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#include <cmath> |
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#include "Mat3x3d.hpp" |
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#include "Roll.hpp" |
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#include "SimInfo.hpp" |
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//////////////////////////////////////////////////////////////////////////////// |
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//Implementation of DCRollAFunctor |
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//////////////////////////////////////////////////////////////////////////////// |
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int DCRollAFunctor::operator()(ConstraintAtom* consAtom1, ConstraintAtom* consAtom2){ |
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Vector3d posA; |
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Vector3d posB; |
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Vector3d oldPosA; |
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Vector3d oldPosB; |
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Vector3d velA; |
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Vector3d velB; |
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Vector3d pab; |
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Vector3d tempPab; |
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Vector3d rab; |
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Vector3d zetaA; |
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Vector3d zetaB; |
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Vector3d zeta; |
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Vector3d consForce; |
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Vector3d bondDirUnitVec; |
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double dx, dy, dz; |
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double rpab; |
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double rabsq, pabsq, rpabsq; |
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double diffsq; |
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double gab; |
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double dt; |
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double pabDotZeta; |
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double pabDotZeta2; |
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double zeta2; |
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double forceScalar; |
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dt = info->dt; |
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consAtom1->getOldPos(oldPosA.vec); |
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consAtom2->getOldPos(oldPosB.vec); |
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consAtom1->getPos(posA.vec); |
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consAtom2->getPos(posB.vec); |
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//discard the vector convention in alan tidesley's code |
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//rij = rj - ri; |
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pab = posB - posA; |
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//periodic boundary condition |
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info->wrapVector(pab.vec); |
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pabsq = dotProduct(pab, pab); |
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rabsq = curPair->getBondLength2(); |
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diffsq = pabsq -rabsq; |
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if (fabs(diffsq) > (consTolerance * rabsq * 2)){ |
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rab = oldPosB - oldPosA; |
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info->wrapVector(rab.vec); |
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//rpab = dotProduct(rab, pab); |
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//rpabsq = rpab * rpab; |
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//if (rpabsq < (rabsq * -diffsq)){ |
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// return consFail; |
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//} |
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bondDirUnitVec = pab; |
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bondDirUnitVec.normalize(); |
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calcZeta(consAtom1, bondDirUnitVec, zetaA); |
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calcZeta(consAtom2, bondDirUnitVec, zetaB); |
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zeta = zetaA + zetaB; |
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zeta2 = dotProduct(zeta, zeta); |
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pabDotZeta = dotProduct(pab, zeta); |
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pabDotZeta2 = pabDotZeta * pabDotZeta; |
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//solve quadratic equation |
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//dt^4 * zeta^2 * G^2 + 2* h^2 * pab * zeta * G + pab^2 - d^2 |
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//dt : time step |
