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using namespace std; |
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namespace OpenMD { |
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bool Sticky::initialized_ = false; |
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ForceField* Sticky::forceField_ = NULL; |
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map<int, AtomType*> Sticky::StickyMap; |
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map<pair<AtomType*, AtomType*>, StickyInteractionData> Sticky::MixingMap; |
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Sticky* Sticky::_instance = NULL; |
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Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {} |
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Sticky* Sticky::Instance() { |
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if (!_instance) { |
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_instance = new Sticky(); |
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} |
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return _instance; |
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} |
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StickyParam Sticky::getStickyParam(AtomType* atomType) { |
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// Do sanity checking on the AtomType we were passed before |
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} |
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} |
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RealType Sticky::getStickyCut(int atid) { |
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if (!initialized_) initialize(); |
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std::map<int, AtomType*> :: const_iterator it; |
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it = StickyMap.find(atid); |
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if (it == StickyMap.end()) { |
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sprintf( painCave.errMsg, |
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"Sticky::getStickyCut could not find atid %d in StickyMap\n", |
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(atid)); |
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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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AtomType* atype = it->second; |
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return MixingMap[make_pair(atype, atype)].rbig; |
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} |
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void Sticky::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
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RealType rij, RealType r2, RealType sw, |
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RealType &vpair, RealType &pot, |
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RotMat3x3d A1, RotMat3x3d A2, Vector3d &f1, |
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Vector3d &t1, Vector3d &t2) { |
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// This routine does only the sticky portion of the SSD potential |
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// [Chandra and Ichiye, J. Chem. Phys. 111, 2701 (1999)]. |
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// The Lennard-Jones and dipolar interaction must be handled separately. |
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// We assume that the rotation matrices have already been calculated |
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// and placed in the A array. |
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/** |
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* This function does the sticky portion of the SSD potential |
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* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701 |
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* (1999)]. The Lennard-Jones and dipolar interaction must be |
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* handled separately. We assume that the rotation matrices have |
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* already been calculated and placed in the A1 & A2 entries in the |
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* idat structure. |
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*/ |
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void Sticky::calcForce(InteractionData idat) { |
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if (!initialized_) initialize(); |
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pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
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pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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StickyInteractionData mixer = MixingMap[key]; |
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RealType w0 = mixer.w0; |
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RealType rbig = mixer.rbig; |
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bool isPower = mixer.isPower; |
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if (rij <= rbig) { |
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if (idat.rij <= rbig) { |
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RealType r3 = r2 * rij; |
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RealType r5 = r3 * r2; |
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RealType r3 = idat.r2 * idat.rij; |
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RealType r5 = r3 * idat.r2; |
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RotMat3x3d A1trans = A1.transpose(); |
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RotMat3x3d A2trans = A2.transpose(); |
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RotMat3x3d A1trans = idat.A1.transpose(); |
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RotMat3x3d A2trans = idat.A2.transpose(); |
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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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Vector3d ri = A1 * d; |
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Vector3d ri = idat.A1 * idat.d; |
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// negative sign because this is the vector from j to i: |
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Vector3d rj = -A2 * d; |
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Vector3d rj = - idat.A2 * idat.d; |
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RealType xi = ri.x(); |
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RealType yi = ri.y(); |
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RealType sp = 0.0; |
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RealType dspdr = 0.0; |
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if (rij < ru) { |
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if (rij < rl) { |
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if (idat.rij < ru) { |
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if (idat.rij < rl) { |
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s = 1.0; |
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dsdr = 0.0; |
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} else { |
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// we are in the switching region |
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pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(rij); |
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pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(idat.rij); |
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s = res.first; |
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dsdr = res.second; |
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} |
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} |
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if (rij < rup) { |
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if (rij < rlp) { |
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if (idat.rij < rup) { |
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if (idat.rij < rlp) { |
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sp = 1.0; |
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dspdr = 0.0; |
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} else { |
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// we are in the switching region |
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pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(rij); |
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pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(idat.rij); |
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sp = res.first; |
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dspdr = res.second; |
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} |
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RealType w = wi+wj; |
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RealType zif = zi/rij - 0.6; |
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RealType zis = zi/rij + 0.8; |
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RealType zif = zi/idat.rij - 0.6; |
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RealType zis = zi/idat.rij + 0.8; |
