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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 <iostream> |
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#include <functional> |
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#include "types/MoleculeStamp.hpp" |
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#include "utils/Tuple.hpp" |
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|
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namespace oopse { |
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MoleculeStamp::MoleculeStamp() { |
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DefineParameter(Name, "name"); |
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|
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deprecatedKeywords_.insert("nAtoms"); |
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deprecatedKeywords_.insert("nBonds"); |
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deprecatedKeywords_.insert("nBends"); |
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deprecatedKeywords_.insert("nTorsions"); |
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deprecatedKeywords_.insert("nRigidBodies"); |
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deprecatedKeywords_.insert("nCutoffGroups"); |
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|
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} |
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|
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MoleculeStamp::~MoleculeStamp() { |
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|
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} |
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|
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bool MoleculeStamp::addAtomStamp( AtomStamp* atom) { |
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bool ret = addIndexSensitiveStamp(atomStamps_, atom); |
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if (!ret) { |
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std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName() << " Molecule\n"; |
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} |
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return ret; |
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|
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} |
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|
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bool MoleculeStamp::addBondStamp( BondStamp* bond) { |
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bondStamps_.push_back(bond); |
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return true; |
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} |
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|
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bool MoleculeStamp::addBendStamp( BendStamp* bend) { |
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bendStamps_.push_back(bend); |
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return true; |
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} |
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|
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bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) { |
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torsionStamps_.push_back(torsion); |
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return true; |
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} |
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|
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bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) { |
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bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody); |
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if (!ret) { |
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std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName() << " Molecule\n"; |
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} |
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return ret; |
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} |
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|
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bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) { |
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cutoffGroupStamps_.push_back(cutoffgroup); |
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return true; |
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} |
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|
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bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) { |
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return addIndexSensitiveStamp(fragmentStamps_, fragment); |
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} |
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|
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void MoleculeStamp::validate() { |
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DataHolder::validate(); |
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|
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atom2Rigidbody.resize(getNAtoms()); |
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// negative number means atom is a free atom, does not belong to rigidbody |
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//every element in atom2Rigidbody has unique negative number at the very beginning |
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for(int i = 0; i < atom2Rigidbody.size(); ++i) { |
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atom2Rigidbody[i] = -1 - i; |
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} |
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for (int i = 0; i < getNRigidBodies(); ++i) { |
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RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
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std::vector<int> members = rbStamp->getMembers(); |
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for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) { |
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atom2Rigidbody[*j] = i; |
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} |
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} |
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|
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checkAtoms(); |
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checkBonds(); |
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fillBondInfo(); |
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checkBends(); |
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checkTorsions(); |