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// pab : |
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//G : constraint force scalar |
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//d: equilibrium bond length |
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if (pabDotZeta2 - zeta2 * diffsq < 0) |
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return consFail; |
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//forceScalar = (pabDotZeta + sqrt(pabDotZeta2 - zeta2 * diffsq)) / dt * dt * zeta2; |
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forceScalar = diffsq / (2 * dt * dt * pabDotZeta); |
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//forceScalar = 1 / forceScalar; |
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consForce = forceScalar * bondDirUnitVec; |
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//integrate consRB1 using constraint force; |
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integrate(consAtom1, consForce); |
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//integrate consRB2 using constraint force; |
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integrate(consAtom2, -consForce); |
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return consSuccess; |
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} |
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else |
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return consAlready; |
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} |
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void DCRollAFunctor::calcZeta(ConstraintAtom* consAtom, const Vector3d& bondDir, Vector3d&zeta){ |
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double invMass; |
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invMass = 1.0 / consAtom ->getMass(); |
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zeta = invMass * bondDir; |
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} |
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void DCRollAFunctor::integrate(ConstraintAtom* consAtom, const Vector3d& force){ |
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StuntDouble* sd; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d tempPos; |
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Vector3d tempVel; |
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double mass; |
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double dt; |
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dt = info->dt; |
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sd = consAtom->getStuntDouble(); |
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sd->getVel(vel.vec); |
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sd->getPos(pos.vec); |
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mass = sd->getMass(); |
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tempVel = dt/mass * force; |
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tempPos = dt * tempVel; |
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vel += tempVel; |
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pos += tempPos; |
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sd->setVel(vel.vec); |
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sd->setPos(pos.vec); |
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} |
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int DCRollAFunctor::operator()(ConstraintRigidBody* consRB1, ConstraintRigidBody* consRB2){ |
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Vector3d posA; |
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Vector3d posB; |
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Vector3d oldPosA; |
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Vector3d oldPosB; |
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Vector3d velA; |
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Vector3d velB; |
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Vector3d pab; |
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Vector3d tempPab; |
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Vector3d rab; |
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Vector3d zetaA; |
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Vector3d zetaB; |
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Vector3d zeta; |
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Vector3d consForce; |
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Vector3d bondDirUnitVec; |
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double dx, dy, dz; |
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double rpab; |
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double rabsq, pabsq, rpabsq; |
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double diffsq; |
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double gab; |
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double dt; |
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double pabDotZeta; |
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double pabDotZeta2; |
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double zeta2; |
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double forceScalar; |
