| 1 |
#include <cmath> |
| 2 |
#include "Atom.hpp" |
| 3 |
#include "SRI.hpp" |
| 4 |
#include "AbstractClasses.hpp" |
| 5 |
#include "SimInfo.hpp" |
| 6 |
#include "ForceFields.hpp" |
| 7 |
#include "Thermo.hpp" |
| 8 |
#include "ReadWrite.hpp" |
| 9 |
#include "Integrator.hpp" |
| 10 |
#include "simError.h" |
| 11 |
|
| 12 |
#ifdef IS_MPI |
| 13 |
#include "mpiSimulation.hpp" |
| 14 |
#endif |
| 15 |
|
| 16 |
// Basic non-isotropic thermostating and barostating via the Melchionna |
| 17 |
// modification of the Hoover algorithm: |
| 18 |
// |
| 19 |
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 20 |
// Molec. Phys., 78, 533. |
| 21 |
// |
| 22 |
// and |
| 23 |
// |
| 24 |
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 25 |
|
| 26 |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 27 |
T( theInfo, the_ff ) |
| 28 |
{ |
| 29 |
int i, j; |
| 30 |
chi = 0.0; |
| 31 |
integralOfChidt = 0.0; |
| 32 |
|
| 33 |
for(i = 0; i < 3; i++) |
| 34 |
for (j = 0; j < 3; j++) |
| 35 |
eta[i][j] = 0.0; |
| 36 |
|
| 37 |
have_tau_thermostat = 0; |
| 38 |
have_tau_barostat = 0; |
| 39 |
have_target_temp = 0; |
| 40 |
have_target_pressure = 0; |
| 41 |
|
| 42 |
have_chi_tolerance = 0; |
| 43 |
have_eta_tolerance = 0; |
| 44 |
have_pos_iter_tolerance = 0; |
| 45 |
|
| 46 |
oldPos = new double[3*nAtoms]; |
| 47 |
oldVel = new double[3*nAtoms]; |
| 48 |
oldJi = new double[3*nAtoms]; |
| 49 |
#ifdef IS_MPI |
| 50 |
Nparticles = mpiSim->getTotAtoms(); |
| 51 |
#else |
| 52 |
Nparticles = theInfo->n_atoms; |
| 53 |
#endif |
| 54 |
|
| 55 |
} |
| 56 |
|
| 57 |
template<typename T> NPTf<T>::~NPTf() { |
| 58 |
delete[] oldPos; |
| 59 |
delete[] oldVel; |
| 60 |
delete[] oldJi; |
| 61 |
} |
| 62 |
|
| 63 |
template<typename T> void NPTf<T>::moveA() { |
| 64 |
|
| 65 |
// new version of NPTf |
| 66 |
int i, j, k; |
| 67 |
DirectionalAtom* dAtom; |
| 68 |
double Tb[3], ji[3]; |
| 69 |
double A[3][3], I[3][3]; |
| 70 |
double angle, mass; |
| 71 |
double vel[3], pos[3], frc[3]; |
| 72 |
|
| 73 |
double rj[3]; |
| 74 |
double instaTemp, instaPress, instaVol; |
| 75 |
double tt2, tb2; |
| 76 |
double sc[3]; |
| 77 |
double eta2ij; |
| 78 |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
| 79 |
double bigScale, smallScale, offDiagMax; |
| 80 |
double COM[3]; |
| 81 |
|
| 82 |
tt2 = tauThermostat * tauThermostat; |
| 83 |
tb2 = tauBarostat * tauBarostat; |
| 84 |
|
| 85 |
instaTemp = tStats->getTemperature(); |
| 86 |
tStats->getPressureTensor(press); |
| 87 |
instaVol = tStats->getVolume(); |
| 88 |
|
| 89 |
tStats->getCOM(COM); |
| 90 |
|
| 91 |
//calculate scale factor of veloity |
| 92 |
for (i = 0; i < 3; i++ ) { |
| 93 |
for (j = 0; j < 3; j++ ) { |
| 94 |
vScale[i][j] = eta[i][j]; |
| 95 |
|
| 96 |
if (i == j) { |
| 97 |
vScale[i][j] += chi; |
| 98 |
} |
| 99 |
} |
| 100 |
} |
| 101 |
|
| 102 |
//evolve velocity half step |
| 103 |
for( i=0; i<nAtoms; i++ ){ |
| 104 |
|
| 105 |
atoms[i]->getVel( vel ); |
| 106 |
atoms[i]->getFrc( frc ); |
| 107 |
|
| 108 |
mass = atoms[i]->getMass(); |
| 109 |
|
| 110 |
info->matVecMul3( vScale, vel, sc ); |
| 111 |
|
| 112 |
for (j=0; j < 3; j++) { |
| 113 |
// velocity half step |
