xc; |
| 700 |
curG = gc; |
| 701 |
curF = fc; |
| 702 |
return LS_SUCCEED; |
| 703 |
} else { |
| 704 |
if (slopeC > 0) |
| 705 |
stepSize *= 0.618034; |
| 706 |
} |
| 707 |
|
| 708 |
maxLSIter = paramSet->getLineSearchMaxIteration(); |
| 709 |
|
| 710 |
iter = 0; |
| 711 |
|
| 712 |
do { |
| 713 |
|
| 714 |
// Select a new trial point. |
| 715 |
|
| 716 |
// If the derivatives at points a & c have different sign we use cubic interpolate |
| 717 |
|
| 718 |
//if (slopeC > 0){ |
| 719 |
|
| 720 |
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
| 721 |
|
| 722 |
mu = sqrt(eta * eta - slopeA * slopeC); |
| 723 |
|
| 724 |
b = a + (c - a) |
| 725 |
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
| 726 |
|
| 727 |
if (b < lsTol) { |
| 728 |
break; |
| 729 |
} |
| 730 |
|
| 731 |
//} |
| 732 |
|
| 733 |
// Take a trial step to this new point - new coords in xb |
| 734 |
|
| 735 |
for(size_t i = 0; i < ndim; i++) { |
| 736 |
xb[i] = curX[i] + direction[i]* b; |
| 737 |
} |
| 738 |
|
| 739 |
//function evaluation |
| 740 |
|
| 741 |
calcG(xb, gb, fb, status); |
| 742 |
|
| 743 |
if (status < 0) { |
| 744 |
if (bVerbose) |
| 745 |
std::cerr << "Function Evaluation Error" << std::endl; |
| 746 |
} |
| 747 |
|
| 748 |
//calculate the derivative at c |
| 749 |
|
| 750 |
slopeB = 0; |
| 751 |
|
| 752 |
for(size_t i = 0; i < ndim; i++) { |
| 753 |
slopeB += gb[i] * direction[i]; |
| 754 |
} |
| 755 |
|
| 756 |
//Amijo Rule to stop the line search |
| 757 |
|
| 758 |
if (fb <= curF + initSlope * ftol * b) { |
| 759 |
curF = fb; |
| 760 |
|
| 761 |
curX = xb; |
| 762 |
|
| 763 |
curG = gb; |
| 764 |
|
| 765 |
return LS_SUCCEED; |
| 766 |
} |
| 767 |
|
| 768 |
if (slopeB < 0 && fb < fa) { |
| 769 |
|
| 770 |
//replace a by b |
| 771 |
|
| 772 |
fa = fb; |
| 773 |
|
| 774 |
a = b; |
| 775 |
|
| 776 |
slopeA = slopeB; |
| 777 |
|
| 778 |
// swap coord a/b |
| 779 |
|
| 780 |
std::swap(xa, xb); |
| 781 |
|
| 782 |
std::swap(ga, gb); |
| 783 |
} else { |
| 784 |
|
| 785 |
//replace c by b |
| 786 |
|
| 787 |
fc = fb; |
| 788 |
|
| 789 |
c = b; |
| 790 |
|
| 791 |
slopeC = slopeB; |
| 792 |
|
| 793 |
// swap coord b/c |
| 794 |
|
| 795 |
std::swap(gb, gc); |
| 796 |
|
| 797 |
std::swap(xb, xc); |
| 798 |
} |
| 799 |
|
| 800 |
iter++; |
| 801 |
} while ((fb > fa || fb > fc) && (iter < maxLSIter)); |
| 802 |
|
| 803 |
if (fb < curF || iter >= maxLSIter) { |
| 804 |
|
| 805 |
//could not find a lower value, we might just go uphill. |
| 806 |
|
| 807 |
return LS_ERROR; |
| 808 |
} |
| 809 |
|
| 810 |
//select the end point |
| 811 |
|
| 812 |
if (fa <= fc) { |
| 813 |
curX = xa; |
| 814 |
|
| 815 |
curG = ga; |
| 816 |
|
| 817 |
curF = fa; |
| 818 |
} else { |
| 819 |
curX = xc; |
| 820 |
|
| 821 |
curG = gc; |
| 822 |
|
| 823 |
curF = fc; |
| 824 |
