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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <algorithm> |
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#include "primitives/RigidBody.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ |
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|
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} |
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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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//((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
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|
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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(a * refOrients_[i]); |
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} |
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} |
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|
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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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//((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
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|
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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(a * refOrients_[i]); |
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} |
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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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|
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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(a * refOrients_[i], snapshotNo); |
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} |
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} |
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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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|
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std::vector<double> RigidBody::getGrad() { |
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std::vector<double> 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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Vector3d ephi; |
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Vector3d etheta; |
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Vector3d epsi; |
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|
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force = getFrc(); |
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torque =getTrq(); |
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myEuler = getA().toEulerAngles(); |
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|
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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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|
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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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|
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// get unit vectors along the phi, theta and psi rotation axes |
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|
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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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|
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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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|
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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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|
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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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|
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for (int j = 0; j < 3; j++ ) { |
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|
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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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} |
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|
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return grad; |
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} |
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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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|
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/**@todo need modification */ |
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void RigidBody::calcRefCoords() { |
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double 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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mtmp = atoms_[i]->getMass(); |
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mass_ += mtmp; |
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refCOM += refCoords_[i]*mtmp; |
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} |
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refCOM /= mass_; |
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|
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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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} |
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|
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// Moment of Inertia calculation |
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Mat3x3d Itmp(0.0); |
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|
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for (std::size_t i = 0; i < atoms_.size(); i++) { |
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mtmp = atoms_[i]->getMass(); |
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Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
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double r2 = refCoords_[i].lengthSquare(); |
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Itmp(0, 0) += mtmp * r2; |
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Itmp(1, 1) += mtmp * r2; |
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Itmp(2, 2) += mtmp * r2; |
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} |
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|
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//diagonalize |
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Vector3d evals; |
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Mat3x3d::diagonalize(Itmp, evals, sU_); |
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|
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// zero out I and then fill the diagonals with the moments of inertia: |
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inertiaTensor_(0, 0) = evals[0]; |
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inertiaTensor_(1, 1) = evals[1]; |
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inertiaTensor_(2, 2) = evals[2]; |
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|
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int nLinearAxis = 0; |
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for (int i = 0; i < 3; i++) { |
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if (fabs(evals[i]) < oopse::epsilon) { |
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linear_ = true; |
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linearAxis_ = i; |
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++ nLinearAxis; |
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} |
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} |
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|
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if (nLinearAxis > 1) { |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
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"\tmoment of inertia. This can happen in one of three ways:\n" |
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"\t 1) Only one atom was specified, or \n" |
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"\t 2) All atoms were specified at the same location, or\n" |
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"\t 3) The programmers did something stupid.\n" |
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"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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|
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void RigidBody::calcForcesAndTorques() { |
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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 frc(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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|
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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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|
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frc += afrc; |
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|
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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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|
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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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|
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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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|
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setFrc(frc); |
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setTrq(trq); |
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|
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} |
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|
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void RigidBody::updateAtoms() { |
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unsigned int i; |
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Vector3d ref; |
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Vector3d apos; |
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DirectionalAtom* dAtom; |
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Vector3d pos = getPos(); |
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RotMat3x3d a = getA(); |
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|
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for (i = 0; i < atoms_.size(); i++) { |
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|
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ref = body2Lab(refCoords_[i]); |
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|
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apos = pos + ref; |
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|
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atoms_[i]->setPos(apos); |
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|
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if (atoms_[i]->isDirectional()) { |
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|
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dAtom = (DirectionalAtom *) atoms_[i]; |
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dAtom->setA(a * refOrients_[i]); |
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//dAtom->rotateBy( A ); |
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} |
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|
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} |
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|