| 114 |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 115 |
} |
| 116 |
|
| 117 |
atoms[i]->setVel( vel ); |
| 118 |
|
| 119 |
if( atoms[i]->isDirectional() ){ |
| 120 |
|
| 121 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 122 |
|
| 123 |
// get and convert the torque to body frame |
| 124 |
|
| 125 |
dAtom->getTrq( Tb ); |
| 126 |
dAtom->lab2Body( Tb ); |
| 127 |
|
| 128 |
// get the angular momentum, and propagate a half step |
| 129 |
|
| 130 |
dAtom->getJ( ji ); |
| 131 |
|
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for (j=0; j < 3; j++) |
| 133 |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 134 |
|
| 135 |
// use the angular velocities to propagate the rotation matrix a |
| 136 |
// full time step |
| 137 |
|
| 138 |
dAtom->getA(A); |
| 139 |
dAtom->getI(I); |
| 140 |
|
| 141 |
// rotate about the x-axis |
| 142 |
angle = dt2 * ji[0] / I[0][0]; |
| 143 |
this->rotate( 1, 2, angle, ji, A ); |
| 144 |
|
| 145 |
// rotate about the y-axis |
| 146 |
angle = dt2 * ji[1] / I[1][1]; |
| 147 |
this->rotate( 2, 0, angle, ji, A ); |
| 148 |
|
| 149 |
// rotate about the z-axis |
| 150 |
angle = dt * ji[2] / I[2][2]; |
| 151 |
this->rotate( 0, 1, angle, ji, A); |
| 152 |
|
| 153 |
// rotate about the y-axis |
| 154 |
angle = dt2 * ji[1] / I[1][1]; |
| 155 |
this->rotate( 2, 0, angle, ji, A ); |
| 156 |
|
| 157 |
// rotate about the x-axis |
| 158 |
angle = dt2 * ji[0] / I[0][0]; |
| 159 |
this->rotate( 1, 2, angle, ji, A ); |
| 160 |
|
| 161 |
dAtom->setJ( ji ); |
| 162 |
dAtom->setA( A ); |
| 163 |
} |
| 164 |
} |
| 165 |
|
| 166 |
// advance chi half step |
| 167 |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 168 |
|
| 169 |
// calculate the integral of chidt |
| 170 |
integralOfChidt += dt2*chi; |
| 171 |
|
| 172 |
// advance eta half step |
| 173 |
|
| 174 |
for(i = 0; i < 3; i ++) |
| 175 |
for(j = 0; j < 3; j++){ |
| 176 |
if( i == j) |
| 177 |
eta[i][j] += dt2 * instaVol * |
| 178 |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 179 |
else |
| 180 |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 181 |
} |
| 182 |
|
| 183 |
//save the old positions |
| 184 |
for(i = 0; i < nAtoms; i++){ |
| 185 |
atoms[i]->getPos(pos); |
| 186 |
for(j = 0; j < 3; j++) |
| 187 |
oldPos[i*3 + j] = pos[j]; |
| 188 |
} |
| 189 |
|
| 190 |
//the first estimation of r(t+dt) is equal to r(t) |
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|
| 192 |
for(k = 0; k < 4; k ++){ |
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|
| 194 |
for(i =0 ; i < nAtoms; i++){ |
| 195 |
|
| 196 |
atoms[i]->getVel(vel); |
| 197 |
atoms[i]->getPos(pos); |
| 198 |
|
| 199 |
for(j = 0; j < 3; j++) |
| 200 |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
| 201 |
|
| 202 |
info->matVecMul3( eta, rj, sc ); |
| 203 |
|
| 204 |
for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
| 206 |
|
| 207 |
atoms[i]->setPos( pos ); |
| 208 |
|
| 209 |
} |
| 210 |
|
| 211 |
if (nConstrained) { |
| 212 |
constrainA(); |
| 213 |
} |
| 214 |
} |
| 215 |
|
| 216 |
|
| 217 |
// Scale the box after all the positions have been moved: |
| 218 |
|
| 219 |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 220 |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 221 |
