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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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#ifndef TYPES_MOLECULESTAMP_HPP |
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#define TYPES_MOLECULESTAMP_HPP |
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#include <vector> |
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#include <utility> |
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#include "types/AtomStamp.hpp" |
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#include "types/BondStamp.hpp" |
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#include "types/BendStamp.hpp" |
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#include "types/TorsionStamp.hpp" |
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#include "types/RigidBodyStamp.hpp" |
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#include "types/CutoffGroupStamp.hpp" |
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#include "types/FragmentStamp.hpp" |
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|
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namespace oopse { |
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class MoleculeStamp : public DataHolder { |
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DeclareParameter(Name, std::string); |
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public: |
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MoleculeStamp(); |
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virtual ~MoleculeStamp(); |
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|
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bool addAtomStamp( AtomStamp* atom); |
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bool addBondStamp( BondStamp* bond); |
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bool addBendStamp( BendStamp* bend); |
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bool addTorsionStamp( TorsionStamp* torsion); |
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bool addRigidBodyStamp( RigidBodyStamp* rigidbody); |
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bool addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup); |
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bool addFragmentStamp( FragmentStamp* fragment); |
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|
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int getNAtoms() { return atomStamps_.size(); } |
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int getNBonds() { return bondStamps_.size(); } |
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int getNBends() { return bendStamps_.size(); } |
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int getNTorsions() { return torsionStamps_.size(); } |
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int getNRigidBodies() { return rigidBodyStamps_.size(); } |
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int getNCutoffGroups() { return cutoffGroupStamps_.size(); } |
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int getNIntegrable() { return nintegrable_;} |
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virtual void validate(); |
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|
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AtomStamp* getAtomStamp(int index) { return atomStamps_[index]; } |
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BondStamp* getBondStamp(int index) { return bondStamps_[index]; } |
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BendStamp* getBendStamp(int index) { return bendStamps_[index]; } |
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TorsionStamp* getTorsionStamp(int index) { return torsionStamps_[index]; } |
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RigidBodyStamp* getRigidBodyStamp(int index) { return rigidBodyStamps_[index]; } |
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CutoffGroupStamp* getCutoffGroupStamp(int index) { return cutoffGroupStamps_[index]; } |
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FragmentStamp* getFragmentStamp(int index) { return fragmentStamps_[index]; } |
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|
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bool isBondInSameRigidBody(BondStamp*bond); |
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bool isAtomInRigidBody(int atomIndex); |
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bool isAtomInRigidBody(int atomIndex, int& whichRigidBody, |
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int& consAtomIndex); |
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std::vector<std::pair<int, int> > getJointAtoms(int rb1, int rb2); |
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|
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private: |
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|
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void fillBondInfo(); |
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void checkAtoms(); |
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void checkBonds(); |
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void checkBends(); |
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void checkTorsions(); |
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void checkRigidBodies(); |
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void checkCutoffGroups(); |
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void checkFragments(); |
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template <class Cont, class T> |
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bool addIndexSensitiveStamp(Cont& cont, T* stamp) { |
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typename Cont::iterator i; |
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int index = stamp->getIndex(); |
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bool ret = false; |
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size_t size = cont.size(); |
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|
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if (size >= index +1) { |
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if (cont[index]!= NULL) { |
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ret = false; |
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}else { |
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cont[index] = stamp; |
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ret = true; |
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} |
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} else { |
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cont.insert(cont.end(), index - cont.size() + 1, NULL); |
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cont[index] = stamp; |
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ret = true; |
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} |
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|
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return ret; |
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} |
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|
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std::vector<AtomStamp*> atomStamps_; |
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std::vector<BondStamp*> bondStamps_; |
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std::vector<BendStamp*> bendStamps_; |
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std::vector<TorsionStamp*> torsionStamps_; |
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std::vector<RigidBodyStamp*> rigidBodyStamps_; |
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std::vector<CutoffGroupStamp*> cutoffGroupStamps_; |
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std::vector<FragmentStamp*> fragmentStamps_; |
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std::vector<int> atom2Rigidbody; |
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int nintegrable_; |
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}; |
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|
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} |
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#endif |