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checkRigidBodies(); |
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checkCutoffGroups(); |
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checkFragments(); |
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|
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int nrigidAtoms = 0; |
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for (int i = 0; i < getNRigidBodies(); ++i) { |
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RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
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nrigidAtoms += rbStamp->getNMembers(); |
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} |
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nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms; |
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|
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} |
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|
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void MoleculeStamp::checkAtoms() { |
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std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL)); |
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if (ai != atomStamps_.end()) { |
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std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n"; |
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} |
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|
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//make sure index is not out of range |
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int natoms = getNAtoms(); |
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for(int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp = getBondStamp(i); |
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if (bondStamp->getA() >= natoms && bondStamp->getB() >= natoms) { |
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std::cout << "Error in Molecule " << getName() << ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n"; |
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} |
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} |
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} |
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|
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void MoleculeStamp::checkBonds() { |
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//make sure bonds are unique |
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std::set<std::pair<int, int> > allBonds; |
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for(int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp= getBondStamp(i); |
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std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB()); |
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//make sure bondTuple.first is always less than or equal to bondTuple.third |
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if (bondPair.first > bondPair.second) { |
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std::swap(bondPair.first, bondPair.second); |
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} |
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|
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std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair); |
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if ( iter != allBonds.end()) { |
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std::cout << "Error in Molecule " << getName() << ": " << "Bond appears multiple times\n"; |
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} else { |
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allBonds.insert(bondPair); |
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} |
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} |
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|
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//make sure atoms belong to same rigidbody do not bond to each other |
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for(int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp = getBondStamp(i); |
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if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) { |
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std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
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} |
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} |
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|
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} |
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|
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struct BendLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> { |
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bool operator()(IntTuple3 b1, IntTuple3 b2) { |
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return b1.first < b2.first |
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|| (!(b2.first < b1.first) && b1.second < b2.second) |
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|| (!(b2.first < b1.first) && !(b2.second < b2.second) && b1.third < b2.third); |
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} |
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}; |
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|
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void MoleculeStamp::checkBends() { |
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for(int i = 0; i < getNBends(); ++i) { |
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BendStamp* bendStamp = getBendStamp(i); |
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std::vector<int> bendAtoms = bendStamp->getMembers(); |
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std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
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if (j != bendAtoms.end()) { |
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std::cout << "Error in Molecule " << getName(); |
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} |
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|
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if (bendAtoms.size() == 2 ) { |
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if (!bendStamp->haveGhostVectorSource()) { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n"; |
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}else{ |
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int ghostIndex = bendStamp->getGhostVectorSource(); |
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if (ghostIndex < getNAtoms()) { |
