| 1 |
#include <iostream> |
| 2 |
#include <cstdlib> |
| 3 |
#include <cmath> |
| 4 |
|
| 5 |
#ifdef IS_MPI |
| 6 |
#include "mpiSimulation.hpp" |
| 7 |
#include <unistd.h> |
| 8 |
#endif //is_mpi |
| 9 |
|
| 10 |
#include "Integrator.hpp" |
| 11 |
#include "simError.h" |
| 12 |
|
| 13 |
|
| 14 |
Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
| 15 |
|
| 16 |
info = theInfo; |
| 17 |
myFF = the_ff; |
| 18 |
isFirst = 1; |
| 19 |
|
| 20 |
molecules = info->molecules; |
| 21 |
nMols = info->n_mol; |
| 22 |
|
| 23 |
// give a little love back to the SimInfo object |
| 24 |
|
| 25 |
if( info->the_integrator != NULL ) delete info->the_integrator; |
| 26 |
info->the_integrator = this; |
| 27 |
|
| 28 |
nAtoms = info->n_atoms; |
| 29 |
|
| 30 |
// check for constraints |
| 31 |
|
| 32 |
constrainedA = NULL; |
| 33 |
constrainedB = NULL; |
| 34 |
constrainedDsqr = NULL; |
| 35 |
moving = NULL; |
| 36 |
moved = NULL; |
| 37 |
oldPos = NULL; |
| 38 |
|
| 39 |
nConstrained = 0; |
| 40 |
|
| 41 |
checkConstraints(); |
| 42 |
} |
| 43 |
|
| 44 |
Integrator::~Integrator() { |
| 45 |
|
| 46 |
if( nConstrained ){ |
| 47 |
delete[] constrainedA; |
| 48 |
delete[] constrainedB; |
| 49 |
delete[] constrainedDsqr; |
| 50 |
delete[] moving; |
| 51 |
delete[] moved; |
| 52 |
delete[] oldPos; |
| 53 |
} |
| 54 |
|
| 55 |
} |
| 56 |
|
| 57 |
void Integrator::checkConstraints( void ){ |
| 58 |
|
| 59 |
|
| 60 |
isConstrained = 0; |
| 61 |
|
| 62 |
Constraint *temp_con; |
| 63 |
Constraint *dummy_plug; |
| 64 |
temp_con = new Constraint[info->n_SRI]; |
| 65 |
nConstrained = 0; |
| 66 |
int constrained = 0; |
| 67 |
|
| 68 |
SRI** theArray; |
| 69 |
for(int i = 0; i < nMols; i++){ |
| 70 |
|
| 71 |
theArray = (SRI**) molecules[i].getMyBonds(); |
| 72 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
| 73 |
|
| 74 |
constrained = theArray[j]->is_constrained(); |
| 75 |
|
| 76 |
if(constrained){ |
| 77 |
|
| 78 |
dummy_plug = theArray[j]->get_constraint(); |
| 79 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
| 80 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
| 81 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 82 |
|
| 83 |
nConstrained++; |
| 84 |
constrained = 0; |
| 85 |
} |
| 86 |
} |
| 87 |
|
| 88 |
theArray = (SRI**) molecules[i].getMyBends(); |
| 89 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
| 90 |
|
| 91 |
constrained = theArray[j]->is_constrained(); |
| 92 |
|
| 93 |
if(constrained){ |
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|
| 95 |
dummy_plug = theArray[j]->get_constraint(); |
| 96 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
| 97 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
| 98 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 99 |
|
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nConstrained++; |
| 101 |
constrained = 0; |
| 102 |
} |
| 103 |
} |
| 104 |
|
| 105 |
theArray = (SRI**) molecules[i].getMyTorsions(); |
| 106 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
| 107 |
|
| 108 |
constrained = theArray[j]->is_constrained(); |