|
| 222 |
bigScale = 1.0; |
| 223 |
smallScale = 1.0; |
| 224 |
offDiagMax = 0.0; |
| 225 |
|
| 226 |
for(i=0; i<3; i++){ |
| 227 |
for(j=0; j<3; j++){ |
| 228 |
|
| 229 |
// Calculate the matrix Product of the eta array (we only need |
| 230 |
// the ij element right now): |
| 231 |
|
| 232 |
eta2ij = 0.0; |
| 233 |
for(k=0; k<3; k++){ |
| 234 |
eta2ij += eta[i][k] * eta[k][j]; |
| 235 |
} |
| 236 |
|
| 237 |
scaleMat[i][j] = 0.0; |
| 238 |
// identity matrix (see above): |
| 239 |
if (i == j) scaleMat[i][j] = 1.0; |
| 240 |
// Taylor expansion for the exponential truncated at second order: |
| 241 |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 242 |
|
| 243 |
if (i != j) |
| 244 |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 245 |
offDiagMax = fabs(scaleMat[i][j]); |
| 246 |
} |
| 247 |
|
| 248 |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 249 |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 250 |
} |
| 251 |
|
| 252 |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 253 |
sprintf( painCave.errMsg, |
| 254 |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 255 |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 256 |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 257 |
" [%lf\t%lf\t%lf]\n" |
| 258 |
" [%lf\t%lf\t%lf]\n", |
| 259 |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 260 |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 261 |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 262 |
painCave.isFatal = 1; |
| 263 |
simError(); |
| 264 |
} else if (offDiagMax > 0.1) { |
| 265 |
sprintf( painCave.errMsg, |
| 266 |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 267 |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 268 |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 269 |
" [%lf\t%lf\t%lf]\n" |
| 270 |
" [%lf\t%lf\t%lf]\n", |
| 271 |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 272 |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 273 |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 274 |
painCave.isFatal = 1; |
| 275 |
simError(); |
| 276 |
} else { |
| 277 |
info->getBoxM(hm); |
| 278 |
info->matMul3(hm, scaleMat, hmnew); |
| 279 |
info->setBoxM(hmnew); |
| 280 |
} |
| 281 |
|
| 282 |
} |
| 283 |
|
| 284 |
template<typename T> void NPTf<T>::moveB( void ){ |
| 285 |
|
| 286 |
//new version of NPTf |
| 287 |
int i, j, k; |
| 288 |
DirectionalAtom* dAtom; |
| 289 |
double Tb[3], ji[3]; |
| 290 |
double vel[3], myVel[3], frc[3]; |
| 291 |
double mass; |
| 292 |
|
| 293 |
double instaTemp, instaPress, instaVol; |
| 294 |
double tt2, tb2; |
| 295 |
double sc[3]; |
| 296 |
double press[3][3], vScale[3][3]; |
| 297 |
double oldChi, prevChi; |
| 298 |
double oldEta[3][3], prevEta[3][3], diffEta; |
| 299 |
|
| 300 |
tt2 = tauThermostat * tauThermostat; |
| 301 |
tb2 = tauBarostat * tauBarostat; |
| 302 |
|
| 303 |
// Set things up for the iteration: |
| 304 |
|
| 305 |
oldChi = chi; |
| 306 |
|
| 307 |
for(i = 0; i < 3; i++) |
| 308 |
for(j = 0; j < 3; j++) |
| 309 |
oldEta[i][j] = eta[i][j]; |
| 310 |
|
| 311 |
for( i=0; i<nAtoms; i++ ){ |
| 312 |
|
| 313 |
atoms[i]->getVel( vel ); |
| 314 |
|
| 315 |
