--- branches/development/src/nonbonded/Electrostatic.cpp 2011/06/21 06:34:35 1586 +++ branches/development/src/nonbonded/Electrostatic.cpp 2011/11/22 20:38:56 1665 @@ -34,9 +34,10 @@ * work. Good starting points are: * * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). - * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [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 @@ -52,16 +53,19 @@ namespace OpenMD { namespace OpenMD { Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false), - forceField_(NULL), info_(NULL), haveCutoffRadius_(false), - haveDampingAlpha_(false), haveDielectric_(false), + forceField_(NULL), info_(NULL), + haveCutoffRadius_(false), + haveDampingAlpha_(false), + haveDielectric_(false), haveElectroSpline_(false) - {} + {} void Electrostatic::initialize() { - + Globals* simParams_ = info_->getSimParams(); summationMap_["HARD"] = esm_HARD; + summationMap_["NONE"] = esm_HARD; summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION; summationMap_["SHIFTED_POTENTIAL"] = esm_SHIFTED_POTENTIAL; summationMap_["SHIFTED_FORCE"] = esm_SHIFTED_FORCE; @@ -114,7 +118,7 @@ namespace OpenMD { sprintf( painCave.errMsg, "Electrostatic::initialize: Unknown electrostaticSummationMethod.\n" "\t(Input file specified %s .)\n" - "\telectrostaticSummationMethod must be one of: \"none\",\n" + "\telectrostaticSummationMethod must be one of: \"hard\",\n" "\t\"shifted_potential\", \"shifted_force\", or \n" "\t\"reaction_field\".\n", myMethod.c_str() ); painCave.isFatal = 1; @@ -247,7 +251,12 @@ namespace OpenMD { preRF2_ = 2.0 * preRF_; } - RealType dx = cutoffRadius_ / RealType(np_ - 1); + // Add a 2 angstrom safety window to deal with cutoffGroups that + // have charged atoms longer than the cutoffRadius away from each + // other. Splining may not be the best choice here. Direct calls + // to erfc might be preferrable. + + RealType dx = (cutoffRadius_ + 2.0) / RealType(np_ - 1); RealType rval; vector rvals; vector yvals; @@ -444,12 +453,13 @@ namespace OpenMD { RealType ct_i, ct_j, ct_ij, a1; RealType riji, ri, ri2, ri3, ri4; RealType pref, vterm, epot, dudr; + RealType vpair(0.0); RealType scale, sc2; RealType pot_term, preVal, rfVal; RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj; RealType preSw, preSwSc; RealType c1, c2, c3, c4; - RealType erfcVal, derfcVal; + RealType erfcVal(1.0), derfcVal(0.0); RealType BigR; Vector3d Q_i, Q_j; @@ -460,6 +470,12 @@ namespace OpenMD { Vector3d rhatdot2, rhatc4; Vector3d dVdr; + // variables for indirect (reaction field) interactions for excluded pairs: + RealType indirect_Pot(0.0); + RealType indirect_vpair(0.0); + Vector3d indirect_dVdr(V3Zero); + Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero); + pair res; if (!initialized_) initialize(); @@ -484,8 +500,12 @@ namespace OpenMD { bool j_is_SplitDipole = data2.is_SplitDipole; bool j_is_Quadrupole = data2.is_Quadrupole; - if (i_is_Charge) + if (i_is_Charge) { q_i = data1.charge; + if (idat.excluded) { + *(idat.skippedCharge2) += q_i; + } + } if (i_is_Dipole) { mu_i = data1.dipole_moment; @@ -518,9 +538,14 @@ namespace OpenMD { duduz_i = V3Zero; } - if (j_is_Charge) + if (j_is_Charge) { q_j = data2.charge; + if (idat.excluded) { + *(idat.skippedCharge1) += q_j; + } + } + if (j_is_Dipole) { mu_j = data2.dipole_moment; uz_j = idat.eFrame2->getColumn(2); @@ -560,9 +585,13 @@ namespace OpenMD { if (j_is_Charge) { if (screeningMethod_ == DAMPED) { // assemble the damping variables - res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); - erfcVal = res.first; - derfcVal = res.second; + //res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); + //erfcVal = res.first; + //derfcVal = res.second; + + erfcVal = erfc(dampingAlpha_ * *(idat.rij)); + derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2)); + c1 = erfcVal * riji; c2 = (-derfcVal + c1) * riji; } else { @@ -581,21 +610,30 @@ namespace OpenMD { dudr = *(idat.sw) * preVal * (c2c_ - c2); } else if (summationMethod_ == esm_REACTION_FIELD) { - rfVal = *(idat.electroMult) * preRF_ * *(idat.rij) * *(idat.rij) ; + rfVal = preRF_ * *(idat.rij) * *(idat.rij); + vterm = preVal * ( riji + rfVal ); dudr = *(idat.sw) * preVal * ( 2.0 * rfVal - riji ) * riji; + + // if this is an excluded pair, there are still indirect + // interactions via the reaction field we must worry about: + if (idat.excluded) { + indirect_vpair += preVal * rfVal; + indirect_Pot += *(idat.sw) * preVal * rfVal; + indirect_dVdr += *(idat.sw) * preVal * 2.0 * rfVal * riji * rhat; + } + } else { - vterm = preVal * riji * erfcVal; + vterm = preVal * riji * erfcVal; dudr = - *(idat.sw) * preVal * c2; } - - *(idat.vpair) += vterm; - epot += *(idat.sw) * vterm; - dVdr += dudr * rhat; + vpair += vterm; + epot += *(idat.sw) * vterm; + dVdr += dudr * rhat; } if (j_is_Dipole) { @@ -608,12 +646,23 @@ namespace OpenMD { ri3 = ri2 * riji; vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) ); - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j); duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) ); + // Even if we excluded this pair from direct interactions, + // we still have the reaction-field-mediated charge-dipole + // interaction: + + if (idat.excluded) { + indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij); + indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij); + indirect_dVdr += preSw * preRF2_ * uz_j; + indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij); + } + } else { // determine the inverse r used if we have split dipoles if (j_is_SplitDipole) { @@ -629,9 +678,11 @@ namespace OpenMD { if (screeningMethod_ == DAMPED) { // assemble the damping variables - res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); - erfcVal = res.first; - derfcVal = res.second; + //res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); + //erfcVal = res.first; + //derfcVal = res.second; + erfcVal = erfc(dampingAlpha_ * *(idat.rij)); + derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2)); c1 = erfcVal * ri; c2 = (-derfcVal + c1) * ri; c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri; @@ -646,7 +697,7 @@ namespace OpenMD { // calculate the potential pot_term = scale * c2; vterm = -pref * ct_j * pot_term; - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; // calculate derivatives for forces and torques @@ -666,9 +717,11 @@ namespace OpenMD { if (screeningMethod_ == DAMPED) { // assemble the damping variables - res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); - erfcVal = res.first; - derfcVal = res.second; + //res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); + //erfcVal = res.first; + //derfcVal = res.second; + erfcVal = erfc(dampingAlpha_ * *(idat.rij)); + derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2)); c1 = erfcVal * riji; c2 = (-derfcVal + c1) * riji; c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji; @@ -693,7 +746,7 @@ namespace OpenMD { qyy_j * (cy2*c3 - c2ri) + qzz_j * (cz2*c3 - c2ri) ); vterm = pref * pot_term; - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; // calculate derivatives for the forces and torques @@ -721,12 +774,23 @@ namespace OpenMD { ri3 = ri2 * riji; vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) ); - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i); duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) ); + + // Even if we excluded this pair from direct interactions, + // we still have the reaction-field-mediated