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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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|
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#include "primitives/DirectionalAtom.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) |
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: Atom(dAtomType){ |
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objType_= otDAtom; |
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if (dAtomType->isMultipole()) { |
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electroBodyFrame_ = dAtomType->getElectroBodyFrame(); |
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} |
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|
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//check if one of the diagonal inertia tensor of this directional atom is zero |
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int nLinearAxis = 0; |
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Mat3x3d inertiaTensor = getI(); |
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for (int i = 0; i < 3; i++) { |
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if (fabs(inertiaTensor(i, 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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"Directional Atom warning.\n" |
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"\tOOPSE found more than one axis in this directional atom with a vanishing \n" |
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"\tmoment of inertia."); |
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painCave.isFatal = 0; |
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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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Mat3x3d DirectionalAtom::getI() { |
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return static_cast<DirectionalAtomType*>(getAtomType())->getI(); |
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} |
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|
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void DirectionalAtom::setPrevA(const RotMat3x3d& a) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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if (atomType_->isMultipole()) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
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} |
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} |
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|
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|
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void DirectionalAtom::setA(const RotMat3x3d& a) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
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if (atomType_->isMultipole()) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
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} |
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} |
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|
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void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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|
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if (atomType_->isMultipole()) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
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} |
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} |
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|
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void DirectionalAtom::rotateBy(const RotMat3x3d& m) { |
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setA(m *getA()); |
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} |
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|
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std::vector<double> DirectionalAtom::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 DirectionalAtom::accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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|
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} |
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|
