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#include "Shake.hpp" |
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#include "SimInfo.hpp" |
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#include <cmath> |
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#include "simError.h" |
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#include "MatVec3.h" |
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//////////////////////////////////////////////////////////////////////////////// |
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//Implementation of DCShakeFunctor |
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//////////////////////////////////////////////////////////////////////////////// |
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int DCShakeFunctor::operator()(ConstraintAtom* consAtom1, ConstraintAtom* consAtom2){ |
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double posA[3]; |
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double posB[3]; |
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double oldPosA[3]; |
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double oldPosB[3]; |
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double velA[3]; |
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double velB[3]; |
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double pab[3]; |
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double rab[3]; |
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double rma, rmb; |
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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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|
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dt = info->dt; |
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|
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consAtom1->getPos(posA); |
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consAtom2->getPos(posB); |
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|
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|
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pab[0] = posA[0] - posB[0]; |
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pab[1] = posA[1] - posB[1]; |
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pab[2] = posA[2] - posB[2]; |
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|
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//periodic boundary condition |
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|
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info->wrapVector(pab); |
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|
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pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
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|
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rabsq = curPair->getBondLength2(); |
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diffsq = rabsq - pabsq; |
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|
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// the original rattle code from alan tidesley |
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if (fabs(diffsq) > (consTolerance * rabsq * 2)){ |
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|
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consAtom1->getOldPos(oldPosA); |
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consAtom2->getOldPos(oldPosB); |
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|
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rab[0] = oldPosA[0] - oldPosB[0]; |
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rab[1] = oldPosA[1] - oldPosB[1]; |
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rab[2] = oldPosA[2] - oldPosB[2]; |
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|
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info->wrapVector(rab); |
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|
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rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
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|
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rpabsq = rpab * rpab; |
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|
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|
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if (rpabsq < (rabsq * -diffsq)){ |
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return consFail; |
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} |
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|
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rma = 1.0 / consAtom1->getMass(); |
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rmb = 1.0 / consAtom2->getMass(); |
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|
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gab = diffsq / (2.0 * (rma + rmb) * rpab); |
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|
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dx = rab[0] * gab; |
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dy = rab[1] * gab; |
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dz = rab[2] * gab; |
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|
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//set atom1's position |
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posA[0] += rma * dx; |
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posA[1] += rma * dy; |
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posA[2] += rma * dz; |
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consAtom1->setPos(posA); |
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|
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//set atom2's position |
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posB[0] -= rmb * dx; |
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posB[1] -= rmb * dy; |
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posB[2] -= rmb * dz; |
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consAtom2->setPos(posB); |
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|
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//dx = dx / dt; |
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//dy = dy / dt; |
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//dz = dz / dt; |
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|
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////set atom1's velocity |
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//consAtom1->getVel(velA); |
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//velA[0] += rma * dx; |
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//velA[1] += rma * dy; |
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//velA[2] += rma * dz; |
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//consAtom1->setVel(velA); |
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|
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////set atom2's velocity |
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//consAtom2->getVel(velB); |
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//velB[0] -= rmb * dx; |
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//velB[1] -= rmb * dy; |
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//velB[2] -= rmb * dz; |
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//consAtom2->setVel(velB); |
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|
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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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} |
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|
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|
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int DCShakeFunctor::operator()(ConstraintAtom* consAtom,ConstraintRigidBody* consRB){ |
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return consElemHandlerFail; |
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} |
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|
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/** |
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* QSHAKE Algorithm |
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* Reference |
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* T.R. Forester and W. Smith, SHAKE, Rattle and Roll: Efficient Constraint Algorithms for Linked |
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* Rigid Bodies, J. Comp. Chem., 19(1), 102 -111 (1998) |
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*/ |
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int DCShakeFunctor::operator()(ConstraintRigidBody* consRB1, ConstraintRigidBody* consRB2){ |
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double posA[3]; |
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double posB[3]; |
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double oldPosA[3]; |
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double oldPosB[3]; |
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double velA[3]; |
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double velB[3]; |
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double pab[3]; |
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double tempPab[3]; |
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double rab[3]; |
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double rma, rmb; |
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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 dt2; |
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double consForce[3]; |
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|
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const int conRBMaxIter = 10; |
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|
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dt = info->dt; |
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dt2 = dt * dt; |
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|
