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namespace OpenMD { |
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< |
MAW::MAW() : name_("MAW"), initialized_(false), forceField_(NULL), |
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< |
shiftedPot_(false), shiftedFrc_(false) {} |
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> |
MAW::MAW() : name_("MAW"), initialized_(false), forceField_(NULL) {} |
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void MAW::initialize() { |
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
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NonBondedInteractionType* nbt; |
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+ |
ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
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nbt = nbiTypes->nextType(j)) { |
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if (nbt->isMAW()) { |
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< |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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< |
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< |
GenericData* data = nbt->getPropertyByName("MAW"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "MAW::initialize could not find\n" |
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"\tMAW parameters for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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< |
painCave.isFatal = 1; |
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simError(); |
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} |
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MAWData* mawData = dynamic_cast<MAWData*>(data); |
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if (mawData == NULL) { |
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> |
keys = nbiTypes->getKeys(j); |
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> |
AtomType* at1 = forceField_->getAtomType(keys[0]); |
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> |
AtomType* at2 = forceField_->getAtomType(keys[1]); |
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> |
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> |
MAWInteractionType* mit = dynamic_cast<MAWInteractionType*>(nbt); |
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> |
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> |
if (mit == NULL) { |
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sprintf( painCave.errMsg, |
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"MAW::initialize could not convert GenericData to\n" |
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"\tMAWData for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->getName().c_str()); |
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"MAW::initialize could not convert NonBondedInteractionType\n" |
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"\tto MAWInteractionType for %s - %s interaction.\n", |
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at1->getName().c_str(), |
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at2->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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MAWParam mawParam = mawData->getData(); |
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RealType De = mawParam.De; |
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RealType beta = mawParam.beta; |
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RealType Re = mawParam.Re; |
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RealType ca1 = mawParam.ca1; |
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RealType cb1 = mawParam.cb1; |
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RealType De = mit->getD(); |
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RealType beta = mit->getBeta(); |
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RealType Re = mit->getR(); |
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RealType ca1 = mit->getCA1(); |
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RealType cb1 = mit->getCB1(); |
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addExplicitInteraction(atypes.first, atypes.second, |
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addExplicitInteraction(at1, at2, |
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De, beta, Re, ca1, cb1); |
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} |
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} |
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if (!initialized_) initialize(); |
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map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it; |
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it = MixingMap.find(idat.atypes); |
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it = MixingMap.find( idat.atypes ); |
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if (it != MixingMap.end()) { |
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MAWInteractionData mixer = (*it).second; |
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if (j_is_Metal) { |
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// rotate the inter-particle separation into the two different |
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// body-fixed coordinate systems: |
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r = idat.A1 * idat.d; |
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Atrans = idat.A1.transpose(); |
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r = *(idat.A1) * *(idat.d); |
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Atrans = idat.A1->transpose(); |
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} else { |
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// negative sign because this is the vector from j to i: |
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r = -idat.A2 * idat.d; |
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Atrans = idat.A2.transpose(); |
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r = -*(idat.A2) * *(idat.d); |
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Atrans = idat.A2->transpose(); |
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} |
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// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
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RealType expt = -beta*(idat.rij - R_e); |
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RealType expt = -beta*( *(idat.rij) - R_e); |
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RealType expfnc = exp(expt); |
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RealType expfnc2 = expfnc*expfnc; |
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myPot = D_e * (expfnc2 - 2.0 * expfnc); |
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myDeriv = 2.0 * D_e * beta * (expfnc - expfnc2); |
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if (MAW::shiftedPot_ || MAW::shiftedFrc_) { |
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exptC = -beta*(idat.rcut - R_e); |
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if (idat.shiftedPot || idat.shiftedForce) { |
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exptC = -beta*( *(idat.rcut) - R_e); |
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expfncC = exp(exptC); |
