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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 "config.h" |
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#include <cmath> |
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#include "primitives/GhostBend.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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namespace OpenMD { |
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|
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/**@todo still a lot left to improve*/ |
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void GhostBend::calcForce(RealType& angle, bool doParticlePot) { |
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DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_); |
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|
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = ghostAtom->getPos(); |
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|
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Vector3d r21 = pos1 - pos2; |
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RealType d21 = r21.length(); |
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|
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RealType d21inv = 1.0 / d21; |
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|
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// we need the transpose of A to get the lab fixed vector: |
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Vector3d r23 = ghostAtom->getA().transpose().getColumn(2); |
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RealType d23 = r23.length(); |
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|
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RealType d23inv = 1.0 / d23; |
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|
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RealType cosTheta = dot(r21, r23) / (d21 * d23); |
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|
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//check roundoff |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
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} else if (cosTheta < -1.0) { |
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cosTheta = -1.0; |
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} |
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|
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RealType theta = acos(cosTheta); |
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|
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RealType dVdTheta; |
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|
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bendType_->calcForce(theta, potential_, dVdTheta); |
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|
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RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
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|
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if (fabs(sinTheta) < 1.0E-6) { |
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sinTheta = 1.0E-6; |
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} |
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|
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RealType commonFactor1 = dVdTheta / sinTheta * d21inv; |
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RealType commonFactor2 = dVdTheta / sinTheta * d23inv; |
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|
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Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta); |
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Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta); |
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|
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// Total force in current bend is zero |
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|
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atom1_->addFrc(force1); |
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ghostAtom->addFrc(-force1); |
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|
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ghostAtom->addTrq( cross(r23, force3) ); |
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if(doParticlePot) { |
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atom1_->addParticlePot(potential_); |
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ghostAtom->addParticlePot(potential_); |
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} |
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|
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angle = theta /M_PI * 180.0; |
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|
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} |
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} //end namespace OpenMD |
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|