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consRB1->getOldAtomPos(oldPosA); |
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consRB2->getOldAtomPos(oldPosB); |
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|
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|
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for(int i=0 ; i < conRBMaxIter; i++){ |
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consRB1->getCurAtomPos(posA); |
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consRB2->getCurAtomPos(posB); |
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|
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|
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pab[0] = posA[0] - posB[0]; |
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pab[1] = posA[1] - posB[1]; |
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pab[2] = posA[2] - posB[2]; |
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|
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//periodic boundary condition |
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|
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info->wrapVector(pab); |
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|
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pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
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|
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rabsq = curPair->getBondLength2(); |
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diffsq = rabsq - pabsq; |
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|
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// the original rattle code from alan tidesley |
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if (fabs(diffsq) > (consTolerance * rabsq * 2)){ |
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|
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rab[0] = oldPosA[0] - oldPosB[0]; |
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rab[1] = oldPosA[1] - oldPosB[1]; |
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rab[2] = oldPosA[2] - oldPosB[2]; |
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|
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info->wrapVector(rab); |
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|
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rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
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|
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rpabsq = rpab * rpab; |
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|
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|
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if (rpabsq < (rabsq * -diffsq)){ |
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return consFail; |
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} |
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|
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//rma = 1.0 / consRB1->getMass(); |
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//rmb = 1.0 / consRB2->getMass(); |
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|
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tempPab[0] = pab[0] / sqrt(pabsq); |
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tempPab[1] = pab[1] / sqrt(pabsq); |
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tempPab[2] = pab[2] / sqrt(pabsq); |
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|
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rma = getEffInvMass(consRB1, tempPab); |
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|
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tempPab[0] = -tempPab[0]; |
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tempPab[1] = -tempPab[1]; |
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tempPab[2] = -tempPab[2]; |
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rmb = getEffInvMass(consRB2, tempPab); |
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|
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gab = diffsq / (2.0* dt * dt * (rma + rmb) * rpab) ; |
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consForce[0] = rab[0] * gab; |
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consForce[1] = rab[1] * gab; |
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consForce[2] = rab[2] * gab; |
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|
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//integrate consRB1 using constraint force; |
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integrate(consRB1,consForce); |
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|
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//integrate consRB2 using constraint force; |
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consForce[0] = -consForce[0]; |
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consForce[1] = -consForce[1]; |
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consForce[2] = -consForce[2]; |
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integrate(consRB2,consForce); |
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|
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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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|
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return consExceedMaxIter; |
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} |
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|
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double DCShakeFunctor::getEffInvMass(ConstraintRigidBody* consRB, double bondDir[3]){ |
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double effInvMass; //effective inversse mass |
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double effInvMassCorr; //correction for effective inverse mass |
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double aTrans[3][3]; |
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double a[3][3]; |
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|
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double IFrame[3][3]; |
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double IBody[3][3]; |
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double invI[3][3]; |
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double refCoor[3]; |
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double refCrossBond[3]; |
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double tempVec1[3]; |
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double tempVec2[3]; |
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|
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effInvMass = 1.0 / consRB ->getMass(); |
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|
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consRB->getRefCoor(refCoor); |
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consRB->getA(a); |
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consRB->getI(IBody); |
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|
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crossProduct3(refCoor, bondDir, refCrossBond); |
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|
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matMul3(a, IBody, IFrame); |
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|
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invertMat3(IFrame, invI); |
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|
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matVecMul3(invI, refCrossBond, tempVec1); |
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|
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crossProduct3(tempVec1, refCoor, tempVec2); |
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|
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effInvMassCorr = dotProduct3(tempVec1, bondDir); |
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|
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effInvMass += effInvMassCorr; |
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|
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return effInvMass; |
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} |
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|
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void DCShakeFunctor::integrate(ConstraintRigidBody* consRB, double force[3]){ |
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|
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} |
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//////////////////////////////////////////////////////////////////////////////// |
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//Implementation of JCShakeFunctor |
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//////////////////////////////////////////////////////////////////////////////// |
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int JCShakeFunctor::operator()(ConstraintAtom* consAtom1, ConstraintAtom* consAtom2){ |
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return consElemHandlerFail; |
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} |
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|
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|
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|
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int JCShakeFunctor::operator()(ConstraintAtom* consAtom,ConstraintRigidBody* consRB){ |
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return consElemHandlerFail; |
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|
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} |
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|
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int JCShakeFunctor::operator()(ConstraintRigidBody* consRB1, ConstraintRigidBody* consRB2){ |
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return consElemHandlerFail; |
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} |