| 109 |
|
| 110 |
if(constrained){ |
| 111 |
|
| 112 |
dummy_plug = theArray[j]->get_constraint(); |
| 113 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
| 114 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 116 |
|
| 117 |
nConstrained++; |
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constrained = 0; |
| 119 |
} |
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} |
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} |
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|
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if(nConstrained > 0){ |
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|
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isConstrained = 1; |
| 126 |
|
| 127 |
if(constrainedA != NULL ) delete[] constrainedA; |
| 128 |
if(constrainedB != NULL ) delete[] constrainedB; |
| 129 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
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|
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constrainedA = new int[nConstrained]; |
| 132 |
constrainedB = new int[nConstrained]; |
| 133 |
constrainedDsqr = new double[nConstrained]; |
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|
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for( int i = 0; i < nConstrained; i++){ |
| 136 |
|
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constrainedA[i] = temp_con[i].get_a(); |
| 138 |
constrainedB[i] = temp_con[i].get_b(); |
| 139 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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} |
| 141 |
|
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|
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// save oldAtoms to check for lode balanceing later on. |
| 144 |
|
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oldAtoms = nAtoms; |
| 146 |
|
| 147 |
moving = new int[nAtoms]; |
| 148 |
moved = new int[nAtoms]; |
| 149 |
|
| 150 |
oldPos = new double[nAtoms*3]; |
| 151 |
} |
| 152 |
|
| 153 |
delete[] temp_con; |
| 154 |
} |
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|
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|
| 157 |
void Integrator::integrate( void ){ |
| 158 |
|
| 159 |
int i, j; // loop counters |
| 160 |
|
| 161 |
double runTime = info->run_time; |
| 162 |
double sampleTime = info->sampleTime; |
| 163 |
double statusTime = info->statusTime; |
| 164 |
double thermalTime = info->thermalTime; |
| 165 |
|
| 166 |
double currSample; |
| 167 |
double currThermal; |
| 168 |
double currStatus; |
| 169 |
double currTime; |
| 170 |
|
| 171 |
int calcPot, calcStress; |
| 172 |
int isError; |
| 173 |
|
| 174 |
|
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|
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tStats = new Thermo( info ); |
| 177 |
statOut = new StatWriter( info ); |
| 178 |
dumpOut = new DumpWriter( info ); |
| 179 |
|
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atoms = info->atoms; |
| 181 |
DirectionalAtom* dAtom; |
| 182 |
|
| 183 |
dt = info->dt; |
| 184 |
dt2 = 0.5 * dt; |
| 185 |