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const int conRBMaxIter = 100; |
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dt = info->dt; |
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consRB1->getOldAtomPos(oldPosA.vec); |
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consRB2->getOldAtomPos(oldPosB.vec); |
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for(int i=0 ; i < conRBMaxIter; i++){ |
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consRB1->getCurAtomPos(posA.vec); |
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consRB2->getCurAtomPos(posB.vec); |
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//discard the vector convention in alan tidesley's code |
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//rij = rj - ri; |
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pab = posB - posA; |
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//periodic boundary condition |
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info->wrapVector(pab.vec); |
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pabsq = dotProduct(pab, pab); |
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rabsq = curPair->getBondLength2(); |
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diffsq = pabsq -rabsq; |
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if (fabs(diffsq) > (consTolerance * rabsq * 2)){ |
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rab = oldPosB - oldPosA; |
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info->wrapVector(rab.vec); |
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bondDirUnitVec = rab; |
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bondDirUnitVec.normalize(); |
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calcZeta(consRB1, bondDirUnitVec, zetaA); |
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calcZeta(consRB2, bondDirUnitVec, zetaB); |
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zeta = zetaA + zetaB; |
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zeta2 = dotProduct(zeta, zeta); |
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pabDotZeta = dotProduct(pab, zeta); |
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pabDotZeta2 = pabDotZeta * pabDotZeta; |
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//solve quadratic equation |
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//dt^4 * zeta^2 * G^2 + 2* h^2 * pab * zeta * G + pab^2 - d^2 |
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//dt : time step |
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// pab : |
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//G : constraint force scalar |
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//d: equilibrium bond length |
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if (pabDotZeta2 - zeta2 * diffsq < 0){ |
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cerr << "DCRollAFunctor::operator() Error: Constraint Fail at " << info->getTime() << endl; |
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return consFail; |
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} |
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//if pabDotZeta is close to 0, we can't neglect the square term |
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if(fabs(pabDotZeta) < consTolerance) |
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forceScalar = (pabDotZeta - sqrt(pabDotZeta2 - zeta2 * diffsq)) / dt * dt * zeta2; |
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else |
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forceScalar = diffsq / (2 * dt * dt * pabDotZeta); |
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// |
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consForce = forceScalar * bondDirUnitVec; |
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//integrate consRB1 using constraint force; |
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integrate(consRB1, consForce); |
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//integrate consRB2 using constraint force; |
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integrate(consRB2, -consForce); |
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} |
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else{ |
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if (i ==0) |
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return consAlready; |
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else |
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return consSuccess; |
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} |
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} |
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cerr << "DCRollAFunctor::operator() Error: can not constrain the bond within maximum iteration at " << info->getTime() << endl; |
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return consExceedMaxIter; |
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} |
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void DCRollAFunctor::calcZeta(ConstraintRigidBody* consRB, const Vector3d& bondDir, Vector3d& zeta){ |
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double invMass; |
