| 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). |
| 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 <stdio.h> |
| 223 |
|
dw2 = 1.0; |
| 224 |
|
} |
| 225 |
|
|
| 226 |
< |
GBInteractionData mixer; |
| 226 |
> |
GBInteractionData mixer1, mixer2; |
| 227 |
|
|
| 228 |
|
// Cleaver paper uses sqrt of squares to get sigma0 for |
| 229 |
|
// mixed interactions. |
| 230 |
|
|
| 231 |
< |
mixer.sigma0 = sqrt(d1*d1 + d2*d2); |
| 232 |
< |
mixer.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
| 233 |
< |
mixer.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
| 234 |
< |
mixer.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / |
| 231 |
> |
mixer1.sigma0 = sqrt(d1*d1 + d2*d2); |
| 232 |
> |
mixer1.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
| 233 |
> |
mixer1.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
| 234 |
> |
mixer1.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / |
| 235 |
|
((l2*l2 + d1*d1) * (l1*l1 + d2*d2)); |
| 236 |
+ |
|
| 237 |
+ |
mixer2.sigma0 = mixer1.sigma0; |
| 238 |
+ |
// xa2 and xai2 for j-i pairs are reversed from the same i-j pairing. |
| 239 |
+ |
// Swapping the particles reverses the anisotropy parameters: |
| 240 |
+ |
mixer2.xa2 = mixer1.xai2; |
| 241 |
+ |
mixer2.xai2 = mixer1.xa2; |
| 242 |
+ |
mixer2.x2 = mixer1.x2; |
| 243 |
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|
| 244 |
|
// assumed LB mixing rules for now: |
| 245 |
|
|
| 246 |
< |
mixer.dw = 0.5 * (dw1 + dw2); |
| 247 |
< |
mixer.eps0 = sqrt(e1 * e2); |
| 246 |
> |
mixer1.dw = 0.5 * (dw1 + dw2); |
| 247 |
> |
mixer1.eps0 = sqrt(e1 * e2); |
| 248 |
> |
|
| 249 |
> |
mixer2.dw = mixer1.dw; |
| 250 |
> |
mixer2.eps0 = mixer1.eps0; |
| 251 |
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|
| 252 |
|
RealType er = sqrt(er1 * er2); |
| 253 |
< |
RealType ermu = pow(er,(1.0 / mu_)); |
| 253 |
> |
RealType ermu = pow(er, (RealType(1.0) / mu_)); |
| 254 |
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RealType xp = (1.0 - ermu) / (1.0 + ermu); |
| 255 |
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RealType ap2 = 1.0 / (1.0 + ermu); |
| 256 |
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|
| 257 |
< |
mixer.xp2 = xp * xp; |
| 258 |
< |
mixer.xpap2 = xp * ap2; |
| 259 |
< |
mixer.xpapi2 = xp / ap2; |
| 257 |
> |
mixer1.xp2 = xp * xp; |
| 258 |
> |
mixer1.xpap2 = xp * ap2; |
| 259 |
> |
mixer1.xpapi2 = xp / ap2; |
| 260 |
|
|
| 261 |
+ |
mixer2.xp2 = mixer1.xp2; |
| 262 |
+ |
mixer2.xpap2 = mixer1.xpap2; |
| 263 |
+ |
mixer2.xpapi2 = mixer1.xpapi2; |
| 264 |
+ |
|
| 265 |
|
// only add this pairing if at least one of the atoms is a Gay-Berne atom |
| 266 |
|
|
| 267 |
|
if (atomType->isGayBerne() || atype2->isGayBerne()) { |
| 270 |
|
key1 = make_pair(atomType, atype2); |
| 271 |
|
key2 = make_pair(atype2, atomType); |
| 272 |
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|
| 273 |
< |
MixingMap[key1] = mixer; |
| 273 |
> |
MixingMap[key1] = mixer1; |
| 274 |
|
if (key2 != key1) { |