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if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; |
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} |
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if (!getAtomStamp(ghostIndex)->haveOrientation()) { |
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std::cout << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; |
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} |
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}else { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n"; |
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} |
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} |
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} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) { |
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std::cout << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; |
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} |
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} |
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|
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for(int i = 0; i < getNBends(); ++i) { |
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BendStamp* bendStamp = getBendStamp(i); |
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std::vector<int> bendAtoms = bendStamp->getMembers(); |
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std::vector<int> rigidSet(getNRigidBodies(), 0); |
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std::vector<int>::iterator j; |
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for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) { |
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int rigidbodyIndex = atom2Rigidbody[*j]; |
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if (rigidbodyIndex >= 0) { |
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++rigidSet[rigidbodyIndex]; |
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if (rigidSet[rigidbodyIndex] > 1) { |
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std::cout << "Error in Molecule " << getName() << ": "; |
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//std::cout << "atoms of bend " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
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} |
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} |
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} |
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} |
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|
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|
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std::set<IntTuple3, BendLessThan> allBends; |
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std::set<IntTuple3, BendLessThan>::iterator iter; |
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for(int i = 0; i < getNBends(); ++i) { |
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BendStamp* bendStamp= getBendStamp(i); |
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std::vector<int> bend = bendStamp->getMembers(); |
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if (bend.size() == 2) { |
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// in case we have two ghost bend. For example, |
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// bend { |
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// members (0, 1); |
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// ghostVectorSource = 0; |
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// } |
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// and |
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// bend { |
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// members (0, 1); |
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// ghostVectorSource = 0; |
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// } |
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// In order to distinguish them. we expand them to Tuple3. |
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// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1) |
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int ghostIndex = bendStamp->getGhostVectorSource(); |
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std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex); |
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if (j != bend.end()) { |
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bend.insert(j, ghostIndex); |
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} |
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} |
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|
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IntTuple3 bendTuple(bend[0], bend[1], bend[2]); |
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//make sure bendTuple.first is always less than or equal to bendTuple.third |
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if (bendTuple.first > bendTuple.third) { |
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std::swap(bendTuple.first, bendTuple.third); |
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} |
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|
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iter = allBends.find(bendTuple); |
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if ( iter != allBends.end()) { |
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std::cout << "Error in Molecule " << getName() << ": " << "Bend appears multiple times\n"; |
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} else { |
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allBends.insert(bendTuple); |
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} |
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} |
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|
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for (int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp = getBondStamp(i); |
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int a = bondStamp->getA(); |
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int b = bondStamp->getB(); |
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|
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AtomStamp* atomA = getAtomStamp(a); |
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AtomStamp* atomB = getAtomStamp(b); |
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|
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//find bend c--a--b |
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AtomStamp::AtomIter ai; |
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for(int c= atomA->getFirstBonedAtom(ai);c != -1;c = atomA->getNextBonedAtom(ai)) |
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{ |