for (j=0; j < 3; j++) |
| 316 |
oldVel[3*i + j] = vel[j]; |
| 317 |
|
| 318 |
if( atoms[i]->isDirectional() ){ |
| 319 |
|
| 320 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 321 |
|
| 322 |
dAtom->getJ( ji ); |
| 323 |
|
| 324 |
for (j=0; j < 3; j++) |
| 325 |
oldJi[3*i + j] = ji[j]; |
| 326 |
|
| 327 |
} |
| 328 |
} |
| 329 |
|
| 330 |
// do the iteration: |
| 331 |
|
| 332 |
instaVol = tStats->getVolume(); |
| 333 |
|
| 334 |
for (k=0; k < 4; k++) { |
| 335 |
|
| 336 |
instaTemp = tStats->getTemperature(); |
| 337 |
tStats->getPressureTensor(press); |
| 338 |
|
| 339 |
// evolve chi another half step using the temperature at t + dt/2 |
| 340 |
|
| 341 |
prevChi = chi; |
| 342 |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 343 |
|
| 344 |
for(i = 0; i < 3; i++) |
| 345 |
for(j = 0; j < 3; j++) |
| 346 |
prevEta[i][j] = eta[i][j]; |
| 347 |
|
| 348 |
//advance eta half step and calculate scale factor for velocity |
| 349 |
|
| 350 |
for(i = 0; i < 3; i ++) |
| 351 |
for(j = 0; j < 3; j++){ |
| 352 |
if( i == j) { |
| 353 |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 354 |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 355 |
vScale[i][j] = eta[i][j] + chi; |
| 356 |
} else { |
| 357 |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 358 |
vScale[i][j] = eta[i][j]; |
| 359 |
} |
| 360 |
} |
| 361 |
|
| 362 |
for( i=0; i<nAtoms; i++ ){ |
| 363 |
|
| 364 |
atoms[i]->getFrc( frc ); |
| 365 |
atoms[i]->getVel(vel); |
| 366 |
|
| 367 |
mass = atoms[i]->getMass(); |
| 368 |
|
| 369 |
for (j = 0; j < 3; j++) |
| 370 |
myVel[j] = oldVel[3*i + j]; |
| 371 |
|
| 372 |
info->matVecMul3( vScale, myVel, sc ); |
| 373 |
|
| 374 |
// velocity half step |
| 375 |
for (j=0; j < 3; j++) { |
| 376 |
// velocity half step (use chi from previous step here): |
| 377 |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 378 |
} |
| 379 |
|
| 380 |
atoms[i]->setVel( vel ); |
| 381 |
|
| 382 |
if( atoms[i]->isDirectional() ){ |
| 383 |
|
| 384 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 385 |
|
| 386 |
// get and convert the torque to body frame |
| 387 |
|
| 388 |
dAtom->getTrq( Tb ); |
| 389 |
dAtom->lab2Body( Tb ); |
| 390 |
|
| 391 |
for (j=0; j < 3; j++) |
| 392 |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 393 |
|
| 394 |
dAtom->setJ( ji ); |
| 395 |
} |
| 396 |
} |
| 397 |
|
| 398 |
if (nConstrained) { |
| 399 |
constrainB(); |
| 400 |
} |
| 401 |
|
| 402 |
diffEta = 0; |
| 403 |
for(i = 0; i < 3; i++) |
| 404 |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 405 |
|
| 406 |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
| 407 |
break; |
| 408 |
} |
| 409 |
|
| 410 |
//calculate integral of chidt |
| 411 |
integralOfChidt += dt2*chi; |
| 412 |
|
| 413 |
} |
| 414 |
|
| 415 |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 416 |
int i,j; |
| 417 |
|
| 418 |
chi = 0.0; |
| 419 |
|
| 420 |
for(i = 0; i < 3; i++) |
| 421 |
for (j = 0; j < 3; j++) |
| 422 |
eta[i][j] = 0.0; |
| 423 |
|
| 424 |
} |
| 425 |
|
| 426 |
template<typename T> int NPTf<T>::readyCheck() { |
| 427 |
|
| 428 |
//check parent's readyCheck() first |
| 429 |
if (T::readyCheck() == -1) |
| 430 |
return -1; |
| 431 |
|
| 432 |
