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/* |
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* Copyright (c) 2009 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, 234107 (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 "restraints/ObjectRestraint.hpp" |
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|
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namespace OpenMD { |
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|
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void ObjectRestraint::calcForce(Vector3d struc) { |
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|
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pot_ = 0.0; |
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if (restType_ & rtDisplacement) { |
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Vector3d del = struc - refPos_; |
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RealType r = del.length(); |
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Vector3d frc = -kDisp_ * del; |
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RealType p = 0.5 * kDisp_ * del.lengthSquare(); |
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|
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pot_ = p; |
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force_ = frc * scaleFactor_; |
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if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r,p); |
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} |
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} |
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|
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void ObjectRestraint::calcForce(Vector3d struc, RotMat3x3d A) { |
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|
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calcForce(struc); |
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|
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// rtDisplacement is 1, so anything higher than that requires orientations: |
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if (restType_ > 1) { |
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|
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Vector3d tBody(0.0); |
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|
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RotMat3x3d temp = A * refA_.transpose(); |
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Quat4d quat = temp.toQuaternion(); |
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|
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RealType twistAngle; |
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Vector3d swingAxis; |
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RealType swingX, swingY; |
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|
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quat.toSwingTwist(swingX, swingY, twistAngle); |
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|
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|
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RealType p; |
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Vector3d tTwist, tSwing; |
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|
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if (restType_ & rtTwist){ |
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RealType dTwist = twistAngle - twist0_; |
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/// RealType dVdtwist = kTwist_ * sin(dTwist); |
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/// p = kTwist_ * (1.0 - cos(dTwist) ); |
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RealType dVdtwist = kTwist_ * dTwist; |
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p = 0.5 * kTwist_ * dTwist * dTwist; |
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pot_ += p; |
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tBody -= dVdtwist * V3Z; |
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if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
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} |
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|
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if (restType_ & rtSwingX){ |
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RealType dSwingX = swingX - swingX0_; |
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/// RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX); |
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/// p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
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RealType dVdswingX = kSwingX_ * dSwingX; |
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p = 0.5 * kSwingX_ * dSwingX * dSwingX; |
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pot_ += p; |
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tBody -= dVdswingX * V3X; |
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if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p); |
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} |
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|
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if (restType_ & rtSwingY){ |
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RealType dSwingY = swingY - swingY0_; |
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/// RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY); |
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/// p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
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RealType dVdswingY = kSwingY_ * dSwingY; |
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p = 0.5 * kSwingX_ * dSwingY * dSwingY; |
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pot_ += p; |
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tBody -= dVdswingY * V3Y; |
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if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p); |
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} |
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|
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Vector3d tLab = A.transpose() * tBody; |
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torque_ = tLab * scaleFactor_; |
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} |
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} |
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} |
