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#include "utils/simError.h" |
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#include "utils/NumericConstant.hpp" |
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namespace oopse { |
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RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ |
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RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), |
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inertiaTensor_(0.0){ |
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} |
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void RigidBody::setPrevA(const RotMat3x3d& a) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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for (int i =0 ; i < atoms_.size(); ++i){ |
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if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
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} |
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} |
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} |
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void RigidBody::setA(const RotMat3x3d& a) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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} |
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} |
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} |
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void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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//((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
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for (int i =0 ; i < atoms_.size(); ++i){ |
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if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
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} |
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} |
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} |
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Mat3x3d RigidBody::getI() { |
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return inertiaTensor_; |
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} |
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std::vector<double> RigidBody::getGrad() { |
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std::vector<double> grad(6, 0.0); |
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std::vector<RealType> RigidBody::getGrad() { |
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std::vector<RealType> grad(6, 0.0); |
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Vector3d force; |
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Vector3d torque; |
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Vector3d myEuler; |
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double phi, theta, psi; |
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double cphi, sphi, ctheta, stheta; |
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RealType phi, theta, psi; |
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RealType cphi, sphi, ctheta, stheta; |
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Vector3d ephi; |
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Vector3d etheta; |
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Vector3d epsi; |
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force = getFrc(); |
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torque =getTrq(); |
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myEuler = getA().toEulerAngles(); |
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phi = myEuler[0]; |
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theta = myEuler[1]; |
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psi = myEuler[2]; |
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cphi = cos(phi); |
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sphi = sin(phi); |
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ctheta = cos(theta); |
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stheta = sin(theta); |
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// get unit vectors along the phi, theta and psi rotation axes |
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ephi[0] = 0.0; |
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ephi[1] = 0.0; |
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ephi[2] = 1.0; |
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etheta[0] = cphi; |
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etheta[1] = sphi; |
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etheta[2] = 0.0; |
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epsi[0] = stheta * cphi; |
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epsi[1] = stheta * sphi; |
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epsi[2] = ctheta; |
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//gradient is equal to -force |
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for (int j = 0 ; j<3; j++) |
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grad[j] = -force[j]; |
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for (int j = 0; j < 3; j++ ) { |
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grad[3] += torque[j]*ephi[j]; |
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grad[4] += torque[j]*etheta[j]; |
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grad[5] += torque[j]*epsi[j]; |
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} |
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return grad; |
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} |
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void RigidBody::accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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/**@todo need modification */ |
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void RigidBody::calcRefCoords() { |
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double mtmp; |
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RealType mtmp; |
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Vector3d refCOM(0.0); |
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mass_ = 0.0; |
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for (std::size_t i = 0; i < atoms_.size(); ++i) { |
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refCOM += refCoords_[i]*mtmp; |
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} |
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refCOM /= mass_; |
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// Next, move the origin of the reference coordinate system to the COM: |
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for (std::size_t i = 0; i < atoms_.size(); ++i) { |
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refCoords_[i] -= refCOM; |
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Mat3x3d IAtom(0.0); |
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mtmp = atoms_[i]->getMass(); |
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IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
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double r2 = refCoords_[i].lengthSquare(); |
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RealType r2 = refCoords_[i].lengthSquare(); |
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IAtom(0, 0) += mtmp * r2; |
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IAtom(1, 1) += mtmp * r2; |
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IAtom(2, 2) += mtmp * r2; |
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Itmp += IAtom; |
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//project the inertial moment of directional atoms into this rigid body |
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if (atoms_[i]->isDirectional()) { |
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Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; |
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Vector3d apos; |
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Vector3d rpos; |
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Vector3d frc(0.0); |
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Vector3d trq(0.0); |
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Vector3d trq(0.0); |
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Vector3d pos = this->getPos(); |
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for (int i = 0; i < atoms_.size(); i++) { |
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if (atoms_[i]->isDirectional()) { |
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atrq = atoms_[i]->getTrq(); |
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trq += atrq; |
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} |
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} |
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} |
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addFrc(frc); |
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addTrq(trq); |
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} |
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Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
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Vector3d afrc; |
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Vector3d atrq; |
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Vector3d apos; |
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Vector3d rpos; |
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Vector3d dfrc; |
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Vector3d frc(0.0); |
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Vector3d trq(0.0); |
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Vector3d pos = this->getPos(); |
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Mat3x3d tau_(0.0); |
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for (int i = 0; i < atoms_.size(); i++) { |
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afrc = atoms_[i]->getFrc(); |
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apos = atoms_[i]->getPos(); |
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rpos = apos - pos; |
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frc += afrc; |
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trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
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trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
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trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
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// If the atom has a torque associated with it, then we also need to |
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// migrate the torques onto the center of mass: |
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if (atoms_[i]->isDirectional()) { |
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atrq = atoms_[i]->getTrq(); |
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trq += atrq; |
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} |
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tau_(0,0) -= rpos[0]*afrc[0]; |
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tau_(0,1) -= rpos[0]*afrc[1]; |
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tau_(0,2) -= rpos[0]*afrc[2]; |
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tau_(1,0) -= rpos[1]*afrc[0]; |
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tau_(1,1) -= rpos[1]*afrc[1]; |
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tau_(1,2) -= rpos[1]*afrc[2]; |
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tau_(2,0) -= rpos[2]*afrc[0]; |
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tau_(2,1) -= rpos[2]*afrc[1]; |
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tau_(2,2) -= rpos[2]*afrc[2]; |
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} |
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addFrc(frc); |
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addTrq(trq); |
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> |
return tau_; |
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} |
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void RigidBody::updateAtoms() { |