charge-dipole + // interaction: + + if (idat.excluded) { + indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij); + indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij); + indirect_dVdr += -preSw * preRF2_ * uz_i; + indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij); + } } else { @@ -744,9 +808,11 @@ namespace OpenMD { if (screeningMethod_ == DAMPED) { // assemble the damping variables - res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); - erfcVal = res.first; - derfcVal = res.second; + //res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); + //erfcVal = res.first; + //derfcVal = res.second; + erfcVal = erfc(dampingAlpha_ * *(idat.rij)); + derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2)); c1 = erfcVal * ri; c2 = (-derfcVal + c1) * ri; c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri; @@ -761,7 +827,7 @@ namespace OpenMD { // calculate the potential pot_term = c2 * scale; vterm = pref * ct_i * pot_term; - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; // calculate derivatives for the forces and torques @@ -784,7 +850,7 @@ namespace OpenMD { vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) - preRF2_ * ct_ij ); - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; a1 = 5.0 * ct_i * ct_j - ct_ij; @@ -794,6 +860,13 @@ namespace OpenMD { duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j); duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i); + if (idat.excluded) { + indirect_vpair += - pref * preRF2_ * ct_ij; + indirect_Pot += - preSw * preRF2_ * ct_ij; + indirect_duduz_i += -preSw * preRF2_ * uz_j; + indirect_duduz_j += -preSw * preRF2_ * uz_i; + } + } else { if (i_is_SplitDipole) { @@ -816,9 +889,11 @@ namespace OpenMD { } if (screeningMethod_ == DAMPED) { // assemble damping variables - res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); - erfcVal = res.first; - derfcVal = res.second; + //res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); + //erfcVal = res.first; + //derfcVal = res.second; + erfcVal = erfc(dampingAlpha_ * *(idat.rij)); + derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2)); c1 = erfcVal * ri; c2 = (-derfcVal + c1) * ri; c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri; @@ -843,7 +918,7 @@ namespace OpenMD { // calculate the potential pot_term = (ct_ij * c2ri - ctidotj * c3); vterm = pref * pot_term; - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; // calculate derivatives for the forces and torques @@ -867,9 +942,11 @@ namespace OpenMD { if (screeningMethod_ == DAMPED) { // assemble the damping variables - res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); - erfcVal = res.first; - derfcVal = res.second; + //res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) ); + //erfcVal = res.first; + //derfcVal = res.second; + erfcVal = erfc(dampingAlpha_ * *(idat.rij)); + derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2)); c1 = erfcVal * riji; c2 = (-derfcVal + c1) * riji; c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji; @@ -895,7 +972,7 @@ namespace OpenMD { qzz_i * (cz2 * c3 - c2ri) ); vterm = pref * pot_term; - *(idat.vpair) += vterm; + vpair += vterm; epot += *(idat.sw) * vterm; // calculate the derivatives for the forces and torques @@ -910,126 +987,44 @@ namespace OpenMD { } } - (*(idat.pot))[ELECTROSTATIC_FAMILY] += epot; - *(idat.f1) += dVdr; - if (i_is_Dipole || i_is_Quadrupole) - *(idat.t1) -= cross(uz_i, duduz_i); - if (i_is_Quadrupole) { - *(idat.t1) -= cross(ux_i, dudux_i); - *(idat.t1) -= cross(uy_i, duduy_i); - } - - if (j_is_Dipole || j_is_Quadrupole) - *(idat.t2) -= cross(uz_j, duduz_j); - if (j_is_Quadrupole) { - *(idat.t2) -= cross(uz_j, dudux_j); - *(idat.t2) -= cross(uz_j, duduy_j); - } + if (!idat.excluded) { + *(idat.vpair) += vpair; + (*(idat.pot))[ELECTROSTATIC_FAMILY] += epot; + *(idat.f1) += dVdr; + + if (i_is_Dipole || i_is_Quadrupole) + *(idat.t1) -= cross(uz_i, duduz_i); + if (i_is_Quadrupole) { + *(idat.t1) -= cross(ux_i, dudux_i); + *(idat.t1) -= cross(uy_i, duduy_i); + } + + if (j_is_Dipole || j_is_Quadrupole) + *(idat.t2) -= cross(uz_j, duduz_j); + if (j_is_Quadrupole) { + *(idat.t2) -= cross(uz_j, dudux_j); + *(idat.t2) -= cross(uz_j, duduy_j); + } - return; - } + } else { - void Electrostatic::calcSkipCorrection(InteractionData &idat) { + // only accumulate the forces and torques resulting from the + // indirect reaction field terms. - if (!initialized_) initialize(); - - ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first]; - ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second]; - - // logicals - - bool i_is_Charge = data1.is_Charge; - bool i_is_Dipole = data1.is_Dipole; - - bool j_is_Charge = data2.is_Charge; - bool j_is_Dipole = data2.is_Dipole; - - RealType q_i, q_j; - - // The skippedCharge computation is needed by the real-space cutoff methods - // (i.e. shifted force and shifted potential) - - if (i_is_Charge) { - q_i = data1.charge; - *(idat.skippedCharge2) += q_i; - } - - if (j_is_Charge) { - q_j = data2.charge; - *(idat.skippedCharge1) += q_j; - } - - // the rest of this function should only be necessary for reaction field. - - if (summationMethod_ == esm_REACTION_FIELD) { - RealType riji, ri2, ri3; - RealType mu_i, ct_i; - RealType mu_j, ct_j; - RealType preVal, rfVal, vterm, dudr, pref, myPot(0.0); - Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat; - - // some variables we'll need independent of electrostatic type: + *(idat.vpair) += indirect_vpair; + (*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot; + *(idat.f1) += indirect_dVdr; - riji = 1.0 / *(idat.rij) ; - rhat = *(idat.d) * riji; - - if (i_is_Dipole) { - mu_i = data1.dipole_moment; - uz_i = idat.eFrame1->getColumn(2); - ct_i = dot(uz_i, rhat); - duduz_i = V3Zero; - } - - if (j_is_Dipole) { - mu_j = data2.dipole_moment; - uz_j = idat.eFrame2->getColumn(2); - ct_j = dot(uz_j, rhat); - duduz_j = V3Zero; - } - - if (i_is_Charge) { - if (j_is_Charge) { - preVal = *(idat.electroMult) * pre11_ * q_i * q_j; - rfVal = preRF_ * *(idat.rij) * *(idat.rij) ; - vterm = preVal * rfVal; - myPot += *(idat.sw) * vterm; - dudr = *(idat.sw) * preVal * 2.0 * rfVal * riji; - dVdr += dudr * rhat; - } - - if (j_is_Dipole) { - ri2 = riji * riji; - ri3 = ri2 * riji; - pref = *(idat.electroMult) * pre12_ * q_i * mu_j; - vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) ); - myPot += *(idat.sw) * vterm; - dVdr += - *(idat.sw) * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j); - duduz_j += - *(idat.sw) * pref * rhat * (ri2 - preRF2_ * *(idat.rij) ); - } - } - if (i_is_Dipole) { - if (j_is_Charge) { - ri2 = riji * riji; - ri3 = ri2 * riji; - pref = *(idat.electroMult) * pre12_ * q_j * mu_i; - vterm = - pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) ); - myPot += *(idat.sw) * vterm; - dVdr += *(idat.sw) * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i); - duduz_i += *(idat.sw) * pref * rhat * (ri2 - preRF2_ * *(idat.rij)); - } - } - - // accumulate the forces and torques resulting from the self term - (*(idat.pot))[ELECTROSTATIC_FAMILY] += myPot; - *(idat.f1) += dVdr; - if (i_is_Dipole) - *(idat.t1) -= cross(uz_i, duduz_i); + *(idat.t1) -= cross(uz_i, indirect_duduz_i); if (j_is_Dipole) - *(idat.t2) -= cross(uz_j, duduz_j); + *(idat.t2) -= cross(uz_j, indirect_duduz_j); } - } + + + return; + } void Electrostatic::calcSelfCorrection(SelfData &sdat) { RealType mu1, preVal, chg1, self;