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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "restraints/MolecularRestraint.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "math/SVD.hpp" |
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#include <utility> |
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|
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//using namespace JAMA; |
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|
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namespace OpenMD { |
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|
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|
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void MolecularRestraint::calcForce(std::vector<Vector3d> struc, |
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Vector3d molCom){ |
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|
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assert(struc.size() == ref_.size()); |
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|
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std::vector<Vector3d>::iterator it; |
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|
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// clear out initial values: |
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pot_ = 0.0; |
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for(it = forces_.begin(); it != forces_.end(); ++it) |
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(*it) = 0.0; |
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|
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|
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if (restType_ & rtDisplacement) { |
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Vector3d del = molCom - refCom_; |
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|
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RealType r = del.length(); |
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RealType p = 0.5 * kDisp_ * r * r; |
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|
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pot_ += p; |
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|
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restInfo_[rtDisplacement] = std::make_pair(r, p); |
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|
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for(it = forces_.begin(); it != forces_.end(); ++it) |
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(*it) = -kDisp_ * del * scaleFactor_; |
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} |
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|
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for(it = struc.begin(); it != struc.end(); ++it) |
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(*it) -= molCom; |
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|
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// rtDisplacement = 1, so anything higher than that requires orientations: |
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if (restType_ > 1) { |
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Vector3d tBody(0.0); |
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|
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Mat3x3d R(0.0); |
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|
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for (int n = 0; n < struc.size(); n++){ |
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|
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/* |
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* correlation matrix R: |
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* R(i,j) = sum(over n): y(n,i) * x(n,j) |
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* where x(n) and y(n) are two vector sets |
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*/ |
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|
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R += outProduct(struc[n], ref_[n]); |
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} |
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|
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// SVD class uses dynamic matrices, so we must wrap the correlation |
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// matrix before calling SVD and then unwrap the results into Mat3x3d |
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// and Vector3d before we use them. |
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|
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DynamicRectMatrix<RealType> Rtmp(3, 3, 0.0); |
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DynamicRectMatrix<RealType> vtmp(3, 3); |
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DynamicVector<RealType> stmp(3); |
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DynamicRectMatrix<RealType> wtmp(3, 3); |
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|
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Rtmp.setSubMatrix(0, 0, R); |
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|
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// Heavy lifting goes here: |
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|
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JAMA::SVD<RealType> svd(Rtmp); |
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|
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svd.getU(vtmp); |
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svd.getSingularValues(stmp); |
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svd.getV(wtmp); |
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|
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Mat3x3d v; |
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Vector3d s; |
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Mat3x3d w_tr; |
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|
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vtmp.getSubMatrix(0, 0, v); |
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stmp.getSubVector(0, s); |
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wtmp.getSubMatrix(0, 0, w_tr); |
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|
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bool is_reflection = (v.determinant() * w_tr.determinant()) < 0.0; |
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|
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if (is_reflection){ |
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v(2, 0) = -v(2, 0); |
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v(2, 1) = -v(2, 1); |
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v(2, 2) = -v(2, 2); |
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} |
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|
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RotMat3x3d Atrans = v * w_tr.transpose(); |
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RotMat3x3d A = Atrans.transpose(); |
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|
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Vector3d eularAngles = A.toEulerAngles(); |
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|
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|
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RealType twistAngle, swingAngle; |
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Vector3d swingAxis; |
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|
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Quat4d quat = A.toQuaternion(); |
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|
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RealType tw, sx, sy, ttw, swingX, swingY; |
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quat.toSwingTwist(swingX, swingY, twistAngle); |
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|
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RealType dVdtwist, dVdswing, dVdswingX, dVdswingY; |
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RealType dTwist, dSwing, dSwingX, dSwingY; |
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RealType p; |
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|
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if (restType_ & rtTwist){ |
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dTwist = twistAngle - twist0_; |
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dVdtwist = kTwist_ * sin(dTwist) ; |
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p = kTwist_ * (1.0 - cos(dTwist) ) ; |
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pot_ += p; |
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tBody -= dVdtwist * V3Z; |
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restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
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} |
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|
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// if (restType_ & rtSwing){ |
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// dSwing = swingAngle - swing0_; |
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// dVdswing = kSwing_ * 2.0 * sin(2.0 * dSwing); |
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// p = kSwing_ * (1.0 - cos(2.0 * dSwing)); |
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// pot_ += p; |
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// tBody -= dVdswing * swingAxis; |
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// restInfo_[rtSwing] = std::make_pair(swingAngle, p); |
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// } |
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|
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if (restType_ & rtSwingX){ |
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dSwingX = swingX - swingX0_; |
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dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX); |
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p = kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
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pot_ += p; |
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tBody -= dVdswingX * V3X; |
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restInfo_[rtSwingX] = std::make_pair(swingX, p); |
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} |
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if (restType_ & rtSwingY){ |
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dSwingY = swingY - swingY0_; |
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dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY); |
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p = kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
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pot_ += p; |
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tBody -= dVdswingY * V3Y; |
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restInfo_[rtSwingY] = std::make_pair(swingY, p); |
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} |
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|
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|
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RealType t2 = dot(tBody, tBody); |
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|
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Vector3d rLab, rBody, txr, fBody, fLab; |
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|
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for (int i = 0; i < struc.size(); i++) { |
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|
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rLab = struc[i]; |
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rBody = A * rLab; |
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|
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txr = cross(tBody, rBody); |
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fBody = txr * t2; |
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fLab = Atrans * fBody; |
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fLab *= scaleFactor_; |
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|
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forces_[i] += fLab; |
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} |
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|
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// test the force vectors and see if it is the right orientation |
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// std::cout << struc.size() << std::endl << std::endl; |
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// for (int i = 0; i != struc.size(); ++i){ |
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// std::cout << "H\t" << struc[i].x() << "\t" << struc[i].y() << "\t" << struc[i].z() << "\t"; |
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// std::cout << forces_[i].x() << "\t" << forces_[i].y() << "\t" << forces_[i].z() << std::endl; |
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// } |
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} |
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} |
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} |
