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/* |
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* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project |
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* |
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* Contact: gezelter@openscience.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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#include "primitives/DirectionalAtom.hpp" |
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|
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namespace OpenMD { |
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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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} |
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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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((snapshotMan_->getPrevSnapshot())->*storage_).unitVector[localIndex_] = a.inverse() * sU_.getColumn(2); |
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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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((snapshotMan_->getCurrentSnapshot())->*storage_).unitVector[localIndex_] = a.inverse() * sU_.getColumn(2); |
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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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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).unitVector[localIndex_] = a.inverse() * sU_.getColumn(2); |
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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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void DirectionalAtom::setUnitFrameFromEuler(double phi, double theta, double psi) { |
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sU_.setupRotMat(phi,theta,psi); |
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} |
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|
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std::vector<double> DirectionalAtom::getGrad() { |
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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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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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|
