--- branches/development/src/nonbonded/GB.cpp 2011/06/14 20:41:44 1582 +++ branches/development/src/nonbonded/GB.cpp 2012/02/16 15:59:20 1674 @@ -36,7 +36,8 @@ * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -222,31 +223,45 @@ namespace OpenMD { dw2 = 1.0; } - GBInteractionData mixer; + GBInteractionData mixer1, mixer2; // Cleaver paper uses sqrt of squares to get sigma0 for // mixed interactions. - mixer.sigma0 = sqrt(d1*d1 + d2*d2); - mixer.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); - mixer.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); - mixer.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / + mixer1.sigma0 = sqrt(d1*d1 + d2*d2); + mixer1.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); + mixer1.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); + mixer1.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / ((l2*l2 + d1*d1) * (l1*l1 + d2*d2)); + + mixer2.sigma0 = mixer1.sigma0; + // xa2 and xai2 for j-i pairs are reversed from the same i-j pairing. + // Swapping the particles reverses the anisotropy parameters: + mixer2.xa2 = mixer1.xai2; + mixer2.xai2 = mixer1.xa2; + mixer2.x2 = mixer1.x2; // assumed LB mixing rules for now: - mixer.dw = 0.5 * (dw1 + dw2); - mixer.eps0 = sqrt(e1 * e2); + mixer1.dw = 0.5 * (dw1 + dw2); + mixer1.eps0 = sqrt(e1 * e2); + + mixer2.dw = mixer1.dw; + mixer2.eps0 = mixer1.eps0; RealType er = sqrt(er1 * er2); - RealType ermu = pow(er,(1.0 / mu_)); + RealType ermu = pow(er, (RealType(1.0) / mu_)); RealType xp = (1.0 - ermu) / (1.0 + ermu); RealType ap2 = 1.0 / (1.0 + ermu); - mixer.xp2 = xp * xp; - mixer.xpap2 = xp * ap2; - mixer.xpapi2 = xp / ap2; + mixer1.xp2 = xp * xp; + mixer1.xpap2 = xp * ap2; + mixer1.xpapi2 = xp / ap2; + mixer2.xp2 = mixer1.xp2; + mixer2.xpap2 = mixer1.xpap2; + mixer2.xpapi2 = mixer1.xpapi2; + // only add this pairing if at least one of the atoms is a Gay-Berne atom if (atomType->isGayBerne() || atype2->isGayBerne()) { @@ -255,9 +270,9 @@ namespace OpenMD { key1 = make_pair(atomType, atype2); key2 = make_pair(atype2, atomType); - MixingMap[key1] = mixer; + MixingMap[key1] = mixer1; if (key2 != key1) { - MixingMap[key2] = mixer; + MixingMap[key2] = mixer2; } } } @@ -352,17 +367,16 @@ namespace OpenMD { + 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / (1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * (x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); - Vector3d rhat = *(idat.d) / *(idat.rij); Vector3d rxu1 = cross(*(idat.d), ul1); Vector3d rxu2 = cross(*(idat.d), ul2); Vector3d uxu = cross(ul1, ul2); - + (*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); *(idat.f1) += dUdr * rhat + dUda * ul1 + dUdb * ul2; *(idat.t1) += dUda * rxu1 - dUdg * uxu; - *(idat.t2) += dUdb * rxu2 - dUdg * uxu; + *(idat.t2) += dUdb * rxu2 + dUdg * uxu; *(idat.vpair) += U * *(idat.sw); return; @@ -379,18 +393,18 @@ namespace OpenMD { RealType d1 = gb1.GB_d; RealType l1 = gb1.GB_l; // sigma is actually sqrt(2)*l for prolate ellipsoids - cut = max(cut, 2.5 * sqrt(2.0) * max(d1, l1)); + cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); } else if (atypes.first->isLennardJones()) { - cut = max(cut, 2.5 * getLJSigma(atypes.first)); + cut = max(cut, RealType(2.5) * getLJSigma(atypes.first)); } if (atypes.second->isGayBerne()) { GayBerneParam gb2 = getGayBerneParam(atypes.second); RealType d2 = gb2.GB_d; RealType l2 = gb2.GB_l; - cut = max(cut, 2.5 * sqrt(2.0) * max(d2, l2)); + cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); } else if (atypes.second->isLennardJones()) { - cut = max(cut, 2.5 * getLJSigma(atypes.second)); + cut = max(cut, RealType(2.5) * getLJSigma(atypes.second)); } return cut;