| 263 |
|
} |
| 264 |
|
} |
| 265 |
|
|
| 266 |
< |
void GB::calcForce(InteractionData idat) { |
| 266 |
> |
void GB::calcForce(InteractionData &idat) { |
| 267 |
|
|
| 268 |
|
if (!initialized_) initialize(); |
| 269 |
|
|
| 270 |
< |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 271 |
< |
GBInteractionData mixer = MixingMap[key]; |
| 270 |
> |
GBInteractionData mixer = MixingMap[*(idat.atypes)]; |
| 271 |
|
|
| 272 |
|
RealType sigma0 = mixer.sigma0; |
| 273 |
|
RealType dw = mixer.dw; |
| 279 |
|
RealType xpap2 = mixer.xpap2; |
| 280 |
|
RealType xpapi2 = mixer.xpapi2; |
| 281 |
|
|
| 282 |
< |
Vector3d ul1 = idat.A1.getRow(2); |
| 283 |
< |
Vector3d ul2 = idat.A2.getRow(2); |
| 282 |
> |
Vector3d ul1 = idat.A1->getRow(2); |
| 283 |
> |
Vector3d ul2 = idat.A2->getRow(2); |
| 284 |
|
|
| 285 |
|
RealType a, b, g; |
| 286 |
|
|
| 287 |
< |
bool i_is_LJ = idat.atype1->isLennardJones(); |
| 288 |
< |
bool j_is_LJ = idat.atype2->isLennardJones(); |
| 289 |
< |
|
| 287 |
> |
bool i_is_LJ = idat.atypes->first->isLennardJones(); |
| 288 |
> |
bool j_is_LJ = idat.atypes->second->isLennardJones(); |
| 289 |
> |
|
| 290 |
|
if (i_is_LJ) { |
| 291 |
|
a = 0.0; |
| 292 |
|
ul1 = V3Zero; |
| 293 |
|
} else { |
| 294 |
< |
a = dot(idat.d, ul1); |
| 294 |
> |
a = dot(*(idat.d), ul1); |
| 295 |
|
} |
| 296 |
|
|
| 297 |
|
if (j_is_LJ) { |
| 298 |
|
b = 0.0; |
| 299 |
|
ul2 = V3Zero; |
| 300 |
|
} else { |
| 301 |
< |
b = dot(idat.d, ul2); |
| 301 |
> |
b = dot(*(idat.d), ul2); |
| 302 |
|
} |
| 303 |
|
|
| 304 |
|
if (i_is_LJ || j_is_LJ) |
| 306 |
|
else |
| 307 |
|
g = dot(ul1, ul2); |
| 308 |
|
|
| 309 |
< |
RealType au = a / idat.rij; |
| 310 |
< |
RealType bu = b / idat.rij; |
| 309 |
> |
RealType au = a / *(idat.rij); |
| 310 |
> |
RealType bu = b / *(idat.rij); |
| 311 |
|
|
| 312 |
|
RealType au2 = au * au; |
| 313 |
|
RealType bu2 = bu * bu; |
| 320 |
|
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 321 |
|
RealType e2 = 1.0 - Hp; |
| 322 |
|
RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
| 323 |
< |
RealType BigR = dw*sigma0 / (idat.rij - sigma + dw*sigma0); |
| 323 |
> |
RealType BigR = dw*sigma0 / (*(idat.rij) - sigma + dw*sigma0); |
| 324 |
|
|
| 325 |
|
RealType R3 = BigR*BigR*BigR; |
| 326 |
|
RealType R6 = R3*R3; |
| 328 |
|
RealType R12 = R6*R6; |
| 329 |
|
RealType R13 = R6*R7; |
| 330 |
|
|
| 331 |
< |
RealType U = idat.vdwMult * 4.0 * eps * (R12 - R6); |
| 331 |
> |
RealType U = *(idat.vdwMult) * 4.0 * eps * (R12 - R6); |
| 332 |
|
|
| 333 |
|
RealType s3 = sigma*sigma*sigma; |
| 334 |
|
RealType s03 = sigma0*sigma0*sigma0; |
| 335 |
|
|
| 336 |
< |
RealType pref1 = - idat.vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * idat.rij); |
| 336 |
> |
RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 337 |
> |
(e2 * *(idat.rij)); |
| 338 |
|
|
| 339 |
< |
RealType pref2 = idat.vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*idat.rij*s03); |
| 339 |
> |
RealType pref2 = *(idat.vdwMult) * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) / |