| 275 |
< |
MixingMap[key2] = mixer; |
| 275 |
> |
MixingMap[key2] = mixer2; |
| 276 |
|
} |
| 277 |
|
} |
| 278 |
|
} |
| 279 |
|
} |
| 280 |
|
|
| 281 |
< |
void GB::calcForce(InteractionData idat) { |
| 281 |
> |
void GB::calcForce(InteractionData &idat) { |
| 282 |
|
|
| 283 |
|
if (!initialized_) initialize(); |
| 284 |
|
|
| 285 |
< |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 271 |
< |
GBInteractionData mixer = MixingMap[key]; |
| 285 |
> |
GBInteractionData mixer = MixingMap[idat.atypes]; |
| 286 |
|
|
| 287 |
|
RealType sigma0 = mixer.sigma0; |
| 288 |
|
RealType dw = mixer.dw; |
| 294 |
|
RealType xpap2 = mixer.xpap2; |
| 295 |
|
RealType xpapi2 = mixer.xpapi2; |
| 296 |
|
|
| 297 |
< |
Vector3d ul1 = idat.A1.getRow(2); |
| 298 |
< |
Vector3d ul2 = idat.A2.getRow(2); |
| 297 |
> |
Vector3d ul1 = idat.A1->getRow(2); |
| 298 |
> |
Vector3d ul2 = idat.A2->getRow(2); |
| 299 |
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|
| 300 |
|
RealType a, b, g; |
| 301 |
|
|
| 302 |
< |
bool i_is_LJ = idat.atype1->isLennardJones(); |
| 303 |
< |
bool j_is_LJ = idat.atype2->isLennardJones(); |
| 304 |
< |
|
| 302 |
> |
bool i_is_LJ = idat.atypes.first->isLennardJones(); |
| 303 |
> |
bool j_is_LJ = idat.atypes.second->isLennardJones(); |
| 304 |
> |
|
| 305 |
|
if (i_is_LJ) { |
| 306 |
|
a = 0.0; |
| 307 |
|
ul1 = V3Zero; |
| 308 |
|
} else { |
| 309 |
< |
a = dot(idat.d, ul1); |
| 309 |
> |
a = dot(*(idat.d), ul1); |
| 310 |
|
} |
| 311 |
|
|
| 312 |
|
if (j_is_LJ) { |
| 313 |
|
b = 0.0; |
| 314 |
|
ul2 = V3Zero; |
| 315 |
|
} else { |
| 316 |
< |
b = dot(idat.d, ul2); |
| 316 |
> |
b = dot(*(idat.d), ul2); |
| 317 |
|
} |
| 318 |
|
|
| 319 |
|
if (i_is_LJ || j_is_LJ) |
| 321 |
|
else |
| 322 |
|
g = dot(ul1, ul2); |
| 323 |
|
|
| 324 |
< |
RealType au = a / idat.rij; |
| 325 |
< |
RealType bu = b / idat.rij; |
| 324 |
> |
RealType au = a / *(idat.rij); |
| 325 |
> |
RealType bu = b / *(idat.rij); |
| 326 |
|
|
| 327 |
|
RealType au2 = au * au; |
| 328 |
|
RealType bu2 = bu * bu; |
| 335 |
|
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 336 |
|
RealType e2 = 1.0 - Hp; |
| 337 |
|
RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
| 338 |
< |
RealType BigR = dw*sigma0 / (idat.rij - sigma + dw*sigma0); |
| 338 |
> |
RealType BigR = dw*sigma0 / (*(idat.rij) - sigma + dw*sigma0); |
| 339 |
|
|
| 340 |
|
RealType R3 = BigR*BigR*BigR; |
| 341 |
|
RealType R6 = R3*R3; |
| 343 |
|
RealType R12 = R6*R6; |
| 344 |
|
RealType R13 = R6*R7; |
| 345 |
|
|
| 346 |
< |
RealType U = idat.vdwMult * 4.0 * eps * (R12 - R6); |
| 346 |
> |
RealType U = *(idat.vdwMult) * 4.0 * eps * (R12 - R6); |
| 347 |
|
|
| 348 |
|
RealType s3 = sigma*sigma*sigma; |
| 349 |
|
RealType s03 = sigma0*sigma0*sigma0; |
| 350 |
|
|
| 351 |
< |
RealType pref1 = - idat.vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * idat.rij); |
| 351 |
> |
RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 352 |
> |
(e2 * *(idat.rij)); |
| 353 |
|
|
| 354 |
< |