|
| 186 |
// initialize the forces before the first step |
| 187 |
|
| 188 |
myFF->doForces(1,1); |
| 189 |
|
| 190 |
if( info->setTemp ){ |
| 191 |
|
| 192 |
tStats->velocitize(); |
| 193 |
} |
| 194 |
|
| 195 |
dumpOut->writeDump( 0.0 ); |
| 196 |
statOut->writeStat( 0.0 ); |
| 197 |
|
| 198 |
calcPot = 0; |
| 199 |
calcStress = 0; |
| 200 |
currSample = sampleTime; |
| 201 |
currThermal = thermalTime; |
| 202 |
currStatus = statusTime; |
| 203 |
currTime = 0.0;; |
| 204 |
|
| 205 |
|
| 206 |
readyCheck(); |
| 207 |
|
| 208 |
#ifdef IS_MPI |
| 209 |
strcpy( checkPointMsg, |
| 210 |
"The integrator is ready to go." ); |
| 211 |
MPIcheckPoint(); |
| 212 |
#endif // is_mpi |
| 213 |
|
| 214 |
|
| 215 |
pos = Atom::getPosArray(); |
| 216 |
vel = Atom::getVelArray(); |
| 217 |
frc = Atom::getFrcArray(); |
| 218 |
trq = Atom::getTrqArray(); |
| 219 |
Amat = Atom::getAmatArray(); |
| 220 |
|
| 221 |
while( currTime < runTime ){ |
| 222 |
|
| 223 |
if( (currTime+dt) >= currStatus ){ |
| 224 |
calcPot = 1; |
| 225 |
calcStress = 1; |
| 226 |
} |
| 227 |
|
| 228 |
integrateStep( calcPot, calcStress ); |
| 229 |
|
| 230 |
currTime += dt; |
| 231 |
|
| 232 |
if( info->setTemp ){ |
| 233 |
if( currTime >= currThermal ){ |
| 234 |
tStats->velocitize(); |
| 235 |
currThermal += thermalTime; |
| 236 |
} |
| 237 |
} |
| 238 |
|
| 239 |
if( currTime >= currSample ){ |
| 240 |
dumpOut->writeDump( currTime ); |
| 241 |
currSample += sampleTime; |
| 242 |
} |
| 243 |
|
| 244 |
if( currTime >= currStatus ){ |
| 245 |
statOut->writeStat( currTime ); |
| 246 |
calcPot = 0; |
| 247 |
calcStress = 0; |
| 248 |
currStatus += statusTime; |
| 249 |
} |
| 250 |
|
| 251 |
#ifdef IS_MPI |
| 252 |
strcpy( checkPointMsg, |
| 253 |
"successfully took a time step." ); |
| 254 |
MPIcheckPoint(); |
| 255 |
#endif // is_mpi |
| 256 |
|
| 257 |
} |
| 258 |
|
| 259 |
dumpOut->writeFinal(); |
| 260 |
|
| 261 |
delete dumpOut; |
| 262 |
delete statOut; |
| 263 |
} |
| 264 |
|
| 265 |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
| 266 |
|
| 267 |
|
| 268 |
|
| 269 |
// Position full step, and velocity half step |
| 270 |
|
| 271 |
preMove(); |
| 272 |
moveA(); |
| 273 |
if( nConstrained ) constrainA(); |
| 274 |
|
| 275 |
// calc forces |
| 276 |
|
| 277 |
myFF->doForces(calcPot,calcStress); |
| 278 |
|
| 279 |
// finish the velocity half step |
| 280 |
|
| 281 |
moveB(); |
| 282 |
if( nConstrained ) constrainB(); |
| 283 |
|
| 284 |
} |
| 285 |
|
| 286 |
|
| 287 |
void Integrator::moveA( void ){ |
| 288 |
|
| 289 |
int i,j,k; |
| 290 |
int atomIndex, aMatIndex; |
| 291 |
DirectionalAtom* dAtom; |
| 292 |
double Tb[3]; |
| 293 |
double ji[3]; |
| 294 |
double angle; |
| 295 |
|
| 296 |
for( i=0; i<nAtoms; i++ ){ |
| 297 |
atomIndex = i * 3; |
| 298 |
aMatIndex = i * 9; |
| 299 |
|
| 300 |
// velocity half step |
| 301 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 302 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 303 |
|
| 304 |
// position whole step |
| 305 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 306 |