| 340 |
> |
(dw* *(idat.rij) * s03); |
| 341 |
|
|
| 342 |
< |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*idat.rij/s3 + H)); |
| 342 |
> |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0 * sigma0 * |
| 343 |
> |
*(idat.rij) / s3 + H)); |
| 344 |
|
|
| 345 |
|
RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
| 346 |
|
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
| 354 |
|
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 355 |
|
|
| 356 |
|
|
| 357 |
< |
Vector3d rhat = idat.d / idat.rij; |
| 358 |
< |
Vector3d rxu1 = cross(idat.d, ul1); |
| 359 |
< |
Vector3d rxu2 = cross(idat.d, ul2); |
| 357 |
> |
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 358 |
> |
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 359 |
> |
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 360 |
|
Vector3d uxu = cross(ul1, ul2); |
| 361 |
|
|
| 362 |
< |
idat.pot += U*idat.sw; |
| 363 |
< |
idat.f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 364 |
< |
idat.t1 += dUda * rxu1 - dUdg * uxu; |
| 365 |
< |
idat.t2 += dUdb * rxu2 - dUdg * uxu; |
| 366 |
< |
idat.vpair += U*idat.sw; |
| 362 |
> |
idat.pot[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 363 |
> |
*(idat.f1) += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 364 |
> |
*(idat.t1) += dUda * rxu1 - dUdg * uxu; |
| 365 |
> |
*(idat.t2) += dUdb * rxu2 - dUdg * uxu; |
| 366 |
> |
*(idat.vpair) += U * *(idat.sw); |
| 367 |
|
|
| 368 |
|
return; |
| 369 |
|
|
| 370 |
|
} |
| 371 |
|
|
| 372 |
< |
RealType GB::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 372 |
> |
RealType GB::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 373 |
|
if (!initialized_) initialize(); |
| 374 |
|
|
| 375 |
|
RealType cut = 0.0; |
| 376 |
|
|
| 377 |
< |
if (at1->isGayBerne()) { |
| 378 |
< |
GayBerneParam gb1 = getGayBerneParam(at1); |
| 377 |
> |
if (atypes.first->isGayBerne()) { |
| 378 |
> |
GayBerneParam gb1 = getGayBerneParam(atypes.first); |
| 379 |
|
RealType d1 = gb1.GB_d; |
| 380 |
|
RealType l1 = gb1.GB_l; |
| 381 |
|
// sigma is actually sqrt(2)*l for prolate ellipsoids |
| 382 |
|
cut = max(cut, 2.5 * sqrt(2.0) * max(d1, l1)); |
| 383 |
< |
} else if (at1->isLennardJones()) { |
| 384 |
< |
cut = max(cut, 2.5 * getLJSigma(at1)); |
| 383 |
> |
} else if (atypes.first->isLennardJones()) { |
| 384 |
> |
cut = max(cut, 2.5 * getLJSigma(atypes.first)); |
| 385 |
|
} |
| 386 |
|
|
| 387 |
< |
if (at2->isGayBerne()) { |
| 388 |
< |
GayBerneParam gb2 = getGayBerneParam(at2); |
| 387 |
> |
if (atypes.second->isGayBerne()) { |
| 388 |
> |
GayBerneParam gb2 = getGayBerneParam(atypes.second); |
| 389 |
|
RealType d2 = gb2.GB_d; |
| 390 |
|
RealType l2 = gb2.GB_l; |
| 391 |
|
cut = max(cut, 2.5 * sqrt(2.0) * max(d2, l2)); |
| 392 |
< |
} else if (at1->isLennardJones()) { |
| 393 |
< |
cut = max(cut, 2.5 * getLJSigma(at2)); |
| 392 |
> |
} else if (atypes.second->isLennardJones()) { |
| 393 |
> |
cut = max(cut, 2.5 * getLJSigma(atypes.second)); |
| 394 |
|
} |
| 395 |
|
|
| 396 |
|
return cut; |