RealType pref2 = idat.vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*idat.rij*s03); |
| 354 |
> |
RealType pref2 = *(idat.vdwMult) * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) / |
| 355 |
> |
(dw* *(idat.rij) * s03); |
| 356 |
|
|
| 357 |
< |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*idat.rij/s3 + H)); |
| 357 |
> |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0 * sigma0 * |
| 358 |
> |
*(idat.rij) / s3 + H)); |
| 359 |
|
|
| 360 |
|
RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
| 361 |
|
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
| 367 |
|
+ 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / |
| 368 |
|
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 369 |
|
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 353 |
– |
|
| 370 |
|
|
| 371 |
< |
Vector3d rhat = idat.d / idat.rij; |
| 372 |
< |
Vector3d rxu1 = cross(idat.d, ul1); |
| 373 |
< |
Vector3d rxu2 = cross(idat.d, ul2); |
| 371 |
> |
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 372 |
> |
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 373 |
> |
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 374 |
|
Vector3d uxu = cross(ul1, ul2); |
| 359 |
– |
|
| 360 |
– |
idat.pot += U*idat.sw; |
| 361 |
– |
idat.f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 362 |
– |
idat.t1 += dUda * rxu1 - dUdg * uxu; |
| 363 |
– |
idat.t2 += dUdb * rxu2 - dUdg * uxu; |
| 364 |
– |
idat.vpair += U*idat.sw; |
| 375 |
|
|
| 376 |
+ |
(*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 377 |
+ |
*(idat.f1) += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 378 |
+ |
*(idat.t1) += dUda * rxu1 - dUdg * uxu; |
| 379 |
+ |
*(idat.t2) += dUdb * rxu2 + dUdg * uxu; |
| 380 |
+ |
*(idat.vpair) += U * *(idat.sw); |
| 381 |
+ |
|
| 382 |
|
return; |
| 383 |
|
|
| 384 |
|
} |
| 385 |
+ |
|
| 386 |
+ |
RealType GB::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 387 |
+ |
if (!initialized_) initialize(); |
| 388 |
+ |
|
| 389 |
+ |
RealType cut = 0.0; |
| 390 |
+ |
|
| 391 |
+ |
if (atypes.first->isGayBerne()) { |
| 392 |
+ |
GayBerneParam gb1 = getGayBerneParam(atypes.first); |
| 393 |
+ |
RealType d1 = gb1.GB_d; |
| 394 |
+ |
RealType l1 = gb1.GB_l; |
| 395 |
+ |
// sigma is actually sqrt(2)*l for prolate ellipsoids |
| 396 |
+ |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); |
| 397 |
+ |
} else if (atypes.first->isLennardJones()) { |
| 398 |
+ |
cut = max(cut, RealType(2.5) * getLJSigma(atypes.first)); |
| 399 |
+ |
} |
| 400 |
+ |
|
| 401 |
+ |
if (atypes.second->isGayBerne()) { |
| 402 |
+ |
GayBerneParam gb2 = getGayBerneParam(atypes.second); |
| 403 |
+ |
RealType d2 = gb2.GB_d; |
| 404 |
+ |
RealType l2 = gb2.GB_l; |
| 405 |
+ |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); |
| 406 |
+ |
} else if (atypes.second->isLennardJones()) { |
| 407 |
+ |
cut = max(cut, RealType(2.5) * getLJSigma(atypes.second)); |
| 408 |
+ |
} |
| 409 |
+ |
|
| 410 |
+ |
return cut; |
| 411 |
+ |
} |
| 412 |
|
} |
| 413 |
|
|
