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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. 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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* 3. 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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|
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#include "primitives/Inversion.hpp" |
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#include "fstream" |
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|
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namespace oopse { |
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|
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Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, |
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Atom *atom4, InversionType *it) : |
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atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), |
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inversionType_(it) { } |
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|
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void Inversion::calcForce(RealType& angle) { |
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|
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// In OOPSE's version of an inversion, the central atom |
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// comes first. However, to get the planarity in a typical cosine |
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// version of this potential (i.e. Amber-style), the central atom |
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// is treated as atom *3* in a standard torsion form: |
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|
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Vector3d pos1 = atom2_->getPos(); |
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Vector3d pos2 = atom3_->getPos(); |
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Vector3d pos3 = atom1_->getPos(); |
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Vector3d pos4 = atom4_->getPos(); |
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|
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/*std::ofstream myfile; |
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myfile.open("Inversion", std::ios::app); |
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myfile << atom1_->getType() << " - atom1; " |
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<< atom2_->getType() << " - atom2; " |
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<< atom3_->getType() << " - atom3; " |
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<< atom4_->getType() << " - atom4; " |
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<< std::endl; |
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*/ |
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Vector3d r31 = pos1 - pos3; |
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Vector3d r23 = pos3 - pos2; |
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Vector3d r43 = pos3 - pos4; |
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|
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// Calculate the cross products and distances |
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Vector3d A = cross(r31, r43); |
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RealType rA = A.length(); |
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Vector3d B = cross(r43, r23); |
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RealType rB = B.length(); |
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//Vector3d C = cross(r23, A); |
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//RealType rC = C.length(); |
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|
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A.normalize(); |
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B.normalize(); |
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//C.normalize(); |
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|
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// Calculate the sin and cos |
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RealType cos_phi = dot(A, B) ; |
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if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" |
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<< std::endl;} |
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if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" |
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<< std::endl;} |
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//std::cout << "We actually use this inversion!!!!" << std::endl; |
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|
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RealType dVdcosPhi; |
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//cos_phi = 2.0*cos_phi*cos_phi - 1.0; |
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inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
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Vector3d f1 ; |
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Vector3d f2 ; |
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Vector3d f3 ; |
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|
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Vector3d dcosdA = (cos_phi * A - B) /rA; |
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Vector3d dcosdB = (cos_phi * B - A) /rB; |
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|
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f1 = dVdcosPhi * cross(r43, dcosdA); |
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f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
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f3 = dVdcosPhi * cross(dcosdB, r43); |
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|
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// In OOPSE's version of an improper torsion, the central atom |
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// comes first. However, to get the planarity in a typical cosine |
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// version of this potential (i.e. Amber-style), the central atom |
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// is treated as atom *3* in a standard torsion form: |
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|
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// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon) |
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// OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
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|
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// Confusing enough? Good. |
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|
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atom2_->addFrc(f1); |
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atom1_->addFrc(f2 - f1 + f3); |
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atom4_->addFrc(-f2); |
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atom3_->addFrc(-f3); |
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|
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angle = acos(cos_phi) /M_PI * 180.0; |
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} |
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|
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} |