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Vector3d tempVec1; |
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Vector3d tempVec2; |
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Vector3d refCoor; |
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Vector3d refCrossBond; |
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Mat3x3d IBody; |
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Mat3x3d invIBody; |
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Mat3x3d invILab; |
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Mat3x3d a; |
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Mat3x3d aTrans; |
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invMass = 1.0 / consRB ->getMass(); |
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zeta = invMass * bondDir; |
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consRB->getRefCoor(refCoor.vec); |
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//consRB->getA(a.element); |
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consRB->getOldA(a.element); |
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consRB->getI(IBody.element); |
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aTrans = a.transpose(); |
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invIBody = IBody.inverse(); |
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invILab = aTrans * invIBody * a; |
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refCrossBond = crossProduct(aTrans *refCoor, bondDir); |
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tempVec1 = invILab * refCrossBond; |
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tempVec2 = crossProduct(tempVec1, aTrans *refCoor); |
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zeta += tempVec2; |
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} |
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void DCRollAFunctor::integrate(ConstraintRigidBody* consRB, const Vector3d& consForce){ |
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RigidBody* rb; |
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Vector3d frc; |
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Vector3d totConsForce; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d Tb; |
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Vector3d ji; |
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Vector3d refCoor; |
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Vector3d consTorque; |
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Vector3d totConsTorque; |
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Mat3x3d a; |
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double mass; |
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double dt; |
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double dtOver2; |
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const double eConvert = 4.184e-4; |
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dt = info->dt; |
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dtOver2 = dt /2; |
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//restore to old status |
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consRB->restoreUnconsStatus(); |
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//accumulate constraint force; |
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consRB->addConsForce(consForce/eConvert); |
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totConsForce = consRB->getConsForce(); |
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rb = consRB->getRigidBody(); |
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rb->addFrc(totConsForce.vec); |
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rb->getVel(vel.vec); |
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rb->getPos(pos.vec); |
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rb->getFrc(frc.vec); |
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mass = rb->getMass(); |
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// velocity half step |
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vel += eConvert * dtOver2 / mass * frc; |
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// position whole step |
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pos += dt * vel; |
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rb->setVel(vel.vec); |
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rb->setPos(pos.vec); |
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//evolve orientational part |
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consRB->getRefCoor(refCoor.vec); |
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rb->getA(a.element); |
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//calculate constraint torque in lab frame |
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consTorque = crossProduct(a.transpose() * refCoor, consForce); |
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consRB->addConsTorque(consTorque/eConvert); |
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//add constraint torque |
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totConsTorque = consRB->getConsTorque(); |
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rb->addTrq(totConsTorque.vec); |