pos[j] += dt * vel[j]; |
| 307 |
|
| 308 |
|
| 309 |
if( atoms[i]->isDirectional() ){ |
| 310 |
|
| 311 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 312 |
|
| 313 |
// get and convert the torque to body frame |
| 314 |
|
| 315 |
Tb[0] = dAtom->getTx(); |
| 316 |
Tb[1] = dAtom->getTy(); |
| 317 |
Tb[2] = dAtom->getTz(); |
| 318 |
|
| 319 |
dAtom->lab2Body( Tb ); |
| 320 |
|
| 321 |
// get the angular momentum, and propagate a half step |
| 322 |
|
| 323 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 324 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 325 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 326 |
|
| 327 |
// use the angular velocities to propagate the rotation matrix a |
| 328 |
// full time step |
| 329 |
|
| 330 |
// rotate about the x-axis |
| 331 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 332 |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 333 |
|
| 334 |
// rotate about the y-axis |
| 335 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 336 |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 337 |
|
| 338 |
// rotate about the z-axis |
| 339 |
angle = dt * ji[2] / dAtom->getIzz(); |
| 340 |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 341 |
|
| 342 |
// rotate about the y-axis |
| 343 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 344 |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 345 |
|
| 346 |
// rotate about the x-axis |
| 347 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 348 |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 349 |
|
| 350 |
dAtom->setJx( ji[0] ); |
| 351 |
dAtom->setJy( ji[1] ); |
| 352 |
dAtom->setJz( ji[2] ); |
| 353 |
} |
| 354 |
|
| 355 |
} |
| 356 |
} |
| 357 |
|
| 358 |
|
| 359 |
void Integrator::moveB( void ){ |
| 360 |
int i,j,k; |
| 361 |
int atomIndex; |
| 362 |
DirectionalAtom* dAtom; |
| 363 |
double Tb[3]; |
| 364 |
double ji[3]; |
| 365 |
|
| 366 |
for( i=0; i<nAtoms; i++ ){ |
| 367 |
atomIndex = i * 3; |
| 368 |
|
| 369 |
// velocity half step |
| 370 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 371 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 372 |
|
| 373 |
if( atoms[i]->isDirectional() ){ |
| 374 |
|
| 375 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 376 |
|
| 377 |
// get and convert the torque to body frame |
| 378 |
|
| 379 |
Tb[0] = dAtom->getTx(); |
| 380 |
Tb[1] = dAtom->getTy(); |
| 381 |
Tb[2] = dAtom->getTz(); |
| 382 |
|
| 383 |
dAtom->lab2Body( Tb ); |
| 384 |
|
| 385 |
// get the angular momentum, and complete the angular momentum |
| 386 |
// half step |
| 387 |
|
| 388 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 389 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 390 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 391 |
|
| 392 |
dAtom->setJx( ji[0] ); |
| 393 |
dAtom->setJy( ji[1] ); |
| 394 |
dAtom->setJz( ji[2] ); |
| 395 |
} |
| 396 |
} |
| 397 |
|
| 398 |
} |
| 399 |
|
| 400 |
void Integrator::preMove( void ){ |
| 401 |
int i; |
| 402 |
|
| 403 |
if( nConstrained ){ |
| 404 |
|
| 405 |