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if(b == c) |
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continue; |
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|
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IntTuple3 newBend(c, a, b); |
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if (newBend.first > newBend.third) { |
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std::swap(newBend.first, newBend.third); |
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} |
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|
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if (allBends.find(newBend) == allBends.end() ) { |
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allBends.insert(newBend); |
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BendStamp * newBendStamp = new BendStamp(); |
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newBendStamp->setMembers(newBend); |
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addBendStamp(newBendStamp); |
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} |
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} |
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|
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//find bend a--b--c |
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for(int c= atomB->getFirstBonedAtom(ai);c != -1;c = atomB->getNextBonedAtom(ai)) |
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{ |
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if(a == c) |
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continue; |
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|
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IntTuple3 newBend( a, b, c); |
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if (newBend.first > newBend.third) { |
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std::swap(newBend.first, newBend.third); |
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} |
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if (allBends.find(newBend) == allBends.end() ) { |
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allBends.insert(newBend); |
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BendStamp * newBendStamp = new BendStamp(); |
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newBendStamp->setMembers(newBend); |
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addBendStamp(newBendStamp); |
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} |
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} |
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} |
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|
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} |
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|
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struct TorsionLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> { |
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bool operator()(IntTuple4 t1, IntTuple4 t2) { |
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|
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return t1.first < t2.first |
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|| (!(t2.first < t1.first) && t1.second < t2.second) |
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|| (!(t2.first < t1.first) && !(t2.second < t2.second) && t1.third < t2.third) |
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||(!(t2.first < t1.first) && !(t2.second < t2.second) && !(t2.third < t1.third) && t1.fourth < t2.fourth); |
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} |
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|
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|
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|
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}; |
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|
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|
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void MoleculeStamp::checkTorsions() { |
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for(int i = 0; i < getNTorsions(); ++i) { |
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TorsionStamp* torsionStamp = getTorsionStamp(i); |
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std::vector<int> torsionAtoms = torsionStamp->getMembers(); |
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std::vector<int> rigidSet(getNRigidBodies(), 0); |
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std::vector<int>::iterator j; |
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for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) { |
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int rigidbodyIndex = atom2Rigidbody[*j]; |
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if (rigidbodyIndex >= 0) { |
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++rigidSet[rigidbodyIndex]; |
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if (rigidSet[rigidbodyIndex] > 1) { |
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std::cout << "Error in Molecule " << getName() << ": "; |
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//std::cout << "atoms of torsion " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
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} |
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} |
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} |
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} |
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|
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std::set<IntTuple4, TorsionLessThan> allTorsions; |
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std::set<IntTuple4, TorsionLessThan>::iterator iter; |
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for(int i = 0; i < getNTorsions(); ++i) { |
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TorsionStamp* torsionStamp= getTorsionStamp(i); |
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std::vector<int> torsion = torsionStamp->getMembers(); |
| 366 |
if (torsion.size() == 3) { |
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int ghostIndex = torsionStamp->getGhostVectorSource(); |
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std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex); |
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if (j != torsion.end()) { |
| 370 |
torsion.insert(j, ghostIndex); |
| 371 |
} |
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} |
| 373 |
|
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IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]); |
| 375 |
if (torsionTuple.first > torsionTuple.fourth) { |
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std::swap(torsionTuple.first, torsionTuple.fourth); |