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//get and convert the torque to body frame |
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rb->getTrq(Tb.vec); |
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rb->lab2Body(Tb.vec); |
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//get the angular momentum, and propagate a half step |
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rb->getJ(ji.vec); |
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ji += eConvert * dtOver2 * Tb; |
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rotationPropagation( rb, ji.vec ); |
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rb->setJ(ji.vec); |
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} |
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void DCRollAFunctor::rotationPropagation(StuntDouble* sd, double ji[3]){ |
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double angle; |
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double A[3][3], I[3][3]; |
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int i, j, k; |
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double dtOver2; |
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double dt; |
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dt = info->dt; |
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dtOver2 = dt /2; |
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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sd->getA(A); |
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sd->getI(I); |
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if (sd->isLinear()) { |
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i = sd->linearAxis(); |
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j = (i+1)%3; |
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k = (i+2)%3; |
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angle = dtOver2 * ji[j] / I[j][j]; |
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this->rotate( k, i, angle, ji, A ); |
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angle = dt* ji[k] / I[k][k]; |
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this->rotate( i, j, angle, ji, A); |
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angle = dtOver2 * ji[j] / I[j][j]; |
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this->rotate( k, i, angle, ji, A ); |
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} else { |
392 |
|
|
// rotate about the x-axis |
393 |
|
|
angle = dtOver2 * ji[0] / I[0][0]; |
394 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
395 |
|
|
|
396 |
|
|
// rotate about the y-axis |
397 |
|
|
angle = dtOver2 * ji[1] / I[1][1]; |
398 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
399 |
|
|
|
400 |
|
|
// rotate about the z-axis |
401 |
tim |
1452 |
angle = dt * ji[2] / I[2][2]; |
402 |
tim |
1254 |
this->rotate( 0, 1, angle, ji, A); |
403 |
|
|
|
404 |
|
|
// rotate about the y-axis |
405 |
|
|
angle = dtOver2 * ji[1] / I[1][1]; |
406 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
407 |
|
|
|
408 |
|
|
// rotate about the x-axis |
409 |
|
|
angle = dtOver2 * ji[0] / I[0][0]; |
410 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
411 |
|
|
|
412 |
|
|
} |
413 |
|
|
sd->setA( A ); |
414 |
|
|
} |
415 |
|
|
|
416 |
|
|
void DCRollAFunctor::rotate(int axes1, int axes2, double angle, double ji[3], double A[3][3]){ |
417 |
|
|
int i, j, k; |
418 |
|
|
double sinAngle; |
419 |
|
|
double cosAngle; |
420 |
|
|
double angleSqr; |
421 |
|
|
double angleSqrOver4; |
422 |
|
|
double top, bottom; |
423 |
|
|
double rot[3][3]; |
424 |
|
|
double tempA[3][3]; |
425 |
|
|
double tempJ[3]; |
426 |
|
|
|
427 |
|
|
// initialize the tempA |
428 |
|
|
|
429 |
|
|
for (i = 0; i < 3; i++){ |
430 |
|
|
for (j = 0; j < 3; j++){ |
431 |
|
|
tempA[j][i] = A[i][j]; |
432 |
|
|
} |
433 |
|
|
} |
434 |
|
|
|
435 |
|
|
// initialize the tempJ |
436 |
|
|
|
437 |
|
|
for (i = 0; i < 3; i++) |
438 |
|
|
tempJ[i] = ji[i]; |
439 |
|
|
|
440 |
|
|
// initalize rot as a unit matrix |
441 |
|
|
|
442 |
|
|
rot[0][0] = 1.0; |
443 |
|
|
rot[0][1] = 0.0; |
444 |
|
|
rot[0][2] = 0.0; |
445 |
|
|
|
446 |
|
|
rot[1][0] = 0.0; |
447 |
|
|
rot[1][1] = 1.0; |
448 |
|
|
rot[1][2] = 0.0; |
449 |
|
|
|
450 |
|
|
rot[2][0] = 0.0; |
451 |
|
|
rot[2][1] = 0.0; |
452 |
|
|
rot[2][2] = 1.0; |
453 |
|
|
|
454 |
|
|
// use a small angle aproximation for sin and cosine |
455 |
|
|
|
456 |
|
|
angleSqr = angle * angle; |
457 |
|
|
angleSqrOver4 = angleSqr / 4.0; |
458 |
|
|
top = 1.0 - angleSqrOver4; |
459 |
|
|
bottom = 1.0 + angleSqrOver4; |
460 |
|
|
|
461 |
|
|
cosAngle = top / bottom; |
462 |
|
|
sinAngle = angle / bottom; |
463 |
|
|
|
464 |
|
|
rot[axes1][axes1] = cosAngle; |
465 |
|
|
rot[axes2][axes2] = cosAngle; |
466 |
|
|
|
467 |
|
|
rot[axes1][axes2] = sinAngle; |
468 |
|
|
rot[axes2][axes1] = -sinAngle; |
469 |
|
|
|
470 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
471 |
|
|
|
472 |
|
|
for (i = 0; i < 3; i++){ |
473 |
|
|
ji[i] = 0.0; |
474 |
|
|
for (k = 0; k < 3; k++){ |
475 |
|
|
ji[i] += rot[i][k] * tempJ[k]; |
476 |
|
|
} |
477 |
|
|
} |
478 |
|
|
|
479 |
|
|
// rotate the Rotation matrix acording to: |
480 |
|
|
// A[][] = A[][] * transpose(rot[][]) |