// if( oldAtoms != nAtoms ){ |
| 406 |
|
| 407 |
// // save oldAtoms to check for lode balanceing later on. |
| 408 |
|
| 409 |
// oldAtoms = nAtoms; |
| 410 |
|
| 411 |
// delete[] moving; |
| 412 |
// delete[] moved; |
| 413 |
// delete[] oldPos; |
| 414 |
|
| 415 |
// moving = new int[nAtoms]; |
| 416 |
// moved = new int[nAtoms]; |
| 417 |
|
| 418 |
// oldPos = new double[nAtoms*3]; |
| 419 |
// } |
| 420 |
|
| 421 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
| 422 |
} |
| 423 |
} |
| 424 |
|
| 425 |
void Integrator::constrainA(){ |
| 426 |
|
| 427 |
int i,j,k; |
| 428 |
int done; |
| 429 |
double pxab, pyab, pzab; |
| 430 |
double rxab, ryab, rzab; |
| 431 |
int a, b; |
| 432 |
double rma, rmb; |
| 433 |
double dx, dy, dz; |
| 434 |
double rpab; |
| 435 |
double rabsq, pabsq, rpabsq; |
| 436 |
double diffsq; |
| 437 |
double gab; |
| 438 |
int iteration; |
| 439 |
|
| 440 |
|
| 441 |
|
| 442 |
for( i=0; i<nAtoms; i++){ |
| 443 |
|
| 444 |
moving[i] = 0; |
| 445 |
moved[i] = 1; |
| 446 |
} |
| 447 |
|
| 448 |
|
| 449 |
iteration = 0; |
| 450 |
done = 0; |
| 451 |
while( !done && (iteration < maxIteration )){ |
| 452 |
|
| 453 |
done = 1; |
| 454 |
for(i=0; i<nConstrained; i++){ |
| 455 |
|
| 456 |
a = constrainedA[i]; |
| 457 |
b = constrainedB[i]; |
| 458 |
|
| 459 |
if( moved[a] || moved[b] ){ |
| 460 |
|
| 461 |
pxab = pos[3*a+0] - pos[3*b+0]; |
| 462 |
pyab = pos[3*a+1] - pos[3*b+1]; |
| 463 |
pzab = pos[3*a+2] - pos[3*b+2]; |
| 464 |
|
| 465 |
//periodic boundary condition |
| 466 |
pxab = pxab - info->box_x * copysign(1, pxab) |
| 467 |
* int( fabs(pxab) / info->box_x + 0.5); |
| 468 |
pyab = pyab - info->box_y * copysign(1, pyab) |
| 469 |
* int( fabs(pyab) / info->box_y + 0.5); |
| 470 |
pzab = pzab - info->box_z * copysign(1, pzab) |
| 471 |
* int( fabs(pzab) / info->box_z + 0.5); |
| 472 |
|
| 473 |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
| 474 |
rabsq = constrainedDsqr[i]; |
| 475 |
diffsq = pabsq - rabsq; |
| 476 |
|
| 477 |
// the original rattle code from alan tidesley |
| 478 |
if (fabs(diffsq) > tol*rabsq*2) { |
| 479 |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
| 480 |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
| 481 |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
| 482 |
|
| 483 |
rxab = rxab - info->box_x * copysign(1, rxab) |
| 484 |
* int( fabs(rxab) / info->box_x + 0.5); |
| 485 |
ryab = ryab - info->box_y * copysign(1, ryab) |
| 486 |
* int( fabs(ryab) / info->box_y + 0.5); |
| 487 |
rzab = rzab - info->box_z * copysign(1, rzab) |
| 488 |
* int( fabs(rzab) / info->box_z + 0.5); |
| 489 |
|
| 490 |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
| 491 |
rpabsq = rpab * rpab; |
| 492 |
|
| 493 |
|
| 494 |
if (rpabsq < (rabsq * -diffsq)){ |
| 495 |
#ifdef IS_MPI |
| 496 |
a = atoms[a]->getGlobalIndex(); |
| 497 |
b = atoms[b]->getGlobalIndex(); |
| 498 |
#endif //is_mpi |
| 499 |
sprintf( painCave.errMsg, |
| 500 |
"Constraint failure in constrainA at atom %d and %d\n.", |
| 501 |
a, b ); |
| 502 |
painCave.isFatal = 1; |
| 503 |
simError(); |