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expfnc2C = expfncC*expfncC; |
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} |
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if (MAW::shiftedPot_) { |
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if (idat.shiftedPot) { |
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myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 0.0; |
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< |
} else if (MAW::shiftedFrc_) { |
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> |
} else if (idat.shiftedForce) { |
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myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 2.0 * D_e * beta * (expfnc2C - expfnc2C); |
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< |
myPotC += myDerivC * (idat.rij - idat.rcut); |
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myPotC += myDerivC * ( *(idat.rij) - *(idat.rcut) ); |
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} else { |
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myPotC = 0.0; |
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myDerivC = 0.0; |
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RealType y2 = y * y; |
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RealType z2 = z * z; |
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RealType r3 = idat.r2 * idat.rij; |
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RealType r4 = idat.r2 * idat.r2; |
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> |
RealType r3 = *(idat.r2) * *(idat.rij) ; |
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> |
RealType r4 = *(idat.r2) * *(idat.r2); |
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// angular modulation of morse part of potential to approximate |
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// the squares of the two HOMO lone pair orbitals in water: |
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// Vmorse(r)*[a*x2/r2 + b*z/r + (1-a-b)] |
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RealType Vmorse = (myPot - myPotC); |
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RealType Vang = ca1 * x2 / idat.r2 + cb1 * z / idat.rij + (0.8 - ca1 / 3.0); |
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< |
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RealType pot_temp = idat.vdwMult * Vmorse * Vang; |
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idat.vpair += pot_temp; |
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idat.pot[0] += idat.sw * pot_temp; |
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> |
RealType Vang = ca1 * x2 / *(idat.r2) + |
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> |
cb1 * z / *(idat.rij) + (0.8 - ca1 / 3.0); |
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> |
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RealType pot_temp = *(idat.vdwMult) * Vmorse * Vang; |
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> |
*(idat.vpair) += pot_temp; |
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(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
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< |
Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) / idat.rij; |
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< |
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Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / idat.r2 - cb1 * x * z / r3, |
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-2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3, |
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-2.0 * ca1 * x2 * z / r4 + cb1 / idat.rij - cb1 * z2 / r3); |
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> |
Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) / *(idat.rij) ; |
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Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / *(idat.r2) - cb1 * x * z / r3, |
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-2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3, |
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-2.0 * ca1 * x2 * z / r4 + cb1 / *(idat.rij) - cb1 * z2 / r3); |
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// chain rule to put these back on x, y, z |
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Vector3d dvdr = Vang * dVmorsedr + Vmorse * dVangdr; |
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// Torques for Vang using method of Price: |
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// S. L. Price, A. J. Stone, and M. Alderton, Mol. Phys. 52, 987 (1984). |
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< |
Vector3d dVangdu = Vector3d(cb1 * y / idat.rij, |
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2.0 * ca1 * x * z / idat.r2 - cb1 * x / idat.rij, |
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-2.0 * ca1 * y * x / idat.r2); |
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> |
Vector3d dVangdu = Vector3d(cb1 * y / *(idat.rij) , |
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2.0 * ca1 * x * z / *(idat.r2) - cb1 * x / *(idat.rij), |
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-2.0 * ca1 * y * x / *(idat.r2)); |
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// do the torques first since they are easy: |
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// remember that these are still in the body fixed axes |
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< |
Vector3d trq = idat.vdwMult * Vmorse * dVangdu * idat.sw; |
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> |
Vector3d trq = *(idat.vdwMult) * Vmorse * dVangdu * *(idat.sw); |
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// go back to lab frame using transpose of rotation matrix: |
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if (j_is_Metal) { |
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< |
idat.t1 += Atrans * trq; |
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> |
*(idat.t1) += Atrans * trq; |
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} else { |
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< |
idat.t2 += Atrans * trq; |
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> |
*(idat.t2) += Atrans * trq; |
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} |
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// Now, on to the forces (still in body frame of water) |
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< |
Vector3d ftmp = idat.vdwMult * idat.sw * dvdr; |
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> |
Vector3d ftmp = *(idat.vdwMult) * *(idat.sw) * dvdr; |
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// rotate the terms back into the lab frame: |
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Vector3d flab; |
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flab = - Atrans * ftmp; |
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} |
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< |
idat.f1 += flab; |
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> |
*(idat.f1) += flab; |
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} |
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return; |
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