| 377 |
std::swap(torsionTuple.second, torsionTuple.third); |
| 378 |
} |
| 379 |
|
| 380 |
iter = allTorsions.find(torsionTuple); |
| 381 |
if ( iter == allTorsions.end()) { |
| 382 |
allTorsions.insert(torsionTuple); |
| 383 |
} else { |
| 384 |
std::cout << "Error in Molecule " << getName() << ": " << "Torsion appears multiple times\n"; |
| 385 |
} |
| 386 |
} |
| 387 |
|
| 388 |
for (int i = 0; i < getNBonds(); ++i) { |
| 389 |
BondStamp* bondStamp = getBondStamp(i); |
| 390 |
int b = bondStamp->getA(); |
| 391 |
int c = bondStamp->getB(); |
| 392 |
|
| 393 |
AtomStamp* atomB = getAtomStamp(b); |
| 394 |
AtomStamp* atomC = getAtomStamp(c); |
| 395 |
|
| 396 |
AtomStamp::AtomIter ai2; |
| 397 |
AtomStamp::AtomIter ai3; |
| 398 |
|
| 399 |
for(int a = atomB->getFirstBonedAtom(ai2);a != -1;a = atomB->getNextBonedAtom(ai2)) |
| 400 |
{ |
| 401 |
if(a == c) |
| 402 |
continue; |
| 403 |
|
| 404 |
for(int d = atomC->getFirstBonedAtom(ai3);d != -1;d = atomC->getNextBonedAtom(ai3)) |
| 405 |
{ |
| 406 |
if(d == b) |
| 407 |
continue; |
| 408 |
|
| 409 |
IntTuple4 newTorsion(a, b, c, d); |
| 410 |
//make sure the first element is always less than or equal to the fourth element in IntTuple4 |
| 411 |
if (newTorsion.first > newTorsion.fourth) { |
| 412 |
std::swap(newTorsion.first, newTorsion.fourth); |
| 413 |
std::swap(newTorsion.second, newTorsion.third); |
| 414 |
} |
| 415 |
if (allTorsions.find(newTorsion) == allTorsions.end() ) { |
| 416 |
allTorsions.insert(newTorsion); |
| 417 |
TorsionStamp * newTorsionStamp = new TorsionStamp(); |
| 418 |
newTorsionStamp->setMembers(newTorsion); |
| 419 |
addTorsionStamp(newTorsionStamp); |
| 420 |
} |
| 421 |
} |
| 422 |
} |
| 423 |
} |
| 424 |
|
| 425 |
} |
| 426 |
|
| 427 |
void MoleculeStamp::checkRigidBodies() { |
| 428 |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
| 429 |
if (ri != rigidBodyStamps_.end()) { |
| 430 |
std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
| 431 |
} |
| 432 |
|
| 433 |
for (int i = 0; i < getNRigidBodies(); ++i) { |
| 434 |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
| 435 |
std::vector<int> rigidAtoms = rbStamp ->getMembers(); |
| 436 |
std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 437 |
if (j != rigidAtoms.end()) { |
| 438 |
std::cout << "Error in Molecule " << getName(); |
| 439 |
} |
| 440 |
|
| 441 |
} |
| 442 |
} |
| 443 |
|
| 444 |
void MoleculeStamp::checkCutoffGroups() { |
| 445 |
|
| 446 |
for(int i = 0; i < getNCutoffGroups(); ++i) { |
| 447 |
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
| 448 |
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
| 449 |
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 450 |
if (j != cutoffGroupAtoms.end()) { |
| 451 |
std::cout << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; |
| 452 |
} |
| 453 |
} |
| 454 |
} |
| 455 |
|
| 456 |
void MoleculeStamp::checkFragments() { |
| 457 |
|
| 458 |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
| 459 |
if (fi != fragmentStamps_.end()) { |
| 460 |
std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
| 461 |
} |
| 462 |
|
| 463 |
} |
| 464 |
|
| 465 |
void MoleculeStamp::fillBondInfo() { |
| 466 |
|
| 467 |
for (int i = 0; i < getNBonds(); ++i) { |
| 468 |
BondStamp* bondStamp = getBondStamp(i); |
| 469 |
int a = bondStamp->getA(); |
| 470 |
int b = bondStamp->getB(); |
| 471 |
AtomStamp* atomA = getAtomStamp(a); |
| 472 |
AtomStamp* atomB = getAtomStamp(b); |
| 473 |
atomA->addBond(i); |
| 474 |
atomA->addBondedAtom(b); |
| 475 |
atomB->addBond(i); |
| 476 |
atomB->addBondedAtom(a); |
| 477 |
|
| 478 |
} |
| 479 |
} |
| 480 |
|
| 481 |
|
| 482 |
|
| 483 |
//Function Name: isBondInSameRigidBody |
| 484 |
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
| 485 |
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
| 486 |
int rbA; |
| 487 |
int rbB; |
| 488 |
int consAtomA; |
| 489 |
int consAtomB; |
| 490 |
|
| 491 |
if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
| 492 |
return false; |
| 493 |
|
| 494 |
if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
| 495 |
return false; |
| 496 |
|
| 497 |
if(rbB == rbA) |
| 498 |
return true; |
| 499 |
else |
| 500 |
return false; |
| 501 |
} |
| 502 |
|
| 503 |
// Function Name: isAtomInRigidBody |
| 504 |
//return false if atom does not belong to a rigid body, otherwise return true |
| 505 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
| 506 |
int whichRigidBody; |
| 507 |
int consAtomIndex; |
| 508 |
|
| 509 |
return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex); |
| 510 |
|
| 511 |
} |
| 512 |
|
| 513 |
// Function Name: isAtomInRigidBody |
| 514 |
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
| 515 |
//and consAtomIndex |
| 516 |
//atomIndex : the index of atom in component |
| 517 |
//whichRigidBody: the index of rigidbody in component |
| 518 |
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
| 519 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
| 520 |
RigidBodyStamp* rbStamp; |
| 521 |
int numRb; |
| 522 |
int numAtom; |
| 523 |
|
| 524 |
whichRigidBody = -1; |
| 525 |
consAtomIndex = -1; |
| 526 |
|
| 527 |
numRb = this->getNRigidBodies(); |
| 528 |
|
| 529 |
for(int i = 0 ; i < numRb; i++){ |
| 530 |
rbStamp = this->getRigidBodyStamp(i); |
| 531 |
numAtom = rbStamp->getNMembers(); |
| 532 |
for(int j = 0; j < numAtom; j++) |
| 533 |
if (rbStamp->getMemberAt(j) == atomIndex){ |
| 534 |
whichRigidBody = i; |
| 535 |
consAtomIndex = j; |
| 536 |
return true; |
| 537 |
} |
| 538 |
} |
| 539 |
|
| 540 |
return false; |
| 541 |
|
| 542 |
} |
| 543 |
|
| 544 |
//return the position of joint atom apears in rigidbody's definition |
| 545 |
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
| 546 |
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
| 547 |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
| 548 |
RigidBodyStamp* rbStamp1; |
| 549 |
RigidBodyStamp* rbStamp2; |
| 550 |
int natomInRb1; |
| 551 |
int natomInRb2; |
| 552 |
int atomIndex1; |
| 553 |
int atomIndex2; |
| 554 |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
| 555 |
|
| 556 |
rbStamp1 = this->getRigidBodyStamp(rb1); |
| 557 |
natomInRb1 =rbStamp1->getNMembers(); |
| 558 |
|
| 559 |
rbStamp2 = this->getRigidBodyStamp(rb2); |
| 560 |
natomInRb2 =rbStamp2->getNMembers(); |
| 561 |
|
| 562 |
for(int i = 0; i < natomInRb1; i++){ |
| 563 |
atomIndex1 = rbStamp1->getMemberAt(i); |
| 564 |
|
| 565 |
for(int j= 0; j < natomInRb1; j++){ |
| 566 |
atomIndex2 = rbStamp2->getMemberAt(j); |
| 567 |
|
| 568 |
if(atomIndex1 == atomIndex2){ |
| 569 |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
| 570 |
break; |
| 571 |
} |
| 572 |
|
| 573 |
} |
| 574 |
|
| 575 |
} |
| 576 |
|
| 577 |
return jointAtomIndexPair; |
| 578 |
} |
| 579 |
|
| 580 |
} |