| 504 |
} |
| 505 |
|
| 506 |
rma = 1.0 / atoms[a]->getMass(); |
| 507 |
rmb = 1.0 / atoms[b]->getMass(); |
| 508 |
|
| 509 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
| 510 |
dx = rxab * gab; |
| 511 |
dy = ryab * gab; |
| 512 |
dz = rzab * gab; |
| 513 |
|
| 514 |
pos[3*a+0] += rma * dx; |
| 515 |
pos[3*a+1] += rma * dy; |
| 516 |
pos[3*a+2] += rma * dz; |
| 517 |
|
| 518 |
pos[3*b+0] -= rmb * dx; |
| 519 |
pos[3*b+1] -= rmb * dy; |
| 520 |
pos[3*b+2] -= rmb * dz; |
| 521 |
|
| 522 |
dx = dx / dt; |
| 523 |
dy = dy / dt; |
| 524 |
dz = dz / dt; |
| 525 |
|
| 526 |
vel[3*a+0] += rma * dx; |
| 527 |
vel[3*a+1] += rma * dy; |
| 528 |
vel[3*a+2] += rma * dz; |
| 529 |
|
| 530 |
vel[3*b+0] -= rmb * dx; |
| 531 |
vel[3*b+1] -= rmb * dy; |
| 532 |
vel[3*b+2] -= rmb * dz; |
| 533 |
|
| 534 |
moving[a] = 1; |
| 535 |
moving[b] = 1; |
| 536 |
done = 0; |
| 537 |
} |
| 538 |
} |
| 539 |
} |
| 540 |
|
| 541 |
for(i=0; i<nAtoms; i++){ |
| 542 |
|
| 543 |
moved[i] = moving[i]; |
| 544 |
moving[i] = 0; |
| 545 |
} |
| 546 |
|
| 547 |
iteration++; |
| 548 |
} |
| 549 |
|
| 550 |
if( !done ){ |
| 551 |
|
| 552 |
sprintf( painCave.errMsg, |
| 553 |
"Constraint failure in constrainA, too many iterations: %d\n", |
| 554 |
iteration ); |
| 555 |
painCave.isFatal = 1; |
| 556 |
simError(); |
| 557 |
} |
| 558 |
|
| 559 |
} |
| 560 |
|
| 561 |
void Integrator::constrainB( void ){ |
| 562 |
|
| 563 |
int i,j,k; |
| 564 |
int done; |
| 565 |
double vxab, vyab, vzab; |
| 566 |
double rxab, ryab, rzab; |
| 567 |
int a, b; |
| 568 |
double rma, rmb; |
| 569 |
double dx, dy, dz; |
| 570 |
double rabsq, pabsq, rvab; |
| 571 |
double diffsq; |
| 572 |
double gab; |
| 573 |
int iteration; |
| 574 |
|
| 575 |
for(i=0; i<nAtoms; i++){ |
| 576 |
moving[i] = 0; |
| 577 |
moved[i] = 1; |
| 578 |
} |
| 579 |
|
| 580 |
done = 0; |
| 581 |
iteration = 0; |
| 582 |
while( !done && (iteration < maxIteration ) ){ |
| 583 |
|
| 584 |
for(i=0; i<nConstrained; i++){ |
| 585 |
|
| 586 |
a = constrainedA[i]; |
| 587 |
b = constrainedB[i]; |
| 588 |
|
| 589 |
if( moved[a] || moved[b] ){ |
| 590 |
|
| 591 |
vxab = vel[3*a+0] - vel[3*b+0]; |
| 592 |
vyab = vel[3*a+1] - vel[3*b+1]; |
| 593 |
vzab = vel[3*a+2] - vel[3*b+2]; |
| 594 |
|
| 595 |
rxab = pos[3*a+0] - pos[3*b+0]; |
| 596 |
ryab = pos[3*a+1] - pos[3*b+1]; |
| 597 |
rzab = pos[3*a+2] - pos[3*b+2]; |
| 598 |
|
| 599 |
rxab = rxab - info->box_x * copysign(1, rxab) |
| 600 |
* int( fabs(rxab) / info->box_x + 0.5); |
| 601 |
ryab = ryab - info->box_y * copysign(1, ryab) |
| 602 |
* int( fabs(ryab) / info->box_y + 0.5); |
| 603 |
rzab = rzab - info->box_z * copysign(1, rzab) |
| 604 |
* int( fabs(rzab) / info->box_z + 0.5); |
| 605 |
|
| 606 |
rma = 1.0 / atoms[a]->getMass(); |
| 607 |
rmb = 1.0 / atoms[b]->getMass(); |
| 608 |
|
| 609 |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
| 610 |
|
| 611 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
| 612 |
|
| 613 |
if (fabs(gab) > tol) { |
| 614 |
|
| 615 |
dx = rxab * gab; |
| 616 |
dy = ryab * gab; |
| 617 |
dz = rzab * gab; |
