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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 <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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//return the position of joint atom apears in rigidbody's definition |
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//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
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//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
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vector<pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
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std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
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RigidBodyStamp* rbStamp1; |
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RigidBodyStamp* rbStamp2; |
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int natomInRb1; |
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int natomInRb2; |
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int atomIndex1; |
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int atomIndex2; |
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vector<pair<int, int> > jointAtomIndexPair; |
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std::vector<std::pair<int, int> > jointAtomIndexPair; |
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|
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rbStamp1 = this->getRigidBody(rb1); |
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natomInRb1 =rbStamp1->getNMembers(); |
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atomIndex2 = rbStamp2->getMember(j); |
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|
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if(atomIndex1 == atomIndex2){ |
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jointAtomIndexPair.push_back(make_pair(i, j)); |
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jointAtomIndexPair.push_back(std::make_pair(i, j)); |
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break; |
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} |
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|