481 |
|
|
|
482 |
|
|
|
483 |
|
|
// NOte for as yet unknown reason, we are performing the |
484 |
|
|
// calculation as: |
485 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
486 |
|
|
|
487 |
|
|
for (i = 0; i < 3; i++){ |
488 |
|
|
for (j = 0; j < 3; j++){ |
489 |
|
|
A[j][i] = 0.0; |
490 |
|
|
for (k = 0; k < 3; k++){ |
491 |
|
|
A[j][i] += tempA[i][k] * rot[j][k]; |
492 |
|
|
} |
493 |
|
|
} |
494 |
|
|
} |
495 |
|
|
} |
496 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
497 |
|
|
//Implementation of DCRollBFunctor |
498 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
499 |
|
|
int DCRollBFunctor::operator()(ConstraintRigidBody* consRB1, ConstraintRigidBody* consRB2){ |
500 |
tim |
1255 |
Vector3d posA; |
501 |
|
|
Vector3d posB; |
502 |
|
|
Vector3d velA; |
503 |
|
|
Vector3d velB; |
504 |
|
|
Vector3d pab; |
505 |
|
|
Vector3d rab; |
506 |
|
|
Vector3d vab; |
507 |
tim |
1284 |
Vector3d zetaA; |
508 |
|
|
Vector3d zetaB; |
509 |
|
|
Vector3d zeta; |
510 |
tim |
1255 |
Vector3d consForce; |
511 |
|
|
Vector3d bondDirUnitVec; |
512 |
|
|
double dt; |
513 |
tim |
1284 |
double pabDotvab; |
514 |
|
|
double pabDotZeta; |
515 |
|
|
double pvab; |
516 |
tim |
1255 |
|
517 |
tim |
1452 |
const int conRBMaxIter = 20; |
518 |
tim |
1255 |
|
519 |
|
|
dt = info->dt; |
520 |
|
|
|
521 |
|
|
for(int i=0 ; i < conRBMaxIter; i++){ |
522 |
|
|
consRB1->getCurAtomPos(posA.vec); |
523 |
|
|
consRB2->getCurAtomPos(posB.vec); |
524 |
tim |
1284 |
pab = posB - posA; |
525 |
tim |
1255 |
|
526 |
|
|
//periodic boundary condition |
527 |
|
|
info->wrapVector(pab.vec); |
528 |
tim |
1284 |
|
529 |
|
|
consRB1->getCurAtomVel(velA.vec); |
530 |
|
|
consRB2->getCurAtomVel(velB.vec); |
531 |
|
|
vab = velB -velA; |
532 |
tim |
1255 |
|
533 |
tim |
1284 |
pvab = dotProduct(pab, vab); |
534 |
tim |
1255 |
|
535 |
tim |
1284 |
if (fabs(pvab) > consTolerance ){ |
536 |
tim |
1255 |
|
537 |
|
|
|
538 |
|
|
bondDirUnitVec = pab; |
539 |
|
|
bondDirUnitVec.normalize(); |
540 |
|
|
|
541 |
tim |
1284 |
getZeta(consRB1, bondDirUnitVec, zetaA); |
542 |
|
|
getZeta(consRB2, bondDirUnitVec, zetaB); |
543 |
|
|
zeta = zetaA + zetaB; |
544 |
tim |
1255 |
|
545 |
tim |
1284 |
pabDotZeta = dotProduct(pab, zeta); |
546 |
|
|
|
547 |
tim |
1452 |
consForce = 2 * pvab / (dt * pabDotZeta) * bondDirUnitVec; |
548 |
tim |
1255 |
//integrate consRB1 using constraint force; |
549 |
tim |
1284 |
integrate(consRB1, consForce); |
550 |
tim |
1255 |
|
551 |
|
|
//integrate consRB2 using constraint force; |
552 |
|
|
integrate(consRB2, -consForce); |
553 |
|
|
|
554 |
|
|
} |
555 |
|
|
else{ |
556 |
|
|
if (i ==0) |
557 |
|
|
return consAlready; |
558 |
|
|
else |
559 |
|
|
return consSuccess; |
560 |
|
|
} |
561 |
|
|
} |
562 |
|
|
|
563 |
tim |
1284 |
cerr << "DCRollBFunctor::operator() Error: can not constrain the bond within maximum iteration at " << info->getTime() << endl; |
564 |
tim |
1255 |
return consExceedMaxIter; |
565 |
|
|
|
566 |
tim |
1254 |
} |
567 |
|
|
|
568 |
tim |
1284 |
void DCRollBFunctor::getZeta(ConstraintRigidBody* consRB, const Vector3d& bondDir, Vector3d& zeta){ |
569 |
tim |
1255 |
double invMass; |
570 |
|
|
Vector3d tempVec1; |
571 |
|
|
Vector3d tempVec2; |
572 |
|
|
Vector3d refCoor; |
573 |
|
|
Vector3d refCrossBond; |
574 |
|
|
Mat3x3d IBody; |
575 |
tim |
1284 |
Mat3x3d ILab; |
576 |
tim |
1255 |
Mat3x3d invIBody; |
577 |
tim |
1284 |
Mat3x3d invILab; |
578 |
tim |
1255 |
Mat3x3d a; |
579 |
|
|
|
580 |
|
|
invMass = 1.0 / consRB ->getMass(); |
581 |
tim |
1254 |
|
582 |
tim |
1284 |
zeta = invMass * bondDir; |
583 |
tim |
1255 |
|
584 |
|
|
consRB->getRefCoor(refCoor.vec); |
585 |
|
|
consRB->getA(a.element); |
586 |
|
|
consRB->getI(IBody.element); |
587 |
|
|
|
588 |
|
|
invIBody = IBody.inverse(); |
589 |
|
|
|
590 |
tim |
1452 |
|
591 |
|
|
refCrossBond = crossProduct(refCoor, a * bondDir); |
592 |
tim |
1255 |
|
593 |
tim |
1452 |
tempVec1 = invIBody * refCrossBond; |
594 |
tim |
1255 |
|
595 |
tim |
1452 |
tempVec2 = (a * tempVec1.makeSkewMat()).transpose() * refCoor; |
596 |
|
|
|
597 |
|
|
zeta += tempVec2; |
598 |
tim |
1255 |
|
599 |
tim |
1254 |
} |
600 |
|
|
|
601 |
|
|
void DCRollBFunctor::integrate(ConstraintRigidBody* consRB, const Vector3d& force){ |
602 |
tim |
1255 |
Vector3d vel; |
603 |
|
|
Vector3d ji; |
604 |
tim |
1284 |
Vector3d tempJi; |
605 |
|
|
Vector3d tempTrq; |
606 |
|
|
Vector3d refCoor; |
607 |
tim |
1255 |
double mass; |
608 |
|
|
double dtOver2; |
609 |
tim |
1452 |
Mat3x3d a; |
610 |
tim |
1255 |
StuntDouble* sd; |
611 |
|
|
|
612 |
|
|
sd = consRB->getStuntDouble(); |
613 |
|
|
dtOver2 = info->dt/2; |
614 |
tim |
1254 |
|
615 |
tim |
1284 |
sd->getVel(vel.vec); |
616 |
tim |
1255 |
mass = sd->getMass(); |
617 |
tim |
1284 |
vel +=dtOver2 /mass * force; |
618 |
tim |
1255 |
sd->setVel(vel.vec); |
619 |
|
|
|
620 |
|
|
if (sd->isDirectional()){ |
621 |
tim |
1452 |
sd->getA(a.element); |
622 |
|
|
consRB->getRefCoor(refCoor.vec); |
623 |
|
|
tempTrq = crossProduct(refCoor, a *force); |
624 |
|
|
|
625 |
tim |
1284 |
tempJi = dtOver2* tempTrq; |
626 |
tim |
1255 |
sd->getJ(ji.vec); |
627 |
tim |
1284 |
ji += tempJi; |
628 |
tim |
1255 |
sd->setJ(ji.vec); |
629 |
|
|
} |
630 |
|
|
|
631 |
|
|
} |