| 618 |
|
| 619 |
vel[3*a+0] += rma * dx; |
| 620 |
vel[3*a+1] += rma * dy; |
| 621 |
vel[3*a+2] += rma * dz; |
| 622 |
|
| 623 |
vel[3*b+0] -= rmb * dx; |
| 624 |
vel[3*b+1] -= rmb * dy; |
| 625 |
vel[3*b+2] -= rmb * dz; |
| 626 |
|
| 627 |
moving[a] = 1; |
| 628 |
moving[b] = 1; |
| 629 |
done = 0; |
| 630 |
} |
| 631 |
} |
| 632 |
} |
| 633 |
|
| 634 |
for(i=0; i<nAtoms; i++){ |
| 635 |
moved[i] = moving[i]; |
| 636 |
moving[i] = 0; |
| 637 |
} |
| 638 |
|
| 639 |
iteration++; |
| 640 |
} |
| 641 |
|
| 642 |
if( !done ){ |
| 643 |
|
| 644 |
|
| 645 |
sprintf( painCave.errMsg, |
| 646 |
"Constraint failure in constrainB, too many iterations: %d\n", |
| 647 |
iteration ); |
| 648 |
painCave.isFatal = 1; |
| 649 |
simError(); |
| 650 |
} |
| 651 |
|
| 652 |
} |
| 653 |
|
| 654 |
|
| 655 |
|
| 656 |
|
| 657 |
|
| 658 |
|
| 659 |
|
| 660 |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
| 661 |
double A[9] ){ |
| 662 |
|
| 663 |
int i,j,k; |
| 664 |
double sinAngle; |
| 665 |
double cosAngle; |
| 666 |
double angleSqr; |
| 667 |
double angleSqrOver4; |
| 668 |
double top, bottom; |
| 669 |
double rot[3][3]; |
| 670 |
double tempA[3][3]; |
| 671 |
double tempJ[3]; |
| 672 |
|
| 673 |
// initialize the tempA |
| 674 |
|
| 675 |
for(i=0; i<3; i++){ |
| 676 |
for(j=0; j<3; j++){ |
| 677 |
tempA[j][i] = A[3*i + j]; |
| 678 |
} |
| 679 |
} |
| 680 |
|
| 681 |
// initialize the tempJ |
| 682 |
|
| 683 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
| 684 |
|
| 685 |
// initalize rot as a unit matrix |
| 686 |
|
| 687 |
rot[0][0] = 1.0; |
| 688 |
rot[0][1] = 0.0; |
| 689 |
rot[0][2] = 0.0; |
| 690 |
|
| 691 |
rot[1][0] = 0.0; |
| 692 |
rot[1][1] = 1.0; |
| 693 |
rot[1][2] = 0.0; |
| 694 |
|
| 695 |
rot[2][0] = 0.0; |
| 696 |
rot[2][1] = 0.0; |
| 697 |
rot[2][2] = 1.0; |
| 698 |
|
| 699 |
// use a small angle aproximation for sin and cosine |
| 700 |
|
| 701 |
angleSqr = angle * angle; |
| 702 |
angleSqrOver4 = angleSqr / 4.0; |
| 703 |
top = 1.0 - angleSqrOver4; |
| 704 |
bottom = 1.0 + angleSqrOver4; |
| 705 |
|
| 706 |
cosAngle = top / bottom; |
| 707 |
sinAngle = angle / bottom; |
| 708 |
|
| 709 |
rot[axes1][axes1] = cosAngle; |
| 710 |
rot[axes2][axes2] = cosAngle; |
| 711 |
|
| 712 |
rot[axes1][axes2] = sinAngle; |
| 713 |
rot[axes2][axes1] = -sinAngle; |
| 714 |
|
| 715 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
| 716 |
|
| 717 |
for(i=0; i<3; i++){ |
| 718 |
ji[i] = 0.0; |
| 719 |
for(k=0; k<3; k++){ |
| 720 |
ji[i] += rot[i][k] * tempJ[k]; |
| 721 |
} |
| 722 |
} |
| 723 |
|
| 724 |
// rotate the Rotation matrix acording to: |
| 725 |
// A[][] = A[][] * transpose(rot[][]) |
| 726 |
|
| 727 |
|
| 728 |
// NOte for as yet unknown reason, we are performing the |
| 729 |
// calculation as: |
| 730 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
| 731 |
|
| 732 |
for(i=0; i<3; i++){ |
| 733 |
for(j=0; j<3; j++){ |
| 734 |
A[3*j + i] = 0.0; |
| 735 |
for(k=0; k<3; k++){ |
| 736 |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
| 737 |
} |
| 738 |
} |
| 739 |
} |
| 740 |
} |
