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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "primitives/DirectionalAtom.hpp" |
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#include "types/DirectionalAdapter.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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#include "utils/simError.h" |
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namespace OpenMD { |
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|
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DirectionalAtom::DirectionalAtom(AtomType* dAtomType) |
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: Atom(dAtomType) { |
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objType_= otDAtom; |
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|
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DirectionalAdapter da = DirectionalAdapter(dAtomType); |
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I_ = da.getI(); |
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|
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MultipoleAdapter ma = MultipoleAdapter(dAtomType); |
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if (ma.isMultipole()) { |
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electroBodyFrame_ = ma.getElectroBodyFrame(); |
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} |
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|
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// Check if one of the diagonal inertia tensor of this directional |
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// 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)) < OpenMD::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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"\tOpenMD 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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Mat3x3d DirectionalAtom::getI() { |
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return I_; |
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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<RealType> DirectionalAtom::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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RealType phi, theta; |
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// RealType 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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|
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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] = -sphi; |
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//etheta[1] = cphi; |
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//etheta[2] = 0.0; |
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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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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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