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RealType zjf = zj/rij - 0.6; |
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RealType zjs = zj/rij + 0.8; |
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RealType zjf = zj/idat.rij - 0.6; |
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RealType zjs = zj/idat.rij + 0.8; |
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RealType wip = zif*zif*zis*zis - w0; |
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RealType wjp = zjf*zjf*zjs*zjs - w0; |
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Vector3d dwip(-2.0*xi*zi*uglyi/r3, |
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-2.0*yi*zi*uglyi/r3, |
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2.0*(1.0/rij - zi2/r3)*uglyi); |
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2.0*(1.0/idat.rij - zi2/r3)*uglyi); |
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Vector3d dwjp(-2.0*xj*zj*uglyj/r3, |
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-2.0*yj*zj*uglyj/r3, |
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2.0*(1.0/rij - zj2/r3)*uglyj); |
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2.0*(1.0/idat.rij - zj2/r3)*uglyj); |
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Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3, |
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4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3, |
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4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3, |
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- 8.0*xj*yj*zj/r3); |
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Vector3d dwipdu(2.0*yi*uglyi/rij, |
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-2.0*xi*uglyi/rij, |
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Vector3d dwipdu(2.0*yi*uglyi/idat.rij, |
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-2.0*xi*uglyi/idat.rij, |
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0.0); |
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Vector3d dwjpdu(2.0*yj*uglyj/rij, |
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-2.0*xj*uglyj/rij, |
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Vector3d dwjpdu(2.0*yj*uglyj/idat.rij, |
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-2.0*xj*uglyj/idat.rij, |
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0.0); |
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if (isPower) { |
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dspdr = 0.0; |
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} |
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vpair += 0.5*(v0*s*w + v0p*sp*wp); |
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pot += 0.5*(v0*s*w + v0p*sp*wp)*sw; |
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idat.vpair += 0.5*(v0*s*w + v0p*sp*wp); |
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idat.pot += 0.5*(v0*s*w + v0p*sp*wp)*idat.sw; |
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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 ti = 0.5*sw*(v0*s*dwidu + v0p*sp*dwipdu); |
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Vector3d tj = 0.5*sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
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Vector3d ti = 0.5*idat.sw*(v0*s*dwidu + v0p*sp*dwipdu); |
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Vector3d tj = 0.5*idat.sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
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// go back to lab frame using transpose of rotation matrix: |
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t1 += A1trans * ti; |
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t2 += A2trans * tj; |
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idat.t1 += A1trans * ti; |
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idat.t2 += A2trans * tj; |
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// Now, on to the forces: |
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// first rotate the i terms back into the lab frame: |
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Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * sw; |
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Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * sw; |
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Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * idat.sw; |
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Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * idat.sw; |
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Vector3d fii = A1trans * radcomi; |
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Vector3d fjj = A2trans * radcomj; |
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// now assemble these with the radial-only terms: |
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f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * d / rij + fii - fjj); |
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> |
idat.f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * idat.d / |
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idat.rij + fii - fjj); |
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} |
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return; |
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} |
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void Sticky::do_sticky_pair(int *atid1, int *atid2, RealType *d, |
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RealType *r, RealType *r2, RealType *sw, |
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RealType *vpair, RealType *pot, RealType *A1, |
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RealType *A2, RealType *f1, |
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RealType *t1, RealType *t2) { |
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|
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if (!initialized_) initialize(); |
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AtomType* atype1 = StickyMap[*atid1]; |
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AtomType* atype2 = StickyMap[*atid2]; |
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|
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Vector3d disp(d); |
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Vector3d frc(f1); |
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Vector3d trq1(t1); |
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Vector3d trq2(t2); |
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RotMat3x3d Ai(A1); |
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RotMat3x3d Aj(A2); |
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|
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calcForce(atype1, atype2, disp, *r, *r2, *sw, *vpair, *pot, |
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Ai, Aj, frc, trq1, trq2); |
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|
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f1[0] = frc.x(); |
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f1[1] = frc.y(); |
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f1[2] = frc.z(); |
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t1[0] = trq1.x(); |
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t1[1] = trq1.y(); |
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t1[2] = trq1.z(); |
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t2[0] = trq2.x(); |
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t2[1] = trq2.y(); |
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t2[2] = trq2.z(); |
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|
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return; |
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} |
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} |
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extern "C" { |
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|
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#define fortranGetStickyCut FC_FUNC(getstickycut, GETSTICKYCUT) |
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#define fortranDoStickyPair FC_FUNC(do_sticky_pair, DO_STICKY_PAIR) |
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|
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RealType fortranGetStickyCut(int* atid) { |
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return OpenMD::Sticky::Instance()->getStickyCut(*atid); |
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} |
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void fortranDoStickyPair(int *atid1, int *atid2, RealType *d, RealType *r, |
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RealType *r2, RealType *sw, RealType *vpair, RealType *pot, |
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RealType *A1, RealType *A2, RealType *f1, |
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RealType *t1, RealType *t2){ |
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return OpenMD::Sticky::Instance()->do_sticky_pair(atid1, atid2, d, r, r2, |
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sw, vpair, pot, A1, A2, |
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f1, t1, t2); |
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} |
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} |