} |
| 825 |
|
| 826 |
return LS_SUCCEED; |
| 827 |
} |
| 828 |
|
| 829 |
void Minimizer::minimize() { |
| 830 |
int convgStatus; |
| 831 |
int stepStatus; |
| 832 |
int maxIter; |
| 833 |
int writeFreq; |
| 834 |
int nextWriteIter; |
| 835 |
Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot(); |
| 836 |
DumpWriter dumpWriter(info); |
| 837 |
StatsBitSet mask; |
| 838 |
mask.set(Stats::TIME); |
| 839 |
mask.set(Stats::POTENTIAL_ENERGY); |
| 840 |
StatWriter statWriter(info->getStatFileName(), mask); |
| 841 |
|
| 842 |
init(); |
| 843 |
|
| 844 |
writeFreq = paramSet->getWriteFreq(); |
| 845 |
|
| 846 |
nextWriteIter = writeFreq; |
| 847 |
|
| 848 |
maxIter = paramSet->getMaxIteration(); |
| 849 |
|
| 850 |
for(curIter = 1; curIter <= maxIter; curIter++) { |
| 851 |
stepStatus = step(); |
| 852 |
|
| 853 |
//if (usingShake) |
| 854 |
// preMove(); |
| 855 |
|
| 856 |
if (stepStatus < 0) { |
| 857 |
saveResult(); |
| 858 |
|
| 859 |
minStatus = MIN_LSERROR; |
| 860 |
|
| 861 |
std::cerr |
| 862 |
<< "Minimizer Error: line search error, please try a small stepsize" |
| 863 |
<< std::endl; |
| 864 |
|
| 865 |
return; |
| 866 |
} |
| 867 |
|
| 868 |
//save snapshot |
| 869 |
info->getSnapshotManager()->advance(); |
| 870 |
//increase time |
| 871 |
curSnapshot->increaseTime(1); |
| 872 |
|
| 873 |
if (curIter == nextWriteIter) { |
| 874 |
nextWriteIter += writeFreq; |
| 875 |
calcF(); |
| 876 |
dumpWriter.writeDumpAndEor(); |
| 877 |
statWriter.writeStat(curSnapshot->statData); |
| 878 |
} |
| 879 |
|
| 880 |
convgStatus = checkConvg(); |
| 881 |
|
| 882 |
if (convgStatus > 0) { |
| 883 |
saveResult(); |
| 884 |
|
| 885 |
minStatus = MIN_CONVERGE; |
| 886 |
|
| 887 |
return; |
| 888 |
} |
| 889 |
|
| 890 |
prepareStep(); |
| 891 |
} |
| 892 |
|
| 893 |
if (bVerbose) { |
| 894 |
std::cout << "Minimizer Warning: " << minimizerName |
| 895 |
<< " algorithm did not converge within " << maxIter << " iteration" |
| 896 |
<< std::endl; |
| 897 |
} |
| 898 |
|
| 899 |
minStatus = MIN_MAXITER; |
| 900 |
|
| 901 |
saveResult(); |
| 902 |
} |
| 903 |
|
| 904 |
|
| 905 |
RealType Minimizer::calcPotential() { |
| 906 |
forceMan->calcForces(); |
| 907 |
|
| 908 |
Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 909 |
RealType potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 910 |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 911 |
RealType potential; |
| 912 |
|
| 913 |
#ifdef IS_MPI |
| 914 |
MPI_Allreduce(&potential_local, &potential, 1, MPI_REALTYPE, MPI_SUM, |
| 915 |
MPI_COMM_WORLD); |
| 916 |
#else |
| 917 |
potential = potential_local; |
| 918 |
#endif |
| 919 |
|
| 920 |
//save total potential |
| 921 |
curSnapshot->statData[Stats::POTENTIAL_ENERGY] = potential; |
| 922 |
return potential; |
| 923 |
} |
| 924 |
|
| 925 |
} |