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} |
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|
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|
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bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { |
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if (index < atoms_.size()) { |
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|
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Vector3d ref = body2Lab(refCoords_[index]); |
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pos = getPos() + ref; |
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return true; |
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} else { |
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std::cerr << index << " is an invalid index, current rigid body contains " |
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<< atoms_.size() << "atoms" << std::endl; |
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return false; |
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} |
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} |
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|
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bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { |
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std::vector<Atom*>::iterator i; |
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i = std::find(atoms_.begin(), atoms_.end(), atom); |
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if (i != atoms_.end()) { |
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//RigidBody class makes sure refCoords_ and atoms_ match each other |
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Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); |
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pos = getPos() + ref; |
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return true; |
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} else { |
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std::cerr << "Atom " << atom->getGlobalIndex() |
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<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
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return false; |
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} |
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} |
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bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { |
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|
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//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
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|
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if (index < atoms_.size()) { |
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|
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Vector3d velRot; |
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Mat3x3d skewMat;; |
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Vector3d ref = refCoords_[index]; |
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Vector3d ji = getJ(); |
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Mat3x3d I = getI(); |
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|
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skewMat(0, 0) =0; |
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skewMat(0, 1) = ji[2] /I(2, 2); |
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skewMat(0, 2) = -ji[1] /I(1, 1); |
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|
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skewMat(1, 0) = -ji[2] /I(2, 2); |
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skewMat(1, 1) = 0; |
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skewMat(1, 2) = ji[0]/I(0, 0); |
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|
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skewMat(2, 0) =ji[1] /I(1, 1); |
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skewMat(2, 1) = -ji[0]/I(0, 0); |
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skewMat(2, 2) = 0; |
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|
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velRot = (getA() * skewMat).transpose() * ref; |
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|
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vel =getVel() + velRot; |
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return true; |
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|
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} else { |
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std::cerr << index << " is an invalid index, current rigid body contains " |
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<< atoms_.size() << "atoms" << std::endl; |
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return false; |
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} |
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} |
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|
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bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { |
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|
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std::vector<Atom*>::iterator i; |
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i = std::find(atoms_.begin(), atoms_.end(), atom); |
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if (i != atoms_.end()) { |
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return getAtomVel(vel, i - atoms_.begin()); |
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} else { |
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std::cerr << "Atom " << atom->getGlobalIndex() |
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<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
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return false; |
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} |
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} |
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|
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bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { |
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if (index < atoms_.size()) { |
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|
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coor = refCoords_[index]; |
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return true; |
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} else { |
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std::cerr << index << " is an invalid index, current rigid body contains " |
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<< atoms_.size() << "atoms" << std::endl; |
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return false; |
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} |
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|
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} |
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|
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bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { |
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std::vector<Atom*>::iterator i; |
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i = std::find(atoms_.begin(), atoms_.end(), atom); |
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if (i != atoms_.end()) { |
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//RigidBody class makes sure refCoords_ and atoms_ match each other |
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coor = refCoords_[i - atoms_.begin()]; |
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return true; |
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} else { |
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std::cerr << "Atom " << atom->getGlobalIndex() |
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<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
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return false; |
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} |
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|
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} |
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|
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|
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void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
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|
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Vector3d coords; |
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Vector3d euler; |
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|
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|
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atoms_.push_back(at); |
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|
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if( !ats->havePosition() ){ |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tAtom %s does not have a position specified.\n" |
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"\tThis means RigidBody cannot set up reference coordinates.\n", |
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ats->getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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coords[0] = ats->getPosX(); |
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coords[1] = ats->getPosY(); |
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coords[2] = ats->getPosZ(); |
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|
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refCoords_.push_back(coords); |
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|
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RotMat3x3d identMat = RotMat3x3d::identity(); |
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|
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if (at->isDirectional()) { |
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|
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if( !ats->haveOrientation() ){ |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tAtom %s does not have an orientation specified.\n" |
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"\tThis means RigidBody cannot set up reference orientations.\n", |
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ats->getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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euler[0] = ats->getEulerPhi(); |
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euler[1] = ats->getEulerTheta(); |
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euler[2] = ats->getEulerPsi(); |
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|
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RotMat3x3d Atmp(euler); |
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refOrients_.push_back(Atmp); |
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|
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}else { |
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refOrients_.push_back(identMat); |
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} |
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|
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|
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} |
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|
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} |
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|