// First check to see if we have a target temperature. |
| 433 |
// Not having one is fatal. |
| 434 |
|
| 435 |
if (!have_target_temp) { |
| 436 |
sprintf( painCave.errMsg, |
| 437 |
"NPTf error: You can't use the NPTf integrator\n" |
| 438 |
" without a targetTemp!\n" |
| 439 |
); |
| 440 |
painCave.isFatal = 1; |
| 441 |
simError(); |
| 442 |
return -1; |
| 443 |
} |
| 444 |
|
| 445 |
if (!have_target_pressure) { |
| 446 |
sprintf( painCave.errMsg, |
| 447 |
"NPTf error: You can't use the NPTf integrator\n" |
| 448 |
" without a targetPressure!\n" |
| 449 |
); |
| 450 |
painCave.isFatal = 1; |
| 451 |
simError(); |
| 452 |
return -1; |
| 453 |
} |
| 454 |
|
| 455 |
// We must set tauThermostat. |
| 456 |
|
| 457 |
if (!have_tau_thermostat) { |
| 458 |
sprintf( painCave.errMsg, |
| 459 |
"NPTf error: If you use the NPTf\n" |
| 460 |
" integrator, you must set tauThermostat.\n"); |
| 461 |
painCave.isFatal = 1; |
| 462 |
simError(); |
| 463 |
return -1; |
| 464 |
} |
| 465 |
|
| 466 |
// We must set tauBarostat. |
| 467 |
|
| 468 |
if (!have_tau_barostat) { |
| 469 |
sprintf( painCave.errMsg, |
| 470 |
"NPTf error: If you use the NPTf\n" |
| 471 |
" integrator, you must set tauBarostat.\n"); |
| 472 |
painCave.isFatal = 1; |
| 473 |
simError(); |
| 474 |
return -1; |
| 475 |
} |
| 476 |
|
| 477 |
|
| 478 |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 479 |
// of particles, so no subtraction or addition of constraints or |
| 480 |
// orientational degrees of freedom: |
| 481 |
|
| 482 |
NkBT = (double)Nparticles * kB * targetTemp; |
| 483 |
|
| 484 |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 485 |
// than the barostat (when there are particles with orientational degrees |
| 486 |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
| 487 |
|
| 488 |
fkBT = (double)info->ndf * kB * targetTemp; |
| 489 |
|
| 490 |
return 1; |
| 491 |
} |
| 492 |
|
| 493 |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 494 |
|
| 495 |
double conservedQuantity; |
| 496 |
double Energy; |
| 497 |
double thermostat_kinetic; |
| 498 |
double thermostat_potential; |
| 499 |
double barostat_kinetic; |
| 500 |
double barostat_potential; |
| 501 |
double trEta; |
| 502 |
double a[3][3], b[3][3]; |
| 503 |
|
| 504 |
Energy = tStats->getTotalE(); |
| 505 |
|
| 506 |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 507 |
(2.0 * eConvert); |
| 508 |
|
| 509 |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 510 |
|
| 511 |
info->transposeMat3(eta, a); |
| 512 |
info->matMul3(a, eta, b); |
| 513 |
trEta = info->matTrace3(b); |
| 514 |
|
| 515 |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
| 516 |
(2.0 * eConvert); |
| 517 |
|
| 518 |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 519 |
eConvert; |
| 520 |
|
| 521 |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 522 |
barostat_kinetic + barostat_potential; |
| 523 |
|
| 524 |
cout.width(8); |
| 525 |
cout.precision(8); |
| 526 |
|
| 527 |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 528 |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 529 |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 530 |
|
| 531 |
return conservedQuantity; |
| 532 |
} |
