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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, 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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/** |
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* @file Bond.hpp |
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* @author tlin |
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* @date 11/01/2004 |
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* @version 1.0 |
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*/ |
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|
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|
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#ifndef PRIMITIVES_BOND_HPP |
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#define PRIMITIVES_BOND_HPP |
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|
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#include "primitives/ShortRangeInteraction.hpp" |
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#include "primitives/Atom.hpp" |
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#include "types/BondType.hpp" |
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|
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namespace OpenMD { |
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|
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class Bond : public ShortRangeInteraction { |
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public: |
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Bond(Atom* atom1, Atom* atom2, BondType* bt) : ShortRangeInteraction(), |
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bondType_(bt) { |
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atoms_.resize(2); |
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atoms_[0] = atom1; |
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atoms_[1] = atom2; |
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} |
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virtual ~Bond() {} |
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void calcForce(bool doParticlePot) { |
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RealType len; |
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RealType dvdr; |
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Vector3d r12; |
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Vector3d force; |
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|
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r12 = atoms_[1]->getPos() - atoms_[0]->getPos(); |
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len = r12.length(); |
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bondType_->calcForce(len, potential_, dvdr); |
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|
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force = r12 * (-dvdr / len); |
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|
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atoms_[0]->addFrc(-force); |
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atoms_[1]->addFrc(force); |
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if (doParticlePot) { |
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atoms_[0]->addParticlePot(potential_); |
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atoms_[1]->addParticlePot(potential_); |
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} |
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} |
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|
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RealType getValue(int snap) { |
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Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap); |
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return r12.length(); |
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} |
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|
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RealType getPotential() { |
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return potential_; |
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} |
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|
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Atom* getAtomA() { |
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return atoms_[0]; |
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} |
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|
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Atom* getAtomB() { |
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return atoms_[1]; |
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} |
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|
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BondType* getBondType() { |
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return bondType_; |
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} |
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|
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virtual std::string getName() { return name_;} |
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/** Sets the name of this bond for selections */ |
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virtual void setName(const std::string& name) { name_ = name; } |
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|
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void accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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|
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private: |
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RealType potential_; |
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BondType* bondType_; /**< bond type */ |
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std::string name_; |
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|
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}; |
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} //end namespace OpenMD |
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#endif //PRIMITIVES_BOND_HPP |
